pag-r
April 28, 2021, 7:35am
1
After:
sudo dnf system-upgrade reboot
And reboot I get below error in /var/log/dnf.log
2021-04-28T09:11:18+0200 INFO Last metadata expiration check: 0:33:32 ago on Wed 28 Apr 2021 08:37:45 CEST.
2021-04-28T09:11:18+0200 DDEBUG timer: sack setup: 5875 ms
2021-04-28T09:11:26+0200 DEBUG --> Starting dependency resolution
2021-04-28T09:11:26+0200 DEBUG --> Finding unneeded leftover dependencies
2021-04-28T09:11:27+0200 DEBUG --> Finished dependency resolution
2021-04-28T09:11:27+0200 DDEBUG timer: depsolve: 1098 ms
2021-04-28T09:11:27+0200 SUBDEBUG
Traceback (most recent call last):
File "/usr/lib/python3.9/site-packages/dnf/cli/main.py", line 130, in cli_run
ret = resolving(cli, base)
File "/usr/lib/python3.9/site-packages/dnf/cli/main.py", line 166, in resolving
base.resolve(cli.demands.allow_erasing)
File "/usr/lib/python3.9/site-packages/dnf/base.py", line 848, in resolve
raise exc
dnf.exceptions.DepsolveError:
Problem: The operation would result in removing the following protected packages: kernel-core
2021-04-28T09:11:27+0200 CRITICAL Error:
Problem: The operation would result in removing the following protected packages: kernel-core
2021-04-28T09:11:27+0200 INFO (try to add '--skip-broken' to skip uninstallable packages)
2021-04-28T09:11:27+0200 DDEBUG Cleaning up.
I’ve upgrade Fedora multiple times (starting from Fedora 29 onwards) w/o any major issues.
1 Like
Hi @pag-r , welcome to the forum! Please take a moment to go through the introductory posts in the #start-here category if you’ve not had a chance to do that yet.
Can you please provide more information on what you did before you got to this stage. For example, before rebooting, did you follow the correct steps here? I.e. was your system up to date?
Can you also please post the output of
fpaste --sysinfo --printonly
and
rpm -qa \*kernel\*
pag-r
April 28, 2021, 7:57am
3
Hi @ankursinha . Thx for your reply.DNF System Upgrade :: Fedora Docs . I had one more issue with rdma-core, but I’ve fixed it by removing: dnf remove rdma-core.i686. System is up-to-date.
rpm -qa \*kernel\*
kernel-srpm-macros-1.0-3.fc33.noarch
abrt-addon-kerneloops-2.14.5-1.fc33.x86_64
libreport-plugin-kerneloops-2.14.0-15.fc33.x86_64
kernel-core-5.11.15-200.fc33.x86_64
kernel-modules-5.11.15-200.fc33.x86_64
kernel-5.11.15-200.fc33.x86_64
kernel-modules-extra-5.11.15-200.fc33.x86_64
kernel-devel-5.11.15-200.fc33.x86_64
kernel-debug-devel-5.11.15-200.fc33.x86_64
kernel-core-5.11.16-200.fc33.x86_64
kernel-modules-5.11.16-200.fc33.x86_64
kernel-5.11.16-200.fc33.x86_64
kernel-modules-extra-5.11.16-200.fc33.x86_64
kernel-headers-5.11.16-200.fc33.x86_64
kernel-devel-5.11.16-200.fc33.x86_64
kernel-debug-devel-5.11.16-200.fc33.x86_64
=== fpaste 0.4.1.1 System Information ===
* OS Release (cat /etc/*-release | uniq):
