getopt/0000755000176000001440000000000012210054615011600 5ustar ripleyusersgetopt/COPYING0000644000176000001440000004325412206012161012636 0ustar ripleyusers GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) 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We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. 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If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. getopt/inst/0000755000176000001440000000000012210024307012550 5ustar ripleyusersgetopt/inst/tests/0000755000176000001440000000000012210024622013712 5ustar ripleyusersgetopt/inst/tests/test-getopt.R0000644000176000001440000001073012210024617016321 0ustar ripleyuserscontext("Testing getopt") test_that("getopt works as expected", { spec = matrix(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" ), ncol=4, byrow=TRUE); expect_equal(sort_list(getopt(spec, c('-c', '-1', '-m', '-1.2'))), sort_list(list(ARGS=character(0), count=-1, mean=-1.2))); expect_equal(sort_list(getopt(spec, c('-v', '-m', '3'))), sort_list(list(ARGS=character(0), verbose=1, mean=3))); expect_equal(sort_list(getopt(spec, c('-m', '3', '-v'))), sort_list(list(ARGS=character(0), mean=3, verbose=1))); expect_equal(sort_list(getopt(spec, c('-m', '3', '-v', '2', '-v'))), sort_list(list(ARGS=character(0), mean=3, verbose=1))); expect_equal(sort_list(getopt(spec, c('-O', '-', '-m', '3'))), sort_list(list(ARGS=character(0), output="-", mean=3))); expect_equal(sort_list(getopt(spec, c('-O', '-', '-m', '3'))), sort_list(getopt(spec, c('-m', '3', '-O', '-')))); expect_equal(sort_list(getopt(spec, c('-de'))), sort_list(getopt(spec, c('-ed')))); expect_equal(sort_list(getopt(spec, c('-de'))), sort_list(list(ARGS=character(0), dummy1=TRUE, dummy2=TRUE))); expect_equal(sort_list(getopt(spec, c('-de', '1'))), sort_list(list(ARGS=character(0), dummy1=TRUE, dummy2=NA))); expect_equal(sort_list(getopt(spec, c('--verbose'))), sort_list(list(ARGS=character(0), verbose=1))); expect_equal(sort_list(getopt(spec, c('--verbose', '--help'))), sort_list(list(ARGS=character(0), verbose=1, help=TRUE))); expect_equal(sort_list(getopt(spec, c('--verbose', '--mean', '5'))), sort_list(list(ARGS=character(0), verbose=1, mean=5))); expect_equal(sort_list(getopt(spec, c('--mean=5'))), sort_list(list(ARGS=character(0), mean=5))); expect_equal(sort_list(getopt(spec, c('--verbose', '--mean=5', '--sd', '5'))), sort_list(list(ARGS=character(0), verbose=1, mean=5, sd=5))); expect_equal(sort_list(getopt(spec, c('--verbose', '--mean=5', '--sd', '5'))), sort_list(getopt(spec, c('--mean=5', '--sd', '5', '--verbose')))); spec = c( 'date' , 'd', 1, "character", 'help' , 'h', 0, "logical", 'getdata' , 'g', 0, "logical", 'market' , 'm', 1, "character", 'threshold', 't', 1, "double" ); spec2 <- matrix(spec, ncol=4, byrow=TRUE) # should give warning is spec is not matrix expect_that(getopt(spec, c('--date','20080421','--market','YM','--getdata')), gives_warning()); expect_equal(sort_list(getopt(spec2, c('--date','20080421','--market','YM','--getdata'))), sort_list(list(ARGS=character(0), date='20080421', market='YM', getdata=TRUE))) expect_equal(sort_list(getopt(spec2, c('--date','20080421','--market','YM','--getdata'))), sort_list(getopt(spec2, c('--date','20080421','--getdata','--market','YM')))); expect_that(getopt(spec2, c('--date','20080421','--getdata','--market','YM'),debug=TRUE), prints_text("processing ")); expect_that(print(getopt(spec2, c('--date','20080421','--getdata','--market','YM'),usage=TRUE)), prints_text("Usage: ")); }) test_that("numeric is cast to double", { # Feature reported upstream (optparse) by Miroslav Posta spec = matrix(c("count", "c", 1, "integer"), ncol=4, byrow=TRUE) getopt(spec, c("-c", "-55")) spec = matrix(c("count", "c", 1, "numeric"), ncol=4, byrow=TRUE) getopt(spec, c("-c", "-55.0")) }) test_that("don't throw error if multiple