Peleg,
At the very least you need to remove the old MySQL before attempting to install the new one.
You would need to run something like:
# rpm -e mysql-3.23.58-9
I'm in the middle of upgrading to MySQL 4.1 and I got stuck with Apache - I can't get Perl/DBI to work with MySQL 4.1 in Apache but I did manage to install MySQL itself and 4.1 is at this moment running smoothly on my machine.
Now, when you run the rpm -e line mentioned above to remove the old mysql, you'll almost certainly get dependency errors. You will have to remove all the various packages mentioned in these error messages before it's possible to remove the old mysql. It took me a while to work through this clearing out process. I don't know how to automate it and I don't want to yet because the process gave me more insight into what goes into a Fedora distribution.
Once all the dependent packages are safely removed (and if you change your mind, they are, after all, on your installation disks so they are easy to re-install) you should be able to install MySQL 5 smoothly.
It seems worth mentioning that you need to install about five MySQL RPMs usually - the server, the client, some shared libraries and heaven knows what else - look at the download page at the mysql website. If you can decipher it all I take my hat off to you.
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