Arduino Yun is a ATMega32U4-based board, like other ATMega32U4-based Arduino boards, such as Arduino Leonardo, Micro, the SPI is only available on the ICSP header:
MOSI - Yun has it on ICSP Pin 4
MISO - Yun has it on ICSP Pin 1
SCK - Yun has it on ICSP pin 3
SS - Yun has no dedicated pin, use any digital data pin
You can find out the ICSP header pin ...