Solved How to exclude packages from pkg

Most of my system has packages installed through ports-mgmt/pkg, with one package editors/emacs-devel manually compiled through the ports system because I need to use my own compilation options with it.
With this, I run into problems with pkg and the port conflicting, when the port has an update, pkg picks that up and when I run pkg upgrade it says:
Installed packages to be REINSTALLED:
    emacs-devel-,2 (options changed)

But I don't want this port to be reinstalled as a package, because then it will not have the options I compiled it with, it will be the generic binary version from pkg, how do I stop this conflict, or am I not understanding something correctly?