Failed to load file through getopt package in R - r

Question

I am trying to use getopt package to open my file but the codes seem not working:
> library(getopt)
args <- commandArgs(trailingOnly = FALSE)
spec = matrix(c(
'help' , 'h', 0, "character",
'input' , 'i', 1, "file",
'output' , 'o', 1, "character"), byrow=TRUE, ncol=4)
opt = getopt(spec)
if(opt$input){
file <- read.table(args[1])
}
print(file)
I am trying to use command line to run the codes like:
Rscript --slave filename.R -i file.txt
The error information is:
Error in storage.mode(peek.optstring) <- mode : invalid value
Calls: getopt ... tryCatch -> tryCatchList -> tryCatchOne -> doTryCatch
Execution halted
Can someone help me out?

Answer 1

You need to test the components, and if -i filename.txt is given then opt$file is what you use to access it.
A repaired version is
#!/usr/bin/Rscript
library(getopt)
spec <- matrix(c(
'help' , 'h', 0, "character",
'input' , 'i', 1, "character",
'output' , 'o', 1, "character"),
byrow=TRUE, ncol=4)
opt <- getopt(spec)
if ( !is.null(opt$input) ) {
file <- read.table(opt$input)
}
print(file)
I used to use this package quite a bit, but these days I much prefer docopt which is even easier to use and more featureful.

Answer 2

In case others run into this same problem, I got the same error message
Error in getopt_options(object, args) :
Error in storage.mode(this.argument) <- mode : invalid value
Calls: parse_args -> parse_options -> getopt_options
My error turned out to be from accidentally misspelling my type argument:
make_option(c("--chr_len"), type = 'chaqracter', default = NULL, help = "file path: length of all chromosomes")
This error was resolved when I fixed the spelling
make_option(c("--chr_len"), type = 'character', default = NULL, help = "file path: length of all chromosomes")