[Rd] conflicting imports despite using importFrom in NAMESPACE

[peter dalgaard]

I'd suspect that the Imports: line in DESCRIPTION imports the full namespaces, including conflicting items, on top of importFrom items. Does it not help to use Depends: instead?

-pd


On Jun 5, 2013, at 18:48 , Jombart, Thibaut wrote:

> 
> Dear all, 
> 
> It is my understanding that using 'importFrom' in the NAMESPACE of a package allows to avoid conflicts between different packages defining objects with identical names. However, I can still see conflicts while loading the package using 'library'.
> 
> Here is a toy example, with a package 'foo' importing 'as.igraph' from the igraph package, and 'nj' from ape.
> 
> 'foo' uses the following DESCRIPTION file:
> ----------------------
> Package: foo
> Version: 0.0-0
> Date: 2013/06/04
> Title: foo
> Author:  John Doe
> Maintainer: John Doe <jdoe at nowhere.org>
> Imports: igraph, ape
> Description: just a test.
> License: GPL (>=2)
> LazyLoad: yes
> ----------------------
> 
> And the following NAMESPACE:
> ----------------------
> ## Export all names
> exportPattern(".")
> 
> ## Export all classes
> exportClassPattern(".")
> 
> ## Import all packages listed as Imports or Depends
> importFrom(igraph, as.igraph)
> importFrom(ape, nj)
> ----------------------
> 
> The check (R 3.0.1) passes without warnings, but then when loading the package:
>> library(foo)
> Warning messages:
> 1: replacing previous import ‘as.igraph’ when loading ‘ape’ 
> 2: replacing previous import ‘edges’ when loading ‘ape’ 
>> 
> 
> I would have assumed only ape::nj and igraph::as.igraph would be imported when loading 'foo', so this conflict should not occur.
> 
> There is probably something simple I have missed as I have just began to pay attention to NAMESPACES recently. Reading this post:
> http://stackoverflow.com/questions/8637993/better-explanation-of-when-to-use-imports-depends
> clarified things a bit, but I still don't understand the warning above.
> 
> Any clarification will be much appreciated.
> 
> All the best
> 
> Thibaut
> 
> -- 
> ######################################
> Dr Thibaut JOMBART
> MRC Centre for Outbreak Analysis and Modelling
> Department of Infectious Disease Epidemiology
> Imperial College - School of Public Health
> St Mary’s Campus
> Norfolk Place
> London W2 1PG
> United Kingdom
> Tel. : 0044 (0)20 7594 3658
> t.jombart at imperial.ac.uk
> http://sites.google.com/site/thibautjombart/
> http://adegenet.r-forge.r-project.org/
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com