[Bioc-devel] NAMESPACE question
robert.castelo at upf.edu
Thu Oct 9 17:00:47 CEST 2014
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:
map <- sim.map(len=100, n.mar=10, anchor.tel=FALSE, eq.spacing=TRUE,
eqtlcross <- eQTLcross(map)
eqtlcross <- addGenes(eqtlcross, 5)
eqtlcross <- addeQTL(eqtlcross, "g1", location=map[])
sim.eqtl <- reQTLcross(eqtlcross, rho=0.5, a=1)
cross <- sim.cross(map, sim.eqtl, n.ind=100)
gstarts <-runif(5, min=range(map[]), max=range(map[]))
annot <- data.frame(chr=rep(names(map), 5),
## 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,
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF8 LC_NUMERIC=C
 LC_MONETARY=en_US.UTF8 LC_MESSAGES=en_US.UTF8
 LC_ADDRESS=C LC_TELEPHONE=C
attached base packages:
 stats4 parallel stats graphics grDevices utils datasets
other attached packages:
 IRanges_1.99.28 S4Vectors_0.2.4 BiocGenerics_0.11.5
 vimcom_0.9-93 setwidth_1.0-3 colorout_1.0-2
loaded via a namespace (and not attached):
 annotate_1.43.5 AnnotationDbi_1.27.16 base64enc_0.1-2
 BBmisc_1.7 Biobase_2.25.0
 Biostrings_2.33.14 bitops_1.0-6 brew_1.0-6
 codetools_0.2-9 DBI_0.3.1 digest_0.6.4
 foreach_1.4.2 futile.logger_1.3.7
 GenomicAlignments_1.1.30 GenomicFeatures_1.17.19
 grid_3.1.0 iterators_1.0.7 lambda.r_1.1.6
 Matrix_1.1-4 mvtnorm_1.0-0 RCurl_1.95-4.3
 Rsamtools_1.17.34 RSQLite_0.11.4
 stringr_0.6.2 tools_3.1.0 XML_3.98-1.1
 XVector_0.5.8 zlibbioc_1.11.1
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
>> 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
> 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()).
>> 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)
>>> so it's important that your code clearly distinguish between
>>> 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
>>> 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:
>>> 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!
>>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
Robert Castelo, PhD
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
More information about the Bioc-devel