This simple change to your FreeBSD system will force cPanel to start using the port tree to upgrade all your applications.
WARNING: After making this change, be prepared to spend an hour or longer waiting for all updates to complete. As a comparison, I'm running FreeBSD 5.4 on a Dual Operton with Dual SCSI drives and it took 55 minutes to complete the entrie upgrade process on a very fast machine .If you are running on anything less than a P4 you will be waiting much longer than 1hr for all services to be upgraded.
I suggest you only do this when your server is the least busy and in the wee hours of the morning. If you your /usr partition is more than 80% FULL procede with caution as it could fill up with work files during upgrade. Mine was at 76% capacity when starting the upgrade from ports, and at times it went as high as 86%. If everything is configured in / you are free to proceed.
Remove file and back it up.
CODE
mv /var/cpanel/usebsdpkgs /var/cpanel/usebsdpkgs.bak
Start the upgrade of all outdated ports: (See Warning Above)
CODE
/scripts/upcp
MySQL should upgrade to the latest version available during the upgrade process.
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