sudo letsencrypt renew --agree-tos
Processing /etc/letsencrypt/renewal/xxxx.conf
2016-10-01 23:19:38,838:WARNING:letsencrypt.cli:Attempting to renew cert from /etc/letsencrypt/renewal/xxx.conf produced an unexpected error: The requested apache plugin does not appear to be installed. Skipping.
All renewal attempts failed. The following certs could not be renewed:
/etc/letsencrypt/live/xxx/fullchain.pem (failure)
1 renew failure(s), 0 parse failure(s)
The apache plugin is packaged separately on Ubuntu, you might need to run sudo apt-get install python-letsencrypt-apache to get it.
That being said, there are some known configuration incompatibilities between more recent versions of letsencrypt-auto/certbot-auto and the slightly outdated version of the client in Ubuntu, so you might be better off sticking with that or starting with a clean /etc/letsencrypt directory. Can’t hurt to try though, worst case you’ll get another error.
$ sudo letsencrypt renew --agree-tos
Processing /etc/letsencrypt/renewal/xxxx.conf
2016-10-10 15:03:10,665:WARNING:letsencrypt.cli:Attempting to renew cert from /etc/letsencrypt/renewal/xxxx.conf produced an unexpected error: ‘server’. Skipping.
All renewal attempts failed. The following certs could not be renewed:
/etc/letsencrypt/livexxxx/fullchain.pem (failure)
1 renew failure(s), 0 parse failure(s)
Yep, that’s one of the known configuration incompatibilities. You could delete your current configuration (delete /etc/letsencrypt - though having a backup can’t hurt) and start from scratch, or continue using certbot-auto (as described here - the instructions for Trusty work on Xenial as well).
(Note: certbot-auto was previously known as letsencrypt-auto.)