Rscript stuck on a system call to python

Question

I have a periodic script running at background in my Ubuntu Server. If I execute it in RStudio, everything works as expected. But when I execute via terminal with Rscript, it gets stuck when calling a python script (it isn't always... but many times it gets stuck there). (I know it gets stuck there because when I stop the Rscript, it always tells me it was running my python script). I have chmod 777 'ed to that python script but no clue.

This worked normally until some days ago, doesn't know why.

The Rscript sentence:

Rscript /home/XXX/XXX/scriptServicioBBDDHS.R

The place where it stops in the R code:

outputMACs <- system(ignore.stdout = F, ignore.stderr = T, 
                   "python3 /home/XXX/XXX/MACsPrincipal.py 'Y.Y.Y.Y' 'user' 'password'", intern = T)

The python script is an API for a MikroTik router. It gets stuck when trying to read the response from the router. In this sentence:

r = select.select([s, sys.stdin], [], [], None)

I put you the code in the main() of the python script:

def main():
    s = None
    for res in socket.getaddrinfo(sys.argv[1], "8728", socket.AF_UNSPEC, socket.SOCK_STREAM):
        af, socktype, proto, canonname, sa = res
        try:
             s = socket.socket(af, socktype, proto)
        except (socket.error, msg):
            s = None
            continue
        try:
            s.connect(sa)
        except (socket.error, msg):
            s.close()
            s = None
            continue
        break
    if s is None:
        print ('could not open socket')
        sys.exit(1)

    apiros = ApiRos(s);
    apiros.login(sys.argv[2], sys.argv[3]);

    inputsentence = ['/ip/hotspot/active/print', '=detail=']
    apiros.writeSentence(inputsentence)

    t_end = time.time() + 2
    while time.time() < t_end:
        r = select.select([s, sys.stdin], [], [], None)
        if s in r[0]:
            # something to read in socket, read sentence
            x = apiros.readSentence()

Thank you for your help. This script used to always work when I first used it in the beggining, using the crontab. Now it just fails.

Sergio.

Answer 1

I found a possible bug in the MikroTik API. The problem was in the sentence

r = select.select([s, sys.stdin], [], [], None)

I had to rewrite it to omit the sys.stdin

r = select.select(s, [], [], 0.0)

And for that to work I have to do a system call via R with the following arguments:

system(ignore.stdout = F, ignore.stderr = T, "python3 /home/XXX/XXX/MACsPrincipal.py 'Y.Y.Y.Y' 'user' 'password'", intern = T)

It doesn't work if you don't ignore the stderr output.