diff --git a/DESCRIPTION b/DESCRIPTION index 6641714e..13bcd966 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: rdev Title: R Development Tools -Version: 1.15.5 +Version: 1.15.6 Authors@R: person("John", "Benninghoff", , "jbenninghoff@mac.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6230-4742")) @@ -59,7 +59,7 @@ Suggests: xaringanExtra VignetteBuilder: knitr -Config/rdev/last-upkeep: 2025-10-24 +Config/rdev/last-upkeep: 2026-01-01 Config/testthat/edition: 3 Encoding: UTF-8 Language: en-US diff --git a/LICENSE b/LICENSE index 1d31cccd..65f8cd14 100644 --- a/LICENSE +++ b/LICENSE @@ -1,2 +1,2 @@ -YEAR: 2025 +YEAR: 2026 COPYRIGHT HOLDER: John Benninghoff diff --git a/LICENSE.md b/LICENSE.md index 99b3e0c5..e542f081 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,6 +1,6 @@ # MIT License -Copyright (c) 2025 John Benninghoff +Copyright (c) 2026 John Benninghoff Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/NEWS.md b/NEWS.md index 1da83f73..0a2126d0 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# rdev 1.15.6 + +* Added instructions for YAML chunk syntax update to `upkeep_checklist()` + +* 2026 Upkeep + # rdev 1.15.5 * Added items for ggplot2 version 4 upgrade and switch to YAML chunk [options](https://yihui.org/knitr/options/) to `upkeep_checklist()` diff --git a/R/upkeep.R b/R/upkeep.R index f5690c93..e10d0d64 100644 --- a/R/upkeep.R +++ b/R/upkeep.R @@ -114,7 +114,16 @@ upkeep_checklist <- function(last_upkeep = last_upkeep_year()) { # nolint: cyclo "Update for ggplot2 [version 4](https://tidyverse.org/blog/2025/09/ggplot2-4-0-0/)", uses_ggplot2 ), - todo("Switch to chunk option YAML [syntax](https://yihui.org/knitr/options/"), + todo("Switch to chunk option YAML [syntax](https://yihui.org/knitr/options/)"), + "", + "Update to YAML chunk syntax using:", + "", + "```", + paste0( + 'lapply(list.files(pattern = "\\\\.Rmd$", recursive = TRUE), knitr::convert_chunk_header, ', + 'output = identity, type = "yaml", width = 100)' + ), + "```", "" ) } diff --git a/README.md b/README.md index 37307922..50b35915 100644 --- a/README.md +++ b/README.md @@ -234,20 +234,20 @@ ci() #> * creating vignettes ... OK #> * checking for LF line-endings in source and make files and shell scripts #> * checking for empty or unneeded directories -#> * building ‘rdev_1.15.5.tar.gz’ +#> * building ‘rdev_1.15.6.tar.gz’ #> #> ── R CMD check ───────────────────────────────────────────────────────────────── -#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/Rtmpqk420B/file11cd6e62afeb/rdev.Rcheck’ +#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpqNxoSE/file820a21bb3a1a/rdev.Rcheck’ #> * using R version 4.5.2 (2025-10-31) #> * using platform: aarch64-apple-darwin20 #> * R was compiled by #> Apple clang version 16.0.0 (clang-1600.0.26.6) #> GNU Fortran (GCC) 14.2.0 -#> * running under: macOS Sequoia 15.7.2 +#> * running under: macOS Sequoia 15.7.3 #> * using session charset: UTF-8 #> * using option ‘--no-manual’ #> * checking for file ‘rdev/DESCRIPTION’ ... OK -#> * this is package ‘rdev’ version ‘1.15.5’ +#> * this is package ‘rdev’ version ‘1.15.6’ #> * package encoding: UTF-8 #> * checking package namespace information ... OK #> * checking package dependencies ... OK @@ -302,8 +302,8 @@ ci() #> * DONE #> #> Status: OK -#> ── R CMD check results ──────────────────────────────────────── rdev 1.15.5 ──── -#> Duration: 28.9s +#> ── R CMD check results ──────────────────────────────────────── rdev 1.15.6 ──── +#> Duration: 26.8s #> #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔ ``` diff --git a/docs/404.html b/docs/404.html index e2943a4d..7d1b6a31 100644 --- a/docs/404.html +++ b/docs/404.html @@ -27,7 +27,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 12553ff4..dfab1761 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 @@ -43,7 +43,7 @@ -YEAR: 2025 +YEAR: 2026 COPYRIGHT HOLDER: John Benninghoff diff --git a/docs/LICENSE.html b/docs/LICENSE.html index e0b51245..5b4bd80e 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 @@ -45,7 +45,7 @@ -Copyright (c) 2025 John Benninghoff +Copyright (c) 2026 John Benninghoff Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/docs/TODO.html b/docs/TODO.html index 54531c5c..c7d6aaed 100644 --- a/docs/TODO.html +++ b/docs/TODO.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/articles/analysis-package-layout.html b/docs/articles/analysis-package-layout.html index e4cf9fc7..1b2a7ae6 100644 --- a/docs/articles/analysis-package-layout.html +++ b/docs/articles/analysis-package-layout.html @@ -26,7 +26,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/articles/index.html b/docs/articles/index.html index d8c5f629..529459e5 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/articles/rdev.html b/docs/articles/rdev.html index fc067e9c..0593987f 100644 --- a/docs/articles/rdev.html +++ b/docs/articles/rdev.html @@ -26,7 +26,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/articles/style-guide.html b/docs/articles/style-guide.html index 6aa8477f..2f58d77f 100644 --- a/docs/articles/style-guide.html +++ b/docs/articles/style-guide.html @@ -26,7 +26,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/authors.html b/docs/authors.html index 8087f6ae..2531cdba 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 @@ -55,15 +55,15 @@ Authors Citation Source: DESCRIPTION - Benninghoff J (2025). + Benninghoff J (2026). rdev: R Development Tools. -R package version 1.15.5, https://jabenninghoff.github.io/rdev/. +R package version 1.15.6, https://jabenninghoff.github.io/rdev/. @Manual{, title = {rdev: R Development Tools}, author = {John Benninghoff}, - year = {2025}, - note = {R package version 1.15.5}, + year = {2026}, + note = {R package version 1.15.6}, url = {https://jabenninghoff.github.io/rdev/}, } diff --git a/docs/index.html b/docs/index.html index 4aa17d3a..6c94b20a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -29,7 +29,7 @@ rdev - 1.15.5 + 1.15.6 @@ -279,20 +279,20 @@ Workflow#> * creating vignettes ... OK #> * checking for LF line-endings in source and make files and shell scripts #> * checking for empty or unneeded directories -#> * building ‘rdev_1.15.5.tar.gz’ +#> * building ‘rdev_1.15.6.tar.gz’ #> #> ── R CMD check ───────────────────────────────────────────────────────────────── -#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/Rtmpqk420B/file11cd6e62afeb/rdev.Rcheck’ +#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpqNxoSE/file820a21bb3a1a/rdev.Rcheck’ #> * using R version 4.5.2 (2025-10-31) #> * using platform: aarch64-apple-darwin20 #> * R was compiled by #> Apple clang version 16.0.0 (clang-1600.0.26.6) #> GNU Fortran (GCC) 14.2.0 -#> * running under: macOS Sequoia 15.7.2 +#> * running under: macOS Sequoia 15.7.3 #> * using session charset: UTF-8 #> * using option ‘--no-manual’ #> * checking for file ‘rdev/DESCRIPTION’ ... OK -#> * this is package ‘rdev’ version ‘1.15.5’ +#> * this is package ‘rdev’ version ‘1.15.6’ #> * package encoding: UTF-8 #> * checking package namespace information ... OK #> * checking package dependencies ... OK @@ -347,8 +347,8 @@ Workflow#> * DONE #> #> Status: OK -#> ── R CMD check results ──────────────────────────────────────── rdev 1.15.5 ──── -#> Duration: 28.9s +#> ── R CMD check results ──────────────────────────────────────── rdev 1.15.6 ──── +#> Duration: 26.8s #> #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔ diff --git a/docs/news/index.html b/docs/news/index.html index 6fe02b7f..eb93a788 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 @@ -43,6 +43,11 @@ Source: NEWS.md + +rdev 1.15.6 +Added instructions for YAML chunk syntax update to upkeep_checklist() +2026 Upkeep + rdev 1.15.5 Added items for ggplot2 version 4 upgrade and switch to YAML chunk options to upkeep_checklist() diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index bc3339e6..b1f59a59 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -5,7 +5,7 @@ articles: analysis-package-layout: analysis-package-layout.html rdev: rdev.html style-guide: style-guide.html -last_built: 2025-12-07T01:08Z +last_built: 2026-01-01T17:24Z urls: reference: https://jabenninghoff.github.io/rdev/reference article: https://jabenninghoff.github.io/rdev/articles diff --git a/docs/reference/build_analysis_site.html b/docs/reference/build_analysis_site.html index d79ca48f..006658ca 100644 --- a/docs/reference/build_analysis_site.html +++ b/docs/reference/build_analysis_site.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/build_quarto_site.html b/docs/reference/build_quarto_site.html index 12b5c9c3..780cba92 100644 --- a/docs/reference/build_quarto_site.html +++ b/docs/reference/build_quarto_site.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/build_rdev_site.html b/docs/reference/build_rdev_site.html index 3ae90702..9739ca51 100644 --- a/docs/reference/build_rdev_site.html +++ b/docs/reference/build_rdev_site.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/check_renv.html b/docs/reference/check_renv.html index c5a328a2..21daa60a 100644 --- a/docs/reference/check_renv.html +++ b/docs/reference/check_renv.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/ci.html b/docs/reference/ci.html index b53aca9b..536e806e 100644 --- a/docs/reference/ci.html +++ b/docs/reference/ci.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/create_github_repo.html b/docs/reference/create_github_repo.html index 64d86fed..b29d94e3 100644 --- a/docs/reference/create_github_repo.html +++ b/docs/reference/create_github_repo.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/deps_check.html b/docs/reference/deps_check.html index 7ef71723..52d8798f 100644 --- a/docs/reference/deps_check.html +++ b/docs/reference/deps_check.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/get_license.html b/docs/reference/get_license.html index 6f9c9a8b..81c4c3c1 100644 --- a/docs/reference/get_license.html +++ b/docs/reference/get_license.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/get_release.html b/docs/reference/get_release.html index 0ca0d739..7e7a75cf 100644 --- a/docs/reference/get_release.html +++ b/docs/reference/get_release.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/html_url_check.html b/docs/reference/html_url_check.html index db3c55ca..f0fd416b 100644 --- a/docs/reference/html_url_check.html +++ b/docs/reference/html_url_check.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/index.html b/docs/reference/index.html index 558ea10e..e0cacb73 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/init.html b/docs/reference/init.html index 1ff4593e..7a4f0187 100644 --- a/docs/reference/init.html +++ b/docs/reference/init.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/lint_all.html b/docs/reference/lint_all.html index 739870a3..b2065ca9 100644 --- a/docs/reference/lint_all.html +++ b/docs/reference/lint_all.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/local_temppkg.html b/docs/reference/local_temppkg.html index 514a9532..60f2fb1b 100644 --- a/docs/reference/local_temppkg.html +++ b/docs/reference/local_temppkg.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/merge_release.html b/docs/reference/merge_release.html index 8fca7a1a..206ecf16 100644 --- a/docs/reference/merge_release.html +++ b/docs/reference/merge_release.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/new_branch.html b/docs/reference/new_branch.html index 4d7e8ca3..f37dd977 100644 --- a/docs/reference/new_branch.html +++ b/docs/reference/new_branch.html @@ -11,7 +11,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/open_files.html b/docs/reference/open_files.html index 0acdd5d2..bf7e7a89 100644 --- a/docs/reference/open_files.html +++ b/docs/reference/open_files.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/package_downloads.html b/docs/reference/package_downloads.html index cd089a90..3d6dc214 100644 --- a/docs/reference/package_downloads.html +++ b/docs/reference/package_downloads.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/package_type.html b/docs/reference/package_type.html index b431a4d0..37fb1ca7 100644 --- a/docs/reference/package_type.html +++ b/docs/reference/package_type.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/quickstart.html b/docs/reference/quickstart.html index 58c803f0..8d64c67e 100644 --- a/docs/reference/quickstart.html +++ b/docs/reference/quickstart.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/rdev-package.html b/docs/reference/rdev-package.html index 8157d725..3b750b19 100644 --- a/docs/reference/rdev-package.html +++ b/docs/reference/rdev-package.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/rmd_metadata.html b/docs/reference/rmd_metadata.html index 1ac42c78..49b3f9c0 100644 --- a/docs/reference/rmd_metadata.html +++ b/docs/reference/rmd_metadata.html @@ -11,7 +11,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/setup_analysis.html b/docs/reference/setup_analysis.html index 56e4e9c9..53286229 100644 --- a/docs/reference/setup_analysis.html +++ b/docs/reference/setup_analysis.html @@ -11,7 +11,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/setup_rdev.html b/docs/reference/setup_rdev.html index 2232dc54..ac0a1050 100644 --- a/docs/reference/setup_rdev.html +++ b/docs/reference/setup_rdev.html @@ -11,7 +11,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/sort_file.html b/docs/reference/sort_file.html index 7723a5f5..ede073ff 100644 --- a/docs/reference/sort_file.html +++ b/docs/reference/sort_file.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/sort_rbuildignore.html b/docs/reference/sort_rbuildignore.html index 08b088d6..d5ce6c2d 100644 --- a/docs/reference/sort_rbuildignore.html +++ b/docs/reference/sort_rbuildignore.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/spell_check_notebooks.html b/docs/reference/spell_check_notebooks.html index af40ce85..f3d6639d 100644 --- a/docs/reference/spell_check_notebooks.html +++ b/docs/reference/spell_check_notebooks.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/stage_release.html b/docs/reference/stage_release.html index abfcca8f..904da2b9 100644 --- a/docs/reference/stage_release.html +++ b/docs/reference/stage_release.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/style_all.html b/docs/reference/style_all.html index 492a60db..9d7c44dc 100644 --- a/docs/reference/style_all.html +++ b/docs/reference/style_all.html @@ -11,7 +11,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/to_document.html b/docs/reference/to_document.html index 8633425f..0bae7946 100644 --- a/docs/reference/to_document.html +++ b/docs/reference/to_document.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/unfreeze.html b/docs/reference/unfreeze.html index 8463c07e..f76dcd30 100644 --- a/docs/reference/unfreeze.html +++ b/docs/reference/unfreeze.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/update_wordlist_notebooks.html b/docs/reference/update_wordlist_notebooks.html index 6370b682..82141255 100644 --- a/docs/reference/update_wordlist_notebooks.html +++ b/docs/reference/update_wordlist_notebooks.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/upkeep_checklist.html b/docs/reference/upkeep_checklist.html index 35400929..bb5c6d49 100644 --- a/docs/reference/upkeep_checklist.html +++ b/docs/reference/upkeep_checklist.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/urlchecker-reexports.html b/docs/reference/urlchecker-reexports.html index f29748a1..c82feb1e 100644 --- a/docs/reference/urlchecker-reexports.html +++ b/docs/reference/urlchecker-reexports.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_analysis_package.html b/docs/reference/use_analysis_package.html index 95d562f2..1cdae3ce 100644 --- a/docs/reference/use_analysis_package.html +++ b/docs/reference/use_analysis_package.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_codecov.html b/docs/reference/use_codecov.html index 3fa77728..7257c608 100644 --- a/docs/reference/use_codecov.html +++ b/docs/reference/use_codecov.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_gitattributes.html b/docs/reference/use_gitattributes.html index dc2bc433..28c29903 100644 --- a/docs/reference/use_gitattributes.html +++ b/docs/reference/use_gitattributes.html @@ -11,7 +11,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_lintr.html b/docs/reference/use_lintr.html index 0a6ca6e3..66d891c4 100644 --- a/docs/reference/use_lintr.html +++ b/docs/reference/use_lintr.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_package_r.html b/docs/reference/use_package_r.html index 2ef540e8..ddc94bf5 100644 --- a/docs/reference/use_package_r.html +++ b/docs/reference/use_package_r.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_rdev_package.html b/docs/reference/use_rdev_package.html index e71363c8..069e4f20 100644 --- a/docs/reference/use_rdev_package.html +++ b/docs/reference/use_rdev_package.html @@ -9,7 +9,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_rdev_pkgdown.html b/docs/reference/use_rdev_pkgdown.html index 97cd4993..e3363042 100644 --- a/docs/reference/use_rdev_pkgdown.html +++ b/docs/reference/use_rdev_pkgdown.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_rprofile.html b/docs/reference/use_rprofile.html index 96863db7..14503e29 100644 --- a/docs/reference/use_rprofile.html +++ b/docs/reference/use_rprofile.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_spelling.html b/docs/reference/use_spelling.html index 57471cb7..ead59f4f 100644 --- a/docs/reference/use_spelling.html +++ b/docs/reference/use_spelling.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_todo.html b/docs/reference/use_todo.html index 83fe6e16..ebc1bd9f 100644 --- a/docs/reference/use_todo.html +++ b/docs/reference/use_todo.