Merge pull request #3 from bedapub/devel

Addressing suggestions raised by CRAN reviewers

Author: Accio

.Rbuildignore

@@ -18,3 +18,5 @@
 ^bin$
 ^CRAN-SUBMISSION$
 ^CRAN-PREPARATION\.md$
+^CRAN-FEEDBACK\.md$
+cran-fixes.patch

.gitignore

@@ -7,3 +7,6 @@ symbols.rds
 *.dll
 .Rhistory
 .Rproj.user
+cran-fixes.patch
+*.tar.gz
+ribiosArg.Rcheck

DESCRIPTION

@@ -9,10 +9,13 @@ Authors@R:
            role = c("aut", "cre", "ctb"),
            email = "jitao_david.zhang@roche.com",
            comment = c(ORCID="0000-0002-3085-0909")),
-    person("F.Hoffmann-La Roche AG", role="cph"))
+    person(given = "Balazs",
+           family = "Banfai",
+           role = "ctb"))
 Description: Provides functions to handle command-line arguments for R
     scripting. It enables building stand-alone R programs that accept and
-    parse command-line options in BIOS style.
+    parse command-line options in 'BIOS' style.
+    Zhang (2025) <https://github.com/bedapub/ribiosArg>.
 Depends:
     R (>= 3.4.0),
     ribiosUtils

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(argGet)
 export(argGetPos)
+export(argIsInit)
 export(argParse)
 export(argPresent)
 export(existArg)

NEWS

@@ -1,3 +1,8 @@
+2026-02-12: v1.5-1
+  + Add R-level guards in argPresent, argGet, and argGetPos to return safe defaults when the parser is uninitialized
+  + Export argIsInit() for users to check parser initialization status
+  + argParse returns silently instead of stopping when no script context is detected (fixes --run-donttest examples)
+
 2015-09-04: v1.1-18
   + rarg_parse: fixed a bug caused by passing SEXP as a size_t object
 

NEWS.md

@@ -1,5 +1,4 @@
 #' Parser of command-line parameters in BIOS style
-#' @aliases argIsInit
 #' @aliases argPresent
 #'
 #' @param optargs String describing optional arguments. Syntax: \code{<optname1>[,paramcnt1] <optname2>[,paramcnt2]\dots}. Example: \dQuote{verbose outfile,1} means the command line has the syntax \code{prog [-verbose] [outfile name]}. It can be an empty string to express \dQuote{no options}. The value for \code{paramcnt} is 0.
@@ -37,7 +36,7 @@
 #' @useDynLib ribiosArg, .registration=TRUE, .fixes="C_"
 #' 
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' argParse("verbose threshold,2", "infile outfile",
 #'          usage="prog [-infile ]infile [-outfile ]outfile [-verbose] [-threshold MIN MAX]")
 #' argIsInit()
@@ -70,8 +69,8 @@ argParse <- function(optargs, reqargs, usage=paste(scriptName(), "-h"), strict=T
     efind <- which(isE)
     allComm <- allComm[-(1:(efind+1))]
   } else {
-    stop("This should not happen: no parameters in the form of '-f' or '--f' is detected. Please contact the developer")
-  } 
+    return(invisible(NULL))
+  }
   comm <- allComm[!grepl("^--", allComm)]
   ## the following code was valid till R-3.0.x. 
   ##  if("--args" %in% allComm) {
@@ -114,6 +113,10 @@ argParse <- function(optargs, reqargs, usage=paste(scriptName(), "-h"), strict=T
   }
 }
 
+#' Check whether the argument parser has been initialized
+#'
+#' @return Logical, \code{TRUE} if \code{argParse} has been called, \code{FALSE} otherwise.
+#' @export
 argIsInit <- function() .Call(C_rarg_isInit)
 
 #' Test whether the given option is present in the command line or not
@@ -127,6 +130,7 @@ argPresent <- function(opt) {
         message("[DEBUGGIING] The script is running in an interactive session, e.g. debugging mode. FALSE is returned")
         return(FALSE)
     }
+    if(!isTRUE(argIsInit())) return(FALSE)
   .Call(C_rarg_present, opt)
 }
 
