similar to: namespaces and S4 methods/classes

I have a question about what to do in the following situation (please bear with the setup): Package A defines an S4 generic 'foo' and as well as S4 methods for 'foo' and has exportMethods("foo") in its NAMESPACE file. Package B defines another method for 'foo' for class "bar" and has importFrom(A, "foo") exportMethods("foo")

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

Dear list, I have another (again possibly boneheaded) puzzle about importing, again encapsulated in a nearly trivial package. (The package is posted at <http://www.math.mcmaster.ca/bolker/misc/coefsumtest_0.001.tar.gz>.) The package consists (only) of the following S3 method definitions: coeftab <- function(object, ...) UseMethod("coeftab",object) coeftab.default <-

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 R devels, let's say I have three packages "pkg1", "pkg2" and "pkg3" which all contain new S4 classes and methods. Where "pkg3" depends on "pkg2" and "pkg2" depends on "pkg1". Moreover, all three packages have namespaces. 1) I use ".onLoad <- function(lib, pkg) require(methods)". Do I also have to

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

Late to the show on this release, unfortunately. One of our production packages no longer builds under R-2.15.0 with the following message. ** testing if installed package can be loaded Error: Function found when exporting methods from the namespace 'SuperCurve' which is not S4 generic: 'image' Possibly relevant clues follow: ## From R/AllGenerics.R if

If a package defined an S3 generic and an S4 generic for the same function (so as to add methods for S4 classes to the existing code), how do I set up the namespace to have them exported? With import(stats) exportMethods(bigglm) importClassesFrom(DBI) useDynLib(biglm) export(biglm) export(bigglm) in NAMESPACE, the S3 generic is not exported. > methods("bigglm") [1] bigglm.RODBC*

Hi, I'm hoping to get some clarification of the intent of some of directives used in NAMESPACE files. 1. Is import(somePkg) also intended to import all classes and methods that are exported via exportClasses and exportMethods in somePkg? I think import pulls in classes and methods, but it isn't clear from the docs whether this is as intended. 2. What is exportMethods intended

pkgA's NAMESPACE has importFrom(graphics, plot) exportClasses("A") exportMethods("plot") R/foo.R has setClass("A") setMethod("plot", "A", function(x, y, ...) {}) During R CMD INSTALL pkgA_1.0.tar.gz we are told ** preparing package for lazy loading Creating a generic function for 'plot' from package

> R.version.string [1] "R Under development (unstable) (2012-02-26 r58493)" In the recent addition "It is important if you export S4 methods that the corresponding generics are available: the requirementa on this are stricter as from R 2.15.0. You may for example need to import plot from graphics to make visible a function to be converted into its implicit generic. But it is

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")})

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

Hello R-Team, May you help me to post a 'S4-creating Package Problem'? Thanks already now for supporting. The problem sounds like: Hello R forum, while compiling my R-package these 'Warnings' occur: ... Warnung in matchSignature(signature, fdef, where) : in the method signature for function "plot" no definition for class: "prediction" Warnung in

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",

Dear R People: I'm still struggling with sending methods and classes as part of creating a new package. Where does the .onLoad function go? Within R itself or in a file in one of the new package directories? Here are my latest efforts: Here's the last part of the woof1-Ex.Rout > library('woof1') Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =

The package 'graph' defines classes graph and graphNEL (extending graph) and a union,graph,graph-method. These are all exported and fully documented. The package 'GSEABase' Imports: graph and importClassesFrom(graph, graphNEL). GSEABase defines methods on union for its own classes (not graph / graphNEL), and has exportMethods(union). union,graph,graph-method is not used in

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",

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

Hi, I have a S4 based package package that was loading fine on R 2.5.0 on both OS X and Linux. I was checking the package against 2.5.1 and doing R CMD check does not give any warnings. So I next built the package and installed it. Though the package installed fine I noticed the following message: Loading required package: methods Error in loadNamespace(package, c(which.lib.loc, lib.loc),