“PHP Warning: Module *** already loaded” seems to be a very common warning for freshly installed PHP. If you happen to see the example below here then this post may help you
PHP Warning: Module 'json' already loaded in Unknown on line 0
In this case, the reason may be that the modules json is loaded twice, look into the php.ini files and find this line and comment it out with a comma
Don’t forget to look into both /etc/php5/cli and /etc/php5/apache2 if the warning appears both in your command line and web server.
There is a chance that you have installed the php5-json package in your Linux system and it also enable the extension somewhere in a config file therefore the duplication occurs. I would recommend to use the package from your distro repositories to make sure that everything is up to date.