similar to: S4 Methods dispatch

Hi, I encounter a problem with method dispatch with S4 classes, using the 'sealed' parameter in setClass. See that example below: setClass("X",representation(x="numeric"),sealed=TRUE) setGeneric("foo",function(x) standardGeneric("foo")) setMethod("foo",signature("X"),function(x) print("foo(X)")) x <-

What a delicious example! (I'm taking the liberty of sharing it with r-devel, since it raises some good issues.) You have two questions, presumably: 1 - how could the order of the setMethod calls make a difference in the results? 2 - what's causing the infinite loop & how could it be avoided, reliably? Second question first. The danger sign is the "vector" method:

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

I use 2 packages that both implement a S4 plot method, where one package depends on the other (the bioconductor package globaltest which depends on multtest). When the plot method is used from within the package, it seems the default plot method is used, and an error is generated. When the method is invoked from the console, the plot is created correctly. I have reproduced this with 2 small

Hello, I'm trying to get S4 dispatch on S3 "connection" objects. So I do : setOldClass( "connection" ) and then : setGeneric( "bling", function(object) standardGeneric( "bling" ) ) setMethod( "bling", "connection", function(object) cat( "gotcha ", as.integer(object), "\n" ) ) but I get : f <- file(

Hello, I'm trying to make .DollarNames generic and implement a method for it in a package. .DollarNames is the function that is now called to get completion possibilities. My R code looks like this: setGeneric( ".DollarNames" ) setClass("track", representation(x="numeric", y="numeric")) ## A class extending the previous, adding one more

Dear list, is it possible that method dispatch checks for superclasses/virtual classes before checking "ANY"? I'd like to build a generic initialization method for all my Reference Class (say "MyDataFrame") objects by having them inherit from class, say "MyRefClassVirtual" (which would have to be a virtual S4 class; there are no virtual Reference Classes,

Hello, This problem originally surfaced as an interaction between 'brms', 'rstan' and 'Rcpp' [1]: a call to dimnames() from the 'brms' package on an object of an S4 class owned by the 'rstan' package tried to load its namespace. rstan:::.onLoad needs to load Rcpp modules, which uses load actions and reference classes. Since methods:::.findInheritedMethods

Hello, I am writing an interface to some functions from the CRAN package pamr, which is poorly written. I have a S4 method I declared with setMethod. I'd like to provide a signature of "pamrtrained" which is the class of object that training creates. The last two lines of code of pamr.train are : class(junk) = "pamrtrained" junk How can I dispatch on these kinds

>>>>> Ivan Krylov via R-devel >>>>> on Fri, 27 Sep 2024 13:32:27 +0300 writes: > Hello, > This problem originally surfaced as an interaction between 'brms', > 'rstan' and 'Rcpp' [1]: a call to dimnames() from the 'brms' package on > an object of an S4 class owned by the 'rstan' package tried to

I have been running into difficulties with dispatching on an S4 class defined in the SparseM package, when the method calls are inside a function passed as the f= argument to optimize() in functions in the spdep package. The S4 methods are typically defined as: setMethod("det","matrix.csr", function(x, ...) det(chol(x))^2) that is within setMethod() rather than by name before

Hi all, I recently encountered some unexpected behavior with S4 generics dispatching on `...`, which I described in http://stackoverflow.com/questions/43499203/use-callnextmethod-with-dotsmethods TL;DR: `callNextMethod()` doesn't work in methods dispatching on `...`, and arguments of such methods are resolved differently than the arguments of methods dispatching on formal arguments. Could

Hi, after updating R 2.5.0 devel yesterday we today observed many new unexpected failures in our daily package build and test system runs, which can be traced to recent changes in the implementation in try() (as noted in NEWS). Investigating this new implementation I come across an issue in conjuntion with using S4 classes and methods. try(expr) does not return an object with attribute

Hello, I've been attempting to make a generic method that dispatches on the first argument, which can be either an S3 or an S4 class. This is as far as I've gotten. Any suggestions about what to try next ? library(aroma.affymetrix) library(GenomicRanges) setGeneric("analyse", function(x, y, ...) standardGeneric("analyse")) setMethodS3("analyse",

Hi, I'm trying to create a new S4 class (myMatrix) which for now just extends dgCMatrix (from package Matrix). Then I want to use "[" which is defined in Matrix. Out of the box with "[" (defined in Matrix) I lose the class information and the result is an object of class dgCMatrix. If I specify a "["-method for myMatrix, it is not used because a signature

Loading an S4 object from a file without first loading the library sometimes (?, the example below and actual example involves a virtual base class and the show generic) leads to incorrect dispatch (to the base class method). The attached package reproduces the problem. It has setClass("A") setClass("B", contains="A") setMethod("show", "A",

If I have a class Foo, then i can write an S3 method for sum for it: >setClass("Foo",representation(a="integer"));aFoo=new("Foo",a=c(1:3,NA)) >sum.Foo <- function(x,na.rm){print(x);print(na.rm);sum(x at a,na.rm=na.rm)} >sum(aFoo) But how do I write an S4 method for this? All my attempts to do so have foundered. For example

Hi all, I am having a little problem with S4 group generics (apologies if I get some terminology wrong below). I'm finding I can set methods for some group generic functions, but not others: > setClass("foo", representation(data="numeric")) > x <- new("foo", data=1:10) ## Setting "Ops" works just as expected: > setMethod("Ops",

Hi, I ran into the following peculiarity involving S4 method dispatch and namespaces. I develop a package which have a namespace and which depends on 'pixmap' package, which itself does not have a namespace. Now, in my package I have a class which has a slot for objects from class "pixmap" and I want to have a "plot" method for this new class. Not to clutter the

In this post https://stat.ethz.ch/pipermail/bioc-devel/2013-March/004152.html a package author reports that S4 dispatch fails. I can reproduce this with a PkgA (attached; 'intervals' is a relatively light-weight CRAN package) that has DESCRIPTION with Depends: intervals Imports: graphics NAMESPACE: importFrom(graphics, "plot") export("plot")