Warning: The SSH and rkhunter configuration options should be the same: SSH configuration option 'PermitRootLogin': yes

Warning: The SSH and rkhunter configuration options should be the same:
SSH configuration option 'PermitRootLogin': yes
Rkhunter configuration option 'ALLOW_SSH_ROOT_USER': no

you can change the /etc/ssh/sshd_config and set:

PermitRootLogin no

http://debianforum.de/forum/viewtopic.php?f=37&t=109601