You have granted a user package with Cron Jobs ticked, but when the user creates a cron job from DirectAdmin or from the shell, they got:
saputra@cana:~$ crontab -l
/etc/cron.deny: Permission denied
You (saputra) are not allowed to use this program (crontab)
See crontab(1) for more...
If you want to add any extra modules to PHP, they'll most likely need to be compiled in. Any module that needs to be compiled in will have a --with-gmp type flag which will need to be used.
First, figure out which configure file your system is using. Type: