For the record, that's exactly the response you get when there is no ADC at the expected address (I2C: 0x4D). Which suggests tool and h/w don't match. What does i2cdetect -y 0 produce?
root@Omega-67F5:~# i2cdetect -y 0
@György-Farkas it seems setting the inputs 'fast-gpio set-input 15' as well as 16 and 17 makes the touch screen work in the dock (while omega is plugged in), but causes the touch screen to think its repeatedly being tapped without actually tapping it. The first touch works, but then the screen acts as if its being touched everywhere. For example I have three buttons which when tapped change colour, what happens is when I tap one button it changes colour and then all of a sudden the other buttons start changing colours and flickering (as if i am tapping them when I am not). (without the omega plugged in touch screen doesnt respond).
WHEREAS in the Arduino Uno (not dock) touch screen works perfectly.
It seems to me that the current wifi kernel module is unable to correctly interpret one or more of these ASCII characters and since it's a closed source component, you cannot examine it to find out why.
You might want to log a ticket on the Onion helpdesk and provide them with these ASCII characters, together with a pointer to this thread and a request to troubleshoot the wifi module. Perhaps that way they can enhance the module with some new functionality or a bug fix, whatever may be necessary?
Apart from that, or perhaps changing your SSID's, I'm not really sure what else to suggest.
Same SD card works fine on another Omega2+ so I'm less likely to think its the card. Supply voltage looks good as well, 3.45v (need to adjust regulator resistors to bring that down to 3.3v) That's a good path to check and more data sheet driven then my approach of swapping the cards and performing a functional check.
I saw that diagram with those pinouts as well but isn't EPHY_APGIO_AIO_EN set in software and not affected by the boot pins?
After a few hours of experimenting here the issue turned out to be a relatively strong pulldown on GPIO45. This was affecting a boot pin. Looking at http://plan44.ch/downloads/Onion-Omega2-Pinout-annotated.png and the MT7688 data sheet though it isn't clear exactly what the issue is. Measuring the module itself there is a 4.7k pullup to 3.3V on that pin, so no need for external strapping. Pulling that pin down would appear to be enabling JTAG mode, page 33 of the MT7688 data sheet fyi.
JTAG pins look entirely separate from SD interface pins though so maybe I'm close on the bootstrap pin issue but off on the effect? I still can't figure out why everything would boot fine if that GPIO45 was strapped low (overriding the 4.7k pullup) but just the SD card wouldn't be working......
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