R help - Jan 2009 - Sweave: conflict between setwd and \SweaveOpts{prefix.string=}

Hello

I think there is a conflict between setwd() and 
\SweaveOpts{prefix.string=}. In the same document, those both command 
get Sweave confuse the files and directories. See:

say my .Rnw document is in File1

If one inserts some setwd() for another file:
-setwd(File2)

then the command \SweaveOpts{prefix.string=graphics/Rplots} will search 
the "graphics" folder in File2 because of command setwd(File2) and not
in File1 where the .Rnw file is and as is said in Sweave Manual A10.

Hence Latex get really confused and does not work anymore: the command 
\includegraphics looks for folder "graphics" in the usual File1 but 
those can have been stored in File2.

I tried to add some:
\usepackage{graphicx}
\graphicspath{{../File2/graphics/}}
but resulot was not so convincing

Is there anyway to avoid this? Thanks!

Matthieu Stigler wrote:
> Hello
>
> I think there is a conflict between setwd() and 
> \SweaveOpts{prefix.string=}. In the same document, those both command 
> get Sweave confuse the files and directories. See:
>
> say my .Rnw document is in File1
>
> If one inserts some setwd() for another file:
> -setwd(File2)
>
> then the command \SweaveOpts{prefix.string=graphics/Rplots} will search 
> the "graphics" folder in File2 because of command setwd(File2)
and not
> in File1 where the .Rnw file is and as is said in Sweave Manual A10.
>
> Hence Latex get really confused and does not work anymore: the command 
> \includegraphics looks for folder "graphics" in the usual File1
but
> those can have been stored in File2.
>
> I tried to add some:
> \usepackage{graphicx}
> \graphicspath{{../File2/graphics/}}
> but resulot was not so convincing
>
> Is there anyway to avoid this? Thanks!
>   
You could use a fully qualified prefix, so it doesn't matter what the 
current directory is when you save a plot.

Or you could avoid setwd().

Or you could change back to the original directory before drawing a plot.

It would probably make sense for Sweave to do the last of these 
internally:  it is mixing up characteristics of the session it's running 
in with characteristics of the session it is running.  However, this is 
a pretty strange case, and I'm not sure fixing it will be a high priority.

Duncan Murdoch

Have you tried specifying an absolute path in prefix.string instead of a
relative one?

HTH,

Thierry 


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be 
www.inbo.be 

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Matthieu Stigler
Verzonden: dinsdag 20 januari 2009 12:53
Aan: r-help at r-project.org
Onderwerp: [R] Sweave: conflict between setwd and
\SweaveOpts{prefix.string=}

Hello

I think there is a conflict between setwd() and 
\SweaveOpts{prefix.string=}. In the same document, those both command 
get Sweave confuse the files and directories. See:

say my .Rnw document is in File1

If one inserts some setwd() for another file:
-setwd(File2)

then the command \SweaveOpts{prefix.string=graphics/Rplots} will search 
the "graphics" folder in File2 because of command setwd(File2) and not
in File1 where the .Rnw file is and as is said in Sweave Manual A10.

Hence Latex get really confused and does not work anymore: the command 
\includegraphics looks for folder "graphics" in the usual File1 but 
those can have been stored in File2.

I tried to add some:
\usepackage{graphicx}
\graphicspath{{../File2/graphics/}}
but resulot was not so convincing

Is there anyway to avoid this? Thanks!

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