From recent discussion on the users@ mailing list: pkg_chk is a known method for upgrading pkgsrc packages; the problem with it is that it removes existing packages, builds the new versions, then installs them. It has problems; this leaves a system without software for the length of the build time, and if a build dependency fails, the previously installed software is not restored. There are other solutions. There’s pkgmanager, or using a jail/chroot environment to build binary packages and then install using those, which the not-yet-ported pkg_comp can help with.