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Oct 4, 2015 7:34 AM in response to deadvibesby Jason L,Howdy deadvibes,
Welcome to Apple Support Communities.
If I understand correctly, you're unable to upgrade to OS X El Capitan on your MacBook Pro because of an alert message related to the file system needing repair. The article below provides a lot of great information and troubleshooting tips that should help you resolve any file system issues with your device.
Resolve startup issues and perform disk maintenance with Disk Utility and fsck - Apple Support
Ciao.
