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11-pattern-substitutions.md

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Pattern Substitutions

Gaston Sanchez

Learning Objectives

  • Basics of pattern substitutions
  • Use the wildcard function
  • Use the % operator

Motivation

Let’s consider the example used in the previous two lessons. This involves executing four R scripts—script1.R, script2.R, script3.R, script4.R— in batch mode via the command R CMD BATCH --no-save.

We’ve seen the naive option of writing a Makefile like this:

.PHONY: all clean

all: script1.Rout script2.Rout script3.Rout script4.Rout

script1.Rout: script1.R
    R CMD BATCH --no-save script1.R

script2.Rout: script2.R
    R CMD BATCH --no-save script2.R

script3.Rout: script3.R
    R CMD BATCH --no-save script3.R

script4.Rout: script4.R
    R CMD BATCH --no-save script4.R

clean:
    rm -f *.Rout

A makefile like the one above is obviously not very efficient. Instead, we can define a variable rcmd that refers to the R command in each recipe.

Likewise, we can use a pattern rule for all the targets:

%.Rout: %.R
    $(rcmd) $<

All the previous elements can be combined in the following makefile:

rcmd = R CMD BATCH --no-save

.PHONY: all clean

all: script1.Rout script2.Rout script3.Rout script4.Rout

%.Rout: %.R
    $(rcmd) $<

clean:
    rm -f *.Rout

As you can tell, the only part that still has some repetition has to do with the prerequisites of the target all (i.e. all the .Rout files).

It would be nice if you could group all the .Rout in one single variable. Let’s see how to do this.

Using the wildcard function

Remember Make’s wildcard function? We can use it to define a variable with the list of input .R files:

rfiles = $(wildcard *.R)

The good news is that we have a variable rfiles that contains the names of all the R script files. The problem now is how to take advantage of rfiles?

You may be tempted to do something like this (with some tragic consequences):

rcmd = R CMD BATCH --no-save
rfiles = $(wildcard *.R)

$(rfiles)out: $(rfiles)
    $(rcmd) $(rfiles)

Using Pattern Substitution

To create a variable that contains the name of the .Rout files, we are going to use the function patsubst (for pattern substitution).

The idea is to take advantage of the variable rfiles—which has the value: script1.R script2.R script3.R script4.R—and define a pattern of characters to be substituted.

The function patsubst has the following usage:

$(patsubst pattern,replacement,text)

patsubst finds whitespace-separated words in text that match the provided pattern and replaces them with the specified replacement.

A pattern may contain a % which acts as a wildcard, matching any number of any characters within a word. If replacement also contains a %, the % is replaced by the text that matched the % in pattern. Only the first % in the pattern and replacement is treated this way; any subsequent % is unchanged.

In our example, we can use patsubst to create the variable rout like thi:

rfiles = $(wildcard *.R)

rout = $(patsubst %.R,%.Rout,$(rfiles))

  • %.R is the pattern to be match in the provided text

  • $(rfiles) is the provided text (i.e. script1.R script2.R script3.R script4.R)

  • %.Rout is the replacement

In other words, patsubst will look for the pattern .R in rfiles, and will replace the pattern with .Rout. This implies that rout will be a text formed by: script1.Rout script2.Rout script3.Rout script4.Rout.

Having obtained the variable rout with the list of output files, we can complete the Makefile as follows:

rcmd = R CMD BATCH --no-save
rfiles = $(wildcard *.R)

rout = $(patsubst %.R,%.Rout,$(rfiles))

all: $(rout)

%.Rout: %.R
    $(rcmd) $<

clean:
    rm -f *.Rout

Note that the variable rout is used as the prerequisite of the target all. You don’t need to write a long list of prequisites for all.

Make Documentation

Functions for String Substitution and Analysis