PHP allows to disabled functions. This directive can be used to increase system security as it can prevent potentially unsecure scripts to access system commands eg. to install rootkits. This is an example that disallows many functions that might be used by hackers:

disable_functions =
    dl,escapeshellarg,escapeshellcmd,exec,leak,passthru,pcntl_exec,posix_kill,posix_mkfifo,posix_setpgid,
    posix_setsid,posix_setuid,proc_get_status,proc_nice,proc_open,proc_terminate,shell_exec,system

This statement can only be configured in php.ini file.
You need to check carefully if any of your installed scripts needs any of this functions as it might break it.