similar to: S3 generic/method consistency issue with R CMD check

i believe the following is true but would appreciate confirmation that it is intended behavior and will continue: if a default argument is employed in the definition of a generic function, and the generic is called with the argument in question (call it 'ARG') missing, then the method for signature (..., ARG = "missing", ...) will be called by 'standardGeneric'

please see the code below. foo2 fails to dispatch correctly, but foo does fine. i have tried 'cacheMetaData(1)' and a number of different variants of 'cacheGenericsMetaData', on the possibility there is a caching issue. but i still can't sort it out. also one general question: does it really matter what's in the body of the function definition in a

Hello. This question concerns the Methods package. I have created a new class and am trying to set a method for it for S4 group generic "Summary". I have run into some signature problems. An example: > setClass("track", representation(x="numeric", y="character")) [1] "track" > setGeneric("max", group="Summary")

Hi, I define a generic function that has many parameters (~20). I then want to define methods for the generic function with setMethod. The default behavior for setGeneric is to allow dispatching on any argument in the def function, expect ... For example, # define a generic function setGeneric("test", useAsDefault=FALSE,

I'm hoping that someone with deeper insight into S4 than I, that is to say virtually everyone reading this list, could help resolve the following problem in SparseM. We have setGeneric("backsolve", function(r, x, k = NULL, upper.tri = NULL, transpose = NULL, twice = TRUE, ...) standardGeneric("backsolve"), useAsDefault= function(r, x,

Hi I want to create a new generic method, but I end up with an error (evaluation nested too deeply). see the transcript below. The function beginYear.Fun() works, but not beginYear. I have no idea why. Any ideas welcome, Rainer > setClass("fun", representation(x = "numeric")) [1] "fun" > new("fun") An object of class ?fun? Slot "x":

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",

Full_Name: Bert Gunter Version: 2.1.1 OS: Windows 2000 Submission from: (NULL) (192.12.78.250) There appears to be either a bug or documentation problem in setMethod/setGeneric with how default arguments are handled. The setMethod Help says: ****** Method definitions can have default expressions for arguments. If those arguments are then missing in the call to the generic function, the default

Hello everyone, I encountered the following confusing behavior of 'deparse' and 'substitute' while programming with S4 classes (see example below). It seems like the presence of '...' argument in the definition of the generic generates the problem. I have no clue why, can anyone explain that to me? Are there any "workarounds"? Thanks a lot for your time!

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

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' )

hi. below is a small test case (hopefully minimal, though i'm still a bit confused about initializers). i would have guessed (and maybe i still would have been right) that one could re-use the name of a generic function for functions with different numbers of arguments. in the case below, class A's bB() queries the status of a single A object, so bB(A) (where here "A" is an

Hello, If the signature of a method defines which generic it implements then I'm confused about why this minimal example I invented won't work : setGeneric("myFun", function(rs, ...){standardGeneric("myFun")}) setGeneric("myFun", function(cs, ...){standardGeneric("myFun")}) setMethod("myFun", "numeric", function(rs, colour =

Hi, i have used S4 classes to implement a unified access to random number generators (package rstream on CRAN). I have used a construct to allow optional arguments: if(!isGeneric("rstream.sample")) setGeneric("rstream.sample", function(stream,...) standardGeneric("rstream.sample")) setMethod("rstream.sample",

For learning purposes mainly I attempted to implement hashes/maps/dictionaries (Python lingua) as S4 classes, see the coding below. I came across some rough S4 edges, but in the end it worked (for one dictionary). When testing ones sees that the dictionaries D1 and D2 share their environments D1 at hash and D2 at hash, though I thought a new and empty environment would be generated each time

Hello, the last command (isGeneric) in following R-code (attached) produces different output, depending on wheter 1.8.0 alpha or 1.7.1 is used. Is that to be expected ? Both R Versions were started with option vanilla --------------------------------------------------- R.1.7.1: --------------------------------------------------- > version _ platform i686-pc-linux-gnu arch i686

Hi, I want to set a default value in a method of a generic function. This seems as though it should be possible. From R help on setMethod... Method definitions can have default expressions for arguments. If those arguments are then missing in the call to the generic function, the default expression in the method is used. If the method definition has no default for the

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

Dear list, I'm trying to write a class for Gaussian error propagation of measured values and their (estimated) errors, > setClass("sec", representation(val="numeric", err="numeric")) I've already successfully implemented basic arithmetics using mostly the "Arith" group generics. But I'm running into trouble when trying to get signif() to

Hi, I found the following on Windows 2000/NT R Version 1.9.1 (2004-06-21) (also Version 1.9.0): The S4 group "Math" doesn't work as documented; i.e., "log", "log10", "gamma" and "lgamma" are included in the documentation but don't work. See example code below. Moreover, what about 'genericForPrimitive' which is used in