similar to: Why S4 methods of S3 'base' generics are not used in 'base' functions ?

Dear list, It seems that a package (pkgB) using another package (pkgA) with S4 generics formed by taking existing functions (for example 'plot') must not import the existing functions ('plot') in its namespace to avoid the warning "replacing previous import: plot". Suppose we use the simple 'import' directive in the name space of pkgB. pkgA and pkgB files would

Hi all, this question has already been posted on stackoverflow, however without success, see also http://stackoverflow.com/questions/27886535/proper-way-to-use-cbind-rbind-with-s4-classes-in-package. I have written a package using S4 classes and would like to use the functions rbind, cbind with these defined classes. Since it does not seem to be possible to define rbind and cbind directly as S4

I'd like to suggest that whenever there is no S3 method implementation available for a particular class, that the error message would also report the class structure of the object dispatched on. Example: foo <- function(...) UseMethod("foo") foo.ClassA <- function(object, ...) { cat("foo() for ClassA called.\n") } > foo(structure(1, class="ClassA"))

>>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>> on Sat, 24 Jan 2015 06:39:37 -0800 writes: > On Sat, Jan 24, 2015 at 12:58 AM, Mario Annau > <mario.annau at gmail.com> wrote: >> Hi all, this question has already been posted on >> stackoverflow, however without success, see also >>

>>>>> Michael Lawrence <lawrence.michael at gene.com> >>>>> on Sun, 1 Feb 2015 19:23:06 -0800 writes: > I've implemented the proposed changes in > R-devel. Minimally tested, so please try it. It should > delegate to r/cbind2 when there is at least one S4 > argument and S3 dispatch fails (so you'll probably want to

A general goal for the next version of R is to make S4 and S3 play better together. As mentioned in a previous thread, one limitation has been that S3 generic functions, specifically the UseMethod() call, did not make use of S4 inheritance when dispatching on general S4 objects. This has been fixed in a version committed today (updated to rev 52267). The code change is not large, but it

Are you able to create a reproducible example, somehow? Thanks, Michael On Mon, Feb 9, 2015 at 2:28 PM, Mario Annau <mario.annau at gmail.com> wrote: > Hi Michael, > I've tested your change in r67699 (using r67773) and the function now > correctly dispatches to r/cbind2 within the R-session without > bind_activation(TRUE). However, running unit tests using R CMD check I

Dear all, In R-devel I have noticed the new approach for the "ts" class in the package "methods". the "structure" behaviour of "ts" is not always kept when one uses "ts" objects and objects of classes which extend the virtual class "structure". As a short example: ## this works fine setClass("foo", representation(header =

>>>>> Mario Annau <mario.annau at gmail.com> >>>>> on Wed, 11 Feb 2015 20:18:53 +0100 writes: > sorry - I just got irritated by my different R-versions. > The behaviour I described in the previous mail was discovered using R > 3.1.2 without bind_activation(TRUE). In r67773 all calls are delegated > to r/cbind.matrix and not

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,...)

Hi, I'm a R newbie and want to accelerate the following pre-filtering step of a data set with more than 115,000 rows : #----------------- # Function to filter out constant data columns filter.const<-function(X, vectors=c('column', 'row'), tol=0){ realdata=c() filteredX<-matrix() if( vectors[1] == 'row' ){ for( row in (1:nrow(X)) ){ if(

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

What is the best way to produce a barplot from my data? I would like the barplot to show each person with the values stacked val1+val2+val3, so there is one bar for each person When I use barplot(data.matrix(realdata)), it shows one bar for each value instead. To post here, I created an artificical data set, but it works fine. fakedata <- as.data.frame(list(LETTERS[1:3])) colnames(fakedata)

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",

Dear all, I asked this question on r-package-devel but Martin Maechler pointed out this was more suited on R-devel. So here it goes: per the manual, one should create and register both the S3 and a S4 method if one needs a method for an S4 class for a function using S3 dispatching. This is cumbersome, and not very optimal. I was wondering if there's a better way to do this. Currently I

Dear developers, the implementation of S4 generics for existing S3 ones in the base package is concerned to be a threat to quick startup times [1]. But since S4 is promoted, and S3/S4 interoperability a pain when package developing [2], are there efforts to improve the situation? E.g. an S3 free system, etc. A good thing [2] is the package 'stats4', including some setGeneric calls (e.g.

If someone is able, can you tell me if there is a better way to do this? More specifically, do I have to rewrite all of the data members stuff and extend stuff of parent class in the child class? See below. Thanks in advance! Example 1: setConstructorS3("ClassA", function(A,x) { if(missing(A))A=15; if(missing(x))x=NA; extend(Object(), "ClassA", .size = A, .x=x

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

I have J Chambers wonderful text ( Software for data Analysis) and I've been trying my hand at some very routine S4 OOP development. One of the things I was trying to do was to create some very basic S4 classes. The first was simply a class that had a data.frame as part of its representation. setClass("df",representation(dirframe="data.frame")) The object basically

Can anyone help me figure out the right way to import a method that is defined as S3 in one package and S4 in another? Specifically: profile() is defined as an S3 method in the stats package: function (fitted, ...) UseMethod("profile") <bytecode: 0xa4cd6e8> <environment: namespace:stats> In stats4 it is defined as an S4 method: stats4:::profile standardGeneric for