On hte mac using El capitan, You nolonger can do a permissions repir--they took that capability out of the disk Utility
How to Repair Verify Disk Permissions in OS X El Capitan
Open the Terminal application (found in /Applications/Utilities/) and use the following syntax to verify a volumes permissions, this will verify the default root volume of a Mac:
sudo /usr/libexec/repair_packages --verify --standard-pkgs /
If you want to verify permissions on a different drive, specify the volume rather than “/”
Can't hurt to run the Disk First Aid too.
Also a good fix is to Reboot in Safe Mode (hold down Shift Key when rebooting). Then reboot normally. Lots of house cleaning going on when you do a Safe Mode boot. Verifies your startup disk, and attempts to repair directory issues if needed