[BioC] warning in lumi

[Martin Morgan]

On 02/22/2012 09:16 AM, Martin Morgan wrote:
> On 02/22/2012 07:56 AM, Francesco Mancuso wrote:
>> Dear all,
>> I am the author of a CRAN package (HumMeth27QCReport) that denpends on
>> lumi.
>> Every time I call the lumi package I obtain the following warning:
>>
>> "
>> Functions for exporting methods must have been made generic,
>> explicitly or implicitly; not true when loading ‘lumi’ for ‘summary’
>> "
>>
>> Since this error comes not only when I try to build ny package but also
>> when I require lumi from normal R command line, I think this is a
>> problem in lumi package itself. Am I correct?
>> Is there the possibility to solve it?
>
> Hi Francesco -- we are addressing these warnings in a number of Bioc
> packages; this particular problem was fixed in the devel branch last
> night. Martin

Maybe to provide developers with a little insight on this --

Previously, in a NAMESPACE file one might

   importFrom(graphics, plot)

'plot' is a standard R function in graphics. and then somewhere in the 
package code say

   setMethod(plot, "MyClass", ...)

This would implicitly promote 'plot' from a standard R function to an S4 
generic, and then associate a method for plotting instances of MyClass. 
Common practice was to then add to the NAMESPACE

   exportMethods(plot)

This now generates a warning (soon to be an error, if I understand 
R-core's intentions), because the plot method is exported without a 
generic on which to export it. The solution is to explicitly create a 
generic for 'plot', and to export (and document) that, as well.

Several functions, including plot, are 'promoted' in this way 
independently in different packages. This means that there would be many 
separate plot generics on which to hang methods and the user would 
potentially have to resolve dispatch to the package -- lumi::plot(...). 
The BiocGenerics package has been developed to provide a central 
location for generic definition, in hopes of avoiding this conflict. The 
BiocGenerics package creates commonly used generics, and these are made 
available to other packages. So the changes to lumi are

   1. Add Imports: BiocGenerics to the DESCRIPTION file
   2. Add importFrom(BiocGenerics, plot) to the NAMESPACE file
   3. Remove importFrom(graphics, plot) from the NAMESPACE file

If the generic were not defined in BiocGenerics, the solution would be

   0. Tell us (via the bioc-devel list) that foo should be in BiocGenerics?
   1. Introduce an explicit generic with setGeneric...
   2. Perhaps provide an S3 version of the S4 method, see ?Methods
   3. Export and document the explicit generic

Martin

>
> r62969 | mtmorgan at fhcrc.org | 2012-02-21 20:37:50 -0800 (Tue, 21 Feb
> 2012) | 6 lines
>
> code tidyup
>
> - avoid implicit plot, summary generic with BiocGenerics
> - avoid partial matching
> - remove empty documentation sections
>
>
>>
>> Many thanks,
>> Francesco
>>
>>
>> > sessionInfo()
>> R Under development (unstable) (2012-01-30 r58238)
>> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>>
>> locale:
>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] lumi_2.7.2 nleqslv_1.9.2 methylumi_2.1.13
>> Biobase_2.15.3 BiocGenerics_0.1.4
>>
>> loaded via a namespace (and not attached):
>> [1] affy_1.33.2 affyio_1.23.1 annotate_1.33.1
>> AnnotationDbi_1.17.15 BiocInstaller_1.3.7 DBI_0.2-5
>> grid_2.15.0 hdrcde_2.15
>> [9] IRanges_1.13.20 KernSmooth_2.23-7 lattice_0.20-0
>> MASS_7.3-16 Matrix_1.0-3 mgcv_1.7-13
>> nlme_3.1-103 preprocessCore_1.17.1
>> [17] RSQLite_0.11.1 tools_2.15.0 xtable_1.6-0
>> zlibbioc_1.1.1
>>
>>
>>
>>
>>
>>
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>
>


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