makefile

# makefile: Rnw -> tex -> pdf
# v 2.0
# .Rnw extension is automatically added
file_name = probability_dna

$(file_name).pdf: $(file_name).tex
	# protection against biber error
	# http://tex.stackexchange.com/questions/140814/
	rm -rf `biber --cache`

	# create pdf
	# will automatically run pdflatex/biber if necessary
	latexmk -xelatex -shell-escape $(file_name).tex
	# arara -v $(file_name).tex

	# clean auxillary files
	# latexmk -c $(file_name).tex

# $(file_name).tex : $(file_name).Rnw
#	Rscript -e "library(knitr); knit('$(file_name).Rnw')"


clean:
	-rm $(file_name).pdf 
	-rm $(file_name).fls 
	-rm $(file_name).log 
	-rm $(file_name).out 
	-rm $(file_name).aux 
	-rm $(file_name).fdb_latexmk 
	-rm $(file_name)-concordance.tex
	-rm $(file_name).idx
	-rm $(file_name).idx
	-rm $(file_name).ilg
	-rm $(file_name).toc
	-rm $(file_name).ind
	-rm $(file_name).bbl
	-rm $(file_name).run.xml
	-rm $(file_name).xdv
	-rm $(file_name).bcf
	-rm $(file_name).blg
	-rm $(file_name).synctex.gz