"The SPI pins are also connected to the AR9331 gpio pins, where it has been implemented in software the SPI interface. This means that the ATMega32u4 and the AR9331 can also communicate using the SPI protocol."
Please see this at http://arduino.cc/en/Main/ArduinoBoardYun.
Make above statement true, we need have either kernel driver kmod-spi-tty-ds ... DogStick SPI TTY Driver or kmod-spi-gpio-custom ... Custom GPIO-based SPI device
kmod-spi-tty-ds is no longer exist after Yun software departure from Linino. kmod-spi-gpio-custom is required much newer kernel than 3.3.8 which Yun has.