matches match one argument fully", { # test if partial name matches fully, # still throw error if multiple matches and doesn't match both fully # feature request from Jonas Zimmermann spec = matrix(c( 'foo' , 'f', 0, "logical", 'foobar' , 'b', 0, "logical", 'biz' , 'z', 0, "logical" ), ncol=4, byrow=TRUE) expect_that(getopt(spec, c('--fo')), throws_error()) expect_equal(getopt(spec, c('--foo')), sort_list(list(ARGS=character(0), foo=TRUE))) }) context("Test sort_list") test_that("sort_list works as expected", { expect_equal(sort_list(list(a = 3, b = 2)), sort_list(list(b = 2, a = 3))) expect_false(identical(sort_list(list(b = 3, a = 2)), list(b = 3, a = 2))) }) getopt/tests/0000755000176000001440000000000012210024370012735 5ustar ripleyusersgetopt/tests/run-all.R0000644000176000001440000000007612141060751014443 0ustar ripleyuserslibrary("testthat") library("getopt") test_package("getopt") getopt/NAMESPACE0000644000176000001440000000007612210022616013016 0ustar ripleyusersexport(get_Rscript_filename) export(getopt) export(sort_list) getopt/NEWS0000644000176000001440000000152412210041077012277 0ustar ripleyusersgetopt 1.20.0 ============= * Type of "numeric" in spec automatically cast to "double". Previously users might have had an error passing negative numbers if they accidentally specified "numeric" instead of "double". * Project website moved to https://github.com/trevorld/getopt * Exports new function ``sort_list``. getopt 1.19.1 ============= * If a passed in option matches multiple options in the getopt specification but matches one exactly then `getopt` now uses that value instead of throwing a "long flag is ambiguous" error. getopt 1.19.0 ============= * Exports new function `get_Rscript_filename` that returns name of calling script, `getopt` now uses this function value as default for `command` argument * Documentation improved and now highlights differences between `getopt` and `optparse` packages for new undecided users getopt/R/0000755000176000001440000000000012210037706012003 5ustar ripleyusersgetopt/R/utils.R0000644000176000001440000000313412210037610013261 0ustar ripleyusers# Copyright (c) 2011-2013 Trevor L. Davis # # This file is free software: you may copy, redistribute and/or modify it # under the terms of the GNU General Public License as published by the # Free Software Foundation, either version 2 of the License, or (at your # option) any later version. # # This file is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . #' Returns file name of calling Rscript #' #' \code{get_Rscript_filename} returns the file name of calling Rscript #' @return A string with the filename of the calling script. #' If not found (i.e. you are in a interactive session) returns NA. #' #' @export get_Rscript_filename <- function() { prog <- sub("--file=", "", grep("--file=", commandArgs(), value=TRUE)[1]) if( .Platform$OS.type == "windows") { prog <- gsub("\\\\", "\\\\\\\\", prog) } prog } #' Recursively sorts a list #' #' \code{sort_list} returns a sorted list #' @param unsorted_list A list. #' @return A sorted list. #' @export sort_list <- function(unsorted_list) { for(ii in seq(along=unsorted_list)) { if(is.list(unsorted_list[[ii]])) { unsorted_list[[ii]] <- sort_list(unsorted_list[[ii]]) } } unsorted_list[sort(names(unsorted_list))] } getopt/R/getopt.R0000644000176000001440000004456112210037704013440 0ustar ripleyusers# Copyright (c) 2008-2010 Allen Day # Copyright (c) 2011-2013 Trevor L. Davis # # This file is free software: you may copy, redistribute and/or modify it # under the terms of the GNU General Public License as published by the # Free Software Foundation, either version 2 of the License, or (at your # option) any later version. # # This file is distributed in the hope that it will be useful, but # WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program. If not, see . #' 