Hi Martin,
thanks, this is reassuring - I'm assuming it is just a problem on my computer
then.
Thanks for pointing out the exportPattern("."). For some purposes I actually
ended up needing to export some hidden functions, but I guess I could just not
export these and reference to them explicitly using ':::'.
Best
Thibaut
________________________________________
From: Martin Morgan [mtmor...@fhcrc.org]
Sent: 05 June 2013 20:19
To: peter dalgaard
Cc: Jombart, Thibaut; r-devel@r-project.org
Subject: Re: [Rd] conflicting imports despite using importFrom in NAMESPACE
On 06/05/2013 11:59 AM, peter dalgaard wrote:
> 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?
I think of Imports: and Depends: as different -- presumably the end user has no
need for ape / igraph beyond the functionality provided by the new package.
For what it's worth, with a minimal package (attached, modulo the mailman gods),
$ tree PkgA
PkgA
├── DESCRIPTION
├── NAMESPACE
└── R
1 directory, 2 files
and with DESCRIPTION / NAMESPACE as below, I don't see any warning about
replacing previous imports
$ R --vanilla
> library(PkgA)
> sessionInfo()
R version 3.0.1 beta (2013-05-07 r62721)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] PkgA_1.2.3
loaded via a namespace (and not attached):
[1] ape_3.0-8 grid_3.0.1 igraph_0.6.5-2 lattice_0.20-15
[5] nlme_3.1-109
likewise with R version 3.0.1 beta (2013-05-07 r62721).
Also I don't think exportPattern(".") is to be recommended; see section 1.5.1 of
Writing R Extensions (though as a lazy programmer I kind of like the pattern
"^[^\\.]").
Martin Morgan
> -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 <j...@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.jomb...@imperial.ac.uk
>> http://sites.google.com/site/thibautjombart/
>> http://adegenet.r-forge.r-project.org/
>> ______________________________________________
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
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