Writing Frictionless R Package Wrappers — Building A Basic R Package

This article is originally published at https://rud.is/b

Before we start wrapping foreign language code we need to make sure that basic R packages can be created. If you’ve followed along from the previous post you have everything you need to get started here. Just to make sure, you should be able to fire up a new RStudio session and execute the following R code and see similar output. If not, you’ll need to go through the steps and resources outlined there before continuing.

pkgbuild::check_build_tools()
### Your system is ready to build packages!

Also: the {bookdown} version should now always match the blog post (apart from some verbiage changes to denote it’s in a book vs a series of blog posts). You can refer to it at any time via — https://rud.is/books/writing-frictionless-r-package-wrappers/.

Configuring {devtools}

We’re going to rely on the {devtools} package for many operations and the first thing you should do now is execute help("create", "devtools") in an RStudio R console to see the package documentation page where you’ll see guidance pointing you to devtools::use_description() that lists some R session options() that you can set to make your package development life much easier and quicker. Specifically, it lets you know that you can setup your ~/.Rprofile to include the certain options settings which will automatically fill in fields each time you create a new package vs you either specifying these fields manually in the package creation GUI or as parameters to devtools::create().

A good, minimal setup would be something like:

options(
  usethis.description = list(
    `Authors@R` = 'person("Some", "One", email = "[email protected]", role = c("aut", "cre"),
                          comment = c(ORCID = "YOUR-ORCID-ID"))',
    License = "MIT + file LICENSE"
  )
)

NOTE: If you do not have an “ORCID” you really should get one (they’re free!) by heading over to
— https://orcid.org/ — and filling in some basic information.

Take a moment to edit your ~/.Rprofile. If you’re not sure about how to do that there is an excellent chapter in Efficient R Programming¹ which walks you through the process.

Once you’ve added or verified these new options() settings, restart your R session.

Creating A Package

We’re almost ready to create and build a basic R package. All R packages live in a package directory and I highly suggest creating a packages directory right off your home directory (e.g. “~/packages“) or someplace where you’ll be able to keep them all organized and accessible. The rest of these posts will assume you’re using “~/packages” as the

With {devtools} now pre-configured, use the RStudio R Console pane to execute the following code which should produce similar output and open up a new RStudio session with the new package directory:

devtools::create("~/packages/myfirstpackage") 
## ✔ Creating '/Users/someuser/packages/myfirstpackage/'
## ✔ Setting active project to '/Users/someuser/packages/myfirstpackage'
## ✔ Creating 'R/'
## ✔ Writing 'DESCRIPTION'
## Package: myfirstpackage
## Title: What the Package Does (One Line, Title Case)
## Version: 0.0.0.9000
## Authors@R (parsed):
##     * Bob Rudis <[email protected]> [aut, cre] (<https://orcid.org/0000-0001-5670-2640>)
## Description: What the package does (one paragraph).
## License: MIT + file LICENSE
## Encoding: UTF-8
## LazyData: true
## ✔ Writing 'NAMESPACE'
## ✔ Writing 'myfirstpackage.Rproj'
## ✔ Adding '.Rproj.user' to '.gitignore'
## ✔ Adding '^myfirstpackage\\.Rproj$', '^\\.Rproj\\.user$' to '.Rbuildignore'
## ✔ Opening '/Users/someuser/packages/myfirstpackage/' in new RStudio session
## ✔ Setting active project to '<no active project>'

The directory structure will look like this:

.
├── DESCRIPTION
├── NAMESPACE
├── R/
└── myfirstpackage.Rproj

At this point we still do not have a “perfect” R package. To prove this, use the R console to run devtools::check() and — after some rather verbose output — you’ll see the following lines at the end:

> checking DESCRIPTION meta-information ... WARNING
  Invalid license file pointers: LICENSE

0 errors ✓ | 1 warning x | 0 notes ✓

Since we’re saying that our package will be using the MIT license, we need to ensure there’s an associated LICENSE file which we can do by executing usethis::use_mit_license() which will create the necessary files and ensure the License field in the DESCRIPTION file is formatted properly.

If you run devtools::check() again, now, your final line should report:

## 0 errors ✓ | 0 warnings ✓ | 0 notes ✓

and the package directory tree should look like this:

├── DESCRIPTION
├── LICENSE
├── LICENSE.md
├── NAMESPACE
├── R/
└── myfirstpackage.Rproj

Rounding Out The Corners

While we have a minimum viable package there are a few other steps we should take during this setup phase. First we’ll setup our package to use {roxygen2}² for documenting functions, declaring NAMESPACE imports, and other helper-features that will be introduced in later posts. We can do this via usethis::use_roxygen_md():

usethis::use_roxygen_md()
## ✔ Setting Roxygen field in DESCRIPTION to 'list(markdown = TRUE)'
## ✔ Setting RoxygenNote field in DESCRIPTION to '7.0.2'
## ● Run `devtools::document()`

We won’t run devtools::document() just yet, though. Before we do that we’ll also create an R file where we can store top-level package introduction/meta-information:

usethis::use_package_doc()
## ✔ Writing 'R/myfirstpackage-package.R'

Now, our directory tree should look like:

.
├── DESCRIPTION
├── LICENSE
├── LICENSE.md
├── NAMESPACE
├── R
│   └── myfirstpackage-package.R
└── myfirstpackage.Rproj

Now, run devtools::document() which will translate the {roxygen2} comments into a properly-formatted R documentation file and regenerate the NAMESPACE file (as we’ll be managing package imports and exports via {roxygen2} comments). The directory tree will now look like:

.
├── DESCRIPTION
├── LICENSE
├── LICENSE.md
├── NAMESPACE
├── R
│   └── myfirstpackage-package.R
├── man
│   └── myfirstpackage-package.Rd
└── myfirstpackage.Rproj

and, we can now re-run devtools::check() to make sure we have the three “0’s” we’re aiming for each time we check our package for errors.

