workflow between Latex and R screwed - r

Question

Trying to write my second Latex file
\documentclass{article}
\title{simple Sweave script}
\usepackage{/Users/Brenden/Documents/R/R-2.15.1/share/texmf/tex/latex/Sweave}
\begin{document}
\maketitle
This is a simple script to demonstrate Sweave. Let's
begin by generating some results
<<>>=
x=rnorm(30)
y=rnorm(30)
mean(x)
cor(x,y)
#
and follow that up with some random text
\end{document}
File saved with .Rnw as extension. I could then use Sweave under R to convert the file to tex. I then run pdflatex under cmd to get my .pdf file. R is stored under /Users/Brenden/Documents. MiKTex is stored under /Users/Brenden/Desktop.
It is said that usually the line of "usepackage" is not needed, as when I run Sweave under R, a line of "usepackage{Sweave}" will be added to the tex file which is stored under /Users/Brenden/Documents. However, if I don't put in userpackage line, when I run pdflatex under cmd (either under /Documents or /Desktop), I got a messsage that says "Sweave.sty not found". So I have been through this trouble by always adding a line of usepackage with a detailed path to help circumvent the problem. Although the "Sweave.sty not found" problem is circumvented, I do notice that when I run pdflatex under cmd, I got the response
LaTeX Warning: You have requested package '/Users/Brenden/Documents/R/R-
2.15.1/share/texmf/tex/latex/Sweave', but the package provides "Sweave'.
Then it runs through several files with .sty under MiKTex
(C:\Users\Brenden\Desktop\MiKTex\tex\latex\base\ifthen.sty)
(C:\Users\Brenden\Desktop\MiKTex\tex\latex\graphics\graphicx.sty)
(C:\Users\Brenden\Desktop\MiKTex\tex\latex\graphics\keyval.sty)
(C:\Users\Brenden\Desktop\MiKTex\tex\latex\graphics\graphics.sty)
(C:\Users\Brenden\Desktop\MiKTex\tex\latex\graphics\trig.sty)
...
to eventually create a .pdf
From another post on Stackoverflow, it is said, "That path is set automatically when you install LaTeX; it's your personal texmf tree and you can put any style or class files you want LaTeX to find there. The directory names don't matter, it searches recursively in them for Sweave.sty". To me, however, clearly my MiKTex could not find the Sweave.sty unless I specify the path. And even with the path specification, LaTex still gives me a warning. Could someone explain to me where I screwed up (during installing MiKTex, perhaps? ) so that I could help MiKtex find its way to Sweave without my specifying the path?
Thank you.

Answer 1

In the MiKTeX Settings program, there is a tab called "Roots". It is there that you can specify where additional .sty files can be found. In your case, I believe that you will want to add C:\Users\Brenden\Documents\R\R-2.15.1\share\texmf as an additional root. Doing this, any of the TeX programs will be able to find Sweave.sty whether run from inside R or from the command line.

Answer 2

It is annoying to be always distracted by little devils like this (new concept texmf tree, endless environment variables TEXINPUTS, SWEAVE_STYLEPATH_DEFAULT, ...). You will never worry about LaTeX packages if you use knitr, and if you like the Sweave style, you can simply put render_sweave() in the document like:
\documentclass{article}
\title{simple Sweave script}
<<setup, include=FALSE>>=
render_sweave()
#
\begin{document}
\maketitle
This is a simple script to demonstrate Sweave. Let's
begin by generating some results
<<>>=
x=rnorm(30)
y=rnorm(30)
mean(x)
cor(x,y)
#
and follow that up with some random text
\end{document}
Save it as, say, test.Rnw and compile it with
library(knitr); knit('test.Rnw') # or knit2pdf('test.Rnw')
And I guess you are probably better off without render_sweave() (i.e. use the default LaTeX style in knitr).

Answer 3

I suspect the path referred to in the other post is the path to your personal texmf tree, which is not where Sweave puts it. One option is to move it to your personal texmf tree, but the usual method nowadays, I believe, is to run pdflatex from within R, like this:
texi2dvi("foo.tex", pdf = TRUE)
I think you can also have Sweave add the full path automatically by adding
export SWEAVE_STYLEPATH_DEFAULT="TRUE"
to your .bashrc file, or whatever the equivalent would be on your system.

Answer 4

At the command line, R CMD sets up the environment with variables appropriate for running R, for instance on Windows
C:\Users\mtmorgan> "c:\Program Files\R\R-2.15.1\bin\R" CMD set
includes (this is not found if one types set at the command line)
TEXINPUTS=.;c:/PROGRA~1/R/R-215~1/.1/share/texmf/tex/latex;
and so
C:\Users\mtmorgan> "c:\Program Files\R\R-2.15.1\bin\R" CMD pdflatex myfile.tex
will find Sweave.sty. Also, tools::texi2dvi can be invoked from within R.

Answer 5

I eventually end up with the following solution:
install.packages("tinytex")
require("tinytex")}
install_tinytex(force = TRUE)
Sweave( "Report.Rnw" , encoding = "utf8" )
xelatex('Report.tex')
This code install TinyTex, then you can compile with pdflatex(), xelatex() or lualatex().