@@ -147,14 +151,15 @@ argPresent <- function(opt) {
 #' @seealso \code{\link{argParse}}, \code{\link{argGet}}, and \code{\link{argPresent}}
 #'
 #' @examples
-#' \dontrun{argGetPos("thresholds", ind=2)}
+#' \donttest{argGetPos("thresholds", ind=2)}
 #'
 #' @export 
 argGetPos <- function(opt, ind=1L, default=NULL, choices=NULL) {
   if(isDebugging()) {
     message("[DEBUGGIING] The script is running in an interactive session, e.g. debugging mode. Default value is returned")
     return(default)
-  }  
+  }
+  if(!isTRUE(argIsInit())) return(default)
   if(argPresent(opt)) {
       res <- .Call(C_rarg_getPos, opt,as.integer(ind))
       if(!is.null(choices) && !res %in% choices)
@@ -182,14 +187,15 @@ argGetPos <- function(opt, ind=1L, default=NULL, choices=NULL) {
 #' @seealso \code{\link{argParse}}, \code{\link{argGetPos}}, and \code{\link{argPresent}}
 #'
 #' @examples
-#' \dontrun{argGet("infile")}
+#' \donttest{argGet("infile")}
 #'
 #' @export
 argGet <- function(opt, default=NULL, choices=NULL) {
   if(isDebugging()) {
     message("[DEBUGGIING] The script is running in an interactive session, e.g. debugging mode. Default value is returned")
     return(default)
   }
+  if(!isTRUE(argIsInit())) return(default)
   if(argPresent(opt)) {
       res <- .Call(C_rarg_get, opt)
       if(!is.null(choices) && !res %in% choices) {

R/argparse.R

@@ -13,6 +13,7 @@
 #' @param failVal If the parsing failed (for example length not correct, or non-numeric values were provided, this value will be returned
 #' @param sep Separator in the character string, default ","
 #'
+#' @return A numeric vector of the parsed values, or \code{failVal} if parsing fails.
 #' @seealso \code{\link{argGet}}
 #' 
 #' @export
@@ -127,6 +128,7 @@ parsePairs <- function(str, collapse=",", sep="=",
 #' @param make.names Should names be converted to adhere to the rule of variable names in R
 #' @param verbose Logical vector
 #'
+#' @return A factor with the specified levels.
 #' @export
 #' @examples
 #' makeFactor(c("A", "B", "C", "C", "A"), levels=LETTERS[3:1])
@@ -178,6 +180,7 @@ makeFactor <- function(groups, levels=NULL, make.names=TRUE, verbose=FALSE) {
 #' @param make.names Logical, should names be converted to adhere to the rule of variable names in R
 #' @param collapse Character used in \code{relevels} to collapse different levels
 #'
+#' @return A factor parsed from the input string with the specified levels.
 #' @export
 #' @examples
 #' parseFactor("A,B,C,B,A", rlevels="A,B,C")
@@ -194,14 +197,14 @@ makeFactor <- function(groups, levels=NULL, make.names=TRUE, verbose=FALSE) {
 #' groups <- factor(c("B", "C", "A", "D"), levels=c("D","C","A","B"))
 #' makeFactor(groups)
 #' 
-#' \dontrun{
+#' \donttest{
 #' groups <- c("ATest", "Control", "Control", "ATest")
 #' levels <- c("Control", "ATest", "Unknown")
 #' makeFactor(groups, levels)
 #' 
 #' groups <- c("ATest", "Control", "Control", "ATest", "BTest")
 #' levels <- c("Control", "ATest")
-#' makeFactor(groups, levels)
+#' try(makeFactor(groups, levels))
 #' }
 #' 
 parseFactor <- function(str, rlevels=NULL, make.names=TRUE, collapse=",") { ## CL=command line
@@ -233,6 +236,7 @@ isDir <- function(str) file.info(str)$isdir
 #' @param recursive In cse of directory or compressed files, whether files should be found recursively
 #' @param ignore.case In case of directory or compressed files, whether case should be ignored
 #'
+#' @return A character vector of file paths.
 #' @importFrom ribiosUtils extname
 #' @importFrom utils untar unzip
 #' @export

R/parseFuncs.R

@@ -1,7 +1,9 @@
-#' Command-line argument handling for R scripting
-#' @docType package
-#' @description Provides command-line argument handling for R scripting
+#' @keywords internal
+"_PACKAGE"
+
+#' ribiosIO
+#' ribiosIO provides Command-line argument handling for R scripting
 #' @author Jitao David Zhang <jitao_david.zhang@roche.com>
 #' @useDynLib ribiosArg, .registration=TRUE, .fixes="C_"
-#' @name ribiosArg-package
+#' @name ribiosArg
 NULL

R/ribiosArg.R

@@ -1,17 +1,19 @@
 #' Prepare the environment for a script
-#' @aliases initScript
-#' 
+#'
 #' This function is called at the beginning of an Rscript, in order to
 #' prepare the R environment to run in a script setting.
 #'
-#' @return Only side effect is used
-#' 
+#' @return No return value, called for side effects.
+#'
+#' @aliases initScript
 #' @export
 #' @examples
-#' \dontrun{
+#' \donttest{
 #'   scriptInit()
 #' }
 scriptInit <- function() {
+  old <- options()
+  on.exit(options(old))
   if(interactive()) {
     setDebug()
   } else {