DEPEND is needed in order to run the configure script. RDEPEND is dubious, however the beep-config script relies only on the existance on the binary /usr/bin/pkg-config, and as such its a hard dependency. The patch is simple, RDEPEND=">=dev-util/pkgconfig-0.9.0"
Added RDEPEND with comment on all ebuilds in the tree (-r2, -r3 and -r4). Thanks for your report spider, this has been committed and you have been mentioned on the commit msg :)