Upgrade not possible due to corrupt table in mariaDB

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  • Nextcloud Server version (e.g., 29.x.x):
    • 29.0.0.19
  • Operating system and version (e.g., Ubuntu 24.04):
    • Freebsd 13 Jail
  • Web server and version (e.g, Apache 2.4.25):
    • apache24-2.4.62
  • Reverse proxy and version _(e.g. nginx 1.27.2)
    • nginx 1.26.2_8,3
  • PHP version (e.g, 8.3):
    • 8.2.25
  • Is this the first time you’ve seen this error? (Yes / No):
    • no
  • When did this problem seem to first start?
    • earlier upgrades, but did not break
  • Installation method (e.g. AIO, NCP, Bare Metal/Archive, etc.)
    • FreeBSD jails
  • Are you using Cloudflare, mod_security, or similar? (Yes / No)
    • no

Summary of the issue you are facing:

Web based upgrade did not work.
Tried manual install afterwards directly to 30.0.2
did occ upgrade, gave error 2006, mysql server has gone away.
“Exception: Database error when running migration 1020Date20240403003535 for app files_trashbin”

  • occ migrations:preview 30.0.2’
    Addition of column ‘deleted_by’ (string) to table ‘files_trash’

  • SHOW TABLES; # in mariadb nextcloud database:
    No tables called ‘files_trash’

Log entries

Nextcloud

Please provide the log entries from your Nextcloud log that are generated during the time of problem (via the Copy raw option from Administration settings->Logging screen or from your nextcloud.log located in your data directory). Feel free to use a pastebin/gist service if necessary.

