[Bug]: "MySQL server has gone away" error when attempting to enable Bookmarks 12.0.0

[buttercannon]

⚠️ This issue respects the following points: ⚠️

• [X] This is a bug, not a question or a configuration/webserver/proxy issue.
• [X] This issue is not already reported on Github (I've searched it).
• [X] Nextcloud Server is up to date. See Maintenance and Release Schedule for supported versions.
• [X] Nextcloud Server is running on 64bit capable CPU, PHP and OS.
• [X] I agree to follow Nextcloud's Code of Conduct.

Bug description

When attempting to enable the Bookmarks app, I get the following error Database error when running migration 004005000Date20210918124721 for app bookmarks An exception occurred while executing a query: SQLSTATE[HY000]: General error: 2006 MySQL server has gone away

Steps to reproduce

1. Click "Enable" on the Bookmarks app.

Expected behavior

Bookmarks app enabled without error.

Installation method

Community Manual installation with Archive

Operating system

Debian/Ubuntu

PHP engine version

PHP 8.0

Web server

Apache (supported)

Database engine version

MariaDB

Is this bug present after an update or on a fresh install?

Updated to a major version (ex. 22.2.3 to 23.0.1)

Are you using the Nextcloud Server Encryption module?

Encryption is Disabled

What user-backends are you using?

• [X] Default user-backend (database)
• [ ] LDAP/ Active Directory
• [ ] SSO - SAML
• [ ] Other

Configuration report

{
    "system": {
        "passwordsalt": "***REMOVED SENSITIVE VALUE***",
        "secret": "***REMOVED SENSITIVE VALUE***",
        "trusted_domains": [
            "localhost",
            "nc.zenpanda.me",
            "nc"
        ],
        "datadirectory": "***REMOVED SENSITIVE VALUE***",
        "dbtype": "mysql",
        "version": "25.0.2.3",
        "overwrite.cli.url": "http:\/\/localhost",
        "dbname": "***REMOVED SENSITIVE VALUE***",
        "dbhost": "***REMOVED SENSITIVE VALUE***",
        "dbport": "",
        "dbtableprefix": "oc_",
        "dbuser": "***REMOVED SENSITIVE VALUE***",
        "dbpassword": "***REMOVED SENSITIVE VALUE***",
        "default_phone_region": "US",
        "engine": "innodb row_format=dynamic",
        "installed": true,
        "instanceid": "***REMOVED SENSITIVE VALUE***",
        "maintenance": false,
        "memcache.local": "\\OC\\Memcache\\APCu",
        "memcache.locking": "\\OC\\Memcache\\Redis",
        "redis": {
            "host": "***REMOVED SENSITIVE VALUE***",
            "port": 6379
        },
        "loglevel": 2,
        "mysql.utf8mb4": true,
        "theme": "",
        "app_install_overwrite": [
            "calendar",
            "twofactor_totp"
        ],
        "twofactor_enforced": "false",
        "twofactor_enforced_groups": [],
        "twofactor_enforced_excluded_groups": [],
        "trashbin_retention_obligation": "auto, 30",
        "updater.release.channel": "stable",
        "mail_smtpmode": "smtp",
        "mail_sendmailmode": "smtp"
    }
}

