similar to: S4: When is validObject issued? (or why S4 is killing me:( ..

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"),

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"),

Hi all, I am having trouble extending S4 classes in cases where I'm using both validity and initialize methods. I've read as much S4 information as I can find, but I've yet to have that "a-ha" moment. In my application, I am using validity methods to guard against inappropriate input data that my code has no way of handling, and initialize methods to detect and deal

Dear useRs and wizaRds, I am currently developing a set of functions using S4 classes. On the way I encountered the problem exemplified with the code below. For some reason the 'validity' method does not seem to work, i.e. does not check for errors in the specification of the slots of the defined class. Any hints? My understanding of the whole S4 system was that validity checks are made

I thought that 'validity' defined in 'setClass' should be called in 'new'. Could somebody let me know why 'validity' is not called? How to make it be called? > setClass( + Class='A', + representation=representation( + x='numeric' + ), + validity=function(object){ + cat("~~~ A: inspector ~~~\n") +

Dear UseRs, A simple class inheritance example: > setClass("test",representation(a="numeric")) > setMethod("initialize","test", function(.Object,x,...){ print("Initialization!!!") callNextMethod(.Object,a=x,...) }) > new("test",x=23) [1] "Initialization!!!" An

Hello list, I'm having troubles setting up a basic calss hierarchy with S4. Here is a simplified schema of what I'd like to do: - Two classes: A and B that extends A - Ensure that the slots added by B are consistent with the slots of A - Let A initialize itself (I'm not supposed to know the internal cooking of A) - By default set the slots of B based on the slots that A initialized

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",

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

Hi the list. I try to learn the S4 programming. I find the wiki and several doc. But I still have few questions... 1. To define 'representation', we can use two syntax : - representation=list(temps = 'numeric',traj = 'matrix') - representation(temps = 'numeric',traj = 'matrix') Is there any difference ? 2. 'validityMethod' check the

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

Hi all, After an upgrade from R_2.10.1 to R_2.11.1 I am now getting the following error: Error: evaluation nested too deeply: infinite recursion / options(expressions=)? This occurs in the initialize method of S4 classes where I was initialising attributes eg: .Object[['realtimeState']] <- list() I can avoid this new error by altering the code to do: .Object$realtimeState <-

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

Hello, Thomas Stabla (statho3@web.de) has already sent this question to R-help, Wed, 12 Nov 2003 21:21:31 +0100, but we are not sure whether we should better post this mail to this audience than to R-help: --------------------------------------------------------------------- We are using S4-classes and want to force a validity check when an object is created. How can this be done, when an

Suppose you have a class, say sex, for lack of a better example, and you are tempted, in defining the behavior of the call, is(x,"sex") to check whether certain basic features are satisfied, not to just trust the claim that x is specified to be of class "sex". `Without delving into details further sanity checking of the structure of the object is sometimes prudent to avoid

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, 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)

I have a class that extends array and my method for "[" stops with an error: > setClass("A", contains="array") [1] "A" > setMethod("[", "A", function(x, i, j, ..., drop = TRUE) new("A", callNextMethod())) [1] "[" > a<-new("A",array(1:12,c(4,3,1))) > a An object of class "A" , , 1

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

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",