{"reqId":"RsT81eo5grx2prMReCm0","level":0,"time":"2024-11-26T11:46:19+00:00","remoteAddr":"","user":"--","app":"core","method":"","url":"/occ","message":"starting upgrade from 29.0.0.19 to 30.0.2.2","userAgent":"--","version":"29.0.0.19","data":{"app":"core"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":1,"time":"2024-11-26T11:46:19+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"OC\\Repair\\Events\\RepairStepEvent: Repair step: Repair MySQL collation","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":1,"time":"2024-11-26T11:46:19+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"OC\\Repair\\Events\\RepairInfoEvent: Repair info: All tables already have the correct collation -> nothing to do","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":1,"time":"2024-11-26T11:46:19+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"OC\\Repair\\Events\\RepairStepEvent: Repair step: Copy data from accounts table when migrating from ownCloud","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":1,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"OC\\Repair\\Events\\RepairStepEvent: Repair step: Drop account terms table when migrating from ownCloud","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":1,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"\\OC\\Updater::dbUpgradeBefore: Updating database schema","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":1,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"\\OC\\Updater::dbUpgrade: Updated database","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
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{"reqId":"RsT81eo5grx2prMReCm0","level":0,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"no app in context","method":"","url":"/occ","message":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1","userAgent":"--","version":"29.0.0.19","exception":{"Exception":"Exception","Message":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1","Code":0,"Trace":[{"file":"/usr/local/www/nextcloud/lib/private/DB/ConnectionAdapter.php","line":50,"function":"executeQuery","class":"OC\\DB\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/QueryBuilder/QueryBuilder.php","line":289,"function":"executeQuery","class":"OC\\DB\\ConnectionAdapter","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/BackgroundJob/JobList.php","line":127,"function":"executeQuery","class":"OC\\DB\\QueryBuilder\\QueryBuilder","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/BackgroundJob/JobList.php","line":47,"function":"has","class":"OC\\BackgroundJob\\JobList","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Setup.php","line":416,"function":"add","class":"OC\\BackgroundJob\\JobList","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":227,"function":"installBackgroundJobs","class":"OC\\Setup","type":"::"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":98,"function":"doUpgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/core/Command/Upgrade.php","line":190,"function":"upgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Command/Command.php","line":326,"function":"execute","class":"OC\\Core\\Command\\Upgrade","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":1078,"function":"run","class":"Symfony\\Component\\Console\\Command\\Command","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":324,"function":"doRunCommand","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":175,"function":"doRun","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Console/Application.php","line":183,"function":"run","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/console.php","line":87,"function":"run","class":"OC\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/occ","line":11,"args":["/usr/local/www/nextcloud/console.php"],"function":"require_once"}],"File":"/usr/local/www/nextcloud/lib/private/DB/Connection.php","Line":402,"message":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1","tables":["oc_jobs"],"reads":["oc_jobs"],"exception":{},"CustomMessage":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":0,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"no app in context","method":"","url":"/occ","message":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1","userAgent":"--","version":"29.0.0.19","exception":{"Exception":"Exception","Message":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1","Code":0,"Trace":[{"file":"/usr/local/www/nextcloud/lib/private/DB/ConnectionAdapter.php","line":50,"function":"executeQuery","class":"OC\\DB\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/QueryBuilder/QueryBuilder.php","line":289,"function":"executeQuery","class":"OC\\DB\\ConnectionAdapter","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/BackgroundJob/JobList.php","line":127,"function":"executeQuery","class":"OC\\DB\\QueryBuilder\\QueryBuilder","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/BackgroundJob/JobList.php","line":47,"function":"has","class":"OC\\BackgroundJob\\JobList","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Setup.php","line":417,"function":"add","class":"OC\\BackgroundJob\\JobList","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":227,"function":"installBackgroundJobs","class":"OC\\Setup","type":"::"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":98,"function":"doUpgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/core/Command/Upgrade.php","line":190,"function":"upgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Command/Command.php","line":326,"function":"execute","class":"OC\\Core\\Command\\Upgrade","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":1078,"function":"run","class":"Symfony\\Component\\Console\\Command\\Command","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":324,"function":"doRunCommand","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":175,"function":"doRun","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Console/Application.php","line":183,"function":"run","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/console.php","line":87,"function":"run","class":"OC\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/occ","line":11,"args":["/usr/local/www/nextcloud/console.php"],"function":"require_once"}],"File":"/usr/local/www/nextcloud/lib/private/DB/Connection.php","Line":402,"message":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1","tables":["oc_jobs"],"reads":["oc_jobs"],"exception":{},"CustomMessage":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":0,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"no