[Bioc-devel] Imports, depends and warnings

Morgan, Martin Martin.Morgan at roswellpark.org
Thu Mar 3 10:08:59 CET 2016


Your description is not clear enough. See the github repository branch

https://github.com/mtmorgan/PkgA/tree/import-conflict

which imports NMF and ggplot2 without any warning during

R CMD build PkgA
R CMD check PkgA_0.0.1.tar.gz

with

$ R --version|head -n3
R Under development (unstable) (2016-02-27 r70232) -- "Unsuffered Consequences"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)


________________________________________
From: Federico Marini <marinif at uni-mainz.de>
Sent: Thursday, March 3, 2016 3:44 AM
To: Morgan, Martin; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Imports, depends and warnings

With the minimal working example, alone the importing of NMF raises the
warning, so I guess this is due to that particular package.

Should I contact the author of that in hope he adapts its NAMESPACE to
have some nicer behavior? (or would be *just that* warning "fine" for
the Bioc ecosystem?)


Cheers,
Federico


On 02.03.16 20:41, Morgan, Martin wrote:
> 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).
>
> Martin
>
> ________________________________________
> 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
>
> --
> 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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>
> This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.

--
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


This email message may contain legally privileged and/or confidential information.  If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited.  If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.


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