I'm unfamiliar with "pkgdb". What does it do?
When you change a huge number of dependencies by deleting gnome and/or X11, it's a good idea to upgrade the pakacge database:
The pkgdb command is a tool to create or update the system package data-
base which is used by the portupgrade(1) tool suite. It maintains a hash
that maps an installed file to a package name, a hash that maps a package
to an origin, and a list of installed packages.
[ ... ]
The pkgdb command also works as an interactive tool for fixing the pack-
age registry database when -F is specified. It helps you resolve stale
dependencies, unlink cyclic dependencies, complete stale or missing ori-
gins and remove duplicates. You should run this command periodically so
portupgrade(1) and other pkg_* tools can work effectively and reliably.You might find that portupgrade wants to pull in X11 again for some port that was left over; you will then need to either delete such ports, or recompile them without X11, or find an alternate, etc depending on the specifics.
-- -Chuck
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