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/reference/use_upkeep_issue.html b/docs/reference/use_upkeep_issue.html index f694eace..03e449b1 100644 --- a/docs/reference/use_upkeep_issue.html +++ b/docs/reference/use_upkeep_issue.html @@ -13,7 +13,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/search.json b/docs/search.json index d9037fe9..b92b1f31 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"https://jabenninghoff.github.io/rdev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2025 John Benninghoff Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"content","dir":"","previous_headings":"","what":"Content","title":"TODO","text":"Add README.Rmd Update DESCRIPTION use description data README.Rmd Add ORCID Update ORCID details","code":""},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"package","dir":"","previous_headings":"","what":"Package","title":"TODO","text":"Write utility function sort .Rbuildignore Implement pkgdown Add links / update Rd formatting function documentation. Add dummy imports silence R CMD check note per tidyverse Migrate build_analysis_site() rdev Switch development version styler (1.3.2.9000) new release becomes available Validate lint_all works expected within ci Add ‘create package’ workflow example README, remove TODO section “Analysis package creation process” Move _pkgdown.yml repository root make projects discoverable pgkdown GitHub query Update README.Rmd template dynamically generate list notebooks analysis Automate release process Automate creation feature branches, including ‘Bump version’ using desc::desc_bump_version(\"dev\") Add check stage_release() look missing topics _pkgdown.yml reference section Update use_rdev_package() Handle .Rmd files already html_document section Move rmd_metadata() README-analysis.Rmd rdev package Add tests per comments R/ reading package book, documentation Update Roxygen comments reading package book, documentation, review merge duplicate Roxygen docs Write manual regression test script (notes R commands) vignette validate ‘Creating Packages’ ‘GitHub Releases’ Add messages, warnings build_analysis_site() report progress Add function spell check notebooks Automate branch protection Address issue https://github.com/r-lib/usethis/issues/1568, closed Add dplyr running use_analysis_package() Consider switching getOption(\"pkgType\") source per R options per R macOS FAQ, “CRAN build guaranteed compatible package binaries CRAN (Bioconductor).” Support creating repos organizations Consider incorporating GitHub description DESCRIPTION Create wrapper spelling includes notebooks package spell checking, WORDLIST Add spell_check_test_notebooks() function CI spellchecks notebooks Convert manual tests (Setup.Rmd) R Script can run within package created create_github_repo() Add function add missing (notebook) dependencies DESCRIPTION, see renv::dependencies() desc::desc_get_deps() Add check_renv() ci() stop renv::status() date Replace proof-docs urlchecker, support checking GitHub Pages docs directory using url_db_from_HTML_files (ask PR accepted) Move scripts tools inst/bin similar, per Stack Overflow R Packages Switch development versions styler (1.3.2.9000) lintr (2.0.1.9000) new release becomes available - needed address bugs current release versions, 1.3.2 2.0.1. Add trailing slash GitHub Pages URL Update lint_all() lint types, including .Rpres Add custom CSS files _site.yml analysis notebook templates control font size, described article, possibly using bs_theme(), since pkgdown customizes default using build_bslib() (issue exists unsupported Safari 14 Safari 15) Remove pkgdown/extra.css https://github.com/r-lib/pkgdown/issues/2377 accepted Establish default knitr options, including knitr::opts_chunk$set(fig.align = \"center\"), add analysis template, also review settings Advanced R Use Project Templates like vertical? Add CSS R Markdown Template instead assets/extra.css? Move shift-heading-level-: 1 _quarto.yml analysis/_metadata.yml, TODO.md renders properly Remove preset: bootstrap workaround pkgdown 2.0.8+ released (per https://github.com/r-lib/pkgdown/issues/2376) Replace GITHUB_PAT .Renviron gitcreds Review use usethis functions, including pull request helpers Update tests new testthat features (testthat::auto_test_package(), testthat::describe(), Reporters, testthat::local_mocked_bindings()) Replace dev = TRUE logic renv 1.1.6+ released; see renv #1695, #2190 Update errors messages reading Advanced R Conditions re-reading Tidyverse Style Guide Reduce number Imports, per R CMD check:","code":"> devtools::check() ... > checking package dependencies ... NOTE Imports includes 30 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally."},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"github","dir":"","previous_headings":"","what":"GitHub","title":"TODO","text":"Use standard R CMD check Use lintr Faster CI checks Switch full R CMD check ? Update GitHub Actions r-lib examples Run test coverage Skip CI checks changes docs/ directory Add GitHub Action html/link checking using something like htmlproofer Autobuild docs/ like pkgdown ?","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to rdev","text":"rdev supports personal workflow, including creation traditional R packages R Analysis Packages (vignette(\"analysis-package-layout\")), enforcing consistency across packages, providing Continuous Integration/Continuous Delivery (CI/CD) automation. use tools rdev improve code quality, speed development R code, publish results analyses R Quarto Notebooks HTML make accessible non-R users.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to rdev","text":"current R development environment uses Homebrew, rig, RStudio, GitHub, collection R packages including rdev, Visual Studio Code, Vim.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"homebrew","dir":"Articles","previous_headings":"Installation","what":"Homebrew","title":"Introduction to rdev","text":"use Homebrew Bundle install software systems; basic macOS working environment published GitHub macos-env.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"installing-r","dir":"Articles","previous_headings":"Installation","what":"Installing R","title":"Introduction to rdev","text":"rig supports installation multiple versions official R binaries, use reproducibility. install R using rig, first install rig: install desired versions R. following installs R 3.6 4.5 ARM based macs (2025-10-08): Note : don’t use pak, rig installs default, yet fully supported renv. oldest version R install 3.6, since RStudio now requires R 3.6 newer (version 2024.04.00) Since ARM binary release R 3.6 (oldrel/6) R 4.0 (oldrel/5), install Intel binaries run Rosetta 2.","code":"brew tap r-lib/rig brew install --cask rig rig install oldrel/6 --without-pak --arch x86_64 rig install oldrel/5 --without-pak --arch x86_64 rig install oldrel/4 --without-pak rig install oldrel/3 --without-pak rig install oldrel/2 --without-pak rig install oldrel/1 --without-pak rig install oldrel --without-pak rig install release --without-pak rig default release"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"development-tools","dir":"Articles","previous_headings":"Installation","what":"Development Tools","title":"Introduction to rdev","text":"Well, obviously, use RStudio. RStudio leading IDE R development integrates many R packages, although sometimes falls short; use GitHub command line Git, occasionally Visual Studio Code (better support markdown) Vim (faster types edits). Posit developing next-generation R Python IDE based Visual Studio Code, Positron. ’ve tried using Positron, ’ve found many missing features replace RStudio development, including: Lack notebook-style interface RMarkdown Quarto documents support lintr command History package Build panes , first two showstoppers missing panes nearly . RStudio, GitHub desktop client, Visual Studio Code easily installed using Homebrew: recommended change default settings .RData RStudio (Options > General > Basic > Workspace): Uncheck “Restore .Data workspace startup” Set “Save workspace .Data exit” “Never” Vim installed default macOS Unix-like systems.","code":"brew install --cask rstudio brew install --cask github brew install --cask visual-studio-code"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"packages","dir":"Articles","previous_headings":"Installation","what":"Packages","title":"Introduction to rdev","text":"Managing packages environments challenge modern languages. Thankfully R doesn’t level challenge python, even ruby, managing packages available within project best practice. use renv purpose, use renv install manage packages projects. setup-r script rdev installs base set packages needed run rdev R User Library. streamlined version script included . chown command needed allow updating base packages using RStudio Packages “Update” function. generally update packages RStudio projects open starting development, update packages projects using renv::update(). ’re installing (development) versions packages GitHub, recommended set personal access token using usethis::create_github_token() adding Git credential store using gitcreds::gitcreds_set(). can verify GitHub set following usethis recommendations usethis::git_sitrep().","code":"# fix rig permissions sudo chown -R \"$(whoami)\":admin /Library/Frameworks/R.framework/Versions/*/Resources/library RVERSION=\"$(Rscript -e 'cat(as.character(getRversion()[1,1:2]))')\" USERLIB=\"$HOME/Library/R/$(uname -m)/${RVERSION}/library\" DEVPKG='c(\"renv\", \"styler\", \"lintr\", \"miniUI\", \"languageserver\", \"rmarkdown\", \"devtools\", \"available\")' GITPKG='c(\"jabenninghoff/rdev\")' if [ ! -d \"${USERLIB}\" ] then mkdir -p \"${USERLIB}\" fi echo \"install.packages(${DEVPKG}, repos=\\\"https://cloud.r-project.org\\\", lib=\\\"${USERLIB}\\\")\" | R --no-save echo \"remotes::install_github(${GITPKG}, lib=\\\"${USERLIB}\\\")\" | R --no-save"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"further-reading","dir":"Articles","previous_headings":"Installation","what":"Further Reading","title":"Introduction to rdev","text":"workflow heavily influenced DevOps movement research DevOps Research Assessment (DORA) team Google started Dr. Nicole Forsgren. research shows technical non-technical capabilities improve outcomes. functions included rdev support many technical capabilities, including: Code maintainability Continuous delivery Continuous integration Deployment automation Shifting left security Test automation Trunk-based development Version control outline SIRAcon 2022 talk, “Making R Work (Automation)” available GitHub siracon2022.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"rdev-conventions","dir":"Articles","previous_headings":"","what":"rdev conventions","title":"Style Guide","text":"rdev uses mix Google tidyverse conventions.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"naming-conventions","dir":"Articles","previous_headings":"rdev conventions","what":"Naming conventions","title":"Style Guide","text":"rdev follows tidyverse naming convention snake_case.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"right-hand-assignment","dir":"Articles","previous_headings":"rdev conventions","what":"Right-hand assignment","title":"Style Guide","text":"rdev follows Google’s style guide, use right-hand assignment.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"returns","dir":"Articles","previous_headings":"rdev conventions","what":"Returns","title":"Style Guide","text":"rdev typically uses implicit returns unless needed flow control construct specific return structure.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"qualifying-namespaces","dir":"Articles","previous_headings":"rdev conventions","what":"Qualifying namespaces","title":"Style Guide","text":"Use @import @importFrom discouraged, instead using :: functions defined R/. exception infix functions (%name%), always imported, using roxygen @importFrom. Within R Quarto Notebooks, use library() encouraged readability.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"package-level-documentation","dir":"Articles","previous_headings":"rdev conventions","what":"Package-level documentation","title":"Style Guide","text":"rdev package documentation lives R/package.R. Additionally, use base R encouraged within functions defined R/ (control dependencies), tidyverse R encouraged within notebooks readability. R Markdown documents generally wrap width code, exceptions R Notebook ‘description line’ (first non-blank line body), long hyperlinks.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"styler","dir":"Articles","previous_headings":"","what":"styler","title":"Style Guide","text":"rdev package implements styler using styler defaults, permanent caching enabled (options(styler.cache_root = \"styler-perm\")). style_all() function applies tidyverse style R Quarto files (R, Rprofile, Rmd, Rnw, qmd) package directory structure.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"lintr","dir":"Articles","previous_headings":"","what":"lintr","title":"Style Guide","text":"lint_all() function lints R Quarto files (R, Rmd, qmd, Rnw, Rhtml, Rpres, Rrst, Rtex, Rtxt) lintr using opinionated configuration (.lintr): settings deliberately chosen meet specific goals:","code":"linters: linters_with_tags( tags = NULL, implicit_integer_linter = NULL, line_length_linter(100), missing_package_linter = NULL, namespace_linter = NULL, nonportable_path_linter = NULL, paste_linter(allow_file_path = \"always\"), todo_comment_linter = NULL, undesirable_function_linter( within(all_undesirable_functions, rm(ifelse, library, require, structure)) ), undesirable_operator_linter(all_undesirable_operators), unnecessary_concatenation_linter(allow_single_expression = FALSE), unused_import_linter( except_packages = c(\"bit64\", \"data.table\", \"tidyverse\", pkgload::pkg_name(\".\")) ) )"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"use-all-linters","dir":"Articles","previous_headings":"lintr","what":"Use all linters","title":"Style Guide","text":"selects linters, including new Google linters. selecting linters, just defaults, forces evaluation new linters added lintr. Specific linters disabled configured per rdev style.","code":"linters: linters_with_tags( tags = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-implicit-integers","dir":"Articles","previous_headings":"lintr","what":"Allow implicit integers","title":"Style Guide","text":"implicit integer linter checks integers explicitly typed using form 1L. , safer, implicit integers common practice, including output dput():","code":"implicit_integer_linter = NULL, dput(character(0L)) #> character(0)"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"set-line-length","dir":"Articles","previous_headings":"lintr","what":"Set line length","title":"Style Guide","text":"line length 100 reasonable width working RStudio IDE laptop.","code":"line_length_linter(100),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"use-renv-for-missing-packages","dir":"Articles","previous_headings":"lintr","what":"Use renv for missing packages","title":"Style Guide","text":"missing package linter namespace linter check packages referenced code installed. rdev uses renv manage packages, better job detecting missing packages, including complaining current package (\".\") installed.","code":"missing_package_linter = NULL, namespace_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-non-portable-paths","dir":"Articles","previous_headings":"lintr","what":"Allow non-portable paths","title":"Style Guide","text":"non-portable path linter generates many false positives, including calls fs, essentially makes UNIX-style paths portable across operating systems. Similarly, allow_file_path default option \"double_slash\" generates false positives used fs.","code":"nonportable_path_linter = NULL, paste_linter(allow_file_path = \"always\"),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-todo-comments","dir":"Articles","previous_headings":"lintr","what":"Allow TODO comments","title":"Style Guide","text":"rdev conventions encourage use # TODO: comments convenient way identifying needed planned updates inline.","code":"todo_comment_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"disallow-almost-all-undesirable-functions-and-operators","dir":"Articles","previous_headings":"lintr","what":"Disallow almost all undesirable functions and operators","title":"Style Guide","text":"Enable undesirable functions operators, just defaults, except ifelse() succinct /else block, library(), require(), structure(). Use require() within .Rprofile library() within R Markdown documents appropriate common practice, although neither used within package code. structure() useful comparing test results values generated dput().","code":"undesirable_function_linter( within(all_undesirable_functions, rm(ifelse, library, require, structure)) ), undesirable_operator_linter(all_undesirable_operators),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"enforce-strict-unnecessary-concatenation","dir":"Articles","previous_headings":"lintr","what":"Enforce strict unnecessary concatenation","title":"Style Guide","text":"Enforce stricter version unnecessary concatenation linter.","code":"unnecessary_concatenation_linter(allow_single_expression = FALSE),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"verify-imported-packages-are-used","dir":"Articles","previous_headings":"lintr","what":"Verify imported packages are used","title":"Style Guide","text":"Verify imported packages used, except packages attached side effects, current package (support package development).","code":"unused_import_linter( except_packages = c(\"bit64\", \"data.table\", \"tidyverse\", pkgload::pkg_name(\".\")) ) )"},{"path":"https://jabenninghoff.github.io/rdev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Benninghoff. Author, maintainer.","code":""},{"path":"https://jabenninghoff.github.io/rdev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Benninghoff J (2025). rdev: R Development Tools. R package version 1.15.5, https://jabenninghoff.github.io/rdev/.","code":"@Manual{, title = {rdev: R Development Tools}, author = {John Benninghoff}, year = {2025}, note = {R package version 1.15.5}, url = {https://jabenninghoff.github.io/rdev/}, }"},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"R Development Tools","text":"R Development Tools: opinionated collection development tools, packages, utilities. Feel free use /fork project!","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"R Development Tools","text":"can install development version rdev GitHub : using renv:","code":"# install.packages(\"remotes\") remotes::install_github(\"jabenninghoff/rdev\") # install.packages(\"renv\") renv::install(\"jabenninghoff/rdev\")"},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"development","dir":"","previous_headings":"","what":"Development","title":"R Development Tools","text":"Changelog: See “Changelog” NEWS.md. Planned: TODO","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"creating-packages","dir":"","previous_headings":"","what":"Creating Packages","title":"R Development Tools","text":"rdev supports creation new R packages following rdev conventions well new R Analysis packages. typical setup workflow (per ?quickstart) : Use available::available() check package name project open, run create_github_repo() initialize GitHub R repository Without committing git, run init() newly created project Manually update Title Description fields DESCRIPTION file without committing Run setup_analysis() setup_rdev() configure package analysis package rdev package respectively. Update TODO.md, NEWS.md, README.Rmd, DESCRIPTION needed Re-run check_renv(), ci() validate package Commit git begin development","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"github-releases","dir":"","previous_headings":"","what":"GitHub Releases","title":"R Development Tools","text":"rdev automates workflow creating GitHub releases along updating GitHub pages either standard R packages R analysis packages, using release notes format NEWS.md. typical development workflow : Bump version create new feature branch new_branch() Write things Update release notes new version NEWS.md, following conventions described get_release() Finalize release merge changes git Run stage_release() create new pull request GitHub using details derived NEWS.md, including updating README GitHub pages pull request reviewed passes required status checks, accept staged release merge_release(), merges pull request, cleans branches, publishes new GitHub release Feature branches can merged without starting new release; stage_release() just requires everything committed, including new release notes NEWS.md running. ready release, stage_release() use existing branch feature branch, create new release branch default.","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"workflow","dir":"","previous_headings":"","what":"Workflow","title":"R Development Tools","text":"workflow, typically check renv start: also ci() function run continuous integration tests locally:","code":"library(rdev) check_renv() #> renv::status(dev = TRUE) #> No issues found -- the project is in a consistent state. #> #> renv::clean() #> - No stale package locks were found. #> - No temporary directories were found in the project library. #> - The project has been cleaned. ci() #> renv::status(dev = TRUE) #> No issues found -- the project is in a consistent state. #> #> missing_deps() #> Finding R package dependencies ... Done! #> renv::dependencies() not in DESCRIPTION: #> #> pkgdown::check_pkgdown() #> ✔ No problems found. #> #> style_all() #> Styling 69 files: #> .Rprofile ✔ #> README.Rmd ✔ #> inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd ✔ #> inst/templates/analysis.qmd ✔ #> inst/templates/changelog.qmd ✔ #> inst/templates/index.qmd ✔ #> inst/templates/package.R ✔ #> inst/templates/README-analysis.Rmd ✔ #> inst/templates/README-rdev.Rmd ✔ #> inst/templates/spelling.R ✔ #> inst/templates/test-spelling.R ✔ #> R/build.R ✔ #> R/ci.R ✔ #> R/helpers.R ✔ #> R/init.R ✔ #> R/package.R ✔ #> R/release.R ✔ #> R/setup.R ✔ #> R/to_document.R ✔ #> R/upkeep.R ✔ #> R/urlchecker.R ✔ #> R/utils.R ✔ #> tests/spelling.R ✔ #> tests/testthat.R ✔ #> tests/manual/setup.Rmd ✔ #> tests/manual/test-new-repo-1.R ✔ #> tests/manual/test-new-repo-2.R ✔ #> tests/manual/test-new-repo-3-analysis.R ✔ #> tests/manual/test-new-repo-3-package.R ✔ #> tests/testthat/test-build.R ✔ #> tests/testthat/test-ci.R ✔ #> tests/testthat/test-helpers.R ✔ #> tests/testthat/test-init.R ✔ #> tests/testthat/test-inst.R ✔ #> tests/testthat/test-release.R ✔ #> tests/testthat/test-setup.R ✔ #> tests/testthat/test-spelling.R ✔ #> tests/testthat/test-to_document.R ✔ #> tests/testthat/test-upkeep.R ✔ #> tests/testthat/test-utils.R ✔ #> tests/testthat/test-ci/test-revealjs.qmd ✔ #> tests/testthat/test-ci/test.Rprofile ✔ #> tests/testthat/test-ci/testcode_1.R ✔ #> tests/testthat/test-ci/testcode_2.R ✔ #> tests/testthat/test-ci/testcode.qmd ✔ #> tests/testthat/test-ci/testcode.Rmd ✔ #> tests/testthat/test-ci/testcode.Rnw ✔ #> tests/testthat/test-ci/packrat/test.R ✔ #> tests/testthat/test-ci/R/RcppExports.R ✔ #> tests/testthat/test-ci/renv/test.R ✔ #> tests/testthat/test-to_document/document.Rmd ✔ #> tests/testthat/test-to_document/docx.qmd ✔ #> tests/testthat/test-to_document/extra-spaces.Rmd ✔ #> tests/testthat/test-to_document/minimal-document.Rmd ✔ #> tests/testthat/test-to_document/minimal-docx.qmd ✔ #> tests/testthat/test-to_document/minimal.qmd ✔ #> tests/testthat/test-to_document/minimal.Rmd ✔ #> tests/testthat/test-to_document/multiple.Rmd ✔ #> tests/testthat/test-to_document/no-format.qmd ✔ #> tests/testthat/test-to_document/no-front-matter.Rmd ✔ #> tests/testthat/test-to_document/no-output.Rmd ✔ #> tests/testthat/test-to_document/no-yaml.qmd ✔ #> tests/testthat/test-to_document/no-yaml.Rmd ✔ #> tests/testthat/test-to_document/valid.qmd ✔ #> tests/testthat/test-to_document/valid.Rmd ✔ #> tests/testthat/test-to_document/with-code.Rmd ✔ #> vignettes/analysis-package-layout.Rmd ✔ #> vignettes/rdev.Rmd ✔ #> vignettes/style-guide.Rmd ✔ #> ─────────────────────────────────────────────────────── #> Status Count Legend #> ✔ 69 File unchanged. #> ℹ 0 File changed. #> ✖ 0 Styling threw an error. #> ─────────────────────────────────────────────────────── #> #> lint_all() #> #> devtools::document() #> ℹ Updating rdev documentation #> ℹ Loading rdev #> #> desc::desc_normalize() #> #> extra_deps() #> Finding R package dependencies ... Done! #> desc::desc_get_deps() not found by renv: #> # A tibble: 3 × 3 #> type package version #> #> 1 Suggests covr * #> 2 Suggests diffviewer * #> 3 Suggests DT * #> #> spelling::update_wordlist() #> No changes required to /Users/agamemnon/GitHub/rdev/inst/WORDLIST #> #> url_check() #> html_url_check() #> # A tibble: 2 × 9 #> URL From Status Message New CRAN Spaces R root #> #> 1 http://covr.r-lib.org/ref… 200 OK http… \"\" \"\" \"\" /Use… #> 2 http://r-lib.github.io/rc… 200 OK http… \"\" \"\" \"\" /Use… #> #> Setting env vars: NOT_CRAN=\"true\", CI=\"true\" #> rcmdcheck::rcmdcheck(args = \"--no-manual\", error_on = \"warning\") #> ── R CMD build ───────────────────────────────────────────────────────────────── #> * checking for file ‘.../DESCRIPTION’ ... OK #> * preparing ‘rdev’: #> * checking DESCRIPTION meta-information ... OK #> * installing the package to build vignettes #> * creating vignettes ... OK #> * checking for LF line-endings in source and make files and shell scripts #> * checking for empty or unneeded directories #> * building ‘rdev_1.15.5.tar.gz’ #> #> ── R CMD check ───────────────────────────────────────────────────────────────── #> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/Rtmpqk420B/file11cd6e62afeb/rdev.Rcheck’ #> * using R version 4.5.2 (2025-10-31) #> * using platform: aarch64-apple-darwin20 #> * R was compiled by #> Apple clang version 16.0.0 (clang-1600.0.26.6) #> GNU Fortran (GCC) 14.2.0 #> * running under: macOS Sequoia 15.7.2 #> * using session charset: UTF-8 #> * using option ‘--no-manual’ #> * checking for file ‘rdev/DESCRIPTION’ ... OK #> * this is package ‘rdev’ version ‘1.15.5’ #> * package encoding: UTF-8 #> * checking package namespace information ... OK #> * checking package dependencies ... OK #> * checking if this is a source package ... OK #> * checking if there is a namespace ... OK #> * checking for executable files ... OK #> * checking for hidden files and directories ... OK #> * checking for portable file names ... OK #> * checking for sufficient/correct file permissions ... OK #> * checking whether package ‘rdev’ can be installed ... OK #> * checking installed package size ... OK #> * checking package directory ... OK #> * checking ‘build’ directory ... OK #> * checking DESCRIPTION meta-information ... OK #> * checking top-level files ... OK #> * checking for left-over files ... OK #> * checking index information ... OK #> * checking package subdirectories ... OK #> * checking code files for non-ASCII characters ... OK #> * checking R files for syntax errors ... OK #> * checking whether the package can be loaded ... OK #> * checking whether the package can be loaded with stated dependencies ... OK #> * checking whether the package can be unloaded cleanly ... OK #> * checking whether the namespace can be loaded with stated dependencies ... OK #> * checking whether the namespace can be unloaded cleanly ... OK #> * checking loading without being on the library search path ... OK #> * checking dependencies in R code ... OK #> * checking S3 generic/method consistency ... OK #> * checking replacement functions ... OK #> * checking foreign function calls ... OK #> * checking R code for possible problems ... OK #> * checking Rd files ... OK #> * checking Rd metadata ... OK #> * checking Rd cross-references ... OK #> * checking for missing documentation entries ... OK #> * checking for code/documentation mismatches ... OK #> * checking Rd \\usage sections ... OK #> * checking Rd contents ... OK #> * checking for unstated dependencies in examples ... OK #> * checking installed files from ‘inst/doc’ ... OK #> * checking files in ‘vignettes’ ... OK #> * checking examples ... OK #> * checking for unstated dependencies in ‘tests’ ... OK #> * checking tests ... #> Running ‘spelling.R’ #> Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK #> Running ‘testthat.R’ #> OK #> * checking for unstated dependencies in vignettes ... OK #> * checking package vignettes ... OK #> * checking re-building of vignette outputs ... OK #> * DONE #> #> Status: OK #> ── R CMD check results ──────────────────────────────────────── rdev 1.15.5 ──── #> Duration: 28.9s #> #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build Analysis Site — build_analysis_site","title":"Build Analysis Site — build_analysis_site","text":"build_analysis_site() wrapper pkgdown::build_site_github_pages() adds 'Analysis' menu containing rendered versions .Rmd files analysis/.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build Analysis Site — build_analysis_site","text":"","code":"build_analysis_site(pkg = \".\", ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build Analysis Site — build_analysis_site","text":"pkg Path package. Currently, pkg = \".\" supported. ... additional arguments passed pkgdown::build_site_github_pages() (implemented)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build Analysis Site — build_analysis_site","text":"rmarkdown _site.yml yaml, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build Analysis Site — build_analysis_site","text":"run, build_analysis_site(): Reads base pkgdown::pkgdown settings pkgdown/_base.yml Writes base settings _pkgdown.yml Creates template using pkgdown::template_navbar() inserts analysis menu links html versions .Rmd file analysis/ Writes template _pkgdown.yml Updates README.md running devtools::build_readme() (README.Rmd exists) update list notebooks Runs pkgdown::build_site_github_pages() install = TRUE new_process = TRUE Creates _site.yml file based final _pkgdown.yml clones pkgdown::pkgdown navbar temporary build directory Copies following analysis/ build directory: *.Rmd, assets/, data/, import/, rendered/ Changes *.Rmd html_notebook html_document using to_document() Builds site using rmarkdown::render_site() using modified html_document output settings render files look feel html_notebook Moves rendered files docs/: *.html, assets/, rendered/, without overwriting build_analysis_site() fail error files analysis/*.Rmd, pkgdown/_base.yml exist.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"continuous-integration","dir":"Reference","previous_headings":"","what":"Continuous Integration","title":"Build Analysis Site — build_analysis_site","text":"build_rdev_site() build_analysis_site() meant used part CI/CD workflow, temporarily set environment variable CI == \"TRUE\" build fail non-internal topics included reference index page per pkgdown::build_reference().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"supported-file-types","dir":"Reference","previous_headings":"","what":"Supported File Types","title":"Build Analysis Site — build_analysis_site","text":"build_quarto_site() supports R Markdown (.Rmd) Quarto (.qmd) notebooks analysis directory interchangeably, build_analysis_site() supports .Rmd files .","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build Quarto Site — build_quarto_site","title":"Build Quarto Site — build_quarto_site","text":"build_quarto_site() wrapper quarto::quarto_render() also updates README.md optionally deletes Quarto _freeze directory fully re-render site.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build Quarto Site — build_quarto_site","text":"","code":"build_quarto_site(input = NULL, as_job = FALSE, unfreeze = FALSE, ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build Quarto Site — build_quarto_site","text":"input input file project directory rendered (defaults rendering project current working directory). as_job Render RStudio background job. Default \"auto\", render individual documents normally projects background jobs. Use quarto.render_as_job R option control default globally. unfreeze TRUE, delete Quarto _freeze directory fully re-render site. ... Arguments passed quarto::quarto_render().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build Quarto Site — build_quarto_site","text":"run, build_quarto_site() calls: devtools::build_readme() unfreeze() (unfreeze = TRUE) quarto::quarto_render()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"supported-file-types","dir":"Reference","previous_headings":"","what":"Supported File Types","title":"Build Quarto Site — build_quarto_site","text":"build_quarto_site() supports R Markdown (.Rmd) Quarto (.qmd) notebooks analysis directory interchangeably, build_analysis_site() supports .Rmd files .","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build rdev Site — build_rdev_site","title":"Build rdev Site — build_rdev_site","text":"build_rdev_site() wrapper pkgdown::build_site_github_pages() optimized rdev workflow updates README.md performs clean GitHub pages build using pkgdown.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build rdev Site — build_rdev_site","text":"","code":"build_rdev_site(pkg = \".\", ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build rdev Site — build_rdev_site","text":"pkg Path package. Currently, pkg = \".\" supported. ... additional arguments passed pkgdown::build_site_github_pages() (implemented)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build rdev Site — build_rdev_site","text":"run, build_rdev_site() calls: devtools::build_readme() pkgdown::build_site_github_pages() install = TRUE new_process = TRUE","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"continuous-integration","dir":"Reference","previous_headings":"","what":"Continuous Integration","title":"Build rdev Site — build_rdev_site","text":"build_rdev_site() build_analysis_site() meant used part CI/CD workflow, temporarily set environment variable CI == \"TRUE\" build fail non-internal topics included reference index page per pkgdown::build_reference().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":null,"dir":"Reference","previous_headings":"","what":"Check renv — check_renv","title":"Check renv — check_renv","text":"Runs renv status(dev = TRUE), clean(), optionally update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check renv — check_renv","text":"","code":"check_renv(update = rlang::is_interactive())"},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check renv — check_renv","text":"update run renv::update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check renv — check_renv","text":"","code":"if (FALSE) { # \\dontrun{ check_renv() check_renv(update = FALSE) } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Local CI — ci","title":"Local CI — ci","text":"Run continuous integration tests locally.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Local CI — ci","text":"","code":"ci( renv = TRUE, missing = TRUE, pkgdown = TRUE, styler = NULL, lintr = TRUE, document = TRUE, normalize = TRUE, extra = TRUE, spelling = TRUE, urls = TRUE, rcmdcheck = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Local CI — ci","text":"renv check renv::status(dev = TRUE) missing run missing_deps() pkgdown check pkgdown::check_pkgdown() _pkgdown.yml exists styler style files using style_all(), see details lintr lint files using lint_all() document run devtools::document() normalize run desc::desc_normalize() extra run extra_deps() spelling update spelling WORDLIST urls validate URLs url_check() html_url_check() rcmdcheck run R CMD check using: rcmdcheck::rcmdcheck(args = \"–-manual\", error_on = \"warning\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Local CI — ci","text":"renv::status(dev = TRUE) synchronized, ci() stop. missing_deps() returns missing dependencies, ci() stop. pkgdown::check_pkgdown() halt ci() error _pkgdown.yml invalid. styler set NULL (default), style_all() run uncommitted changes git. Setting value TRUE FALSE overrides check. lint_all() finds lints, ci() stop open RStudio markers pane. Output missing, extra, urls printed tibble improved readability console.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Local CI — ci","text":"","code":"if (FALSE) { # \\dontrun{ ci() ci(styler = TRUE) ci(styler = FALSE, rcmdcheck = FALSE) } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":null,"dir":"Reference","previous_headings":"","what":"Create rdev GitHub repository — create_github_repo","title":"Create rdev GitHub repository — create_github_repo","text":"Create, configure, clone, open new GitHub R package repository following rdev conventions.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create rdev GitHub repository — create_github_repo","text":"","code":"create_github_repo( repo_name, repo_desc = \"\", private = FALSE, org = NULL, host = getOption(\"rdev.host\") )"},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create rdev GitHub repository — create_github_repo","text":"repo_name name GitHub repository create repo_desc description GitHub repository create private TRUE, creates private repository. org organization create repository . NULL, create repository active user's account. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create rdev GitHub repository — create_github_repo","text":"return value gh::gh() creating repository, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create rdev GitHub repository — create_github_repo","text":"run, create_github_repo(): Creates new GitHub repository using gh::gh() license template get_license() Activates Dependabot alerts per getOption(\"rdev.dependabot\", default = TRUE) Activates Dependabot security updates per getOption(\"rdev.dependabot\", default = TRUE) Adds branch protection default branch (private FALSE) Clones repository locally usethis::create_from_github() Creates basic package using usethis::create_package() running interactively, repository automatically opened RStudio, GitHub Desktop, default browser","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"github-actions","dir":"Reference","previous_headings":"","what":"GitHub Actions","title":"Create rdev GitHub repository — create_github_repo","text":"GitHub Actions can disabled setting rdev.github.actions FALSE: options(rdev.github.actions = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Create rdev GitHub repository — create_github_repo","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check dependencies — missing_deps","title":"Check dependencies — missing_deps","text":"Check dependencies DESCRIPTION.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check dependencies — missing_deps","text":"","code":"missing_deps(exclude_base = TRUE) extra_deps()"},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check dependencies — missing_deps","text":"exclude_base exclude packages installed R missing dependencies","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check dependencies — missing_deps","text":"data.frame either renv::dependencies() desc::desc_get_deps().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check dependencies — missing_deps","text":"missing_deps() reports renv::dependencies() DESCRIPTION. extra_deps() reports desc::desc_get_deps() found renv. current package (pkgload::pkg_name(\".\")) renv (renv.lock ) automatically removed renv::dependencies(), along 'base' R packages exclude_base TRUE (base, compiler, datasets, grDevices, graphics, grid, methods, parallel, splines, stats, stats4, tcltk, tools, utils).","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":null,"dir":"Reference","previous_headings":"","what":"Get license option — get_license","title":"Get license option — get_license","text":"Retrieve validate rdev.license option.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get license option — get_license","text":"","code":"get_license()"},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get license option — get_license","text":"license string, one c(\"mit\", \"gpl\", \"lgpl\", \"proprietary\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get license option — get_license","text":"rdev.license must one c(\"mit\", \"gpl\", \"lgpl\", \"proprietary\"), defaults \"mit\". rdev.license \"proprietary\", rdev.license.copyright (name copyright holder) must also set.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Get release details — get_release","title":"Get release details — get_release","text":"Extract release version release notes NEWS.md.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get release details — get_release","text":"","code":"get_release(pkg = \".\", filename = \"NEWS.md\")"},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get release details — get_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get release details — get_release","text":"list containing package, version release notes first release contained NEWS.md","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get release details — get_release","text":"get_release() assumes NEWS.md contains markdown release notes, release header format: \"# \" followed release notes, expects first line NEWS.md release header.