I now stumbled upon similar case, if not the same with another board. I was able to connect access point of Omega2S and open putty to run commands. After I have run command wifisetup and select option 1, link with omega broke, and I think it also rebooted. I'm not sure about all circumstances, as I didn't connect via serial port.
Then I made conection with O2S again and check ifconfig.
I noticed that there is suspecious eth0.1 interface. So I decided to run command ifconfig eth0.1 down to disable that interface.
Then I tried to run wifisetup and this time it was succesful! I managed to finish instalation of all needed software and it works like a charm.
I can't check if it's the same with one that I had problems with, as it is not on it's board anymore, but for this one it worked.
@György-Farkas Well I have tried pull down resistors, but the problem is that those pins aren't floating from the beginning, as probably the internal multiplexer does something before loading the kernel. As shown on logic analyser graph pins actually go high for around 7 sec and have 1us pulses every 25us or so, which are then detected by 74hc595. DPIO 11 doesn't have those pulses, but stays high (output state) till you don't run a scriptwhere you set the output to low on other side others - 17, 16, 15 go to floating state after that.
I then decided I will go with i2c port expander for more safe and predictable operation. MCP23008 is quiet handy as they are used in relay dock and have libraries written for it.
The jist of it is that you'll need to use the Build System to do your cross compiling. If you need a separate library for your program, it will first have to be built by the build system before you can include it in your program.
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