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CI/CD Workshop | R in Pharma 2022

R in Pharma 2022 CI/CD workshop repository.

Full workshop video available here: https://www.youtube.com/watch?v=OcNzurpCCpY

Presentation video available here: https://www.youtube.com/watch?v=8HPpdv8crHo

Exercises

Exercise 1

Fix issues identified by R CMD check workflow.

Click here for a hint 🔎 A unit test is failing for hello.R.


Click here for the solution ✅ The expected message should be Welcome to the R/Pharma CI/CD workshop! (R/Pharma is missing from the message) in the tests/testthat/test-hello.R file.

Exercise 2

Fix broken links after implementing the Check URLs workflow.

Click here for a hint 🔎 An R/Pharma link is broken in the NEWS.md file.


Click here for the solution ✅ The rinpharma website domain is incorrectly set as .xcom. It should be .com.

Exercise 3

Find and fix all spelling errors determined by the Spellcheck workflow.

Click here for a hint 🔎 One or more words are misspelled in the NEWS.md file.


Click here for the solution ✅ The word link is misspelled as linke in NEWS.md. The word strangephrase should be strange phrase in NEWS.md. Fix the spelling first in the NEWS.md file. Next, simply run spelling::update_wordlist(confirm=“Yes”) to add technical jargon to the wordlist.

Exercise 4

Fix code style errors implementing the Style workflow.

Click here for a hint 🔎 There’s a minor style issue in the R/hello.R file.


Click here for the solution ✅ Simply run styler::style_file(“R/hello.R”) to automatically style the file.

Exercise 5

Reduce the cyclomatic complexity identified by the Lint Code Base workflow.

Click here for a hint 🔎 The issue is manifested in the R/hello.R file.


Click here for the solution ✅ Reduce the number of if statements to reduce the cyclomatic complexity in the R/hello.R file for the linter_ex() function. Run styler::style_file(“R/hello.R”) to fix style issues, if any. Then, run lintr::lint_package() iteratively to determine whether the issue has been resolved.

Exercise 6

Update man pages based on the errors reported by the ROxygen workflow.

Click here for a hint 🔎 Function documentation is not up-to-date for R/cicdworkshop-package.R and the linter_ex() function.


Click here for the solution ✅ Simply run roxygen2::roxygenize(‘.’, roclets = c(‘rd’, ‘collate’, ‘namespace’)) or devtools::document() to automatically update all man pages.

Exercise 7

Increase code coverage for the package.

Click here for a hint 🔎 Add a simple unit test for the linter_ex() function defined in the R/hello.R file.


Click here for the solution ✅

Run covr::package_coverage() to note the current code coverage.

In the tests/testthat/test-hello.R file, add the following test:

test_that("linter_ex is surprised", {
  expect_message(
    linter_ex("lint"),
    "^Whoa!\\n"
  )
})

Run tests locally by executing devtools::test() to make sure that the tests succeed.

Then, run covr::package_coverage() to see that the code coverage has increased.

Exercise 8

Publish a website for your package using GitHub Pages.

Click here for a hint 🔎 Update the _pkgdown.yml and add the pkgdown workflow.


Click here for the solution ✅ Update the url by replacing pharmaverse with your GitHub username and repository name.