Fedora release 33 (Thirty Three)
NAME=Fedora
VERSION="33 (Workstation Edition)"
ID=fedora
VERSION_ID=33
VERSION_CODENAME=""
PLATFORM_ID="platform:f33"
PRETTY_NAME="Fedora 33 (Workstation Edition)"
ANSI_COLOR="0;38;2;60;110;180"
LOGO=fedora-logo-icon
CPE_NAME="cpe:/o:fedoraproject:fedora:33"
HOME_URL="https://fedoraproject.org/"
DOCUMENTATION_URL="https://docs.fedoraproject.org/en-US/fedora/f33/system-administrators-guide/"
SUPPORT_URL="https://fedoraproject.org/wiki/Communicating_and_getting_help"
BUG_REPORT_URL="https://bugzilla.redhat.com/"
REDHAT_BUGZILLA_PRODUCT="Fedora"
REDHAT_BUGZILLA_PRODUCT_VERSION=33
REDHAT_SUPPORT_PRODUCT="Fedora"
REDHAT_SUPPORT_PRODUCT_VERSION=33
PRIVACY_POLICY_URL="https://fedoraproject.org/wiki/Legal:PrivacyPolicy"
VARIANT="Workstation Edition"
VARIANT_ID=workstation
Fedora release 33 (Thirty Three)
* Kernel (uname -r ; cat /proc/cmdline):
5.11.16-200.fc33.x86_64
BOOT_IMAGE=(hd0,msdos1)/vmlinuz-5.11.16-200.fc33.x86_64 root=/dev/mapper/fedora_fornost-root ro rd.lvm.lv=fedora_fornost/root rd.luks.uuid=luks-4a44cae0-007a-46d3-8c74-27b4703d3163 rd.lvm.lv=fedora_fornost/swap rhgb quiet systemd.unified_cgroup_hierarchy=0
* Desktop(s) Running (ps -eo comm= | grep -E '(gnome-session|startkde|startactive|xfce.?-session|fluxbox|blackbox|hackedbox|ratpoison|enlightenment|icewm-session|od-session|wmaker|wmx|openbox-lxde|openbox-gnome-session|openbox-kde-session|mwm|e16|fvwm|xmonad|sugar-session|mate-session|lxqt-session|cinnamon)' ):
gnome-session-b
gnome-session-c
gnome-session-b
* Desktop(s) Installed (ls -m /usr/share/xsessions/ | sed 's/\.desktop//g' ):
dwm, dwm-user, gnome-classic, gnome,
gnome-xorg, openbox
* SELinux Status (sestatus):
SELinux status: disabled
* SELinux Errors (without results: "selinuxenabled && journalctl --since yesterday |grep avc: | grep -Eo comm="[^ ]+" | sort |uniq -c |sort -rn"):
N/A
* CPU Model (grep 'model name' /proc/cpuinfo | awk -F: '{print $2}' | uniq -c |
sed -re 's/^ +//' ):
4 Intel(R) Core(TM) i7-2620M CPU @ 2.70GHz
* 64-bit Support (grep -q ' lm ' /proc/cpuinfo && echo Yes || echo No):
Yes
* Hardware Virtualization Support (grep -Eq '(vmx|svm)' /proc/cpuinfo && echo Yes || echo No):
Yes
* Load average (uptime):
09:55:05 up 43 min, 1 user, load average: 0.77, 0.62, 0.43
* Memory usage (free -m):
total used free shared buff/cache available
Mem: 7833 1616 4332 403 1883 5560
Swap: 3899 0 3899
* Top 5 CPU hogs (ps axuScnh | awk '$2!=4171' | sort -rnk3 | head -5):
1000 2886 14.7 5.5 3501528 443800 ? Sl 09:16 5:39 firefox
1000 2978 6.5 3.0 2926240 245540 ? Sl 09:16 2:30 Web Content
1000 2209 3.8 2.2 3949680 183388 ? Ssl 09:12 1:37 gnome-shell
1000 3028 1.9 5.1 3155688 416212 ? Sl 09:16 0:45 Web Content
0 1 1.6 0.1 106872 14324 ? Ss 09:11 0:42 systemd
* Top 5 Memory hogs (ps axuScnh | sort -rnk4 | head -5):
