5 Publication

R/Pharma workshop: Good Software Engineering Practice for R Packages

Daniel Sabanes Bove

October 28, 2024

Website with pkgdown

Setup of pkgdown

  • pkgdown makes it quick and easy to build a website for your package
  • After installing pkgdown, run usethis::use_pkgdown() to get started
  • Main configuration happens in _pkgdown.yml file
  • Many customizations can be applied, but bulk of work during development is updating the reference section with names of .Rd files

Example _pkgdown.yml File

---
url: https://openpharma.github.io/mmrm/latest-tag

template:
  bootstrap: 5
  params:
    ganalytics: UA-125641273-1

navbar:
  right:
    - icon: fa-github
      href: https://github.com/openpharma/mmrm

reference:
  - title: Package
    contents:
      - mmrm-package
  - title: Functions
    contents:
      - mmrm
      - fit_mmrm
      - mmrm_control
      - fit_single_optimizer
      - refit_multiple_optimizers
      - df_1d
      - df_md
      - component

Publication as GitHub Page

  • It’s helpful for users to read the website online
  • GitHub is very helpful here because:
    • A separate branch, gh-pages, stores the rendered website
    • GitHub actions automatically render the website when the main branch is updated
  • To get started, use usethis::use_pkgdown_github_pages()
    • Or, manually deploy site with pkgdown::deploy_to_branch()

Licensing, Open sourcing, Versioning

Licensing

  • High level categorization of licenses:
    • “Permissive”: Relaxed. Can be freely copied, modified, published (under the same license).
    • “Copyleft”: Stricter. Same rights need to be preserved in derivative works.
  • R itself is licensed under GPL, but packages can choose, e.g.:
    • usethis::use_mit_license() for permissive MIT
    • usethis::use_gpl_license() for copyleft GPL
  • Include minimum version, e.g. GPL (>= 3)

Licensing (cont’d)

  • Need to be careful here when you bundle any code from other software
    • Care must be taken that any copyright/license statements from copied or modified code are preserved and authorship is not misrepresented
  • Are the licenses of your package and the source compatible?
    • e.g. cannot copy/paste code from a GPL package and publish in an MIT package
  • LICENSE file optionally can contain further restrictions of the license

Open Sourcing

  • The easiest way to “open source” your R package is to make the GitHub repository public
  • This allows for easy open source contributions from other developers via pull requests
  • Please check with your organization first:
    • Are they ok to publish the software?
    • What is the appropriate copyright holder?
  • Also allows bugs to be filed and to have the GitHub issues page in the package description

Versioning

  • The Version field defines the package version
  • Syntax: Three integers separated by . or -
    • Canonical form is: x.y-z, equivalent to x.y.z
  • Useful conventions of “semantic versioning”:
    • x is major: Increment this for breaking changes
    • y is minor: Increment this for new features
    • z is patch: Increment this for bug fixes only
    • x.y.z.9000 and count up during development
    • usethis::use_version() can help with this

Checks Before Release

CRAN (The Comprehensive R Archive Network)

  • CRAN is the central repository for R packages
  • It has additional requirements beyond the standard package ones, which are described in the Repository Policy
  • Submitting a package indicates agreement with the policy
  • In particular: “The time of the volunteers is CRAN’s most precious resource, and they reserve the right to remove or modify packages on CRAN without notice or explanation (although notification will usually be given).”

CRAN (cont’d)

  • Only source packages can be submitted
    • But .rda data files are allowed
  • Need single designated maintainer (person, not mailing list)
    • Additional Contact field could be used
  • Citations in author-year style, followed by <doi:...>
  • Reducing run time of tests, checks, examples, vignettes is important
  • Need to provide cross-platform portable code: CRAN runs checks on Windows, Mac, several Linux OS

CRAN (cont’d)

❗ A CRAN submission can be punishing, painful, and nerve-racking:

The first release of the rpact package took 5 weeks and 6 submission attempts; painful experiences:

  • Some Linux machines may generate different random numbers than expected (despite setting a seed)
  • Not only errors and warnings lead to the rejection of a submitted package, but also notes
  • Your local Windows test system may be much faster than the CRAN system (e.g., 5 times)
  • Don’t use “R Package for” in your package title
  • The description of the package must be provided with a doi reference

CRAN (cont’d)

Example message informing about the rejection of the last rpact submission:

Dear maintainer,

package rpact_3.3.2.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
Windows: 00check.log Status: OK, Debian: 00check.log Status: OK

Please fix all problems and resubmit a fixed version via the webform.

Best regards,
CRAN teams’ auto-check service

r-devel-windows-x86_64 Check: Result: NA, Maintainer: ‘Friedrich Pahlke’
r-devel-windows-x86_64 Check: Overall checktime, Result: NOTE, Overall checktime 12 min > 10 min
r-devel-linux-x86_64-debian-gcc Check: Result: Note_to_CRAN_maintainers Maintainer: ‘Friedrich Pahlke’

R-Hub to the Rescue

  • Free R CMD check runs on different operating systems before submitting to CRAN
  • Supported by the R consortium
  • Now works with GitHub Actions:
    1. Put your package in a GitHub repository
    2. Use rhub::rhub_setup() for setting up the GitHub action
    3. Push this change to GitHub
    4. Use rhub::rhub_check() to check your package

GitHub

Tags

  • Tags are a feature of Git, i.e., not specific to GitHub
  • Git can tag specific points in the code history as being important
  • Typically, for each release, create a tag vx.y.z
  • The value here is that users can later check out the package in the state of this release version
    • Download in R: remotes::install_github("org/package", ref = "vx.y.z")
    • Comparison of versions are also possible, etc.

Tags: Example

Releases

  • Based on Git tags, and a feature of GitHub
  • Are “deployable software packages to make them available for a wider audience to download and use”
  • Contain release notes and links to the binary package files for download
    • However, for R packages these tar.gz package files are rarely used directly

Releases: Example

Bioconductor

A Note on Bioconductor

  • The Bioconductor project develops, supports, and disseminates open source software for the analysis of biological assays
  • Like CRAN, Bioconductor has additional package requirements
  • Packages are peer reviewed by community members
  • New packages and updates to existing packages are released semi-annually
  • Software is expected to be interoperable with other Bioconductor packages through the re-use of common data structures and infrastructure

References

License Information

Good Software Engineering Practice for R Packages - Home | Slides | License