It sounds like the line is configured to be a clock signal, perhaps it is 
in MODE 6 (mcasp0_aclkr_mux3)?

What dtb/overlays are you using when booting?

On Tuesday, December 1, 2015 at 1:30:56 PM UTC-6, [email protected] wrote:
>
> After booting Debian for Beaglebone Black I looked at P9 pin 12 (GPIO 1 
> 28) on an oscilloscope, their is a positive 65ms wide positive pulse that 
> repeats approximately every second. 
>
> Is this pin not set up as a GPIO pin? 
>
> I tried 
>
> echo 60 > /sys/class/gpio/export
>
>
> However when I tried 
>
> ls -al /sys/class/gpio
>
>
> after this gpio60 did not show up. 
>

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