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Juergen Rose

2012-Mar-28 12:08 UTC

[R] getopt does not work as expected!

I have the following script (also attached):

#!/usr/bin/Rscript

spec=matrix(c(
  'verbose', 'v', 1, "integer",
  'help'   , 'h', 0, "logical"
  ),ncol=4, byrow=TRUE)
spec.dim=dim(spec)
spec.opt.long=spec[,1]
spec.opt.short=spec[,2]
spec.opt.l <- spec.dim[1]

infile <- "test.dat"
args=commandArgs(TRUE);    l=length(args)
self = commandArgs()[1];

usage <- function() {
  print(sprintf("Usage: %s [--verbose|-v] [--help,-h]
[infile.dat]"),self)
  print(sprintf("                       default infile.dat = '%
s'",infile))
}

library('getopt')

opt = getopt(spec,debug=TRUE);
if ( !is.null(opt$help) ) {
  ## get the script name (only works when invoked with Rscript).
  usage()
  print("------   before 'q(status=0)' ------")
  q(status=0);
}

if ( is.null(opt$verbose ) ) { opt$verbose = 0 }
if ( is.na(opt$verbose ) ) { opt$verbose = 0 }

print(sprintf("%s:  do something with %s!",self,infile))


If I run this script from the command line, I get the output:

rose at moose:/home_moose/rose/Txt/src/Test/R(24)$ ./getopt_test.R 
[1] "/usr/lib64/R/bin/exec/R: do something with test.dat!"

Why is commandArgs()[1] = "/usr/lib64/R/bin/exec/R" and not
"getopt_test.R" as described by the help (?getopt)?

rose at moose:/home_moose/rose/Txt/src/Test/R(25)$ ./getopt_test.R -h
[1] "processing -h"
[1] "  short option: -h"
[1] "Usage: getopt_test.R [--verbose|-v] [--help,-h] [infile.dat]"
[1] "                       default infile.dat = 'test.dat'"
[1] "------   before 'q(status=0)' ------"
rose at moose:/home_moose/rose/Txt/src/Test/R(26)$ ./getopt_test.R --help
[1] "processing --help"
[1] "  long option: --help"
[1] "    dangling flag"
[1] "Usage: getopt_test.R [--verbose|-v] [--help,-h] [infile.dat]"
[1] "                       default infile.dat = 'test.dat'"
[1] "------   before 'q(status=0)' ------"
rose at moose:/home_moose/rose/Txt/src/Test/R(27)$ ./getopt_test.R -b
[1] "processing -b"
[1] "  short option: -b"
Fehler in getopt(spec, debug = TRUE) : short flag "b" is invalid
Ausf?hrung angehalten

Last three commands worked as expected.

rose at moose:/home_moose/rose/Txt/src/Test/R(28)$ ./getopt_test.R --b
[1] "processing --b"
[1] "  long option: --b"
[1] "    dangling flag"
Fehler in getopt(spec, debug = TRUE) : flag "b" requires an argument
Ausf?hrung angehalten

That the command stopped is OK, but I expected the error message like
"long flag "b" is invalid".

rose at moose:/home_moose/rose/Txt/src/Test/R(29)$ ./getopt_test.R bla.dat
[1] "processing bla.dat"
Fehler in getopt(spec, debug = TRUE) : 
  "bla.dat" is not a valid option, or does not support an argument
Ausf?hrung angehalten

This behaviour I don't like at all. Why getopt does not distinguish
beetween options starting with alt least one hyphen and normal arguments
starting without hyphen? How it is possible to handle such a situation?
Have I myself to split the arguments into two lists, one with hyphen and
one without hyphen, and then pass only this list with hyphen to getopt?
Or is there a better solution?

Regards Juergen

-------------- next part --------------
#!/usr/bin/Rscript

spec=matrix(c(
  'verbose', 'v', 1, "integer",
  'help'   , 'h', 0, "logical"
  ),ncol=4, byrow=TRUE)
spec.dim=dim(spec)
spec.opt.long=spec[,1]
spec.opt.short=spec[,2]
spec.opt.l <- spec.dim[1]

infile <- "test.dat"
args=commandArgs(TRUE);    l=length(args)
self = commandArgs()[1];

usage <- function() {
  print(sprintf("Usage: getopt_test.R [--verbose|-v] [--help,-h]
[infile.dat]"))
  print(sprintf("                       default infile.dat =
'%s'",infile))
}

library('getopt')

opt = getopt(spec,debug=TRUE);
#opt = getopt(spec);
#print(opt,usage=TRUE)

## help was asked for.
if ( !is.null(opt$help) ) {
  ## get the script name (only works when invoked with Rscript).
  self = commandArgs()[1];
  ## print a friendly message and exit with a non-zero error code
  usage()
  print("------   before 'q(status=0)' ------")
  q(status=0);
}

## set some reasonable defaults for the options that are needed,
## but were not specified.
if ( is.null(opt$verbose ) ) { opt$verbose = 0 }
if ( is.na(opt$verbose ) ) { opt$verbose = 0 }

print(sprintf("%s: do something with %s!",self,infile))

Juergen Rose

2012-Mar-30 21:09 UTC

head link

[R] getopt does not work as expected!

