Let's Encrypt not installing

After following the Debian 8.4 perfect server instructions, I get this error:

Code:

root@mx:/opt/certbot# ./certbot-auto
Upgrading certbot-auto 0.9.3 to 0.10.1...
Replacing certbot-auto...
Creating virtual environment...
Installing Python packages...
Installation succeeded.
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Certbot doesn't know how to automatically configure the web server on this system. However, it can still get a certificate for you. Please run "certbot-auto certonly" to do so. You'll need to manually configure your web server to use the resulting certificate.
root@mx:/opt/certbot#

Any Ideas?
letsencrypt.log shows:

Code:

2017-01-17 05:04:05,316:DEBUG:certbot.main:Root logging level set at 20
2017-01-17 05:04:05,317:INFO:certbot.main:Saving debug log to /var/log/letsencrypt/letsencrypt.log
2017-01-17 05:04:05,317:DEBUG:certbot.main:certbot version: 0.10.1
2017-01-17 05:04:05,317:DEBUG:certbot.main:Arguments: []
2017-01-17 05:04:05,318:DEBUG:certbot.main:Discovered plugins: PluginsRegistry(PluginEntryPoint#standalone,PluginEntryPoint#manual,PluginEntryPoint#nginx,PluginEntryPoint#web$
2017-01-17 05:04:05,318:DEBUG:certbot.plugins.selection:Requested authenticator None and installer None
2017-01-17 05:04:06,211:DEBUG:certbot.plugins.disco:Other error:(PluginEntryPoint#apache): There has been an error in parsing the file /etc/apache2/sites-available/xxxxxxxx$
Traceback (most recent call last):
  File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot/plugins/disco.py", line 114, in prepare
    self._initialized.prepare()
  File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot_apache/configurator.py", line 191, in prepare
    self.check_parsing_errors("httpd.aug")
  File "/root/.local/share/letsencrypt/local/lib/python2.7/site-packages/certbot_apache/augeas_configurator.py", line 77, in check_parsing_errors
    raise errors.PluginError(msg)
PluginError: There has been an error in parsing the file /etc/apache2/sites-available/xxxxxxxxx.vhost.err on line 102: Syntax error
2017-01-17 05:04:06,212:DEBUG:certbot.plugins.selection:No candidate plugin
2017-01-17 05:04:06,212:DEBUG:certbot.plugins.selection:Selected authenticator None and installer None

 

I ran this command:

Code:

rm /etc/apache2/sites-available/*.err

and the problem went away. However then I get another screen that is not in the documentation:

Code:

root@mx:/opt/certbot# ./certbot-auto
Saving debug log to /var/log/letsencrypt/letsencrypt.log

Which names would you like to activate HTTPS for?
-------------------------------------------------------------------------------
...
51: www.xxxxxxxxx.com
-------------------------------------------------------------------------------
Select the appropriate numbers separated by commas and/or spaces, or leave input
blank to select all options shown (Enter 'c' to cancel):

 

Looks like it's working now.

 

However it is acting strange. I can't create the cert from the control panel. I click on the Lets Encrypt option under the website and save. When I go back and look the check marks are gone, and I get an email saying
17.01.2017-00:25 - WARNING - Let's Encrypt SSL Cert for: xxxxxxxx.com could not be issued.

However I can create it manually running ./certbot-auto --apache and it works just fine, but never shows on the website tab.

 

I removed it with:
rm -rf /etc/letsencrypt/archive/[sitename]/
rm -rf /etc/letsencrypt/live/[sitename]/
rm -rf /etc/letsencrypt/renewal/[sitename].conf
and the apache definitions in sites-enabled.
The tried to do it though the control panel but I get the same issue. The SSL and LetsENcrypt option become blank after it runs the process.

 

It is a subdomain, but why would that not matter when I do it manually?

 

I turned auto-subdomain off, as the site has no aliases. Then it all seems to work. Thanks!

 

For each sub/domain LE requires a CNAME or A record in the DNS. Not sure if wildcard DNS entries work.