There is no repair permissions in El Capitan. They are protected behind rootless. And get updated when you do updates. It is no longer necessary by the user to do anymore. (Thus no more option.)
Quote from the release notes.
"System file permissions are automatically protected, and updated during Software Updates. The Repair Permissions function is no longer necessary."
"Repair permission" does not repair random things, only the operating system permission, so it would still be useless. You should check the disk in Disk Utility.