1000 2886 14.7 5.5 3501528 443800 ? Sl 09:16 5:39 firefox
1000 3028 1.9 5.1 3155688 416212 ? Sl 09:16 0:45 Web Content
1000 2978 6.5 3.0 2926240 245540 ? Sl 09:16 2:30 Web Content
1000 3171 1.4 2.8 28014748 231756 ? Sl 09:16 0:32 WebExtensions
1000 3019 0.3 2.3 2853400 184972 ? Sl 09:16 0:08 Web Content
* Disk space usage (df -hT):
Filesystem Type Size Used Avail Use% Mounted on
devtmpfs devtmpfs 3.9G 0 3.9G 0% /dev
tmpfs tmpfs 3.9G 1.6M 3.9G 1% /dev/shm
tmpfs tmpfs 1.6G 1.8M 1.6G 1% /run
tmpfs tmpfs 4.0M 0 4.0M 0% /sys/fs/cgroup
/dev/mapper/fedora_fornost-root ext4 45G 36G 6.4G 85% /
tmpfs tmpfs 3.9G 16K 3.9G 1% /tmp
/dev/sdc1 ext4 976M 181M 729M 20% /boot
/dev/mapper/fedora_fornost-home ext4 61G 50G 8.6G 86% /home
tmpfs tmpfs 784M 144K 784M 1% /run/user/1000
* Block devices (blkid):
/dev/sda1: LABEL="ZastrzeM-EM-<one przez system" BLOCK_SIZE="512" UUID="B84ADCBA4ADC771A" TYPE="ntfs" PARTUUID="558bbc28-01"
/dev/sda2: BLOCK_SIZE="512" UUID="80D6E196D6E18D2A" TYPE="ntfs" PARTUUID="558bbc28-02"
/dev/sda3: BLOCK_SIZE="512" UUID="E64650B446508769" TYPE="ntfs" PARTUUID="558bbc28-03"
/dev/sda4: UUID="2e5132d6-7091-4781-965a-927773383994" UUID_SUB="1212a382-293a-4258-9fab-4a536f82bb24" BLOCK_SIZE="4096" TYPE="btrfs" PARTUUID="558bbc28-04"
/dev/sdb1: LABEL="System" BLOCK_SIZE="512" UUID="D4287AAC287A8CEC" TYPE="ntfs" PARTUUID="6ee6939d-01"
/dev/sdb2: LABEL="Nowy" BLOCK_SIZE="512" UUID="EC66AA0666A9D19E" TYPE="ntfs" PARTUUID="6ee6939d-02"
/dev/sdc1: LABEL="vg-boot" UUID="79d248b4-461f-4f48-a1b7-a6d398f8a54f" BLOCK_SIZE="4096" TYPE="ext4" PARTUUID="42a204ab-01"
/dev/sdc2: UUID="4a44cae0-007a-46d3-8c74-27b4703d3163" TYPE="crypto_LUKS" PARTUUID="42a204ab-02"
/dev/mapper/luks-4a44cae0-007a-46d3-8c74-27b4703d3163: UUID="aQu18B-WHRz-Xq6M-5Uuy-vc2r-TpQR-4DIpCG" TYPE="LVM2_member"
/dev/mapper/fedora_fornost-root: LABEL="lv-root" UUID="ad321cac-5352-48a3-b3e5-1a9b3cb4ab30" BLOCK_SIZE="4096" TYPE="ext4"
/dev/mapper/fedora_fornost-swap: LABEL="lv-swap" UUID="4618c673-ece6-4d8e-8470-22d015dc855e" TYPE="swap"
/dev/mapper/fedora_fornost-home: LABEL="lv-home" UUID="88c5b5f9-9ed8-45d4-b764-3046c0bb546b" BLOCK_SIZE="4096" TYPE="ext4"
* PCI devices (lspci -nn):
00:00.0 Host bridge [0600]: Intel Corporation 2nd Generation Core Processor Family DRAM Controller [8086:0104] (rev 09)
00:02.0 VGA compatible controller [0300]: Intel Corporation 2nd Generation Core Processor Family Integrated Graphics Controller [8086:0126] (rev 09)
00:16.0 Communication controller [0780]: Intel Corporation 6 Series/C200 Series Chipset Family MEI Controller #1 [8086:1c3a] (rev 04)
00:16.3 Serial controller [0700]: Intel Corporation 6 Series/C200 Series Chipset Family KT Controller [8086:1c3d] (rev 04)
00:19.0 Ethernet controller [0200]: Intel Corporation 82579LM Gigabit Network Connection (Lewisville) [8086:1502] (rev 04)
