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The --upgrade-system-tables option was used, user tables won't be touched.
Phase 1/8: Checking and upgrading mysql database
Processing databases
mysql
mysql.column_stats OK
mysql.columns_priv OK
mysql.db OK
mysql.event OK
mysql.func OK
mysql.global_priv OK
mysql.gtid_slave_pos OK
mysql.help_category OK
mysql.help_keyword OK
mysql.help_relation OK
mysql.help_topic OK
mysql.index_stats OK
mysql.innodb_index_stats
Error : Unknown storage engine 'InnoDB'
error : Corrupt
mysql.innodb_table_stats
Error : Unknown storage engine 'InnoDB'
error : Corrupt
mysql.plugin OK
mysql.proc OK
mysql.procs_priv OK
mysql.proxies_priv OK
mysql.roles_mapping OK
mysql.servers OK
mysql.table_stats OK
mysql.tables_priv OK
mysql.time_zone OK
mysql.time_zone_leap_second OK
mysql.time_zone_name OK
mysql.time_zone_transition OK
mysql.time_zone_transition_type OK
mysql.transaction_registry
Error : Unknown storage engine 'InnoDB'
error : Corrupt
Repairing tables
mysql.innodb_index_stats
Error : Unknown storage engine 'InnoDB'
error : Corrupt
mysql.innodb_table_stats
Error : Unknown storage engine 'InnoDB'
error : Corrupt
mysql.transaction_registry
Error : Unknown storage engine 'InnoDB'
error : Corrupt
Phase 2/8: Installing used storage engines... Skipped
Phase 3/8: Running 'mysql_fix_privilege_tables'
Phase 4/8: Fixing views... Skipped
Phase 5/8: Fixing table and database names ... Skipped
Phase 6/8: Checking and upgrading tables... Skipped
Phase 7/8: uninstalling plugins
Phase 8/8: Running 'FLUSH PRIVILEGES'
OK
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