I was also able to update on Gutsy without issue:
Preparing to replace mysql-server-5.0 5.0.45-1ubuntu2 (using .../mysql-
server-5.0_5.0.45-1ubuntu3_i386.deb) ...
Setting up mysql-server-5.0 (5.0.45-1ubuntu3) ...
* Stopping MySQL database server mysqld
[ OK ]
* Starting MySQL database server mysqld
[ OK ]
* Checking for corrupt, not cleanly closed and upgrade needing tables.
Again, I used "sudo apt-get update; sudo apt-get upgrade" and not aptitude so I
guess it could be an aptitude issue?
--
MySQL server fails to upgrade in Gutsy
https://bugs.launchpad.net/bugs/153221
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