00:1a.0 USB controller [0c03]: Intel Corporation 6 Series/C200 Series Chipset Family USB Enhanced Host Controller #2 [8086:1c2d] (rev 04)
00:1b.0 Audio device [0403]: Intel Corporation 6 Series/C200 Series Chipset Family High Definition Audio Controller [8086:1c20] (rev 04)
00:1c.0 PCI bridge [0604]: Intel Corporation 6 Series/C200 Series Chipset Family PCI Express Root Port 1 [8086:1c10] (rev b4)
00:1c.1 PCI bridge [0604]: Intel Corporation 6 Series/C200 Series Chipset Family PCI Express Root Port 2 [8086:1c12] (rev b4)
00:1c.4 PCI bridge [0604]: Intel Corporation 6 Series/C200 Series Chipset Family PCI Express Root Port 5 [8086:1c18] (rev b4)
00:1d.0 USB controller [0c03]: Intel Corporation 6 Series/C200 Series Chipset Family USB Enhanced Host Controller #1 [8086:1c26] (rev 04)
00:1f.0 ISA bridge [0601]: Intel Corporation QM67 Express Chipset LPC Controller [8086:1c4f] (rev 04)
00:1f.2 SATA controller [0106]: Intel Corporation 6 Series/C200 Series Chipset Family 6 port Mobile SATA AHCI Controller [8086:1c03] (rev 04)
00:1f.3 SMBus [0c05]: Intel Corporation 6 Series/C200 Series Chipset Family SMBus Controller [8086:1c22] (rev 04)
03:00.0 Network controller [0280]: Intel Corporation Centrino Advanced-N 6205 [Taylor Peak] [8086:0085] (rev 34)
0d:00.0 SD Host controller [0805]: Ricoh Co Ltd MMC/SD Host Controller [1180:e822] (rev 08)
* USB devices (lsusb):
Bus 002 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 001 Device 003: ID 046d:c52b Logitech, Inc. Unifying Receiver
Bus 001 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
* DRM Information (journalctl -k -b | grep -o 'kernel:.*drm.*$' | cut -d ' ' -f 2- ):
[drm] Initialized i915 1.6.0 20201103 for 0000:00:02.0 on minor 0
fbcon: i915drmfb (fb0) is primary device
i915 0000:00:02.0: [drm] fb0: i915drmfb frame buffer device
* Xorg modules (grep LoadModule /var/log/Xorg.0.log ~/.local/share/xorg/Xorg.0.log | cut -d \" -f 2 | xargs):
* GL Support (glxinfo | grep -E "OpenGL version|OpenGL renderer"):
OpenGL renderer string: Mesa DRI Intel(R) HD Graphics 3000 (SNB GT2)
OpenGL version string: 3.0 Mesa 20.3.5
* Xorg errors (without results: "grep '^\[.*(EE)' /var/log/Xorg.0.log ~/.local/share/xorg/Xorg.0.log | cut -d ':' -f 2- "):
N/A
* Kernel buffer tail (dmesg | tail):
[ 35.451915] virbr0: port 1(virbr0-nic) entered blocking state
[ 35.451922] virbr0: port 1(virbr0-nic) entered disabled state
[ 35.451976] device virbr0-nic entered promiscuous mode
[ 35.868622] virbr0: port 1(virbr0-nic) entered blocking state
[ 35.868629] virbr0: port 1(virbr0-nic) entered listening state
[ 35.908543] virbr0: port 1(virbr0-nic) entered disabled state
[ 38.287453] rfkill: input handler disabled
[ 73.362418] rfkill: input handler enabled
[ 78.075152] rfkill: input handler disabled
[ 1544.781975] logitech-hidpp-device 0003:046D:101B.0004: HID++ 1.0 device connected.
