Letsencrypt tab disappeared + Editing virtual server's "enabled features" is extremely limited ! How did this happen?

Hello,

A few days ago I started receiving emails complaining about Letsencrypt. Example:

An error occurred requesting a new certificate for mydomain.com, www.mydomain.com from Let’s Encrypt : Domain has no website, and DNS-based validation is not possible.
<<<

The domain does have a website (though DNS is hosted elsewhere).
When I tried to manually renew the certificate I noticed that the TAB Letsencrypt does not even exist.
On the current certificate details it does show the letsencrypt valid cert with 19 days until expiry however I cannot renew it!

Also, I noticed that while trying to view the server’s “enabled features” it ONLY shows “MariaDB database enabled” but nothing more!

Digging deeper, I found that if I go to System Settings > Features and Plugins and click the “Show Domains” action to see the list, mydomain.com is not listed. Others are.

What is happening here?
This must have been the result of an update as I only noticed it now.

Please help :frowning:

SYSTEM INFORMATION
OS type and version CentOS Linux 7.9.2009
Webmin version 1.999
Virtualmin version 7.1

UPDATE:

Digging deeper i realized that inside the “Features and Plugins” page the only ticked item was the MariaDB database! No idea how this happened as I am only user acting as root on the server.
However: While I enabled most of the features virtualmin is complaining on Spam/Virus and ProFTP items as follows:

Failed to save enabled features : The ClamAV program does not appear to be installed on your system. Either adjust the path on the module configuration page, or disable this feature.
and
Failed to save enabled features : An error was found in the ProFTPD configuration template : Missing User directive. This must be fixed by editing the Default Settings on the Server Templates page
<<<

ClamAv is installed:

clamav 0.103.7-1.el7
clamav-data 0.103.7-1.el7
clamav-filesystem 0.103.7-1.el7
clamav-lib 0.103.7-1.el7
clamav-update 0.103.7-1.el7

While trying to enable ProFTP I am getting:

Failed to save enabled features : An error was found in the ProFTPD configuration template : Missing User directive. This must be fixed by editing the Default Settings on the Server Templates page
<<<

and if I go the template (the default one) I see that the directives part is empty!
I am trying to replicate the directives from another server however when I try to save I am getting:

Failed to save server template : Cannot write to directory /etc/webmin/virtual-server/
<<

I stopped here as I realize that probably too many things have gone bad, most probably due the recent updates.
Any ideas how do I fix cannot write to directory problem? I am of course logged in as root.

Help… :-/

@netizen,

Why are you attempting to adjust global features to solve an issue with a single domain?

You need to go to “Edit Virtual Server” page for the domain, then enable or disable features there.

Aside from that, if you require more help, more info would be required to accurately guide you.

If you’d like, send me a private message and we can discuss further.

*** Pro, Affordable, Trusted Virtualmin assistant https://tpnassist.com ***

Thank you for replying.
This is not affecting one domain only. Maybe I was not clear when I was writing parts of the post.

A) All domains had only MariaDB available to be selected. No other feature was showing there to enabled/disabled.
This prompted me to go to “Features and Plugins” where I realised that all of them were unticked. And I mean all of them.
I started enabling them until I got stopped on the “Virus filtering” with the ClamAv “does not appear to be installed on your system” error. However ClamAv is installed (versions in my post).
(Note that the LetsEncrypt problem is now gone at this stage).

B) I also got stopped when trying to enable ProFTPd due to missing directives. When I tried to insert them it would now allow me to save with the error: “Failed to save server template : Cannot write to directory /etc/webmin/virtual-server/
Searching the forums a solution was to reinstall virtualmin however I don’t think this a good idea on a server that domains exist already.
I think the solution is that I need to grant access to all webmin users as per post:
https://archive.virtualmin.com/node/12693
Not sure how to do that without reinstalling on top of the existing installation.

All this mess clearly was caused by a server update without me realising when it happened.