Commit 59f61a77 authored by Dirk Eddelbuettel's avatar Dirk Eddelbuettel

Import Upstream version 1.14

Package: getopt
Type: Package
Title: C-like getopt behavior.
Version: 1.14
Date: 2008-04-29
Author: Allen Day <>
Maintainer: Allen Day <>
Description: Use this with Rscript to write ``#!'' shebang scripts that accept short and long flags/options.
License: GPL
Packaged: Wed Apr 30 02:13:57 2008; allenday
This diff is collapsed.
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ C-like getopt behavior }
getopt is primarily intended to be used with ``\link{Rscript}''. It facilitates writing
``\#!'' shebang scripts that accept short and long flags/options. It can also
be used from ``R'' directly, but is probably less useful in this context.
getopt() returns a \link{list} data structure containing \link{names} of the
flags that were present in the \link{character} \link{vector} passed in under
the \emph{opt} argument. Each value of the \link{list} is coerced to the data
type specified according to the value of the \emph{spec} argument. See below
for details.
Notes on naming convention:
1. An \emph{option} is one of the shell-split input strings.
2. A \emph{flag} is a type of \emph{option}. a \emph{flag} can be defined
as having no \emph{argument} (defined below), a required \emph{argument}, or an
optional \emph{argument}.
3. An \emph{argument} is a type of \emph{option}, and is the value associated
with a flag.
4. A \emph{long flag} is a type of \emph{flag}, and begins with the string
``--''. If the \emph{long flag} has an associated \emph{argument}, it may be
delimited from the \emph{long flag} by either a trailing \emph{=}, or may be
the subsequent \emph{option}.
5. A \emph{short flag} is a type of \emph{flag}, and begins with the string
``-''. If a \emph{short flag} has an associated \emph{argument}, it is the
subsequent \emph{option}. \emph{short flags} may be bundled together, sharing
a single leading ``-'', but only the final \emph{short flag} is able to have a
corresponding \emph{argument}.
\usage{getopt( spec=NULL, opt=commandArgs(TRUE), command=strsplit(commandArgs(FALSE)[4],"=")[[1]][2], usage=FALSE, debug=FALSE )}
%- maybe also 'usage' for other objects documented here.
The getopt specification, or spec of what options are considered valid. The
specification must be either a 4-5 column \link{matrix}, or a \link{character}
\link{vector} coercible into a 4 column \link{matrix} using
\link{matrix}(x,ncol=4,byrow=TRUE) command. The \link{matrix}/\link{vector}
Column 1: the \emph{long flag} name. A multi-\link{character} string.
Column 2: \emph{short flag} alias of Column 1. A single-\link{character}
Column 3: \emph{Argument} mask of the \emph{flag}. An \link{integer}.
Possible values: 0=no argument, 1=required argument, 2=optional argument.
Column 4: Data type to which the \emph{flag}'s argument shall be cast using
\link{storage.mode}. A multi-\link{character} string. This only
considered for same-row Column 3 values of {1,2}. Possible values:
\link{logical}, \link{integer}, \link{double}, \link{complex},
Column 5 (optional): A brief description of the purpose of the option.
The terms \emph{option}, \emph{flag}, \emph{long flag}, \emph{short flag},
and \emph{argument} have very specific meanings in the context of this
document. Read the ``Description'' section for definitions.
This defaults to the return value of \link{commandArgs}(TRUE).
If R was invoked directly via the ``R'' command, this corresponds
to all arguments passed to R after the ``--args'' flag.
If R was invoked via the ``\link{Rscript}'' command, this corresponds to all
arguments after the name of the R script file.
Read about \link{commandArgs} and \link{Rscript} to learn more.
The string to use in the usage message as the name of the script. See
argument \emph{usage}.
If TRUE, argument \emph{opt} will be ignored and a usage statement (character
string) will be generated and returned from \emph{spec}.
This is used internally to debug the getopt() function itself.
Current issues:
1. No support for multiple, identical flags, e.g. for "-m 3 -v 5 -v", the
trailing "-v" overrides the preceding "-v 5", result is v=TRUE (or equivalent
2. No support for multi-valued flags, e.g.
"--libpath=/usr/local/lib --libpath=/tmp/foo".
