[Bioc-devel] GenomicFeatures namespace warning

Hahne, Florian florian.hahne at novartis.com
Mon Aug 20 11:33:37 CEST 2012

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
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)


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