* Last few reboots (last -x -n10 reboot runlevel):
runlevel (to lvl 5) 5.11.16-200.fc33 Wed Apr 28 09:12 still running
reboot system boot 5.11.16-200.fc33 Wed Apr 28 11:12 still running
reboot system boot 5.11.16-200.fc33 Wed Apr 28 11:11 - 09:11 (-1:59)
runlevel (to lvl 5) 5.11.16-200.fc33 Wed Apr 28 09:03 - 09:10 (00:06)
reboot system boot 5.11.16-200.fc33 Wed Apr 28 11:03 - 09:10 (-1:53)
reboot system boot 5.11.16-200.fc33 Wed Apr 28 11:02 - 09:03 (-1:59)
runlevel (to lvl 5) 5.11.16-200.fc33 Wed Apr 28 08:54 - 09:02 (00:07)
reboot system boot 5.11.16-200.fc33 Wed Apr 28 10:54 - 09:02 (-1:52)
reboot system boot 5.11.16-200.fc33 Wed Apr 28 10:53 - 08:53 (-1:59)
runlevel (to lvl 5) 5.11.15-200.fc33 Mon Apr 26 15:51 - 08:52 (1+17:01)
wtmp begins Fri Dec 16 20:51:43 2016
* DNF Repositories (dnf repolist):
repo id repo name
brave-browser-rpm-release.s3.brave.com_x86_64_ created by dnf config-manager from https://brave-browser-rpm-release.s3.brave.com/x86_64/
copr:copr.fedorainfracloud.org:nunodias:nixnote2 Copr repo for nixnote2 owned by nunodias
docker-ce-stable Docker CE Stable - x86_64
fedora Fedora 33 - x86_64
fedora-cisco-openh264 Fedora 33 openh264 (From Cisco) - x86_64
fedora-modular Fedora Modular 33 - x86_64
google-chrome google-chrome
nordvpn NordVPN YUM repository - x86_64
nordvpn-noarch NordVPN YUM repository - noarch
rpmfusion-free RPM Fusion for Fedora 33 - Free
rpmfusion-free-updates RPM Fusion for Fedora 33 - Free - Updates
rpmfusion-nonfree RPM Fusion for Fedora 33 - Nonfree
rpmfusion-nonfree-updates RPM Fusion for Fedora 33 - Nonfree - Updates
rpmsphere RPM Sphere - Basearch
rpmsphere-noarch RPM Sphere - Noarch
teams teams
updates Fedora 33 - x86_64 - Updates
updates-modular Fedora Modular 33 - x86_64 - Updates
* DNF Extras (dnf -C list extras):
Last metadata expiration check: 2:23:48 ago on Wed 28 Apr 2021 07:31:20 CEST.
Extra Packages
ICAClient.x86_64 20.06.0.15-0 @@commandline
bind-export-libs.x86_64 32:9.11.11-1.fc30 @updates
brscan-skey.x86_64 0.2.4-1 @System
brscan4.x86_64 0.4.6-1 @System
chef-workstation.x86_64 0.17.5-1.el7 @@commandline
citrix-hdx-realtime-media-engine.x86_64 2.9.100-2419 @System
clang5.0-libs.x86_64 5.0.1-6.fc30 @fedora
clang6.0-libs.x86_64 6.0.1-8.fc30 @fedora
codium.x86_64 1.55.2-1618361370.el8 @@commandline
dcpl2530dwpdrv.i386 4.0.0-1 @System
dwm.x86_64 6.1-8.module_f31+5349+00dfe6a5 @fedora-modular
dwm-user.x86_64 6.1-8.module_f31+5349+00dfe6a5 @fedora-modular
java-9-openjdk-headless.x86_64 1:9.0.4.11-6.fc28 @fedora
jp2a.x86_64 1.0.7-6.fc32 @fedora
libblockdev-vdo.x86_64 2.24-2.fc32 @updates
mongo-tools.x86_64 3.6.3-0.5.20180319git2b10d84.fc29 @fedora
pam_krb5.x86_64 2.4.13-14.fc31 @fedora
recordmydesktop.x86_64 0.3.8.1-19.fc27 @fedora
recoverjpeg.x86_64 2.6.1-6.fc29 @fedora
tabish-eeyek-fonts.noarch 1.0-13.fc29 @fedora
* Last 20 packages installed (rpm -qa --nodigest --nosignature --last | head -20):
gpg-pubkey-45719a39-5f2c0192 Wed 28 Apr 2021 08:44:42 CEST
gpg-pubkey-c2d4e821-5e7252b8 Wed 28 Apr 2021 07:46:02 CEST
gdk-pixbuf2-modules-2.42.6-1.fc33.i686 Wed 28 Apr 2021 07:35:25 CEST
gdk-pixbuf2-2.42.6-1.fc33.i686 Wed 28 Apr 2021 07:35:21 CEST
kernel-debug-devel-5.11.16-200.fc33.x86_64 Wed 28 Apr 2021 07:34:49 CEST
kernel-devel-5.11.16-200.fc33.x86_64 Wed 28 Apr 2021 07:34:38 CEST
