[Bioc-devel] problem with S4 class/methods documentation

[mattia pelizzola]

Hi,

I have a warning on the check report of my package MEDME (BioC 2.3
devel) that I do not know how to deal with. I can't reproduce the same
warning on my computer so it is difficult test possible solutions as I
continuously have to wait for the online update. This warning is
consistent over all the tested OSs:

* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'MEDMEset,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.


Unfortunately, I have no idea what the " siglist
'MEDMEset,ANY,ANY,ANY' " refers to.

Regarding the "[" method, here are some extracts from my MEDMEset-class.Rd file.
I already included an alias for the "[" method:

\name{MEDMEset-class}
\docType{class}
\alias{MEDMEset-class}
\alias{[,MEDMEset-method}
.....



as well as the method description:

......
\section{Methods}{
  \describe{
    \item{[}{\code{signature(x = "MEDMEset")}: subsets the object
based on its probes and/or samples}
.......


I used the promptClass function to generate a first version of this Rd
file. I did not use the promptMethods function though, and it is not
clear to me when to use it.

Many thanks for any advice,

mattia