From t.jombart at imperial.ac.uk  Fri May 21 17:34:26 2010
From: t.jombart at imperial.ac.uk (Jombart, Thibaut)
Date: Fri, 21 May 2010 16:34:26 +0100
Subject: [Rd] S4 method defined but not used
Message-ID: <0B75A6276180B546A1CA8D2B46E7580503362D5194@ICEXM3.ic.ac.uk>

Dear R developers, 

I am having a slightly weird issue with a S4 method defined in my package adegenet 1.2-4, with R 2.11.0. As far as I know, the problem is new, and the code implementing the method has not changed for more than a year and worked well so far.

The problem is the following. I define, in the package, a method "[" for the S4 class 'genind'. The method's definition is:
setMethod("[", signature(x="genind", i="ANY", j="ANY", drop="ANY"), function(x, i, j, ..., loc=NULL, treatOther=TRUE, drop=FALSE) { 
... ## code of the function
})

When sourcing the code directly from R, this method is found and used normally. However, when loading the package, the method does not seem to be "found" any longer by the dispatcher. For instance, here is an error I get:
### R code
> library(adegenet)
> data(nancycats) # nancycat is a S4 object with class 'genind'
> class(nancycats)
[1] "genind"
attr(,"package")
[1] "adegenet"
> nancycats[1]
Error in nancycats[1] : object of type 'S4' is not subsettable # "[" IS NOT USED HERE
### end R code

And still, the method is defined in the environment:
### R code
> showMethods("[", class="genind")
Function: [ (package base)
x="genind"

> findMethods("[", classes="genind")$genind
Method Definition:

function (x, i, j, ..., drop = FALSE) 
{
    .local <- function (x, i, j, ..., loc = NULL, treatOther = TRUE, 
        drop = FALSE) 
    {
        if (missing(i)) 
            i <- TRUE
        if (missing(j)) 
            j <- TRUE
        pop <- NULL

... # rest of the code of the function
### end R code

findMethods and showMethods find the method. However, getMethod doesn't:
### R code
> getMethod("[","genind")
Error in getMethod("[", "genind") : 
  No method found for function "[" and signature genind
### end R code

Now, if I just try the same thing after sourcing the code of the method manually, everything works fine. showMethods then reads:
### R code
> showMethods("[", classes="genind")
Function: [ (package base)
x="genind"
x="genind", i="ANY", j="ANY", drop="ANY"
x="genind", i="numeric", j="missing", drop="missing"
    (inherited from: x="genind", i="ANY", j="ANY", drop="ANY")
### end R code

My R version/session is:
### R code
> R.version
               _                            
platform       i686-pc-linux-gnu            
arch           i686                         
os             linux-gnu                    
system         i686, linux-gnu              
status                                      
major          2                            
minor          11.0                         
year           2010                         
month          04                           
day            22                           
svn rev        51801                        
language       R                            
version.string R version 2.11.0 (2010-04-22)

> sessionInfo()
R version 2.11.0 (2010-04-22) 
i686-pc-linux-gnu 

locale:
 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] adegenet_1.2-4 MASS_7.3-5    

loaded via a namespace (and not attached):
[1] graph_1.26.0  phylobase_0.5 tcltk_2.11.0  tools_2.11.0 

### end R code

R was compiled from the sources. All packages are up-to-date (as of the 21 May 2010). My system is a Ubuntu 10.04 (32 bits), with kernel 2.6.31-20-generic. I could not reproduce the problem using R 2.11.0 on Windows Vista, or on Debian testing (R 2.11.0 compiled from the sources). The package adegenet does not have a namespace. The error arises whether using a field 'Collate' in DESCRIPTION, or not. I checked that the source file is indeed sourced when loading the package: it is. The method "[" is not defined by any other package for 'genind' objects.

I would be pleased to get any piece of insight, advice, or explanation for this issue. Thanks in advance for your time.

Best regards,

Thibaut Jombart.


-- 
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary?s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/



[Rd] S4 method defined but not used
Jombart, Thibaut