From D.Strbenac at garvan.org.au  Fri Apr 15 05:00:21 2011
From: D.Strbenac at garvan.org.au (Dario Strbenac)
Date: Fri, 15 Apr 2011 13:00:21 +1000 (EST)
Subject: [Rd] DESCRIPTION file and Rd examples
Message-ID: <20110415130021.BLM73721@gimr.garvan.unsw.edu.au>

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)
    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



[Rd] DESCRIPTION file and Rd examples
Dario Strbenac