Hello,
I have a beaglebone black, and I am having some serious problems with the 
GPIO configuration, trying to migrate our working ubuntu 14.04 installation 
to ubuntu 16.04. The beaglebone sits on a specifically constructed board, 
that needs some GPIOs and the CAN-bus working, to function properly. As a 
starting point, I took the preconfigured 16.04 image from 
http://elinux.org/BeagleBoardUbuntu#Ubuntu_.2816.04.29 and installed the 
modified 4.4 kernel (--bone-kernel --lts-4_4 as described here: 
http://elinux.org/Beagleboard:BeagleBoneBlack_Debian#Mainline_.284.4.x_lts.29). 


I modified a dts script for a CAN overlay and got it working. Then, using 
Adafruit with python3, I got the required GPIOs configured. However 
autostart of CAN and GPIOs works only, if I force the respective init.d 
script to start after $network, which could pose a problem later, as the 
power supply for our wlan rounter is powered on using GPIOs.

Nonetheless, the resulting entries in /sys/class/gpio are:
    gpio115, gpio26, gpio38, gpio44, gpio46, gpio48, gpio63, gpio65
    
With the respective device trees in:
    /sys/devices/platform/ocp/44e07000.gpio/gpio/
    gpio26 (LED)

    /sys/devices/platform/ocp/481ac000.gpio/gpio/
    gpio65 (LED)

    /sys/devices/platform/ocp/4804c000.gpio/gpio (wird in der BBB_Setup.py 
benutzt)
    gpio38 (scanner_running)
    gpio44 (LED)
    gpio46 (LED)
    gpio48 (scanner_pwr)
    gpio63 (LED)

    /sys/devices/platform/ocp/481ae000.gpio/gpio/
    gpio115 (motor_pwr)

At this point, I am able to power up the motor with gpio115 and four of the 
LEDs (gpio44, gpio46, gpio26, gpio65) via python or writing to the value 
files in the device tree.
Unfortunately gpio48 always stays at measured 0.9V, regardless of the 
values written to the value file or the output commands issued using python 
and gpio63 always outputs something similar to a HIGH signal. As I 
suspected some other conflicting capes, I copied the system from eMMC to 
uSD and disabled the eMMC and HDMI/HDMI-audio capes in /boot/uEnv.txt. The 
slots in /sys/bus/platform/devices/bone_capemgr/slots now show only the CAN 
and the Adafruit capes. pinmux-pins and pingroups in 
/sys/kernel/debug/pinctrl/44e10800.pinmux look, as if all required pins are 
configured as GPIO unclaimed. However gpio48 and gpio63 still do not react 
to any output commands. Then I tried to build a device tree overlay using 
the patched version of the dtc compiler and configuring the required pins 
to work as outputs in mode7. Loading this cape gives me a probably kernel 
related error(see cape-error.log) that does not occur, if w1-gpio and 
w1-term are loaded using modprobe in advance. Regardless of this cape being 
loaded, gpio48 and gpio63 are still not working.

I made some logs, that may be helpful with the diagnosis of the problem:
www.defi1.de/beaglebone/cape-slots.log (slots right after booting)
www.defi1.de/beaglebone/dmesg.log (kernel message log right after booting)
www.defi1.de/beaglebone/cape-error.log (error in kernel message log when 
trying to load my custom cape)
www.defi1.de/beaglebone/overlays.log (the device tree overlays created with 
Adafruit)
www.defi1.de/beaglebone/pinmux-pins.log
www.defi1.de/beaglebone/piongroups.log

Any help on this would be appreciated.


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