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}. #' #' Many users wonder whether they should use the getopt package, optparse package, #' or argparse package. #' Here is some of the major differences: #' #' Features available in \code{getopt} unavailable in \code{optparse} #' #' 1. As well as allowing one to specify options that take either #' no argument or a required argument like \code{optparse}, #' \code{getopt} also allows one to specify option with an optional argument. #' #' Some features implemented in \code{optparse} package unavailable in \code{getopt} #' #' 1. Limited support for capturing positional arguments after the optional arguments #' when \code{positional_arguments} set to TRUE in \code{parse_args} #' #' 2. Automatic generation of an help option and printing of help text when encounters an "-h" #' #' 3. Option to specify default arguments for options as well the #' variable name to store option values #' #' There is also new package \code{argparse} introduced in 2012 which contains #' all the features of both getopt and optparse but which has a dependency on #' Python 2.7 or 3.2+ and has not been used in production since 2008 or 2009 #' like the getopt and optparse packages. #' #' Some Features unlikely to be implemented in \code{getopt}: #' #' 1. 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 #' typecast). #' #' 2. Support for multi-valued flags, e.g. "--libpath=/usr/local/lib #' --libpath=/tmp/foo". #' #' 3. Support for lists, e.g. "--define os=linux --define os=redhat" would #' set result$os$linux=TRUE and result$os$redhat=TRUE. #' #' 4. Support for incremental, argument-less flags, e.g. "/path/to/script #' -vvv" should set v=3. #' #' 5. Support partial-but-unique string match on options, e.g. "--verb" and #' "--verbose" both match long flag "--verbose". #' #' 6. No support for mixing in positional arguments or extra arguments that #' don't match any options. For example, you can't do "my.R --arg1 1 foo bar #' baz" and recover "foo", "bar", "baz" as a list. Likewise for "my.R foo #' --arg1 1 bar baz". #' #' @aliases getopt getopt-package #' @param spec 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} #' contains: #' #' 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} #' string. #' #' 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}, \link{character}. #' If \link{numeric} is encountered then it will be converted to double. #' #' 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. #' @param opt 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. #' @param command The string to use in the usage message as the name of the #' script. See argument \emph{usage}. #' @param usage If TRUE, argument \emph{opt} will be ignored and a usage #' statement (character string) will be generated and returned from \emph{spec}. #' @param debug This is used internally to debug the getopt() function itself. #' @author Allen Day #' @seealso \code{\link{getopt}} #' @keywords data #' @export #' @examples #' #' #!/path/to/Rscript #' library('getopt'); #' #get options, using the spec as defined by the enclosed list. #' #we read the options from the default: commandArgs(TRUE). #' spec = matrix(c( #' 'verbose', 'v', 2, "integer", #' 'help' , 'h', 0, "logical", #' 'count' , 'c', 1, "integer", #' 'mean' , 'm', 1, "double", #' 'sd' , 's', 1, "double" #' ), byrow=TRUE, ncol=4); #' opt = getopt(spec); #' #' # if help was asked for print a friendly message #' # and exit with a non-zero error code #' if ( !is.null(opt$help) ) { #' cat(getopt(spec, usage=TRUE)); #' q(status=1); #' } #' #' #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$verbose ) { write("writing...",stderr()); } #' #' #do some operation based on user input. #' cat(paste(rnorm(opt$count,mean=opt$mean,sd=opt$sd),collapse="\n")); #' cat("\n"); #' #' #signal success and exit. #' #q(status=0); getopt = function (spec=NULL,opt=commandArgs(TRUE),command=get_Rscript_filename(),usage=FALSE,debug=FALSE) { # littler compatibility - map argv vector to opt if (exists("argv", where = .GlobalEnv, inherits = FALSE)) { opt = get("argv", envir = .GlobalEnv); } ncol=4; maxcol=6; col.long.name = 1; col.short.name = 2; col.has.argument = 3; col.mode = 4; col.description = 5; flag.no.argument = 0; flag.required.argument = 1; flag.optional.argument = 2; result = list(); result$ARGS = vector(mode="character"); #no spec. fail. if ( is.null(spec) ) { stop('argument "spec" must be non-null.'); #spec is not a matrix. attempt to coerce, if possible. issue a warning. } else if ( !is.matrix(spec) ) { if ( length(spec)/4 == as.integer(length(spec)/4) ) { warning('argument "spec" was coerced to a 4-column (row-major) matrix. use a matrix to prevent the coercion'); spec = matrix( spec, ncol=ncol, byrow=TRUE ); } else { stop('argument "spec" must be a matrix, or a character vector with length divisible by 4, rtfm.'); } #spec is a matrix, but it has too few columns. } else if ( dim(spec)[2] < ncol ) { stop(paste('"spec" should have at least ",ncol," columns.',sep='')); #spec is a matrix, but it has too many columns. } else if ( dim(spec)[2] > maxcol ) { stop(paste('"spec" should have no more than ",maxcol," columns.',sep='')); #spec is a matrix, and it has some optional columns. } else if ( dim(spec)[2] != ncol ) { ncol = dim(spec)[2]; } #sanity check. make sure long names are unique, and short names are unique. if ( length(unique(spec[,col.long.name])) != length(spec[,col.long.name]) ) { stop(paste('redundant long names for flags (column ',col.long.name,').',sep='')); } if ( length(na.omit(unique(spec[,col.short.name]))) != length(na.omit(spec[,col.short.name])) ) { stop(paste('redundant short names for flags (column ',col.short.name,').',sep='')); } # convert numeric type to double type spec[,4] <- gsub("numeric", "double", spec[,4]) # if usage=TRUE, don't process opt, but generate a usage string from the data in spec if ( usage ) { ret = ''; ret = paste(ret,"Usage: ",command,sep=''); for ( j in 1:(dim(spec))[1] ) { ret = paste(ret,' [-[-',spec[j,col.long.name],'|',spec[j,col.short.name],']',sep=''); if (spec[j,col.has.argument] == flag.no.argument) { ret = paste(ret,']',sep=''); } else if (spec[j,col.has.argument] == flag.required.argument) { ret = paste(ret,' <',spec[j,col.mode],'>]',sep=''); } else if (spec[j,col.has.argument] == flag.optional.argument) { ret = paste(ret,' [<',spec[j,col.mode],'>]]',sep=''); } } # include usage strings if ( ncol >= 5 ) { max.long = max(apply(cbind(spec[,col.long.name]),1,function(x)length(strsplit(x,'')[[1]]))); ret = paste(ret,"\n",sep=''); for (j in 1:(dim(spec))[1] ) { ret = paste(ret,sprintf(paste(" -%s|--%-",max.long,"s %s\n",sep=''), spec[j,col.short.name],spec[j,col.long.name],spec[j,col.description] ),sep=''); } } else { ret = paste(ret,"\n",sep=''); } return(ret); } #XXX check spec validity here. e.g. column three should be convertible to integer i = 1; while ( i <= length(opt) ) { if ( debug ) print(paste("processing",opt[i])); current.flag = 0; #XXX use NA optstring = opt[i]; #long flag if ( substr(optstring, 1, 2) == '--' ) { if ( debug ) print(paste(" long option:",opt[i])); optstring = substring(optstring,3); this.flag = NA; this.argument = NA; kv = strsplit(optstring, '=')[[1]]; if ( !is.na(kv[2]) ) { this.flag = kv[1]; this.argument = paste(kv[-1], collapse="="); } else { this.flag = optstring; } rowmatch = grep( this.flag, spec[,col.long.name],fixed=TRUE ); #long flag is invalid, matches no options if ( length(rowmatch) == 0 ) { stop(paste('long flag "', this.flag, '" is invalid', sep='')); #long flag is ambiguous, matches too many options } else if ( length(rowmatch) > 1 ) { # check if there is an exact match and use that rowmatch = which(this.flag == spec[,col.long.name]) if(length(rowmatch) == 