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 filesand 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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PkgA.tar.gz
Description: GNU Zip compressed data
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