sys-libs/pam-1.0.0 creates a directory "/var/lib/run/sepermit", which, presumably should be "/var/run/sepermit". Portage runs configure with --localstatedir=/var/lib by default, but it needs to be --localstatedir=/var in this case. Reproducible: Always
I've overridden it on emake/emake install rather than at configure so that if in the future it will have other stuff in /var that should go to /var/lib it won't move them incorrectly.