WowAce

What steps will reproduce the problem?
1. Load character into game.
2.
3.

What is the expected output? What do you see instead?

What version of the product are you using?
v1.90

Do you have an error log of what happened?
Message: Interface\FrameXML\AlertFrames.lua:291: attempt to index global 'GarrisonMissionAlertSystem' (a function value)
Time: 07/22/16 18:31:02
Count: 1
Stack: [C]: ?
Interface\FrameXML\AlertFrames.lua:291: in function <Interface\FrameXML\AlertFrames.lua:203>

Locals:

Please provide any additional information below.

same here

As a replacement for hooking pre-7.0 GarrisonMissionAlertFrame_ShowAlert and GarrisonBuildingAlertFrame_ShowAlert, you are hooking GarrisonMissionAlertSystem and GarrisonBuildingAlertSystem, which are supposed to be tables. You probably should be hooking the AddAlert method instead, in the aforementioned tables and also in GarrisonShipMissionAlertSystem.

However, in 7.0 starting the minimap icon pulse animation has been moved from the previous _ShowAlert functions / current AddAlert methods, to AlertFrame:OnEvent method which calls the correct AddAlert method on certain events. You could try hooking that instead and filtering out the relevant events "GARRISON_MISSION_FINISHED" and "GARRISON_BUILDING_ACTIVATABLE".

EDIT: Trying to read through Blizzard's code, it looks like the pulse-hiding was broken even in 6.2.4 and older, if Blizzard notifications were enabled, because they directly call :Play on the animationgroup, bypassing the hooked _ShowPulse and _HidePulse in Minimap.lua. Now in 7.0, if the notification code path didn't error out trying to index a function, it would be broken even if Blizzard notifications are hidden. I will write an in-game bug report, but I'm not sure if they care about "bugs" that only surface with addons.