similar to: Namespaces and S4 Generics

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,

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")

In > R.version.string [1] "R Under development (unstable) (2011-12-15 r57901)" section 1.6.6 of 'Writing R Extensions' says Note that exporting methods on a generic in the namespace will also export the generic, and exporting a generic in the namespace will also export its methods. and Note that importMethodsFrom will also import any generics defined in

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

In the last few days I've received couple of messages pointing out that our SparseM package fails to install on the patched version of 1.7.0. Laurent Gaultier kindly suggested that replacing: setGeneric("as.matrix.csr") by setGeneric("as.matrix.csr", function(x, nrow, ncol, eps) standardGeneric("as.matrix.csr")) was sufficient to fix the problem.

There seems to be a bug arising when using multiple S4 generics with "..." as the signature. The following code works as expected: ############################################################## > setGeneric("rbind", function(..., deparse.level=1) standardGeneric("rbind"), + signature = "...") Creating a generic for "rbind" in

Hi, I'm developing in S4 and I wanted to see the methods for a specific class using showMethods but I didn't succed. Can someone help ? See the example below. setClass("myclass", representation( name ="character" ) ) setGeneric("mymeth", function(obj, ...){ standardGeneric("mymeth") } ) setMethod("mymeth",

Hi the list When two setGeneric occurs on the same function, the second erage the first and erase all the function previously define. Is it possible to prevent that ? Is it possible to declare a setGeneric that can not be erased later ? Something like the |sealed for setMethod...| || |Thanks| || Christophe

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")

In > R.version.string [1] "R Under development (unstable) (2011-12-15 r57901)" PkgA promotes 'unique' to a generic and exports that DESCRIPTION: Imports: methods R/f.R: setGeneric("unique") NAMESPACE: export(unique) and PkgB creates and exports a method on unique DESCRIPTION Imports: methods, PkgA R/f.R: setClass("B",

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

Hi the list, I define a method that want to change an object without assignation (foo(x) and not x<-foo(x)) using deparse and assign. But when the argument of the method does not match *exactly* with the definition of the generic function, assign does not work... Anything wrong? Christophe #------ Does not work ------#

Hi, S4 method dispatch can be very slow. Would it be reasonable to cache the most recent dispatch, anticipating the next invocation will be on the same type? This would be very helpful in loops. fun0 <- function(x) sapply(x, paste, collapse="+") fun1 <- function(x) { paste <- selectMethod(paste, class(x[[1]])) sapply(x, paste,

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, This strange warning happen sometimes when running 'R CMD check': * checking whether the package can be loaded with stated dependencies ... WARNING Error : .onLoad failed in loadNamespace() for ?pkgB?, details: call: length(new("A")) error: could not find function "loadMethod" Error: package/namespace load failed for ?pkgB? Execution halted

Dear all, I am experiencing some problems with S4 method overloading. I have defined a generic for graphics:plot, using setGeneric("plot", useAsDefault = plot) and with importFrom('graphics', 'plot') and exportMethods('plot') in the NAMESPACE file of pkg A. I then proceed to define a method for signature c('myS4class', 'missing'). This works

I have been trying to write a new class that reimplements the vector class. As a test of my overloading I decided to try and and call t.test on two vectors which were objects of my class rather than the default class. The overloaded length I wrote seems to work correctly. I used setMethod("length", "myvector", ...) setMethod("mean", "myvector", ...)

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. I am trying to write an S4 method for rbind(). I have a class of objects called 'mdm', and I want to be able to rbind() them to one another. I do not want the method for rbind() to coerce anything to an mdm object. I want rbind(x1,x2,x1,x2) to work as expected [ie rbind() should take any number of arguments]. This is what I have so far: setGeneric(".rbind_pair",

Hi there, I'm working with an object whose internal data representation is very different from a data.frame (data is stored as a list of big.matrix objects from the bigmemory package) but to which I'd like to give users data.frame-like access. I've implemented names very easily as follows: setMethod("names", signature = "my.dataset", definition = function (x) {