--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/getopt.R	Fri Jun 26 09:45:41 2020 -0400
@@ -0,0 +1,773 @@
+# Copyright (c) 2008-2010 Allen Day
+# Copyright (c) 2011-2013 Trevor L. Davis <trevor.l.davis@stanford.edu>  
+#  
+# Modified by J.Vandel 2017 to consider situation of multiple identical flag
+# and concatenate as a vector the set of parameter for the same flag instead of
+# keeping only the last value as done by the previous version.
+#
+#  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 <http://www.gnu.org/licenses/>.  
+
+#' 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];
+          #don't need here to remove the last value of the vector as argument is in the same string as
+          #the flag name "--flag=argument" so no spurious TRUE was added
+          result[[spec[rowmatch, col.long.name]]] = c(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]]] = c(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]]] = c(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]]] = c(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];
+          #remove the last argument put in result for current.flag that should be a TRUE and concatenate argument with previous ones
+          result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]][-length(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];
+          #remove the last argument put in result for current.flag that should be a TRUE and concatenate argument with previous ones
+          result[[spec[current.flag, col.long.name]]] =c(result[[spec[current.flag, col.long.name]]][-length(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]]] = c(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]]] = c(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]]] = c(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);
+}
+
+
+
+#########################
+#set a modified version using only long named parameters 
+
+getoptLong = 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],']',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("--%-",max.long,"s    %s\n",sep='')
+                                ,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];
+          #don't need here to remove the last value of the vector as argument is in the same string as
+          #the flag name "--flag=argument" so no spurious TRUE was added
+          result[[spec[rowmatch, col.long.name]]] = c(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]]] = c(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]]] = c(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]]] = c(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];
+          #remove the last argument put in result for current.flag that should be a TRUE and concatenate argument with previous ones
+          result[[spec[current.flag, col.long.name]]] = c(result[[spec[current.flag, col.long.name]]][-length(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];
+          #remove the last argument put in result for current.flag that should be a TRUE and concatenate argument with previous ones
+          result[[spec[current.flag, col.long.name]]] =c(result[[spec[current.flag, col.long.name]]][-length(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]]] = c(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]]] = c(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]]] = c(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);
+}
+