System Shell

This is not a comprehensive lesson on using a command line interface (CLI), but we will be writing some shell code today. If you’re interested in learning more, I’d point you to the Software Carpentry lesson on The Unix Shell.

This will be, perhaps, the trickiest part of this workshop since the exact syntax and results will vary from platform to platform. Unfortunately, I have very little experience with macOS, so we might find it difficult to troubleshoot problems with the shell on Mac, and I apologize in advance for having mostly Windows-specific examples. I’ll try to generalize as much as I can.

Getting Started

Start by opening your favorite command line interface.

But Brian, I don’t have a favorite command line interface.

Neither do I. I have done a bit of dabbling, but I mostly use Window’s default, cmd.exe, even though I have PowerShell and Git bash ready to go. -1 nerd point for me 🤓 👎

If you don’t have a favorite, either, open the default:

  • Windows: cmd.exe
  • macOS: Terminal.app

(If you do have a favorite, you probably don’t need this module.)

If you start cmd.exe it should look something like this:

If you start Terminal.app, it should look something like this:

Besides the monotype font, they look pretty different (and I’m not talking about the background color!)

The cmd.exe prompt tells you what directory (folder) you are in. Mine says C:\Users\bsmit>. The C: indicates which “drive” I’m working on, which can be a physical drive (like a hard drive or a DVD drive) or a virtual drive (like a network location). By convention, C: always refers to the primary hard drive on a PC. (Fun fact, A: and B: were both reserved for floppy disk drives). Then comes the BACKSLASH. Windows is weird in that it is the only major operating system that uses the backslash (\) instead of the forward slash (/) to separate directories. Users\bsmit means I’m in a folder on my C: drive that is called Users and then a folder inside that called bsmit. On Windows, this folder is tied to your “user profile”. Finally, the > signals the end of the prompt, i.e., that’s where you start typing commands.

The Terminal.app has some slightly different information. The example I downloaded from the internet says MacBook-Pro-9:~ helloigor$ (the rest is a command). The first part is the machine you are connected to, most likely your local machine. In this case, it is called MacBook-Pro-9. The colon comes next, and then the directory (folder). On Unix-like systems (macOS and Linux), the tilde (~) refers to your root directory, or the base directory from which you navigate to all other directories on your machine. The next bit (here, helloigor) is your username, and the $ indicates the end of the prompt, i.e., that’s where you start typing commands.

Recall from the last module that there is a command to print out the contents of a directory. On Windows, type dir and on Mac type ls. Then press Enter.

Getting Around

What if we want to go somewhere else? In both command lines, we can use cd to change directory. We can then type either a full path or a relative path.

Say I am in a directory on my Windows machine called C:\User\bsmit. I print out my directory and I see a folder in my current location called Documents. The full path to the Documents folder is C:\User\bsmit\Documents, but relative to my current location, the path is simply Documents. As long as I am currently in C:\User\bsmit, I can get to documents by using cd and the relative path:

C:\Users\bsmit> cd Documents
C:\Users\bsmit\Documents>

This is way more convenient than typing out the full path, but if I’m in a completely different directory, perhaps the full path will be more appropriate. No matter where I am on my computer, I can get back to documents with:

C:\Windows\System32> cd C:\Users\bsmit\Documents
C:\Users\bsmit\Documents>

Now say I am in C:\Users\bsmit, and I want to get to my R library at C:\Users\bsmit\Documents\R\win-library\4.0\. If I want to use a relative path, I can do it all at once, or one folder at a time (which might be useful if I don’t know exactly where I’m going and I need to print the directory contents each time). Either approach will work:

C:\Users\bsmit> cd Documents\R\win-library\4.0
C:\Users\bsmit\Documents\R\win-library\4.0>

OR

C:\Users\bsmit> cd Documents
C:\Users\bsmit\Documents> cd R
C:\Users\bsmit\Documents\R> cd win-library
C:\Users\bsmit\Documents\R\win-library> cd 4.0
C:\Users\bsmit\Documents\R\win-library\4.0>

If I want to go up a level (to the parent directory), I can type cd ... If I want to go up two levels, I can type cd ..\...

C:\Users\bsmit\Documents\R\win-library\4.0> cd ..
C:\Users\bsmit\Documents\R\win-library>
C:\Users\bsmit\Documents\R\win-library> cd ..\..
C:\Users\bsmit\Documents>

Full paths and relative paths are fundamental concepts in computing, relevant to us whether we are working with R, from the command line, or in countless other contexts.

Running Programs

Now that we know how to get around, how do we run a program? Well, we can navigate to the program’s directory and then type the program’s name. This would be calling the program using its relative path. For example, I can run R from the command line:

C:\Users\bsmit> cd C:\Program Files\R\R-4.0.3\bin
C:\Program Files\R\R-4.0.3\bin> R.exe

We can also call programs using their absolute path without changing directories. (Note that we need double quotes here because of the space in Program Files. One good reason not to have spaces in your directories or filenames).

C:\Users\bsmit> "C:\Program Files\R\R-4.0.3\bin\R.exe"

We’ll see why this is useful later.

The System PATH

What if, for example, we needed to run R often from different directories? We might get pretty tired of typing C:\Program Files\R\R-4.0.3\bin\R.exe every time we need to run it.

Your operating system has a list of directories where commonly used programs live. That list is called the system PATH (usually written in all caps to distinguish from the path to a resource). If your program’s directory is on the PATH, you can omit the path when you call your program. For example, if C:\Program Files\R\R-4.0.3\bin\ was on my system’s path (it isn’t), I could be anywhere on my machine and type:

C:\Users\bsmit> R.exe

The PATH is a convenient way for other programs to know where a resource lives. For example, if you’re working in R on Windows and you want to build a package from source, R needs to know where the various Rtools *.exes live. It doesn’t necessarily know how your computer is setup or what your directory structure looks like. But if the path to Rtools is on the PATH, it doesn’t need to know. (Which is exactly why any of us using Windows had to add Rtools to the PATH when we installed it).

You might want to know what directories are on your path.

On Windows:

C:\Users\bsmit> PATH
PATH=C:\Rtools\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;C:\Program Files\Git\cmd;C:\Users\bsmit\AppData\Local\Microsoft\WindowsApps;C:\Users\bsmit\AppData\Roaming\TinyTeX\bin\win32;C:\Hugo\bin;

On Mac:

$ echo $PATH

Conclusion

This is hardly even a basic introduction to the system shell, but hopefully it gives us the basics we need for this workshop. There are a variety of programs you can use to run a shell, but cmd.exe is the default on Windows and Terminal.app is the default on Mac. While they look different, they have similar functionality. Both shells use cd to change directories. Both shells use relative paths and absolute paths. And both shells use a variable called PATH to store common paths to programs (.exe or .app).

The shell is very powerful, and if you can get some experience using it, you’ll unlock a much more efficient way to interact with your computer.

Workshop Table of Contents