# R Cran Knowledge Patch > R / CRAN - Skill: `nevaberry/r-cran-knowledge-patch` (Agent Skill, multi-file: 7 files) - Install (CLI): `npx skillmds@latest add nevaberry/r-cran-knowledge-patch` - Raw SKILL.md: https://api.skillmd.com/api/skills/nevaberry/r-cran-knowledge-patch/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Coding & Dev Tools - License: MIT - Author: nevaberry (https://skillmd.com/u/nevaberry) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/nevaberry/r-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](references/language-and-runtime.md) | Base functions, argument matching, strings, tables, session options, archives, methods, bindings, and corrected edge cases | | [statistics-and-graphics.md](references/statistics-and-graphics.md) | Statistical inference, GLMs, time-series decomposition, matrix factorization, plotting, and graphics behavior | | [package-build-and-native-code.md](references/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](references/documentation-and-weaving.md) | Rd links and equations, generated references, installed README files, LaTeX compatibility, Sweave, and tangling | | [cran-policy.md](references/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](references/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 `.binary.` 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](references/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.