Roxygen: how to set a default parameter including backslash ('\') to functions

Question

I use Roxygen to generate Rd files of my packages under development, but I have some problems with functions with default parameter set to '\n', e.g.:

  lineCount <- function(text, sep='\n') {
       ...
   }

Which purpose is to count new line ('\n') characters in a string. The problem is that R CMD check gives a warning about:

Codoc mismatches from documentation object 'lineCount':
lineCount
  Code: function(text, sep = "\n")
  Docs: function(text, sep = " ")
  Mismatches in argument default values:
    Name: 'sep' Code: "\n" Docs: " "

The problem seems to me that caused by writing to the Rd file (writing to standard LaTeX files via cat() always requires to double escape characters for some purpose, e.g.: \\newline - as I experienced). If I put an extra backslash to the separator, like:

  lineCount <- function(text, sep='\\n') {
       ...
   }

The problem still presists, as in the code it looks like '\\n', but in the docs (Rd files) it looks '\n'.

Is there an easy solution for my problem? May be an extra tag in Roxygen which could define how to write the function's params to the Rd file? Sorry if asked too obvious a question, but I am lost after Google-ing for a while.

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History: http://permalink.gmane.org/gmane.comp.lang.r.roxygen/24

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UPDATE: use roxygen2!

Answer 1

I also ran into problems with too much escaped " and vanishing \t. I ended up changing the parse.formals function in roxygen's Rd2.R as follows:

  parse.formals <- function(partitum) {
    formals <- partitum$formals
    if (!is.null(formals)) {
      formals <- lapply(formals, trim)
      formals <- lapply(formals, paste, collapse=" ")
      name.defaults <- zip.c(names(formals), formals)
      args <-
        do.call(paste, c(Map(function(name.default) {
          name <- car(name.default)
          default <- cadr(name.default)
          if (! is.character (default)) {  # too much escaped. 
                                           # Not sure when escaping is needed. 
                                           # param = c ("x", "y", "z") works now
            default <- gsubfn("\"(.*)\"",
                              function(x)
                              sprintf("\"%s\"", gsub("\"", "\\\\\"", x)),
                              as.character(default))
          }
          default <- gsub ("\t", "\\\\t", default) # the tabs and newlines are already
          default <- gsub ("\n", "\\\\n", default) # tab and newline here.
          if (is.null.string(default))
            name
          else
            sprintf('%s=%s', name, default)
        },
                             name.defaults),
                         sep=', '))

      append.Rd(usageTag(parse.function.name(partitum), args))
    }
  }

Hope that helps and doesn't break anything else.

Answer 2

I came across this problem also, i.e. I had split="\+" and split="\|" in various functions.

The .Rd files actually also represent these as split="\+" and split="\|", but then whatever reads .Rd files in R CMD check turned them into split="+" and split="\|", and caused the error.

If the .Rd files had split="\\+" and split="\\|" it would then get read correctly.

My solution was to run this on the /man/ directory with the .Rd files, just before R CMD check:

perl -e 's/("\\\|")/"\\\\\|"/g;' -pi $(find BioGeoBEARS/man -type f)

perl -e 's/("\\+")/"\\\\+"/g;' -pi $(find BioGeoBEARS/man -type f)

Took a bit of trial and error, but it works!

Cheers! Nick

Answer 3

I had the same problem. I ended-up overriding default usage field as produced by roxygen from the source code with @usage. E.g. the R source file contains

#' @usage sourceall(dir = getwd(), pattern = ".*\\\\.R", ...)
sourceall <- function( dir=getwd(), pattern=".*\\.R", ... )
{
    blah blah
}

Answer 4

I experienced similar problem with roxygen2 v6.0.1.

# this caused errors in R CMD check (non-ASCII chars)
f <- function(x, y, chr = "\u279B")

# this was ok
f <- function(x, y, chr = intToUtf8(0x279B))

In your case, with the newline character, it should also work:

lineCount <- function(text, sep = intToUtf8(10))

Answer 5

Well, frack me, the comment box escapes backslash characters! I refuse to add to the madness and add backslashes to escape the blackslashes in the perl code which escape the backslashes in the .Rd files which escape the backlashes in R.

Just double all backslashes.

Or hmm code tags:

perl -e 's/("\\\\\|")/"\\\\\\\\\|"/g;' -pi $(find BioGeoBEARS/man -type f)

perl -e 's/("\\\\\+")/"\\\\\\\\\+"/g;' -pi $(find BioGeoBEARS/man -type f)

Yeah that's good.