FreeBSD: Mixing packages and ports

You need to remember that pkg and ports register installed software in the same place (an SQLite database in /var/db/pkg). Neither system records any additional information that a particular piece of software was installed as a pre-compiled package, or as a port. Thus, once a piece of software is installed by either approach, the tools have no way of knowing how it was installed.

When you selected GTK2 support for the editors/vim port, that was registered in the package database. When you later ran pkg upgrade, pkg looked at the package data for vim, and found that GTK2 support had been enabled in the installed version, whereas it is not enabled in the pre-compiled package. pkg upgrade is doing exactly what it should - finding any installed packages that are different from the available pre-compiled packages, and attempting to upgrade them. Those differences can be in version number, dependency graph, compile-time options, etc.

The proper way to prevent pkg from considering a port or package (once installed, there is no difference, as far as the tools are concerned) that you want to protect is to use the pkg lock command.

Alternatively, if you find yourself changing options on a number of ports, you might consider installing poudriere and maintaining your own package repository. It takes a bit of setting up, and works best if your build host has a ZFS storage pool, although it will work if you don't have ZFS; it is a very flexible and convenient way to manage custom software builds.

I think ports-mgmt/portconf will do what do you want:

Portconf is a simple framework to set ports options in an universal way. Knobs set to specific ports are honoured by portmaster, portupgrade, portmanager and 'make install'.

Check more in pkg-message.