seeing an S4 method, not using it
Hi Thibaut -- The short answer seems to be that this is fixed in the devel implementation of S4 (at least, my effort at reproducing this was successful in 2.7 but not R version 2.8.0 Under development (unstable) (2008-05-22 r45762)). I think it is like this http://tolstoy.newcastle.edu.au/R/e2/devel/07/09/4469.html My understanding of the problem is that when the object is read in the necessary package is 'load'ed but not 'attach'ed -- R knows about the class definition, etc, but methods and functions from the package are not on the search path, i.e., after reading your data object, the result of search() does not contain the package. When you 'show' your object, S4 tries to find an appropriate method, but does not. So it uses the default, and makes a note that your object should be printed with that. After printing, showMethods('show') will indicate that your object has a 'show' method inherited from 'ANY'. Unfortunately, if you now load the package, nothing good happens -- the appropriate show method is available, but S4 thinks that it already knows a method for your object (the 'ANY' method) so does not find your version. Confusing, isn't it? Martin
Thibaut Jombart wrote:
Dear list, here is a problem I met when trying to use a method for an S4 object, without loading the package in which the method was defined. I do not know if this is a bug, or a mistake of mine. Normally, I think the package in which the appropriate method is defined is loaded automatically when calling the method. The problem is that if the package is indeed loaded automatically, the appropriate method is not used. An example using the package pixmap (but I obtained similar results with S4 objects from adegenet and phylobase packages): ##### in one R session
> library(pixmap)
> foo <- new("pixmap")
## here the object is printed with the appropriate show method.
> foo
Pixmap image Type : pixmap Size : 0x0 Resolution : 0x0 Bounding box : 0 0 0 0
> setClass("myClass", contains="pixmap") # used later
[1] "myClass"
> foo2 <- new("myClass")
## show is ok too
> foo2
Pixmap image Type : myClass Size : 0x0 Resolution : 0x0 Bounding box : 0 0 0 0 save.image() ##### after closing R and starting a new session, loading the .RData ##### (pixmap is not loaded)
> foo
Loading required package: pixmap ## <-- pixmap loaded automatically An object of class ?pixmap? Slot "size": [1] 0 0 Slot "cellres": [1] 0 0 Slot "bbox": [1] 0 0 0 0 Slot "bbcent": logical(0) ## the object is not printed correctly. Yet:
> getMethod("show","pixmap")
Method Definition:
function (object)
{
cat("Pixmap image\n")
cat(" Type :", class(object), "\n")
cat(" Size :", paste(object at size, collapse = "x"),
"\n")
cat(" Resolution :", paste(object at cellres, collapse = "x"),
"\n")
cat(" Bounding box :", object at bbox, "\n")
if (is(object, "pixmapIndexed"))
cat(" Nr. of colors :", length(unique(as(object at index,
"vector"))), "of", length(object at col), "\n")
cat("\n")
}
<environment: 0x89b0e38>
Signatures:
object
target "pixmap"
defined "pixmap"
More surprisingly, the printing of foo2 is correct:
> foo2
Pixmap image Type : myClass Size : 0x0 Resolution : 0x0 Bounding box : 0 0 0 0 Plus, detaching the package pixmap and re-loading it did not help. I tried to trace the show method to get an idea of what was going on, but 'tracing' the problem, solved the problem (!). I used:
> trace("show",browser, signature="pixmap")
> foo
Tracing structure(function (object) .... on entry Called from: eval(expr, envir, enclos) Browse[1]> Pixmap image Type : pixmap Size : 0x0 Resolution : 0x0 Bounding box : 0 0 0 0
> tracingState(FALSE) > foo
Pixmap image
Type : pixmap
Size : 0x0
Resolution : 0x0
Bounding box : 0 0 0 0
Running debug on trace, I found that the correct show method was used
after this command line:
methods::.TraceWithMethods("show", browser, signature = "pixmap", where
= .GlobalEnv)
But I admit I did not go much further in .TraceWithMethods.
I did not find related topics among known bugs (S4methods section), yet
I found this possibly related topic:
http://tolstoy.newcastle.edu.au/R/e2/devel/07/05/3111.html
but this did not give me an answer.
Is this a normal behaviour?
Here is my sessionInfo (second session):
> sessionInfo()
R version 2.7.0 (2008-04-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] datasets utils stats graphics grDevices methods base other attached packages: [1] pixmap_0.4-7 ade4_1.4-8 MASS_7.2-42 loaded via a namespace (and not attached): [1] tools_2.7.0 My OS is an Ubuntu 8.04 for 32bits systems. Thanks in advance. Best regards, Thibaut.
Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793