I've been following the Getting started with Sweave guide and created a new project folder called MISC with a subfolder called Sweave.
I've placed my sample .Rnw file in this folder together with a copy of the Sweave.sty file. I then changed my R working directory to MISC\Sweave. Sweave does create the TEX file without problems, but then complains:
Project output file format not set in project
I've checked the project properties and I can't quite work out where I should set it. Any ideas?
P.S.: Does this mean that I will have to set this up for every single project I want to Sweave?
Since your .tex file is located in a folder within your project folder, you will have to add the directory/folder name to your specified .tex and .pdf filenames.
Project Properties > Latex Project Properties
for your 'MISC' project folder, the first text box, Main TeX File, should be something like '/Sweave/myfile.tex' where 'myfile.tex' is the name of your Sweave document with the .tex extension.To answer your P.S., if every project is in a separate project folder, you will have to set this up for every project since you have to specify single main .tex and output files.