app in context","method":"","url":"/occ","message":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1","userAgent":"--","version":"29.0.0.19","exception":{"Exception":"Exception","Message":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1","Code":0,"Trace":[{"file":"/usr/local/www/nextcloud/lib/private/DB/ConnectionAdapter.php","line":50,"function":"executeQuery","class":"OC\\DB\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/QueryBuilder/QueryBuilder.php","line":289,"function":"executeQuery","class":"OC\\DB\\ConnectionAdapter","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/BackgroundJob/JobList.php","line":127,"function":"executeQuery","class":"OC\\DB\\QueryBuilder\\QueryBuilder","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/BackgroundJob/JobList.php","line":47,"function":"has","class":"OC\\BackgroundJob\\JobList","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Setup.php","line":418,"function":"add","class":"OC\\BackgroundJob\\JobList","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":227,"function":"installBackgroundJobs","class":"OC\\Setup","type":"::"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":98,"function":"doUpgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/core/Command/Upgrade.php","line":190,"function":"upgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Command/Command.php","line":326,"function":"execute","class":"OC\\Core\\Command\\Upgrade","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":1078,"function":"run","class":"Symfony\\Component\\Console\\Command\\Command","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":324,"function":"doRunCommand","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":175,"function":"doRun","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Console/Application.php","line":183,"function":"run","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/console.php","line":87,"function":"run","class":"OC\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/occ","line":11,"args":["/usr/local/www/nextcloud/console.php"],"function":"require_once"}],"File":"/usr/local/www/nextcloud/lib/private/DB/Connection.php","Line":402,"message":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1","tables":["oc_jobs"],"reads":["oc_jobs"],"exception":{},"CustomMessage":"dirty table reads: SELECT `id` FROM `*PREFIX*jobs` WHERE (`class` = :dcValue1) AND (`argument_hash` = :dcValue2) LIMIT 1"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":1,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"\\OC\\Updater::appUpgradeStarted: Updating <files_trashbin> ...","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":3,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"no app in context","method":"","url":"/occ","message":"Database error when running migration 1020Date20240403003535 for app files_trashbin\nAn exception occurred while executing a query: SQLSTATE[HY000]: General error: 2006 MySQL server has gone away","userAgent":"--","version":"29.0.0.19","exception":{"Exception":"Exception","Message":"Database error when running migration 1020Date20240403003535 for app files_trashbin\nAn exception occurred while executing a query: SQLSTATE[HY000]: General error: 2006 MySQL server has gone away","Code":0,"Trace":[{"file":"/usr/local/www/nextcloud/lib/private/legacy/OC_App.php","line":736,"function":"migrate","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":323,"function":"updateApp","class":"OC_App","type":"::","args":["*** sensitive parameters replaced 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General error: 2006 MySQL server has gone away","Code":2006,"Trace":[{"file":"/usr/local/www/nextcloud/3rdparty/doctrine/dbal/src/Driver/PDO/Connection.php","line":39,"function":"new","class":"Doctrine\\DBAL\\Driver\\PDO\\Exception","type":"::"},{"file":"/usr/local/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1211,"function":"exec","class":"Doctrine\\DBAL\\Driver\\PDO\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/doctrine/dbal/src/Connections/PrimaryReadReplicaConnection.php","line":292,"function":"executeStatement","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/Connection.php","line":462,"function":"executeStatement","class":"Doctrine\\DBAL\\Connections\\PrimaryReadReplicaConnection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/Migrator.php","line":142,"function":"executeStatement","class":"OC\\DB\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/Migrator.php","line":47,"function":"applySchema","class":"OC\\DB\\Migrator","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/Connection.php","line":791,"function":"migrate","class":"OC\\DB\\Migrator","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/MigrationService.php","line":515,"function":"migrateToSchema","class":"OC\\DB\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/MigrationService.php","line":395,"function":"executeStep","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/legacy/OC_App.php","line":736,"function":"migrate","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":323,"function":"updateApp","class":"OC_App","type":"::","args":["*** sensitive