I'm also having problems with libgpiod - it simply does not work on a BBB with kernel 4.14.71-ti-r80. Cape universal is disabled, relevant pins are not exported via sysfs gpio interface.
Example: I'm trying to set P9.23 a.k.a. gpio number 49 (gpiochip 1, pin 17) and absolutely nothing happens. The pin stays in some high-z state, measuring 0.6 volts:
$ sudo gpioset gpiochip1 17=0
$ sudo gpioset gpiochip1 17=1
Running "gpioinfo gpiochip1" shows my pin as output, while it's definitely not that:
...
line 17: "GPMC_A1" unused output active-high
...
Also tried to control each of the user LEDs on pins 21-24 on the same port with very strange results. I managed to switch on usr1 or usr2 and no further changes are possible - the one LED won't turn off and the others won't turn on. Also wrote a small C program which uses the "linux/gpio.h" API - doesn't do anything useful to any of the pins.
Am I missing something here?
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Kind regars,
Tarmo