[Solved] Had a power outage while updating my fedora system, and now dnf has file conflicts. Is it recoverable?
The system booted normally after the energy was cut, but if I try to run a dnf update again, I get this error:
<span style="color:#323232;">Last metadata expiration check: 0:51:09 ago on Fri 26 Jan 2024 05:02:36 PM -03.
</span><span style="color:#323232;">Dependencies resolved.
</span><span style="color:#323232;">
</span><span style="color:#323232;"> Problem: The operation would result in removing the following protected packages: systemd, systemd-udev
</span><span style="color:#323232;">================================================================================
</span><span style="color:#323232;"> Package                         Arch     Version               Repo       Size
</span><span style="color:#323232;">================================================================================
</span><span style="color:#323232;">Upgrading:
</span><span style="color:#323232;"> ImageMagick                     x86_64   1:7.1.1.26-2.fc39     updates    81 k
</span><span style="color:#323232;"> ImageMagick-c++                 x86_64   1:7.1.1.26-2.fc39     updates   201 k
</span><span style="color:#323232;"> at-spi2-atk                     i686     2.50.1-1.fc39         updates    92 k
</span><span style="color:#323232;"> at-spi2-core                    i686     2.50.1-1.fc39         updates   378 k
</span><span style="color:#323232;"> atk                             i686     2.50.1-1.fc39         updates    82 k
</span><span style="color:#323232;"> bluez-libs                      i686     5.72-1.fc39           updates    88 k
</span><span style="color:#323232;"> chkconfig                       x86_64   1.26-1.fc39           updates   176 k
</span><span style="color:#323232;"> crun                            x86_64   1.13-1.fc39           updates   218 k
</span><span style="color:#323232;"> darktable                       x86_64   4.6.0-1.fc39          updates   7.2 M
</span><span style="color:#323232;"> device-mapper-persistent-data   x86_64   1.0.9-1.fc39          updates   1.0 M
</span><span style="color:#323232;"> eog                             x86_64   45.2-1.fc39           updates   1.6 M
</span><span style="color:#323232;"> epiphany-runtime                x86_64   1:45.2-1.fc39         updates   853 k
</span><span style="color:#323232;"> fluidsynth-libs                 x86_64   2.3.4-2.fc39          updates   235 k
</span><span style="color:#323232;"> folks                           x86_64   1:0.15.7-1.fc39       updates   588 k
</span><span style="color:#323232;"> gnome-maps                      x86_64   45.3-1.fc39           updates   1.0 M
</span><span style="color:#323232;"> gtk3                            i686     3.24.41-1.fc39        updates   5.8 M
</span><span style="color:#323232;"> gtk3-devel                      x86_64   3.24.41-1.fc39        updates   4.3 M
</span><span style="color:#323232;"> gvfs-afc                        x86_64   1.52.2-1.fc39         updates    57 k
</span><span style="color:#323232;"> gvfs-afp                        x86_64   1.52.2-1.fc39         updates    67 k
</span><span style="color:#323232;"> gvfs-archive                    x86_64   1.52.2-1.fc39         updates    23 k
</span><span style="color:#323232;"> gvfs-fuse                       x86_64   1.52.2-1.fc39         updates    29 k
</span><span style="color:#323232;"> gvfs-goa                        x86_64   1.52.2-1.fc39         updates    67 k
</span><span style="color:#323232;"> gvfs-gphoto2                    x86_64   1.52.2-1.fc39         updates    61 k
