From mtmorgan at fhcrc.org  Sat Apr 16 05:34:54 2011
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Fri, 15 Apr 2011 20:34:54 -0700
Subject: [Rd] DESCRIPTION file and Rd examples
In-Reply-To: <13B22E72-633B-452F-8F9C-1BB16A444EEB@r-project.org>
References: <20110415130021.BLM73721@gimr.garvan.unsw.edu.au>
	<13B22E72-633B-452F-8F9C-1BB16A444EEB@r-project.org>
Message-ID: <4DA90E5E.9020109@fhcrc.org>

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
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


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[Rd] DESCRIPTION file and Rd examples
Martin Morgan