similar to: S4-based package failure: setGeneric example#1

Nevermind, I figured out my problem after looking at the packS4 package. I didn't realize that package.skeleton would build invalid R code. The warning hints at that, but I interpreted the warning to mean that the package.skeleton-generated code should be *edited*, and none of my edits gave me a workable package. Now I realize that the S4-driven code from package.skeleton can simply be

I created some S4 objects that are essentially data frame objects. The S4 object definitions were necessary to verify data integrity and force a standardized data format. I am, however, finding myself redefining all the typical generic functions so that I can still manipulate my S4 objects as if they were data frames ... I have used setMethod to set methods for "subset",

PkgA wishes to write a method for 'unique' on S4 class 'A'. ?Methods indicates that one should setGeneric("unique") setClass("A") unique.A <- function(x, incomparables=FALSE, ...) {} setMethod(unique, "A", unique.A) Both S3 and S4 methods need to be exported in the NAMESPACE import(methods) S3method(unique, A)

Hi R version 2.4.0 alpha (2006-09-06 r39158) MacOSX 10.4.7 There was a thread some time ago as to whether the structure created by package.skeleton() would pass R CMD check. I have an example where package.skeleton() gives an R file that gives an error when sourced. If I type setClass("brob", representation = representation

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:

Hello everyone. R-2.12.0, suse linux 11.3. I am debugging a package that uses S4 methods and R CMD check gives the following warning: > Warning in methods::findMethods(g, env) : > non-generic function 'mdm' given to findMethods() > See the information on DESCRIPTION files in the chapter 'Creating R > packages' of the 'Writing R Extensions' manual. I

Hi, We are developing a package using S4 classes. The S4 classes are wrappers to C++ classes. So S4 classes contain an integer that is the memory address of one C++ object. If an user calls the rm() function, the C++ object must be deleted. But our generic rm() function apparently doesn't work. Here is the code: # The class setClass("component",

I'm experimenting with a few model-fitting classes of my own. I'm leaning towards using S4 for my classes, but the R functions I'd want to override (residuals, predict, etc.) are all S3 methods. As I understand it, I could do setGeneric("residuals"), then add S4 specializations to it. However, I don't understand the full consequences of doing this. Are there any

Hello developeRs, Apologies in advance for a rather long email, but to describe the problem, I need to step through many details. I have been working on a new dispatching system (futile.paradigm on CRAN) based on functional programming concepts that is an alternative to S3 and S4 dispatching. I use a declarative syntax using guard statements to control the dispatching between function variants. I

My question has two parts. The first is with regard to the frame or environment in which generic functions are defined in packages. It seems as though they are defined (i.e. exist as objects) in frame 1, even when defined in a package. The following is a short example: setClass("track",representation(x="numeric",y="numeric")) plotTrack <- function(x,y,...)

Some quick questions about S4 methods. Does the typing of S4 methods mean that lazy evaluation is no longer possible? It seems that you would need to evaluate the arguments to determine their type at dispatch. Second, what role, if any, do default arguments play in S4 methods? I notice that you can put default arguments into generics but that the dispatch is still done on the type of the

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' )

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

Dear List Members, I'm struggling with the documentation of a generic S4 replacement method. I've created a S4 method "lows" via setGeneric("lows", function(object) standardGeneric("lows")) setGeneric("lows<-", function(object, value) standardGeneric("lows<-")) setMethod("lows", "myClass", function(object) {

Thank you Michael for updating the 3.4 branch, the `callNextMethod()` now works for `...` methods as expected. However, I'm still missing your other patch fixing the handling of arguments in `...` methods. It would be really great if this bugfix could be integrated into the 3.4 branch as well, such that the following code doesn't result in an error. Cheers, Andrzej f = function(x,

The problem is not specific to redefining the q function, but to the interaction of assignInNamespace and setGeneric. The latter requires, roughtly, that the environment of the function being replaced by an S4 generic is (or is the descendent of) the environment in which it lives. E.g., the following demonstrates the problem % R --quiet --vanilla > assignInNamespace("plot",

I've installed R-devel R Under development (unstable) (2014-07-09 r66111) Platform: x86_64-apple-darwin13.1.0 (64-bit) and am trying to resolve some problems that I am seeing with my SparseM package. In prior versions I explicitly had: setGeneric("image", function(x, ...) standardGeneric("image")) and then used setMethod to define a method for the class matrix.csr but

I have encountered an issue which I have been unable to resolve, involving an S3 generic (print) being declared S4 generic in a package, and the method being exported. This all works fine - the problem occurs when I try to import the method to another package. Here is the bit that works fine. ------------- #the .r file for package bar

Hello all, I'd like to report a problem related to S4 classes. Platform: Mac G4/400 PCI (PPC-architecture) Mac OS 10.4.8 R 2.4.1 for Mac OS X (CRAN binary, 2006-12-19) w/ R.app 1.18 Last December, Simon Urbanek confirmed that the issue is not platform related, and that it is most likely a bug. He suggested to post my report to "the appropriate mailing list" -- I choose r-devel.

Hi the list I am creating a package and I have a problem to define a S4 method for plot. I define a class 'A' and a class 'B'. I want to define a function plot for signature c(A,missing) and another method plot for signature c(A,B). My code is the following : In /package/R/ directory: --- main.R --- setGeneric("plot",function(x,y,...){standardGeneric("plot")})