[BioC] help needed in namespace definition

[Hervé Pagès]

Hi Frederic,

On 11-08-12 11:09 AM, Frederic Fournier wrote:
> Hello,
>
> I'm in need of some help with what I think is namespace administration. I'm
> modifying some methods of the package PICS so that they can take GRanges
> object (from the GenomicRanges package) as input.
> In doing so, I want to use the method as.data.frame(GRanges) defined in the
> GenomicRanges package.
>
> But when I try to transform a GRanges object in a data.frame, I get this
> error:
> "Error in as.data.frame.default(gr, row.names = NULL, optional = FALSE) :
>    cannot coerce class '"GRanges"' into a data.frame"
>
> In the DESCRIPTION file of the package, I have included
>      "Imports: ..., GenomicRanges, ..."
>
> In the NAMESPACE file of the package, I have included:
>       "importFrom(GenomicRanges)
>       importClassesFrom(GenomicRanges, GRanges)
>       importMethodsFrom(GenomicRanges, as.data.frame)"
>
> If I do a showMethods("as.data.frame") from PICS namespace environment, I
> get:
>> showMethods(as.data.frame)
> Function: as.data.frame (package base)
> x="ANY"
> x="AtomicList"
> x="DataFrame"
> x="DataFrameList"
> x="GappedAlignments"
> x="GappedRanges"
> x="GenomicRanges"
> x="GRangesList"
> ...
>
> which shows that the "as.data.frame" method defined in GenomicRanges is
> available (x="GRanges" is inherited from x="GenomicRanges"), but still, I
> can't use as.data.frame on a GRanges object without getting this error:
> "Error in as.data.frame.default(gr, row.names = NULL, optional = FALSE) :
>    cannot coerce class '"GRanges"' into a data.frame"
>
> Any idea what I am doing wrong?

Importing as.data.frame from IRanges seems to solve the problem.
as.data.frame is implicitly turned into an S4 generic when IRanges is
installed. Output of R CMD INSTALL IRanges:

   ...
   Creating a generic function for "as.data.frame" from package "base" 
in package “IRanges”
   ...

Cheers,
H.

>
> Also, if anyone knows a good source of information on the syntax to use in
> the NAMESPACE and DESCRIPTION files?
>
> Thank you very much!
>
> Frederic
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319