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.geistlin...@bio.ifi.lmu.de _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel