[R] Cryptic error with Roxygen

[ONKELINX, Thierry]

Dear all,

I'm using Roxygen for the first time and I'm getting a rather cryptic
error message. I must be doing something wrong but I have no clue what
is it. Any suggestions?

Regards,

Thierry

roxygenize("AFLP", roxygen.dir = "AFLP", copy.package = FALSE,
unlink.target = FALSE)
Writing AFLP.outlier to AFLP/man/AFLP.outlier.Rd
Writing AFLP.outlier to AFLP/man/AFLP.outlier.Rd
Error in col(m) : 
  a matrix-like object is required as argument to 'row/col'

traceback()
14: col(m)
13: split.default(m, col(m))
12: split(m, col(m))
11: zip(c, ...)
10: zip.c(names(formals), formals)
9: parse.formals(partitum)
8: parse.usage(partitum)
7: function (partitum) 
   {
       assign.parent("params", NULL, environment())
       assign.parent("examples", NULL, environment())
       parse.name(partitum)
       parse.usage(partitum)
   }(list(assignee = "AFLP.outlier", formals = list(Replicate =
"data.frame(PC = character(), Replicate = character(), Observed =
numeric())", 
       Specimen = "data.frame(PC = character(), Specimen = character(),
Observed = numeric())", 
       Marker = "data.frame(PC = character(), Marker = numeric(),
Observed = numeric())", 
       Residual = c("data.frame(PC = character(), Replicate =
character(), Marker = numeric(), ", 
       "    Observed = numeric())")), srcref = list(filename =
"AFLP/R/AFLP-outlier.R", 
       lloc = c(26L, 1L, 31L, 1L, 1L, 1L))))
6: do.call(proc, list(...))
5: maybe.call(pre.parse, partitum)
4: roclet$parse.parsed(parse.files(...))
3: function (...) 
   roclet$parse.parsed(parse.files(...))("AFLP/R/AFLP-outlier.R", 
       "AFLP/R/AFLP-package.R", "AFLP/R/as-AFLP.R", "AFLP/R/is-AFLP.R")
2: do.call(Rd$parse, files)
1: roxygenize("AFLP", roxygen.dir = "AFLP", copy.package = FALSE, 
       unlink.target = FALSE)


#content of AFLP-outlier.R

#' Holds the outliers of an AFLP project
#' @method AFLP outlier
#' @param Replicate a dataframe with the name of the primer combination
(PC), 
#' 		the name of the replicate and the observed value of the
outlier
#' @param Specimen a dataframe with the name of the primer combination
(PC), 
#' 		the name of the specimen and the observed value of the
outlier
#' @param Marker a dataframe with the name of the primer combination
(PC), 
#' 		the name of the marker and the observed value of the
outlier
#' @param Residual a dataframe with the name of the primer combination
(PC), 
#' 		the name of the replicate, the name of the marker and
the observed value
#' 		of the outlier
#' @return An object of the AFLP.outlier class
#' @author Thierry Onkelinx \email{Thierry.Onkelinx@@inbo.be}
#' @examples 
#' AFLP.outlier()

setClass("AFLP.outlier",
	representation = representation(Replicate = "data.frame",
Specimen = "data.frame",
		Marker = "data.frame", Residual = "data.frame"),
	prototype = prototype(Replicate = data.frame(PC = character(),
Replicate = character(), Observed = numeric()),
		Specimen = data.frame(PC = character(), Specimen =
character(), Observed = numeric()),
		Marker = data.frame(PC = character(), Marker =
numeric(), Observed = numeric()),
		Residual = data.frame(PC = character(), Replicate =
character(), Marker = numeric(), Observed = numeric()))
)

AFLP.outlier <- function(Replicate = data.frame(PC = character(),
Replicate = character(), Observed = numeric()), 
		Specimen = data.frame(PC = character(), Specimen =
character(), Observed = numeric()), 
		Marker = data.frame(PC = character(), Marker =
numeric(), Observed = numeric()), 
		Residual = data.frame(PC = character(), Replicate =
character(), Marker = numeric(), Observed = numeric())){
	new("AFLP.outlier", Replicate = Replicate, Specimen = Specimen,
Marker = Marker, Residual = Residual)
}


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey


Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer 
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in  this message 
and any annex are purely those of the writer and may not be regarded as stating 
an official position of INBO, as long as the message is not confirmed by a duly 
signed document.