Dnf update reports problems and conflicts after upgrade to Fedora 41

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1

Hello,

After an upgrade to Fedora 41 I tried to update using dnf. This caused many issues. Below is the output of “sudo dnf update”:

Last metadata expiration check: 2:19:00 ago on Sat 16 Nov 2024 13:32:34 CET.
Dependencies resolved.

 Problem 1: package gnome-control-center-46.5-1.fc40.x86_64 from updates requires gnome-control-center-filesystem = 46.5-1.fc40, but none of the providers can be installed
  - cannot install both gnome-control-center-filesystem-46.5-1.fc40.noarch from updates and gnome-control-center-filesystem-47.1.1-1.fc41.noarch from @System
  - cannot install the best update candidate for package gnome-control-center-46.4-1.fc40.x86_64
  - problem with installed package gnome-control-center-filesystem-47.1.1-1.fc41.noarch
 Problem 2: package ibus-1.5.30-7.fc40.x86_64 from updates requires ibus-libs(x86-64) = 1.5.30-7.fc40, but none of the providers can be installed
  - cannot install both ibus-libs-1.5.30-7.fc40.x86_64 from updates and ibus-libs-1.5.31-1.fc41.x86_64 from @System
  - cannot install the best update candidate for package ibus-1.5.30-6.fc40.x86_64
  - problem with installed package ibus-libs-1.5.31-1.fc41.x86_64
 Problem 3: cannot install both ibus-libs-1.5.30-7.fc40.x86_64 from updates and ibus-libs-1.5.31-1.fc41.x86_64 from @System
  - package ibus-gtk2-1.5.30-7.fc40.x86_64 from updates requires ibus-libs(x86-64) = 1.5.30-7.fc40, but none of the providers can be installed
  - cannot install the best update candidate for package ibus-libs-1.5.30-6.fc40.x86_64
  - cannot install the best update candidate for package ibus-gtk2-1.5.30-6.fc40.x86_64
 Problem 4: cannot install both ibus-libs-1.5.30-7.fc40.x86_64 from updates and ibus-libs-1.5.31-1.fc41.x86_64 from @System
  - package ibus-gtk3-1.5.30-7.fc40.x86_64 from updates requires ibus-libs(x86-64) = 1.5.30-7.fc40, but none of the providers can be installed
  - cannot install the best update candidate for package ibus-libs-1.5.31-1.fc41.x86_64
  - cannot install the best update candidate for package ibus-gtk3-1.5.30-6.fc40.x86_64
 Problem 5: package kf6-breeze-icons-6.8.0-1.fc40.x86_64 from updates requires breeze-icon-theme = 6.8.0-1.fc40, but none of the providers can be installed
  - cannot install both breeze-icon-theme-6.8.0-1.fc40.noarch from updates and breeze-icon-theme-6.8.0-1.fc41.noarch from @System
  - cannot install the best update candidate for package kf6-breeze-icons-6.7.0-1.fc40.x86_64
  - problem with installed package breeze-icon-theme-6.8.0-1.fc41.noarch
 Problem 6: krb5-libs-1.21.3-2.fc40.i686 from updates  does not belong to a distupgrade repository
  - cannot install both krb5-libs-1.21.3-2.fc40.x86_64 from updates and krb5-libs-1.21.3-3.fc41.x86_64 from @System
  - cannot install the best update candidate for package krb5-libs-1.21.3-1.fc40.i686
  - problem with installed package krb5-libs-1.21.3-3.fc41.x86_64
 Problem 7: package libkworkspace6-6.2.3-1.fc40.x86_64 from updates requires plasma-workspace-common = 6.2.3-1.fc40, but none of the providers can be installed
  - cannot install both plasma-workspace-common-6.2.3-1.fc40.x86_64 from updates and plasma-workspace-common-6.2.3-1.fc41.x86_64 from @System
  - cannot install the best update candidate for package libkworkspace6-6.2.2-1.fc40.x86_64
  - problem with installed package plasma-workspace-common-6.2.3-1.fc41.x86_64
 Problem 8: cannot install both python3-botocore-1.35.59-1.fc40.noarch from updates and python3-botocore-1.35.55-1.fc41.noarch from @System
  - package python3-s3transfer-0.10.3-1.fc41.noarch from @System requires (python3.13dist(botocore) < 2~a0 with python3.13dist(botocore) >= 1.33.2), but none of the providers can be installed
  - cannot install the best update candidate for package python3-botocore-1.35.54-1.fc40.noarch
  - problem with installed package python3-s3transfer-0.10.3-1.fc41.noarch
 Problem 9: package python3-s3transfer-0.10.3-1.fc41.noarch from @System requires (python3.13dist(botocore) < 2~a0 with python3.13dist(botocore) >= 1.33.2), but none of the providers can be installed
  - cannot install both python3-botocore-1.35.59-1.fc40.noarch from updates and python3-botocore-1.35.55-1.fc41.noarch from @System
  - cannot install the best update candidate for package python3-s3transfer-0.10.3-1.fc40.noarch
  - cannot install the best update candidate for package python3-botocore-1.35.55-1.fc41.noarch
 Problem 10: package webkit2gtk4.1-2.46.3-1.fc40.x86_64 from updates requires javascriptcoregtk4.1(x86-64) = 2.46.3-1.fc40, but none of the providers can be installed
  - cannot install both javascriptcoregtk4.1-2.46.3-1.fc40.x86_64 from updates and javascriptcoregtk4.1-2.46.3-1.fc41.x86_64 from @System
  - cannot install the best update candidate for package webkit2gtk4.1-2.46.1-1.fc40.x86_64
  - problem with installed package javascriptcoregtk4.1-2.46.3-1.fc41.x86_64
 Problem 11: package webkitgtk6.0-2.46.3-1.fc40.x86_64 from updates requires javascriptcoregtk6.0(x86-64) = 2.46.3-1.fc40, but none of the providers can be installed
  - cannot install both javascriptcoregtk6.0-2.46.3-1.fc40.x86_64 from updates and javascriptcoregtk6.0-2.46.3-1.fc41.x86_64 from @System
  - cannot install the best update candidate for package webkitgtk6.0-2.46.1-1.fc40.x86_64
  - problem with installed package javascriptcoregtk6.0-2.46.3-1.fc41.x86_64
 Problem 12: package libkworkspace6-6.2.3-1.fc40.x86_64 from updates requires plasma-workspace-common = 6.2.3-1.fc40, but none of the providers can be installed
  - cannot install both plasma-workspace-common-6.2.3-1.fc40.x86_64 from updates and plasma-workspace-common-6.2.3-1.fc41.x86_64 from @System
  - package kde-cli-tools-6.2.3-1.fc40.x86_64 from updates requires libkworkspace6(x86-64) >= 6.2.3, but none of the providers can be installed
  - cannot install the best update candidate for package plasma-workspace-common-6.2.2-1.fc40.x86_64
  - cannot install the best update candidate for package kde-cli-tools-6.2.2-1.fc40.x86_64
 Problem 13: cannot install both python3-botocore-1.35.59-1.fc40.noarch from updates and python3-botocore-1.35.55-1.fc41.noarch from @System
  - package python3-s3transfer-0.10.3-1.fc41.noarch from @System requires (python3.13dist(botocore) < 2~a0 with python3.13dist(botocore) >= 1.33.2), but none of the providers can be installed
  - package python3-boto3-1.35.59-1.fc40.noarch from updates requires (python3.12dist(botocore) < 1.36~~ with python3.12dist(botocore) >= 1.35.59), but none of the providers can be installed
