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

Ludwig Geistlinger Ludwig.Geistlinger at bio.ifi.lmu.de
Wed Jun 24 19:36:42 CEST 2015

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

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

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.


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

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