</span><span style="color:#323232;"> gvfs-mtp                        x86_64   1.52.2-1.fc39         updates    61 k
</span><span style="color:#323232;"> iwlegacy-firmware               noarch   20240115-2.fc39       updates   146 k
</span><span style="color:#323232;"> iwlwifi-dvm-firmware            noarch   20240115-2.fc39       updates   1.8 M
</span><span style="color:#323232;"> iwlwifi-mvm-firmware            noarch   20240115-2.fc39       updates    50 M
</span><span style="color:#323232;"> kde-settings                    noarch   39.1-1.fc39           updates    40 k
</span><span style="color:#323232;"> krb5-libs                       i686     1.21.2-3.fc39         updates   809 k
</span><span style="color:#323232;"> libblockdev-lvm-dbus            x86_64   3.1.0-1.fc39          updates    48 k
</span><span style="color:#323232;"> libblockdev-plugins-all         x86_64   3.1.0-1.fc39          updates    10 k
</span><span style="color:#323232;"> libdecor                        i686     0.2.2-1.fc39          updates    60 k
</span><span style="color:#323232;"> libdrm                          i686     2.4.120-1.fc39        updates   172 k
</span><span style="color:#323232;"> libertas-firmware               noarch   20240115-2.fc39       updates   1.3 M
</span><span style="color:#323232;"> libmwaw                         x86_64   0.3.22-1.fc39         updates   2.6 M
</span><span style="color:#323232;"> libpeas                         x86_64   2.0.1-1.fc39          updates   117 k
</span><span style="color:#323232;"> librbd1                         x86_64   2:18.2.1-4.fc39       updates   3.5 M
</span><span style="color:#323232;"> libva                           i686     2.20.0-2.fc39         updates   113 k
</span><span style="color:#323232;"> libwpg                          x86_64   0.3.4-1.fc39          updates    74 k
</span><span style="color:#323232;"> libwps                          x86_64   0.4.14-1.fc39         updates   879 k
</span><span style="color:#323232;"> libxmlb                         x86_64   0.3.15-1.fc39         updates   115 k
</span><span style="color:#323232;"> lutris                          x86_64   0.5.16-2.fc39         updates   1.9 M
</span><span style="color:#323232;"> papirus-icon-theme              noarch   20231201-2.fc39       updates    39 M
</span><span style="color:#323232;"> perl-common-sense               x86_64   3.7.5-15.fc39         updates    29 k
</span><span style="color:#323232;"> publicsuffix-list-dafsa         noarch   20240107-1.fc39       updates    58 k
</span><span style="color:#323232;"> python3-audit                   x86_64   3.1.2-6.fc39          updates    87 k
</span><span style="color:#323232;"> python3-beautifulsoup4          noarch   4.12.3-1.fc39         updates   320 k
</span><span style="color:#323232;"> python3-blockdev                x86_64   3.1.0-1.fc39          updates    37 k
</span><span style="color:#323232;"> python3-fonttools               x86_64   4.43.1-1.fc39         updates   2.9 M
</span><span style="color:#323232;"> python3-jinja2                  noarch   3.1.3-1.fc39          updates   507 k
</span><span style="color:#323232;"> python3-pyatspi                 noarch   2.46.1-1.fc39         updates   112 k
</span><span style="color:#323232;"> python3-pyrate-limiter          noarch   3.2.0-1.fc39          updates    65 k
</span><span style="color:#323232;"> qadwaitadecorations-qt6         x86_64   0.1.3-5.fc39          updates    65 k
</span><span style="color:#323232;"> qt5-srpm-macros                 noarch   5.15.12-1.fc39        updates   8.4 k
</span><span style="color:#323232;"> readline                        i686     8.2-6.fc39            updates   218 k
