This one-line command will edit the /etc/rkhunter.conf file to permit root logins via SSH. This does not make your system any more or less secure, it just disables the (daily) warning message.
perl -i -p -e 's/\#ALLOW_SSH_ROOT_USER=0/ALLOW_SSH_ROOT_USER=1/' \
/etc/rkhunter.conf
More on using Perl as an in-place editor here.
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