The other day, I updated some packages using pkg. The default version of PHP went from 5.4 to 5.6. I ended up doing what /usr/dports/UPGRADING says and making a list of all PHP packages on my system, before removing PHP and its dependencies. I then reinstalled the packages that used PHP, bringing the needed packages back in at the right version. pkg 1.4 didn’t handle the transition cleanly, unfortunately. I also had to specify mod_php56 because pkg was trying to get the 5.4 version despite it not being default.
None of these are insurmountable problems, but it never hurts to be forewarned. pkg 1.5 is on the horizon and may have an easier time with sorting these types of dependency/version changes. This may apply to FreeBSD in addition to DragonFly.