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check URLs in HTML files — html_url_check","title":"Check URLs in HTML files — html_url_check","text":"Runs urlchecker::url_check() database created using url_db_from_HTML_files function tools package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check URLs in HTML files — html_url_check","text":"","code":"html_url_check( path = \"docs\", parallel = TRUE, pool = curl::new_pool(), progress = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check URLs in HTML files — html_url_check","text":"path Path directory HTML files parallel TRUE, check URLs parallel pool multi handle created curl::new_pool(). NULL use global pool. progress Whether show progress bar parallel checks","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check URLs in HTML files — html_url_check","text":"url_checker_db object (invisibly). check_url_db object added class custom print method.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize rdev package — init","title":"Initialize rdev package — init","text":"Initialize rdev package within newly created create_github_repo() project creating new git branch, committing changes, running use_rdev_package().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize rdev package — init","text":"","code":"init()"},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Initialize rdev package — init","text":"init() stop rlang::is_interactive() FALSE. running init(), update Title Description fields DESCRIPTION file without committing run either setup_analysis() setup_rdev() per quickstart.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Lint all files — lint_all","title":"Lint all files — lint_all","text":"Lint files project. Implemented wrapper lintr::lint_dir().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lint all files — lint_all","text":"","code":"lint_all( pattern = \"(?i)[.](r|rmd|qmd|rnw|rhtml|rpres|rrst|rtex|rtxt)$\", exclusions = list(\"renv\", \"packrat\", \"R/RcppExports.R\"), ... )"},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lint all files — lint_all","text":"pattern regex pattern files, default take files extensions .R, .Rmd, .qmd, .Rnw, .Rhtml, .Rpres, .Rrst, .Rtex, .Rtxt, ignoring case. exclusions exclusions exclude(), relative package path. ... Arguments passed lintr::lint_dir parse_settings Logical. Whether try parse settings. Otherwise, default_settings() used. TRUE default linting files, opposed text=. path base directory project (lint_dir()) package (lint_package()). relative_path TRUE, file paths printed using path relative base directory. FALSE, use full absolute path. show_progress Logical controlling whether show linting progress cli::cli_progress_along(). default behavior show progress interactive() sessions running testthat suite.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lint all files — lint_all","text":"list lint objects.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lint all files — lint_all","text":"","code":"if (FALSE) { # \\dontrun{ lint_all() lint_all(\"analysis\") } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":null,"dir":"Reference","previous_headings":"","what":"Temporary package — local_temppkg","title":"Temporary package — local_temppkg","text":"Temporarily create rdev R analysis package, automatically removed afterwards.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Temporary package — local_temppkg","text":"","code":"local_temppkg(dir = fs::file_temp(), type = \"usethis\", env = parent.frame())"},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Temporary package — local_temppkg","text":"dir Path package directory, created necessary, defaults fs::file_temp(). type type package create, one \"usethis\" - usethis::create_package(), \"rdev\" - use_rdev_package(), \"analysis\" - use_analysis_package(use_quarto = FALSE), \"quarto\" - use_analysis_package(use_quarto = TRUE). env Environment passed withr::defer(), defaults parent.frame().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Temporary package — local_temppkg","text":"Path temporary package directory.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Temporary package — local_temppkg","text":"Used internally testing rdev automation. Based usethis case study testthat.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Temporary package — local_temppkg","text":"","code":"if (FALSE) { # \\dontrun{ test_that(\"local_temppkg creates a directory\", { dir <- usethis::ui_silence(local_temppkg()) expect_true(fs::dir_exists(dir)) }) } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Merge staged GitHub release — merge_release","title":"Merge staged GitHub release — merge_release","text":"Merge pull request staged stage_release() create new release GitHub.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merge staged GitHub release — merge_release","text":"","code":"merge_release(pkg = \".\", filename = \"NEWS.md\", host = getOption(\"rdev.host\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merge staged GitHub release — merge_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merge staged GitHub release — merge_release","text":"list containing results pull request merge GitHub release, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Merge staged GitHub release — merge_release","text":"Manually verify status checks completed running, merge_release() currently validate status checks successful. run, merge_release(): Determines staged release title NEWS.md using get_release() Selects GitHub pull request matches staged release title, stops less one matching PR using gh::gh() Verifies staged pull request ready merged checking locked, draft, mergeable, rebaseable flags Merges pull request default branch using \"Rebase merge\" using gh::gh() Deletes pull request branch remotely locally using gh::gh() gert::git_branch_delete() Updates default branch gert::git_pull() Adds version tag DESCRIPTION commit message \"GitHub release \" gert::git_tag_create() pushes using gert::git_tag_push() Create GitHub release newly created tag, name \"\" release notes body, using gh::gh()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Merge staged GitHub release — merge_release","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":null,"dir":"Reference","previous_headings":"","what":"Start a new branch — new_branch","title":"Start a new branch — new_branch","text":"Create new \"feature\" branch current default branch project git repository using gert::git_branch_create() bump 'dev' version 9000 desc::desc_bump_version().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start a new branch — new_branch","text":"","code":"new_branch(name, bump_ver = TRUE, current = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start a new branch — new_branch","text":"name name new branch. bump_ver TRUE, bump 'dev' version 9000, see details. current create new branch currently active branch (TRUE) default branch (FALSE), see details.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start a new branch — new_branch","text":"new branch created checked exist local remote. version DESCRIPTION 3 components (release version) bump_ver TRUE (default), fourth component, 'dev' bumped 9000 checked new branch. version already 4 components, changed. current = FALSE (default), new branch created default branch determined usethis::git_default_branch().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Open rdev files — open_files","title":"Open rdev files — open_files","text":"Open standard set files editing RStudio.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Open rdev files — open_files","text":"","code":"open_files(files = c(\"TODO.md\", \"NEWS.md\", \"README.Rmd\", \"DESCRIPTION\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Open rdev files — open_files","text":"files vector files open.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Open rdev files — open_files","text":"named character vector files opened.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Open rdev files — open_files","text":"default, open_files() opens four documents RStudio: TODO.md, NEWS.md, README.Rmd, DESCRIPTION. open_files() stop error RStudio running.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize package downloads — package_downloads","title":"Summarize package downloads — package_downloads","text":"wrapper cranlogs::cran_downloads() summarizes number package downloads RStudio CRAN mirror.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize package downloads — package_downloads","text":"","code":"package_downloads(packages, when = \"last-month\")"},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize package downloads — package_downloads","text":"packages character vector packages query. period summarize, one last-day, last-week last-month (default).","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize package downloads — package_downloads","text":"data frame containing total number downloads package specified period, sorted popularity.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize package downloads — package_downloads","text":"default, summary last month.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine rdev package type — package_type","title":"Determine rdev package type — package_type","text":"Use heuristics (strict = FALSE) presence specific files (strict = TRUE) determine package type. one files found, package strictly determined:","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine rdev package type — package_type","text":"","code":"package_type(pkg = \".\", strict = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine rdev package type — package_type","text":"pkg path package strict strictly determine package type (see description)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine rdev package type — package_type","text":"type string, one c(\"unknown\", rdev\", \"analysis\", \"quarto\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine rdev package type — package_type","text":"_quarto.yml found, type quarto pkgdown/_base.yml found, type analysis _pkgdown.yml found, type rdev package_type return unknown strict = TRUE none files present. strict checking disabled, package assumed analysis analysis directory present, rdev .","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/quickstart.html","id":null,"dir":"Reference","previous_headings":"","what":"rdev Quick Start — quickstart","title":"rdev Quick Start — quickstart","text":"Quick start guide creating new rdev analysis package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/quickstart.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rdev Quick Start — quickstart","text":"quickly create configure new rdev analysis package, use following commands: project open, run create_github_repo() initialize GitHub R repository Without committing git, run init() newly created project Manually update Title Description fields DESCRIPTION file without committing Run setup_analysis() setup_rdev() configure package analysis package rdev package respectively. Manually update .gitignore: remove docs/ exclusion add line breaks , package configuration complete ready development.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rdev-package.html","id":null,"dir":"Reference","previous_headings":"","what":"rdev: R Development Tools — rdev-package","title":"rdev: R Development Tools — rdev-package","text":"opinionated collection development tools, packages, utilities.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/rdev-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rdev: R Development Tools — rdev-package","text":"Maintainer: John Benninghoff jbenninghoff@mac.com (ORCID)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get analysis notebook metadata — rmd_metadata","title":"Get analysis notebook metadata — rmd_metadata","text":"Extract YAML front matter 'description' line analysis notebook, construct URL notebook's location GitHub pages.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get analysis notebook metadata — rmd_metadata","text":"","code":"rmd_metadata(file_path)"},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get analysis notebook metadata — rmd_metadata","text":"file_path Path analysis notebook","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get analysis notebook metadata — rmd_metadata","text":"Named list containing analysis notebook title, URL, date, description","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get analysis notebook metadata — rmd_metadata","text":"'description' line first non-blank line body R notebook serves brief description work. quarto packages, rmd_metadata() extract YAML front matter description Quarto format (.qmd) notebooks.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up analysis package — setup_analysis","title":"Set up analysis package — setup_analysis","text":"Set analysis package within rdev package newly initialized init(), updating Title Description DESCRIPTION, committing changes running use_analysis_package(), use_spelling(), ci().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up analysis package — setup_analysis","text":"","code":"setup_analysis(use_quarto = TRUE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up analysis package — setup_analysis","text":"use_quarto TRUE (default), use Quarto publishing (build_quarto_site()), otherwise use build_analysis_site().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set up analysis package — setup_analysis","text":"setup_analysis() stop rlang::is_interactive() FALSE, run open_files() running RStudio.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up rdev package — setup_rdev","title":"Set up rdev package — setup_rdev","text":"Set rdev package traditional package development running init() updating Title Description DESCRIPTION, committing changes running use_rdev_pkgdown(), use_spelling(), use_codecov(), ci().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up rdev package — setup_rdev","text":"","code":"setup_rdev()"},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set up rdev package — setup_rdev","text":"setup_rdev() stop rlang::is_interactive() FALSE, run open_files() running RStudio.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort file — sort_file","title":"Sort file — sort_file","text":"Sorts file using R sort().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort file — sort_file","text":"","code":"sort_file(filename)"},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort file — sort_file","text":"filename file sorted","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort file — sort_file","text":"","code":"if (FALSE) { # \\dontrun{ sort_file(\".Rbuildignore\") } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_rbuildignore.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort .Rbuildignore file — sort_rbuildignore","title":"Sort .Rbuildignore file — sort_rbuildignore","text":"Sorts .Rbuildignore file using sort_file().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_rbuildignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort .Rbuildignore file — sort_rbuildignore","text":"","code":"sort_rbuildignore()"},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":null,"dir":"Reference","previous_headings":"","what":"Spell Check Notebooks — spell_check_notebooks","title":"Spell Check Notebooks — spell_check_notebooks","text":"Perform spell check notebooks spelling::spell_check_files().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spell Check Notebooks — spell_check_notebooks","text":"","code":"spell_check_notebooks( path = \"analysis\", regexp = \"[.][Rq]md$\", use_wordlist = TRUE, lang = NULL )"},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spell Check Notebooks — spell_check_notebooks","text":"path character vector one paths. regexp regular expression (e.g. [.]csv$) passed grep() filter paths. use_wordlist ignore words package WORDLIST file. lang set Language field DESCRIPTION e.g. \"en-US\" \"en-GB\". supporting languages, see hunspell vignette.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spell Check Notebooks — spell_check_notebooks","text":"lang NULL (default), get language DESCRIPTION using desc::desc_get_field().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Stage a GitHub release — stage_release","title":"Stage a GitHub release — stage_release","text":"Open GitHub pull request new release NEWS.md. Approve, merge, create release using merge_release().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stage a GitHub release — stage_release","text":"","code":"stage_release( pkg = \".\", filename = \"NEWS.md\", unfreeze = FALSE, host = getOption(\"rdev.host\") )"},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stage a GitHub release — stage_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md. unfreeze TRUE, delete Quarto _freeze directory fully re-render site. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stage a GitHub release — stage_release","text":"results GitHub pull request, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Stage a GitHub release — stage_release","text":"run, stage_release(): Extracts release version release notes NEWS.md using get_release() Validates version conforms rdev conventions (#.#.#) release notes empty Verifies version tag already exist using gert::git_tag_list() Checks uncommitted changes stops exist using gert::git_status() Creates new branch default branch (gert::git_branch() == usethis::git_default_branch()) using gert::git_branch_create() Updates Version DESCRIPTION desc::desc_set_version(), commits push git message \"GitHub release \" using gert::git_add(), gert::git_commit() gert::git_push() Runs build_quarto_site() (_quarto.yml exists), build_analysis_site() (pkgdown/_base.yml exists) build_rdev_site() (_pkgdown.yml exists), commits pushes changes () git message: \" release \" Opens pull request title \" \" release notes body using gh::gh()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Stage a GitHub release — stage_release","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Style all files — style_all","title":"Style all files — style_all","text":"Style files project. Implemented wrapper styler::style_dir() defaults styling .R, .Rprofile, .Rmd, .Rmarkdown, .Rnw, .qmd files, excluding files packrat, renv, R/RcppExports.R.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Style all files — style_all","text":"","code":"style_all( path = \".\", filetype = c(\"R\", \"Rprofile\", \"Rmd\", \"Rmarkdown\", \"Rnw\", \"Qmd\"), exclude_dirs = c(\"packrat\", \"renv\"), exclude_files = \"R/RcppExports.R\", ... )"},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Style all files — style_all","text":"path Path directory files transform. filetype Vector file extensions indicating file types styled. Case ignored, . optional, e.g. c(\".R\",\".Rmd\"), c(\"r\", \"rmd\"). Supported values (standardization) : \"qmd\", \"r\", \"rmd\", \"rmarkdown\", \"rnw\", \"rprofile\". Rmarkdown treated Rmd. exclude_dirs Character vector directories exclude (recursively). exclude_files Character vector regular expressions files excluded styling. ... Arguments passed styler::style_dir style function creates style guide use, default tidyverse_style. used except construct argument transformers. See style_guides() details. transformers set transformer functions. argument conveniently constructed via style argument .... See 'Examples'. recursive logical value indicating whether files sub directories path styled well. include_roxygen_examples Whether style code roxygen examples. base_indention Integer scalar indicating many spaces whole output text indented. Note splitting line add base_indention spaces code case multi-line strings present. See 'Examples'. dry indicate whether styler run dry mode, .e. refrain writing back files .