[Bioc-devel] NAMESPACE question
Martin Morgan
mtmorgan at fhcrc.org
Thu Oct 9 18:33:28 CEST 2014
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>
>>>>
>>>>
>>>
>>
>>
>
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