[Bioc-devel] GenomicFeatures namespace warning

[Martin Morgan]

On 08/20/2012 02:33 AM, Hahne, Florian wrote:
> Hi Marc,I get a strange namespace warning in one of my packages which seem
> to originate from GenomicFeatures:** testing if installed package can be
> loaded
> Warning: No function found corresponding to methods exports from
> ŒGenomicFeatures¹ for: ŒseqnameStyle¹
>
> The strange thing is that I am importing some methods and classes from
> your package, but never touch seqnameStyle:
>
> importClassesFrom(GenomicFeatures, "TranscriptDb")
> importMethodsFrom(GenomicFeatures, isActiveSeq, "isActiveSeq<-", exonsBy,
> transcriptsBy, transcripts)
>
> The generic is defined in GenomicRanges, and I am at a complete loss now
> why I am seeing this warning. I neither import nor explicitly call
> seqnameStyle from GenomicFeatures, and simply importing the generic from
> GenomicRanges in my package names pace doesn't seem to do the trick,
> either. I suspect that you are doing something funky in your package name
> space. You seem to export a method for seqnameStyle without ever importing
> the generic, and while your own package depends on GenomicRanges that will
> work when directly loading GenomicFeatures, but everybody who imports from
> it will not see it. To make a long story short:
> I think you need to add seqnameStyle to your importFrom(GenomicRanges) to
> fix that problem.
>
> As a more general remark (and maybe Martin can chime in here): If you
> depend on a package A shouldn't you also import the whole package name
> space into your own package B? Otherwise all those functions that are
> exported in A will not be available in anybody else's package C which
> imports from B. (B gets loaded but not attached, thus A does not get
> attached, thus nothing in A.namespace is available to C)

Hi Florian -- I think your analysis is correct, but also that B should 
just import what it needs from A. Likewise, C should import what it 
needs from B, and also import what it needs from A.

Certainly it would be wrong if B's package code relied on a function 
A::foo that was only available because A was attached -- B should 
importFrom(A, foo).

Martin

>
> Cheers,
> Florian
>


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