[Bioc-devel] Fwd: Question about a package submission

[Ioannis Vardaxis]

Ioannis Vardaxis
Stipendiat NTNU
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Fra: "bioconductorseattle at gmail.com<mailto:bioconductorseattle at gmail.com>" <bioconductorseattle at gmail.com<mailto:bioconductorseattle at gmail.com>>
Dato: 26. oktober 2016 kl. 00.55.14 CEST
Til: Ioannis Vardaxis <ioannis.vardaxis at math.ntnu.no<mailto:ioannis.vardaxis at math.ntnu.no>>
Emne: Re: Question about a package submission

On 10/25/2016 06:52 PM, Ioannis Vardaxis wrote:
Hi,

I have a problem documenting multiple functions in one rd file using
roxygen2. I tried to find the solution on the internet with no results.
I have for example 2 plot functions for class1 and class2 and I want to
make a plot-method.R as the Bioconductor guideline suggests.

What I have in the plot-method.R is the following code:

Please ask questions about Bioconductor package development on the bioc-devel mailing list.

https://stat.ethz.ch/mailman/listinfo/bioc-devel

Martin


#' @title Plot methods
#' @author ...
#'
#' @references ...
#'
#' @description something
#' @param x An x of correct class.
#' @param ... something
#'
#' @seealso something
#'
#' @rdname plot
#  @export plot
#' @include AllClasses.R #this where class1 and class2 are defined.
#?#'?packages I need
#' @importFrom plyr ddply . ldply laply
#' @importFrom utils methods
#' @importFrom S4Vectors metadata

#define the plot function which is in base in R:
plot <- function(x, ...){
   UseMethod("plot")
}


#define the other plot function for my classes:
#?class1
#' @rdname plot
#' @method plot class1
#' @return something
#' @export
plot.class1=function(x,...){
   code
}
#?class2
#' @rdname plot
#' @method plot class2
#' @return something
#' @export
plot.class2=function(x,...){
   code
}



When I generate with roxygen I am then able to write ??Mypkg::plot and I
get nice rd files. However when I try to use plot for an x object of
class1 or class2 then I get the following error:
Error in as.vector(x, mode = "numeric") :
 no method for coercing this S4 class to a vector


If on the other hand I remove the first code:
plot <- function(x, ...){
UseMethod("plot")
}


Then I am able to run the plot functions correctly with no error, but then
in the help in R I have to write ??Mypkg::plot.class1 and the main
S3method is plot.class1.
How can I solve this in a way that I write ??Mypkg::plot and get all the
methods in one script and at the same time the plot.class1,2 work properly?






Best,
Ioannis


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