Open phpMyAdmin in a browser and log in as root.
Create a database called phpmyadmin
Create a user called pma and set the “host” to the hostname or IP address of your web server (if the web server and MySQL are on the same box use localhost), make a note of the password, and grant the new user full control over the phpmyadmin database. It is recommended that this user does not have access to anything other than this database.
Go to the phpMyAdmin installation directory, where you should find a sub-directory called sql.
In sql you will find a file called create_tables.sql. Open it in a text editor.
In phpMyAdmin, select the phpmyadmin database and click on the “SQL” tab.
Copy/paste the entire text from create_tables.sql into the text box, and run the query.
Open the config.inc.php file in the phpMyAdmin install directory, and add the following lines (or change the existing settings if they are already there):
$cfg[‘Servers’][1][‘pmadb’] = ‘phpmyadmin’;
$cfg[‘Servers’][1][‘controluser’] = ‘pma’;
$cfg[‘Servers’][1][‘controlpass’] = ‘
// Note: The list below may grow as PMA evolves and more control tables are added
// Use your common sense! Don’t just blindly copypasta, look at what it means!
$cfg[‘Servers’][1][‘bookmarktable’] = ‘pma_bookmark’;
$cfg[‘Servers’][1][‘relation’] = ‘pma_relation’;
$cfg[‘Servers’][1][‘userconfig’] = ‘pma_userconfig’;
$cfg[‘Servers’][1][‘table_info’] = ‘pma_table_info’;
$cfg[‘Servers’][1][‘column_info’] = ‘pma_column_info’;
$cfg[‘Servers’][1][‘history’] = ‘pma_history’;
$cfg[‘Servers’][1][‘recent’] = ‘pma_recent’;
$cfg[‘Servers’][1][‘table_uiprefs’] = ‘pma_table_uiprefs’;
$cfg[‘Servers’][1][‘tracking’] = ‘pma_tracking’;
$cfg[‘Servers’][1][‘table_coords’] = ‘pma_table_coords’;
$cfg[‘Servers’][1][‘pdf_pages’] = ‘pma_pdf_pages’;
$cfg[‘Servers’][1][‘designer_coords’] = ‘pma_designer_coords’;
Save and close the file.
IMPORTANT – PMA loads the config on login, evaluates it and stores it into the session data so the message will not disappear until you do this:
Log out of phpMyAdmin and log in again
Problem solved.
If you got here and you are using Debian/Ubuntu (or any other dpkg based distro), execute the following command:
sudo dpkg-reconfigure phpmyadmin
The phpmyadmin package contains the script to perform this operation for you, all it needs is a user with permissions. sudo is not required if you’re logged in as root, of course.
EDIT: It might be worth trying to drop the current phpmyadmin user.