parameters replaced ***"]},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":234,"function":"doAppUpgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":98,"function":"doUpgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/core/Command/Upgrade.php","line":190,"function":"upgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Command/Command.php","line":326,"function":"execute","class":"OC\\Core\\Command\\Upgrade","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":1078,"function":"run","class":"Symfony\\Component\\Console\\Command\\Command","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":324,"function":"doRunCommand","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":175,"function":"doRun","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Console/Application.php","line":183,"function":"run","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/console.php","line":87,"function":"run","class":"OC\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/occ","line":11,"args":["/usr/local/www/nextcloud/console.php"],"function":"require_once"}],"File":"/usr/local/www/nextcloud/3rdparty/doctrine/dbal/src/Driver/PDO/Exception.php","Line":28,"Previous":{"Exception":"PDOException","Message":"SQLSTATE[HY000]: General error: 2006 MySQL server has gone away","Code":"HY000","Trace":[{"file":"/usr/local/www/nextcloud/3rdparty/doctrine/dbal/src/Driver/PDO/Connection.php","line":33,"function":"exec","class":"PDO","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/doctrine/dbal/src/Connection.php","line":1211,"function":"exec","class":"Doctrine\\DBAL\\Driver\\PDO\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/doctrine/dbal/src/Connections/PrimaryReadReplicaConnection.php","line":292,"function":"executeStatement","class":"Doctrine\\DBAL\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/Connection.php","line":462,"function":"executeStatement","class":"Doctrine\\DBAL\\Connections\\PrimaryReadReplicaConnection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/Migrator.php","line":142,"function":"executeStatement","class":"OC\\DB\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/Migrator.php","line":47,"function":"applySchema","class":"OC\\DB\\Migrator","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/Connection.php","line":791,"function":"migrate","class":"OC\\DB\\Migrator","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/MigrationService.php","line":515,"function":"migrateToSchema","class":"OC\\DB\\Connection","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/DB/MigrationService.php","line":395,"function":"executeStep","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/legacy/OC_App.php","line":736,"function":"migrate","class":"OC\\DB\\MigrationService","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":323,"function":"updateApp","class":"OC_App","type":"::","args":["*** sensitive parameters replaced ***"]},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":234,"function":"doAppUpgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Updater.php","line":98,"function":"doUpgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/core/Command/Upgrade.php","line":190,"function":"upgrade","class":"OC\\Updater","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Command/Command.php","line":326,"function":"execute","class":"OC\\Core\\Command\\Upgrade","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":1078,"function":"run","class":"Symfony\\Component\\Console\\Command\\Command","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":324,"function":"doRunCommand","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/3rdparty/symfony/console/Application.php","line":175,"function":"doRun","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/lib/private/Console/Application.php","line":183,"function":"run","class":"Symfony\\Component\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/console.php","line":87,"function":"run","class":"OC\\Console\\Application","type":"->"},{"file":"/usr/local/www/nextcloud/occ","line":11,"args":["/usr/local/www/nextcloud/console.php"],"function":"require_once"}],"File":"/usr/local/www/nextcloud/3rdparty/doctrine/dbal/src/Driver/PDO/Connection.php","Line":33}}},"message":"Database error when running migration 1020Date20240403003535 for app files_trashbin\nAn exception occurred while executing a query: SQLSTATE[HY000]: General error: 2006 MySQL server has gone away","exception":{},"CustomMessage":"Database error when running migration 1020Date20240403003535 for app files_trashbin\nAn exception occurred while executing a query: SQLSTATE[HY000]: General error: 2006 MySQL server has gone away"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":3,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"\\OC\\Updater::failure: Exception: Database error when running migration 1020Date20240403003535 for app files_trashbin\nAn exception occurred while executing a query: SQLSTATE[HY000]: General error: 2006 MySQL server has gone away","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":3,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"\\OC\\Updater::updateEnd: Update failed","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":1,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"\\OC\\Updater::maintenanceActive: Maintenance mode is kept active","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}
{"reqId":"RsT81eo5grx2prMReCm0","level":1,"time":"2024-11-26T11:46:20+00:00","remoteAddr":"","user":"--","app":"updater","method":"","url":"/occ","message":"\\OC\\Updater::resetLogLevel: Reset log level to Warning(2)","userAgent":"--","version":"29.0.0.19","data":{"app":"updater"}}

