R devel - Jun 2013 - conflicting imports despite using importFrom in NAMESPACE

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/

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/
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
-- 
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