Likely your problem is taht you have not "identified" your device to github:
I managed it this way:
Generate SSH key at your device (RPI)
$ ssh-keygen -t rsa -b 4096 -C youreEmailAddress@github
Presse Enter to accept default location
Press Enter twice to set pass phrase to none.
Print new SSH key to screen
$ cat ls .ssh/id_rsa.pub
Select and copy the printed SSH key to github at: https://github.com/settings/keys
Now your device is accepted by github.
I hope it helps.