As per the actual message… you get to see this while the server is processing the update. In this particular case, the upgrade to PMS 1.40.0 contains a significant amount of updates to the database structure. Depending on the size of your database and how powerful you server is, this might take a moment.
From the release announcement:
Please also be patient when updating to this version if you have a very large database and allow the upgrade process to finish.
