Well I seem to have pulled off the upgrade to MySQL 4.1 but not without hitches. First off, and annoyingly, the upgrade instructions insist on having MySQL shutdown and removed during the installation, so all MySQL dependent services were offline while it compiled. Secondly, the first time I installed it, the reloading of the data bases didn’t take with an error 1071, something about a key sizes being a maximum of 1000 bytes. After a quick fall back (first time I’ve used quickpkg, and damn useful it was) I took a guess que from the forums and added the ‘latin1′ use flag. That seemed to do the trick and the second time around has taken. Still, a damn lot of work, and downtime for a mandatory upgrade due to a GLSA. Looking at the GLSA, it doesn’t even seem to mention the upgrade guide or that any problems might be encountered. Most frustrating.
Oh well, hopefully we can go back to a more stable life now that this is over.