[Bioc-devel] NAMESPACE question
Robert Castelo
robert.castelo at upf.edu
Thu Oct 9 17:00:47 CEST 2014
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...]
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
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