From D.Strbenac at garvan.org.au  Mon Apr 18 04:00:06 2011
From: D.Strbenac at garvan.org.au (Dario Strbenac)
Date: Mon, 18 Apr 2011 12:00:06 +1000 (EST)
Subject: [Rd] DESCRIPTION file and Rd examples
Message-ID: <20110418120006.BLN05010@gimr.garvan.unsw.edu.au>

It turns out what I needed was IRanges in the Imports: field. I assumed that require(GenomicRanges) at the top of my function would, as a result of loading GenomicRanges, implicitly already know about all the IRanges classes, because GenomicRanges itself depends on them.

---- Original message ----
>Date: Fri, 15 Apr 2011 20:34:54 -0700
>From: Martin Morgan <mtmorgan at fhcrc.org>  
>Subject: Re: [Rd] DESCRIPTION file and Rd examples  
>To: Simon Urbanek <simon.urbanek at r-project.org>
>Cc: D.Strbenac at garvan.org.au, r-devel at r-project.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
>
>
>-- 
>Computational Biology
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
>Location: M1-B861
>Telephone: 206 667-2793


--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia



[Rd] DESCRIPTION file and Rd examples
Dario Strbenac