Updated: 29 September 2026 · Applies to: dnf and RPM 4.16 to 4.19 on AlmaLinux and Rocky Linux 9 and 10, RHEL 9 and 10
When the RPM package database cannot be opened, dnf and rpm stop with errors such as:
error: sqlite failure: CREATE TABLE IF NOT EXISTS 'Packages' (...): database disk image is malformed error: cannot open Packages index using sqlite - No such file or directory (2) error: cannot open Packages database in /var/lib/rpm
dnf shows the same lines. We reproduced them on AlmaLinux 9 with a damaged copy of the database. On CentOS 7 (end of life since June 2024), yum reported the same problem as Error: rpmdb open failed.
On CentOS 7 and older this usually came from stale Berkeley DB lock files (/var/lib/rpm/__db.*), and old guides tell you to delete them. Current AlmaLinux, Rocky Linux and RHEL releases store the database in a single SQLite file, so there are no __db files to delete, and yum clean headers or dbcache no longer exist. Work through these checks instead.
1. Is another package tool running?
pgrep -a 'rpm|dnf|yum|packagekit'
If an update is running, for example from dnf-automatic or PackageKit, wait for it to finish. Stop PackageKit with systemctl stop packagekit if it holds the database.
2. Is the disk full?
df -h / /var /usr df -i / /var
A full file system, or one without free inodes, is a common cause. Free space first, then try again.
3. Clean dnf's cache
dnf clean all dnf makecache
This only removes downloaded repository data and packages; it does not touch the installed-package database. If dnf still fails with the same error, the database itself is damaged.
4. Rebuild the database
cp -a "$(rpm -E %_dbpath)" /root/rpmdb-backup-$(date +%F) rpmdb --verifydb rpmdb --rebuilddb rpm -qa | wc -l
Back up first, as shown. After the rebuild, rpm -qa should list your packages again and dnf check should report no problems. For the full procedure, including what to do if the rebuild fails, see how to recover from a corrupt RPM database.
Then update
dnf upgrade
Official documentation: RPM documentation and dnf command reference.
