Turn a 'cmd_assign' Call Into a Makefile Rule

Extract a call to cmd_assign() from an R script, and turn it into a Makefile rule.

Usage

extract_make(path_file, dir_make = NULL)

Arguments

path_file

A path from dir_make to the R scripe containing the call to cmd_assign().

dir_make

The directory that contains the Makefile. The default is the current working directory.

Value

extract_make() is typically called for its side effect, which is to print a Makefile rule. However, extract_make() invisibly returns a text string with the rule.

The components of a Makefile rule

A Makefile rule produced by extract_make() normally looks something like this:

out/model.rds: src/model.R \
  data/cleaned.rds
       Rscript $^ $@ --use_log=TRUE

In this rule

• out/model.rds is the "target", i.e. the file that the rule creates;

• src/model.R and data/timeseries.rds are "prerequisites", i.e. files that are used to create the target;

• \ is a "line continuation character";

• at the start of the third line is a tab, telling make that the recipe for creating the target from the starts here;

• Rscript is a call to utils::Rscript();

• $^ is an automatic variable meaning "all the prerequisites" and $@ is an automatic variable meaning "the target", so that Rscript $^ $@ expands to Rscript src/model.R data/cleaned.rds out/model.rds; and

• --use_log=TRUE is a named argument that Rscript passes to src/model.R

Using extract_make() to build a data analysis workflow

• Step 1. Write the R file that carries out the step in analysis (eg tidying data, fitting a model, making a graph.) This file will contain a call to cmd_assign(), and will appear in the first line of the Makefile rule. When writing and testing the file, use cmd_assign() interactively.

• Step 2. Once the R file is working correctly, call extract_make(), and add the rule to your Makefile.

When using extract_make(), it is a good idea to set the current working directory to the project directory (something that will happen automatically if you are using RStudio projects.)

Location of the Makefile

The Makefile normally sets at the top of the project, so that the project folder looks something like this:

Makefile
- data/
- src/
- out/
report.qmd

Identifying file arguments

To construct the Makefile rule, extract_make() needs to be able to pick out arguments that refer to file names. To do so, it uses the following heuristic:

• if the call includes arguments whose names start with a dot, then these arguments are assumed to refer to file names;

• otherwise, find arguments whose values actually are file names (as determined by file.exists()), or that look like they could be.

References

• Project Management with Make Makefiles in data analysis workflows

• GNU make Definitive guide

• Command-Line Programs Introduction to Rscript

See also

• extract_shell() Shell script equivalent of extract_make()

• makefile() Create a Makefile from calls to cmd_assign()

• cmd_assign() Process command line arguments

• Quick Start Guide How to use cmd_assign()

• Modular Workflows for Data Analysis Safe, flexible data analysis workflows

• littler Alternative to Rscript

Examples

library(fs)
library(withr)
with_tempdir({

  ## create 'src'  directory
  dir_create("src")

  ## put an R script containing a call to
  ## 'cmd_assign' in the 'src' directory
  writeLines(c("cmd_assign(x = 1, .out = 'out/results.rds')",
               "results <- x + 1",
               "saveRDS(results, file = .out)"),
             con = "src/results.R")

  ## call 'extract_make()'
  extract_make(path_file = "src/results.R",
               dir_make = ".")

})
#> out/results.rds: ./src/results.R
#> 	Rscript $^ $@ --x=1