Dnf system-upgrade fails from F39->F40 KDE Spin

Again like many I have issues upgrading a F39 install to F40.

I have to use traditional Fedora on that PC as it is a dualboot with Windows. While Kinoite had no issues at all, system upgrades on traditional Fedora dont work well at all and are often broken for me.

Here I get the issue that the upgrade would remove many packages and one of them seems protected. Trying to remove it, prompts me to remove the entire plasma desktop.

user@PC:~$ sudo dnf system-upgrade download --releasever=40 --allowerasing --best
Before you continue ensure that your system is fully upgraded by running "dnf --refresh upgrade". Do you want to continue [y/N]: y
Fedora 40 - x86_64                                                                                                                                          147 kB/s |  28 kB     00:00    
Fedora 40 openh264 (From Cisco) - x86_64                                                                                                                    9.2 kB/s | 989  B     00:00    
Fedora 40 - x86_64 - Updates                                                                                                                                117 kB/s |  27 kB     00:00    
No match for group package "nafees-pakistani-naskh-fonts"
No match for group package "ibus-bogo"
No match for group package "lohit-malayalam-fonts"
No match for group package "wget"
No match for group package "lohit-nepali-fonts"
No match for group package "nafees-riqa-fonts"
No match for group package "khotkeys"
No match for group package "layla-arcyarc-fonts"
No match for group package "eosrei-emojione-fonts"
No match for group package "layla-boxer-fonts"
No match for group package "baekmuk-ttf-gulim-fonts"
No match for group package "baekmuk-ttf-hline-fonts"
No match for group package "google-noto-sans-phags-pa-fonts"
No match for group package "samyak-gujarati-fonts"
No match for group package "kf5-baloo-file"
No match for group package "kalapi-fonts"
No match for group package "multican"
No match for group package "layla-ruqaa-fonts"
No match for group package "fontawesome-fonts"
No match for group package "layla-koufi-fonts"
No match for group package "passwd"
No match for group package "nafees-pakistani-web-naskh-fonts"
No match for group package "kde-print-manager"
No match for group package "nafees-nastaleeq-fonts"
No match for group package "samyak-malayalam-fonts"
No match for group package "cdac-sakal-marathi-fonts"
No match for group package "baekmuk-ttf-dotum-fonts"
No match for group package "paktype-ajrak-fonts"
No match for group package "nafees-naskh-fonts"
No match for group package "layla-diwani-fonts"
No match for group package "baekmuk-ttf-batang-fonts"
No match for group package "samyak-devanagari-fonts"
No match for group package "lohit-tamil-classical-fonts"
No match for group package "nafees-tehreer-naskh-fonts"
No match for group package "layla-digital-fonts"
No match for group package "nafees-web-naskh-fonts"
No match for group package "google-noto-looped-thai-fonts"
No match for group package "samyak-odia-fonts"
No match for group package "scim-sayura"
No match for group package "layla-thuluth-fonts"
No match for group package "layla-basic-arabic-fonts"
No match for group package "kf5-audiocd-kio"
No match for group package "samyak-tamil-fonts"
Error: 
 Problem: The operation would result in removing the following protected packages: setup
(try to add '--skip-broken' to skip uninstallable packages)
1 Like

Removed kinoite

What is the output of the dnf with the skip broken?
I suspect there is a conflict that is triggering the cascade of failures.
Can you also set the locale to en_us so the messages are in english?

1 Like

Maybe I am totally wrong but can it be your F39 is using Plasma 5 and while doing the upgrade to F40 you’re also upgrading to Plasma 6? Can that be the reason Plasma is completely deleted?

1 Like

I would suggest to remove the file /etc/dnf/protected.d/setup.conf and see what happens.

The problem is that when dnf reports that a protected package would be removed, it would prevent the list of to-be removed packages to be shown. And to find out what is going on, we would need that list.

As the package setup is required by a lot of other packages, it would never be removed anyway without removing all the other packages as well.

That setting was already used.

