On 10/05/2014 01:39 PM, Robert Castelo wrote:
hi,
i have the following warning message when installing the devel version
(0.99.5) of my package 'qpgraph':
** testing if installed package can be loaded
Warning: replacing previous import by 'IRanges::as.vector' when loading
'qpgraph'
* DONE (qpgraph)
after investigating the issue i think it has to do with the fact that in
the NAMESPACE of 'qpgraph' i'm importing the whole Matrix package and
later the 'as.vector()' method defined in IRanges. The NAMESPACE file
looks like this:
useDynLib(qpgraph)
import(methods)
import(graph)
import(Matrix)
... (few lines later) ...
importMethodsFrom(IRanges,
as.vector)
... (rest of the file) ...
from what i have learned while reading documentation and googling about
this issue, it seems that the solution would be to import every
function/method i use from Matrix before i do the import from IRanges,
but i use the dspMatrix-class all over the package and i don't know how
would i find out what set of functions/methods i have to explicitly
import. i can import a few of the methods from Matrix i know from the
top of my head that the package is using but i'm afraid i'll be missing
other methods that will break the package when using it in situations
outside current examples and unit tests.
i'd appreciate if you have a suggestion about what to do in this situation.
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.
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) about
what functionality is being imported.
Martin
thanks!
robert.
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