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makefile
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# 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