1 Like

Doh. I meant without --skip-broken

1 Like

can you show:
sudo dnf repolist
sudo dnf list installed passwd shadow-utils

Yes thats true. And it should not be a problem. I suppose the packages may need to be unprotected but the metapackage plasma-desktop is removed @barryascott among others.

user@PC:~$ LANG=C
user@PC:~$ sudo dnf system-upgrade download --releasever=40              
[sudo] password for user: 
Before you continue ensure that your system is fully upgraded by running "dnf --refresh upgrade". Do you want to continue [y/N]: y
Fedora 40 - x86_64                                     122 kB/s |  28 kB     00:00    
Fedora 40 openh264 (From Cisco) - x86_64               7.9 kB/s | 989  B     00:00    
Fedora 40 - x86_64 - Updates                           163 kB/s |  27 kB     00:00    
Fedora 40 - x86_64 - Updates                           2.0 MB/s | 1.8 MB     00:00    
No match for group package "nafees-web-naskh-fonts"
No match for group package "samyak-malayalam-fonts"
No match for group package "wget"
No match for group package "samyak-tamil-fonts"
No match for group package "scim-sayura"
No match for group package "baekmuk-ttf-gulim-fonts"
No match for group package "layla-ruqaa-fonts"
No match for group package "ibus-bogo"
No match for group package "nafees-naskh-fonts"
No match for group package "layla-koufi-fonts"
No match for group package "baekmuk-ttf-batang-fonts"
No match for group package "layla-diwani-fonts"
No match for group package "google-noto-looped-thai-fonts"
No match for group package "paktype-ajrak-fonts"
No match for group package "layla-boxer-fonts"
No match for group package "eosrei-emojione-fonts"
No match for group package "nafees-pakistani-naskh-fonts"
No match for group package "samyak-gujarati-fonts"
No match for group package "nafees-riqa-fonts"
No match for group package "layla-digital-fonts"
No match for group package "kde-print-manager"
No match for group package "nafees-tehreer-naskh-fonts"
No match for group package "lohit-malayalam-fonts"
No match for group package "kf5-baloo-file"
No match for group package "lohit-nepali-fonts"
No match for group package "layla-thuluth-fonts"
No match for group package "khotkeys"
No match for group package "lohit-tamil-classical-fonts"
No match for group package "samyak-devanagari-fonts"
No match for group package "kf5-audiocd-kio"
No match for group package "nafees-nastaleeq-fonts"
No match for group package "cdac-sakal-marathi-fonts"
No match for group package "layla-arcyarc-fonts"
No match for group package "layla-basic-arabic-fonts"
No match for group package "nafees-pakistani-web-naskh-fonts"
No match for group package "passwd"
No match for group package "google-noto-sans-phags-pa-fonts"
No match for group package "baekmuk-ttf-hline-fonts"
No match for group package "samyak-odia-fonts"
No match for group package "baekmuk-ttf-dotum-fonts"
No match for group package "fontawesome-fonts"
No match for group package "multican"
No match for group package "kalapi-fonts"
Error: 
 Problem: The operation would result in removing the following protected packages: setup
(try to add '--skip-broken' to skip uninstallable packages)

Oh well…

user@PC:~$ sudo dnf repolist
repo id                                                                              repo name
fedora                                                                               Fedora 39 - x86_64
fedora-cisco-openh264                                                                Fedora 39 openh264 (From Cisco) - x86_64
updates                                                                              Fedora 39 - x86_64 - Updates
user@PC:~$ sudo dnf list installed passwd shadow-utils
Installed Packages
shadow-utils.x86_64                                                                         2:4.14.0-2.fc39                                                                         @updates
shadow-utils.x86_64                                                                         2:4.15.1-2.fc40  

Another case where the dnf system upgrade is completely broken I guess…

Doing a normal dnf upgrade pulls down f39 packages with tons of errors, while I already have some f40 packages installed.

That looks like a partial upgrade.
you may want to do:
sudo dnf distro-sync
sudo dnf remove --duplicates

And see if that cleans it up.

1 Like

distro sync gives me tons of dependency errors where Plasma 5 packages cannot be installed because they depend on unavailable outdated dependencies.

Is there no way to just rebase to the next vanilla OS??..

