pkgcheck News

0.2.0.00x (current dev version)

Major changes

• Removed all remotes deps on other ropensci-review-tools pkgs in preparation for CRAN release

New checks added

• Checks for ROR and ORCID entries (#243; thanks to @Aariq).
• Check for pkgdown structure finally refined and activated (#100; thanks to @maelle).

Minor changes

• Removed internal get_gh_token() fn, replaced with gh::gh_token().

0.1.3

Minor changes

• Fix bug in sub-directory check
• Update network plot to align with new pkgstats d3.js plots (pkgstats#118)
• Fix goodpractice section numbering for srr pkgs (#400; thanks to @adamhsparks)
• Wrap markdown-rendered gp Roxygen2 tags in backticks to avoid pinging on GitHub (#402; thanks to @adamhsparks).

0.1.2

New checks and check improvements

• Removed numerous skip_on_os() conditions in tests (#378)
• Added check to make sure statistical standards document compliance for at least one specific category, not just general.
• Added check for packages using statistical standards only in a single directory or file (check-srr), improving detection of incomplete standards adoption.
• Elevated sp to the “truly obsolete” category in the obsolete-package-deps check.
• Added rm_global_assign_in_memoise to handle <<- within memoise calls, preventing false positives in the global-assignment check.
• Fixed output of obsolete_pkg_deps function and improved ordering of checks via order_checks.

Infrastructure and CI

• Added dependabot.yml to keep GitHub Actions dependencies up to date; bumped actions/checkout, actions/github-script, docker/build-push-action, docker/setup-buildx-action, and docker/login-action to current versions.
• Updated check-standard workflow; improved test-coverage workflow.
• Switched off bspm before final sf reinstall in Dockerfile to fix library-linkage issues; re-installed sf at end of Docker script.
• Added all packages from r-universe-org/base-image to Dockerfile.
• Updated test snapshots for new srr standards (v0.2) and for changes in pkgstats output.

Bug fixes

• Fixed minor bug in parse_pkg_deps and order_checks.
• Fixed catch lintr errors so that lintr failures no longer crash the full check run.
• Improved render_markdown/render_md2html and added examples and return values to all exported functions.

Documentation

• Updated README to describe the package-check workflow more clearly.
• Updated monthly GHA workflow message.
• Renamed render_markdown to render_md2html for clarity.
• Added pkgcheck GitHub Action integration (add pkgcheck action).

0.1.1

New checks

• Added check-fns-have-return-vals: flags exported functions whose roxygen documentation lacks a @return tag.
• Added check-default-branch: warns when the default git branch is not main.
• Implemented a three-way symbol set (heavy_check_mark, eyes, heavy_multiplication_x) to distinguish clear passes, marginal results, and clear failures across all check output.

Check improvements

• Rewrote the srr failure message to list each missing standard individually, making it actionable for package authors.
• Improved fns_have_return_vals to use tools::parse_Rd instead of roxygen2 for parsing return values, making it more robust.
• Removed fns_have_return_vals from the print method; results now appear only in the summary method.
• Fixed print output when an srr check fails entirely.

Documentation and vignettes

• Restructured README with a clearer check-by-check guide.
• Added list-checks vignette documenting every check.
• Updated all pkgchk_ function documentation pages; added roxygen2 family tags throughout.
• Added @schneiderpy to the contributors list.

Infrastructure

• Switched Docker base image from bspm to r2u for faster, more reliable package installation.
• Switched Dockerfile base OS from ubuntugis to ubuntugis-unstable to fix spatial library compatibility.
• Added missing roxygen2 family tag for the check-has-codemeta family.
• Moved seasonal packages from the roreviewapi Dockerfile to this one.
• Updated allcontributors list.

0.1.0

New checks

• Added check-unique-fn-names: verifies that no exported function name duplicates a name already used by a CRAN package (fn_names_on_cran).
• Added check-renv / renv_activated: detects packages where renv is activated in the project, which can interfere with dependency resolution.

Check improvements

• Renamed has_renv check to renv_activated with an improved user-facing message.
• Changed misc_check_counts to a dedicated summary function replacing has_misc_checks.
• Improved format-checks.R to handle checks with empty print methods.
• Fixed check_left_assigns to correctly handle edge cases.
• Fixed pkgchk_fns_have_exs to exclude package and data docTypes from the examples check.
• Added rm_global_assigns_in_ref_class to avoid false positives from <<- inside R5/Reference Class definitions.

