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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