No: the solution is: initialize the serial port correctly!

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our current arduino does not function correctly after a reboot
the way to fix is, is to flash the arduino at every boot

do: apt-get install gcc-avr avr-libc avrdude

avrdude is the program we need

compile the desired arduino program and grab the .hex file from /tmp/build.blah

the .hex can be uploaded to the arduino by doing:

avrdude -C/usr/share/arduino/hardware/tools/avrdude.conf -patmega328p -carduino -P/dev/ttyUSB1 -b115200 -D -Uflash:w:driekleurenIR.cpp.hex:i