Today I tried to update all packages with sudo dnf --refresh upgrade command in my Fedora 35 desktop. During the package update, I encountered with this issue - error: rpmdb: damaged header #5904 retrieved -- skipping.
I kept getting this error a lot. I couldn't update the Fedora system. After a couple web searches, I found that the RPM database is corrupted for some reason.
If you ever stuck into a situation like mine, you can easily solve the "rpmdb damaged header" error by rebuilding the RPM database as shown in the following steps.
Fix error: rpmdb: damaged header in Fedora
Backup corrupted RPM database, just in case:
$ mv /var/lib/rpm/__db* /var/lib/rpm/old/
Next, delete the RPM database using command:
$ sudo rm -f /var/lib/rpm/__db*
Next, reset the SELinux security context for /var/lib/rpm/ directory to its default values using restorecon command:
$ sudo restorecon -Rv /var/lib/rpm
Finally, rebuild the RPM database to fix rpmdb damaged header error in Fedora, RHEL and its clones like CentOS, AlmaLinux and Rocky Linux:
$ sudo rpmdb --rebuilddb
You will not see any output in the terminal. If you want to see what's going on in the background, use -v flag.
$ sudo rpmdb --rebuilddb -v
And then update/upgrade Fedora system as usual.
$ sudo dnf update --refresh
Now, I can able to update the system without any issues.
Copr repo for fedy owned by kwizart 921 B/s | 3.3 kB 00:03 Copr repo for Signal-Desktop owned by luminoso 8.7 kB/s | 3.3 kB 00:00 Copr repo for PyCharm owned by phracek 567 B/s | 3.3 kB 00:05 Fedora 35 - x86_64 5.1 kB/s | 5.3 kB 00:01 Fedora 35 openh264 (From Cisco) - x86_64 2.0 kB/s | 989 B 00:00 Fedora Modular 35 - x86_64 17 kB/s | 5.2 kB 00:00 Fedora 35 - x86_64 - Updates 13 kB/s | 4.4 kB 00:00 Fedora 35 - x86_64 - Updates 210 kB/s | 1.7 MB 00:08 Fedora Modular 35 - x86_64 - Updates 26 kB/s | 6.6 kB 00:00 google-chrome 4.8 kB/s | 1.3 kB 00:00 RPM Fusion for Fedora 35 - Free 4.4 kB/s | 6.2 kB 00:01 RPM Fusion for Fedora 35 - Free - Updates 6.2 kB/s | 5.8 kB 00:00 RPM Fusion for Fedora 35 - Nonfree 7.1 kB/s | 6.7 kB 00:00 RPM Fusion for Fedora 35 - Nonfree - NVIDIA Dri 6.8 kB/s | 6.4 kB 00:00 RPM Fusion for Fedora 35 - Nonfree - Steam 6.5 kB/s | 6.1 kB 00:00 RPM Fusion for Fedora 35 - Nonfree - Updates 6.6 kB/s | 6.2 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Upgrading: cmake-filesystem x86_64 3.22.0-4.fc35 updates 18 k cpp x86_64 11.2.1-7.fc35 updates 10 M gcc x86_64 11.2.1-7.fc35 updates 31 M gcc-gdb-plugin x86_64 11.2.1-7.fc35 updates 147 k glibc x86_64 2.34-10.fc35 updates 2.0 M [...] python3-pikepdf x86_64 4.1.0-1.fc35 updates 500 k virt-viewer x86_64 11.0-1.fc35 updates 324 k xxhash-libs x86_64 0.8.1-1.fc35 updates 40 k zram-generator x86_64 1.1.1-3.fc35 updates 397 k zram-generator-defaults noarch 1.1.1-3.fc35 updates 9.6 k Transaction Summary ================================================================================ Upgrade 49 Packages Total download size: 134 M Is this ok [y/N]: y
Hope this helps.
