sys-libs/pam-1.1.5 creates /var/run/sepermit during compilation which, of course, is not available after reboot as /var/run now on tmpfs. I really don't know what's the purpose of this dir, but portage gave me the warning, so you see this bug report. Reproducible: Always
There is an inconsistency in values of sepermitlockdir: $ grep sepermitlockdir= pam-1.1.6-r1.ebuild emake sepermitlockdir="${EPREFIX}/run/sepermit" emake sepermitlockdir="${EPREFIX}/run/sepermit" check sepermitlockdir="${EPREFIX}/var//sepermit"
Reopening, see previous comment.
Don't reopen bugs in the future for stuff like that. There was a brainfreeze, and was reported separately, and has been fixed already.
OK. Sorry.