tar of Pkgs A, B, C attached. Martin On 12/15/2011 03:34 PM, Martin Morgan wrote:
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 the namespace on those methods However, if 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", representation(b="numeric")) setMethod(unique, "B", function(x, incomparables=FALSE, ...) unique(x@b)) NAMESPACE: importFrom(PkgA, unique) exportClasses(B) exportMethods(unique) and PkgC wants to import PkgB's classes and methods DESCRIPTION Imports: methods, PkgB R/f.R cunique <- function(x) unique(x) NAMESPACE importMethodsFrom(PkgB, unique) export(cunique) then (a) the 'unique' generic is not available to the user of PkgB > library(PkgB) > unique(new("B", b=1:5)) Error in unique.default(new("B", b = 1:5)) : unique() applies only to vectors and (b) the generic has not been imported to PkgC's namespace > cunique(new("B", b=1:5)) Error in unique.default(b) : unique() applies only to vectors A workaround is for PkgB to also export(unique), and for PkgC to also importFrom(PkgA, unique), but is this the intention? This is arising from Bioconductor efforts to place commonly promoted functions and S3 classes into a single package, to avoid conflicts when the same function is promoted independently by several packages. Martin
-- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
PkgABC.tar
Description: Unix tar archive
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