Error occurred while checking server setup, but there are not

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Nextcloud version (eg, 20.0.5): 26.0.1
Operating system and version (eg, Ubuntu 20.04): docker-fpm @ Raspberry Pi OS 11
Apache or nginx version (eg, Apache 2.4.25): nginx 1.23.4
PHP version (eg, 7.4): 8.1.18

The issue you are facing: On Settings → Overview, I get “Error occurred while checking server setup” but there are no errors - I checked the following:

Is this the first time you’ve seen this error? (Y/N): Y
I start getting this error from the version 26.0.0

Steps to replicate it:

  1. Go to Settings
  2. Go to Administration
  3. Go to Overview

Client side I have the following errors:

GET https://mynas.synology.me/index.php/.well-known/webfinger 404
GET https://mynas.synology.me/index.php/.well-known/nodeinfo 404
GET https://mynas.synology.me/settings/ajax/checksetup 504

The output of your Nextcloud log in Admin > Logging:

No errors

The output of your config.php file in /path/to/nextcloud (make sure you remove any identifiable information!):

<?php
$CONFIG = array (
  'memcache.local' => '\\OC\\Memcache\\APCu',
  'apps_paths' => 
  array (
    0 => 
    array (
      'path' => '/var/www/html/apps',
      'url' => '/apps',
      'writable' => false,
    ),
    1 => 
    array (
      'path' => '/var/www/html/custom_apps',
      'url' => '/custom_apps',
      'writable' => true,
    ),
  ),
  'overwritehost' => 'mynas.synology.me',
  'overwriteprotocol' => 'https',
  'trusted_proxies' => 
  array (
    0 => 'mynas.synology.me',
    1 => '192.168.2.100',
  ),
  'instanceid' => 'ocxoalcueoiu',
  'passwordsalt' => 'dgdfsadg/toP',
  'secret' => 'B7Asafsadfdsfsadf9ng/h',
  'trusted_domains' => 
  array (
    0 => 'mynas.synology.me',
  ),
  'datadirectory' => '/var/www/html/data',
  'dbtype' => 'mysql',
  'version' => '26.0.1.1',
  'overwrite.cli.url' => 'https://mynas.synology.me',
  'dbname' => 'nextcloud',
  'dbhost' => '192.168.2.10:3307',
  'dbport' => '',
  'dbtableprefix' => 'oc_',
  'mysql.utf8mb4' => true,
  'dbuser' => 'nextcloud_usr',
  'dbpassword' => 'JtsadfasdfadsafqwNI',
  'installed' => true,
  'theme' => '',
  'loglevel' => 2,
  'maintenance' => false,
  'mail_smtpmode' => 'smtp',
  'mail_smtphost' => 'smtp.gmail.com',
  'mail_sendmailmode' => 'smtp',
  'mail_from_address' => 'mymail',
  'mail_smtpport' => '465',
  'mail_domain' => 'gmail.com',
  'mail_smtpauth' => 1,
  'mail_smtpname' => 'mymail@gmail.com',
  'mail_smtppassword' => 'asdfsadfsadf',
  'mail_smtpsecure' => 'ssl',
);

The output of your Apache/nginx/system log in /var/log/____:

no errors

Here my nginx.conf file:
Please note I also tried with same results the standard one provided online.

worker_processes auto;

error_log  /var/log/nginx/error.log warn;
pid        /var/run/nginx.pid;


events {
    worker_connections  1024;
}


http {
    include       /etc/nginx/mime.types;
    default_type  application/octet-stream;

    log_format  main  '$remote_addr - $remote_user [$time_local] "$request" '
                      '$status $body_bytes_sent "$http_referer" '
                      '"$http_user_agent" "$http_x_forwarded_for"';

    access_log  /var/log/nginx/access.log  main;

    sendfile        on;
    #tcp_nopush     on;

    # Prevent nginx HTTP Server Detection
    server_tokens   off;

    keepalive_timeout  65;

    #gzip  on;

    upstream php-handler {
        server app:9000;
    }

    server {
        server_name mynas.synology.me;
        listen 80;

        # HSTS settings
        # WARNING: Only add the preload option once you read about
        # the consequences in https://hstspreload.org/. This option
        # will add the domain to a hardcoded list that is shipped
        # in all major browsers and getting removed from this list
        # could take several months.
        #add_header Strict-Transport-Security "max-age=15768000; includeSubDomains; preload;" always;

        # set max upload size
        client_max_body_size 512M;
        fastcgi_buffers 64 4K;

        # Enable gzip but do not remove ETag headers
        gzip on;
        gzip_vary on;
        gzip_comp_level 4;
        gzip_min_length 256;
        gzip_proxied expired no-cache no-store private no_last_modified no_etag auth;
        gzip_types application/atom+xml application/javascript application/json application/ld+json application/manifest+json application/rss+xml application/vnd.geo+json application/vnd.ms-fontobject application/x-font-ttf application/x-web-app-manifest+json application/xhtml+xml application/xml font/opentype image/bmp image/svg+xml image/x-icon text/cache-manifest text/css text/plain text/vcard text/vnd.rim.location.xloc text/vtt text/x-component text/x-cross-domain-policy;

