[Bioc-devel] NAMESPACE question

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.