API and caching

• Moved the cache directory from cache/ to cache/R/ for cleaner organisation.
• Added use_cache parameter to the main pkgcheck function, allowing callers to bypass the cache.
• Renamed cache_pkgstats_component to cache_pkgcheck_... for naming consistency.
• Switched CI-results fetching from httr / jsonlite to jsonlite only.

Infrastructure and CI

• Added goodpractice as a GitHub remote dependency (temporarily removed from CRAN) in all workflows and Dockerfile.
• Moved Julia pre-installation to the Dockerfile; added explicit branch parameter to get_latest_commit.
• Updated roxygen2 to 7.2.1; updated various workflow job names.
• Added use_github_action_pkgcheck documentation; described pkgcheck-action in README.
• Renamed the check workflow job from check to pkgcheck.

Documentation

• Described testing new checks in the “Extending Checks” vignette.

0.0.3

New checks

• Added check-license: validates that the package LICENSE field is a recognised CRAN-compatible identifier (closes #73).
• Added check-pkgdown: detects whether a pkgdown site exists and is configured (closes #100).
• Added check-obsolete-pkg-deps: flags dependencies on packages considered truly or potentially obsolete on CRAN (closes #44).
• Added GitHub-Actions default-branch check: warns when the default branch name differs from main.

Check improvements

• Improved check-fns-have-exs to exclude dataset documentation entries (closes #103).
• Improved check-on-cran with a tryCatch around the CRAN URL test.
• Improved check-scrap to detect the same scrap file appearing in different locations.
• Deactivated the roxygen2 family tag check (closes #100) as it produced many false positives.
• Fixed pkgchk_uses_roxygen2; fixed check_fns_have_exs logic.

Markdown and print output

• Implemented msg_pre / msg_post print sub-methods for all check types, providing a consistent before/after hook pattern (closes #108).
• Added pkgfns_as_details section to markdown output, listing all exported function names in a collapsible block (closes #117, #137).
• Added pkgdeps_as_table section to markdown output, listing package dependencies and their imported call counts.
• Added Bootstrap-style alerts (alert-success, alert-danger) in HTML output (closes #82).
• Added tooltip descriptions to stats summary output (closes #28).
• Implemented markdown rendering of the “extra checks” section (closes #44, #108).
• Fixed checks_to_markdown scrap-check key name.

Dependency data

• Added get_re_exports and ncalls column to the package-dependency summary.
• Added external_fns data item to the checks object, exposing counts of calls to functions in each imported package.

CI and GitHub Actions

• Added use_github_action_pkgcheck / use_github_check function for inserting the pkgcheck GHA template into a package (closes #135).
• Added branch parameter to use_github_action_pkgcheck so the action targets the correct branch (closes #135).
• Added NOT_CRAN environment variable to the GHA template (fixes #134).
• Added read_pkg_guide helper for reading the rOpenSci packaging guide.
• Removed GitLab mirroring workflow (closes #128).
• Added monthly.yaml workflow to send automated monthly check summaries (closes #123).
• Added allcontributors integration.
• Switched visjs path handling to be compatible with GHA runners (closes #127).
• Added note in rendered output when network diagram is generated on GHA (closes #127).

Testing and snapshots

• Added clean-snapshots.R script to normalise platform-specific paths in snapshot output (closes #111).
• All tests now use a local tempdir() as the cache directory, isolating them from the real user cache (closes #113).
• Added test-extra-checks and associated snapshots.
• Added test-order-checks.R.
• Switched to pandoc --wrap=preserve for reproducible HTML snapshot output.
• Added goodpractice = FALSE parameter to the main pkgcheck function, allowing tests (and users) to skip the slow goodpractice step.

Infrastructure

• Replaced ghql dependency with gh for all GitHub API calls (closes #256 prep).
• Replaced httr with httr2 for all HTTP requests.
• Removed cloc dependency.
• Updated Dockerfile: R 4.0 → 4.1, added ubuntugis PPA, pre-installed spatial system libraries, pre-installed arrow, duckdb, sf.
• Added add-apt-repository / software-properties-common to Docker image.
• Added spaceout pre-commit hook; applied consistent whitespace formatting across all source files.
• Updated rappdirs-based cache path to use fs::path_abs.
• Added .onUnload to reset options and environment variables set during package load.

0.0.2

Package rename and restructure

• Renamed the package from an earlier prototype to pkgcheck and updated the object class, all exported function names, and documentation to match (closes #21).
• Restructured the main pkgcheck() object: separated info items (git metadata, pkgstats, srr, CI badges, URLs) from checks items (each individually named pkgchk_*).
• Split the monolithic format-checks.R into collate-checks.R and individual per-check source files under R/check-*.R and R/info-*.R.
• Renamed all collate_* functions to summarise_* for consistency.
• Added a generic summarise_check function dispatched per check type.

