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Make-like build management, reimagined for R.

See below for installation instructions.

The idea

"make", when it works, is wonderful. Being able to change part of a complicated system and the re-make, updating only the parts of the system that have changed is great. While it gets some use It's very heavily tailored towards building software though. While make can be used to create reproducible research workflows (e.g. here and here), it is a challenge.

The idea here is to re-imagine a set of ideas from make but built for R. Rather than having a series of calls to different instances of R (as happens if you run make on R scripts), the idea is to define pieces of a pipeline within an R session. Rather than being language agnostic (like make must be), remake is unapologetically R focussed.

Note: This package is under heavy development (as of May 2015), so things may change under you if you start using this now. However, the core format seems to be working on some nontrivial cases that we are using in our own work. At the same time, if you're willing to have things change around a bit feel free to start using this and post issues with problems/friction/ideas etc and the package will reflect your workflow more.

Note: Between versions 0.1 and 0.2.0 the database format has changed. This will require rebuilding your project. This corresponds to adding the dependency on storr. Everything else should remain unchanged though.

What remake does

You describe the beginning, intermediate and end points of your analysis, and how they flow together.

There might be very few steps or very many, but remake will take care of stepping through the analysis in a correct order (there can be more than one correct order!).


Here's a very simple analysis pipeline that illustrates the basic idea:

  1. Download some data from the web into a local file
  2. Process that file to prepare it for analysis
  3. Create a plot from that file
  4. Create a knitr report that uses the same set of objects

The remakefile that describes this pipline might look like this:

  - code.R

    depends: plot.pdf

    command: download_data(target_name)

    command: process_data("data.csv")

    command: myplot(processed)
    plot: true
    depends: processed
    knitr: true

(this is a yaml file). The full version of this file, with explanations, is here.

You still need to write functions that carry out each step; that might look something like this, but it would define the functions download_data, processs_data and myplot. Remake can then be run from within R:

# [ BUILD ] data.csv            |  download_data("data.csv")
# [ BUILD ] processed           |  processed <- process_data("data.csv")
# [ BUILD ] plot.pdf            |  myplot(processed) # ==> plot.pdf
# [       ] all

The "BUILD": next to each target indicates that it is being run (which may take some time for a complicated step) and after the pipe a call is printed that indicates what is happening (this is a small white lie).

Rerunning remake:

# [    OK ] data.csv
# [    OK ] processed
# [    OK ] plot.pdf
# [       ] all

Everything is up to date, so remake just skips over things.

There are also special knitr targets:

# [    OK ] data.csv
# [    OK ] processed
# [       ] report.Rmd
# [  KNIT ]            |  knitr::knit("report.Rmd", "")

This arranges for the target processed, on which this depends (see the remakefile) to be passed through to knitr, along with all the functions defined in code.R, and builds the report from the knitr source report.Rmd (the source is here). Note that because processed was already up to date, remake skips rebuilding it.

remake can also be run from the command line (outside of R), to make it easy to include as part of a bigger pipeline, perhaps using make! (I do this in my own use of remake).

Rather than require that you buy in to some all-singing, all-dancing workflow tool, remake tries to be agnostic about how you work: there are no special functions within your code that you need to use. You can also create a linear version of your analysis at any time:

# source("code.R")
# download_data("data.csv")
# processed <- process_data("data.csv")
# pdf("plot.pdf")
# myplot(processed)

Other core features:

Real-world examples


Some tutorials on using remake with different datasets.


Install using devtools:


If you don't have devtools installed you will see an error "there is no package called 'devtools'"; if that happens install devtools with install.packages("devtools").

remake depends on several R packages, all of which can be installed from CRAN. The required packages are:

install.packages(c("R6", "yaml", "digest", "crayon", "optparse"))

We also depend on storr for object storage:


richfitz/remake documentation built on May 27, 2019, 8:27 a.m.