similar to: S4: Initialization method called during setClass??

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,...)

Dear Developers, In current implementation of validity method, objects are first coerced to superclass (slots are striped). Thus, it is not possible to write validity method which would perform some checks on children slots. Say, I want to check if number of slots in a class is equal to "n": setClass("A", representation(a="numeric", n="integer"),

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, 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, 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

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, 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 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

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",

Dear All, A small inconsistency (it's probably not even a buglet): > setClass("A", contains="numeric") [1] "A" > names(new("A", c(a=23))) [1] "a" > setClass("B", contains="A") [1] "B" > names(new("B", c(a=23))) NULL > This is exactly that kind of behavior S4 was invented for, you

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

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

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

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, 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 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 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

Hi all, After all these years, I am finally porting some R-2.3.1-based S4 object code to R-2.6.1, dealing with all the S4 object system changes that came in R-2.4.0. I've run across what appears to be some sort of ommission in the implementation of callNextMethod() when used with primitives having group generic methods. In a stock R-2.6.1 patched (happens to be running on AMD64/RHEL 4, but

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") +