        # Pagespeed is not supported by Nextcloud, so if your server is built
        # with the `ngx_pagespeed` module, uncomment this line to disable it.
        #pagespeed off;

        # HTTP response headers borrowed from Nextcloud `.htaccess`
        add_header Referrer-Policy                      "no-referrer"   always;
        add_header X-Content-Type-Options               "nosniff"       always;
        add_header X-Download-Options                   "noopen"        always;
        add_header X-Frame-Options                      "SAMEORIGIN"    always;
        add_header X-Permitted-Cross-Domain-Policies    "none"          always;
        add_header X-Robots-Tag                         "noindex, nofollow"          always;
        add_header X-XSS-Protection                     "1; mode=block" always;

        # Remove X-Powered-By, which is an information leak
        fastcgi_hide_header X-Powered-By;

        # Path to the root of your installation
        root /var/www/html;

        # Specify how to handle directories -- specifying `/index.php$request_uri`
        # here as the fallback means that Nginx always exhibits the desired behaviour
        # when a client requests a path that corresponds to a directory that exists
        # on the server. In particular, if that directory contains an index.php file,
        # that file is correctly served; if it doesn't, then the request is passed to
        # the front-end controller. This consistent behaviour means that we don't need
        # to specify custom rules for certain paths (e.g. images and other assets,
        # `/updater`, `/ocm-provider`, `/ocs-provider`), and thus
        # `try_files $uri $uri/ /index.php$request_uri`
        # always provides the desired behaviour.
        index index.php index.html /index.php$request_uri;

        # Rule borrowed from `.htaccess` to handle Microsoft DAV clients
        location = / {
            if ( $http_user_agent ~ ^DavClnt ) {
                return 302 /remote.php/webdav/$is_args$args;
            }
        }

        location = /robots.txt {
            allow all;
            log_not_found off;
            access_log off;
        }

        #rewrite ^/.well-known/webfinger /public.php?service=webfinger last;

        # Make a regex exception for `/.well-known` so that clients can still
        # access it despite the existence of the regex rule
        # `location ~ /(\.|autotest|...)` which would otherwise handle requests
        # for `/.well-known`.
        location ^~ /.well-known {
            # The rules in this block are an adaptation of the rules
            # in `.htaccess` that concern `/.well-known`.

            location = /.well-known/carddav { return 301 https://$host/remote.php/dav/; }
            location = /.well-known/caldav  { return 301 https://$host/remote.php/dav/; }

            location /.well-known/acme-challenge    { try_files $uri $uri/ =404; }
            location /.well-known/pki-validation    { try_files $uri $uri/ =404; }

            # Let Nextcloud's API for `/.well-known` URIs handle all other
            # requests by passing them to the front-end controller.
            return 301 https://$host/index.php$request_uri;
        }

        # Rules borrowed from `.htaccess` to hide certain paths from clients
        location ~ ^/(?:build|tests|config|lib|3rdparty|templates|data)(?:$|/)  { return 404; }
        location ~ ^/(?:\.|autotest|occ|issue|indie|db_|console)                { return 404; }

        # Ensure this block, which passes PHP files to the PHP process, is above the blocks
        # which handle static assets (as seen below). If this block is not declared first,
        # then Nginx will encounter an infinite rewriting loop when it prepends `/index.php`
        # to the URI, resulting in a HTTP 500 error response.
        location ~ \.php(?:$|/) {
            # Required for legacy support
            rewrite ^/(?!index|remote|public|cron|core\/ajax\/update|status|ocs\/v[12]|updater\/.+|oc[ms]-provider\/.+|.+\/richdocumentscode\/proxy) /index.php$request_uri;

            fastcgi_split_path_info ^(.+?\.php)(/.*)$;
            set $path_info $fastcgi_path_info;

            try_files $fastcgi_script_name =404;

            include fastcgi_params;
            fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
            fastcgi_param PATH_INFO $path_info;
            #fastcgi_param HTTPS on;

            fastcgi_param modHeadersAvailable true;         # Avoid sending the security headers twice
            fastcgi_param front_controller_active true;     # Enable pretty urls
            fastcgi_pass php-handler;

            fastcgi_intercept_errors on;
            fastcgi_request_buffering off;
        }

        location ~ \.(?:css|js|svg|gif)$ {
            try_files $uri /index.php$request_uri;
            expires 6M;         # Cache-Control policy borrowed from `.htaccess`
            access_log off;     # Optional: Don't log access to assets
        }

        location ~ \.woff2?$ {
            try_files $uri /index.php$request_uri;
            expires 7d;         # Cache-Control policy borrowed from `.htaccess`
            access_log off;     # Optional: Don't log access to assets
        }

        # Rule borrowed from `.htaccess`
        location /remote {
            return 301 /remote.php$request_uri;
        }

        location / {
            try_files $uri $uri/ /index.php$request_uri;
        }
    }
}

Solution

Simply increase the timeout; in my case I had to add the following lines to nginx.conf file:

fastcgi_send_timeout 120s;
fastcgi_read_timeout 120s;

In my specific case, though, I am behind a reverse proxy. In other scenario, you may need to increase also the following (always assuming nginx):

proxy_connect_timeout 120s;
proxy_send_timeout 120s;
proxy_read_timeout 120s;