[Bioc-devel] Imports, depends and warnings

Morgan, Martin Martin.Morgan at roswellpark.org
Wed Mar 2 20:41:32 CET 2016

I think the only unavoidable case is when the package you import 'does it wrong'. If that's not the case, then please provide an (easy-to-reproduce -- start with a simple package.skeleton() and add a couple of Imports: and import() statements, rather than providing your current package).


From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Federico Marini <marinif at uni-mainz.de>
Sent: Wednesday, March 2, 2016 10:53 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Imports, depends and warnings

Hi Bioconductors,

I'm on a good way to finalize the pcaExplorer package I presented at the
recent Bioc Developers Meeting.

Trying to keep check and BiocCheck always in the background of my head,
as well as trying to be a good 'package neighbour', I am dealing with
the issue of some "Warning: replacing previous import by..." messages,
when building/loading/checking.

 From my understanding, there might be some cases where this can not be
fixed, probably because an imported package in turn imports itself
another one entirely, making my own import redundant (e.g., ggplot2 for
plotting and NMF for aheatmap give this part:

Warnung: replacing previous import by ‘ggplot2::unit’ when loading ‘NMF’
Warnung: replacing previous import by ‘ggplot2::arrow’ when loading ‘NMF’

This happens even if I specifically just use importFrom in the NAMESPACE.

I'm kind of puzzled on this, so I thought I'd better ask out for some
expert advice on the ML. If required, I could put the package in a
GitHub repository.

Thank you in advance for any help you can provide!


Federico Marini, M.Sc.
Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)
Division Biostatistics and Bioinformatics
University Medical Center of the Johannes Gutenberg University Mainz
Postal address: 55101 Mainz
Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz

Phone: +49 (0) 6131 17-8108
Fax: +49 (0) 6131 17-2968
Web: www.imbei.uni-mainz.de
E-Mail: marinif at uni-mainz.de

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