From skullnobrains:
i’ll give you a little advice if you do not want to stumble across such things again
– update ports tree as root, preferably by using portsnap
do a make clean and chown you whole ports tree before you do anything else
– unless you have a very ggod reason to, just do not update your ports tree
when you do update it, export your portslist, remove all ports and rebuild all ports
– if you do update ports without rebuilding everything
– don’t forget the “-w” option in portmaster
– have a a look at the /usr/ports/UPDATING file before you update things
– do not try partial updates of packages that have too many dependencies (gettext, pango ….)
– use “-r” when necessary, when you are unsure, when you know that will be fast anyway
and use snapshots on /usr if your filesystem handles them when you do such manipulations