  - cannot install the best update candidate for package python3-s3transfer-0.10.3-1.fc41.noarch
  - cannot install the best update candidate for package python3-boto3-1.35.54-1.fc40.noarch
 Problem 14: package kde-cli-tools-6.2.3-1.fc40.x86_64 from updates requires libkworkspace6(x86-64) >= 6.2.3, but none of the providers can be installed
  - problem with installed package kde-cli-tools-6.2.2-1.fc40.x86_64
  - package libkworkspace6-6.2.3-1.fc40.x86_64 from updates requires plasma-workspace-common = 6.2.3-1.fc40, but none of the providers can be installed
  - package kde-cli-tools-6.2.2-1.fc40.x86_64 from @System requires kdesu = 1:6.2.2-1.fc40, but none of the providers can be installed
  - cannot install both plasma-workspace-common-6.2.3-1.fc40.x86_64 from updates and plasma-workspace-common-6.2.3-1.fc41.x86_64 from @System
  - cannot install both kdesu-1:6.2.3-1.fc40.x86_64 from updates and kdesu-1:6.2.2-1.fc40.x86_64 from @System
  - cannot install the best update candidate for package plasma-workspace-common-6.2.3-1.fc41.x86_64
  - cannot install the best update candidate for package kdesu-1:6.2.2-1.fc40.x86_64
==============================================================================================================================================================================================================================================
 Package                                                                   Architecture                                     Version                                                   Repository                                         Size
==============================================================================================================================================================================================================================================
Skipping packages with conflicts:
(add '--best --allowerasing' to command line to force their upgrade):
 breeze-icon-theme                                                         noarch                                           6.8.0-1.fc40                                              updates                                           9.6 M
 gnome-control-center-filesystem                                           noarch                                           46.5-1.fc40                                               updates                                            11 k
 ibus-libs                                                                 x86_64                                           1.5.30-7.fc40                                             updates                                           259 k
 javascriptcoregtk4.1                                                      x86_64                                           2.46.3-1.fc40                                             updates                                           7.6 M
 javascriptcoregtk6.0                                                      x86_64                                           2.46.3-1.fc40                                             updates                                           7.6 M
 kdesu                                                                     x86_64                                           1:6.2.3-1.fc40                                            updates                                           271 k
 krb5-libs                                                                 x86_64                                           1.21.3-2.fc40                                             updates                                           759 k
 plasma-workspace-common                                                   x86_64                                           6.2.3-1.fc40                                              updates                                            43 k
 python3-botocore                                                          noarch                                           1.35.59-1.fc40                                            updates                                           7.4 M
Skipping packages with broken dependencies:
 gnome-control-center                                                      x86_64                                           46.5-1.fc40                                               updates                                           7.0 M
 ibus                                                                      x86_64                                           1.5.30-7.fc40                                             updates                                            14 M
 ibus-gtk2                                                                 x86_64                                           1.5.30-7.fc40                                             updates                                            30 k
 ibus-gtk3                                                                 x86_64                                           1.5.30-7.fc40                                             updates                                            30 k
 kde-cli-tools                                                             x86_64                                           6.2.3-1.fc40                                              updates                                           879 k
 kf6-breeze-icons                                                          x86_64                                           6.8.0-1.fc40                                              updates                                           3.0 M
 libkworkspace6                                                            x86_64                                           6.2.3-1.fc40                                              updates                                           147 k
 python3-boto3                                                             noarch                                           1.35.59-1.fc40                                            updates                                           398 k
 webkit2gtk4.1                                                             x86_64                                           2.46.3-1.fc40                                             updates                                            24 M
 webkitgtk6.0                                                              x86_64                                           2.46.3-1.fc40                                             updates                                            24 M

