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([EMAIL PROTECTED], collapse = "x"),
"\n")
cat(" Resolution :", paste([EMAIL PROTECTED], collapse = "x"),
"\n")
cat(" Bounding box :", [EMAIL PROTECTED], "\n")
if (is(object, "pixmapIndexed"))
cat(" Nr. of colors :", length(unique(as([EMAIL PROTECTED],
"vector"))), "of", length([EMAIL PROTECTED]), "\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
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