</span><span style="color:#323232;"> sos                             noarch   4.6.1-1.fc39          updates   1.2 M
</span><span style="color:#323232;"> syncthing                       x86_64   1.27.2-1.fc39         updates   8.8 M
</span><span style="color:#323232;"> systemd-boot-unsigned           x86_64   254.8-2.fc39          updates    98 k
</span><span style="color:#323232;"> systemd-libs                    i686     254.8-2.fc39          updates   727 k
</span><span style="color:#323232;"> vim-filesystem                  noarch   2:9.1.031-1.fc39      updates    17 k
</span><span style="color:#323232;"> wine                            x86_64   9.0-1.fc39            updates    10 k
</span><span style="color:#323232;"> wine-alsa                       i686     9.0-1.fc39            updates    86 k
</span><span style="color:#323232;"> wine-core                       i686     9.0-1.fc39            updates    88 M
</span><span style="color:#323232;"> wine-opencl                     i686     9.0-1.fc39            updates    72 k
</span><span style="color:#323232;"> wine-pulseaudio                 i686     9.0-1.fc39            updates    62 k
</span><span style="color:#323232;"> wine-twain                      i686     9.0-1.fc39            updates   136 k
</span><span style="color:#323232;"> zenity                          x86_64   4.0.1-1.fc39          updates   3.2 M
</span><span style="color:#323232;">
</span><span style="color:#323232;">Transaction Summary
</span><span style="color:#323232;">================================================================================
</span><span style="color:#323232;">Upgrade  67 Packages
</span><span style="color:#323232;">
</span><span style="color:#323232;">Total size: 233 M
</span><span style="color:#323232;">Is this ok [y/N]: y
</span><span style="color:#323232;">Downloading Packages:
</span><span style="color:#323232;">[SKIPPED] ImageMagick-7.1.1.26-2.fc39.x86_64.rpm: Already downloaded           
</span><span style="color:#323232;">[SKIPPED] ImageMagick-c++-7.1.1.26-2.fc39.x86_64.rpm: Already downloaded       
</span><span style="color:#323232;">[SKIPPED] at-spi2-atk-2.50.1-1.fc39.i686.rpm: Already downloaded               
</span><span style="color:#323232;">[SKIPPED] at-spi2-core-2.50.1-1.fc39.i686.rpm: Already downloaded              
</span><span style="color:#323232;">[SKIPPED] atk-2.50.1-1.fc39.i686.rpm: Already downloaded                       
</span><span style="color:#323232;">[SKIPPED] bluez-libs-5.72-1.fc39.i686.rpm: Already downloaded                  
</span><span style="color:#323232;">[SKIPPED] chkconfig-1.26-1.fc39.x86_64.rpm: Already downloaded                 
</span><span style="color:#323232;">[SKIPPED] crun-1.13-1.fc39.x86_64.rpm: Already downloaded                      
</span><span style="color:#323232;">[SKIPPED] darktable-4.6.0-1.fc39.x86_64.rpm: Already downloaded                
</span><span style="color:#323232;">[SKIPPED] device-mapper-persistent-data-1.0.9-1.fc39.x86_64.rpm: Already downloaded
</span><span style="color:#323232;">[SKIPPED] eog-45.2-1.fc39.x86_64.rpm: Already downloaded                       
</span><span style="color:#323232;">[SKIPPED] epiphany-runtime-45.2-1.fc39.x86_64.rpm: Already downloaded          
</span><span style="color:#323232;">[SKIPPED] fluidsynth-libs-2.3.4-2.fc39.x86_64.rpm: Already downloaded          
</span><span style="color:#323232;">[SKIPPED] folks-0.15.7-1.fc39.x86_64.rpm: Already downloaded                   
</span><span style="color:#323232;">[SKIPPED] gnome-maps-45.3-1.fc39.x86_64.rpm: Already downloaded                
