Why?

May 12, 2011

Makefiles and Sweave

Filed under: Computing, latex, R — Tags: , , , , — csgillespie @ 8:19 pm

A Makefile is a simple text file that controls compilation of a target file. The key benefit of using Makefile is that it uses file time stamps to determine if a particular action is needed. In this post we discuss how to use a simple Makefile that compiles a tex file that contains a number of \include statements. The files referred to by the \include statements are Sweave files.

Suppose we have a master tex file called master.tex. In this file we have:

\include chapter1
\include chapter2
\include chapter3
....

where the files chapter1, chapter2, chapter3 are Sweave files. Ideally, when we compile master.tex, we only want to sweave if the time stamp of chapter1.tex is older than the time stamp of chapter1.Rnw. This conditional compiling is even more important when we have a number of sweave files.

Meta-rules

To avoid duplication in a Makefile, it’s handy to use meta-rules. These rules specify how to convert from one file format to another. For example,

.Rnw.tex:
    R CMD Sweave $<

is a meta rule for converting an Rnw file to a tex file. In the above meta-rule, $< is the filename, i.e. chapter1.Rnw. Other helpful meta rules are:

.Rnw.R:
    R CMD Stangle $<

which is used to convert between Rnw and R files. We will also have a meta-rule for converting from .tex to .pdf.

For meta-rules to work, we have to list all the file suffixes that we will convert between. This means we have to include the following line:

.SUFFIXES: .tex .pdf .Rnw .R

Files to convert

Suppose we have a master tex file called master.tex and a sweave file chapter1.Rnw. This means we need to convert from:

  • master.tex to master.pdf
  • chapter1.Rnw to chapter1.tex
  • chapter1.Rnw to chapter1.R

Obviously, we don’t want to write down every file we need – especially if we have more than one sweave file. Instead, we just want to state the master file and the Rnw files. There are a couple of ways of doing this, however, the following way combines flexibility and simplicity. We first define the master and Rnw files:


##Suppose we have three Sweave files with a single master file
MAIN = master
RNWINCLUDES = chapter1 chapter2 chapter3

Now we add in the relevant file extensions

TEX = $(RNWINCLUDES:=.tex)
RFILES = $(RNWINCLUDES:=.R)
RNWFILES = $(INCLUDES:=.Rnw)

In the Makefile, whenever we use the $(TEX) variable, it is automatically expanded to

chapter1.tex chapter2.tex chapter3.tex

A similar rule applies to $(RFILES) and $(RNWFILES).

Conversion rules

We now define the file conversion rules. When we build our pdf file we want to:

  • build the tex file from Rnw file only if the Rnw files have changed or if the tex file doesn’t exist.
  • build the pdf file from the tex file only if master.tex file has changed or one of the Rnw files has changed, or the pdf file doesn’t exist.

We can accomplish this with the following rule:

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

Typically, I also have a dependencies on a graphics directory and a bibtex file

$(MAIN).pdf: $(TEX) $(MAIN).tex refs.bib graphics/*.pdf

We also have a conversion rule to R files.

R: $(RFILES)

Cleaning up

We also use sweave to clean up after ourselves:

clean:
rm -fv $(MAIN).pdf $(MAIN).tex $(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

The complete Makefile

In the Makefile below:

  • make all – creates master.pdf;
  • make clean – deletes all files created as part of the latex and sweave process;
  • make R – creates the R files from the Rnw files.

.SUFFIXES: .tex .pdf .Rnw .R

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

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

R: $(RFILES)

view: all
    acroread $(MAIN).pdf &

.Rnw.R:
    R CMD Stangle $<

.Rnw.tex:
    R CMD Sweave $<

.tex.pdf:
    pdflatex $<
    bibtex $*
    pdflatex $<
    pdflatex $<

clean:
    rm -fv $(MAIN).pdf $(MAIN).tex $(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

Useful links

  • Jeromy Anglim’s post on Sweave and Make;
  • Ross Ihaka’s Makefile on Sweave;
  • Instead of using a Makefile, you could also use a shell script;
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2 Comments »

  1. Thanks alot for this. It has definitly made my life much easier. I have been trying to get this system to work for my thesis, or joint work. I modified the first few lines of your makefile, so it looks through sub directories for files.

    MAIN = main
    RNWINCLUDES = test
    DIRECTORIES = chapter1 chapter2 chapter3
    TEX = $(DIRECTORIES)/$(RNWINCLUDES:=.tex)
    RFILES = $(DIRECTORIES)/$(RNWINCLUDES:=.R)
    RNWFILES = $(DIRECTORIES)/$(INCLUDES:=.Rnw)

    Comment by Jason — June 21, 2011 @ 12:40 pm

    • Thanks for the tip Jason. Funnily enough, I only had your file structure for my thesis. For papers I can get away with something a bit simpler.

      Comment by csgillespie — July 29, 2011 @ 2:05 pm


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