From ripley at stats.ox.ac.uk  Sun Apr 20 23:00:00 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Sun, 20 Apr 2008 22:00:00 +0100 (BST)
Subject: [Rd] package building problem under Windows Vista
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	<480BA4FE.5020304@stats.uwo.ca>
Message-ID: <alpine.LFD.1.10.0804202135380.30178@gannet.stats.ox.ac.uk>

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
>>>> [1] "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:
>>>>
>>>>     setwd(path.to.tradeCosts-article.Rnw)
>>>>     Sweave("tradeCosts-article.Rnw")
>>>> 
>>>> 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 
> fails.
>
> So I still don't understand why in chunk 17 "pdf" is being used instead of 
> "grDevices::pdf".

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.

Try

options(device="pdf")
example(Sweave)

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



[Rd] package building problem under Windows Vista
Prof Brian Ripley