Please, see the stackoverflow thread first:

The execution of an R script just gets stuck and there is no errors. I need to have a way of figuring out of what is going on.

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I see that you were able to find the answer to this. For the benefit of future readers, I am going to paste your answer here:

So, I do not know why but it was apache2 server problem. I switched to nginx, but then RAM out of memory errors appeared which I fixed by reducing the amount of memory my R script uses:

options(java.parameters = "-Xmx6000m")

It was -Xmx8000m. Then the script was finishing correctly on the server, but on the client I saw 504 gateway timeout errors which I fixed by the solution I found here:

Just created file at /etc/nginx/conf.d/timeout.conf with:

proxy_connect_timeout       3000;
proxy_send_timeout          3000;
proxy_read_timeout          3000;
send_timeout                3000;
After which it finally started working