On newer systems, /run lives on tmpfs and /var/run is a symlink to the same place, so ebuilds should not be installing anything there. The packages immediately become "damaged" after a reboot. Some example offenders: # qcheck cups gdm mariadb wpa_supplicant Checking dev-db/mariadb-5.5.32 ... AFK: /var/run/mysqld/.keep_dev-db_mariadb-0 * 650 out of 651 files are good Checking gnome-base/gdm-3.8.4-r3 ... AFK: /run/gdm/greeter * 167 out of 168 files are good Checking net-print/cups-1.7.0 ... AFK: /var/spool/cups/tmp/.keep_net-print_cups-0 * 464 out of 465 files are good Checking net-wireless/wpa_supplicant-2.0-r2 ... AFK: /var/run/wpa_supplicant AFK: /var/run/wpa_supplicant/.keep_net-wireless_wpa_supplicant-0 * 51 out of 53 files are good #
*** This bug has been marked as a duplicate of bug 493154 ***