Update cran-comments and bits

Author: gregorgorjanc

.gitignore

@@ -5,6 +5,8 @@
 .Ruserdata
 .vscode
 *.Rproj
+cran-comments.html
+cran-comments_files/
 RcppTskit/**/.quarto/
 RcppTskit/inst/doc
 RcppTskit/src/*.o
@@ -15,5 +17,5 @@ RcppTskit/src/Makevars
 RcppTskit/src/Makevars.win
 RcppTskit/vignettes/*.html
 RcppTskit/vignettes/*.R
-RcppTskit/vignettes/*_files
+RcppTskit/vignettes/*_files/
 test.trees

RcppTskit/.Rbuildignore

@@ -11,6 +11,8 @@
 ^\.github$
 ^codecov\.yaml$
 ^cran-comments\.md$
+^cran-comments\.html$
+^cran-comments_files$
 ^inst/examples/create_test\.trees\.R$
 ^inst/examples/create_test\.trees\.py$
 ^inst/examples/explore_reticulate\.R$

RcppTskit/NEWS.md

@@ -10,7 +10,7 @@ This is the first release.
 
 ### Added (new features)
 
-- Initial version of RcppTskit using the tskit C API (version 1.3.0).
+- Initial version of RcppTskit using the tskit C API (1.3.0).
 - TreeSequence R6 class so R code looks Pythonic.
 - `ts_load()` or `TreeSequence$new()` to load a tree sequence from file into R.
 - Methods to summarise a tree sequence and its contents `ts$print()`,
@@ -19,5 +19,5 @@ This is the first release.
 - Method to push tree sequence between R and reticulate Python
   `ts$r_to_py()` and `ts_py_to_r()`.
 - Most methods have an underlying (unexported) C++ function that works with
-  a pointer to tree sequence object,for example, `RcppTskit:::ts_load_ptr()`.
+  a pointer to tree sequence object, for example, `RcppTskit:::ts_load_ptr()`.
 - All implemented functionality is documented and demonstrated with a vignette.

RcppTskit/cran-comments.md

@@ -3,3 +3,27 @@
 0 errors | 0 warnings | 1 note
 
 * This is a new release.
+
+* I have tested on my local MacOS laptop using:
+  `devtools::check()` and
+  `devtools::check(remote = TRUE, manual = TRUE)`. Both pass.
+
+* I have also used R CMD check GitHub action on MacOS, Windows, and
+  Ubunutu (olderelease, release, and devel, and ); all pass as you can
+  see at https://github.com/HighlanderLab/RcppTskit/actions/runs/21542139159.
+
+* `urlchecker::url_check()` also passes.
+
+* On https://win-builder.r-project.org/UmBp28nqBAkU/00check.log
+  I get this warning:
+
+  ```
+  * checking whether package 'RcppTskit' can be installed ... WARNING
+  Found the following significant warnings:
+    ../inst/include/tskit/tskit/core.h:171:21: warning: C++ designated initializers only available with '-std=c++20' or '-std=gnu++20' [-Wc++20-extensions]
+  ```
+
+  Discussion with upstream devs of tskit indicates that this is due
+  to how the build tools have been built for this platform since
+  we could not replicate the warning on any of our platforms even when
+  tweaking the flags - see https://github.com/tskit-dev/tskit/issues/3375.

RcppTskit/notes_pkg_dev.Rmd

@@ -5,8 +5,6 @@
 # TODO: Create a minimal package to demonstrate how to link against RcppTskit and call tskit C API
         https://github.com/HighlanderLab/RcppTskit/issues/48
 
-
-
 TODO: Add citation for tskit to DESCRIPTION file #46
       https://github.com/HighlanderLab/RcppTskit/issues/46
 
@@ -15,13 +13,6 @@ TODO: Add citation for tskit to DESCRIPTION file #46
 #       https://github.com/HighlanderLab/RcppTskit/issues/15
 # remotes::install_github("HighlanderLab/RcppTskit/RcppTskit")
 
-# Main branch
-remotes::install_github("HighlanderLab/RcppTskit/RcppTskit")
-
-# TODO: Create a devel branch #16
-#       https://github.com/HighlanderLab/RcppTskit/issues/16
-# remotes::install_github("HighlanderLab/RcppTskit/RcppTskit@devel")
-
 # TODO: Publish on CRAN #14
 #       https://github.com/HighlanderLab/RcppTskit/issues/14
 
@@ -150,10 +141,7 @@ PATCH version when you make backward compatible bug fixes
 ```
 use_upkeep_issue(year = NULL) # https://usethis.r-lib.org/reference/use_upkeep_issue.html
 use_release_issue(version = NULL) # https://usethis.r-lib.org/reference/use_release_issue.html
-use_cran_comments() # https://usethis.r-lib.org/reference/use_cran_comments.html
-use_github_release(publish = TRUE) # https://usethis.r-lib.org/reference/use_github_release.html
-devtools::release(pkg = ".", check = TRUE)
-# pkg The package to use, can be a file path to the package or a package object. See as.package() for more information
+# just follow tasks in there;)
 ```
 
 ## Setup