</span><span style="color:#323232;">[SKIPPED] gtk3-3.24.41-1.fc39.i686.rpm: Already downloaded                     
</span><span style="color:#323232;">[SKIPPED] gtk3-devel-3.24.41-1.fc39.x86_64.rpm: Already downloaded             
</span><span style="color:#323232;">[SKIPPED] gvfs-afc-1.52.2-1.fc39.x86_64.rpm: Already downloaded                
</span><span style="color:#323232;">[SKIPPED] gvfs-afp-1.52.2-1.fc39.x86_64.rpm: Already downloaded                
</span><span style="color:#323232;">[SKIPPED] gvfs-archive-1.52.2-1.fc39.x86_64.rpm: Already downloaded            
</span><span style="color:#323232;">[SKIPPED] gvfs-fuse-1.52.2-1.fc39.x86_64.rpm: Already downloaded               
</span><span style="color:#323232;">[SKIPPED] gvfs-goa-1.52.2-1.fc39.x86_64.rpm: Already downloaded                
</span><span style="color:#323232;">[SKIPPED] gvfs-gphoto2-1.52.2-1.fc39.x86_64.rpm: Already downloaded            
</span><span style="color:#323232;">[SKIPPED] gvfs-mtp-1.52.2-1.fc39.x86_64.rpm: Already downloaded                
</span><span style="color:#323232;">[SKIPPED] iwlegacy-firmware-20240115-2.fc39.noarch.rpm: Already downloaded     
</span><span style="color:#323232;">[SKIPPED] iwlwifi-dvm-firmware-20240115-2.fc39.noarch.rpm: Already downloaded  
</span><span style="color:#323232;">[SKIPPED] iwlwifi-mvm-firmware-20240115-2.fc39.noarch.rpm: Already downloaded  
</span><span style="color:#323232;">[SKIPPED] kde-settings-39.1-1.fc39.noarch.rpm: Already downloaded              
</span><span style="color:#323232;">[SKIPPED] krb5-libs-1.21.2-3.fc39.i686.rpm: Already downloaded                 
</span><span style="color:#323232;">[SKIPPED] libblockdev-lvm-dbus-3.1.0-1.fc39.x86_64.rpm: Already downloaded     
</span><span style="color:#323232;">[SKIPPED] libblockdev-plugins-all-3.1.0-1.fc39.x86_64.rpm: Already downloaded  
</span><span style="color:#323232;">[SKIPPED] libdecor-0.2.2-1.fc39.i686.rpm: Already downloaded                   
</span><span style="color:#323232;">[SKIPPED] libdrm-2.4.120-1.fc39.i686.rpm: Already downloaded                   
</span><span style="color:#323232;">[SKIPPED] libertas-firmware-20240115-2.fc39.noarch.rpm: Already downloaded     
</span><span style="color:#323232;">[SKIPPED] libmwaw-0.3.22-1.fc39.x86_64.rpm: Already downloaded                 
</span><span style="color:#323232;">[SKIPPED] libpeas-2.0.1-1.fc39.x86_64.rpm: Already downloaded                  
</span><span style="color:#323232;">[SKIPPED] librbd1-18.2.1-4.fc39.x86_64.rpm: Already downloaded                 
</span><span style="color:#323232;">[SKIPPED] libva-2.20.0-2.fc39.i686.rpm: Already downloaded                     
</span><span style="color:#323232;">[SKIPPED] libwpg-0.3.4-1.fc39.x86_64.rpm: Already downloaded                   
</span><span style="color:#323232;">[SKIPPED] libwps-0.4.14-1.fc39.x86_64.rpm: Already downloaded                  
</span><span style="color:#323232;">[SKIPPED] libxmlb-0.3.15-1.fc39.x86_64.rpm: Already downloaded                 
</span><span style="color:#323232;">[SKIPPED] lutris-0.5.16-2.fc39.x86_64.rpm: Already downloaded                  
</span><span style="color:#323232;">[SKIPPED] papirus-icon-theme-20231201-2.fc39.noarch.rpm: Already downloaded    
</span><span style="color:#323232;">[SKIPPED] perl-common-sense-3.7.5-15.fc39.x86_64.rpm: Already downloaded       
</span><span style="color:#323232;">[SKIPPED] publicsuffix-list-dafsa-20240107-1.fc39.noarch.rpm: Already downloaded
</span><span style="color:#323232;">[SKIPPED] python3-audit-3.1.2-6.fc39.x86_64.rpm: Already downloaded            
</span><span style="color:#323232;">[SKIPPED] python3-beautifulsoup4-4.12.3-1.fc39.noarch.rpm: Already downloaded  
