I am having the same issue.
Running this command
/opt/letsencrypt/letsencrypt-auto renew >> /var/log/le-renew.log
From a cron job give me the same error as ZFWT is seeing, However if I run the same command from a terminal it works fine.
I also checked on the lets encrypt log file located in /var/log/letsencrypt
Here is the full log file
Here is a section that I thought was interesting.
2016-07-03 06:00:05,860:INFO:certbot.renewal:Cert is due for renewal, auto-renewing…
2016-07-03 06:00:05,878:DEBUG:certbot.plugins.selection:Requested authenticator apache and installer apache
2016-07-03 06:00:05,940:DEBUG:certbot.plugins.disco:No installation (PluginEntryPoint#apache):
Traceback (most recent call last):
File “/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/plugins/disco.py”, line 105, in prepare
File “/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot_apache/configurator.py”, line 161, in prepare
So from what I gather for some reason it thinks Apache isn’t installed when the cron job runs.
The cron job is running as root, so it shouldn’t be any permission issues.