[Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!

[Martin Morgan]

Your NAMESPACE has

import(ComplexHeatmap)
...
import(pheatmap)

and both packages have a function pheatmap -- the import from ComplexHeatmap is being replaced by the import from pheatmap.

In other places your NAMESPACE has lines like

import(seqinr, except = c(zscore, count, a))

so you'd like to do the same for one or the other of ComplexHeatmap / pheatmap. It looks like the roxygen for this is

#' @rawNamespace import(ComplexHeatmap, except = c(pheatmap))

...but I wonder whether you really want to import both packages?? Does your package really need functionality from each? I see from

  https://bioconductor.org/packages/artMS

that your package has 200 dependencies, which is a lot and means that changes in any of those could break your package -- it sounds like a quite fragile situation.

Martin



On 10/22/20, 2:13 AM, "Bioc-devel on behalf of David Jimenez-Morales" <bioc-devel-bounces using r-project.org on behalf of biodavidjm using gmail.com> wrote:

    Dear bioc team,

    I am getting the following warning
    <http://bioconductor.org/checkResults/devel/bioc-LATEST/artMS/> that I do
    not understand and cannot reproduce locally (and my search online didn't
    help):

    * checking whether package ‘artMS’ can be installed ... WARNING
    Found the following significant warnings:
      Warning: replacing previous import ‘ComplexHeatmap::pheatmap’ by
    ‘pheatmap::pheatmap’ when loading ‘artMS’
    See ‘/home/biocbuild/bbs-3.12-bioc/meat/artMS.Rcheck/00install.out’ for details.

    What does this mean? How could I get rid of the warning?

    Thanks a lot!
    David


    Found the following significant warnings:
      Warning: replacing previous import ‘ComplexHeatmap::pheatmap’ by
    ‘pheatmap::pheatmap’ when loading

    	[[alternative HTML version deleted]]

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