[Bioc-devel] NAMESPACE question

[Robert Castelo]

hi, it happens only with "[", that's why i'm puzzled.

it behaves as if you load a GRanges object 'x' and try to subset it

x[1]

without loading 'GenomicRanges' first.

robert.

On 10/07/2014 05:05 PM, Michael Lawrence wrote:
> Does that happen with the other methods or just "["? As a last resort,
> you could just drop the import (because "[" is a primitive, it should
> just work).
>
> On Tue, Oct 7, 2014 at 3:08 AM, Robert Castelo <robert.castelo at upf.edu
> <mailto:robert.castelo at upf.edu>> wrote:
>
>     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
>         <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:
>
>     importMethodsFrom(__GenomicRanges,
>                        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!
>     robert.
>
>
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>
>

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550