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Message-ID: <BL0PR04MB6609866028E85B2F2D90EF54F91D0@BL0PR04MB6609.namprd04.prod.outlook.com>
Date: 2020-10-22T07:25:49Z
From: Martin Morgan
Subject: [Bioc-devel] Fwd: BioC 3.12 coming soon, package a4 and a4Base need your attention!
In-Reply-To: <CAA+4G_VZNM50PU-uFx1q9CaoNQWieNu5dE-nVxykBfBCbXvL+g@mail.gmail.com>

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 at r-project.org on behalf of biodavidjm at 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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