\"\" \"fail\" write back, latter returns error input code identical result styling. \"\", default, writes back input output styling identical.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Style all files — style_all","text":"","code":"if (FALSE) { # \\dontrun{ style_all() style_all(\"analysis\", filetype = \"Rmd\") } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert R Notebook to html_document — to_document","title":"Convert R Notebook to html_document — to_document","text":"Copies file using fs::file_copy() changes output type yaml front matter html_notebook html_document, removing output types.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert R Notebook to html_document — to_document","text":"","code":"to_document(file_path, new_path, overwrite = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert R Notebook to html_document — to_document","text":"file_path Path source file new_path Path copy converted file using fs::file_copy() overwrite Overwrite file exists, passed fs::file_copy()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert R Notebook to html_document — to_document","text":"Path new file","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert R Notebook to html_document — to_document","text":"","code":"if (FALSE) { # \\dontrun{ to_document(\"notebook.Rmd\", \"document.Rmd\") to_document(\"notebooks_dir/notebook.Rmd\", \"documents_dir\") } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/unfreeze.html","id":null,"dir":"Reference","previous_headings":"","what":"Unfreeze Quarto site — unfreeze","title":"Unfreeze Quarto site — unfreeze","text":"Delete Quarto _freeze directory fully re-render site quarto::quarto_render() called.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/unfreeze.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unfreeze Quarto site — unfreeze","text":"","code":"unfreeze()"},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":null,"dir":"Reference","previous_headings":"","what":"Update WORDLIST from notebooks — update_wordlist_notebooks","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"Update package inst/WORDLIST words spell_check_notebooks().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"","code":"update_wordlist_notebooks( pkg = \".\", vignettes = TRUE, path = \"analysis\", regexp = \"[.][Rq]md$\", confirm = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"pkg path package root directory containing DESCRIPTION file vignettes check rmd rnw files pkg root directory (e.g. readme.md) package vignettes folder. path character vector one paths. regexp regular expression (e.g. [.]csv$) passed grep() filter paths. confirm show changes ask confirmation adding new words list","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"update_wordlist_notebooks customized version spelling::update_wordlist() using code wordlist.R.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/upkeep_checklist.html","id":null,"dir":"Reference","previous_headings":"","what":"Create upkeep checklist — upkeep_checklist","title":"Create upkeep checklist — upkeep_checklist","text":"Build upkeep checklist following format usethis::use_tidy_upkeep_issue().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/upkeep_checklist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create upkeep checklist — upkeep_checklist","text":"","code":"upkeep_checklist(last_upkeep = last_upkeep_year())"},{"path":"https://jabenninghoff.github.io/rdev/reference/upkeep_checklist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create upkeep checklist — upkeep_checklist","text":"last_upkeep Year upkeep last performed.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/upkeep_checklist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create upkeep checklist — upkeep_checklist","text":"Upkeep checklist current year GitHub markdown array.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Functions re-exported from the urlchecker package — urlchecker-reexports","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"functions re-exported urlchecker package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"","code":"url_check( path = \".\", db = NULL, parallel = TRUE, pool = curl::new_pool(), progress = TRUE ) url_update(path = \".\", results = url_check(path))"},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"path Path package db url database parallel TRUE, check URLs parallel pool multi handle created curl::new_pool(). 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install development packages site repository macOS + Homebrew check_renv(): convenience function runs renv status(), clean(), optionally update() (default). style_all(): style .R .Rmd files project using styler lint_all(): lint .R .Rmd files project using lintr sort_file(): sort file using R sort(), similar unix sort command sort_rbuildignore(): sort .Rbuildignore file using sort_file(), unsorted annoying ci(): run continuous integration tests locally: lint, R CMD check, style (default).","code":""}] +[{"path":"https://jabenninghoff.github.io/rdev/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2026 John Benninghoff Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"content","dir":"","previous_headings":"","what":"Content","title":"TODO","text":"Add README.Rmd Update DESCRIPTION use description data README.Rmd Add ORCID Update ORCID details","code":""},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"package","dir":"","previous_headings":"","what":"Package","title":"TODO","text":"Write utility function sort .Rbuildignore Implement pkgdown Add links / update Rd formatting function documentation. Add dummy imports silence R CMD check note per tidyverse Migrate build_analysis_site() rdev Switch development version styler (1.3.2.9000) new release becomes available Validate lint_all works expected within ci Add ‘create package’ workflow example README, remove TODO section “Analysis package creation process” Move _pkgdown.yml repository root make projects discoverable pgkdown GitHub query Update README.Rmd template dynamically generate list notebooks analysis Automate release process Automate creation feature branches, including ‘Bump version’ using desc::desc_bump_version(\"dev\") Add check stage_release() look missing topics _pkgdown.yml reference section Update use_rdev_package() Handle .Rmd files already html_document section Move rmd_metadata() README-analysis.Rmd rdev package Add tests per comments R/ reading package book, documentation Update Roxygen comments reading package book, documentation, review merge duplicate Roxygen docs Write manual regression test script (notes R commands) vignette validate ‘Creating Packages’ ‘GitHub Releases’ Add messages, warnings build_analysis_site() report progress Add function spell check notebooks Automate branch protection Address issue https://github.com/r-lib/usethis/issues/1568, closed Add dplyr running use_analysis_package() Consider switching getOption(\"pkgType\") source per R options per R macOS FAQ, “CRAN build guaranteed compatible package binaries CRAN (Bioconductor).” Support creating repos organizations Consider incorporating GitHub description DESCRIPTION Create wrapper spelling includes notebooks package spell checking, WORDLIST Add spell_check_test_notebooks() function CI spellchecks notebooks Convert manual tests (Setup.Rmd) R Script can run within package created create_github_repo() Add function add missing (notebook) dependencies DESCRIPTION, see renv::dependencies() desc::desc_get_deps() Add check_renv() ci() stop renv::status() date Replace proof-docs urlchecker, support checking GitHub Pages docs directory using url_db_from_HTML_files (ask PR accepted) Move scripts tools inst/bin similar, per Stack Overflow R Packages Switch development versions styler (1.3.2.9000) lintr (2.0.1.9000) new release becomes available - needed address bugs current release versions, 1.3.2 2.0.1. Add trailing slash GitHub Pages URL Update lint_all() lint types, including .Rpres Add custom CSS files _site.yml analysis notebook templates control font size, described article, possibly using bs_theme(), since pkgdown customizes default using build_bslib() (issue exists unsupported Safari 14 Safari 15) Remove pkgdown/extra.css https://github.com/r-lib/pkgdown/issues/2377 accepted Establish default knitr options, including knitr::opts_chunk$set(fig.align = \"center\"), add analysis template, also review settings Advanced R Use Project Templates like vertical? Add CSS R Markdown Template instead assets/extra.css? Move shift-heading-level-: 1 _quarto.yml analysis/_metadata.yml, TODO.md renders properly Remove preset: bootstrap workaround pkgdown 2.0.8+ released (per https://github.com/r-lib/pkgdown/issues/2376) Replace GITHUB_PAT .Renviron gitcreds Review use usethis functions, including pull request helpers Update tests new testthat features (testthat::auto_test_package(), testthat::describe(), Reporters, testthat::local_mocked_bindings()) Replace dev = TRUE logic renv 1.1.6+ released; see renv #1695, #2190 Update errors messages reading Advanced R Conditions re-reading Tidyverse Style Guide Reduce number Imports, per R CMD check:","code":"> devtools::check() ... > checking package dependencies ... NOTE Imports includes 30 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally."},{"path":"https://jabenninghoff.github.io/rdev/TODO.html","id":"github","dir":"","previous_headings":"","what":"GitHub","title":"TODO","text":"Use standard R CMD check Use lintr Faster CI checks Switch full R CMD check ? Update GitHub Actions r-lib examples Run test coverage Skip CI checks changes docs/ directory Add GitHub Action html/link checking using something like htmlproofer Autobuild docs/ like pkgdown ?","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Introduction to rdev","text":"rdev supports personal workflow, including creation traditional R packages R Analysis Packages (vignette(\"analysis-package-layout\")), enforcing consistency across packages, providing Continuous Integration/Continuous Delivery (CI/CD) automation. use tools rdev improve code quality, speed development R code, publish results analyses R Quarto Notebooks HTML make accessible non-R users.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Introduction to rdev","text":"current R development environment uses Homebrew, rig, RStudio, GitHub, collection R packages including rdev, Visual Studio Code, Vim.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"homebrew","dir":"Articles","previous_headings":"Installation","what":"Homebrew","title":"Introduction to rdev","text":"use Homebrew Bundle install software systems; basic macOS working environment published GitHub macos-env.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"installing-r","dir":"Articles","previous_headings":"Installation","what":"Installing R","title":"Introduction to rdev","text":"rig supports installation multiple versions official R binaries, use reproducibility. install R using rig, first install rig: install desired versions R. following installs R 3.6 4.5 ARM based macs (2025-10-08): Note : don’t use pak, rig installs default, yet fully supported renv. oldest version R install 3.6, since RStudio now requires R 3.6 newer (version 2024.04.00) Since ARM binary release R 3.6 (oldrel/6) R 4.0 (oldrel/5), install Intel binaries run Rosetta 2.","code":"brew tap r-lib/rig brew install --cask rig rig install oldrel/6 --without-pak --arch x86_64 rig install oldrel/5 --without-pak --arch x86_64 rig install oldrel/4 --without-pak rig install oldrel/3 --without-pak rig install oldrel/2 --without-pak rig install oldrel/1 --without-pak rig install oldrel --without-pak rig install release --without-pak rig default release"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"development-tools","dir":"Articles","previous_headings":"Installation","what":"Development Tools","title":"Introduction to rdev","text":"Well, obviously, use RStudio. RStudio leading IDE R development integrates many R packages, although sometimes falls short; use GitHub command line Git, occasionally Visual Studio Code (better support markdown) Vim (faster types edits). Posit developing next-generation R Python IDE based Visual Studio Code, Positron. ’ve tried using Positron, ’ve found many missing features replace RStudio development, including: Lack notebook-style interface RMarkdown Quarto documents support lintr command History package Build panes , first two showstoppers missing panes nearly . RStudio, GitHub desktop client, Visual Studio Code easily installed using Homebrew: recommended change default settings .RData RStudio (Options > General > Basic > Workspace): Uncheck “Restore .Data workspace startup” Set “Save workspace .Data exit” “Never” Vim installed default macOS Unix-like systems.","code":"brew install --cask rstudio brew install --cask github brew install --cask visual-studio-code"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"packages","dir":"Articles","previous_headings":"Installation","what":"Packages","title":"Introduction to rdev","text":"Managing packages environments challenge modern languages. Thankfully R doesn’t level challenge python, even ruby, managing packages available within project best practice. use renv purpose, use renv install manage packages projects. setup-r script rdev installs base set packages needed run rdev R User Library. streamlined version script included . chown command needed allow updating base packages using RStudio Packages “Update” function. generally update packages RStudio projects open starting development, update packages projects using renv::update(). ’re installing (development) versions packages GitHub, recommended set personal access token using usethis::create_github_token() adding Git credential store using gitcreds::gitcreds_set(). can verify GitHub set following usethis recommendations usethis::git_sitrep().","code":"# fix rig permissions sudo chown -R \"$(whoami)\":admin /Library/Frameworks/R.framework/Versions/*/Resources/library RVERSION=\"$(Rscript -e 'cat(as.character(getRversion()[1,1:2]))')\" USERLIB=\"$HOME/Library/R/$(uname -m)/${RVERSION}/library\" DEVPKG='c(\"renv\", \"styler\", \"lintr\", \"miniUI\", \"languageserver\", \"rmarkdown\", \"devtools\", \"available\")' GITPKG='c(\"jabenninghoff/rdev\")' if [ ! -d \"${USERLIB}\" ] then mkdir -p \"${USERLIB}\" fi echo \"install.packages(${DEVPKG}, repos=\\\"https://cloud.r-project.org\\\", lib=\\\"${USERLIB}\\\")\" | R --no-save echo \"remotes::install_github(${GITPKG}, lib=\\\"${USERLIB}\\\")\" | R --no-save"},{"path":"https://jabenninghoff.github.io/rdev/articles/rdev.html","id":"further-reading","dir":"Articles","previous_headings":"Installation","what":"Further Reading","title":"Introduction to rdev","text":"workflow heavily influenced DevOps movement research DevOps Research Assessment (DORA) team Google started Dr. Nicole Forsgren. research shows technical non-technical capabilities improve outcomes. functions included rdev support many technical capabilities, including: Code maintainability Continuous delivery Continuous integration Deployment automation Shifting left security Test automation Trunk-based development Version control outline SIRAcon 2022 talk, “Making R Work (Automation)” available GitHub siracon2022.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"rdev-conventions","dir":"Articles","previous_headings":"","what":"rdev conventions","title":"Style Guide","text":"rdev uses mix Google tidyverse conventions.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"naming-conventions","dir":"Articles","previous_headings":"rdev conventions","what":"Naming conventions","title":"Style Guide","text":"rdev follows tidyverse naming convention snake_case.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"right-hand-assignment","dir":"Articles","previous_headings":"rdev conventions","what":"Right-hand assignment","title":"Style Guide","text":"rdev follows Google’s style guide, use right-hand assignment.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"returns","dir":"Articles","previous_headings":"rdev conventions","what":"Returns","title":"Style Guide","text":"rdev typically uses implicit returns unless needed flow control construct specific return structure.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"qualifying-namespaces","dir":"Articles","previous_headings":"rdev conventions","what":"Qualifying namespaces","title":"Style Guide","text":"Use @import @importFrom discouraged, instead using :: functions defined R/. exception infix functions (%name%), always imported, using roxygen @importFrom. Within R Quarto Notebooks, use library() encouraged readability.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"package-level-documentation","dir":"Articles","previous_headings":"rdev conventions","what":"Package-level documentation","title":"Style Guide","text":"rdev package documentation lives R/package.R. Additionally, use base R encouraged within functions defined R/ (control dependencies), tidyverse R encouraged within notebooks readability. R Markdown documents generally wrap width code, exceptions R Notebook ‘description line’ (first non-blank line body), long hyperlinks.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"styler","dir":"Articles","previous_headings":"","what":"styler","title":"Style Guide","text":"rdev package implements styler using styler defaults, permanent caching enabled (options(styler.cache_root = \"styler-perm\")). style_all() function applies tidyverse style R Quarto files (R, Rprofile, Rmd, Rnw, qmd) package directory structure.","code":""},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"lintr","dir":"Articles","previous_headings":"","what":"lintr","title":"Style Guide","text":"lint_all() function lints R Quarto files (R, Rmd, qmd, Rnw, Rhtml, Rpres, Rrst, Rtex, Rtxt) lintr using opinionated configuration (.lintr): settings deliberately chosen meet specific goals:","code":"linters: linters_with_tags( tags = NULL, implicit_integer_linter = NULL, line_length_linter(100), missing_package_linter = NULL, namespace_linter = NULL, nonportable_path_linter = NULL, paste_linter(allow_file_path = \"always\"), todo_comment_linter = NULL, undesirable_function_linter( within(all_undesirable_functions, rm(ifelse, library, require, structure)) ), undesirable_operator_linter(all_undesirable_operators), unnecessary_concatenation_linter(allow_single_expression = FALSE), unused_import_linter( except_packages = c(\"bit64\", \"data.table\", \"tidyverse\", pkgload::pkg_name(\".