BuddyPress.org

@thebigk, if your DB for one reason or another needs repair or optimization, the best way to do that is with a human eye and phpMyAdmin. This should rarely happen however, so you shouldn’t have problems going forward.

The suggested way of upgrading the core is to deactivate all plugins first before you press go. Otherwise those other plugins are trying to load even as WordPress hasn’t fully upgraded itself, which can cause conflicts if the tables or indexes change even slightly.