R devel - May 2009 - S4 method dispatch and namespaces: why is default method selected

Hi,

I ran into the following peculiarity involving S4 method dispatch and
namespaces.

I develop a package which have a namespace and which depends on 'pixmap'
package, which itself does not have a namespace.

Now, in my package I have a class which has a slot for objects from
class "pixmap" and I
want to have a "plot" method for this new class. Not to clutter the
point with
my original code here is a stylized example:


# library(pixmap) # so that the class pixmap is available

# class
setClass("myclass", representation(img="pixmap",
title="character",
other="numeric"))

# method to plot
setMethod("plot", signature(x="myclass",
y="missing"),
function(x, main=x at title, ...)
{
    # plot using the method from pixmap package
    plot(x=x at img, ...)
    title(main=main)
    points(seq(along=x at other), other)
} )


Now, if you try to do this:

library(pixmap)
f <- system.file(file.path("pictures", "logo.ppm"),
package="pixmap")
o <- new("myclass", img=read.pnm(f), title="some title",
other=Inf)
o

# now this works as the plot method for signature x="pixmap"
y="ANY" is
# dispatched correctly
plot(o)



However, when I put all these in a package with Depends field in
DESCRIPTION having: methods, pixmap, and with the following namespace:


importFrom("graphics", "plot")
exportClasses("myclass")
exportMethods("plot")


things stop working (this is from package test):

> f <- system.file(file.path("pictures", "logo.ppm"),
package="pixmap")
> o <- new("myclass", a=read.pnm(f), title="tytul")
> plot(o)
Error in as.double(y) :
  cannot coerce type 'S4' to vector of type 'double'
Calls: plot ... plot -> .local -> plot -> plot.default -> xy.coords
Execution halted



So apparently calling 'plot' dispatches the default method instead of
using the
one from package 'pixmap'. Why?

As far as I understand the documentation and section 10.6 of "Software for
Data
Analysis" the default method should never be selected as far as there are
other
candidates. And there seems to be other candidates, and they seem to be properly
selected if checked using 'selectMethod' (this is from results from
package tests):



> showMethods("plot")
Function: plot (package graphics)
x="ANY", y="ANY"
x="myclass", y="missing"
x="pixmap", y="ANY"

> selectMethod("plot", signature(x="pixmap",
y="missing"))
Method Definition:

function (x, y, ...)
{
    .local <- function (x, y, xlab = "", ylab = "", axes
= FALSE,
        asp = 1, ...)
    {
        x = as(x, "pixmapIndexed")
        X <- seq(x at bbox[1], x at bbox[3], by = x at cellres[1])
        Y <- seq(x at bbox[2], x at bbox[4], by = x at cellres[2])
        image(x = X, y = Y, z = t(x at index[nrow(x at index):1, ,
            drop = FALSE]), col = x at col, xlab = xlab, ylab = ylab,
            axes = axes, asp = asp, ...)
    }
    .local(x, y, ...)
}
<environment: 0x01844e60>

Signatures:
        x        y
target  "pixmap" "missing"
defined "pixmap" "ANY"




> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-pc-mingw32

locale:
LC_COLLATE=Polish_Poland.1250;LC_CTYPE=Polish_Poland.1250;LC_MONETARY=Polish_Poland.1250;LC_NUMERIC=C;LC_TIME=Polish_Poland.1250

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

other attached packages:
[1] pixmap_0.4-9

loaded via a namespace (and not attached):
[1] tools_2.9.0




Thanks in advance!

Best,
Micha?



