From simon.urbanek at r-project.org  Fri Apr 15 20:18:24 2011
From: simon.urbanek at r-project.org (Simon Urbanek)
Date: Fri, 15 Apr 2011 14:18:24 -0400
Subject: [Rd] DESCRIPTION file and Rd examples
In-Reply-To: <20110415130021.BLM73721@gimr.garvan.unsw.edu.au>
References: <20110415130021.BLM73721@gimr.garvan.unsw.edu.au>
Message-ID: <13B22E72-633B-452F-8F9C-1BB16A444EEB@r-project.org>


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
> 
> 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
> 
> 



[Rd] DESCRIPTION file and Rd examples
Simon Urbanek