The --upgrade-system-tables option was used, user tables won't be touched.
Phase 1/7: 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.gtid_slave_pos                               OK
mysql.help_category                                OK
mysql.help_keyword                                 OK
mysql.help_relation                                OK
mysql.help_topic                                   OK
mysql.host                                         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
mysql.user                                         OK

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 2/7: Installing used storage engines... Skipped
Phase 3/7: Fixing views... Skipped
Phase 4/7: Running 'mysql_fix_privilege_tables'
Phase 5/7: Fixing table and database names ... Skipped
Phase 6/7: Checking and upgrading tables... Skipped
Phase 7/7: Running 'FLUSH PRIVILEGES'
OK