On Tue, Oct 7, 2014 at 8:54 AM, Martin Morgan <mtmor...@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.cast...@upf.edu
>>> <mailto:robert.cast...@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@r-project.org <mailto:Bioc-devel@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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