0) { stop(paste('long flag "', this.flag, '" is ambiguous', sep='')); } } #if we have an argument if ( !is.na(this.argument) ) { #if we can't accept the argument, bail out if ( spec[rowmatch, col.has.argument] == flag.no.argument ) { stop(paste('long flag "', this.flag, '" accepts no arguments', sep='')); #otherwise assign the argument to the flag } else { storage.mode(this.argument) = spec[rowmatch, col.mode]; result[spec[rowmatch, col.long.name]] = this.argument; i = i + 1; next; } #otherwise, we don't have an argument } else { #if we require an argument, bail out ###if ( spec[rowmatch, col.has.argument] == flag.required.argument ) { ### stop(paste('long flag "', this.flag, '" requires an argument', sep='')); #long flag has no attached argument. set flag as present. set current.flag so we can peek ahead later and consume the argument if it's there ###} else { result[spec[rowmatch, col.long.name]] = TRUE; current.flag = rowmatch; ###} } #short flag(s) } else if ( substr(optstring, 1, 1) == '-' ) { if ( debug ) print(paste(" short option:",opt[i])); these.flags = strsplit(optstring,'')[[1]]; done = FALSE; for ( j in 2:length(these.flags) ) { this.flag = these.flags[j]; rowmatch = grep( this.flag, spec[,col.short.name],fixed=TRUE ); #short flag is invalid, matches no options if ( length(rowmatch) == 0 ) { stop(paste('short flag "', this.flag, '" is invalid', sep='')); #short flag is ambiguous, matches too many options } else if ( length(rowmatch) > 1 ) { stop(paste('short flag "', this.flag, '" is ambiguous', sep='')); #short flag has an argument, but is not the last in a compound flag string } else if ( j < length(these.flags) & spec[rowmatch,col.has.argument] == flag.required.argument ) { stop(paste('short flag "', this.flag, '" requires an argument, but has none', sep='')); #short flag has no argument, flag it as present } else if ( spec[rowmatch,col.has.argument] == flag.no.argument ) { result[spec[rowmatch, col.long.name]] = TRUE; done = TRUE; #can't definitively process this flag yet, need to see if next option is an argument or not } else { result[spec[rowmatch, col.long.name]] = TRUE; current.flag = rowmatch; done = FALSE; } } if ( done ) { i = i + 1; next; } } #invalid opt if ( current.flag == 0 ) { stop(paste('"', optstring, '" is not a valid option, or does not support an argument', sep='')); #TBD support for positional args #if ( debug ) print(paste('"', optstring, '" not a valid option. It is appended to getopt(...)$ARGS', sep='')); #result$ARGS = append(result$ARGS, optstring); # some dangling flag, handle it } else if ( current.flag > 0 ) { if ( debug ) print(' dangling flag'); if ( length(opt) > i ) { peek.optstring = opt[i + 1]; if ( debug ) print(paste(' peeking ahead at: "',peek.optstring,'"',sep='')); #got an argument. attach it, increment the index, and move on to the next option. we don't allow arguments beginning with '-' UNLESS #specfile indicates the value is an "integer" or "double", in which case we allow a leading dash (and verify trailing digits/decimals). if ( substr(peek.optstring, 1, 1) != '-' | #match negative double ( substr(peek.optstring, 1, 1) == '-' & regexpr('^-[0123456789]*\\.?[0123456789]+$',peek.optstring) > 0 & spec[current.flag, col.mode]== 'double' ) | #match negative integer ( substr(peek.optstring, 1, 1) == '-' & regexpr('^-[0123456789]+$',peek.optstring) > 0 & spec[current.flag, col.mode]== 'integer' ) ) { if ( debug ) print(paste(' consuming argument *',peek.optstring,'*',sep='')); storage.mode(peek.optstring) = spec[current.flag, col.mode]; result[spec[current.flag, col.long.name]] = peek.optstring; i = i + 1; #a lone dash } else if ( substr(peek.optstring, 1, 1) == '-' & length(strsplit(peek.optstring,'')[[1]]) == 1 ) { if ( debug ) print(' consuming "lone dash" argument'); storage.mode(peek.optstring) = spec[current.flag, col.mode]; result[spec[current.flag, col.long.name]] = peek.optstring; i = i + 1; #no argument } else { if ( debug ) print(' no argument!'); #if we require an argument, bail out if ( spec[current.flag, col.has.argument] == flag.required.argument ) { stop(paste('flag "', this.flag, '" requires an argument', sep='')); #otherwise set flag as present. } else if ( spec[current.flag, col.has.argument] == flag.optional.argument | spec[current.flag, col.has.argument] == flag.no.argument ) { x = TRUE; storage.mode(x) = spec[current.flag, col.mode]; result[spec[current.flag, col.long.name]] = x; } else { stop(paste("This should never happen.", "Is your spec argument correct? Maybe you forgot to set", "ncol=4, byrow=TRUE in your matrix call?")); } } #trailing flag without required argument } else if ( spec[current.flag, col.has.argument] == flag.required.argument ) { stop(paste('flag "', this.flag, '" requires an argument', sep='')); #trailing flag without optional argument } else if ( spec[current.flag, col.has.argument] == flag.optional.argument ) { x = TRUE; storage.mode(x) = spec[current.flag, col.mode]; result[spec[current.flag, col.long.name]] = x; #trailing flag without argument } else if ( spec[current.flag, col.has.argument] == flag.no.argument ) { x = TRUE; storage.mode(x) = spec[current.flag, col.mode]; result[spec[current.flag, col.long.name]] = x; } else { stop("this should never happen (2). please inform the author."); } #no dangling flag, nothing to do. } else { } i = i+1; } return(result); } getopt/MD50000644000176000001440000000102212210054615012103 0ustar ripleyusersb234ee4d69f5fce4486a80fdaf4a4263 *COPYING 08656e23fb8bd07c69f68e7d5443f05a *DESCRIPTION dd396c987d24860d37a42fc7541e77b5 *NAMESPACE f651db85028ffd75fd6e59b496a413fe *NEWS 244e1fed9d7aaaffaf66976576c06f9d *R/getopt.R e374b85f40f7549cbdb66c9065c1f1ec *R/utils.R 252fbb7071cd1cc555ca81c8f537a6b9 *inst/tests/test-getopt.R f692f19f2e09013c3d075f6d322473c0 *man/get_Rscript_filename.Rd 7edc52e347b20c53819d16cef5ff8086 *man/getopt.Rd 21469f658334a9ef307e44fcd49a1710 *man/sort_list.Rd 71912d95683c1891b4523acbc554da5e *tests/run-all.R getopt/DESCRIPTION0000644000176000001440000000147512210054615013315 0ustar ripleyusersPackage: getopt Type: Package Title: C-like getopt behavior. Version: 1.20.0 Author: Allen Day. Contributions from Trevor L Davis. Maintainer: Trevor L Davis URL: https://github.com/trevorld/getopt BugReports: https://github.com/trevorld/getopt/issues Description: Package designed to be used with Rscript to write ``#!'' shebang scripts that accept short and long flags/options. Many users will prefer using instead the packages optparse or argparse which add extra features like automatically generated help option and usage, support for default values, positional argument support, etc. License: GPL (>= 2) Suggests: testthat Collate: 'getopt.R' 'utils.R' Packaged: 2013-08-30 07:02:26 UTC; trevorld NeedsCompilation: no Repository: CRAN Date/Publication: 2013-08-30 10:36:29 getopt/man/0000755000176000001440000000000012210022616012347 5ustar ripleyusersgetopt/man/get_Rscript_filename.Rd0000644000176000001440000000054512141060751016774 0ustar ripleyusers\name{get_Rscript_filename} \alias{get_Rscript_filename} \title{Returns file name of calling Rscript} \usage{ get_Rscript_filename() } \value{ A string with the filename of the calling script. If not found (i.e. you are in a interactive session) returns NA. } \description{ \code{get_Rscript_filename} returns the file name of calling Rscript } getopt/man/sort_list.Rd0000644000176000001440000000035412210022616014662 0ustar ripleyusers\name{sort_list} \alias{sort_list} \title{Recursively sorts a list} \usage{ sort_list(unsorted_list) } \arguments{ \item{unsorted_list}{A list.