Edit DESCRIPTION based on CRAN comments

Author: gregorgorjanc

RcppTskit/DESCRIPTION

@@ -1,6 +1,6 @@
 Type: Package
 Package: RcppTskit
-Title: R Access to the Tskit C API
+Title: 'R' Access to the 'tskit C' API
 Version: 0.2.0
 Date: 2026-01-27
 Authors@R: c(
@@ -15,14 +15,14 @@ Description: 'Tskit' enables efficient storage, manipulation, and analysis
     al. (2024) <doi:10.1093/genetics/iyae100>, while `tskit` project is
     described in Jeffrey et al. (2026) <doi:10.48550/arXiv.2602.09649>.
     See also <https://tskit.dev> for project news, documentation, and
-    tutorials.  'Tskit' provides Python, C, and Rust application
-    programming interfaces (APIs). The Python API can be called from R via
+    tutorials. 'Tskit' provides 'Python', 'C', and 'Rust' application
+    programming interfaces (APIs). The 'Python' API can be called from 'R' via
     the 'reticulate' package to load and analyse tree sequences as
     described at <https://tskit.dev/tutorials/tskitr.html>. 'RcppTskit'
-    provides R access to the 'tskit' C API for cases where the
+    provides 'R' access to the 'tskit C' API for cases where the
     'reticulate' option is not optimal; for example, high-performance or
     low-level work with tree sequences. Currently, 'RcppTskit' provides a
-    limited set of R functions because the Python API and 'reticulate'
+    limited set of 'R' functions because the 'Python' API and 'reticulate'
     already covers most needs.
 License: MIT + file LICENSE
 URL: https://github.com/HighlanderLab/RcppTskit

RcppTskit/NEWS.md

@@ -4,7 +4,7 @@ All notable changes to RcppTskit are documented in this file.
 The file format is based on [Keep a Changelog](https://keepachangelog.com),
 and releases adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.2.0] - 2026-02-09
+## [0.2.0] - 2026-02-13
 
 ### Added (new features)
 
@@ -33,6 +33,10 @@ and releases adhere to [Semantic Versioning](https://semver.org/spec/v2.0.0.html
 - We now specify C++20 standard to go around the CRAN Windows issue,
   see #63 for further details.
 
+### Maintenance
+
+- Delete temporary files in examples and tests after use.
+
 - Renamed unexported functions from `RcppTskit:::ts_load_ptr()` to
   `RcppTskit:::ts_ptr_load()`.
 

RcppTskit/R/RcppTskit-package.R

@@ -1,27 +1,27 @@
 # Contains the package description and .onLoad() function
 
 #' @description
-#' `Tskit` enables efficient storage, manipulation, and analysis of
+#' \code{Tskit} enables efficient storage, manipulation, and analysis of
 #' ancestral recombination graphs (ARGs) using succinct tree sequence encoding.
 #' The tree sequence encoding of an ARG is described in Wong et al. (2024)
-#' <doi:10.1093/genetics/iyae100>, while `tskit` project is
+#' <doi:10.1093/genetics/iyae100>, while \code{tskit} project is
 #' described in Jeffrey et al. (2026) <doi:10.48550/arXiv.2602.09649>.
 #' See also https://tskit.dev for project news, documentation, and tutorials.
-#' `Tskit` provides Python, C, and Rust application programming interfaces (APIs).
-#' The Python API can be called from R via the `reticulate` package to
+#' \code{Tskit} provides Python, C, and Rust application programming interfaces (APIs).
+#' The Python API can be called from R via the \code{reticulate} package to
 #' load and analyse tree sequences as described at
 #' https://tskit.dev/tutorials/tskitr.html.
-#' `RcppTskit` provides R access to the `tskit` C API for cases where the
-#' `reticulate` option is not optimal; for example; high-performance or low-level
-#' work with tree sequences. Currently, `RcppTskit` provides a limited set of
-#' R functions because the Python API and `reticulate` already covers most needs.
+#' \code{RcppTskit} provides R access to the \code{tskit} C API for cases where the
+#' \code{reticulate} option is not optimal; for example; high-performance or low-level
+#' work with tree sequences. Currently, \code{RcppTskit} provides a limited set of
+#' R functions because the Python API and \code{reticulate} already covers most needs.
 #' @keywords internal
 #'
 #' @useDynLib RcppTskit, .registration = TRUE
 #' @importFrom methods is
 #' @importFrom R6 R6Class
-#' @importFrom Rcpp registerPlugin cppFunction
-#' @importFrom reticulate is_py_object import py_module_available py_require
+#' @importFrom Rcpp cppFunction registerPlugin
+#' @importFrom reticulate import is_py_object py_module_available py_require
 #'
 #' @examples
 #' vignette(package="RcppTskit")
@@ -32,7 +32,7 @@
 #' (search for cppFunction).
 #
 #' In RcppArmadillo, I do not see any use of Rcpp::registerPlugin(). This is
-#' likely because Armadillo is header-only, so `depends = "RcppArmadillo"` adds
+#' because Armadillo is header-only, so `depends = "RcppArmadillo"` adds
 #' include paths but there is no library to link against. RcppTskit is different
 #' because we must link against the compiled RcppTskit library file. The plugin
 #' (or `PKG_LIBS`) provides linker flags in addition to `depends` for include

RcppTskit/cran-comments.md

@@ -4,6 +4,20 @@
 
 * This is a new release (v0.2.0).
 
+* Re-submitting to CRAN.
+
+* Submitted to CRAN on 2026-02-09 and got feedback to quote
+  Python, C, and Rust and to be mindful about case sensitivity.
+
+  I assume the case sensitivity refers to the use of
+  `Tskit` and `tskit`. I am following the convention from
+  https://tskit.dev to use 'Tskit' at the start of sentences and
+  'tskit' otherwise. I am also following the guidance from
+  the R packages manual & CRAN cookbook to quote program/package name.
+
+  We now also quote Python, C, and Rust (also R for consistency)
+  in the DESCRIPTION file.
+
 * It passes checks on my local MacOS laptop using:
   `devtools::check()` and
   `devtools::check(remote = TRUE, manual = TRUE)`.
@@ -25,7 +39,7 @@
   ```
 
   I have now addressed it by setting CXX_STD = CXX20 in Makevars.in.
-  Note that discussion with upstream devs of tskit indicates that this warning
+  Note that discussion with upstream devs of `tskit` indicates that this warning
   seems to arise from how the build tools have been built for CRAN windows,
   since we could not replicate the warning on any of platforms even when
   tweaking the flags, including Windows. See the above checks and

RcppTskit/man/RcppTskit-package.Rd

@@ -106,6 +106,7 @@ PATCH version when you make backward compatible bug fixes
 ### Removed (now removed features)
 ### Fixed (bug fixes)
 ### Security (vulnerabilities)
+### Maintenance (non-user facing changes, e.g. refactoring, CI updates, etc.)
 ```
 
 ## Prepare for release