I am the current maintainer of math/isabelle.
It gives me great pains to say this, but math/isabelle is too hard to maintain and keep up to date, so I think it would be best if someone else takes over the port, or that it is dropped from the ports tree entirely, since the isabelle developers don't like third-party ports or packages (the old versions like this one are not especially hard to build from source, at least).
At some point I would like to bring this port back from the dead with a current version, but I don't have a timeframe on when that would happen. For now, I'd like to focus more heavily on ML language ports that I use more frequently, such as lang/mlton, lang/urweb, lang/twelf and lang/polyml, especially the first two.
I would advise anyone up for the task of maintaining math/isabelle to look into bringing back polyml support, since it compiles more quickly, making it less likely to time out on port build servers.
Committed, thanks for your work on this port
A commit references this bug:
Date: Fri Feb 20 15:42:45 UTC 2015
New revision: 379437
Submitted by: Timothy Beyer