List of activated Apps

Enabled:
  - activity: 2.17.0
  - admin_audit: 1.15.0
  - calendar: 4.1.2
  - circles: 25.0.0
  - cloud_federation_api: 1.8.0
  - comments: 1.15.0
  - contacts: 5.0.2
  - contactsinteraction: 1.6.0
  - dashboard: 7.5.0
  - dav: 1.24.0
  - federatedfilesharing: 1.15.0
  - federation: 1.15.0
  - files: 1.20.1
  - files_pdfviewer: 2.6.0
  - files_photospheres: 1.25.2
  - files_rightclick: 1.4.0
  - files_sharing: 1.17.0
  - files_trashbin: 1.15.0
  - files_versions: 1.18.0
  - firstrunwizard: 2.14.0
  - logreader: 2.10.0
  - lookup_server_connector: 1.13.0
  - nextcloud_announcements: 1.14.0
  - notes: 4.6.0
  - notifications: 2.13.1
  - oauth2: 1.13.0
  - password_policy: 1.15.0
  - photos: 2.0.1
  - previewgenerator: 5.1.1
  - privacy: 1.9.0
  - provisioning_api: 1.15.0
  - related_resources: 1.0.3
  - serverinfo: 1.15.0
  - settings: 1.7.0
  - sharebymail: 1.15.0
  - support: 1.8.0
  - systemtags: 1.15.0
  - tasks: 0.14.5
  - text: 3.6.0
  - theming: 2.0.1
  - twofactor_backupcodes: 1.14.0
  - twofactor_totp: 7.0.0
  - twofactor_webauthn: 1.0.0
  - unsplash: 2.1.1
  - updatenotification: 1.15.0
  - viewer: 1.9.0
  - workflowengine: 2.7.0
Disabled:
  - apporder: 0.15.0
  - bookmarks: 4.2.2
  - bruteforcesettings
  - electronicsignatures: 2.0.1
  - encryption: 2.8.1
  - end_to_end_encryption: 1.11.1
  - files_external
  - maps: 0.2.1
  - recommendations: 0.8.0
  - survey_client: 1.2.0
  - suspicious_login
  - user_external: 3.1.0
  - user_ldap
  - user_status: 1.0.1
  - weather_status: 1.0.0

Nextcloud Signing status

No errors have been found.

Nextcloud Logs

[settings] Error: Exception: Database error when running migration 004005000Date20210918124721 for app bookmarks
An exception occurred while executing a query: SQLSTATE[HY000]: General error: 2006 MySQL server has gone away at <<closure>>

0. /var/www/nextcloud/lib/private/Installer.php line 153
   OC\DB\MigrationService->migrate()
1. /var/www/nextcloud/apps/settings/lib/Controller/AppSettingsController.php line 451
   OC\Installer->installApp()
2. /var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php line 225
   OCA\Settings\Controller\AppSettingsController->enableApps()
3. /var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php line 133
   OC\AppFramework\Http\Dispatcher->executeController()
4. /var/www/nextcloud/lib/private/AppFramework/App.php line 172
   OC\AppFramework\Http\Dispatcher->dispatch()
5. /var/www/nextcloud/lib/private/Route/Router.php line 298
   OC\AppFramework\App::main()
6. /var/www/nextcloud/lib/base.php line 1047
   OC\Route\Router->match()
7. /var/www/nextcloud/index.php line 36
   OC::handleRequest()

POST /nextcloud/index.php/settings/apps/enable
from <redacted> by admin at 2022-12-28T23:19:28+00:00

Additional info

This is the last entry in the nextcloud.log file.

