Error setting up MySQL: Table 'mysql.plugin' doesn't exist
I have a MySQL 5.7 instance running without problems on Ubuntu 16, but when i try to install any other package or try to update existing ones through apt-get, i get the following error:
# apt-get upgrade
Setting up mysql-server-5.7 (5.7.20-0ubuntu0.16.04.1) ...
Checking if update is needed.
Checking server version.
Running queries to upgrade MySQL server.
mysql_upgrade: [ERROR] 1146: Table 'mysql.plugin' doesn't exist
mysql_upgrade failed with exit status 5
dpkg: error processing package mysql-server-5.7 (--configure):
subprocess installed post-installation script returned error exit status 1
No apport report written because the error message indicates its a followup error from a previous failure.
dpkg: dependency problems prevent configuration of mysql-server:
mysql-server depends on mysql-server-5.7; however:
Package mysql-server-5.7 is not configured yet.
dpkg: error processing package mysql-server (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
mysql-server-5.7
mysql-server
And if i run a mysqlcheck, it looks like some of the system tables exists but others are missing:
mysql.columns_priv OK
mysql.db OK
mysql.engine_cost
Error : Table 'mysql.engine_cost' doesn't exist
status : Operation failed
mysql.event OK
mysql.func OK
mysql.general_log OK
mysql.gtid_executed
Error : Table 'mysql.gtid_executed' doesn't exist
status : Operation failed
mysql.help_category
Error : Table 'mysql.help_category' doesn't exist
status : Operation failed
mysql.help_keyword
Error : Table 'mysql.help_keyword' doesn't exist
status : Operation failed
mysql.help_relation
Error : Table 'mysql.help_relation' doesn't exist
status : Operation failed
mysql.help_topic
Error : Table 'mysql.help_topic' doesn't exist
status : Operation failed
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
Error : Table 'mysql.plugin' doesn't exist
status : Operation failed
mysql.proc OK
mysql.procs_priv OK
mysql.proxies_priv OK
mysql.server_cost
Error : Table 'mysql.server_cost' doesn't exist
status : Operation failed
mysql.servers
Error : Table 'mysql.servers' 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
mysql.slow_log OK
mysql.tables_priv OK
mysql.time_zone
Error : Table 'mysql.time_zone' doesn't exist
status : Operation failed
mysql.time_zone_leap_second
Error : Table 'mysql.time_zone_leap_second' doesn't exist
status : Operation failed
mysql.time_zone_name
Error : Table 'mysql.time_zone_name' doesn't exist
status : Operation failed
mysql.time_zone_transition
Error : Table 'mysql.time_zone_transition' doesn't exist
status : Operation failed
mysql.time_zone_transition_type
Error : Table 'mysql.time_zone_transition_type' doesn't exist
status : Operation failed
mysql.user OK
sys.sys_config
Error : Table 'sys.sys_config' doesn't exist
status : Operation failed
However, the database is correctly running and if I manually check through an SQL, it looks like the tables exist.
mysql> SHOW TABLES;
+---------------------------+
| Tables_in_mysql |
+---------------------------+
| columns_priv |
| db |
| engine_cost |
| event |
| func |
| general_log |
| gtid_executed |
| help_category |
| help_keyword |
| help_relation |
| help_topic |
| innodb_index_stats |
| innodb_table_stats |
| ndb_binlog_index |
| plugin |
| proc |
| procs_priv |
| proxies_priv |
| server_cost |
| servers |
| slave_master_info |
| slave_relay_log_info |
| slave_worker_info |
| slow_log |
| tables_priv |
| time_zone |
| time_zone_leap_second |
| time_zone_name |
| time_zone_transition |
| time_zone_transition_type |
| user |
+---------------------------+
I use the innodb_file_per_table=1 setting, and the owner of /var/lib/mysql directory is correctly set to mysql user.
I would like to fix this issue without dumping existing data, but i'm running out of ideas.
Answer
I had the same problem today and I managed to solve it without the backup - reinstall - restore steps. (Though I had backup and everyone should!)
In my case, there was a plugin.ibd file in /var/lib/mysql/mysql/ directory, and the other missing tables also had files there, but maybe they were incomplete for some reason.
I did the following:
- Moved the files of
mysql.plugintable to another directory, e.g.:mv /var/lib/mysql/mysql/plugin.* /other/place/ - Ran
apt-get upgrade -yto see what happens. The upgrade script recreated themysql.plugintable correctly and complained about another table. - I repeated steps above with the table name the upgrade script told me and after recreating 19 tables this way, the upgrade completed successfully.
All steps I made, as root of course:
cd /var/lib/mysql/mysql
mkdir temp
mv engine_cost.* temp/
mv gtid_executed.* temp/
mv help_category.* temp/
mv help_keyword.* temp/
mv help_relation.* temp/
mv help_topic.* temp/
mv innodb_index_stats.* temp/
mv innodb_table_stats.* temp/
mv plugin.* temp/
mv server_cost.* temp/
mv servers.* temp/
mv slave_master_info.* temp/
mv slave_relay_log_info.* temp/
mv slave_worker_info.* temp/
mv time_zone.* temp/
mv time_zone_leap_second.* temp/
mv time_zone_name.* temp/
mv time_zone_transition.* temp/
mv time_zone_transition_type.* temp/
apt-get upgrade -y
I hope it helps someone.