Transaction Summary
==============================================================================================================================================================================================================================================
Skip  19 Packages

Nothing to do.
Complete!

What is the best way to go about fixing this? The “fc40” in the package names make me suspect they are Fedora 40-specific packages, does that mean I should remove them?

2

f41 hinzugefügt

3

Using the --refresh option it seems I am still on Fedora 40 repositories? How do I make it change to Fedora 41?

4

try
sudo dnf distro-sync --releasever=41 --allowerasing

2 Likes
5

Hello Joe, thanks for your answer. When trying this dnf fails with the error “Problem: The operation would result in removing the following protected packages: NetworkManager, grub2-efi-ia32, grub2-efi-x64, grub2-pc, grub2-tools-minimal, selinux-policy-targeted, setup, sudo”

How do I bypass this? Using skip-broken seems to result in no upgrades being done at all.

6

At least some of the problems have been gone, but I am still on Fedora 40 servers it seems.

7

I found this thread: Server in semi-broken state after dnf system-upgrade - #3 by vwbusguy from some years ago. I tried the fix in the posted GitHub link (Remove duplicates after a botched dnf upgrade · GitHub) and now distro-sync seems to be working.

2 Likes
8

Distro-sync finished without issues and dnf update is in working order again. Going to try rebooting and if that goes smoothly I will mark as fixed.

Edit: Everything smooth after the reboot!

2 Likes
9

This is good news on two accounts - First and most importantly, you were able to fix your system. And second, that script continues to work with dnf5! Now, my hope is that the script won’t be needed by anyone any more moving forward :crossed_fingers: .