[Rd] Problem with S3 to S4 transition

From: Renard Didier <didier.renard_at_mines-paristech.fr>
Date: Tue, 16 Mar 2010 13:26:09 +0100


Hello to everybody

I am developing a package using R and have the following problem:

I used to work in a mixture of S3 and S4 mechanism environment: as a matter of fact, I used to define my classes (say "DB" for illustration) using the setClass function (with representation field), and I was using the S3 implicit mechanism writing the functions: print.DB and plot.DB.

Recently, I read some interesting papers on the use of S4 mechanism and was convinced that I would have some benefit in turning everything on S4 formalism.
This is the reason why I simply renamed my previous functions into DB.print and DB.plot (by analogy with other functions where the Class name is the leading part of the name). My idea was to use the setMethod principle to set the DB.print function as the function for the "print" method on the "DB" class.
Therefore, in the .First.Lib file of my package, I introduced the setMethod line just after the setClass one, as in the following example:

    setClass("DB",

        representation(flag.grid = "logical", ndim = "numeric",
        x0 = "numeric", dx = "numeric", nx = "numeric",
        locators ="character",items = "data.frame"))
    setMethod("show","DB",function(object) DB.print(object))
    setMethod("print",signature(x="DB"),function(x,...) DB.print(x))
    setMethod("plot",signature(x="DB"),function(x,y,...) DB.plot(x))
    setMethod("["  ,signature(x="DB"),db0.getindex)
    setMethod("[<-",signature(x="DB"),db0.setindex)
    setMethod("$" ,signature(x="DB"),db0.get)     setMethod("$<-",signature(x="DB"),db0.set)

As one can notice, I use the same mechanism for SHOW, PLOT and PRINT. Finally I created the package and imagined to use it using library statement

Surprisingly, when I used the library statement, the program tells me:
> standardGeneric for "print" defined from package "base"
> standardGeneric for "plot" defined from package "base"
and creates two objects in the .GlobalEnv, namely "plot" and "print" with the following contents:

> print

standardGeneric for "print" defined from package "base"

function (x, ...)
standardGeneric("print")
<environment: 0xa275c70>
Methods may be defined for arguments: x
Use showMethods("print") for currently available ones.

Nothing similar for "show" although my use of setMethod is the same.

I see a main difference as "show" belongs to the "methods" library whereas the two other belong to the "base" library. Bu t I could not see how to avoid a user of my library to have these message and the two objects created.

I am allowed to set the method as I did (I think that I read something telling me that I could not do it with methods of the "base" library). Otherwiser how can I define the function DB.print as the required method for printing objects belonging to the "DB" class.

Thank in advance for you help.

-- 
Didier RENARD
Centre de Geosciences / Geostatistique
Ecole des Mines de Paris
35 Rue St Honore
77300 Fontainebleau

Tel: (1) 64 69 47 80
Fax: (1) 64 69 47 05


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