The uploaded tar archives were both taken with server stopped. sql_50614 gives no errors in Oracle mysqld 5.6.14. mariadb_100004 has 2 server 10.0.4 sessions in mysql/dwarfstar.err. 2nd session shows the persistent error. Users in database are root/root and dunc/dunc. As root, I used mysql_upgrade -proot

Reproducible on empty datadirs as well (create one by mysql_install_db from 5.6.13, start 10.0.4 on it, run mysql_upgrade, try to use, observe the error).

While technically it is a downgrade (10.0.4 contains InnoDB of 5.6.10), still, it should work whenever possible, and this seems to be the case.

Jan,
Could you please take a look at it along with MDEV-5010?

This is already fixed on more recent version of MariaDB e.g. 10.0.6. Only error I see are:

131120 16:11:10 [ERROR] Missing system table mysql.roles_mapping; please run mysql_upgrade to create it
131120 16:11:10 [ERROR] Incorrect definition of table mysql.event: expected column 'sql_mode' at position
14 to have type set('REAL_AS_FLOAT','PIPES_AS_CONCAT','ANSI_QUOTES','IGNORE_SPACE','IGNORE_BAD_TABLE_OPTIO
NS','ONLY_FULL_GROUP_BY','NO_UNSIGNED_SUBTRACTION','NO_DIR_IN_CREATE','POSTGRESQL','ORACLE','MSSQL','DB2',
'MAXDB','NO_KEY_OPTIONS','NO_TABLE_OPTIONS','NO_FIELD_OPTIONS','MYSQL323','MYSQL40','ANSI','NO_AUTO_VALUE_
ON_ZERO','NO_BACKSLASH_ESCAPES','STRICT_TRANS_TABLES','STRICT_ALL_TABLES','NO_ZERO_IN_DATE','NO_ZERO_DATE'
,'INVALID_DATES','ERROR_FOR_DIVISION_BY_ZERO','TRADITIONAL','NO_AUTO_CREATE_USER','HIGH_NOT_PRECEDENCE','N
O_ENGINE_SUBSTITUTION','PAD_CHAR_TO_FULL_LENGTH'), found type set('REAL_AS_FLOAT','PIPES_AS_CONCAT','ANSI_
QUOTES','IGNORE_SPACE','NOT_USED','ONLY_FULL_GROUP_BY','NO_UNSIGNED_SUBTRACTION','NO_DIR_IN_CREATE','POSTG
RESQL','ORACLE','MSSQL','DB2','MAXDB','NO_KEY_OPTIONS','NO_TABLE_OPTIONS','NO_FIELD_OPTIONS','MYSQL323','M
YSQL40','ANSI','NO_AUTO_VALUE_ON_ZERO','NO_BACKSLASH_ESCAPES','STRICT_TRANS_TABLES','STRICT_A
131120 16:11:10 [ERROR] Event Scheduler: An error occurred when initializing system tables. Disabling the
Event Scheduler.
131120 16:11:10 [Warning] Failed to load slave replication state from table mysql.gtid_slave_pos: 1146: Ta
ble 'mysql.gtid_slave_pos' doesn't exist
131120 16:11:10 [Note] /usr/local/mysql/bin/mysqld: ready for connections.
Version: '10.0.7-MariaDB' socket: '/home/jan/mysql/newdb/mysql.sock2' port: 3306 Source distribution

Started mariadb_10.0.12 with mysql_5.6.16 databaste. also, ran mysql_upgade
Stopped and re-started server. Following messages still appear:

140623 11:27:05 mysqld_safe Starting mysqld daemon with databases from /home/mariadb/mariadb-data
140623 11:27:06 [Note] InnoDB: Using mutexes to ref count buffer pool pages
140623 11:27:06 [Note] InnoDB: The InnoDB memory heap is disabled
140623 11:27:06 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
140623 11:27:06 [Note] InnoDB: Compressed tables use zlib 1.2.3
140623 11:27:06 [Note] InnoDB: Using CPU crc32 instructions
140623 11:27:06 [Note] InnoDB: Initializing buffer pool, size = 4.0G
140623 11:27:06 [Note] InnoDB: Completed initialization of buffer pool
140623 11:27:06 [Note] InnoDB: Highest supported file format is Barracuda.
140623 11:27:06 [Note] InnoDB: 128 rollback segment(s) are active.
140623 11:27:06 [Note] InnoDB: Waiting for purge to start
140623 11:27:06 [Note] InnoDB: Percona XtraDB (http://www.percona.com) 5.6.17-65.0 started; log sequence number 2377750992406
2014-06-23 11:27:06 7fe9ef9f2700 InnoDB: Error: Column last_update in table "mysql"."innodb_table_stats" is BINARY(4) NOT NULL but should be INT NOT NULL (type mismatch).
2014-06-23 11:27:06 7fe9ef9f2700 InnoDB: Error: Fetch of persistent statistics requested for table "mysql"."gtid_slave_pos" 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.
140623 11:27:06 [Note] Server socket created on IP: '0.0.0.0'.
140623 11:27:06 [Note] Event Scheduler: Loaded 0 events
140623 11:27:06 [Note] /home/mariadb/bin/mysqld: ready for connections.
Version: '10.0.12-MariaDB-log' socket: '/home/mariadb/mariadb-data/mariadb.socket' port: 3307 Source distribution

"I'm seeing this error, as well as one of our partners, when doing an upgrade from MySQL 5.6.17 to MariaDB 10.0.12"

The following is just a guess where the problem could be:

In ha_innodb.cc::get_innobase_type_from_mysql_type() we have in 5.6:

case MYSQL_TYPE_TIMESTAMP:
switch (field->real_type())

In MariaDB 10.0 we have:
case MYSQL_TYPE_TIMESTAMP:
if (field->key_type() == HA_KEYTYPE_BINARY)
return(DATA_FIXBINARY);
else
return(DATA_INT);

The likely reason the code is failing in 10.0 is that the field is stored as MYSQL_TYPE_TIMESTAMP2 in the .frm file (as it's exported from 5.6) and either
Field_timestampf() doesn't have field->key_type() to return HA_KEYTYPE_BINARY or the field is not read as a Field_timestampf() in MariaDB 10.0.

