[Bioc-devel] NAMESPACE question

Robert Castelo robert.castelo at upf.edu
Tue Oct 7 12:08:59 CEST 2014

hi Martin,

On 10/06/2014 07:24 PM, Martin Morgan wrote:
> There are two 'as.vector' generics, one defined in Matrix and one in
> BiocGenerics (and made available via IRanges). These generics have
> different methods
>  > showMethods(Matrix::as.vector)
> Function: as.vector (package base)
> x="abIndex", mode="ANY"
> x="abIndex", mode="character"
> x="ANY", mode="ANY"
> x="dgCMatrix", mode="missing"
> x="dgeMatrix", mode="missing"
> x="diagonalMatrix", mode="missing"
> x="dsCMatrix", mode="missing"
> x="ldenseMatrix", mode="missing"
> x="Matrix", mode="missing"
> x="ndenseMatrix", mode="missing"
> x="sparseVector", mode="character"
> x="sparseVector", mode="missing"
>  > showMethods(BiocGenerics::as.vector)
> Function: as.vector (package BiocGenerics)
> x="ANY"
> x="AtomicList"
> x="Rle"
> x="XDouble"
> x="XInteger"
> x="XRaw"
> x="XString"
> x="XStringSet"
> so it's important that your code clearly distinguish between generics.
> One possibility is to remove importMethodsFrom(IRanges, as.vector) from
> the NAMESPACE, and explicitly use IRanges::as.vector(...) in your code.

ok, i've done this as it is the easiest at the moment to meet the 
release schedule. i guess that in the future i should try to avoid using 
the '::' operator by importing exclusively what is needed from each package.

> codetoolsBioC::writeNamespaceImports("qpgraph") might provide you with
> some guidance (it's not 100% reliable; available via svn at
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/codetoolsBioC)
> about what functionality is being imported.

thanks for the heads up about codetoolsBioC, i've tried it out and seen 
that some of the suggested imports are not necessary but some others i 
was really missing them (which makes me wonder how was it possible that 
he package did not break at those points).

one further question related to NAMESPACE. i subset GRanges objects in 
the package via the '[' operator, i've included this into the NAMESPACE 
file as:

                   c, cbind, rbind,
                   "mcols<-", start, end, strand, sort,
                   "[", "[<-", "[[", "[[<-", "$", "$<-")

however, when the package reaches a subset operation x[i] with x being a 
GRanges object, an entire package loading sequence starts:

Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’
[... etc ...]

which may look a bit odd to the user. for every other imported method 
the package uses them silently without loading the corresponding 
package, am i importing '[' for GRanges objects from the wrong package? 
is there a way to import '[' so that my package can use it without 
triggering that package loading sequence?

thanks again!

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