Agent Skills: R and CRAN Knowledge Patch

R and CRAN Knowledge Patch

Use this skill when writing, reviewing, upgrading, building, or submitting R code and R packages. Check the project's R requirement, native-code build settings, package metadata, and target repository before applying a rule.

Reference index

| Reference | Topics | | --- | --- | | language-and-runtime.md | Base functions, argument matching, strings, tables, session options, archives, methods, bindings, and corrected edge cases | | statistics-and-graphics.md | Statistical inference, GLMs, time-series decomposition, matrix factorization, plotting, and graphics behavior | | package-build-and-native-code.md | C++ defaults, native APIs, package formats, integrity and signing, build requirements, checks, and vignette engines | | documentation-and-weaving.md | Rd links and equations, generated references, installed README files, LaTeX compatibility, Sweave, and tangling | | cran-policy.md | Source and licensing, names, dependencies, downloads, Internet resources, compatibility, API coordination, and submission cadence |

Quick reference: breaking and compatibility-sensitive changes

Native package builds

• The default C++ dialect is C++20 where available, with C++17 as the fallback. A package may explicitly request C++17.
• Existing C++11 or C++14 declarations in src/Makevars now select the default dialect instead of those removed standards.
• The R CMD config variable families CXX11 and CXX14 are defunct.
• Remove uses of Rf_isFrame, VECTOR_PTR, and non-API DATAPTR.
• Replace Rf_isFrame with Rf_isDataFrame.
• Treat the pointers returned by CHARACTER_DATA and CHARACTER_POINTER as const.
• Include object-table definitions from R_ext/ObjectTable.h, not R_ext/Callbacks.h.
• Reinstall packages that provide graphics devices because the graphics engine is version 17.

See package-build-and-native-code.md for supported replacements, new device helpers, and stronger check diagnostics.

Runtime and method behavior

• weighted.residuals() on a glm now returns weighted working residuals, not deviance residuals.
• influence.glm() exposes both wt.res and dev.res; related influence measures use Pearson residuals and handle fixed-dispersion models without leave-one-out dispersion estimates.
• plot.lm() no longer adds a smoother to the residuals-versus-leverage panel unless panel.raw = panel.smooth restores it explicitly.
• as.table.ftable() defaults to named.dim = FALSE.
• structure(NULL, name = value) is defunct.
• tk*.slaves() is deprecated; use tk*.child(), which requires Tcl/Tk 8.6 or later.
• Assigning attributes to a primitive function is an error.
• Changing a primitive function's environment is ignored with a warning and is planned to become an error.
• Invalid or unmet requireNamespace(versionCheck = ...) requests no longer pass quietly; unmatched arguments also error even if the namespace is already loaded.
• Values returned by active bindings are marked non-mutable so complex assignment cannot modify the returned object in place unintentionally.

Documentation compatibility

• Cross-package S4 links use \linkS4class[pkg]{Class} and require a dependency on R 4.6.0 or later.
• Use \linkS4methods{} for S4 method documentation and \manual{name}{node} for a section in an R manual.
• The bundled jss.cls works with hyperref 7.01q.

Package distribution

• Binary package tooling must accept custom types named <system>.binary.<build> and the supported compressed tar extensions.
• Tar-based packages can carry a SHA256 manifest and detached SHA256.sig; signing uses GnuPG keyrings under R_HOME/etc/keyrings.
• A rebuilt binary can supersede the same package version through the timestamp in Built.
• R CMD check diagnoses clang -Wkeyword-macro, including macros that mask bool, true, false, or nullptr.

Quick reference: CRAN submission constraints

Source and licensing

• Supply source, or material readily convertible back to source, for every package component. This includes generated configure files, PDF documentation, and Java bytecode.
• Put Java sources in a top-level java directory, or explain there how to obtain them.
• Ensure direct and indirect dependencies do not restrict users or usage.
• The package license must permit CRAN to distribute the package in perpetuity, and a license change must be highlighted on submission.