\")) ) )"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"use-all-linters","dir":"Articles","previous_headings":"lintr","what":"Use all linters","title":"Style Guide","text":"selects linters, including new Google linters. selecting linters, just defaults, forces evaluation new linters added lintr. Specific linters disabled configured per rdev style.","code":"linters: linters_with_tags( tags = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-implicit-integers","dir":"Articles","previous_headings":"lintr","what":"Allow implicit integers","title":"Style Guide","text":"implicit integer linter checks integers explicitly typed using form 1L. , safer, implicit integers common practice, including output dput():","code":"implicit_integer_linter = NULL, dput(character(0L)) #> character(0)"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"set-line-length","dir":"Articles","previous_headings":"lintr","what":"Set line length","title":"Style Guide","text":"line length 100 reasonable width working RStudio IDE laptop.","code":"line_length_linter(100),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"use-renv-for-missing-packages","dir":"Articles","previous_headings":"lintr","what":"Use renv for missing packages","title":"Style Guide","text":"missing package linter namespace linter check packages referenced code installed. rdev uses renv manage packages, better job detecting missing packages, including complaining current package (\".\") installed.","code":"missing_package_linter = NULL, namespace_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-non-portable-paths","dir":"Articles","previous_headings":"lintr","what":"Allow non-portable paths","title":"Style Guide","text":"non-portable path linter generates many false positives, including calls fs, essentially makes UNIX-style paths portable across operating systems. Similarly, allow_file_path default option \"double_slash\" generates false positives used fs.","code":"nonportable_path_linter = NULL, paste_linter(allow_file_path = \"always\"),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"allow-todo-comments","dir":"Articles","previous_headings":"lintr","what":"Allow TODO comments","title":"Style Guide","text":"rdev conventions encourage use # TODO: comments convenient way identifying needed planned updates inline.","code":"todo_comment_linter = NULL,"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"disallow-almost-all-undesirable-functions-and-operators","dir":"Articles","previous_headings":"lintr","what":"Disallow almost all undesirable functions and operators","title":"Style Guide","text":"Enable undesirable functions operators, just defaults, except ifelse() succinct /else block, library(), require(), structure(). Use require() within .Rprofile library() within R Markdown documents appropriate common practice, although neither used within package code. structure() useful comparing test results values generated dput().","code":"undesirable_function_linter( within(all_undesirable_functions, rm(ifelse, library, require, structure)) ), undesirable_operator_linter(all_undesirable_operators),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"enforce-strict-unnecessary-concatenation","dir":"Articles","previous_headings":"lintr","what":"Enforce strict unnecessary concatenation","title":"Style Guide","text":"Enforce stricter version unnecessary concatenation linter.","code":"unnecessary_concatenation_linter(allow_single_expression = FALSE),"},{"path":"https://jabenninghoff.github.io/rdev/articles/style-guide.html","id":"verify-imported-packages-are-used","dir":"Articles","previous_headings":"lintr","what":"Verify imported packages are used","title":"Style Guide","text":"Verify imported packages used, except packages attached side effects, current package (support package development).","code":"unused_import_linter( except_packages = c(\"bit64\", \"data.table\", \"tidyverse\", pkgload::pkg_name(\".\")) ) )"},{"path":"https://jabenninghoff.github.io/rdev/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Benninghoff. Author, maintainer.","code":""},{"path":"https://jabenninghoff.github.io/rdev/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Benninghoff J (2026). rdev: R Development Tools. R package version 1.15.6, https://jabenninghoff.github.io/rdev/.","code":"@Manual{, title = {rdev: R Development Tools}, author = {John Benninghoff}, year = {2026}, note = {R package version 1.15.6}, url = {https://jabenninghoff.github.io/rdev/}, }"},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"R Development Tools","text":"R Development Tools: opinionated collection development tools, packages, utilities. Feel free use /fork project!","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"R Development Tools","text":"can install development version rdev GitHub : using renv:","code":"# install.packages(\"remotes\") remotes::install_github(\"jabenninghoff/rdev\") # install.packages(\"renv\") renv::install(\"jabenninghoff/rdev\")"},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"development","dir":"","previous_headings":"","what":"Development","title":"R Development Tools","text":"Changelog: See “Changelog” NEWS.md. Planned: TODO","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"creating-packages","dir":"","previous_headings":"","what":"Creating Packages","title":"R Development Tools","text":"rdev supports creation new R packages following rdev conventions well new R Analysis packages. typical setup workflow (per ?quickstart) : Use available::available() check package name project open, run create_github_repo() initialize GitHub R repository Without committing git, run init() newly created project Manually update Title Description fields DESCRIPTION file without committing Run setup_analysis() setup_rdev() configure package analysis package rdev package respectively. Update TODO.md, NEWS.md, README.Rmd, DESCRIPTION needed Re-run check_renv(), ci() validate package Commit git begin development","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"github-releases","dir":"","previous_headings":"","what":"GitHub Releases","title":"R Development Tools","text":"rdev automates workflow creating GitHub releases along updating GitHub pages either standard R packages R analysis packages, using release notes format NEWS.md. typical development workflow : Bump version create new feature branch new_branch() Write things Update release notes new version NEWS.md, following conventions described get_release() Finalize release merge changes git Run stage_release() create new pull request GitHub using details derived NEWS.md, including updating README GitHub pages pull request reviewed passes required status checks, accept staged release merge_release(), merges pull request, cleans branches, publishes new GitHub release Feature branches can merged without starting new release; stage_release() just requires everything committed, including new release notes NEWS.md running. ready release, stage_release() use existing branch feature branch, create new release branch default.","code":""},{"path":"https://jabenninghoff.github.io/rdev/index.html","id":"workflow","dir":"","previous_headings":"","what":"Workflow","title":"R Development Tools","text":"workflow, typically check renv start: also ci() function run continuous integration tests locally:","code":"library(rdev) check_renv() #> renv::status(dev = TRUE) #> No issues found -- the project is in a consistent state. #> #> renv::clean() #> - No stale package locks were found. #> - No temporary directories were found in the project library. #> - The project has been cleaned. ci() #> renv::status(dev = TRUE) #> No issues found -- the project is in a consistent state. #> #> missing_deps() #> Finding R package dependencies ... Done! #> renv::dependencies() not in DESCRIPTION: #> #> pkgdown::check_pkgdown() #> ✔ No problems found. #> #> style_all() #> Styling 69 files: #> .Rprofile ✔ #> README.Rmd ✔ #> inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd ✔ #> inst/templates/analysis.qmd ✔ #> inst/templates/changelog.qmd ✔ #> inst/templates/index.qmd ✔ #> inst/templates/package.R ✔ #> inst/templates/README-analysis.Rmd ✔ #> inst/templates/README-rdev.Rmd ✔ #> inst/templates/spelling.R ✔ #> inst/templates/test-spelling.R ✔ #> R/build.R ✔ #> R/ci.R ✔ #> R/helpers.R ✔ #> R/init.R ✔ #> R/package.R ✔ #> R/release.R ✔ #> R/setup.R ✔ #> R/to_document.R ✔ #> R/upkeep.R ✔ #> R/urlchecker.R ✔ #> R/utils.R ✔ #> tests/spelling.R ✔ #> tests/testthat.R ✔ #> tests/manual/setup.Rmd ✔ #> tests/manual/test-new-repo-1.R ✔ #> tests/manual/test-new-repo-2.R ✔ #> tests/manual/test-new-repo-3-analysis.R ✔ #> tests/manual/test-new-repo-3-package.R ✔ #> tests/testthat/test-build.R ✔ #> tests/testthat/test-ci.R ✔ #> tests/testthat/test-helpers.R ✔ #> tests/testthat/test-init.R ✔ #> tests/testthat/test-inst.R ✔ #> tests/testthat/test-release.R ✔ #> tests/testthat/test-setup.R ✔ #> tests/testthat/test-spelling.R ✔ #> tests/testthat/test-to_document.R ✔ #> tests/testthat/test-upkeep.R ✔ #> tests/testthat/test-utils.R ✔ #> tests/testthat/test-ci/test-revealjs.qmd ✔ #> tests/testthat/test-ci/test.Rprofile ✔ #> tests/testthat/test-ci/testcode_1.R ✔ #> tests/testthat/test-ci/testcode_2.R ✔ #> tests/testthat/test-ci/testcode.qmd ✔ #> tests/testthat/test-ci/testcode.Rmd ✔ #> tests/testthat/test-ci/testcode.Rnw ✔ #> tests/testthat/test-ci/packrat/test.R ✔ #> tests/testthat/test-ci/R/RcppExports.R ✔ #> tests/testthat/test-ci/renv/test.R ✔ #> tests/testthat/test-to_document/document.Rmd ✔ #> tests/testthat/test-to_document/docx.qmd ✔ #> tests/testthat/test-to_document/extra-spaces.Rmd ✔ #> tests/testthat/test-to_document/minimal-document.Rmd ✔ #> tests/testthat/test-to_document/minimal-docx.qmd ✔ #> tests/testthat/test-to_document/minimal.qmd ✔ #> tests/testthat/test-to_document/minimal.Rmd ✔ #> tests/testthat/test-to_document/multiple.Rmd ✔ #> tests/testthat/test-to_document/no-format.qmd ✔ #> tests/testthat/test-to_document/no-front-matter.Rmd ✔ #> tests/testthat/test-to_document/no-output.Rmd ✔ #> tests/testthat/test-to_document/no-yaml.qmd ✔ #> tests/testthat/test-to_document/no-yaml.Rmd ✔ #> tests/testthat/test-to_document/valid.qmd ✔ #> tests/testthat/test-to_document/valid.Rmd ✔ #> tests/testthat/test-to_document/with-code.Rmd ✔ #> vignettes/analysis-package-layout.Rmd ✔ #> vignettes/rdev.Rmd ✔ #> vignettes/style-guide.Rmd ✔ #> ─────────────────────────────────────────────────────── #> Status Count Legend #> ✔ 69 File unchanged. #> ℹ 0 File changed. #> ✖ 0 Styling threw an error. #> ─────────────────────────────────────────────────────── #> #> lint_all() #> #> devtools::document() #> ℹ Updating rdev documentation #> ℹ Loading rdev #> #> desc::desc_normalize() #> #> extra_deps() #> Finding R package dependencies ... Done! #> desc::desc_get_deps() not found by renv: #> # A tibble: 3 × 3 #> type package version #> #> 1 Suggests covr * #> 2 Suggests diffviewer * #> 3 Suggests DT * #> #> spelling::update_wordlist() #> No changes required to /Users/agamemnon/GitHub/rdev/inst/WORDLIST #> #> url_check() #> html_url_check() #> # A tibble: 2 × 9 #> URL From Status Message New CRAN Spaces R root #> #> 1 http://covr.r-lib.org/ref… 200 OK http… \"\" \"\" \"\" /Use… #> 2 http://r-lib.github.io/rc… 200 OK http… \"\" \"\" \"\" /Use… #> #> Setting env vars: NOT_CRAN=\"true\", CI=\"true\" #> rcmdcheck::rcmdcheck(args = \"--no-manual\", error_on = \"warning\") #> ── R CMD build ───────────────────────────────────────────────────────────────── #> * checking for file ‘.../DESCRIPTION’ ... OK #> * preparing ‘rdev’: #> * checking DESCRIPTION meta-information ... OK #> * installing the package to build vignettes #> * creating vignettes ... OK #> * checking for LF line-endings in source and make files and shell scripts #> * checking for empty or unneeded directories #> * building ‘rdev_1.15.6.tar.gz’ #> #> ── R CMD check ───────────────────────────────────────────────────────────────── #> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpqNxoSE/file820a21bb3a1a/rdev.Rcheck’ #> * using R version 4.5.2 (2025-10-31) #> * using platform: aarch64-apple-darwin20 #> * R was compiled by #> Apple clang version 16.0.0 (clang-1600.0.26.6) #> GNU Fortran (GCC) 14.2.0 #> * running under: macOS Sequoia 15.7.3 #> * using session charset: UTF-8 #> * using option ‘--no-manual’ #> * checking for file ‘rdev/DESCRIPTION’ ... OK #> * this is package ‘rdev’ version ‘1.15.6’ #> * package encoding: UTF-8 #> * checking package namespace information ... OK #> * checking package dependencies ... OK #> * checking if this is a source package ... OK #> * checking if there is a namespace ... OK #> * checking for executable files ... OK #> * checking for hidden files and directories ... OK #> * checking for portable file names ... OK #> * checking for sufficient/correct file permissions ... OK #> * checking whether package ‘rdev’ can be installed ... OK #> * checking installed package size ... OK #> * checking package directory ... OK #> * checking ‘build’ directory ... OK #> * checking DESCRIPTION meta-information ... OK #> * checking top-level files ... OK #> * checking for left-over files ... OK #> * checking index information ... OK #> * checking package subdirectories ... OK #> * checking code files for non-ASCII characters ... OK #> * checking R files for syntax errors ... OK #> * checking whether the package can be loaded ... OK #> * checking whether the package can be loaded with stated dependencies ... OK #> * checking whether the package can be unloaded cleanly ... OK #> * checking whether the namespace can be loaded with stated dependencies ... OK #> * checking whether the namespace can be unloaded cleanly ... OK #> * checking loading without being on the library search path ... OK #> * checking dependencies in R code ... OK #> * checking S3 generic/method consistency ... OK #> * checking replacement functions ... OK #> * checking foreign function calls ... OK #> * checking R code for possible problems ... OK #> * checking Rd files ... OK #> * checking Rd metadata ... OK #> * checking Rd cross-references ... OK #> * checking for missing documentation entries ... OK #> * checking for code/documentation mismatches ... OK #> * checking Rd \\usage sections ... OK #> * checking Rd contents ... OK #> * checking for unstated dependencies in examples ... OK #> * checking installed files from ‘inst/doc’ ... OK #> * checking files in ‘vignettes’ ... OK #> * checking examples ... OK #> * checking for unstated dependencies in ‘tests’ ... OK #> * checking tests ... #> Running ‘spelling.R’ #> Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK #> Running ‘testthat.R’ #> OK #> * checking for unstated dependencies in vignettes ... OK #> * checking package vignettes ... OK #> * checking re-building of vignette outputs ... OK #> * DONE #> #> Status: OK #> ── R CMD check results ──────────────────────────────────────── rdev 1.15.6 ──── #> Duration: 26.8s #> #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build Analysis Site — build_analysis_site","title":"Build Analysis Site — build_analysis_site","text":"build_analysis_site() wrapper pkgdown::build_site_github_pages() adds 'Analysis' menu containing rendered versions .Rmd files analysis/.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build Analysis Site — build_analysis_site","text":"","code":"build_analysis_site(pkg = \".\", ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build Analysis Site — build_analysis_site","text":"pkg Path package. Currently, pkg = \".\" supported. ... additional arguments passed pkgdown::build_site_github_pages() (implemented)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build Analysis Site — build_analysis_site","text":"rmarkdown _site.yml yaml, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build Analysis Site — build_analysis_site","text":"run, build_analysis_site(): Reads base pkgdown::pkgdown settings pkgdown/_base.yml Writes base settings _pkgdown.yml Creates template using pkgdown::template_navbar() inserts analysis menu links html versions .Rmd file analysis/ Writes template _pkgdown.yml Updates README.md running devtools::build_readme() (README.Rmd exists) update list notebooks Runs pkgdown::build_site_github_pages() install = TRUE new_process = TRUE Creates _site.yml file based final _pkgdown.yml clones pkgdown::pkgdown navbar temporary build directory Copies following analysis/ build directory: *.Rmd, assets/, data/, import/, rendered/ Changes *.Rmd html_notebook html_document using to_document() Builds site using rmarkdown::render_site() using modified html_document output settings render files look feel html_notebook Moves rendered files docs/: *.html, assets/, rendered/, without overwriting build_analysis_site() fail error files analysis/*.Rmd, pkgdown/_base.yml exist.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"continuous-integration","dir":"Reference","previous_headings":"","what":"Continuous Integration","title":"Build Analysis Site — build_analysis_site","text":"build_rdev_site() build_analysis_site() meant used part CI/CD workflow, temporarily set environment variable CI == \"TRUE\" build fail non-internal topics included reference index page per pkgdown::build_reference().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_analysis_site.html","id":"supported-file-types","dir":"Reference","previous_headings":"","what":"Supported File Types","title":"Build Analysis Site — build_analysis_site","text":"build_quarto_site() supports R Markdown (.Rmd) Quarto (.qmd) notebooks analysis directory interchangeably, build_analysis_site() supports .Rmd files .","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build Quarto Site — build_quarto_site","title":"Build Quarto Site — build_quarto_site","text":"build_quarto_site() wrapper quarto::quarto_render() also updates README.md optionally deletes Quarto _freeze directory fully re-render site.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build Quarto Site — build_quarto_site","text":"","code":"build_quarto_site(input = NULL, as_job = FALSE, unfreeze = FALSE, ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build Quarto Site — build_quarto_site","text":"input input file project directory rendered (defaults rendering project current working directory). as_job Render RStudio background job. Default \"auto\", render individual documents normally projects background jobs. Use quarto.render_as_job R option control default globally. unfreeze TRUE, delete Quarto _freeze directory fully re-render site. ... Arguments passed quarto::quarto_render().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build Quarto Site — build_quarto_site","text":"run, build_quarto_site() calls: devtools::build_readme() unfreeze() (unfreeze = TRUE) quarto::quarto_render()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_quarto_site.html","id":"supported-file-types","dir":"Reference","previous_headings":"","what":"Supported File Types","title":"Build Quarto Site — build_quarto_site","text":"build_quarto_site() supports R Markdown (.Rmd) Quarto (.qmd) notebooks analysis directory interchangeably, build_analysis_site() supports .Rmd files .","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":null,"dir":"Reference","previous_headings":"","what":"Build rdev Site — build_rdev_site","title":"Build rdev Site — build_rdev_site","text":"build_rdev_site() wrapper pkgdown::build_site_github_pages() optimized rdev workflow updates README.md performs clean GitHub pages build using pkgdown.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build rdev Site — build_rdev_site","text":"","code":"build_rdev_site(pkg = \".\", ...)"},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build rdev Site — build_rdev_site","text":"pkg Path package. Currently, pkg = \".\" supported. ... additional arguments passed pkgdown::build_site_github_pages() (implemented)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Build rdev Site — build_rdev_site","text":"run, build_rdev_site() calls: devtools::build_readme() pkgdown::build_site_github_pages() install = TRUE new_process = TRUE","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/build_rdev_site.html","id":"continuous-integration","dir":"Reference","previous_headings":"","what":"Continuous Integration","title":"Build rdev Site — build_rdev_site","text":"build_rdev_site() build_analysis_site() meant used part CI/CD workflow, temporarily set environment variable CI == \"TRUE\" build fail non-internal topics included reference index page per pkgdown::build_reference().