ownCloud 8.2.8 to Nextcloud 9.0.54 upgrade error - what to do?

I just upgraded my ownCloud 8.2.8 installation to Nextcloud 9.0.54 using the manual upgrade documentation and at the “occ upgrade” part I get the following error message:

{“reqId”:“85wCet+g1+qejtfkMjDo”,“remoteAddr”:"",“app”:“notifications”,“message”:“Exception: {“Exception”:“Doctrine\\DBAL\\Exception\\TableExistsException”,“Message”:“An exception occurred while executing ‘CREATE TABLE oc_notifications (notification_id INT AUTO_INCREMENT NOT NULL, app VARCHAR(32) NOT NULL, user VARCHAR(64) NOT NULL, timestamp INT DEFAULT 0 NOT NULL, object_type VARCHAR(64) NOT NULL, object_id VARCHAR(64) NOT NULL, subject VARCHAR(64) NOT NULL, subject_parameters LONGTEXT DEFAULT NULL, message VARCHAR(64) DEFAULT NULL, message_parameters LONGTEXT DEFAULT NULL, link VARCHAR(4000) DEFAULT NULL, actions LONGTEXT DEFAULT NULL, INDEX oc_notifications_app (app), INDEX oc_notifications_user (user), INDEX oc_notifications_timestamp (timestamp), INDEX oc_notifications_object (object_type, object_id), PRIMARY KEY(notification_id)) DEFAULT CHARACTER SET utf8 COLLATE utf8_bin ENGINE = InnoDB’:\n\nSQLSTATE[42S01]: Base table or view already exists: 1050 Table ‘oc_notifications’ already exists”,“Code”:0,“Trace”:”#0 \/var\/www\/cloud.mydomain.com\/3rdparty\/doctrine\/dbal\/lib\/Doctrine\/DBAL\/DBALException.php(116): Doctrine\\DBAL\\Driver\\AbstractMySQLDriver->convertException(‘An exception oc…’, Object(Doctrine\\DBAL\\Driver\\PDOException))\n#1 \/var\/www\/cloud.mydomain.com\/3rdparty\/doctrine\/dbal\/lib\/Doctrine\/DBAL\/Connection.php(945): Doctrine\\DBAL\\DBALException::driverExceptionDuringQuery(Object(Doctrine\\DBAL\\Driver\\PDOMySql\\Driver), Object(Doctrine\\DBAL\\Driver\\PDOException), ‘CREATE TABLE o...')\\n#2 \\\/var\\\/www\\\/cloud.mydomain.com\\\/lib\\\/private\\\/db\\\/mdb2schemamanager.php(168): Doctrine\\\\DBAL\\\\Connection->query('CREATE TABLEo…’)\n#3 \/var\/www\/cloud.mydomain.com\/lib\/private\/db\/mdb2schemamanager.php(71): OC\\DB\\MDB2SchemaManager->executeSchemaChange(Object(Doctrine\\DBAL\\Schema\\Schema))\n#4 \/var\/www\/cloud.mydomain.com\/lib\/private\/db.php(173): OC\\DB\\MDB2SchemaManager->createDbFromStructure(’\/var\/www\/cloud…’)\n#5 \/var\/www\/cloud.mydomain.com\/lib\/private\/installer.php(588): OC_DB::createDbFromStructure(’\/var\/www\/cloud…’)\n#6 \/var\/www\/cloud.mydomain.com\/lib\/private\/installer.php(558): OC_Installer::installShippedApp(‘notifications’)\n#7 \/var\/www\/cloud.mydomain.com\/lib\/private\/updater.php(336): OC_Installer::installShippedApps(true)\n#8 \/var\/www\/cloud.mydomain.com\/lib\/private\/updater.php(214): OC\\Updater->doUpgrade(‘9.0.54.5’, ‘8.2.8.2’)\n#9 \/var\/www\/cloud.mydomain.com\/core\/command\/upgrade.php(248): OC\\Updater->upgrade()\n#10 \/var\/www\/cloud.mydomain.com\/3rdparty\/symfony\/console\/Command\/Command.php(259): OC\\Core\\Command\\Upgrade->execute(Object(Symfony\\Component\\Console\\Input\\ArgvInput), Object(Symfony\\Component\\Console\\Output\\ConsoleOutput))\n#11 \/var\/www\/cloud.mydomain.com\/core\/command\/base.php(159): Symfony\\Component\\Console\\Command\\Command->run(Object(Symfony\\Component\\Console\\Input\\ArgvInput), Object(Symfony\\Component\\Console\\Output\\ConsoleOutput))\n#12 \/var\/www\/cloud.mydomain.com\/3rdparty\/symfony\/console\/Application.php(840): OC\\Core\\Command\\Base->run(Object(Symfony\\Component\\Console\\Input\\ArgvInput), Object(Symfony\\Component\\Console\\Output\\ConsoleOutput))\n#13 \/var\/www\/cloud.mydomain.com\/3rdparty\/symfony\/console\/Application.php(192): Symfony\\Component\\Console\\Application->doRunCommand(Object(OC\\Core\\Command\\Upgrade), Object(Symfony\\Component\\Console\\Input\\ArgvInput), Object(Symfony\\Component\\Console\\Output\\ConsoleOutput))\n#14 \/var\/www\/cloud.mydomain.com\/3rdparty\/symfony\/console\/Application.php(123): Symfony\\Component\\Console\\Application->doRun(Object(Symfony\\Component\\Console\\Input\\ArgvInput), Object(Symfony\\Component\\Console\\Output\\ConsoleOutput))\n#15 \/var\/www\/cloud.mydomain.com\/lib\/private\/console\/application.php(146): Symfony\\Component\\Console\\Application->run(NULL, NULL)\n#16 \/var\/www\/cloud.mydomain.com\/console.php(89): OC\\Console\\Application->run()\n#17 \/var\/www\/cloud.mydomain.com\/occ(11): require_once(’\/var\/www\/cloud…’)\n#18 {main}",“File”:"\/var\/www\/cloud.mydomain.com\/3rdparty\/doctrine\/dbal\/lib\/Doctrine\/DBAL\/Driver\/AbstractMySQLDriver.php",“Line”:49}",“level”:3,“time”:“2016-10-31T21:30:56+01:00”,“method”:"–",“url”:"/occ",“user”:"–"}

does this mean my upgrade is messed up? or can I safely continue?

There have been reports before:

even for later upgrades:

All these issues were still reported on OC, but not only there: Owncloud 8.2 to nextcloud 9.0 upgrade error - should I be concerned?

Since nobody really provided a solution, you should probably create an issue on github.com/nextcloud/server/issues