[Bioc-devel] best practice: dependencies of dependencies / no visible global function definition

[Michael Lawrence]

In order for R to find those symbols reliably, you need to import
those functions into your NAMESPACE, and therefore you should ensure
that the Biobase package is listed on the Depends line of your
DESCRIPTION. Your package directly depends on Biobase, so there's no
redundancy by having it listed in Depends.

On Wed, Jun 24, 2015 at 10:36 AM, Ludwig Geistlinger
<Ludwig.Geistlinger at bio.ifi.lmu.de> wrote:
> I'm surely not the first asking this question.
> But as I did not find a clear answer to that (e.g. in the 'Writing R
> extensions' manual or in the diverse posts on this), I risk asking it
> again.
>
> As an example:
>
> I'm dealing a lot with ExpressionSets (from Biobase) and
> GeneSet[Collection]s (from GSEABase) in my package and they are in- &
> outputs of my exported functions, so I want them to be available when my
> package is loaded.
>
> Thus, I would tend to put both, 'Biobase' and 'GSEABase', in the 'Depends'
> field of my DESCRIPTION file and a corresponding 'import' directive in my
> NAMESPACE file.
>
> However, I do know that 'GSEABase' depends on 'Biobase' - so in order to
> be not redundant and keeping the 'Depends' field as small as possible, I
> could also remove 'Biobase' from my 'Depends'.
>
> Now, everything still works fine (building, installing, and I still got
> the ExpressionSets when loading my package), however R CMD CHECK now
> *notes* on many occasions:
>
> no visible global function definition for ‘pData’
> no visible global function definition for ‘exprs’
> no visible global function definition for ‘fData’
> ...
>
> Ok, these are NOTES, but I assume they are there for a reason.
> So, I wonder what a developer's best practice is on that - ignoring the
> notes, adding all Biobase/ExpressionSet functionality via imports, or
> indeed depending on both packages.
>
> Best,
> Ludwig
>
> --
> Dipl.-Bioinf. Ludwig Geistlinger
>
> Lehr- und Forschungseinheit für Bioinformatik
> Institut für Informatik
> Ludwig-Maximilians-Universität München
> Amalienstrasse 17, 2. Stock, Büro A201
> 80333 München
>
> Tel.: 089-2180-4067
> eMail: Ludwig.Geistlinger at bio.ifi.lmu.de
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel