[Akonadi] [Bug 348491] New: Multiple MySQL table structure errors

Sun May 31 11:22:06 BST 2015

https://bugs.kde.org/show_bug.cgi?id=348491

            Bug ID: 348491
           Summary: Multiple MySQL table structure errors
           Product: Akonadi
           Version: 1.13.0
          Platform: Gentoo Packages
                OS: Linux
            Status: UNCONFIRMED
          Severity: major
          Priority: NOR
         Component: server
          Assignee: kdepim-bugs at kde.org
          Reporter: peter at prh.myzen.co.uk

After creating a new user and setting up KMail-2, but before importing KMail-2
messages from an archive made by the previous user,
~/.local/share/akonadi/db_data/mysql.err contains many table structure errors.

Reproducible: Always

$ cat .local/share/akonadi/db_data/mysql.err
2015-05-31 10:29:55 7f1ee1fab740 InnoDB: Warning: Using
innodb_additional_mem_pool_size is DEPRECATED. This option may be removed in
future releases, together with the option innodb_use_sys_malloc and with the
InnoDB's internal memory allocator.
150531 10:29:55 [Note] InnoDB: Using mutexes to ref count buffer pool pages
150531 10:29:55 [Note] InnoDB: The InnoDB memory heap is disabled
150531 10:29:55 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
150531 10:29:55 [Note] InnoDB: Memory barrier is not used
150531 10:29:55 [Note] InnoDB: Compressed tables use zlib 1.2.8
150531 10:29:55 [Note] InnoDB: Using Linux native AIO
150531 10:29:55 [Note] InnoDB: Using CPU crc32 instructions
150531 10:29:55 [Note] InnoDB: Initializing buffer pool, size = 80.0M
150531 10:29:55 [Note] InnoDB: Completed initialization of buffer pool
150531 10:29:55 [Note] InnoDB: The first specified data file ./ibdata1 did not
exist: a new database to be created!
150531 10:29:55 [Note] InnoDB: Setting file ./ibdata1 size to 12 MB
150531 10:29:55 [Note] InnoDB: Database physically writes the file full:
wait...
150531 10:29:55 [Note] InnoDB: Setting log file ./ib_logfile101 size to 64 MB
150531 10:29:56 [Note] InnoDB: Setting log file ./ib_logfile1 size to 64 MB
150531 10:29:56 [Note] InnoDB: Renaming log file ./ib_logfile101 to
./ib_logfile0
150531 10:29:56 [Warning] InnoDB: New log files created, LSN=45781
150531 10:29:56 [Note] InnoDB: Doublewrite buffer not found: creating new
150531 10:29:56 [Note] InnoDB: Doublewrite buffer created
150531 10:29:56 [Note] InnoDB: 128 rollback segment(s) are active.
150531 10:29:56 [Warning] InnoDB: Creating foreign key constraint system
tables.
150531 10:29:56 [Note] InnoDB: Foreign key constraint system tables created
150531 10:29:56 [Note] InnoDB: Creating tablespace and datafile system tables.
150531 10:29:56 [Note] InnoDB: Tablespace and datafile system tables created.
150531 10:29:56 [Note] InnoDB: Waiting for purge to start
150531 10:29:56 [Note] InnoDB:  Percona XtraDB (http://www.percona.com)
5.6.23-72.1 started; log sequence number 0
150531 10:29:56 [ERROR] Can't open and lock privilege tables: Table
'mysql.servers' doesn't exist
150531 10:29:56 [Warning] Can't open and lock time zone table: Table
'mysql.time_zone_leap_second' doesn't exist trying to live without them
150531 10:29:56 [ERROR] Native table 'performance_schema'.'cond_instances' has
the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_waits_current' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_waits_history' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_waits_history_long' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_waits_summary_by_host_by_event_name' has the wrong
structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_waits_summary_by_instance' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_waits_summary_by_thread_by_event_name' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_waits_summary_by_user_by_event_name' has the wrong
structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_waits_summary_by_account_by_event_name' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_waits_summary_global_by_event_name' has the wrong
structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'file_instances' has
the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'file_summary_by_event_name' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'file_summary_by_instance' has the wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'host_cache' has the
wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'mutex_instances' has
the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'objects_summary_global_by_type' has the wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'performance_timers'
has the wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'rwlock_instances'
has the wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'setup_actors' has
the wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'setup_consumers' has
the wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'setup_instruments'
has the wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'setup_objects' has
the wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'setup_timers' has
the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'table_io_waits_summary_by_index_usage' has the wrong
structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'table_io_waits_summary_by_table' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'table_lock_waits_summary_by_table' has the wrong
structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'threads' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_stages_current' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_stages_history' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_stages_history_long' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_stages_summary_by_thread_by_event_name' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_stages_summary_by_account_by_event_name' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_stages_summary_by_user_by_event_name' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_stages_summary_by_host_by_event_name' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_stages_summary_global_by_event_name' has the wrong
structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_statements_current' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_statements_history' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_statements_history_long' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_statements_summary_by_thread_by_event_name' has
the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_statements_summary_by_account_by_event_name' has
the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_statements_summary_by_user_by_event_name' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_statements_summary_by_host_by_event_name' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_statements_summary_global_by_event_name' has the
wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'events_statements_summary_by_digest' has the wrong
structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'users' has the wrong
structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'accounts' has the
wrong structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'hosts' has the wrong
structure
150531 10:29:56 [ERROR] Native table 'performance_schema'.'socket_instances'
has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'socket_summary_by_instance' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'socket_summary_by_event_name' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'session_connect_attrs' has the wrong structure
150531 10:29:56 [ERROR] Native table
'performance_schema'.'session_account_connect_attrs' has the wrong structure
150531 10:29:56 [Warning] Failed to load slave replication state from table
mysql.gtid_slave_pos: 1146: Table 'mysql.gtid_slave_pos' doesn't exist
150531 10:29:56 [Note] Reading of all Master_info entries succeded
150531 10:29:56 [Note] Added new Master_info '' to hash table
150531 10:29:56 [Note] /usr/sbin/mysqld: ready for connections.
Version: '10.0.19-MariaDB'  socket: '/tmp/akonadi-prh.GWFNGt/mysql.socket' 
port: 0  Source distribution
2015-05-31 10:29:56 7f1ee1e80700 InnoDB: Error: Table
"mysql"."innodb_table_stats" not found.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."collectiontable" index
"CollectionTable_parentAndNameIndex" but the required persistent statistics
storage is not present or is corrupted. Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."collectiontable" index
"CollectionTable_enabledIndex" but the required persistent statistics storage
is not present or is corrupted. Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."collectiontable" index
"CollectionTable_syncPrefIndex" but the required persistent statistics storage
is not present or is corrupted. Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."collectiontable" index
"CollectionTable_displayPrefIndex" but the required persistent statistics
storage is not present or is corrupted. Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."collectiontable" index
"CollectionTable_indexPrefIndex" but the required persistent statistics storage
is not present or is corrupted. Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."pimitemtable" index
"PimItemTable_collectionIndex" but the required persistent statistics storage
is not present or is corrupted. Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."pimitemtable" index "PimItemTable_gidIndex" but
the required persistent statistics storage is not present or is corrupted.
Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."pimitemtable" index "PimItemTable_ridIndex" but
the required persistent statistics storage is not present or is corrupted.
Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."parttypetable" index
"PartTypeTable_partTypeNameIndex" but the required persistent statistics
storage is not present or is corrupted. Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."parttable" index "PartTable_pimItemIdTypeIndex"
but the required persistent statistics storage is not present or is corrupted.
Using transient stats instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."collectionattributetable" index
"CollectionAttributeTable_collectionIndex" but the required persistent
statistics storage is not present or is corrupted. Using transient stats
instead.
2015-05-31 10:29:57 7f1ee1e80700 InnoDB: Recalculation of persistent statistics
requested for table "akonadi"."tagattributetable" index
"TagAttributeTable_tagIndex" but the required persistent statistics storage is
not present or is corrupted. Using transient stats instead.
150531 10:53:54 [ERROR] mysqld: Deadlock found when trying to get lock; try
restarting transaction
150531 10:53:54 [ERROR] mysqld: Deadlock found when trying to get lock; try
restarting transaction
150531 10:53:54 [ERROR] mysqld: Deadlock found when trying to get lock; try
restarting transaction
150531 10:53:54 [ERROR] mysqld: Deadlock found when trying to get lock; try
restarting transaction
150531 10:53:54 [ERROR] mysqld: Deadlock found when trying to get lock; try
restarting transaction
150531 10:53:54 [ERROR] mysqld: Deadlock found when trying to get lock; try
restarting transaction
150531 10:54:57 [ERROR] mysqld: Deadlock found when trying to get lock; try
restarting transaction
150531 10:54:57 [ERROR] mysqld: Deadlock found when trying to get lock; try
restarting transaction

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