Upgrading from MySQL 5.0 to MySQL 5.1 or Percona Server 5.1 you may run into issues with mysql_upgrade – it will identify some tables to be upgraded and will attempt to run REPAIR TABLE for them. This will fail with “The storage engine for the table doesn’t support repair” error message. This seems to confuse a lot of people and I’ve seen people doing failsafe upgrade path of dumping and reloading complete database confused by this error message, which of course works, but can take quite a lot of time.
Another solution is to simply run ALTER TABLE tbl ENGINE=INNODB which will rebuild table with new MySQL version and normally will fix issues identified by mysql_upgrade.
You can use mysqlcheck -A –check-upgrade to identify tables which need to be fixed such a way.
With Oracle intentions to make Innodb default storage engine in next MySQL release I’m hopeful minor annoyances like this will be fixed. It should not be that complicated to at least map REPAIR TABLE to null ALTER TABLE which will help with most issues.
There is nice bug filed about it though it only covers documentation aspects.