Names and dependencies

• Check a proposed name case-insensitively against current and past CRAN packages and current Bioconductor packages.
• Package names persist. A takeover normally needs the former maintainer's written agreement unless the package is formally orphaned.
• Strong dependencies in Depends, Imports, and LinkingTo should come from CRAN or the Bioconductor software repository.
• Do not make an orphaned CRAN package a direct or indirect strong dependency. Conditional use through Suggests is allowed but discouraged.
• Document access to nonstandard Suggests or Enhances dependencies and use them conditionally when they are not readily installable on major platforms.

Network, native libraries, and compatibility

• Prefer a suitable installed external library, then bundled source.
• Download only fixed source versions. Precompiled downloads are a last resort and require agreement from the CRAN team.
• Windows and macOS builds must use static libraries.
• Make installation and startup downloads secure, and raise the timeout for downloads larger than a few megabytes.
• Internet-dependent code must fail informatively when a shared resource is unavailable or changes, without causing a check warning or error.
• Minimize shared-resource use and avoid rate-limit responses such as HTTP 429 and 403.
• Target current released CRAN and Bioconductor dependencies, not development versions.

Coordination and cadence

• Agree on significantly disruptive changes with CRAN maintainers well before publicizing them.
• Before changing an API, notify affected reverse-dependency maintainers and allow at least two weeks, preferably longer, for updates.
• Use a higher version for every published-package update; increasing it after each unsuccessful submission is preferred.
• Established packages should normally update no more often than every one to two months, and must not send a replacement while a submission is pending.
• After publication, wait for the CRAN check page to finish updating before submitting a correction; this can take at least 48 hours.

See cran-policy.md for repository metadata, archival risk, back-compatibility-package restrictions, and macbuilder guidance.

Quick reference: commonly used additions

Base R

• list.files(..., fixed = TRUE) matches pattern literally.
• substring() and substr(), including replacement forms, accept an ending index of NULL to mean through the end of the string.
• read.dcf() ignores lines beginning with #.
• ftable() and as.table.ftable() accept perm.
• match.arg(several.ok = "all") selects the new all-values sentinel.
• sequence() can jointly recycle nvec, from, and by with recycle = TRUE or R_sequence_recycle; its default remains backward-compatible for now.
• options(netrc = path) selects a netrc file for basic HTTP authentication with the "libcurl" download method.
• The logical quiet option reflects R --quiet initially and can be changed during the session.

Statistics and plots

• wilcox.test() can perform exact conditional inference with ties and can add up to three Edgeworth correction terms to asymptotic inference.
• stats::free1way() supports likelihood- and permutation-based inference for distribution-free stratified K-sample layouts.
• barplot(orderH = ...) can order each stack by size.
• Histograms, bar plots, bxp(), and box plots support panel.first; bar plots, bxp(), and box plots also support panel.last.
• plot.default(lim2 = TRUE) derives limits from jointly finite x/y pairs.
• plot.data.frame() accepts a formula, and hatvalues() has an nls method.

Documentation and packaging

• Rd can generate citations and reference lists from bibentry data or R/BibTeX bibliographic databases.
• tools::deparseLatex(math = ...) can convert $...$ fields to Rd equation markup.
• Package README.md files are installed and displayed in HTML help.
• tools::analyze_license() computes SPDX license identifiers.
• R CMD build installs a package that provides its own vignette engine before building the vignettes.

Quick reference: corrected edge cases

• stl() validates its 3-by-3 tuning parameters at R level; s.window = 0 no longer crashes and s.window = 1 works.
• zapsmall(x, digits = Inf) returns x when x contains Inf instead of producing all NaN.
• Asymptotic wilcox.test(..., exact = FALSE, correct = k) includes the required dnorm(z) factor, including in the two-sample case.
• as.matrix() on POSIXlt again returns a numeric matrix, while c() and subassignment handle more objects without a "tzone" attribute.
• Pivoted chol() zeroes the trailing submatrix after stopping early, so positive-semidefinite reconstruction remains correct when rank is at least two below dimension.

Use the topic references for the remaining method, formatting, graphics, archive, weaving, native API, and package-policy details.