mysql_upgrade fails from 5.5 to 5.6

[George Ormond Lorch III]

It seems that a basic in place upgrade has problems:
1- create 5.5 server instance with my.cnf and start:
  [client]
  port=10000
  socket=/data/dev/var/test-0/mysql.1/mysql.sock
  [mysqld]
  basedir=/data/bin/ps-5.5
  datadir=/data/dev/var/test-0/mysql.1/data
  tmpdir=/data/dev/var/test-0/mysql.1/tmp
  port=10000
  socket=/data/dev/var/test-0/mysql.1/mysql.sock
  pid-file=/data/dev/var/test-0/mysql.1/mysql.pid
  console
  user=root
  server-id=1
  innodb_buffer_pool_size=512M
  innodb_file_format=barracuda
  innodb_file_per_table=1
  innodb_log_file_size=128M
2- create and load in sakila database
3 - shutdown 5.5 server
4 - create 5.6 server instance with my.cnf
  [client]
  port=10001
  socket=/data/dev/var/test-0/mysql.2/mysql.sock
  [mysqld]
  basedir=/data/bin/ps-5.6
  datadir=/data/dev/var/test-0/mysql.2/data
  tmpdir=/data/dev/var/test-0/mysql.2/tmp
  port=10001
  socket=/data/dev/var/test-0/mysql.2/mysql.sock
  pid-file=/data/dev/var/test-0/mysql.2/mysql.pid
  console
  user=root
  server-id=2
  innodb_buffer_pool_size=512M
  innodb_file_format=barracuda
  innodb_file_per_table=1
  innodb_log_file_size=128M
5 - delete 5.6 data dir and copy over 5.5 data dir to same location
6 - start 5.6 server with --skip-grant-tables
7 - run mysql_upgrade

