[Bioc-devel] NAMESPACE question

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.