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

file /usr/share/mysql/dutch/errmsg.sys from install of MySQL56-server-5.6.39-1.cp1162.x86_64 conflicts with file from package mysql-community-common-5.7.22-1.el6.x86_64

This is a common error during cPanel update- ‘MySQL conflicts with file from package‘.

Being a provider of server support and maintenance service, solving such issues is all in a day’s work for us.

In today’s post, we’ll take a look at this update failure and how we resolve this for our customers.


What is ‘MySQL file conflict’? Why does it cause cPanel update failure?

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 Server Support Engineers here at Bobcares.

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.



The error “MySQL conflicts with file from package” happens in cPanel due to configuration file errors. Today we’ve seen two scenarios where we’ve seen this error occuring and how we resolve it.


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Bobcares is a server management company that helps businesses deliver uninterrupted and secure online services. Our engineers manage close to 51,500 servers that include virtualized servers, cloud infrastructure, physical server clusters, and more.