-R flag is recursive which means it will affect parent directory and all sub directories and files. You have 3 options here really.
1.) just reinstall your system which is nice if you dont want to spend all day figuring out this problem and you didn't have anything you really needed on the system.
2.) extract data then reinstall. if you did have something on there that you needed try booting to a different medium (USB or optical disk) and extracting your file that way then reinstalling.
3.) spend hours trying to figure this problem out before giving up and drinking a 6 pack and playing some video games. then reinstall your system when you're done rethinking your life.
4.) (maybe) get realllllly lucky that someone did that and managed to fix it and that they're not drunk or playing video games so they post the answer in this thread.
Good luck homie