5.6 mysql.log when started with --skip-grant-tables:
2013-07-02 13:13:52 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2013-07-02 13:13:52 11815 [Note] Plugin 'FEDERATED' is disabled.
2013-07-02 13:13:52 11815 [Note] InnoDB: The InnoDB memory heap is disabled
2013-07-02 13:13:52 11815 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2013-07-02 13:13:52 11815 [Note] InnoDB: Compressed tables use zlib 1.2.3
2013-07-02 13:13:52 11815 [Note] InnoDB: Using Linux native AIO
2013-07-02 13:13:52 11815 [Note] InnoDB: Using CPU crc32 instructions
2013-07-02 13:13:52 11815 [Note] InnoDB: Initializing buffer pool, size = 512.0M
2013-07-02 13:13:52 11815 [Note] InnoDB: Completed initialization of buffer pool
2013-07-02 13:13:52 11815 [Note] InnoDB: Highest supported file format is Barracuda.
2013-07-02 13:13:52 11815 [Note] InnoDB: 128 rollback segment(s) are active.
2013-07-02 13:13:52 11815 [Note] InnoDB: Creating tablespace and datafile system tables.
2013-07-02 13:13:52 11815 [Note] InnoDB: Tablespace and datafile system tables created.
2013-07-02 13:13:52 11815 [Note] InnoDB: Waiting for purge to start
2013-07-02 13:13:52 11815 [Note] InnoDB: Percona XtraDB (http://www.percona.com) 5.6.12-60.3 started; log sequence number 8438071
2013-07-02 13:13:52 11815 [Warning] No existing UUID has been found, so we assume that this is the first time that this server has been started. Generating a new UUID: ea327020-e353-11e2-9ce0-000c297bf3c1.
2013-07-02 13:13:52 11815 [Note] Server hostname (bind-address): '*'; port: 10001
2013-07-02 13:13:52 11815 [Note] IPv6 is available.
2013-07-02 13:13:52 11815 [Note] - '::' resolves to '::';
2013-07-02 13:13:52 11815 [Note] Server socket created on IP: '::'.
2013-07-02 13:13:52 11815 [Warning] Info table is not ready to be used. Table 'mysql.slave_master_info' cannot be opened.
2013-07-02 13:13:52 11815 [Warning] Info table is not ready to be used. Table 'mysql.slave_relay_log_info' cannot be opened.
2013-07-02 13:13:52 11815 [ERROR] Column count of mysql.events_waits_current is wrong. Expected 19, found 16. Created with MySQL 50532, now running 50612. Please use mysql_upgrade to fix this error.
2013-07-02 13:13:52 11815 [ERROR] Column count of mysql.events_waits_history is wrong. Expected 19, found 16. Created with MySQL 50532, now running 50612. Please use mysql_upgrade to fix this error.
2013-07-02 13:13:52 11815 [ERROR] Column count of mysql.events_waits_history_long is wrong. Expected 19, found 16. Created with MySQL 50532, now running 50612. Please use mysql_upgrade to fix this error.
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_host_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Incorrect definition of table performance_schema.events_waits_summary_by_thread_by_event_name: expected column 'THREAD_ID' at position 0 to have type bigint(20), found type int(11).
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_user_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_account_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Column count of mysql.file_summary_by_event_name is wrong. Expected 23, found 5. Created with MySQL 50532, now running 50612. Please use mysql_upgrade to fix this error.
2013-07-02 13:13:52 11815 [ERROR] Column count of mysql.file_summary_by_instance is wrong. Expected 25, found 6. Created with MySQL 50532, now running 50612. Please use mysql_upgrade to fix this error.
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'host_cache' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Incorrect definition of table performance_schema.mutex_instances: expected column 'LOCKED_BY_THREAD_ID' at position 2 to have type bigint(20), found type int(11).
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'objects_summary_global_by_type' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Incorrect definition of table performance_schema.rwlock_instances: expected column 'WRITE_LOCKED_BY_THREAD_ID' at position 2 to have type bigint(20), found type int(11).
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'setup_actors' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'setup_objects' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'table_io_waits_summary_by_index_usage' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'table_io_waits_summary_by_table' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'table_lock_waits_summary_by_table' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Column count of mysql.threads is wrong. Expected 14, found 3. Created with MySQL 50532, now running 50612. Please use mysql_upgrade to fix this error.
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_stages_current' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_stages_history' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_stages_history_long' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_stages_summary_by_thread_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_stages_summary_by_account_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_stages_summary_by_user_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_stages_summary_by_host_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_stages_summary_global_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_statements_current' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_statements_history' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_statements_history_long' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_thread_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_account_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_user_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_host_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_statements_summary_global_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'events_statements_summary_by_digest' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'users' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'accounts' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'hosts' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'socket_instances' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'socket_summary_by_instance' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'socket_summary_by_event_name' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'session_connect_attrs' has the wrong structure
2013-07-02 13:13:52 11815 [ERROR] Native table 'performance_schema'.'session_account_connect_attrs' has the wrong structure
2013-07-02 13:13:52 11815 [Note] mysqld: ready for connections.
Version: '5.6.12' socket: '/data/dev/var/test-0/mysql.2/mysql.sock' port: 10001 MySQL Community Server (GPL)
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."actor" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."address" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."category" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."city" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."country" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."customer" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."film" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."film_actor" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."film_category" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."inventory" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."language" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."payment" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."rental" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."staff" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Table "mysql"."innodb_table_stats" not found.
2013-07-02 13:13:52 7fe238071700 InnoDB: Error: Fetch of persistent statistics requested for table "sakila"."store" but the required system tables mysql.innodb_table_stats and mysql.innodb_index_stats are not present or have unexpected structure. Using transient stats instead.
2013-07-02 13:13:53 11815 [Note] mysqld: Normal shutdown
2013-07-02 13:13:53 11815 [Note] Giving 0 client threads a chance to die gracefully
2013-07-02 13:13:53 11815 [Note] Shutting down slave threads
2013-07-02 13:13:53 11815 [Note] Forcefully disconnecting 0 remaining clients
2013-07-02 13:13:53 11815 [Note] Binlog end
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'partition'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'BLACKHOLE'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'ARCHIVE'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_CHANGED_PAGES'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_METRICS'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_CMPMEM'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_CMP'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_LOCKS'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'INNODB_TRX'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'XTRADB_RSEG'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'XTRADB_INTERNAL_HASH_TABLES'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'XTRADB_READ_VIEW'
2013-07-02 13:13:53 11815 [Note] Shutting down plugin 'InnoDB'
2013-07-02 13:13:53 11815 [Note] InnoDB: FTS optimize thread exiting.
2013-07-02 13:13:53 11815 [Note] InnoDB: Starting shutdown...
2013-07-02 13:13:54 11815 [Note] InnoDB: Shutdown completed; log sequence number 8441732
2013-07-02 13:13:54 11815 [Note] Shutting down plugin 'MEMORY'
2013-07-02 13:13:54 11815 [Note] Shutting down plugin 'MyISAM'
2013-07-02 13:13:54 11815 [Note] Shutting down plugin 'MRG_MYISAM'
2013-07-02 13:13:54 11815 [Note] Shutting down plugin 'CSV'
2013-07-02 13:13:54 11815 [Note] Shutting down plugin 'sha256_password'
2013-07-02 13:13:54 11815 [Note] Shutting down plugin 'mysql_old_password'
2013-07-02 13:13:54 11815 [Note] Shutting down plugin 'mysql_native_password'
2013-07-02 13:13:54 11815 [Note] Shutting down plugin 'binlog'
2013-07-02 13:13:54 11815 [Note] mysqld: Shutdown complete

