I finally succeeded to get some data to and from the board by a very clumsy method but it is a beginning. The best would be to have direct access to the SCPI served that is provided on the Red Pitaya and sending string command, or better go thru MathLink but I am not a that level yet. Anyway I just got that, by connecting the ADC to the DAC:

I attach the notebook I just used for this (code summary below). It is emulating the input in a console, sending line command at high level with the commands "acquire" and "generate" provided by the board.
Christian
Open device
pitaya = DeviceOpen[ "Serial", {"COM5", "BaudRate" -> 115200, "ReadBufferSize" -> 16384, "StopBits" -> 1, "Parity" -> None}]
Note that the serial port can be used as a console like with Hypeterminal or PuTTy in Serial Mode.
Generate signal on chanel 1 DAC device
DeviceWrite[pitaya, "generate 1 1 750000 sine" <> "\n"];
Pause[1];
DeviceReadBuffer[pitaya] // FromCharacterCode
Record signal on chanel 1 ADC device (connected to chanel 1 DAC)
AbsoluteTiming[n = 500;(*want n samples*)
DeviceWrite[pitaya, "acquire " <> ToString[n] <> "\n"];
(*the high level "acquire" function that wortks either under SSH terminal or Serial terminal from USB FTDI"*)
s = Table[DeviceReadBuffer[pitaya, "ReadTerminator" -> "\r"], {n + 1}];
DeviceReadBuffer[pitaya]; (*flush the rest*)
s = Cases[s // FromCharacterCode // StringSplit // ToExpression, {_Integer, _Integer}];]
ListPlot[s // Transpose, Joined -> True, PlotRange -> All]
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