[Rd] package building problem under Windows Vista
Prof Brian Ripley
ripley at stats.ox.ac.uk
Sun Apr 20 23:00:00 CEST 2008
On Sun, 20 Apr 2008, Duncan Murdoch wrote:
> On 20/04/2008 1:21 PM, Prof Brian Ripley wrote:
>> On Sun, 20 Apr 2008, Duncan Murdoch wrote:
>>> On 20/04/2008 8:43 AM, Gabor Grothendieck wrote:
>>>> There does seem to be some general problem associated with Sweave
>>>> and graphics when I try it on my Vista system with
>>>>  "R version 2.7.0 RC (2008-04-17 r45367)"
>> There is no evidence whatsoever of 'some general problem', and it is quite
>> specific to that package. We've tested all the CRAN and BioC packages with
>> vignettes, and accounted for all the errors.
>>>> Using tradeCosts-article.Rnw from the tradeCosts package:
>>>> appears to work properly; however, if we try it from the
>>>> command line:
>>>> R CMD Sweave tradeCosts-article.Rnw
>>>> to simulate what happens when trying to build the package it
>>>> indicates that in chunk 2 that pdf is masked from grDevices.
>>> tradeCosts has its own pdf(), which is an S4 generic. Once you have
>>> attached that package, the regular pdf() device driver is hidden. So it
>>> looks as though running Sweave from the R console does the search in the
>>> intended way, but running it from R CMD Sweave finds the tradeCosts
>>> version of pdf() instead of the standard one.
>> Sweave does call grDevices::pdf explicitly. But that's not the issue as
>> R --slave < tradeCosts-article.R
>> also fails at
>> Calls: plot ... barplot -> barplot.default -> par -> pdf -> <Anonymous>
>> So the issue is that pdf() is getting called because no device has been
>> opened, and "pdf" is the default device. That seems quite reasonable to
>> me: if you create a function "pdf" high on the path it indicates that you
>> want that to be the default device. (And the default device is used.)
> I think there may be another problem. Running R on the Stangle output is
> different than running Sweave, because Sweave knows that certain chunks have
> fig=TRUE, and so it should set up the graphics device for them. I don't
> think there's a chunk in that file that does graphics without declaring
> fig=TRUE, so the original Sweave run should succeed, even if the run above
> So I still don't understand why in chunk 17 "pdf" is being used instead of
That's equally true of the example used in example(Sweave), and that puts
up a graphics device, just as this one does.
fig=TRUE asks for *additional* runs with devices set -- see the code in
makeRweaveLatexCodeRunner. If options$eval is true
if(options$eval) err <- evalFunc(ce, options)
is run (and if it isn't options$eps and options$pdf are not reached).
Or look at ?RweaveLatex which says
eval: logical ('TRUE'). If 'FALSE', the code chunk is not
evaluated, and hence no text or graphical output produced.
and see what gets generated.
Or (as I had done), put options(device=grDevice::pdf) in the first chunk
of the tradeCosts example, and see what gets plotted in Rplots.pdf.
Brian D. Ripley, ripley at stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
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