Integrity check results with anomalies

Nextcloud version (eg, 18.0.2): 18.0.6
Operating system and version (eg, Ubuntu 20.04): Ubuntu 18.04
Apache or nginx version (eg, Apache 2.4.25): apache2
PHP version (eg, 7.1): 7.2

The issue you are facing:
Integrity check results with red error message.

Is this the first time you’ve seen this error? (Y/N): N

Steps to replicate it:

  1. Click Settings!
  2. Click Overview!
  3. See the red error message " Some files have not passed the integrity check. Further information on how to resolve this issue can be found in the documentation. (List of invalid files… / Rescan…)"

The output of your Nextcloud log in Admin > Logging:

Debug	cron	Finished OCA\Maps\BackgroundJob\UpdatePhotoByFileJob job with ID 913 in 0 seconds		2020-07-13T17:38:34+0300
Debug	cron	Run OCA\Maps\BackgroundJob\UpdatePhotoByFileJob job with ID 913		2020-07-13T17:38:34+0300
Warning	l10n	Failed to load /projektid/nextcloud/apps/drop_account/l10n/en.json - json error code: 4		2020-07-13T17:38:30+0300
Debug	maps	Could not find resource file "/apps/maps/js/filetypes.js"		2020-07-13T17:29:14+0300
Error	PHP	count(): Parameter must be an array or an object that implements Countable at /projektid/nextcloud/apps/onlyoffice/lib/appconfig.php#477		2020-07-13T17:29:14+0300
Debug	no app in context	Deprecated event type for OCA\Files::loadAdditionalScripts: Symfony\Component\EventDispatcher\GenericEvent		2020-07-13T17:29:14+0300
Error	PHP	count(): Parameter must be an array or an object that implements Countable at /projektid/nextcloud/apps/onlyoffice/lib/appconfig.php#477		2020-07-13T17:29:14+0300

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

<?php
$CONFIG = array (
  'instanceid' => 'oct73v7ell46',
...
  'trusted_domains' =>
  array (
    0 => 'nextcloud.tennis24.ee',
  ),
  'datadirectory' => '/projektid/nextcloud/data',
  'dbtype' => 'mysql',
  'version' => '18.0.6.0',
  'overwrite.cli.url' => 'https://test.tennis24.ee/nextcloud',
  'dbname' => 'nextcloud',
  'dbhost' => 'localhost',
  'dbport' => '',
  'dbtableprefix' => 'oc_',
  'dbuser' => 'nextcloud',
...
  'installed' => true,
  'maintenance' => false,
  'theme' => '',
  'loglevel' => 0,
  'app_install_overwrite' =>
  array (
    0 => 'onlyoffice',
  ),
  'tempdirectory' => '/projektid/nextcloud/data',
  'overwriteprotocol' => 'https',
  'mysql.utf8mb4' => true,
...
  'memcache.local' => '\\OC\\Memcache\\APCu',
);

If I click List of invalid files the result is:

Technical information
=====================
The following list covers which files have failed the integrity check. Please read
the previous linked documentation to learn more about the errors and how to fix
them.

Results
=======
- onlyoffice
	- EXCEPTION
		- OC\IntegrityCheck\Exceptions\InvalidSignatureException
		- Signature data not found.
- onlyoffice-old
	- EXCEPTION
		- Exception
		- App not found
- onlyoffice-veryold
	- EXCEPTION
		- Exception
		- App not found
- maps
	- INVALID_HASH
		- lib/Controller/RoutingController.php
	- EXTRA_FILE
		- lib/Controller/RoutingController.php~

Raw output
==========
Array
(
    [onlyoffice] => Array
        (
            [EXCEPTION] => Array
                (
                    [class] => OC\IntegrityCheck\Exceptions\InvalidSignatureException
                    [message] => Signature data not found.
                )

        )

    [onlyoffice-old] => Array
        (
            [EXCEPTION] => Array
                (
                    [class] => Exception
                    [message] => App not found
                )

        )

    [onlyoffice-veryold] => Array
        (
            [EXCEPTION] => Array
                (
                    [class] => Exception
                    [message] => App not found
                )

        )

    [maps] => Array
        (
            [INVALID_HASH] => Array
                (
                    [lib/Controller/RoutingController.php] => Array
                        (
                            [expected] => a76dc79838a1e32aceb8d4ec917062bbe8dfad71191e02f6b52520d222f15469d7475967645e1062b7e645cfa11adbb8c14b9b1e32fc6799217d28aa9e89a8f2
                            [current] => 5cbb4f7111ae93b0e9bdb9daf880acada819956940030a1b7eb3fa5d4125352e2f8e09f6c79b43c7683e8a4ba4db677bdf81194a4048609a68b1967d6db94e20
                        )

                )

            [EXTRA_FILE] => Array
                (
                    [lib/Controller/RoutingController.php~] => Array
                        (
                            [expected] => 
                            [current] => eed99428fc07ae0cc923efa809cf46f141dd46f3423c95029a95b42ff90733418b2b7b818223daec3c3b6b515d3717403442e89422ec3eed9f24f81fcd81cf29
                        )

                )

        )

)

Once upon a time I had problems with OnlyOffice and renamed the corresponding app folder to onlyoffice-old. I reinstalled the app and then, there were both folders. Then, I saw here the message tha the requested certificate is for onlyoffice-old but there’s onlyoffice. So I decided to rename the old folder to onlyoffice-veryold. It had no influence. So I removed the folder and also removed four onlyoffice-old folders from backup. Then I did a manual integrity check usin occ on onlyoffice-old, onlyoffice and maps and thereafter, I had even more error messages.