Adding these args reduces the issue to the setup package.

user@PC:~$ sudo dnf distro-sync --allowerasing --skip-broken
Last metadata expiration check: 0:04:14 ago on Sun Jul 14 13:53:37 2024.
Error: 
 Problem: The operation would result in removing the following protected packages: setup
user@PC:~$ sudo dnf remove --duplicates
Last metadata expiration check: 0:06:51 ago on Sun Jul 14 13:53:37 2024.
Installed package fonts-filesystem-1:2.0.5-14.fc40.noarch not available.
Installed package fontconfig-2.15.0-4.fc40.x86_64 not available.
Installed package abattis-cantarell-vf-fonts-0.301-12.fc40.noarch not available.
Installed package fedora-logos-38.1.0-5.fc40.noarch not available.
Installed package default-fonts-core-sans-4.0-13.fc40.noarch not available.
Installed package google-noto-sans-vf-fonts-20240301-2.fc40.noarch not available.
Installed package pcre2-syntax-10.42-2.fc40.2.noarch not available.
Installed package pcre2-10.42-2.fc40.2.x86_64 not available.
Installed package libreport-filesystem-2.17.15-1.fc40.noarch not available.
Installed package hunspell-filesystem-1.7.2-7.fc40.x86_64 not available.
Installed package cmake-filesystem-3.28.2-1.fc40.x86_64 not available.
Installed package whois-nls-5.5.20-3.fc40.noarch not available.
Installed package redhat-menus-12.0.2-26.fc40.noarch not available.
Installed package fuse-common-3.16.2-3.fc40.x86_64 not available.
Installed package setup-2.14.5-2.fc40.noarch not available.
Installed package filesystem-3.18-8.fc40.x86_64 not available.
Installed package systemd-255.6-1.fc40.x86_64 not available.
Installed package kbd-2.6.4-3.fc40.x86_64 not available.
Installed package pam-1.6.1-1.fc40.x86_64 not available.
Installed package adwaita-cursor-theme-46.0-1.fc40.noarch not available.
Installed package basesystem-11-20.fc40.noarch not available.
Installed package poppler-data-0.4.11-7.fc40.noarch not available.
Installed package xz-libs-1:5.4.6-3.fc40.x86_64 not available.
Installed package xz-1:5.4.6-3.fc40.x86_64 not available.
Installed package libpng-2:1.6.40-3.fc40.x86_64 not available.
Installed package popt-1.19-6.fc40.x86_64 not available.
Installed package glibc-2.39-13.fc40.x86_64 not available.
Installed package bzip2-libs-1.0.8-18.fc40.x86_64 not available.
Installed package sqlite-libs-3.45.1-2.fc40.x86_64 not available.
Installed package libcom_err-1.47.0-5.fc40.x86_64 not available.
Installed package libxcrypt-4.4.36-5.fc40.x86_64 not available.
Installed package mkpasswd-5.5.20-3.fc40.x86_64 not available.
Installed package json-c-0.17-3.fc40.x86_64 not available.
Installed package libtalloc-2.4.2-1.fc40.x86_64 not available.
Installed package gmp-1:6.2.1-8.fc40.x86_64 not available.
Installed package grep-3.11-7.fc40.x86_64 not available.
Installed package libtdb-1.4.10-1.fc40.x86_64 not available.
Installed package libtevent-0.16.1-1.fc40.x86_64 not available.
Installed package jansson-2.13.1-9.fc40.x86_64 not available.
Installed package libcap-ng-0.8.4-4.fc40.x86_64 not available.
Installed package libffi-3.4.4-7.fc40.x86_64 not available.
Installed package nettle-3.9.1-6.fc40.x86_64 not available.
Installed package libunistring-1.1-7.fc40.x86_64 not available.
Installed package dbus-common-1:1.14.10-3.fc40.noarch not available.
Installed package dbus-1:1.14.10-3.fc40.x86_64 not available.
Installed package lz4-libs-1.9.4-6.fc40.x86_64 not available.
Installed package dbus-libs-1:1.14.10-3.fc40.x86_64 not available.
Installed package libXau-1.0.11-6.fc40.x86_64 not available.
Installed package libxcb-1.17.0-1.fc40.x86_64 not available.
Installed package mpfr-4.2.1-4.fc40.x86_64 not available.
Installed package libref_array-0.1.5-56.fc40.x86_64 not available.
Installed package pixman-0.43.4-1.fc40.x86_64 not available.
Installed package libbasicobjects-0.1.1-56.fc40.x86_64 not available.
Installed package libbrotli-1.1.0-3.fc40.x86_64 not available.
Installed package libcollection-0.7.0-56.fc40.x86_64 not available.
Installed package libdhash-0.5.0-56.fc40.x86_64 not available.
Installed package libtasn1-4.19.0-6.fc40.x86_64 not available.
Installed package lua-libs-5.4.6-5.fc40.x86_64 not available.
Installed package libpsl-0.21.5-3.fc40.x86_64 not available.
Installed package publicsuffix-list-dafsa-20240107-3.fc40.noarch not available.
Installed package xml-common-0.6.3-63.fc40.noarch not available.