I did a quick code check in 10.0 and the code looks correct. We need to check this in a debugger to see why the current code fails.

awesome - thanks for fixing this, Serg!

This is not really fixed up on due usage on CPanel/WHM server running Maria DB 10.0.15

22:27:45 server root@5997911 ~]cPs# tail /var/lib/mysql/server.brandyou.in.err
2015-01-20 22:27:25 7fdb46fb6700 InnoDB: Error: Column last_update in table "mysql"."innodb_table_stats" is BINARY(4) NOT NULL but should be INT NOT NULL (type mismatch).
2015-01-20 22:27:25 7fdb46fb6700 InnoDB: Error: Fetch of persistent statistics requested for table "photoz_wp84"."wp_wfVulnScanners" 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.
2015-01-20 22:27:25 7fdb46fb6700 InnoDB: Error: Column last_update in table "mysql"."innodb_table_stats" is BINARY(4) NOT NULL but should be INT NOT NULL (type mismatch).
2015-01-20 22:27:25 7fdb46fb6700 InnoDB: Error: Column last_update in table "mysql"."innodb_table_stats" is BINARY(4) NOT NULL but should be INT NOT NULL (type mismatch).
2015-01-20 22:27:25 7fdb46fb6700 InnoDB: Error: Column last_update in table "mysql"."innodb_table_stats" is BINARY(4) NOT NULL but should be INT NOT NULL (type mismatch).
2015-01-20 22:27:25 7fdb46fb6700 InnoDB: Error: Fetch of persistent statistics requested for table "photoz_wp84"."wp_wfLockedOut" 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.
2015-01-20 22:27:25 7fdb4cbff700 InnoDB: Error: Column last_update in table "mysql"."innodb_table_stats" is BINARY(4) NOT NULL but should be INT NOT NULL (type mismatch).
2015-01-20 22:27:25 7fdb4cbff700 InnoDB: Error: Fetch of persistent statistics requested for table "photoz_wp84"."wp_wfLeechers" 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.
2015-01-20 22:27:25 7fdb4cbff700 InnoDB: Error: Column last_update in table "mysql"."innodb_table_stats" is BINARY(4) NOT NULL but should be INT NOT NULL (type mismatch).
2015-01-20 22:27:25 7fdb4cbff700 InnoDB: Error: Fetch of persistent statistics requested for table "photoz_wp84"."wp_wfHits" 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.

Does this bug also affect 10.1.7? (note, however, the 1136 error after the other errors)

root@ubu1:/usr/local/mysql# ./scripts/mysql_install_db --user=mysql --basedir=/usr/local/mysql
Installing MariaDB/MySQL system tables in '/var/lib/mysql' ...
2015-10-04 14:30:34 140696390404032 [Note] /usr/local/mysql/bin/mysqld (mysqld 10.1.7-MariaDB-log) starting as process 3431 ...
2015-10-04 14:30:34 140696390404032 [Note] CONNECT: Version 1.03.0007 July 05, 2015
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Using mutexes to ref count buffer pool pages
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: The InnoDB memory heap is disabled
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Memory barrier is not used
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Compressed tables use zlib 1.2.3
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Using Linux native AIO
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Using CPU crc32 instructions
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Initializing buffer pool, size = 256.0M
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Completed initialization of buffer pool
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Highest supported file format is Barracuda.
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: 128 rollback segment(s) are active.
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Waiting for purge to start
2015-10-04 14:30:34 140696390404032 [Note] InnoDB:  Percona XtraDB (http://www.percona.com) 5.6.25-73.1 started; log sequence number 36477166193
2015-10-04 14:30:34 140695473981184 [Note] InnoDB: Dumping buffer pool(s) not yet started
2015-10-04 14:30:34 7ff66e5d5700 InnoDB: Error: Column last_update in table "mysql"."innodb_table_stats" is INT UNSIGNED NOT NULL but should be BINARY(4) NOT NULL (type mismatch).
2015-10-04 14:30:34 7ff66e5d5700 InnoDB: Error: Fetch of persistent statistics requested for table "mysql"."gtid_slave_pos" 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.
ERROR: 1136  Column count doesn't match value count at row 1
2015-10-04 14:30:34 140696390404032 [ERROR] Aborting

2015-10-04 14:30:34 140695457195776 [Note] InnoDB: FTS optimize thread exiting.
2015-10-04 14:30:34 140696390404032 [Note] InnoDB: Starting shutdown...
2015-10-04 14:30:37 140696390404032 [Note] InnoDB: Shutdown completed; log sequence number 36477166203
2015-10-04 14:30:37 140696390404032 [Note] /usr/local/mysql/bin/mysqld: Shutdown complete