cPanel update failed: rpm package conflict: @System and baseos

Symptoms

Package updates are failing with installation conflicts:

CONFIG_TEXT: Pre Maintenance ended, however it did not exit cleanly (256). The following events were logged: "scripts/update-packages". Please check the logs for an indication of what happened

CONFIG_TEXT: [2026-07-09 01:00:08 +0000] [/usr/local/cpanel/scripts/update-packages] Problem 1: package expat-devel-2.5.0-5.el9_7.1.x86_64 from @System requires expat(x86-64) = 2.5.0-5.el9_7.1, but none of the providers can be installed
[2026-07-09 01:00:08 +0000] [/usr/local/cpanel/scripts/update-packages] - cannot install both expat-2.5.0-6.el9.x86_64 from repo.cloudlinux.com_cloudlinux_9_BaseOS_x86_64_os_ and expat-2.5.0-5.el9_7.1.x86_64 from @System
[2026-07-09 01:00:08 +0000] [/usr/local/cpanel/scripts/update-packages] - cannot install both expat-2.5.0-6.el9.x86_64 from repo.cloudlinux.com_cloudlinux_9_BaseOS_x86_64_os_ and expat-2.5.0-5.el9_7.1.x86_64 from baseos
[2026-07-09 01:00:08 +0000] [/usr/local/cpanel/scripts/update-packages] - cannot install the best update candidate for package expat-devel-2.5.0-5.el9_7.1.x86_64
[2026-07-09 01:00:08 +0000] [/usr/local/cpanel/scripts/update-packages] - cannot install the best update candidate for package expat-2.5.0-5.el9_7.1.x86_64

Cause

An additional repository has been added that is causing conflicts when updates are run.

CONFIG_TEXT: repo.cloudlinux.com_cloudlinux_9_BaseOS_x86_64_os_ created by dnf config-manager from https://repo.cloudlinux.com/cloudlinux/9/BaseOS/x86_64/os/

Resolution

Disable the repository repo.cloudlinux.com_cloudlinux_9_BaseOS_x86_64_os_ 

# dnf config-manager --set-disabled repo.cloudlinux.com_cloudlinux_9_BaseOS_x86_64_os_

Additional Resources

How to disable a repository on a RHEL-based system