similar to: Extract callNextMethod "array" calls "matrix"?

Hi, Given a simple three class hierarchy: A <-- B <-- C I want to define an initialize method for each class such that when I call new("C", x=5), the initialize methods for A and B are used to incrementally build the object. When I do what seems obvious to me using callNextMethod, I get an infinite recursion. An example follows... setClass("A",

Hi, I don't understand why this code doesn't work (f(b2)): ///////////////// setClass("B0", representation(b0 = "numeric")) setClass("B1", representation("B0", b1 = "character")) setClass("B2", representation("B1", b2 = "logical")) f <- function(x) class(x) setMethod("f", "B0",

I don't understand why I get the following results. I define two classes 'Base' and 'Derived', the latter of which 'contains' the first. I then define a generic method 'test' and overload it for each of these classes. I call 'callNextMethod()' in the overload for Derived. From the output, it appears that the overload for Base gets called twice. Why is

Hi, there seems to be a possible bug in callNextMethod in conjunction with the [-operator. Relevant info, minimal example and sessionInfo follow below: ############################### setClass("foo", representation = representation(a = "numeric")) setClass("bar", contains = "foo") setMethod( f = "[", signature =

Hello, I experienced a strange behaviour of callNextMethod when used in either initialize or any other S4 function method definition. Help says callNextMethod calls the next inherited method for the current function from where it is called with the same actual (non missing) arguments. This is OK. The problem appears when some formal arguments (in particular, S4 objects) of this function are

Hi, Strange things happen. Here is a simple example: > setClass("A", contains="integer") > setMethod("as.matrix", "A", function(x, ...) t(callNextMethod())) Creating a generic function for ?as.matrix? from package ?base? in the global environment [1] "as.matrix" > a <- new("A", 1:3) > as.matrix(a)

Dear UseRs, Does anyone know when exactly the validity is checked in S4? Documentation is silent:(. Here is a small example: setClass("test1",representation(a="numeric")) setMethod("initialize","test1", function(.Object,...){ a<-runif(1) ## here slot "a" is initialized ## callNextMethod(.Object,a=a,...)

Can someone explain what the problem is when I use the generating function? And how to get debug() to stop in the Superclass initialize method? ---- source ----- setClass("Superclass", representation(id = "character"), contains = "VIRTUAL") setMethod("initialize", signature(.Object = "Superclass"),

Hi all, It seems that there is a use case for obtaining the environment for the "top" promise. By "top", I mean following the promise chain up the call stack until hitting a non-promise. S4 data containers often mimic the API of base R data structures. This means writing S4 methods for functions that quote their arguments, like with() and subset(). The methods package

Hi R-Help, Please consider the following simple case: I have a class like setClass("myClass", representation(x="matrix", y="character")) and I would like to use the method *"["* for a *myClass* objects (but changing the default *drop* argument from TRUE to FALSE): setMethod("[","myClass", function(x,i,j,...,drop=FALSE)

Dear all, I am just writing the documentation file for S4 class 'QualTreeSet' and get the following warning with R CMD check: * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic 'initialize' and siglist 'QualTreeSet' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See the

Hi again, Here is a very simplified version of a class hierarchy defined in the Biobase package (Bioconductor). I post here because this seems to be an S4 related problem: setClass("A", representation(name="character")) setMethod("initialize", "A", function(.Object) {.Object at name <- "I'm an A"; .Object})

Hi the list, I try to use callNextMethod in a setteur ([<-) but it does not work. Any raison ? Any other option ? --- 8< ------------------ ### Class B0 ### setClass("B0" , representation(b0 = "numeric")) setReplaceMethod("[","B0",function(x,i,j,value){x at b0 <- -value}) a <- new("B0") a at b0 <- 3 a a["b0"] <- 3 a

Dear all, Maybe, I am doing something wrong, but using R-2.5.0 on my Intel-Mac, I have problems using function callNextMethod() in method initialize. I am loading the following code as file "testS4.R": setClass("baseClass", representation(myname = "character", mydir = "character", "VIRTUAL"),

I feel tedious when I define a S4 class and the methods. For each method, I have to call both setMethod and setGeneric (or both setReplaceMethod and setGeneric). I would like a more compact grammar so that I can reduce the key strokes. I'm wondering if there is a better way available. setClass( Class='A', representation=representation( x='numeric' )

Dear all Below is the code for "scriptPreFilter.R" which gives the following result: > source("scriptPreFilter.R") > prefltr <- new("PreFilter", mad=c(0.5,0.01)) [1] "------initialize:PreFilter------" [1] "------initialize:Filter------" > str(prefltr) Formal class 'PreFilter' [package ".GlobalEnv"] with 2 slots

Hello R users, I am trying to make a my first package and I get an error that I can understand. The package is build out of three files (one for functions, 1 for s4 classes and 1 for s4 methods). Once I source them I run package.skeleton( name="TDC" ) within a R session and I get Creating directories ... Creating DESCRIPTION ... Creating Read-and-delete-me ... Saving functions and

In the following code, 'multiply' doesn't multiply a at x by 2. I'm wondering how to define a method that can change the slot of a class. $ Rscript setGeneric.R > setClass( + Class='A', + representation=representation( + x='numeric' + ) + ) [1] "A" > > setMethod( + f='initialize', +

Hi, I recently ran into this problem. I couldn't find any mention of it in the setClass documentation. setClass("Foo", representation(file = "character")) setMethod("initialize", "Foo", function(.Object, file) { print(file) }) setClass("Bar", contains = "Foo") And the error: Error in print(file) : argument "file" is

Dear R-users, I am working on a project that uses S4-classes. At some point I encountered the problem - well known to R - that I have to pass 3 different objects to a function, that should modify several slots of them and of course there is no passing by reference in R. Then I read this thread by Steve Lianoglou: https://stat.ethz.ch/pipermail/r-help/2010-August/250468.html, which offers from