Short flag -nl must only be a '-' and a single letter

[jggautier]

Thanks for sharing this really helpful tool!

When I ran the scan.R on the sample data, I got this error message:

Error in make_option(c("-nl", "--nolabels"), type = "logical", dest = "noscanlables", :
Short flag -nl must only be a '-' and a single letter
Execution halted

When I changed -nl to -n on line 69, the code ran without errors.

I'm running R version 3.6.1 (2019-07-05). Maybe I need to use a different version of one of the required packages?