Web Browser

If the problem is related to the Web interface, open your browser inspector Console and Network tabs while refreshing (reloading) and reproducing the problem. Provide any relevant output/errors here that appear.

PASTE

Web server / Reverse Proxy

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

PASTE HERE

Configuration

Nextcloud

The output of occ config:list system or similar is best, but, if not possible, the contents of your config.php file from /path/to/nextcloud is fine (make sure to remove any identifiable information!):

{
    "system": {
        "instanceid": "***REMOVED SENSITIVE VALUE***",
        "passwordsalt": "***REMOVED SENSITIVE VALUE***",
        "secret": "***REMOVED SENSITIVE VALUE***",
        "trusted_domains": [
            "************",
            "********************"
        ],
        "trusted_proxies": "***REMOVED SENSITIVE VALUE***",
        "datadirectory": "***REMOVED SENSITIVE VALUE***",
        "dbtype": "mysql",
        "version": "29.0.0.19",
        "overwrite.cli.url": "http:\/\/*******",
        "dbname": "***REMOVED SENSITIVE VALUE***",
        "dbhost": "***REMOVED SENSITIVE VALUE***",
        "dbport": "",
        "dbtableprefix": "oc_",
        "mysql.utf8mb4": true,
        "dbuser": "***REMOVED SENSITIVE VALUE***",
        "dbpassword": "***REMOVED SENSITIVE VALUE***",
        "installed": true,
        "redis": {
            "host": "***REMOVED SENSITIVE VALUE***",
            "port": 0
        },
        "memcache.local": "\\OC\\Memcache\\APCu",
        "memcache.locking": "\\OC\\Memcache\\Redis",
        "mail_smtphost": "***REMOVED SENSITIVE VALUE***",
        "mail_from_address": "***REMOVED SENSITIVE VALUE***",
        "mail_smtpmode": "smtp",
        "mail_sendmailmode": "smtp",
        "mail_domain": "***REMOVED SENSITIVE VALUE***",
        "mail_smtpauth": 1,
        "mail_smtpauthtype": "PLAIN",
        "mail_smtpport": "587",
        "mail_smtpname": "***REMOVED SENSITIVE VALUE***",
        "mail_smtppassword": "***REMOVED SENSITIVE VALUE***",
        "maintenance_window_start": "1",
        "default_phone_region": "**",
        "overwriteprotocol": "https",
        "overwritehost": "cloud.********.com",
        "overwritewebroot": "\/",
        "htaccess.RewriteBase": "\/",
        "maintenance": true,
        "memories.vod.path": "\/usr\/local\/www\/nextcloud\/apps\/memories\/bin-ext\/go-vod-aarch64",
        "enabledPreviewProviders": [
            "OC\\Preview\\Image",
            "OC\\Preview\\HEIC",
            "OC\\Preview\\TIFF",
            "OC\\Preview\\Movie"
        ],
        "memories.vod.disable": false,
        "memories.vod.ffmpeg": "\/usr\/local\/bin\/ffmpeg",
        "memories.vod.ffprobe": "\/usr\/local\/bin\/ffprobe",
        "memories.exiftool": "\/usr\/local\/www\/nextcloud\/apps\/memories\/bin-ext\/exiftool\/exiftool",
        "preview_ffmpeg_path": "\/usr\/local\/bin\/ffmpeg",
        "theme": "",
        "loglevel": 2,
        "memories.exiftool_no_local": true,
        "memories.vod.external": true,
        "app_install_overwrite": [
            "news"
        ],
        "memories.db.triggers.fcu": true,
        "updater.secret": "***REMOVED SENSITIVE VALUE***"
    }
}

Apps

The output of occ app:list (if possible).

  - cloud_federation_api: 1.13.0
  - contactsinteraction: 1.10.0
  - dav: 1.31.1
  - federatedfilesharing: 1.19.0
  - files: 2.2.0
  - files_downloadlimit: 2.0.0
  - files_external: 1.22.0
  - files_pdfviewer: 2.10.0
  - files_trashbin: 1.19.0
  - logreader: 2.14.0
  - lookup_server_connector: 1.18.0
  - mail: 3.7.12
  - memories: 7.4.1
  - notes: 4.11.0
  - notifications: 2.17.0
  - oauth2: 1.18.1
  - password_policy: 2.0.0
  - photos: 3.0.2
  - previewgenerator: 5.7.0
  - privacy: 1.13.0
  - provisioning_api: 1.19.0
  - recognize: 7.1.0
  - serverinfo: 1.19.0
  - settings: 1.12.0
  - theming: 2.4.0
  - twofactor_backupcodes: 1.18.0
  - twofactor_totp: 11.0.0-dev
  - updatenotification: 1.19.1
  - viewer: 2.3.0
  - workflowengine: 2.11.0
Disabled:
  - activity: 3.0.0 (installed 2.15.0)
  - admin_audit: 1.20.0
  - app_api: 4.0.0
  - bruteforcesettings: 3.0.0 (installed 2.9.0)
  - calendar: 4.7.16 (installed 4.7.16)
  - circles: 30.0.0 (installed 22.1.1)
  - comments: 1.20.1 (installed 1.11.0)
  - contacts: 6.0.1 (installed 6.0.1)
  - dashboard: 7.10.0 (installed 7.1.0)
  - encryption: 2.18.0
  - federation: 1.20.0 (installed 1.11.0)
  - files_reminders: 1.3.0 (installed 1.1.0)
  - files_sharing: 1.22.0 (installed 1.20.0)
  - files_versions: 1.23.0 (installed 1.16.0)
  - firstrunwizard: 3.0.0 (installed 2.11.0)
  - keeporsweep: 0.3.0 (installed 0.3.0)
  - news: 25.0.2 (installed 25.0.2)
  - nextcloud_announcements: 2.0.0 (installed 1.17.0)
  - recommendations: 3.0.0 (installed 1.1.0)
  - related_resources: 1.5.0 (installed 1.3.0)
  - sharebymail: 1.20.0 (installed 1.11.0)
  - support: 2.0.0 (installed 1.5.0)
  - survey_client: 2.0.0 (installed 1.16.0)
  - suspicious_login: 8.0.0 (installed 5.0.0)
  - systemtags: 1.20.0 (installed 1.11.0)
  - text: 4.1.0 (installed 3.9.1)
  - twofactor_nextcloud_notification: 4.0.0
  - user_ldap: 1.21.0
  - user_status: 1.10.0 (installed 1.1.1)
  - weather_status: 1.10.0 (installed 1.1.0)
  - webhook_listeners: 1.1.0-dev