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":null,"dir":"Reference","previous_headings":"","what":"Check renv — check_renv","title":"Check renv — check_renv","text":"Runs renv status(dev = TRUE), clean(), optionally update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check renv — check_renv","text":"","code":"check_renv(update = rlang::is_interactive())"},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check renv — check_renv","text":"update run renv::update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/check_renv.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check renv — check_renv","text":"","code":"if (FALSE) { # \\dontrun{ check_renv() check_renv(update = FALSE) } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":null,"dir":"Reference","previous_headings":"","what":"Local CI — ci","title":"Local CI — ci","text":"Run continuous integration tests locally.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Local CI — ci","text":"","code":"ci( renv = TRUE, missing = TRUE, pkgdown = TRUE, styler = NULL, lintr = TRUE, document = TRUE, normalize = TRUE, extra = TRUE, spelling = TRUE, urls = TRUE, rcmdcheck = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Local CI — ci","text":"renv check renv::status(dev = TRUE) missing run missing_deps() pkgdown check pkgdown::check_pkgdown() _pkgdown.yml exists styler style files using style_all(), see details lintr lint files using lint_all() document run devtools::document() normalize run desc::desc_normalize() extra run extra_deps() spelling update spelling WORDLIST urls validate URLs url_check() html_url_check() rcmdcheck run R CMD check using: rcmdcheck::rcmdcheck(args = \"–-manual\", error_on = \"warning\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Local CI — ci","text":"renv::status(dev = TRUE) synchronized, ci() stop. missing_deps() returns missing dependencies, ci() stop. pkgdown::check_pkgdown() halt ci() error _pkgdown.yml invalid. styler set NULL (default), style_all() run uncommitted changes git. Setting value TRUE FALSE overrides check. lint_all() finds lints, ci() stop open RStudio markers pane. Output missing, extra, urls printed tibble improved readability console.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/ci.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Local CI — ci","text":"","code":"if (FALSE) { # \\dontrun{ ci() ci(styler = TRUE) ci(styler = FALSE, rcmdcheck = FALSE) } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":null,"dir":"Reference","previous_headings":"","what":"Create rdev GitHub repository — create_github_repo","title":"Create rdev GitHub repository — create_github_repo","text":"Create, configure, clone, open new GitHub R package repository following rdev conventions.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create rdev GitHub repository — create_github_repo","text":"","code":"create_github_repo( repo_name, repo_desc = \"\", private = FALSE, org = NULL, host = getOption(\"rdev.host\") )"},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create rdev GitHub repository — create_github_repo","text":"repo_name name GitHub repository create repo_desc description GitHub repository create private TRUE, creates private repository. org organization create repository . NULL, create repository active user's account. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create rdev GitHub repository — create_github_repo","text":"return value gh::gh() creating repository, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create rdev GitHub repository — create_github_repo","text":"run, create_github_repo(): Creates new GitHub repository using gh::gh() license template get_license() Activates Dependabot alerts per getOption(\"rdev.dependabot\", default = TRUE) Activates Dependabot security updates per getOption(\"rdev.dependabot\", default = TRUE) Adds branch protection default branch (private FALSE) Clones repository locally usethis::create_from_github() Creates basic package using usethis::create_package() running interactively, repository automatically opened RStudio, GitHub Desktop, default browser","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"github-actions","dir":"Reference","previous_headings":"","what":"GitHub Actions","title":"Create rdev GitHub repository — create_github_repo","text":"GitHub Actions can disabled setting rdev.github.actions FALSE: options(rdev.github.actions = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/create_github_repo.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Create rdev GitHub repository — create_github_repo","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check dependencies — missing_deps","title":"Check dependencies — missing_deps","text":"Check dependencies DESCRIPTION.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check dependencies — missing_deps","text":"","code":"missing_deps(exclude_base = TRUE) extra_deps()"},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check dependencies — missing_deps","text":"exclude_base exclude packages installed R missing dependencies","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check dependencies — missing_deps","text":"data.frame either renv::dependencies() desc::desc_get_deps().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/deps_check.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check dependencies — missing_deps","text":"missing_deps() reports renv::dependencies() DESCRIPTION. extra_deps() reports desc::desc_get_deps() found renv. current package (pkgload::pkg_name(\".\")) renv (renv.lock ) automatically removed renv::dependencies(), along 'base' R packages exclude_base TRUE (base, compiler, datasets, grDevices, graphics, grid, methods, parallel, splines, stats, stats4, tcltk, tools, utils).","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":null,"dir":"Reference","previous_headings":"","what":"Get license option — get_license","title":"Get license option — get_license","text":"Retrieve validate rdev.license option.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get license option — get_license","text":"","code":"get_license()"},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get license option — get_license","text":"license string, one c(\"mit\", \"gpl\", \"lgpl\", \"proprietary\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_license.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get license option — get_license","text":"rdev.license must one c(\"mit\", \"gpl\", \"lgpl\", \"proprietary\"), defaults \"mit\". rdev.license \"proprietary\", rdev.license.copyright (name copyright holder) must also set.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Get release details — get_release","title":"Get release details — get_release","text":"Extract release version release notes NEWS.md.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get release details — get_release","text":"","code":"get_release(pkg = \".\", filename = \"NEWS.md\")"},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get release details — get_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get release details — get_release","text":"list containing package, version release notes first release contained NEWS.md","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/get_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get release details — get_release","text":"get_release() assumes NEWS.md contains markdown release notes, release header format: \"# \" followed release notes, expects first line NEWS.md release header.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Check URLs in HTML files — html_url_check","title":"Check URLs in HTML files — html_url_check","text":"Runs urlchecker::url_check() database created using url_db_from_HTML_files function tools package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check URLs in HTML files — html_url_check","text":"","code":"html_url_check( path = \"docs\", parallel = TRUE, pool = curl::new_pool(), progress = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check URLs in HTML files — html_url_check","text":"path Path directory HTML files parallel TRUE, check URLs parallel pool multi handle created curl::new_pool(). NULL use global pool. progress Whether show progress bar parallel checks","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/html_url_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check URLs in HTML files — html_url_check","text":"url_checker_db object (invisibly). check_url_db object added class custom print method.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize rdev package — init","title":"Initialize rdev package — init","text":"Initialize rdev package within newly created create_github_repo() project creating new git branch, committing changes, running use_rdev_package().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize rdev package — init","text":"","code":"init()"},{"path":"https://jabenninghoff.github.io/rdev/reference/init.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Initialize rdev package — init","text":"init() stop rlang::is_interactive() FALSE. running init(), update Title Description fields DESCRIPTION file without committing run either setup_analysis() setup_rdev() per quickstart.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Lint all files — lint_all","title":"Lint all files — lint_all","text":"Lint files project. Implemented wrapper lintr::lint_dir().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lint all files — lint_all","text":"","code":"lint_all( pattern = \"(?i)[.](r|rmd|qmd|rnw|rhtml|rpres|rrst|rtex|rtxt)$\", exclusions = list(\"renv\", \"packrat\", \"R/RcppExports.R\"), ... )"},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lint all files — lint_all","text":"pattern regex pattern files, default take files extensions .R, .Rmd, .qmd, .Rnw, .Rhtml, .Rpres, .Rrst, .Rtex, .Rtxt, ignoring case. exclusions exclusions exclude(), relative package path. ... Arguments passed lintr::lint_dir parse_settings Logical. Whether try parse settings. Otherwise, default_settings() used. TRUE default linting files, opposed text=. path base directory project (lint_dir()) package (lint_package()). relative_path TRUE, file paths printed using path relative base directory. FALSE, use full absolute path. show_progress Logical controlling whether show linting progress cli::cli_progress_along(). default behavior show progress interactive() sessions running testthat suite.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Lint all files — lint_all","text":"list lint objects.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/lint_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lint all files — lint_all","text":"","code":"if (FALSE) { # \\dontrun{ lint_all() lint_all(\"analysis\") } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":null,"dir":"Reference","previous_headings":"","what":"Temporary package — local_temppkg","title":"Temporary package — local_temppkg","text":"Temporarily create rdev R analysis package, automatically removed afterwards.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Temporary package — local_temppkg","text":"","code":"local_temppkg(dir = fs::file_temp(), type = \"usethis\", env = parent.frame())"},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Temporary package — local_temppkg","text":"dir Path package directory, created necessary, defaults fs::file_temp(). type type package create, one \"usethis\" - usethis::create_package(), \"rdev\" - use_rdev_package(), \"analysis\" - use_analysis_package(use_quarto = FALSE), \"quarto\" - use_analysis_package(use_quarto = TRUE). env Environment passed withr::defer(), defaults parent.frame().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Temporary package — local_temppkg","text":"Path temporary package directory.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Temporary package — local_temppkg","text":"Used internally testing rdev automation. Based usethis case study testthat.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/local_temppkg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Temporary package — local_temppkg","text":"","code":"if (FALSE) { # \\dontrun{ test_that(\"local_temppkg creates a directory\", { dir <- usethis::ui_silence(local_temppkg()) expect_true(fs::dir_exists(dir)) }) } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Merge staged GitHub release — merge_release","title":"Merge staged GitHub release — merge_release","text":"Merge pull request staged stage_release() create new release GitHub.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Merge staged GitHub release — merge_release","text":"","code":"merge_release(pkg = \".\", filename = \"NEWS.md\", host = getOption(\"rdev.host\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Merge staged GitHub release — merge_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Merge staged GitHub release — merge_release","text":"list containing results pull request merge GitHub release, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Merge staged GitHub release — merge_release","text":"Manually verify status checks completed running, merge_release() currently validate status checks successful. run, merge_release(): Determines staged release title NEWS.md using get_release() Selects GitHub pull request matches staged release title, stops less one matching PR using gh::gh() Verifies staged pull request ready merged checking locked, draft, mergeable, rebaseable flags Merges pull request default branch using \"Rebase merge\" using gh::gh() Deletes pull request branch remotely locally using gh::gh() gert::git_branch_delete() Updates default branch gert::git_pull() Adds version tag DESCRIPTION commit message \"GitHub release \" gert::git_tag_create() pushes using gert::git_tag_push() Create GitHub release newly created tag, name \"\" release notes body, using gh::gh()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/merge_release.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Merge staged GitHub release — merge_release","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":null,"dir":"Reference","previous_headings":"","what":"Start a new branch — new_branch","title":"Start a new branch — new_branch","text":"Create new \"feature\" branch current default branch project git repository using gert::git_branch_create() bump 'dev' version 9000 desc::desc_bump_version().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Start a new branch — new_branch","text":"","code":"new_branch(name, bump_ver = TRUE, current = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Start a new branch — new_branch","text":"name name new branch. bump_ver TRUE, bump 'dev' version 9000, see details. current create new branch currently active branch (TRUE) default branch (FALSE), see details.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/new_branch.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Start a new branch — new_branch","text":"new branch created checked exist local remote. version DESCRIPTION 3 components (release version) bump_ver TRUE (default), fourth component, 'dev' bumped 9000 checked new branch. version already 4 components, changed. current = FALSE (default), new branch created default branch determined usethis::git_default_branch().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Open rdev files — open_files","title":"Open rdev files — open_files","text":"Open standard set files editing RStudio.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Open rdev files — open_files","text":"","code":"open_files(files = c(\"TODO.md\", \"NEWS.md\", \"README.Rmd\", \"DESCRIPTION\"))"},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Open rdev files — open_files","text":"files vector files open.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Open rdev files — open_files","text":"named character vector files opened.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/open_files.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Open rdev files — open_files","text":"default, open_files() opens four documents RStudio: TODO.md, NEWS.md, README.Rmd, DESCRIPTION. open_files() stop error RStudio running.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize package downloads — package_downloads","title":"Summarize package downloads — package_downloads","text":"wrapper cranlogs::cran_downloads() summarizes number package downloads RStudio CRAN mirror.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize package downloads — package_downloads","text":"","code":"package_downloads(packages, when = \"last-month\")"},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize package downloads — package_downloads","text":"packages character vector packages query. period summarize, one last-day, last-week last-month (default).","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize package downloads — package_downloads","text":"data frame containing total number downloads package specified period, sorted popularity.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_downloads.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Summarize package downloads — package_downloads","text":"default, summary last month.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine rdev package type — package_type","title":"Determine rdev package type — package_type","text":"Use heuristics (strict = FALSE) presence specific files (strict = TRUE) determine package type. one files found, package strictly determined:","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine rdev package type — package_type","text":"","code":"package_type(pkg = \".\", strict = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine rdev package type — package_type","text":"pkg path package strict strictly determine package type (see description)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine rdev package type — package_type","text":"type string, one c(\"unknown\", rdev\", \"analysis\", \"quarto\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/package_type.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine rdev package type — package_type","text":"_quarto.yml found, type quarto pkgdown/_base.yml found, type analysis _pkgdown.yml found, type rdev package_type return unknown strict = TRUE none files present. strict checking disabled, package assumed analysis analysis directory present, rdev .","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/quickstart.html","id":null,"dir":"Reference","previous_headings":"","what":"rdev Quick Start — quickstart","title":"rdev Quick Start — quickstart","text":"Quick start guide creating new rdev analysis package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/quickstart.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"rdev Quick Start — quickstart","text":"quickly create configure new rdev analysis package, use following commands: project open, run create_github_repo() initialize GitHub R repository Without committing git, run init() newly created project Manually update Title Description fields DESCRIPTION file without committing Run setup_analysis() setup_rdev() configure package analysis package rdev package respectively. Manually update .gitignore: remove docs/ exclusion add line breaks , package configuration complete ready development.