Installed package libattr-2.5.2-3.fc40.x86_64 not available.
Installed package libsepol-3.6-3.fc40.x86_64 not available.
Installed package libselinux-3.6-4.fc40.x86_64 not available.
Installed package sed-4.9-1.fc40.x86_64 not available.
Installed package findutils-1:4.9.0-8.fc40.x86_64 not available.
Installed package libsemanage-3.6-3.fc40.x86_64 not available.
Installed package audit-libs-4.0.1-1.fc40.x86_64 not available.
Installed package protobuf-c-1.5.0-3.fc40.x86_64 not available.
Installed package file-libs-5.45-4.fc40.x86_64 not available.
Installed package file-5.45-4.fc40.x86_64 not available.
Installed package tcl-1:8.6.13-2.fc40.x86_64 not available.
Installed package fuse-libs-2.9.9-21.fc40.x86_64 not available.
Installed package gdbm-libs-1:1.23-6.fc40.x86_64 not available.
Installed package cyrus-sasl-lib-2.1.28-19.fc40.x86_64 not available.
Installed package cpio-2.15-1.fc40.x86_64 not available.
Installed package libverto-0.3.2-8.fc40.x86_64 not available.
Installed package libb2-0.98.1-11.fc40.x86_64 not available.
Installed package libbpf-2:1.2.0-3.fc40.x86_64 not available.
Installed package graphite2-1.3.14-15.fc40.x86_64 not available.
Installed package voikko-fi-2.5-6.fc40.noarch not available.
Installed package diffutils-3.10-5.fc40.x86_64 not available.
Installed package libdb-5.3.28-61.fc40.x86_64 not available.
Installed package qrencode-libs-4.1.1-7.fc40.x86_64 not available.
Installed package gettext-libs-0.22.5-2.fc40.x86_64 not available.
Installed package pigz-2.8-4.fc40.x86_64 not available.
Installed package jemalloc-5.3.0-6.fc40.x86_64 not available.
Installed package memstrack-0.2.5-4.fc40.x86_64 not available.
Installed package fstrm-0.6.1-10.fc40.x86_64 not available.
Installed package gettext-envsubst-0.22.5-2.fc40.x86_64 not available.
Installed package gettext-runtime-0.22.5-2.fc40.x86_64 not available.
Installed package dbus-broker-36-2.fc40.x86_64 not available.
Installed package libpath_utils-0.2.1-56.fc40.x86_64 not available.
Installed package libini_config-1.3.1-56.fc40.x86_64 not available.
Installed package libsigsegv-2.14-8.fc40.x86_64 not available.
Installed package mpdecimal-2.5.1-9.fc40.x86_64 not available.
Installed package libXext-1.3.6-1.fc40.x86_64 not available.
Installed package libX11-1.8.9-1.fc40.x86_64 not available.
Installed package libXrender-0.9.11-6.fc40.x86_64 not available.
Installed package kbd-misc-2.6.4-3.fc40.noarch not available.
Installed package kbd-legacy-2.6.4-3.fc40.noarch not available.
Installed package gawk-all-langpacks-5.3.0-3.fc40.x86_64 not available.
Installed package gawk-5.3.0-3.fc40.x86_64 not available.
Installed package cairo-1.18.0-3.fc40.x86_64 not available.
Installed package fprintd-pam-1.94.2-11.fc40.x86_64 not available.
Installed package authselect-1.5.0-5.fc40.x86_64 not available.
Installed package harfbuzz-8.4.0-1.fc40.x86_64 not available.
Installed package freetype-2.13.2-5.fc40.x86_64 not available.
Installed package sssd-2.9.4-7.fc40.x86_64 not available.
Installed package authselect-libs-1.5.0-5.fc40.x86_64 not available.
Installed package libutempter-1.2.1-13.fc40.x86_64 not available.
Installed package shadow-utils-2:4.15.1-2.fc40.x86_64 not available.
Installed package logrotate-3.21.0-6.fc40.x86_64 not available.
Installed package libpinyin-data-2.8.1-7.fc40.x86_64 not available.
Installed package pam-libs-1.6.1-1.fc40.x86_64 not available.
Installed package xkeyboard-config-2.41-1.fc40.noarch not available.
Installed package libxkbcommon-1.6.0-2.fc40.x86_64 not available.
Installed package procps-ng-4.0.4-3.fc40.x86_64 not available.
Installed package dracut-101-1.fc40.x86_64 not available.
Installed package bash-5.2.26-3.fc40.x86_64 not available.
Installed package systemd-udev-255.6-1.fc40.x86_64 not available.
Installed package util-linux-2.40.1-1.fc40.x86_64 not available.
Installed package libgcc-14.1.1-1.fc40.x86_64 not available.
Installed package google-noto-fonts-common-20240301-2.fc40.noarch not available.
Installed package kf5-filesystem-5.115.0-1.fc40.x86_64 not available.
Installed package tzdata-2024a-5.fc40.noarch not available.
Installed package glibc-common-2.39-13.fc40.x86_64 not available.
Installed package breeze-gtk-common-6.0.4.1-1.fc40.noarch not available.