{"reqId":"Zr3s20eUvmXpGsoYd8Qb","level":3,"time":"2022-12-28T23:19:28+00:00","remoteAddr":"192.168.1.97","user":"admin","app":"settings","method":"POST","url":"/nextcloud/index.php/settings/apps/enable","message":"could not enable apps","userAgent":"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:108.0) Gecko/20100101 Firefox/108.0","version":"25.0.2.3","exception":{"Exception":"Exception","Message":"Database error when running migration 004005000Date20210918124721 for app bookmarks\nAn exception occurred while executing a query: SQLSTATE[HY000]: General error: 2006 MySQL server has gone away","Code":0,"Trace":[{"file":"/var/www/nextcloud/lib/private/Installer.php","line":153,"function":"migrate","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/var/www/nextcloud/apps/settings/lib/Controller/AppSettingsController.php","line":451,"function":"installApp","class":"OC\\Installer","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php","line":225,"function":"enableApps","class":"OCA\\Settings\\Controller\\AppSettingsController","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php","line":133,"function":"executeController","class":"OC\\AppFramework\\Http\\Dispatcher","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/App.php","line":172,"function":"dispatch","class":"OC\\AppFramework\\Http\\Dispatcher","type":"->"},{"file":"/var/www/nextcloud/lib/private/Route/Router.php","line":298,"function":"main","class":"OC\\AppFramework\\App","type":"::"},{"file":"/var/www/nextcloud/lib/base.php","line":1047,"function":"match","class":"OC\\Route\\Router","type":"->"},{"file":"/var/www/nextcloud/index.php","line":36,"function":"handleRequest","class":"OC","type":"::"}],"File":"/var/www/nextcloud/lib/private/DB/MigrationService.php","Line":420,"Previous":{"Exception":"Doctrine\\DBAL\\Exception\\ConnectionLost","Message":"An exception occurred while executing a query: SQLSTATE[HY000]: General error: 2006 MySQL server has gone away","Code":2006,"Trace":[{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1780,"function":"convert","class":"Doctrine\\DBAL\\Driver\\API\\MySQL\\ExceptionConverter","type":"->"},{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1719,"function":"handleDriverException","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1067,"function":"convertExceptionDuringQuery","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Connection.php","line":261,"function":"executeQuery","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1809,"function":"executeQuery","class":"OC\\DB\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Migrator.php","line":162,"function":"query","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Migrator.php","line":69,"function":"applySchema","class":"OC\\DB\\Migrator","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Connection.php","line":582,"function":"migrate","class":"OC\\DB\\Migrator","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/MigrationService.php","line":531,"function":"migrateToSchema","class":"OC\\DB\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/MigrationService.php","line":416,"function":"executeStep","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/var/www/nextcloud/lib/private/Installer.php","line":153,"function":"migrate","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/var/www/nextcloud/apps/settings/lib/Controller/AppSettingsController.php","line":451,"function":"installApp","class":"OC\\Installer","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php","line":225,"function":"enableApps","class":"OCA\\Settings\\Controller\\AppSettingsController","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php","line":133,"function":"executeController","class":"OC\\AppFramework\\Http\\Dispatcher","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/App.php","line":172,"function":"dispatch","class":"OC\\AppFramework\\Http\\Dispatcher","type":"->"},{"file":"/var/www/nextcloud/lib/private/Route/Router.php","line":298,"function":"main","class":"OC\\AppFramework\\App","type":"::"},{"file":"/var/www/nextcloud/lib/base.php","line":1047,"function":"match","class":"OC\\Route\\Router","type":"->"},{"file":"/var/www/nextcloud/index.php","line":36,"function":"handleRequest","class":"OC","type":"::"}],"File":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Driver/API/MySQL/ExceptionConverter.php","Line":101,"Previous":{"Exception":"Doctrine\\DBAL\\Driver\\PDO\\Exception","Message":"SQLSTATE[HY000]: General error: 2006 MySQL server has gone