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$verbose = 0 }
print(sprintf("%s: do something with %s!",self,infile))
If I run this script from the command line, I get the output:
rose@moose:/home_moose/rose/Txt/src/Test/R(24)$ ./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@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@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@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
Ausführung angehalten
Last three commands worked as expected.
rose@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
Ausführung angehalten
That the command stopped is OK, but I expected the error message like
"long flag "b" is invalid".
rose@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
Ausführung 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
#!/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))
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