How to fix MySQL conflicts with file from package error in cPanel?

Updated: 22 October 2026 · Applies to: cPanel

In a cPanel update, MySQL also gets updated if a new version is available. If for some reason like Config file issue, or RPM errors, etc., MySQL doesn’t get updated, it is said to be a ‘File conflict’ issue.

cPanel update has many prerequisites. One of which is MySQL update. So when MySQL update is not met, it causes cPanel update failure.

How do we fix the conflict?

Note- This is a high level description of the steps taken for resolving the conflict. These are not the exact steps. If you need detailed analysis or urgent help, please contact our Our Experts. 

Customers often prefer the latest MySQL version to be installed in their servers. Automatic MySQL upgrades can fail due to cPanel config file errors. In such cases, we resolve it by:

• Updating MySQL version number in /var/cpanel/cpanel.config.
  • For eg: changing mysql-version from 5.6 to 5.7
• Run the scripts/update_local_rpm_versions command to set the state of the RPM target as ‘installed‘.

There maybe scenarios where the existing MySQL version is preferred. This could be because of dependencies on scripts and databases.

In such scenarios, if RPM duplication is stopping the update, we take the following steps- 

• Run the /scripts/check_cpanel_rpms script to check and correct the installed RPMs.
• Add MySQL as ‘unmanaged‘ in /var/cpanel/rpm.versions.d/local.versions.