Passing The Test

We’re going to want to write and use tests to ensure our package works properly. There are many R package testing frameworks available. To ease the introduction into this process, we’ll use one of the frameworks that came along for the ride when you installed the various packages outlined in the previous post: {testthat}³. Setting up {testthat} is also pretty painless thanks to the {usethis} package we’ve been taking advantage of quite a bit so far. We’ll create the {testthat} overall infrastructure then add a placeholder test script since devtools::check() will complain about no tests being available if we do not have at least a single script it can execute during the test phase of the package checking process.

usethis::use_testthat()
## ✔ Adding 'testthat' to Suggests field in DESCRIPTION
## ✔ Creating 'tests/testthat/'
## ✔ Writing 'tests/testthat.R'
## ● Call `use_test()` to initialize a basic test file and open it for editing.

usethis::use_test("placeholder")
## ✔ Increasing 'testthat' version to '>= 2.1.0' in DESCRIPTION
## ✔ Writing 'tests/testthat/test-placeholder.R'
## ● Modify 'tests/testthat/test-placeholder.R'

The directory tree will now look like this:

.
├── DESCRIPTION
├── LICENSE
├── LICENSE.md
├── NAMESPACE
├── R
│   └── myfirstpackage-package.R
├── man
│   └── myfirstpackage-package.Rd
├── myfirstpackage.Rproj
└── tests
    ├── testthat
    │   └── test-placeholder.R
    └── testthat.R

Run devtools::check() one more time to make sure we’ve got those precious 3 “0’s” one last time.

Getting Things Under Control

We’re almost done! One final step is to turn this directory into a git-managed directory so we can work a bit more safely and eventually share our development work with a broader audience. Provided you followed the outline in the previous post, setting up git is as straightforward as one {usethis} function call:

usethis::use_git()
## ✔ Setting active project to '/Users/someuser/packages/myfirstpackage'
## ✔ Initialising Git repo
## ✔ Adding '.Rhistory', '.RData' to '.gitignore'
## There are 10 uncommitted files:
## * '.gitignore'
## * '.Rbuildignore'
## * 'DESCRIPTION'
## * 'LICENSE'
## * 'LICENSE.md'
## * 'man/'
## * 'myfirstpackage.Rproj'
## * 'NAMESPACE'
## * 'R/'
## * 'tests/'
## Is it ok to commit them?
## 
## 1: For sure
## 2: Negative
## 3: Not now
## 
## Selection: 1
## ✔ Adding files
## ✔ Commit with message 'Initial commit'
## ● A restart of RStudio is required to activate the Git pane
## Restart now?
## 
## 1: Negative
## 2: Not now
## 3: Yup
## 
## Selection: 3

RStudio should have been restarted (so it can add a “Git” pane in case you want to use the GUI to manage git) and the directory tree will now have a .git/ subdirectory that you should (almost) never touch by hand.

The last thing to do is to “vaccinate” your git setup so you don’t leak sensitive or unnecessary files when you (eventually) share your creation with the world:

usethis::git_vaccinate()
## ✔ Adding '.Rproj.user', '.Rhistory', '.Rdata' to '/Users/someuser/.gitignore'

We now have a basic, working R package that is devoid of any real functionality other than that of getting us familiar with the package setup and validation processes. We’ll be building upon this experience in most of the coming posts.

Quick Reference

After ensuring you’ve got the recommended options() in place, here are the steps to setup a new package:

# in any RStudio R Console session
devtools::create("~/packages/THE-PACKAGE-NAME")

# in the newly created package RStudio R Console session:
usethis::use_mit_license()       # need a LICENSE file
usethis::use_roxygen_md()        # use {roxygen2} for documentation and configuration
usethis::use_package_doc()       # setup a package-level manual page
usethis::use_testthat()          # setup testing infrastructure
usethis::use_test("placeholder") # setup a placeholder test file
devtools::document()             # Let {roxygen2} create NAMESPACE entries, build manual pages (and, more later on)
devtools::check()                # looking for the three "0's" that tell us we're ready to roll!
usethis::use_git()               # put the directory under git version control
usethis::git_vaccinate()         # Prevent leaking credentials and other unnecessary filesystem cruft

Rather than re-type devtools::document() (et al) whenever you need to run {roxygen2} or build/check a package you can use RStudio keyboard shortcuts that are designed to seamlessly integrate with the {devtools} ecosystem:

We’ll refer to these operations as “install” (or “build”), “load all”, “test”, “check”, and “document” from now on so you can choose to use the console or the shortcuts as you prefer.

Exercises

Our package may be kinda, well, useless for the moment but that doesn’t mean you can’t show it some love and get some practice in at the same time while things are still relatively straightforward.

• Modify the Title, Version, and Description fields of the DESCRIPTION file and refine them as needed until package checks pass.
• Deliberately mangle parts of the DESCRIPTION file to see what errors or warnings you receive during the package check process.
• Read up on {roxygen2} and add some Sections to it formatted with markdown and/or LaTeX. Re-“document” the package and see how your changes look.
• Edit the test-placeholder.R file and change the placeholder test it created so it fails and then re-check the package to see what warnings or errors show up.
• After you’ve made (valid, working) modifications to any/all of the above and package checks pass, use either the git command line tools or the RStudio Git pane to add your updates to the git tree. Use the resources linked to in the previous post if you need a refresher on how to do that.
• Re-run through all the steps with a brand new package name just to make sure you’re comfortable with the package creation process.

Up Next

In the next installment in the series we will start wrapping by creating a basic wrapper that just calls out to the operating system shell to run commands.

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This article is originally published at https://rud.is/b
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