Makefiles for R/LaTeX projects


31 October 2012

reproducible research

Updated: 21 November 2012

Make is a marvellous tool used by programmers to build software, but it can be used for much more than that. I use make whenever I have a large project involving R files and LaTeX files, which means I use it for almost all of the papers I write, and almost of the consulting reports I produce.

If you are using a Mac or Linux, you will already have make installed. If you are using Windows and have Rtools installed, then you will also have make. Otherwise, Windows users will need to install it. One implementation is in GnuWin.

A typical project of mine will include several R files containing code that fit some models, and generate tables and graphs. I try to set things up so I can re-create all the results by simply running the R files. Then I will have a LaTeX file which contains the paper or report I am writing. The tables and graphs produced by R are pulled in to the LaTeX file. Consequently, all I need to do is run all the R files, and then process the tex file, and the paper/report is generated.

Make relies on a Makefile to determine what it must do. Essentially, a Makefile specifies what files must be generated first, and how to generate them. So I need a Makefile that specifies that all the R files must be processed first, and then the LaTeX file.

The beauty of a Makefile is that it will only process the files that have been updated. It is smart enough not to re-run code if it has already been run. So if nothing has changed, running make does nothing. If only the tex file changes, running make will re-compile the tex document. If the R code has changed, running make will re-run the R code to generate the new tables and graphs, and then re-compile the tex document. All I do is type make and it figures out what is required.

A Makefile for LaTeX

It is easy to tell if the latex document needs compiling — make simply has to check that the pdf version of the document is older than the tex version of the document. Here is a simple Makefile that will just handle a LaTeX document.

TEXFILE= paper
$(TEXFILE).pdf: $(TEXFILE).tex
    latexmk -pdf -quiet $(TEXFILE)

The first line specifies the name of my file, in this case paper.tex. The second line specifies that the pdf file must be created from the tex file, and the last line explains how to do that. MikTeX users might prefer pdftexify instead of latexmk.

To use the above Makefile, copy the code into a plain text file called Makefile and store it in the same directory as your tex file. Change the first line so the name of your tex file (without the extension) is used. Then type make from a command prompt within the same directory as the tex file, and it should do whatever is necessary to convert your tex to pdf.

Of course, you wouldn’t normally bother with a Makefile if that is all it did. But throw in a whole lot of R files, and it becomes very worthwhile.

A Makefile for R and LaTeX

We need a way to allow make to be able to tell if an R file has been run. If the R files are run using


then the output is saved as file.Rout. Then make only has to check if file.Rout is older than file.R.

I also like to strip out all the white space from the pdf figures created in R before I put them in a LaTeX document. There is a nice command pdfcrop which does that. (You should already have it on a Mac or Linux, and also on Windows provided you are using MikTeX.) So I also want my Makefile to crop all images if they have not already been done. Once an image is cropped, an empty file of the form file.pdfcrop is created to indicate that file.pdf has already been cropped.

OK, now we are ready for my marvellous Makefile.

# Usually, only these lines need changing
TEXFILE= paper
FIGDIR= ./figs

# list R files
RFILES := $(wildcard $(RDIR)/*.R)
# pdf figures created by R
PDFFIGS := $(wildcard $(FIGDIR)/*.pdf)
# Indicator files to show R file has run
# Indicator files to show pdfcrop has run
CROP_FILES:= $(PDFFIGS:.pdf=.pdfcrop)


# May need to add something here if some R files depend on others.

$(RDIR)/%.Rout: $(RDIR)/%.R $(RDIR)/functions.R
    R CMD BATCH $<

$(FIGDIR)/%.pdfcrop: $(FIGDIR)/%.pdf
    pdfcrop $< $< && touch $@

# Compile main tex file and show errors
    latexmk -pdf -quiet $(TEXFILE)

# Run R files

# View main tex file
view: $(TEXFILE).pdf
    evince $(TEXFILE).pdf &

# Clean up stray files
    rm -fv $(OUT_FILES)
    rm -fv $(CROP_FILES)
    rm -fv *.aux *.log *.toc *.blg *.bbl *.synctex.gz
    rm -fv *.out *.bcf *blx.bib *.run.xml
    rm -fv *.fdb_latexmk *.fls
    rm -fv $(TEXFILE).pdf

.PHONY: all clean

Download the file here. For most projects I copy this file into the main directory of my project, then all I have to do is modify the first few lines. RDIR specifies where the R files are kept and FIGDIR specifies where the figures are kept. Normally I keep these together, but sometimes they might be in separate directories.

Now make will do everything necessary — run the R files, crop the pdf graphics, and process the latex document. But it won’t do any steps that don’t need doing.

make R will only process the R files.

make view will run the pdf viewer, after updating the pdf file if necessary.

make clean will delete all the files generated by latex or by make, so that the entire process must be run again at the next make command.

Notice that my R files all depend on functions.R. This is a file that contains project-specific functions. If this file is updated, all the other R files will need updating also.

For many projects, some R files will depend on some others having already run. For example, read.R may read in the data and reformat it for analysis, while plot.R might produce some graphs assuming that read.R has already run. To ensure make knows about this dependency, we need to add a line

$(RDIR)/plot.Rout: $(RDIR)/plot.R $(RDIR)/functions.R $(RDIR)/read.R
    R CMD BATCH $<

This should be inserted where I have the comment # May need to add something here if some R files depend on others.

This Makefile works on Linux. Mac and Windows users will need to replace evince by whatever pdf viewer they prefer.