On netbsd-current and dragonflybsd-current I see the same problem with
the latest pkg_chk -i:

$ pkg_chk -i
[ Scan /usr/pkgsrc/packages/All ]
WARNING: No archivers/file-roller/Makefile - package moved or obsolete?
WARNING: No archivers/gtar-base/Makefile - package moved or obsolete?
[lots of snippage]

I think the problem lies wih the PKGSRCDIR variable.  Anyone else
seeing this problem?