[R] Sweave: conflict between setwd and \SweaveOpts{prefix.string=}

[Duncan Murdoch]

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