On 9/1/2010 8:00 PM, Dario Strbenac wrote:
Hello,
I'd like to treat these 2 classes as 1 class for the purpose of method dispatch.
In the first couple of lines of my .R file I have
setGeneric("annotationCounts", function(someArgument1,
someArgument2){standardGeneric("annotationCounts")})
... ...
setClassUnion("sequencingList", c("GenomeDataList", "GRangesList"))
and lower in the file I have
setMethod("annotationCounts", "sequencingList", function(someArgument1,
someArgument2) {
... ...
})
I am wondering if anyone knows what I should do about this warning in R CMD
check ?
* checking whether package 'Repitools' can be installed ... WARNING
Found the following significant warnings:
Warning: Class "GRangesList" is defined (with package slot âGenomicRangesâ)
but no metadata object found to revise superClass information---not exported? Making a
copy in package âRepitoolsâ
Hi Dario --
I think you require a NAMESPACE file with
importClassesFrom(BSgenome, GenomeDataList)
importClassesFrom(GRanges, GRangesList)
And a DESCRIPTION file that has the line
Imports: GRanges, BSgenome
And for my 2 cents I'm not sure that class unions are a good idea --
you're setting up a contract where you're saying you'll support classes
that inherit from not one but two classes, and you'll fulfill the
contract without the author of those classes consenting. This is a
pretty tall order -- much more so than saying Y contains X, where you're
only saying that if Y doesn't behave specially it'll behave like X, or Y
has X, which could say nothing about how much like X a Y is (e.g.,
because there are no user-visible methods to access X directly).
Martin
Thanks,
Dario.
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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--
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
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