</span><span style="color:#323232;">[SKIPPED] python3-blockdev-3.1.0-1.fc39.x86_64.rpm: Already downloaded         
</span><span style="color:#323232;">[SKIPPED] python3-fonttools-4.43.1-1.fc39.x86_64.rpm: Already downloaded       
</span><span style="color:#323232;">[SKIPPED] python3-jinja2-3.1.3-1.fc39.noarch.rpm: Already downloaded           
</span><span style="color:#323232;">[SKIPPED] python3-pyatspi-2.46.1-1.fc39.noarch.rpm: Already downloaded         
</span><span style="color:#323232;">[SKIPPED] python3-pyrate-limiter-3.2.0-1.fc39.noarch.rpm: Already downloaded   
</span><span style="color:#323232;">[SKIPPED] qadwaitadecorations-qt6-0.1.3-5.fc39.x86_64.rpm: Already downloaded  
</span><span style="color:#323232;">[SKIPPED] qt5-srpm-macros-5.15.12-1.fc39.noarch.rpm: Already downloaded        
</span><span style="color:#323232;">[SKIPPED] readline-8.2-6.fc39.i686.rpm: Already downloaded                     
</span><span style="color:#323232;">[SKIPPED] sos-4.6.1-1.fc39.noarch.rpm: Already downloaded                      
</span><span style="color:#323232;">[SKIPPED] syncthing-1.27.2-1.fc39.x86_64.rpm: Already downloaded               
</span><span style="color:#323232;">[SKIPPED] systemd-boot-unsigned-254.8-2.fc39.x86_64.rpm: Already downloaded    
</span><span style="color:#323232;">[SKIPPED] systemd-libs-254.8-2.fc39.i686.rpm: Already downloaded               
</span><span style="color:#323232;">[SKIPPED] vim-filesystem-9.1.031-1.fc39.noarch.rpm: Already downloaded         
</span><span style="color:#323232;">[SKIPPED] wine-9.0-1.fc39.x86_64.rpm: Already downloaded                       
</span><span style="color:#323232;">[SKIPPED] wine-alsa-9.0-1.fc39.i686.rpm: Already downloaded                    
</span><span style="color:#323232;">[SKIPPED] wine-core-9.0-1.fc39.i686.rpm: Already downloaded                    
</span><span style="color:#323232;">[SKIPPED] wine-opencl-9.0-1.fc39.i686.rpm: Already downloaded                  
</span><span style="color:#323232;">[SKIPPED] wine-pulseaudio-9.0-1.fc39.i686.rpm: Already downloaded              
</span><span style="color:#323232;">[SKIPPED] wine-twain-9.0-1.fc39.i686.rpm: Already downloaded                   
</span><span style="color:#323232;">[SKIPPED] zenity-4.0.1-1.fc39.x86_64.rpm: Already downloaded                   
</span><span style="color:#323232;">Running transaction check
</span><span style="color:#323232;">Transaction check succeeded.
</span><span style="color:#323232;">Running transaction test
</span><span style="color:#323232;">The downloaded packages were saved in cache until the next successful transaction.
</span><span style="color:#323232;">You can remove cached packages by executing 'dnf clean packages'.
</span><span style="color:#323232;">Error: Transaction test error:
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">  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
</span><span style="color:#323232;">
</span><span style="color:#323232;">
</span>
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”:
<span style="color:#323232;">Last metadata expiration check: 1:20:21 ago on Fri 26 Jan 2024 05:02:36 PM -03.
</span><span style="color:#323232;">Dependencies resolved.
</span><span style="color:#323232;">
</span><span style="color:#323232;"> Problem: The operation would result in removing the following protected packages: systemd, systemd-udev
</span><span style="color:#323232;">Nothing to do.
</span><span style="color:#323232;">Complete!
</span>
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.
 
                     
                    
Add comment