This FreeBSDDiary article explains how to keep your installed packages from ports up-to-date. “The FreeBSD Diary—Got ports? Here is THE way to upgrade them!”
When I ran pkgdb -F I got some Stale Dependencies I could not solve since somehow installed packages like ImageMagick depended on fontconfig that was not installed. Have no idea how I have ended up in that situation.
But reading on I found information on the pkgdb man-page that said one should run portsdb -Uu after doing a cvsup on the ports tree. I have cvsuped my ports tree several times without running it so now I’m doing that.
cvsup -g -L 2 ./ports-supfile