similar to: Pb with .findInheritedMethods

I am extending a DBI connection by setClass("TSPostgreSQLConnection", contains=c("PostgreSQLConnection","TSdbOptions")) but the first time I use this I am getting a warning when it tries to coerce the TSPostgreSQLConnection to a PostgreSQLConnection. After the first use the warning stops, but the first warning is causing me problems when I do automatic checks

Hello everybody R version 2.4.0 alpha (2006-09-15 r39323), MacOSX 10.4.7 Next S4 problem. I have "brob" objects that are large real numbers, and now I want "glub" numbers that are to be a pair of glubs that represent complex numbers. I want to define binary operator "+" so that if either the left or right argument are glubs, it uses .ArithGlub. If either

Hi, I got the following error. Sorry but this time I couldn't reproduce it with a simple chunk of code: .TM.repl.i.2col(): drop 'matrix' case ... Error in .nextMethod(x = x, i = i, j = j) : 'i' has no integer column number should never happen; please report In addition: Warning messages: 1: Ambiguous method selection for "%*%", target

Hi, I am having some trouble using R 2.13.1 for generating a pmml object of of class "c('randomForest.formula', 'randomForest')" I see that these methods are available: > methods(pmml) [1] pmml.coxph* pmml.hclust* pmml.itemsets* pmml.kmeans* pmml.ksvm* pmml.lm* pmml.multinom* pmml.nnet* pmml.rpart* [10] pmml.rsf* pmml.rules* pmml.survreg*

Hi list, I've got a class B that contains a slot obj of class A. I'd like to be able to call all the methods of class A directly on objects of class B as if I had called the method on slot obj. This without overloading all methods of class A to work on class B. I don't define B as an extension of A, because I want class B to also work with objects of classes that inherit from

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",

Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

I am new to using S4 methods and have run into this problem (on Windows XP using R 2.4.1): I am writing a package in which I use the graph package. I define my own classes of graphs as: setOldClass("graphsh") setOldClass("ugsh") setIs("ugsh", "graphsh") (I know that I "should have" used setClass instead - and I will eventually - but right now

I have an S4 object extending "function". Is it there a good way to access the object (resp. its slots) from within the function in .Data? If I'm reading help files correctly, it is not possible to overload '(' (which would be the most elegant solution, I suppose). I can enclose the slotted data in the function when it is created, but that obviously doesn't work when

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 am having difficulty defining an S4 method for head() and tail(). I can't quite provide minimal self-contained code because the problem appears to require the whole corpus of my package; and there also appears to be a difference between sourcing the lines directly, and having them installed in a package. The lines in question (I think) are: setClass("mdm",

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

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

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 =

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,...)

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)

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