From mtmorgan at fhcrc.org  Wed Dec 11 11:39:52 2013
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Wed, 11 Dec 2013 02:39:52 -0800
Subject: [Rd] Undocumented S4 method Warning For Bracket
In-Reply-To: <ae2b45e5a97f444aaa68bbc850f4b4bd@BLUPR01MB035.prod.exchangelabs.com>
References: <ae2b45e5a97f444aaa68bbc850f4b4bd@BLUPR01MB035.prod.exchangelabs.com>
Message-ID: <52A840F8.1060808@fhcrc.org>

On 12/05/2013 07:00 PM, Dario Strbenac wrote:
> Hello,
>
> With R version 3.0.2 Patched (2013-10-30 r64123) I don't see warnings that I get in R Under development (unstable) (2013-11-03 r64145)
>
> The warnings are like :
>
> Undocumented S4 methods:
>    generic '[' and siglist 'BayMethList,ANY,ANY'
>
> The function actually looks like :
>
> setMethod("[", "BayMethList",
>      function(x, i) {
>    # Code to subset object.
> }
>
> It has 2 parameters, not 3. The warning also happens in R 3.0.2 Release. Has this been fixed in Patched but not in the development version ?
>

Not a complete answer but actually the generic is

 > getGeneric("[")
standardGeneric for "[" defined from package "base"

function (x, i, j, ..., drop = TRUE)
standardGeneric("[", .Primitive("["))
<bytecode: 0x46a54e0>
<environment: 0x4698330>
Methods may be defined for arguments: x, i, j, drop
Use  showMethods("[")  for currently available ones.

and the fact that you've implemented a simpler method signature doesn't change 
the overall signature

 > getMethod("[", "BayMethList")
Method Definition:

function (x, i, j, ..., drop = TRUE)
{
     .local <- function (x, i)
     {
     }
     .local(x, i, ...)
}

Signatures:
         x
target  "BayMethList"
defined "BayMethList"

Notice how your method actually accepts and then silently ignores a 'j' 
argument. A better (?) method definition would be

    setMethod("[", c("BayMethList", "ANY", "missing"),
        function(x, i, j, ..., drop=TRUE) {})

so a user providing a 'j' argument would be told that there was no matching method.

Martin
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>


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[Rd] Undocumented S4 method Warning For Bracket
Martin Morgan