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New Debian testing + MySQL + ISAM == major problem
This would also fit under Databases, but since the trouble is (most likely) Debian specific, I'm putting it here.

If you still have tables in ISAM format, you may want to convert them now. The current testing distribution contains a conflict with libreadline4 which forces an upgrade from MySQL 4.1 -> MySQL 5.0 as soon as any package that depends on libreadline5 is installed/updated.

MySQL 5 then refuses to install when it detects ISAM tables. The only way out is to reinstall libreadline4 (and have APT uninstall all packages that depend on libreadline5) + MySQL 4.1. Then do the conversion, reinstall all the dumped packages again and switch to MySQL 5.0.

(The underlying conflict is caused by readline-common which conflicts with libreadline4/stable. It references libreadline4/unstable, but that one only exists for kfreebsd and the source package is AWOL).

New Clarification?
Are you talking about ISAM or MyISAM tables?

The latter should work - MyISAM tables are still a good choice for certain actions. OTOH, the much older ISAM format probably isn't supported in 5.0 anymore.

Wade.
"Insert crowbar. Apply force."
New ISAM tables as stated
MySQL 5 has indeed dumped support for the format, but it's the way Debian currently does things that causes problems. The root cause is a version requirement on libreadline4 (required by mysql-*-4.1) in the readline-common package (part of libreadline5) which can't be satisfied by anything but unstable/kfreebsd-i386. And the source is missing, so it can't even be recompiled.

What triggered it for me was a rebuild following a harddrive crash. Starting off with a clean Sarge install and adding Eclipse and KDE 3.5 from testing leaves no other option but to install MySQL 5.0. The backup of the mysql directory contained some little used development databases dating back to MySQL 3.x that still had ISAM tables so the 5.0 installation aborted. In the end, I had to back out all the stuff installed from testing to get MySQL 4.1 back on so I could convert the tables.

(But before the crash, MySQL 4.x happily coexisted with Eclipse so something must have moved recently on the readline-common packages as well)
New Well at least all the up-and-down-and-up-grading worked. :-)
"Insert crowbar. Apply force."
New Yep. And now I'm gonna print out the lot, just in case.. ;-)
     Debian testing + MySQL + ISAM == major problem - (scoenye) - (4)
         Clarification? - (static) - (3)
             ISAM tables as stated - (scoenye) - (2)
                 Well at least all the up-and-down-and-up-grading worked. :-) -NT - (static) - (1)
                     Yep. And now I'm gonna print out the lot, just in case.. ;-) -NT - (scoenye)

He's dead, Jim.
60 ms