similar to: Imports/exports of S4 methods

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, 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 <-

The current version of the methods package now has a namespace. Packages using S4 methods and classes can have NAMESPACE files. New directives can be included in NAMESPACE files to import and export classes and methods. Namespaces allow cleaner definition of the API for packages, and are needed for future improvements to R. NOTE: This is a major revision. In principle, it should be back

The current coxme code has functions that depend on bdsmatrix and others that depend on Matrix, both those pacakges define S4 methods for diag. When loaded, the message appears: replacing previous import ?diag? when loading ?Matrix? Questions: 1. Do I need to worry about this? If so, what can I do about it? I suppose I could add an importFrom directive, but it will be a pain unless there

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

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

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

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

We are building a package, and want to create S4 methods for both head and mean for our own BigMatrix class. Following the recommendation in "Writing R Extensions" we use exportMethods instead of export in NAMESPACE (this is described as being "clearer"). This works for head, but not for mean. Obviously we importFrom(utils, head), but don't need to do this for mean,

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

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 =

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)

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

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, 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),

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 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

Dear all, I am encountering a cyclic dependency error when running R CMD check on an R package I wrote (R version 2.6.1, Mac OS X 10.4), see the error message below. Creating a new generic function for "print" in "clValid" Creating a new generic function for "summary" in "clValid" Creating a new generic function for "plot" in

Hello everybody, I have a problem with accessing class attributes. I think it might be due to namespace access restrictions or something similar, but I'm unable to figure it out, maybe someone knows the trick how to do it ... I'm trying to extract some information from the summary object for a model fitted using the lmer function from the lme4 package: smry <- summary(lmer(foo