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

[David Jimenez-Morales]

Thanks a lot, Martin,

I'll take care of that. I guess that's a new function in that package
(because it always worked before)

And yes, I am planning to start removing dependencies. artMS has one
function that tries to help the very inexperienced R users by doing a lot
of things for them out of the box.

Thank you very much!
David

On Thu, Oct 22, 2020 at 12:25 AM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> 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
>
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>
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