Your suggestions worked ok in the example, but in my case there is yet another
package that implements a plot method.
Now the plotting from within the package works, but plotting from outside the
package, on the console, gives an error as if plot.default is invoked.
> class(myplot)
[1] "gt.barplot"
attr(,"package")
[1] "globaltest"
> plot(myplot)
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' and 'y' lengths differ
Rgraphviz implements a plot method on 2 classes: graph and Ragraph
multtest implements a plot method on 1 class: MTP
globaltest, the package i'm working on, depends on multtest, and suggests
Rgraphviz. Class gt.barplot implements a plot method
the output of showMethods("plot")
> showMethods("plot")
Function: plot, (package graphics)
x="ANY"
x="graph"
x="gt.barplot"
x="MTP"
x="Ragraph"
Rgraphviz has a proper NAMESPACE and I created one for multtest that imports
plot from graphics, and exports plot as a method, because they are not
dependent on each other that does seem ok.
In globaltest I import the plot method from multtest.
How to deal with this.
> sessionInfo()
R version 2.4.0 alpha (2006-09-11 r39258)
i386-pc-mingw32
locale:
LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_MONETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.1252
attached base packages:
[1] "splines" "tools" "methods" "stats" "graphics" "grDevices"
[7] "utils" "datasets" "base"
other attached packages:
Rgraphviz geneplotter GOstats Category hgu95av2 genefilter
"1.11.10" "1.11.8" "1.7.11" "1.5.9" "1.13.0" "1.11.8"
RBGL annotate graph Ruuid GO KEGG
"1.9.9" "1.11.5" "1.11.14" "1.11.2" "1.13.0" "1.13.0"
hu6800 globaltest multtest survival vsn golubEsets
"1.13.0" "4.3.5" "1.11.2" "2.28" "1.11.2" "1.3.1"
Biobase
"1.11.34"
===========================================================
John Chambers wrote:
> Good example.
>
>The basic problem is in the NAMESPACE file:
>
>importFrom(graphics, plot)
>
>But the version of plot() in the graphics package is not a generic function.
>Therefore, when your mpplot() calls it there is no >method dispatch.
>
>You need to import the generic version of plot() from minipkg2 (notice that
>there's a message about creating a new generic for >plot() when you install
>minipkg2).
>
>The line in the NAMESPACE file should be:
>
>importFrom(minipkg2, plot)
>
>In your mini-example, there are some additional steps needed, not directly
>related to the problem & possibly not true in the >real example.
>
>1. minipkg2 also needs a NAMESPACE, in which it imports from methods and
>graphics and exports plot and the class mp2.plot >(example attached).
>
>2. Highly recommended though maybe not required here is to use some form of
>saved image, e.g. by including "LazyLoad:yes" in >the two DESCRIPTION files.
>
>John
Oosting, J. (PATH) wrote:
I use 2 packages that both implement a S4 plot method, where one package
depends on the other (the bioconductor package globaltest which depends
on multtest). When the plot method is used from within the package, it
seems the default plot method is used, and an error is generated. When
the method is invoked from the console, the plot is created correctly. I
have reproduced this with 2 small packages (minipkg and minipkg2)
implementing just this part.
I've seen a thread about a similar problem, but that seemed mostly due
to already installed packages not handling the new S4 stuff.
mpplot() is a function that creates a class instance and (usually)
invokes the plot immediately. When the dependency on minipkg2 is removed
from the DESCRIPTION file the first call to mpplot() gives no error and
shows the plot.
Jan Oosting
library(minipkg)
Loading required package: minipkg2
Creating a new generic function for 'plot' in 'minipkg2'
mpplot(1:10)
Error in as.vector(x, "double") : cannot coerce to vector
plot(mpplot(1:10,plot=FALSE)) # this shows a proper plot
showMethods("plot")
Function: plot, (package graphics)
x="ANY"
x="mp.plot"
x="mp2.plot"
sessionInfo()
R version 2.4.0 Under development (unstable) (2006-09-04 r39086)
i386-pc-mingw32
locale:
LC_COLLATE=Dutch_Netherlands.1252;LC_CTYPE=Dutch_Netherlands.1252;LC_MON
ETARY=Dutch_Netherlands.1252;LC_NUMERIC=C;LC_TIME=Dutch_Netherlands.1252
attached base packages:
[1] "methods" "stats" "graphics" "grDevices" "utils"
"datasets"
[7] "base"
other attached packages:
minipkg minipkg2
"1.0.0" "1.0.0"
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