New checks

• check-has-citation: verifies a CITATION file exists (closes #9).
• check-has-codemeta: verifies a codemeta.json file exists (closes #9).
• check-has-contrib: verifies a CONTRIBUTING.md file exists (closes #9, #35).
• check-has-vignette: detects presence of at least one built vignette (improved by Maëlle Salmon).
• check-scrap: detects unwanted files such as .DS_Store in the git tree (closes #27).
• check-pkgname-available: checks that the package name is not already on CRAN.
• check-left-assign: reports use of <- vs = for assignment in function bodies.
• check-fns-have-exs: reports exported functions lacking @examples tags.
• check-on-cran: reports whether the package is already on CRAN.
• check-uses-roxygen2: checks that roxygen2 is used for documentation.
• check-covr: reports test coverage via covr.

Output and print methods

• Added print and summary S3 methods for the pkgcheck class; added dedicated output_pkgchk_* functions for each check type, providing consistent screen and markdown rendering.
• Added checks_to_markdown function that converts the full pkgcheck result to a GitHub-flavoured Markdown string, including a visjs network diagram and an srr standards section.
• Added render_markdown function to render the Markdown string to HTML via rmarkdown.
• Implemented symbol_tck / symbol_crs helpers (tick and cross Unicode symbols) used uniformly across all output functions; added fmt parameter for screen vs. markdown formatting.
• Added order_checks function to control the display sequence of check items in summary output.
• Added list_pkgchecks function (with quiet parameter) to enumerate all currently active checks.
• Added extra_check_prints_from_env allowing extra checks supplied via an environment variable to appear in the print output (closes #40).

goodpractice integration

• Separated goodpractice into its own pkgchk_gp check; divided gp results into four labelled sections (rcmdcheck, cyclocomp, lintr, covr); added lintr section to output (closes #19).
• Added get_gp_report (exported) and local caching of gp results in the cache directory.
• Extended convert_gp_components to produce Markdown-formatted sub-sections.

Statistical software standards (srr)

• Integrated the srr package: captured the srr version, copied the srr Markdown report to the static cache directory, and added srr categories to the print and summary output.
• Added add_srr_categories_from_report function.
• Added separate collate_srr_checks / summarise_srr_checks functions.

Caching and background execution

• Added pkgcheck_bg for running checks in a background callr process (via callr::r_bg), with checks_running_in_bg to detect concurrent runs.
• Added stdout_stderr_cache / logfile_names helpers for routing background-process output to cache files.
• Added cache-directory management via .onLoad: auto-creates pkgcheck and static sub-directories under the rappdirs application directory.

CI and GitHub Actions

• Added ci_badges check: scrapes CI badges from the package README to determine CI provider status (GitHub Actions, Travis, etc.).
• Added ci_results_gh function: fetches GitHub Actions workflow run results directly from the GitHub API via gert and gh.
• Replaced all git remote shell commands with gert equivalents.
• Added use_github_action_pkgcheck stub and pkgdown GitHub Actions workflow.
• Added check-other-OS workflow to test on additional platforms.
• Added Docker image with full system dependencies (R, ctags, gtags, pandoc, visNetwork, spatial libraries); added serve_api function wrapping a plumber API.

API / plumber endpoints (later moved to ‘roreviewapi’)

• Implemented plumber API endpoints: check, goodpractice, srr, log, report, editorcheck; later consolidated into roreviewapi.
• Added dl_gh_repo / dl_repo helpers for downloading package source from GitHub.

Dependency changes

• Added imports: cli, gert, gh, glue, pkgstats, rappdirs, rmarkdown, visNetwork, withr.
• Removed cloc; removed plumber-related files; reduced exported fns.

Documentation

• Added CONTRIBUTING.md (closes #35) and CODE_OF_CONDUCT.md.
• Added “Extending Checks” vignette describing how to add new pkgchk_* checks (closes #29, #36).
• Added “Installation of ctags” vignette.
• Added README sections on checks_to_markdown, the full list of checks, and Docker/API usage.
• Added @maelle (Maëlle Salmon) and @assignUser (Jacob Wujciak-Jens) as package authors.

0.0.1

• Initial release of the package.
• Set up basic package structure: pkgcheck() main function, background-process helper (bg parameter), and pg_report entry point.
• Added rappdirs-based cache directory with cache_dir parameter and corresponding environment variable.
• Added GitHub Actions workflows (check, push-to-gitlab); configured Travis CI.
• Added pkgdown documentation action.
• Added codemeta.json.

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