Am Mittwoch, den 28.03.2012, 14:08 +0200 schrieb Juergen
Rose:> I have the following script (also attached):
> 
...> Ausf?hrung angehalten
> 
> This behaviour I don't like at all. Why getopt does not distinguish
> beetween options starting with alt least one hyphen and normal arguments
> starting without hyphen? How it is possible to handle such a situation?
> Have I myself to split the arguments into two lists, one with hyphen and
> one without hyphen, and then pass only this list with hyphen to getopt?
> Or is there a better solution?
I now extended getopt to mygetopt (look at the attached file), which is
now able to distinguish between options and remaining arguments. But my
solution is longish. I hope somebody can give me a shorter solution.


-------------- next part --------------
#!/usr/bin/Rscript

spec=matrix(c(
  'verbose', 'v', 1, "integer",
  'help'   , 'h', 0, "logical",
  'debug',   'd', 2, "integer"
  ),ncol=4, byrow=TRUE)
spec.dim=dim(spec)
spec.opt.long=spec[,1]
spec.opt.short=spec[,2]
spec.opt.type=spec[,3]
spec.opt.l <- spec.dim[1]

infile <- "test.dat"
args=commandArgs(TRUE);    l.args=length(args)
self = commandArgs()[1];

usage <- function() {
  print(sprintf("Usage: getopt_test.R [--verbose|-v] [--help,-h]
[infile.dat]"))
  print(sprintf("                       default infile.dat =
'%s'",infile))
}

library('getopt')

i.arg=0
i.opt=0
args.new=c()
opts=c()
i=1
if(l.args>=1) {
  while (i <= l.args) {
    print(sprintf("i=%2d  l.args=%2d",i,l.args))
    print(sprintf("i=%2d  args[[%2d]]=%-20s  
substring(args[[i]],1,1)=|%s|",
                  i,i,args[[i]],substring(args[[i]],1,1)))
    if (substring(args[[i]],1,1) == "-") {
      i.opt <- i.arg+1
      opts=c(opts,args[[i]])
      if (spec.opt.type[i]==1) {
        if (i+1 <= l.args) {
          if (substring(args[[i+1]],1,1) != "-") {
            i <- i+1
            opts=c(opts,args[[i]])
          } else {
            print(sprintf("ERROR in parameters, missing value for option
%s",
                          args[[i]]));
            q(status=1)
          }
        } else {
          print(sprintf("ERROR in parameters"));
          q(status=1)
        }
      }
      if (spec.opt.type[i]==2) {
        if (i+1 <= l.args) {
          if (substring(args[[i+1]],1,1) != "-") {
            i <- i+1
            opts=c(opts,args[[i]])
          }
        }
      }
      i <- i+1
    } else {
      i.arg <- i.arg+1
      args.new=c(args.new,args[[i]])
    }
  }
}

opt = getopt(spec,opt=opts,debug=TRUE);
#opt = getopt(spec);
#print(opt,usage=TRUE)

## help was asked for.
if ( !is.null(opt$help) ) {
  ## get the script name (only works when invoked with Rscript).
  self = commandArgs()[1];
  ## print a friendly message and exit with a non-zero error code
  usage()
  print("------   before 'q(status=0)' ------")
  q(status=0);
}

## set some reasonable defaults for the options that are needed,
## but were not specified.
print("before 1st print(opt$verbose)");   print(opt$verbose)
if ( is.null(opt$verbose ) ) { opt$verbose = 0 }
if ( is.na(opt$verbose ) ) { opt$verbose = 0 }
print("before 2nd print(opt$verbose)");   print(opt$verbose)

print(sprintf("%s: do something with %s!",self,infile))

Trevor Davis

2012-Mar-31 00:39 UTC

head link

[R] getopt does not work as expected!

> Why is commandArgs()[1] = "/usr/lib64/R/bin/exec/R" and not
> "getopt_test.R" as described by the help (?getopt)?
That used to work but R changed the behavior of the commandArgs()
function a couple of years ago, I guess the orginal author of getopt
didn't update his example then.

This will do the trick:

args <- commandArgs()
file_index <- grepl("--file=", args)
self <- gsub("--file=", "", args[file_index])
> This behaviour I don't like at all. Why getopt does not distinguish
> beetween options starting with alt least one hyphen and normal arguments
> starting without hyphen? How it is possible to handle such a situation?
> Have I myself to split the arguments into two lists, one with hyphen and
> one without hyphen, and then pass only this list with hyphen to getopt?
> Or is there a better solution?
The author of getopt started but did not finish adding positional
arguments to ``getopt``.  Howevor, positional arguments have been
supported in the ``optparse`` package for over a year if you specify
``positional_args=TRUE`` to the ``parse_args`` function.

- Trevor Davis

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