Installed package mesa-filesystem-24.0.7-3.fc40.x86_64 not available.
Installed package google-noto-sans-fonts-20240301-2.fc40.noarch not available.
Installed package plasma-breeze-common-6.0.4-1.fc40.noarch not available.
Installed package fedora-release-identity-kde-40-39.noarch not available.
Installed package fedora-release-kde-40-39.noarch not available.
Installed package breeze-cursor-theme-6.0.4-1.fc40.noarch not available.
Installed package qt-settings-40.0-1.fc40.noarch not available.
Installed package ncurses-base-6.4-12.20240127.fc40.noarch not available.
Installed package glibc-all-langpacks-2.39-13.fc40.x86_64 not available.
Installed package glibc-gconv-extra-2.39-13.fc40.x86_64 not available.
Installed package ncurses-libs-6.4-12.20240127.fc40.x86_64 not available.
Installed package glibc-langpack-en-2.39-13.fc40.x86_64 not available.
Installed package libstdc++-14.1.1-1.fc40.x86_64 not available.
Installed package libzstd-1.5.6-1.fc40.x86_64 not available.
Installed package libuuid-2.40.1-1.fc40.x86_64 not available.
Installed package libblkid-2.40.1-1.fc40.x86_64 not available.
Installed package expat-2.6.2-1.fc40.x86_64 not available.
Installed package alternatives-1.26-3.fc40.x86_64 not available.
Installed package libX11-xcb-1.8.9-1.fc40.x86_64 not available.
Installed package libcap-2.69-8.fc40.x86_64 not available.
Installed package systemd-libs-255.6-1.fc40.x86_64 not available.
Installed package libusb1-1.0.27-2.fc40.x86_64 not available.
Installed package nspr-4.35.0-22.fc40.x86_64 not available.
Installed package elfutils-libelf-0.191-4.fc40.x86_64 not available.
Installed package grub2-common-1:2.06-121.fc40.noarch not available.
Installed package util-linux-core-2.40.1-1.fc40.x86_64 not available.
Installed package grubby-8.40-75.fc40.x86_64 not available.
Installed package keyutils-libs-1.6.3-3.fc40.x86_64 not available.
Installed package libacl-2.3.2-1.fc40.x86_64 not available.
Installed package readline-8.2-8.fc40.x86_64 not available.
Installed package libmount-2.40.1-1.fc40.x86_64 not available.
Installed package libidn2-2.3.7-1.fc40.x86_64 not available.
Installed package p11-kit-0.25.3-4.fc40.x86_64 not available.
Installed package libnl3-3.9.0-3.fc40.x86_64 not available.
Installed package libsss_idmap-2.9.4-7.fc40.x86_64 not available.
Installed package libgomp-14.1.1-1.fc40.x86_64 not available.
Installed package libfdisk-2.40.1-1.fc40.x86_64 not available.
Installed package libnghttp2-1.59.0-3.fc40.x86_64 not available.
Installed package libsmartcols-2.40.1-1.fc40.x86_64 not available.
Installed package p11-kit-trust-0.25.3-4.fc40.x86_64 not available.
Installed package c-ares-1.28.1-1.fc40.x86_64 not available.
Installed package libipa_hbac-2.9.4-7.fc40.x86_64 not available.
Installed package libsss_nss_idmap-2.9.4-7.fc40.x86_64 not available.
Installed package libsss_sudo-2.9.4-7.fc40.x86_64 not available.
Installed package sssd-common-2.9.4-7.fc40.x86_64 not available.
Installed package libuv-1:1.48.0-1.fc40.x86_64 not available.
Installed package libwacom-data-2.11.0-1.fc40.noarch not available.
Installed package libX11-common-1.8.9-1.fc40.noarch not available.
Installed package grub2-tools-1:2.06-121.fc40.x86_64 not available.
Installed package elfutils-default-yama-scope-0.191-4.fc40.noarch not available.
Installed package elfutils-libs-0.191-4.fc40.x86_64 not available.
Installed package device-mapper-1.02.197-1.fc40.x86_64 not available.
Installed package device-mapper-libs-1.02.197-1.fc40.x86_64 not available.
Installed package systemd-networkd-255.6-1.fc40.x86_64 not available.
Installed package systemd-pam-255.6-1.fc40.x86_64 not available.
Installed package sssd-krb5-common-2.9.4-7.fc40.x86_64 not available.
Installed package sssd-krb5-2.9.4-7.fc40.x86_64 not available.
Installed package sssd-ldap-2.9.4-7.fc40.x86_64 not available.
Installed package sssd-proxy-2.9.4-7.fc40.x86_64 not available.
Installed package sssd-ipa-2.9.4-7.fc40.x86_64 not available.
Installed package qt6-qttranslations-6.7.0-1.fc40.noarch not available.
Installed package libeconf-0.6.2-1.fc40.x86_64 not available.
Installed package appstream-data-40-7.fc40.noarch not available.
Error: 
 Problem: The operation would result in removing the following protected packages: setup, systemd, systemd-udev
(try to add '--skip-broken' to skip uninstallable packages)

