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File System

Gaston Sanchez

Learning Objectives

  • Working with files in various directories
  • Identify relative path names
  • Writing Makefiles with

Files in several directories

The examples covered so far have all the input and output files located in one single directory. But this is rarely how most real projects are structured.

In this lesson, we are going to discuss a toy example of an “article” about the R project. All the directories and files are in the example folder 05-file-system/ which has the following structure:


The idea is to generate an html file R-project.html (containing some text about the R project), that is built with the .md files in sections/.

To make things a bit more interesting, the generated output file will be placed at the level of the parent directory (i.e. 05-file-system/)

Generating the html document

To generate the output R-project.html file from the 3 .md files, you would have to cd into sections/ and then run pandoc like so:

pandoc *.md -s -o R-project.html

But remember that we want R-project.html to be at the parent level. Assuming that you are inside sections/, you would need to mv the output file R-project.html one level up:

mv R-project.html ../

The Makefile

How do you tell Make to switch between sub-directories and move files to different locations? Very easy: using shell commands to navigate the file system.

Here’s how the Makefile looks like:

all: R-project.html

R-project.html: sections/ sections/ sections/
    cd sections; pandoc *.md -s -o R-project.html
    cd sections; mv R-project.html ../

Important things to keep in mind: the Makefile lives at the top level. All dependencies are in the sections/ sub-directory.

  • R-project.html is the target file

  • The dependencies are the markdown files inside the sections/ folder

  • The recipe involves two commands:

    • first we cd into sections/ and then call pandoc
    • then we cd again into sections/ and mv the target file one level up

All the commands for each rule have as a starting point the location where the Makefile is. This is why we need to cd into sections/ in order to run pandoc.

Note the use of the semicolon in the command:

cd sections; pandoc *.md -s -o R-project.html

the semicolon lets us group several related instructions in one single line.

Relative paths of image files

There is one last important detail that we need to mention. As you can tell from the file structure, there is an images/ folder. This is where the PNG files of the R logos are located.

Those logos are used inside the file If you take a look at this file, you will see a couple of lines like these:

### Old and New Logos

![R old logo](images/Rlogo-old.png)

### New Logo

![R new logo](images/Rlogo-new.png)

Pay attention to the path names of each image file. They are paths relative to the location of R-project.html. The output file is located at the top level, and this is exactly where images/ is located too. In this way R-project.html can load correctly the R logos.