gnome-settings-daemon-3.38.2-1.fc33.x86_64 Wed 28 Apr 2021 07:34:30 CEST
kernel-headers-5.11.16-200.fc33.x86_64 Wed 28 Apr 2021 07:34:29 CEST
ostree-libs-2021.2-2.fc33.x86_64 Wed 28 Apr 2021 07:34:28 CEST
perl-version-0.99.29-1.fc33.x86_64 Wed 28 Apr 2021 07:34:21 CEST
google-chrome-stable-90.0.4430.93-1.x86_64 Wed 28 Apr 2021 07:34:18 CEST
kernel-modules-extra-5.11.16-200.fc33.x86_64 Wed 28 Apr 2021 07:33:50 CEST
xdg-desktop-portal-wlr-0.3.0-1.fc33.x86_64 Wed 28 Apr 2021 07:33:49 CEST
slurp-1.3.2-1.fc33.x86_64 Wed 28 Apr 2021 07:33:49 CEST
sane-airscan-0.99.26-1.fc33.x86_64 Wed 28 Apr 2021 07:33:49 CEST
libsane-airscan-0.99.26-1.fc33.x86_64 Wed 28 Apr 2021 07:33:49 CEST
libical-glib-3.0.10-1.fc33.x86_64 Wed 28 Apr 2021 07:33:49 CEST
libical-3.0.10-1.fc33.x86_64 Wed 28 Apr 2021 07:33:49 CEST
kernel-5.11.16-200.fc33.x86_64 Wed 28 Apr 2021 07:33:49 CEST
iniparser-4.1-6.fc33.x86_64 Wed 28 Apr 2021 07:33:49 CEST
* EFI boot manager output (without results: "efibootmgr -v"):
N/A
1 Like
Thanks. That all looks pretty OK, so that’s very odd. Can you check what you’ve set as the installonly_limit in /etc/dnf/dnf.conf?
Did the error only crop up on reboot, and not during the initial transaction test during dnf sytem-upgrade download...?
pag-r
April 28, 2021, 9:55am
5
Error is only visible in the logs after reboot not during the dnf system-upgrade download
# grep installonly_limit /etc/dnf/dnf.conf installonly_limit=2
1 Like
ankursinha
April 28, 2021, 10:09am
6
That looks fine too. Thanks.
So, this is what the docs say about protected packages:
https://rpm-software-management.github.io/dnf-plugins-core/protected_packages.html
The currently booted kernel is protected. When you tried to upgrade, were you booted into the latest kernel (which your fpaste output shows you are booted into now)? The error indicates that you maybe were booted into the older of the two. dnf can keep 2 kernels installed, so it wanted to remove the older one to install the new F34 kernel, but because you were booted into the older one, it was protected and could not be removed. Can you try the upgrade again now that you’re booted into the latest kernel? let us know if you’ve already tried that and still get the error. We’ll look at other possibilities then.
pag-r
April 28, 2021, 10:46am
7
It’t fixed! It turns out that I had to once again run dnf update --refresh and dnf system-upgrade download. There were few new packages and issue has been resolved. Thanks a lot for your help!
1 Like
ankursinha
April 28, 2021, 11:12am
8
Great. Glad that worked. I suspect it was because you weren’t booted into the latest kernel when you’d tried before, and so DNF refused to remove it because it was protected. A workaround would’ve been to increase the installonly_limit to 3 so that DNF didn’t need to remove a kernel for the upgrade at all. Of course, rebooting into the latest version so that DNF can remove the older one is a better solution
I’ve marked your comment as the solution then. (We don’t need to change the topic title on Discourse—marking a comment as the answer puts a nice tickbox next to it etc.)
1 Like
system
May 26, 2021, 11:12am
9
This topic was automatically closed 28 days after the last reply. New replies are no longer allowed.