Tips for increasing the likelihood of a response

  • Use the preformatted text formatting option in the editor for all log entries and configuration output.
  • If screenshots are useful, feel free to include them.
    • If possible, also include key error output in text form so it can be searched for.
  • Try to edit log output only minimally (if at all) so that it can be ran through analyzers / formatters by those trying to help you.
2

The above is the problem, not a missing table. See How to work around “general error: 2006 MySQL server has gone away” and also threads like Mail app causes this error: SQLSTATE general error 2006: MySQL server has gone away

29.0.0.19
[…]
Tried manual install afterwards directly to 30.0.2

For future reference, it’s recommended to update to the latest maintenance release before jumping to a new major version. See How to upgrade.

Web based upgrade did not work.

Not sure the nature of the problem you encountered when using web-mode of the automated updater, but there is separate logging for the Updater (which might offer some clues as to what happened). There is also a command-line mode - which is more reliable (because it avoids things like web infrastructure timeouts among other things). See Upgrade: Troubleshooting for details.

3

Fixed:
Ran every type of mysqlcheck and it just dropped connection.
Decided to just drop table oc_files_trash; and ran again occ upgrade.

i set the Max_allowed_packet to

root@localhost [nextcloud]> SHOW VARIABLES LIKE 'max_allowed_packet';
+--------------------+------------+
| Variable_name      | Value      |
+--------------------+------------+
| max_allowed_packet | 1073741824 |
+--------------------+------------+

i also added wait_timout to 8 hours, but that was already the standard.
Restarted all the services and ran occ upgrade > The same 2006 error persists.

mysql error log:

241127  7:23:40 [ERROR] mysqld got signal 11 ;
Sorry, we probably made a mistake, and this is a bug.

Your assistance in bug reporting will enable us to fix this for the next release.
To report this bug, see https://mariadb.com/kb/en/reporting-bugs

We will try our best to scrape up some info that will hopefully help
diagnose the problem, but since we have already crashed,
something is definitely wrong and this may fail.