3. No support for lists, e.g. "--define os=linux --define os=redhat"
would set result$os$linux=TRUE and result$os$redhat=TRUE.
4. No support for incremental, argument-less flags, e.g. "/path/to/script -vvv"
should set v=3.
5. Need more unit tests (see end of examples section).
6. Support partial-but-unique string match on options, e.g. "--verb" and
"--verbose" both match long flag "--verbose".
\value{ }
\references{ }
\author{ Allen Day }
\note{ }
\seealso{ \code{\link{getopt}} }
#get options, using the spec as defined by the enclosed list.
#we read the options from the default: commandArgs(TRUE).
opt = getopt(c(
'verbose', 'v', 2, "integer",
'help' , 'h', 0, "logical",
'count' , 'c', 1, "integer",
'mean' , 'm', 1, "double",
'sd' , 's', 1, "double"
#help was asked for.
if ( !is.null(opt$help) ) {
#get the script name (only works when invoked with Rscript).
self = commandArgs()[1];
#print a friendly message and exit with a non-zero error code
cat(paste("Usage: ",self," [-[vh]] [-[-mean|m] <mean>] [-[-sd|s] <sd>] [-[-count|c] <count>]\n",sep=""));
#set some reasonable defaults for the options that are needed,
#but were not specified.
if ( is.null(opt$mean ) ) { opt$mean = 0 }
if ( is.null(opt$sd ) ) { opt$sd = 1 }
if ( is.null(opt$count ) ) { opt$count = 10 }
if ( is.null(opt$verbose ) ) { opt$verbose = FALSE }
#print some progress messages to stderr, if requested.
if ( opt$verbose ) { write("writing...",stderr()); }
#do some operation based on user input.
#signal success and exit.
### END ###
#regression tests follow. not part of the example.
spec = c(
'verbose', 'v', 2, "integer",
'help' , 'h', 0, "logical",
'dummy1' , 'd', 0, "logical",
'dummy2' , 'e', 2, "logical",
'count' , 'c', 1, "integer",
'mean' , 'm', 1, "double",
'sd' , 's', 1, "double",
'output' , 'O', 1, "character"
opt = getopt(spec, c('-v', '-m', '3'));
opt = getopt(spec, c('-m', '3', '-v'));
opt = getopt(spec, c('-m', '3', '-v', '2', '-v'));
opt = getopt(spec, c('-O', '-', '-m', '3'));
opt = getopt(spec, c('-m', '3', '-O', '-'));
opt = getopt(spec, c('-de'));
opt = getopt(spec, c('-ed'));
opt = getopt(spec, c('-d'));
opt = getopt(spec, c('-e', '1'));
opt = getopt(spec, c('-de', '1'));
opt = getopt(spec, c('--verbose'));
opt = getopt(spec, c('--help'));
opt = getopt(spec, c('--verbose', '--help'));
opt = getopt(spec, c('--verbose', '--mean', '5'));
opt = getopt(spec, c('--mean=5'));
opt = getopt(spec, c('--verbose', '--mean=5'));
opt = getopt(spec, c('--verbose', '--mean=5', '--sd', '5'));
opt = getopt(spec, c('--mean=5', '--sd', '5', '--verbose'));
opt = getopt(spec, c('--mean=5', '--verbose', '--sd', '5'));
spec = c(
'date' , 'd', 1, "character",
'help' , 'h', 0, "logical",
'getdata' , 'g', 0, "logical",
'market' , 'm', 1, "character",
'threshold', 't', 1, "double"
opt = getopt(spec, c('--date','20080421','--market','YM','--getdata'));
opt = getopt(spec, c('--date','20080421','--getdata','--market','YM'));
opt = getopt(spec, c('--date','20080421','--getdata','--market','YM'),usage=TRUE,debug=TRUE);
print(getopt(spec, c('--date','20080421','--getdata','--market','YM'),usage=TRUE));
\keyword{ data }% at least one, from doc/KEYWORDS
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