[Bioc-devel] NAMESPACE question

[Michael Lawrence]

On Tue, Oct 7, 2014 at 8:54 AM, Martin Morgan <mtmorgan at fhcrc.org> wrote:

> On 10/07/2014 08:15 AM, Robert Castelo wrote:
>
>> 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.
>>
>
> Is there a reproducible example? I see in your code there are several
> places where you require() or library() various packages. I think one of
> these Depends: on GenomicRanges, and the messages you see are the effect of
> moving GenomicRanges from 'loaded' to 'attached'. You can see the effect
> with
>
>   library(qpgraph)
>   sessionInfo()           ## GenomicRanges loaded but not attached
>   library(GenomicRanges)  ## information about the package being attached
>
> Probably in your code you do not actually want to require() ad hoc
> packages and influence the user search path (and implicitly rely on search
> path order for correct functionality), but rather to
> requireNamespace("foo"); foo::fun(...) (or possibly loadNamespace()).
>

This last paragraph should probably be explained in the Bioc coding
standards if it is not already.


>
> Complicated!
>
> Martin
>
>
>
>> 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.
>>>
>>>
>>>     _________________________________________________
>>>     Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing
>>> list
>>>     https://stat.ethz.ch/mailman/__listinfo/bioc-devel
>>>     <https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>>>
>>>
>>>
>>
>
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