Example Makefile used when dealing with Sweave

Makefile

## $* = filename without extension
## $@ = the output file
## $< = the input file

.SUFFIXES: .tex .pdf .Rnw .R

MAIN = lecture
INCLUDES = chapter1 chapter2 chapter3
TEX = $(INCLUDES:=.tex) 
RFILES = $(INCLUDES:=.R)
RNWFILES = $(INCLUDES:=.Rnw)

all: $(TEX) $(MAIN).pdf

$(MAIN).pdf: $(TEX) $(MAIN).tex

R: $(RFILES)

view: all
	xpdf $(MAIN).pdf &

.Rnw.R:
	R CMD Stangle $<

.Rnw.tex:
	Rscript -e "require(highlight); \
	driver = HighlightWeaveLatex(boxes = TRUE);\
	Sweave('$*.Rnw', driver = driver ); "

.tex.pdf:
	rubber --pdf $*.tex # Or use pdflatex

clean:
	rm -fv $(MAIN).pdf $(TEX) $(RFILES)
	rm -fv *.aux *.dvi *.log *.toc *.bak *~ *.blg *.bbl *.lot *.lof
	rm -fv  *.nav *.snm *.out *.pyc \#*\# _region_* _tmp.* *.vrb
	rm -fv Rplots.pdf *.RData movie.csv.gz mygraph*

cleaner:
	make clean
	rm -fv ../graphics/*.pdf
	rm -fvr auto/