[Bioc-devel] NAMESPACE question

Fri Oct 10 12:11:18 CEST 2014

Martin, Hervé,

this is great! thanks for nailing this one down. it wasn't anything 
critical to my package but it was making me feel unsure about how 
namespaces work, and moreover, i've learned the use of 
'requireNamespace()' !!

cheers,
robert.

On 10/09/2014 09:40 PM, Hervé Pagès wrote:
> Hi Robert, Martin,
>
> Yes using requireNamespace() internally is much cleaner than using
> require(). Sorry for that. Just made the change in S4Vectors 0.2.6.
> FYI the need to load IRanges namespace in a couple of places
> inside S4Vectors is temporary and will go away soon.
>
> Cheers,
> H.
>
> On 10/09/2014 09:33 AM, Martin Morgan wrote:
>> On 10/09/2014 08:00 AM, Robert Castelo wrote:
>>> hi Martin,
>>>
>>> thanks for your recommendations regarding the conditional loading of
>>> packages. I
>>> think however, that they are not related to the problem I'm referring.
>>> Let me
>>> put here a reproducible example which works with qpgraph version
>>> 0.99.7 that I
>>> have just pushed to svn:
>>>
>>> library(qtl)
>>> library(qpgraph)
>>>
>>> map <- sim.map(len=100, n.mar=10, anchor.tel=FALSE, eq.spacing=TRUE,
>>> include.x=FALSE)
>>>
>>> eqtlcross <- eQTLcross(map)
>>> eqtlcross <- addGenes(eqtlcross, 5)
>>> eqtlcross <- addeQTL(eqtlcross, "g1", location=map[[1]][1])
>>>
>>> sim.eqtl <- reQTLcross(eqtlcross, rho=0.5, a=1)
>>> cross <- sim.cross(map, sim.eqtl, n.ind=100)
>>>
>>> gstarts <-runif(5, min=range(map[[1]])[1], max=range(map[[1]])[2])
>>>
>>> annot <- data.frame(chr=rep(names(map)[1], 5),
>>> start=gstarts, end=gstarts+1,
>>> strand=rep("+", 5),
>>> row.names=sim.eqtl$model$Y,
>>> stringsAsFactors=FALSE)
>>>
>>> ## the following is the method that triggers the
>>> ## unexpected behavior. Its last but one instruction
>>> ## in line 208 of file qpgraph/R/eQTLnetworkEstimationParam-methods.R
>>> ## is the following:
>>> ##
>>> ## geneAnnotation <- geneAnnotation[genes]
>>> ##
>>> ## and should be using the method "[" imported from GenomicRanges
>>> ## however it starts loading a number of packages to do the job
>>>
>>> param <- eQTLnetworkEstimationParam(cross, geneAnnotation=annot,
>>> genome="simulatedGenome")
>>> Loading required package: parallel
>>>
>>> Attaching package: ‘BiocGenerics’
>>>
>>> The following objects are masked from ‘package:parallel’:
>>>
>>> [...etc...]
>>
>> Hmm, I see that the parallel, BiocGenerics, and stats4 packages are
>> being attached. In a new R session I did this:
>>
>> > trace(loadNamespace, tracer=recover)
>> Tracing function "loadNamespace" in package "base"
>> [1] "loadNamespace"
>> > param <- eQTLnetworkEstimationParam(cross, geneAnnotation=annot,
>> genome="simulatedGenome")
>> Loading required package: parallel
>> Tracing loadNamespace(package, c(which.lib.loc, lib.loc)) on entry
>>
>> Enter a frame number, or 0 to exit
>>
>> 1: eQTLnetworkEstimationParam(cross, geneAnnotation = annot, genome =
>> "simulat
>> 2: geneAnnotation[genes]
>> 3: geneAnnotation[genes]
>> 4: extractROWS(x, i)
>> 5: extractROWS(x, i)
>> 6: extractROWS(seqnames(x), i)
>> 7: extractROWS(seqnames(x), i)
>> 8: suppressWarnings(require(IRanges, quietly = TRUE))
>> 9: withCallingHandlers(expr, warning = function(w)
>> invokeRestart("muffleWarnin
>> 10: require(IRanges, quietly = TRUE)
>> ...
>>
>> and it's likely from
>>
>> ./S4Vectors/R/Rle-class.R: if (!suppressWarnings(require(IRanges,
>> quietly=TRUE)))
>> ./S4Vectors/R/Rle-class.R: if (!suppressWarnings(require(IRanges,
>> quietly=TRUE)))
>>
>> could be addressed with suppressPackageStartupMessages()
>> (less-preferred) or requireNamespace("IRanges") followed by
>> IRanges::...; let's see if we can get that fixed...
>>
>> Martin
>>
>>>
>>> sessionInfo()
>>> R version 3.1.0 (2014-04-10)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF8 LC_NUMERIC=C LC_TIME=en_US.UTF8
>>> LC_COLLATE=en_US.UTF8
>>> [5] LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
>>> LC_PAPER=en_US.UTF8
>>> LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF8
>>> LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats4 parallel stats graphics grDevices utils datasets
>>> methods base
>>>
>>> other attached packages:
>>> [1] IRanges_1.99.28 S4Vectors_0.2.4 BiocGenerics_0.11.5
>>> qpgraph_1.99.7 qtl_1.33-7
>>> [6] vimcom_0.9-93 setwidth_1.0-3 colorout_1.0-2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] annotate_1.43.5 AnnotationDbi_1.27.16 base64enc_0.1-2
>>> BatchJobs_1.4
>>> [5] BBmisc_1.7 Biobase_2.25.0 BiocParallel_0.99.22
>>> biomaRt_2.21.1
>>> [9] Biostrings_2.33.14 bitops_1.0-6 brew_1.0-6
>>> checkmate_1.4
>>> [13] codetools_0.2-9 DBI_0.3.1 digest_0.6.4
>>> fail_1.2
>>> [17] foreach_1.4.2 futile.logger_1.3.7 futile.options_1.0.0
>>> GenomeInfoDb_1.1.23
>>> [21] GenomicAlignments_1.1.30 GenomicFeatures_1.17.19
>>> GenomicRanges_1.17.42
>>> graph_1.43.0
>>> [25] grid_3.1.0 iterators_1.0.7 lambda.r_1.1.6
>>> lattice_0.20-29
>>> [29] Matrix_1.1-4 mvtnorm_1.0-0 RCurl_1.95-4.3
>>> Rgraphviz_2.9.1
>>> [33] Rsamtools_1.17.34 RSQLite_0.11.4 rtracklayer_1.25.17
>>> sendmailR_1.2-1
>>> [37] stringr_0.6.2 tools_3.1.0 XML_3.98-1.1
>>> xtable_1.7-4
>>> [41] XVector_0.5.8 zlibbioc_1.11.1
>>>
>>>
>>> cheers,
>>> robert.
>>>
>>>
>>>
>>> On 10/07/2014 05:54 PM, Martin Morgan 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()).
>>>>
>>>> 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>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>>
>

-- 
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