} } \value{ A sorted list. } \description{ \code{sort_list} returns a sorted list } getopt/man/getopt.Rd0000644000176000001440000001603612210025756014156 0ustar ripleyusers\name{getopt} \alias{getopt} \alias{getopt-package} \title{C-like getopt behavior} \usage{ getopt(spec = NULL, opt = commandArgs(TRUE), command = get_Rscript_filename(), usage = FALSE, debug = FALSE) } \arguments{ \item{spec}{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} contains: 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} string. 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}, \link{character}. If \link{numeric} is encountered then it will be converted to double. 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.} \item{opt}{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.} \item{command}{The string to use in the usage message as the name of the script. See argument \emph{usage}.} \item{usage}{If TRUE, argument \emph{opt} will be ignored and a usage statement (character string) will be generated and returned from \emph{spec}.} \item{debug}{This is used internally to debug the getopt() function itself.} } \description{ 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. } \details{ 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}. Many users wonder whether they should use the getopt package, optparse package, or argparse package. Here is some of the major differences: Features available in \code{getopt} unavailable in \code{optparse} 1. As well as allowing one to specify options that take either no argument or a required argument like \code{optparse}, \code{getopt} also allows one to specify option with an optional argument. Some features implemented in \code{optparse} package unavailable in \code{getopt} 1. Limited support for capturing positional arguments after the optional arguments when \code{positional_arguments} set to TRUE in \code{parse_args} 2. Automatic generation of an help option and printing of help text when encounters an "-h" 3. Option to specify default arguments for options as well the variable name to store option values There is also new package \code{argparse} introduced in 2012 which contains all the features of both getopt and optparse but which has a dependency on Python 2.7 or 3.2+ and has not been used in production since 2008 or 2009 like the getopt and optparse packages. Some Features unlikely to be implemented in \code{getopt}: 1. 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 typecast). 2. Support for multi-valued flags, e.g. "--libpath=/usr/local/lib --libpath=/tmp/foo". 3. Support for lists, e.g. "--define os=linux --define os=redhat" would set result$os$linux=TRUE and result$os$redhat=TRUE. 4. Support for incremental, argument-less flags, e.g. "/path/to/script -vvv" should set v=3. 5. Support partial-but-unique string match on options, e.g. "--verb" and "--verbose" both match long flag "--verbose". 6. No support for mixing in positional arguments or extra arguments that don't match any options. For example, you can't do "my.R --arg1 1 foo bar baz" and recover "foo", "bar", "baz" as a list. Likewise for "my.R foo --arg1 1 bar baz". } \examples{ #!/path/to/Rscript library('getopt'); #get options, using the spec as defined by the enclosed list. #we read the options from the default: commandArgs(TRUE). spec = matrix(c( 'verbose', 'v', 2, "integer", 'help' , 'h', 0, "logical", 'count' , 'c', 1, "integer", 'mean' , 'm', 1, "double", 'sd' , 's', 1, "double" ), byrow=TRUE, ncol=4); opt = getopt(spec); # if help was asked for print a friendly message # and exit with a non-zero error code if ( !is.null(opt$help) ) { cat(getopt(spec, usage=TRUE)); q(status=1); } #set some reasonable defaults for the options that are needed, #but were not specified. if ( is.null(opt$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. cat(paste(rnorm(opt$count,mean=opt$mean,sd=opt$sd),collapse="\\n")); cat("\\n"); #signal success and exit. #q(status=0); } \author{ Allen Day } \seealso{ \code{\link{getopt}} } \keyword{data}