R optparse error with command line arguments

Question

For some reason, the optparse usage in this script breaks:

test.R:

#!/usr/bin/env Rscript
library("optparse")

option_list <- list(
    make_option(c("-n", "--name"), type="character", default=FALSE,
                dest="report_name", help="A different name to use for the file"),
    make_option(c("-h", "--height"), type="numeric", default=12,
                dest = "plot_height", help="Height for plot [default %default]",
                metavar="plot_height"),
    make_option(c("-w", "--width"), type="numeric", default=10,
                dest = "plot_width", help="Width for plot [default %default]",
                metavar="plot_width")
)

opt <- parse_args(OptionParser(option_list=option_list), positional_arguments = TRUE)
print(opt)

report_name <- opt$options$report_name
plot_height <- opt$options$plot_height
plot_width <- opt$options$plot_width

input_dir <- opt$args[1] # input directory

I get this error:

    $ ./test.R --name "report1" --height 42 --width 12 foo
Error in getopt(spec = spec, opt = args) :
  redundant short names for flags (column 2).
Calls: parse_args -> getopt
Execution halted

However, if I remove the "-h" from this line:

make_option(c("--height"), type="numeric", default=12,
                    dest = "plot_height", help="Height for plot [default %default]"

It seems to work fine;

$ ./test.R --name "report1" --height 42 --width 12 foo
$options
$options$report_name
[1] "report1"

$options$plot_height
[1] 42

$options$plot_width
[1] 12

$options$help
[1] FALSE


$args
[1] "foo"

Any ideas what might be going on here?

I am using R 3.3.0 and optparse_1.3.2 (getopt_1.20.0)

Answer 1

The -h flag is reserved by optparse (which is described as a feature of optparse which is not in getopt, from the getopt.R source file on Github):

Some features implemented in optparse package unavailable in getopt:

2. Automatic generation of an help option and printing of help text when encounters an "-h"

Therefore, when the user specifies -h, the sanity check for uniqueness of flags fails. The issue tracker does not seem to have any mention of the need to create a better error message for this case, however.

Finally, note that optparse seems to be invoking getopt, as they have the same author.