Re: [Rd] DESCRIPTION file and Rd examples

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Fri, 15 Apr 2011 20:34:54 -0700

On 04/15/2011 11:18 AM, Simon Urbanek wrote:
>
> On Apr 14, 2011, at 11:00 PM, Dario Strbenac wrote:
>
>> I have a confusing error from R CMD check that I don't get when running the example manually by hand.
>>
>> In the \examples section of an Rd file, I create a GRanges object, then I call a function with the GRanges object, whose first 2 lines are
>>
>> require(GenomicRanges)
>
> require() is doesn't guarantee that the package will load, so I think what you meant to write was more
>
> if (require(GenomicRanges, quietly=TRUE)) {
> ...
>
>> annoDF<- as.data.frame(anno) # anno is the GRanges object.
>>
>> and that second line gives:
>>
>> Error in as.data.frame.default(anno) :
>> cannot coerce class 'structure("GRanges", package = "GenomicRanges")' into a data.frame
>> Calls: annoGR2DF ... annoGR2DF -> .local -> as.data.frame -> as.data.frame.default

Try IRanges::as.data.frame(anno)

I'm guessing that your call finds base::as.data.frame, perhaps because some earlier example has already require'd GenomicRanges, and that it's definition of as.data.frame has been masked some time in between.

It's too complicated to debug in detail; R CMD check produces a file <pkg>.Rcheck/<pkg>-Ex.R that contains the compiled example code, and it is in the evaluation of this file that the error occurs. So you could dissect it to discover the gory details.

Martin

>>
>> I have GenomicRanges listed in my Imports: field, and IRanges in the Suggests: of the DESCRIPTION file (it's require()d elsewhere). I'm trying to avoid putting packages in Depends: , so my package loads fast. Any tips of what I'm not understanding properly ?
>>
>> Thanks.
>>
>> --------------------------------------
>> Dario Strbenac
>> Research Assistant
>> Cancer Epigenetics
>> Garvan Institute of Medical Research
>> Darlinghurst NSW 2010
>> Australia
>>
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>>
>>
>
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