In cPanel server after upgrading MySQL version to 5, PhpMyAdmin shows a warning message as given below

Your PHP MySQL library version 4.1.22 differs from your MySQL server version 5.0.45

CPanel’s internal PHP is not compiled with MySQL 5. That is why you are facing this issue. In order to fix this, perform the following steps.

1) Run the script /scripts/makecpphp
2) Copy the PHP binary inside /var/cpanel/3rdparty//bin/  to  /usr/local/cpanel/3rdparty/bin/

That will fix the problem.