Repair the Hard Drive and Permissions - Yosemite, Mavericks, Mountain Lion or Lion
Boot to the Recovery HD:
Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears.
Repair
When the recovery menu appears select Disk Utility and press the Continue button. After Disk Utility loads select the indented Macintosh HD entry from the the left side list. Click on the First Aid tab, then click on the Repair Disk button. If Disk Utility reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit Disk Utility and return to the main menu. Select Restart from the Apple menu. If you are running El Capitan, then click on the First Aid button in the toolbar. Note, however, that in El Capitan file permissions are locked and protected. They don't require repair.
If you've run another program that has garbaged system files, then you will need to reinstall El Capitan.
Reinstall El Capitan Without Erasing the Drive
Boot to the Recovery HD: Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears.
Repair the Hard Drive and Permissions: Upon startup select Disk Utility from the main menu. Repair the Hard Drive and Permissions as follows.
When the recovery menu appears select Disk Utility and press the Continue button. After Disk Utility loads select the indented Macintosh HD entry from the the left side list. Click on the First Aid button in the toolbar. Wait until the operation completes, then quit Disk Utility and return to the main menu.
Reinstall OS X: Select Reinstall OS X and click on the Continue button.
Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless and more reliable.