away","Code":2006,"Trace":[{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Driver/PDO/Connection.php","line":87,"function":"new","class":"Doctrine\\DBAL\\Driver\\PDO\\Exception","type":"::"},{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1062,"function":"query","class":"Doctrine\\DBAL\\Driver\\PDO\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Connection.php","line":261,"function":"executeQuery","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1809,"function":"executeQuery","class":"OC\\DB\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Migrator.php","line":162,"function":"query","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Migrator.php","line":69,"function":"applySchema","class":"OC\\DB\\Migrator","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Connection.php","line":582,"function":"migrate","class":"OC\\DB\\Migrator","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/MigrationService.php","line":531,"function":"migrateToSchema","class":"OC\\DB\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/MigrationService.php","line":416,"function":"executeStep","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/var/www/nextcloud/lib/private/Installer.php","line":153,"function":"migrate","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/var/www/nextcloud/apps/settings/lib/Controller/AppSettingsController.php","line":451,"function":"installApp","class":"OC\\Installer","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php","line":225,"function":"enableApps","class":"OCA\\Settings\\Controller\\AppSettingsController","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php","line":133,"function":"executeController","class":"OC\\AppFramework\\Http\\Dispatcher","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/App.php","line":172,"function":"dispatch","class":"OC\\AppFramework\\Http\\Dispatcher","type":"->"},{"file":"/var/www/nextcloud/lib/private/Route/Router.php","line":298,"function":"main","class":"OC\\AppFramework\\App","type":"::"},{"file":"/var/www/nextcloud/lib/base.php","line":1047,"function":"match","class":"OC\\Route\\Router","type":"->"},{"file":"/var/www/nextcloud/index.php","line":36,"function":"handleRequest","class":"OC","type":"::"}],"File":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Driver/PDO/Exception.php","Line":26,"Previous":{"Exception":"PDOException","Message":"SQLSTATE[HY000]: General error: 2006 MySQL server has gone away","Code":"HY000","Trace":[{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Driver/PDO/Connection.php","line":82,"function":"query","class":"PDO","type":"->"},{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1062,"function":"query","class":"Doctrine\\DBAL\\Driver\\PDO\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Connection.php","line":261,"function":"executeQuery","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1809,"function":"executeQuery","class":"OC\\DB\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Migrator.php","line":162,"function":"query","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Migrator.php","line":69,"function":"applySchema","class":"OC\\DB\\Migrator","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/Connection.php","line":582,"function":"migrate","class":"OC\\DB\\Migrator","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/MigrationService.php","line":531,"function":"migrateToSchema","class":"OC\\DB\\Connection","type":"->"},{"file":"/var/www/nextcloud/lib/private/DB/MigrationService.php","line":416,"function":"executeStep","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/var/www/nextcloud/lib/private/Installer.php","line":153,"function":"migrate","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/var/www/nextcloud/apps/settings/lib/Controller/AppSettingsController.php","line":451,"function":"installApp","class":"OC\\Installer","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php","line":225,"function":"enableApps","class":"OCA\\Settings\\Controller\\AppSettingsController","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/Http/Dispatcher.php","line":133,"function":"executeController","class":"OC\\AppFramework\\Http\\Dispatcher","type":"->"},{"file":"/var/www/nextcloud/lib/private/AppFramework/App.php","line":172,"function":"dispatch","class":"OC\\AppFramework\\Http\\Dispatcher","type":"->"},{"file":"/var/www/nextcloud/lib/private/Route/Router.php","line":298,"function":"main","class":"OC\\AppFramework\\App","type":"::"},{"file":"/var/www/nextcloud/lib/base.php","line":1047,"function":"match","class":"OC\\Route\\Router","type":"->"},{"file":"/var/www/nextcloud/index.php","line":36,"function":"handleRequest","class":"OC","type":"::"}],"File":"/var/www/nextcloud/3rdparty/doctrine/dbal/src/Driver/PDO/Connection.php","Line":82}}},"message":"could not enable apps","exception":{},"CustomMessage":"could not enable apps"}}

Sorry for the ugly formatting.

[buttercannon]

The app list above has bookmarks at 4.2.2 but, as can be seen in the screenshot, it shows as 12.0.0 on the UI.

I've also tried replacing the oc_appconfig and oc_bookmarks tables and replacing with exact replicas. This worked with some other issues I was having but did not work for this issue.

[buttercannon]

Finally fixed!

First, set up logging of SQL statements executed when enabling the app by using the following commands.

set global log_output = 'table';
set global general_log = 'on';

Then attempted to enable the Bookmarks app which errored as usual and ran the following.

select * from mysql.general_log;

In the morass that followed, a line referencing the oc_bookmarks_root_folders table stuck out. I made a clone of that table, dropped the original, and renamed the clone to the original name. Et voilà! All is now well!