Server version: 10.5.27-MariaDB source revision: 6aa47fae304bd1f3efc0ebd2035bc1481ded73a3
key_buffer_size=134217728
read_buffer_size=131072
max_used_connections=1
max_threads=153
thread_count=1
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 467816 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x81f52dd18
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 0x7fffde549f10 thread_stack 0x49000
0x1347c8c <my_print_stacktrace+0x3c> at /usr/local/libexec/mariadbd
0xcaf144 <handle_fatal_signal+0x284> at /usr/local/libexec/mariadbd
0x801953580 <pthread_sigmask+0x540> at /lib/libthr.so.3
0x801952b3f <pthread_setschedparam+0x82f> at /lib/libthr.so.3
0x7ffffffff2d3 <???> at ???
0x11d6c57 <wsrep_get_domain_id+0xfc687> at /usr/local/libexec/mariadbd
0x11d89dc <wsrep_get_domain_id+0xfe40c> at /usr/local/libexec/mariadbd
0xeb0007 <_Z12check_engineP3THDPKcS2_P14HA_CREATE_INFO+0x2d47> at /usr/local/libexec/mariadbd
0xeacb29 <_Z17mysql_alter_tableP3THDPK25st_mysql_const_lex_stringS3_P14HA_CREATE_INFOP10TABLE_LISTP13Recreate_infoP10Alter_infojP8st_orderbb+0x1c79> at /usr/local/libexec/mariadbd
0xf195fd <_ZN19Sql_cmd_alter_table7executeEP3THD+0x55d> at /usr/local/libexec/mariadbd
0xdf2f58 <_Z21mysql_execute_commandP3THD+0x818> at /usr/local/libexec/mariadbd
0xdeeb79 <_Z11mysql_parseP3THDPcjP12Parser_statebb+0x1b9> at /usr/local/libexec/mariadbd
0xdecfa8 <_Z16dispatch_command19enum_server_commandP3THDPcjbb+0xd28> at /usr/local/libexec/mariadbd
0xdeef83 <_Z10do_commandP3THD+0x223> at /usr/local/libexec/mariadbd
0xf13818 <_Z24do_handle_one_connectionP7CONNECTb+0xd8> at /usr/local/libexec/mariadbd
0xf136a0 <handle_one_connection+0x80> at /usr/local/libexec/mariadbd
0x1066b06 <_ZN11MyCTX_nopad6finishEPhPj+0x14a96> at /usr/local/libexec/mariadbd

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (0x81f5865b0): ALTER TABLE oc_files_trash ADD deleted_by VARCHAR(64) DEFAULT NULL

Connection ID (thread ID): 3
Status: NOT_KILLED

Optimizer switch: index_merge=on,index_merge_union=on,index_merge_sort_union=on,index_merge_intersection=on,index_merge_sort_intersection=off,engine_condition_pushdown=off,index_condition_pushdown=on,derived_merge=on,derived_with_keys=on,firstmatch=on,loosescan=on,materialization=on,in_to_exists=on,semijoin=on,partial_match_rowid_merge=on,partial_match_table_scan=on,subquery_cache=on,mrr=off,mrr_cost_based=off,mrr_sort_keys=off,outer_join_with_cache=on,semijoin_with_cache=on,join_cache_incremental=on,join_cache_hashed=on,join_cache_bka=on,optimize_join_buffer_size=on,table_elimination=on,extended_keys=on,exists_to_in=on,orderby_uses_equalities=on,condition_pushdown_for_derived=on,split_materialized=on,condition_pushdown_for_subquery=on,rowid_filter=on,condition_pushdown_from_having=on,not_null_range_scan=off

The manual page at https://mariadb.com/kb/en/how-to-produce-a-full-stack-trace-for-mariadbd/ contains
information that should help you find out what is causing the crash.
Core pattern: /var/db/system/cores/%N.core

the table in question is indeed available in mariadb.

root@localhost [nextcloud]> SHOW FULL TABLES WHERE TABLES_IN_NEXTCLOUD LIKE '%oc_files_trash%';
+---------------------+------------+
| Tables_in_nextcloud | Table_type |
+---------------------+------------+
| oc_files_trash      | BASE TABLE |
+---------------------+------------+

if i then run: select * from oc_files_trash; and instantly i receive:

ERROR 2013 (HY000): Lost connection to MySQL server during query

However, when run: select * from oc_files_metadata;
it starts spewing out data.

4

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