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Устанавливал через sudo, то есть как бы права суперпользователя нужны? Или под www-data?

Сайт добавлял без www он с www и не отображается у нас никак.

 Ошибки следующие показывает.

Known Problems

There are some errors that we cannot fix properly in the current version. They will be addressed in the next generation version, which is currently being developed.

• No secure protocols supported - if you get this message, but you know that the site supports SSL, wait until the cache expires on its own, then try again, making sure the hostname you enter uses the "www" prefix (e.g., "www.ssllabs.com", not just "ssllabs.com").
• no more data allowed for version 1 certificate - the certificate is invalid; it is declared as version 1, but uses extensions, which were introduced in version 3. Browsers might ignore this problem, but our parser is strict and refuses to proceed. We'll try to find a different parser to avoid this problem.
• Failed to obtain certificate and Internal Error - errors of this type will often be reported for servers that use connection rate limits or block connections in response to unusual traffic. Problems of this type are very difficult to diagnose. If you have access to the server being tested, before reporting a problem to us, please check that there is no rate limiting or IDS in place.
• NetScaler issues - some NetScaler versions appear to reject SSL handshakes that do not include certain suites or handshakes that use a few suites. If the test is failing and there is a NetScaler load balancer in place, that's most likely the reason.
• Unexpected failure - our tests are designed to fail when unusual results are observed. This usually happens when there are multiple TLS servers behind the same IP address. In such cases we can't provide accurate results, which is why we fail.

Common Error Messages

• Connect timed out - server did not respond to our connection request, sometimes before we are dynamically blocked when our tests are detected
• No route to host - unable to reach the server
• Unable to connect to server - failed to connect to the server, it usually happens due to firewall restrictions
• Connection reset - we got disconnected from the server
• Unrecognized SSL message, plaintext connection? - the server responded with plain-text HTTP on HTTPS port
• Received fatal alert: handshake_failure - this is either a faulty SSL server or some other server listening on port 443; if the SSL version of the web site works in your browser, please report this issue to us

Я Ваши инструкции посмотрел выше, но вроде как под убунту можно не вмешиваться, по словам Вадима. Вот и решил попробовать. Но увы...

В cron нужно писать для root (у www-data нет прав на изменения конфигурации веб-сервера, а сертификаты задаются там).

В cron нужно писать команду без --dry-run, иначе возможность обновления сертификатов проверится, но сертификаты не создадутся.

Если это не секретная информация, то легче будет, если вы укажете свой домен и приведете конфиги apache после запуска certbot (как для 80, так и для 443 порта)