Pirate, 90, suffering a long time in here? (12)
I believe the answer is:
penitentiary
'a long time in here?' is the definition.
(type of prison - where people do time)
I don't understand the rest of the clue.
(Other definitions for penitentiary that I've seen before include "stir" , "American prison" , "US prison" , "Senior Catholic" .)