= InnoDB: Missing FILE_CHECKPOINT at 42251 between the checkpoint 42251 and the end 42347.

Try the following command to remove the file, and then restart mysql to see if there is an error?

cd /www/server/data/
mv ibdata1 /tmp/ibdata1.bak
mv ib_logfile0 /tmp/ib_logfile0.bak
mv ib_logfile1 /tmp/ib_logfile1.bak
/etc/init.d/mysqld restart

Deprecation Notice in ./libraries/classes/Di/ReflectorItem.php#82
Method ReflectionParameter::getClass() is deprecated

you need to uninstall the original phpMyAdmin and then re install it to select version 5.2. Unloading phpMyAdmin will not affect the database data, so it is safe to operate.

= Reset mySQL root password

Starting in MariaDB 10.4 onwards, the mysql.user is not a table anymore, thus requiring a new command to reset the password.

mysql -u root -e 'SET PASSWORD FOR `root`@`localhost` = PASSWORD("new_password"); FLUSH PRIVILEGES;'

Change the new_password to your new password.