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.jomb...@imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
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