mysql_upgrade.log
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
Running 'mysqlcheck' with connection arguments: '--socket=/data/dev/var/test-0/mysql.2/mysql.sock'
Running 'mysqlcheck' with connection arguments: '--socket=/data/dev/var/test-0/mysql.2/mysql.sock'
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.host OK
mysql.ndb_binlog_index OK
mysql.plugin OK
mysql.proc OK
mysql.procs_priv OK
mysql.proxies_priv OK
mysql.servers OK
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
performance_schema.cond_instances OK
performance_schema.events_waits_current OK
performance_schema.events_waits_history OK
performance_schema.events_waits_history_long OK
performance_schema.events_waits_summary_by_instance OK
performance_schema.events_waits_summary_by_thread_by_event_name OK
performance_schema.events_waits_summary_global_by_event_name OK
performance_schema.file_instances OK
performance_schema.file_summary_by_event_name OK
performance_schema.file_summary_by_instance OK
performance_schema.mutex_instances OK
performance_schema.performance_timers OK
performance_schema.rwlock_instances OK
performance_schema.setup_consumers OK
performance_schema.setup_instruments OK
performance_schema.setup_timers OK
performance_schema.threads OK
sakila.actor OK
sakila.address OK
sakila.category OK
sakila.city OK
sakila.country OK
sakila.customer OK
sakila.film OK
sakila.film_actor OK
sakila.film_category OK
sakila.film_text OK
sakila.inventory OK
sakila.language OK
sakila.payment OK
sakila.rental OK
sakila.staff OK
sakila.store OK
Running 'mysql_fix_privilege_tables'...
ERROR 1426 (42000) at line 47: Too big precision 14 specified for column 'Timestamp'. Maximum is 6.
ERROR 1426 (42000) at line 49: Too big precision 14 specified for column 'Timestamp'. Maximum is 6.
ERROR 1426 (42000) at line 81: Too big precision 14 specified for column 'Timestamp'. Maximum is 6.
ERROR 1193 (HY000) at line 85: Unknown system variable 'have_csv'
ERROR 1064 (42000) at line 87: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'NULL' at line 1
ERROR 1243 (HY000) at line 88: Unknown prepared statement handler (stmt) given to EXECUTE
ERROR 1243 (HY000) at line 89: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
ERROR 1193 (HY000) at line 93: Unknown system variable 'have_csv'
ERROR 1064 (42000) at line 95: You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near 'NULL' at line 1
ERROR 1243 (HY000) at line 96: Unknown prepared statement handler (stmt) given to EXECUTE
ERROR 1243 (HY000) at line 97: Unknown prepared statement handler (stmt) given to DEALLOCATE PREPARE
ERROR 1426 (42000) at line 483: Too big precision 14 specified for column 'Timestamp'. Maximum is 6.
FATAL ERROR: Upgrade failed

If 5.6 server is restarted without --skip-grant-tables, same errors as those that occur in original are still present

[George Ormond Lorch III (gl-az)]

This is probably upstream but I can not find a report of anything similar (or I am completely missing something).

[George Ormond Lorch III (gl-az)]

Invalid, my test script was pointing to the wrong mysql_upgrade.

[Shahriyar Rzayev (rzayev-sehriyar)]

Percona now uses JIRA for bug reports so this bug report is migrated to: https://jira.percona.com/browse/PS-2983