_________________________
Michal Bojanowski
http://bojan.3e.pl/weblog
http://www.fss.uu.nl/soc/bojanowski
http://www.ifispan.waw.pl/socnierowno

Hi Micha? --

Micha? Bojanowski <michal2992 at gmail.com> writes:
> Hi,
>
> I ran into the following peculiarity involving S4 method dispatch and
> namespaces.
>
> I develop a package which have a namespace and which depends on
'pixmap'
> package, which itself does not have a namespace.
>
> Now, in my package I have a class which has a slot for objects from
> class "pixmap" and I
> want to have a "plot" method for this new class. Not to clutter
the point with
> my original code here is a stylized example:
>
>
> # library(pixmap) # so that the class pixmap is available
>
> # class
> setClass("myclass", representation(img="pixmap",
title="character",
> other="numeric"))
>
> # method to plot
> setMethod("plot", signature(x="myclass",
y="missing"),
> function(x, main=x at title, ...)
> {
>     # plot using the method from pixmap package
>     plot(x=x at img, ...)
>     title(main=main)
>     points(seq(along=x at other), other)
> } )
>
>
> Now, if you try to do this:
>
> library(pixmap)
> f <- system.file(file.path("pictures", "logo.ppm"),
package="pixmap")
> o <- new("myclass", img=read.pnm(f), title="some
title", other=Inf)
> o
>
> # now this works as the plot method for signature x="pixmap"
y="ANY" is
> # dispatched correctly
> plot(o)
>
>
>
> However, when I put all these in a package with Depends field in
> DESCRIPTION having: methods, pixmap, and with the following namespace:
>
>
> importFrom("graphics", "plot")
> exportClasses("myclass")
> exportMethods("plot")
>
>
> things stop working (this is from package test):
>
>
>> f <- system.file(file.path("pictures",
"logo.ppm"), package="pixmap")
>> o <- new("myclass", a=read.pnm(f),
title="tytul")
>> plot(o)
> Error in as.double(y) :
>   cannot coerce type 'S4' to vector of type 'double'
> Calls: plot ... plot -> .local -> plot -> plot.default ->
xy.coords
> Execution halted
>
>
>
> So apparently calling 'plot' dispatches the default method instead
of using the
> one from package 'pixmap'. Why?
Not speaking authoritatively, but plot,myclass,missing-method is
defined in your name space, and so has access only to symbols defined
or imported into the name space. The plot,pixmap,ANY-method is not in
your name space (even though it's on the search path), and so is not
found. Clever of the methods package to keep track of this. I think
the only solution is

  pixmap::plot(x=x at img, ...)

Martin
> As far as I understand the documentation and section 10.6 of "Software
for Data
> Analysis" the default method should never be selected as far as there
are other
> candidates. And there seems to be other candidates, and they seem to be
properly
> selected if checked using 'selectMethod' (this is from results from
> package tests):
>
>
>
>
>> showMethods("plot")
> Function: plot (package graphics)
> x="ANY", y="ANY"
> x="myclass", y="missing"
> x="pixmap", y="ANY"
>
>
>> selectMethod("plot", signature(x="pixmap",
y="missing"))
> Method Definition:
>
> function (x, y, ...)
> {
>     .local <- function (x, y, xlab = "", ylab = "",
axes = FALSE,
>         asp = 1, ...)
>     {
>         x = as(x, "pixmapIndexed")
>         X <- seq(x at bbox[1], x at bbox[3], by = x at cellres[1])
>         Y <- seq(x at bbox[2], x at bbox[4], by = x at cellres[2])
>         image(x = X, y = Y, z = t(x at index[nrow(x at index):1, ,
>             drop = FALSE]), col = x at col, xlab = xlab, ylab = ylab,
>             axes = axes, asp = asp, ...)
>     }
>     .local(x, y, ...)
> }
> <environment: 0x01844e60>
>
> Signatures:
>         x        y
> target  "pixmap" "missing"
> defined "pixmap" "ANY"
>
>
>
>
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-pc-mingw32
>
> locale:
>
LC_COLLATE=Polish_Poland.1250;LC_CTYPE=Polish_Poland.1250;LC_MONETARY=Polish_Poland.1250;LC_NUMERIC=C;LC_TIME=Polish_Poland.1250
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] pixmap_0.4-9
>
> loaded via a namespace (and not attached):
> [1] tools_2.9.0
>
>
>
>
> Thanks in advance!
>
> Best,
> Micha?
>
>
>
> _________________________
> Michal Bojanowski
> http://bojan.3e.pl/weblog
> http://www.fss.uu.nl/soc/bojanowski
> http://www.ifispan.waw.pl/socnierowno
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793