R in Pharma 2022 CI/CD workshop repository.
November 4, 2022
Fix issues identified by R CMD check workflow.
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A unit test is failing forhello.R.
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The expected message should beWelcome to the R/Pharma CI/CD workshop! (R/Pharma is missing from the message) in the tests/testthat/test-hello.R file.
Fix broken links after implementing the Check URLs workflow.
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An R/Pharma link is broken in theNEWS.md file.
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The rinpharma website domain is incorrectly set as.xcom. It should be .com.
Find and fix all spelling errors determined by the Spellcheck workflow.
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One or more words are misspelled in theNEWS.md file.
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The wordlink 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.
Fix code style errors implementing the Style workflow.
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There's a minor style issue in theR/hello.R file.
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Simply runstyler::style_file("R/hello.R") to automatically style the file.
Reduce the cyclomatic complexity identified by the Lint Code Base workflow.
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The issue is manifested in theR/hello.R file.
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Reduce the number of if statements to reduce the cyclomatic complexity in theR/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.
Update man pages based on the errors reported by the ROxygen workflow.
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Function documentation is not up-to-date forR/cicdworkshop-package.R and the linter_ex() function.
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Simply runroxygen2::roxygenize('.', roclets = c('rd', 'collate', 'namespace')) or devtools::document() to automatically update all man pages.
Increase code coverage for the package.
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Add a simple unit test for thelinter_ex() function defined in the R/hello.R file.
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Runcovr::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.
Publish a website for your package using GitHub Pages.
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Update the_pkgdown.yml and add the pkgdown workflow.
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Update theurl by replacing pharmaverse with your GitHub username and repository name.
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