I am upgrading my mysql-5.5 docker container database to mysql-5.6 docker container. I was able to fix all other problems. Finally my server is running with 5.6. But when i run mysql_upgrade i am getting the following error.
ERROR:
root@17aa74cbc5e2# mysql_upgrade -uroot -password           
Warning: Using a password on the command line interface can be insecure.
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/var/run/mysqld/mysqld.sock' 
Warning: Using a password on the command line interface can be insecure.
Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/var/run/mysqld/mysqld.sock' 
Warning: Using a password on the command line interface can be insecure.
mysql.columns_priv                                 OK
mysql.db                                           OK
mysql.event                                        OK
mysql.func                                         OK
mysql.general_log                                  OK
mysql.help_category                                OK
mysql.help_keyword                                 OK
mysql.help_relation                                OK
mysql.help_topic                                   OK
mysql.innodb_index_stats
Error    : Table 'mysql.innodb_index_stats' doesn't exist
status   : Operation failed
mysql.innodb_table_stats
Error    : Table 'mysql.innodb_table_stats' doesn't exist
status   : Operation failed
mysql.ndb_binlog_index                             OK
mysql.plugin                                       OK
mysql.proc                                         OK
mysql.procs_priv                                   OK
mysql.proxies_priv                                 OK
mysql.servers                                      OK
mysql.slave_master_info
Error    : Table 'mysql.slave_master_info' doesn't exist
status   : Operation failed
mysql.slave_relay_log_info
Error    : Table 'mysql.slave_relay_log_info' doesn't exist
status   : Operation failed
mysql.slave_worker_info
Error    : Table 'mysql.slave_worker_info' doesn't exist
status   : Operation failed
mysql.slow_log                                     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.user                                         OK
Repairing tables
mysql.innodb_index_stats
Error    : Table 'mysql.innodb_index_stats' doesn't exist
status   : Operation failed
mysql.innodb_table_stats
Error    : Table 'mysql.innodb_table_stats' doesn't exist
status   : Operation failed
mysql.slave_master_info
Error    : Table 'mysql.slave_master_info' doesn't exist
status   : Operation failed
mysql.slave_relay_log_info
Error    : Table 'mysql.slave_relay_log_info' doesn't exist
status   : Operation failed
mysql.slave_worker_info
Error    : Table 'mysql.slave_worker_info' doesn't exist
status   : Operation failed
Running 'mysql_fix_privilege_tables'...
Warning: Using a password on the command line interface can be insecure.
ERROR 1146 (42S02) at line 62: Table 'mysql.innodb_table_stats' doesn't exist
ERROR 1243 (HY000) at line 63: Unknown prepared statement handler (stmt) given to EXECUTE
ERROR 1243 (HY000) at line 64: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
ERROR 1146 (42S02) at line 66: Table 'mysql.innodb_index_stats' doesn't exist
ERROR 1243 (HY000) at line 67: Unknown prepared statement handler (stmt) given to EXECUTE
ERROR 1243 (HY000) at line 68: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
ERROR 1146 (42S02) at line 81: Table 'mysql.slave_relay_log_info' doesn't exist
ERROR 1243 (HY000) at line 82: Unknown prepared statement handler (stmt) given to EXECUTE
ERROR 1243 (HY000) at line 83: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
ERROR 1146 (42S02) at line 110: Table 'mysql.slave_master_info' doesn't exist
ERROR 1243 (HY000) at line 111: Unknown prepared statement handler (stmt) given to EXECUTE
ERROR 1243 (HY000) at line 112: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
ERROR 1146 (42S02) at line 128: Table 'mysql.slave_worker_info' doesn't exist
ERROR 1243 (HY000) at line 129: Unknown prepared statement handler (stmt) given to EXECUTE
ERROR 1243 (HY000) at line 130: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
ERROR 1146 (42S02) at line 1896: Table 'mysql.slave_master_info' doesn't exist
ERROR 1146 (42S02) at line 1897: Table 'mysql.slave_master_info' doesn't exist
ERROR 1146 (42S02) at line 1898: Table 'mysql.slave_master_info' doesn't exist
ERROR 1146 (42S02) at line 1899: Table 'mysql.slave_worker_info' doesn't exist
ERROR 1146 (42S02) at line 1900: Table 'mysql.slave_relay_log_info' doesn't exist
ERROR 1146 (42S02) at line 1904: Table 'mysql.innodb_table_stats' doesn't exist
ERROR 1146 (42S02) at line 1908: Table 'mysql.innodb_index_stats' doesn't exist
FATAL ERROR: Upgrade failed
				
                        
This is a known bug in MySQL 5.6, it is documented here.
According to the replies to the bug report, you can manually create the missing tables. The structure of the missing tables is provided as attachment here.
Steps to follow:
Drop these tables from Mysql:
innodb_index_stats innodb_table_stats slave_master_info slave_relay_log_info slave_worker_info
Delete
*.frmand*.ibdfiles for the 5 tables above.Create the tables by running the following queries:
Restart your MySQL server.
Run the
mysql_upgradescript.