This looks like the repos are still old

Added dnf

Doing the upgrade, normally I would use --allowerasing to just remove outdated packages, but this seems to not do anything the output is the same. Instead it says I should use --skip-broken which sounds dangerous on a system upgrade as it may lead to outdated packages.

(Updated the first code block)

A lot of those packages were retired during F39/40.

can you manually remove the duplicate shadow-utils package with rpm?
rpm -e --justdb --nodeps shadow-utils-4.15.1-2.fc40.x86_64

And then do the distrosync?

thanks

2 Likes

When upgrading fedora you have to bring it more or less back to an standard setup.
If you install packages where since F39 are orphaned you can really not generalize and say that “traditional Fedora don’t work well at all”

samyak-gujarati-fonts
Package Info

    Upstream: http://sarovar.org/projects/samyak/
    License(s): GPLv3+ with exceptions
    Maintainer: orphan


Source:  https://packages.fedoraproject.org/pkgs/samyak-fonts/samyak-gujarati-fonts/

Files of that package are:

Files

    etc/
        fonts/
            conf.d/
                67-samyak-gujarati.conf
    usr/
        share/
            appdata/
                samyak-gujarati.metainfo.xml
            fontconfig/
                conf.avail/
                    67-samyak-gujarati.conf
            fonts/
                samyak/
                    Samyak-Gujarati.ttf
1 Like

Thanks, that worked. Still with allowerasing distrosync I get the issue with the setup package

But why doesnt --allowerasing just remove them? I didnt install these packages manually.

Also there are some strange groups like passwd and wget

I think that is what @grumpey tries to help you with? Two versions for one package, seeing from your errors you posted above.