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rdev-package.html","id":null,"dir":"Reference","previous_headings":"","what":"rdev: R Development Tools — rdev-package","title":"rdev: R Development Tools — rdev-package","text":"opinionated collection development tools, packages, utilities.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/rdev-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rdev: R Development Tools — rdev-package","text":"Maintainer: John Benninghoff jbenninghoff@mac.com (ORCID)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get analysis notebook metadata — rmd_metadata","title":"Get analysis notebook metadata — rmd_metadata","text":"Extract YAML front matter 'description' line analysis notebook, construct URL notebook's location GitHub pages.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get analysis notebook metadata — rmd_metadata","text":"","code":"rmd_metadata(file_path)"},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get analysis notebook metadata — rmd_metadata","text":"file_path Path analysis notebook","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get analysis notebook metadata — rmd_metadata","text":"Named list containing analysis notebook title, URL, date, description","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/rmd_metadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get analysis notebook metadata — rmd_metadata","text":"'description' line first non-blank line body R notebook serves brief description work. quarto packages, rmd_metadata() extract YAML front matter description Quarto format (.qmd) notebooks.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up analysis package — setup_analysis","title":"Set up analysis package — setup_analysis","text":"Set analysis package within rdev package newly initialized init(), updating Title Description DESCRIPTION, committing changes running use_analysis_package(), use_spelling(), ci().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up analysis package — setup_analysis","text":"","code":"setup_analysis(use_quarto = TRUE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set up analysis package — setup_analysis","text":"use_quarto TRUE (default), use Quarto publishing (build_quarto_site()), otherwise use build_analysis_site().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_analysis.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set up analysis package — setup_analysis","text":"setup_analysis() stop rlang::is_interactive() FALSE, run open_files() running RStudio.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":null,"dir":"Reference","previous_headings":"","what":"Set up rdev package — setup_rdev","title":"Set up rdev package — setup_rdev","text":"Set rdev package traditional package development running init() updating Title Description DESCRIPTION, committing changes running use_rdev_pkgdown(), use_spelling(), use_codecov(), ci().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set up rdev package — setup_rdev","text":"","code":"setup_rdev()"},{"path":"https://jabenninghoff.github.io/rdev/reference/setup_rdev.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set up rdev package — setup_rdev","text":"setup_rdev() stop rlang::is_interactive() FALSE, run open_files() running RStudio.","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort file — sort_file","title":"Sort file — sort_file","text":"Sorts file using R sort().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort file — sort_file","text":"","code":"sort_file(filename)"},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort file — sort_file","text":"filename file sorted","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort file — sort_file","text":"","code":"if (FALSE) { # \\dontrun{ sort_file(\".Rbuildignore\") } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_rbuildignore.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort .Rbuildignore file — sort_rbuildignore","title":"Sort .Rbuildignore file — sort_rbuildignore","text":"Sorts .Rbuildignore file using sort_file().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/sort_rbuildignore.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort .Rbuildignore file — sort_rbuildignore","text":"","code":"sort_rbuildignore()"},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":null,"dir":"Reference","previous_headings":"","what":"Spell Check Notebooks — spell_check_notebooks","title":"Spell Check Notebooks — spell_check_notebooks","text":"Perform spell check notebooks spelling::spell_check_files().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spell Check Notebooks — spell_check_notebooks","text":"","code":"spell_check_notebooks( path = \"analysis\", regexp = \"[.][Rq]md$\", use_wordlist = TRUE, lang = NULL )"},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spell Check Notebooks — spell_check_notebooks","text":"path character vector one paths. regexp regular expression (e.g. [.]csv$) passed grep() filter paths. use_wordlist ignore words package WORDLIST file. lang set Language field DESCRIPTION e.g. \"en-US\" \"en-GB\". supporting languages, see hunspell vignette.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/spell_check_notebooks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spell Check Notebooks — spell_check_notebooks","text":"lang NULL (default), get language DESCRIPTION using desc::desc_get_field().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":null,"dir":"Reference","previous_headings":"","what":"Stage a GitHub release — stage_release","title":"Stage a GitHub release — stage_release","text":"Open GitHub pull request new release NEWS.md. Approve, merge, create release using merge_release().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stage a GitHub release — stage_release","text":"","code":"stage_release( pkg = \".\", filename = \"NEWS.md\", unfreeze = FALSE, host = getOption(\"rdev.host\") )"},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stage a GitHub release — stage_release","text":"pkg path package. Currently, pkg = \".\" supported. filename name file containing release notes, defaults NEWS.md. unfreeze TRUE, delete Quarto _freeze directory fully re-render site. host GitHub host target, passed .api_url argument gh::gh(). unspecified, gh defaults \"https://api.github.com\", although gh's default can customised setting GITHUB_API_URL environment variable. hypothetical GitHub Enterprise instance, either \"https://github.acme.com/api/v3\" \"https://github.acme.com\" acceptable.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stage a GitHub release — stage_release","text":"results GitHub pull request, invisibly","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Stage a GitHub release — stage_release","text":"run, stage_release(): Extracts release version release notes NEWS.md using get_release() Validates version conforms rdev conventions (#.#.#) release notes empty Verifies version tag already exist using gert::git_tag_list() Checks uncommitted changes stops exist using gert::git_status() Creates new branch default branch (gert::git_branch() == usethis::git_default_branch()) using gert::git_branch_create() Updates Version DESCRIPTION desc::desc_set_version(), commits push git message \"GitHub release \" using gert::git_add(), gert::git_commit() gert::git_push() Runs build_quarto_site() (_quarto.yml exists), build_analysis_site() (pkgdown/_base.yml exists) build_rdev_site() (_pkgdown.yml exists), commits pushes changes () git message: \" release \" Opens pull request title \" \" release notes body using gh::gh()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/stage_release.html","id":"host","dir":"Reference","previous_headings":"","what":"Host","title":"Stage a GitHub release — stage_release","text":"Set rdev.host option using GitHub Enterprise server: options(rdev.host = \"https://github.example.com/api/v3\")","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":null,"dir":"Reference","previous_headings":"","what":"Style all files — style_all","title":"Style all files — style_all","text":"Style files project. Implemented wrapper styler::style_dir() defaults styling .R, .Rprofile, .Rmd, .Rmarkdown, .Rnw, .qmd files, excluding files packrat, renv, R/RcppExports.R.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Style all files — style_all","text":"","code":"style_all( path = \".\", filetype = c(\"R\", \"Rprofile\", \"Rmd\", \"Rmarkdown\", \"Rnw\", \"Qmd\"), exclude_dirs = c(\"packrat\", \"renv\"), exclude_files = \"R/RcppExports.R\", ... )"},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Style all files — style_all","text":"path Path directory files transform. filetype Vector file extensions indicating file types styled. Case ignored, . optional, e.g. c(\".R\",\".Rmd\"), c(\"r\", \"rmd\"). Supported values (standardization) : \"qmd\", \"r\", \"rmd\", \"rmarkdown\", \"rnw\", \"rprofile\". Rmarkdown treated Rmd. exclude_dirs Character vector directories exclude (recursively). exclude_files Character vector regular expressions files excluded styling. ... Arguments passed styler::style_dir style function creates style guide use, default tidyverse_style. used except construct argument transformers. See style_guides() details. transformers set transformer functions. argument conveniently constructed via style argument .... See 'Examples'. recursive logical value indicating whether files sub directories path styled well. include_roxygen_examples Whether style code roxygen examples. base_indention Integer scalar indicating many spaces whole output text indented. Note splitting line add base_indention spaces code case multi-line strings present. See 'Examples'. dry indicate whether styler run dry mode, .e. refrain writing back files .\"\" \"fail\" write back, latter returns error input code identical result styling. \"\", default, writes back input output styling identical.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/style_all.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Style all files — style_all","text":"","code":"if (FALSE) { # \\dontrun{ style_all() style_all(\"analysis\", filetype = \"Rmd\") } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert R Notebook to html_document — to_document","title":"Convert R Notebook to html_document — to_document","text":"Copies file using fs::file_copy() changes output type yaml front matter html_notebook html_document, removing output types.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert R Notebook to html_document — to_document","text":"","code":"to_document(file_path, new_path, overwrite = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert R Notebook to html_document — to_document","text":"file_path Path source file new_path Path copy converted file using fs::file_copy() overwrite Overwrite file exists, passed fs::file_copy()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert R Notebook to html_document — to_document","text":"Path new file","code":""},{"path":[]},{"path":"https://jabenninghoff.github.io/rdev/reference/to_document.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert R Notebook to html_document — to_document","text":"","code":"if (FALSE) { # \\dontrun{ to_document(\"notebook.Rmd\", \"document.Rmd\") to_document(\"notebooks_dir/notebook.Rmd\", \"documents_dir\") } # }"},{"path":"https://jabenninghoff.github.io/rdev/reference/unfreeze.html","id":null,"dir":"Reference","previous_headings":"","what":"Unfreeze Quarto site — unfreeze","title":"Unfreeze Quarto site — unfreeze","text":"Delete Quarto _freeze directory fully re-render site quarto::quarto_render() called.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/unfreeze.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Unfreeze Quarto site — unfreeze","text":"","code":"unfreeze()"},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":null,"dir":"Reference","previous_headings":"","what":"Update WORDLIST from notebooks — update_wordlist_notebooks","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"Update package inst/WORDLIST words spell_check_notebooks().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"","code":"update_wordlist_notebooks( pkg = \".\", vignettes = TRUE, path = \"analysis\", regexp = \"[.][Rq]md$\", confirm = TRUE )"},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"pkg path package root directory containing DESCRIPTION file vignettes check rmd rnw files pkg root directory (e.g. readme.md) package vignettes folder. path character vector one paths. regexp regular expression (e.g. [.]csv$) passed grep() filter paths. confirm show changes ask confirmation adding new words list","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/update_wordlist_notebooks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update WORDLIST from notebooks — update_wordlist_notebooks","text":"update_wordlist_notebooks customized version spelling::update_wordlist() using code wordlist.R.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/upkeep_checklist.html","id":null,"dir":"Reference","previous_headings":"","what":"Create upkeep checklist — upkeep_checklist","title":"Create upkeep checklist — upkeep_checklist","text":"Build upkeep checklist following format usethis::use_tidy_upkeep_issue().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/upkeep_checklist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create upkeep checklist — upkeep_checklist","text":"","code":"upkeep_checklist(last_upkeep = last_upkeep_year())"},{"path":"https://jabenninghoff.github.io/rdev/reference/upkeep_checklist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create upkeep checklist — upkeep_checklist","text":"last_upkeep Year upkeep last performed.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/upkeep_checklist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create upkeep checklist — upkeep_checklist","text":"Upkeep checklist current year GitHub markdown array.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Functions re-exported from the urlchecker package — urlchecker-reexports","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"functions re-exported urlchecker package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"","code":"url_check( path = \".\", db = NULL, parallel = TRUE, pool = curl::new_pool(), progress = TRUE ) url_update(path = \".\", results = url_check(path))"},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"path Path package db url database parallel TRUE, check URLs parallel pool multi handle created curl::new_pool(). NULL use global pool. progress Whether show progress bar parallel checks results results url_check.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/urlchecker-reexports.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Functions re-exported from the urlchecker package — urlchecker-reexports","text":"Follow links see urlchecker documentation. urlchecker::url_check() urlchecker::url_update()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":null,"dir":"Reference","previous_headings":"","what":"Use Analysis Package Layout — use_analysis_package","title":"Use Analysis Package Layout — use_analysis_package","text":"Add Analysis Package Layout current package.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use Analysis Package Layout — use_analysis_package","text":"","code":"use_analysis_package(use_quarto = TRUE, prompt = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use Analysis Package Layout — use_analysis_package","text":"use_quarto TRUE (default), use Quarto publishing (build_quarto_site()), otherwise use build_analysis_site(). prompt TRUE, prompt writing renv.lock, passed renv::snapshot().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Use Analysis Package Layout — use_analysis_package","text":"List containing dirs created, rbuildignore lines added .Rbuildignore, gitignore exclusions added .gitignore.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_analysis_package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use Analysis Package Layout — use_analysis_package","text":"run, use_analysis_package(): Creates analysis package directories Adds exclusions .gitignore .Rbuildignore Adds extra.css analysis/assets pkgdown (use_quarto FALSE) fix rendering GitHub-style task lists Adds .nojekyll, _quarto.yml, changelog.qmd, index.qmd analysis/_metadata.yml templates creates _base.yml pkgdown first URL DESCRIPTION Installs README.Rmd template analysis packages, dplyr package needed README.Rmd template","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev code coverage — use_codecov","title":"Use rdev code coverage — use_codecov","text":"Install code coverage usethis::use_coverage(type = \"codecov\"), DT package covr::report(), rdev GitHub action test-coverage.yaml.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev code coverage — use_codecov","text":"","code":"use_codecov(prompt = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev code coverage — use_codecov","text":"prompt TRUE, prompt writing renv.lock, passed renv::snapshot().","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Use rdev code coverage — use_codecov","text":"use_rdev_package(), use_analysis_package() use_codecov() modify README.Rmd, use_codecov() must run last changes overwritten. use_codecov() run use_rdev_package(). Set option rdev.codecov FALSE skip installation codecov.io test-coverage.yaml: options(rdev.codecov = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_codecov.html","id":"github-actions","dir":"Reference","previous_headings":"","what":"GitHub Actions","title":"Use rdev code coverage — use_codecov","text":"GitHub Actions can disabled setting rdev.github.actions FALSE: options(rdev.github.actions = FALSE)","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_gitattributes.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev .gitattributes — use_gitattributes","title":"Use rdev .gitattributes — use_gitattributes","text":"Install rdev .gitattributes template using usethis::use_template() set GitHub Linguist overrides. analysis package detected, RMarkdown enabled language GitHub statistics.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_gitattributes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev .gitattributes — use_gitattributes","text":"","code":"use_gitattributes(open = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_gitattributes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev .gitattributes — use_gitattributes","text":"open Open newly created file editing? Happens RStudio, applicable, via utils::file.edit() otherwise.","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_lintr.html","id":null,"dir":"Reference","previous_headings":"","what":"Use rdev .lintr — use_lintr","title":"Use rdev .lintr — use_lintr","text":"Install rdev .lintr template using usethis::use_template()","code":""},{"path":"https://jabenninghoff.github.io/rdev/reference/use_lintr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Use rdev .lintr — use_lintr","text":"","code":"use_lintr(open = FALSE)"},{"path":"https://jabenninghoff.github.io/rdev/reference/use_lintr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Use rdev .lintr — use_lintr","text":"open Open newly created file editing? 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default Add R Analysis Package layout definition, migrated rtraining Update ci() use style_all() lint_all() consistency Add import directory build_analysis_site() minor updates, improved tests, maintenance","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-031","dir":"Changelog","previous_headings":"","what":"rdev 0.3.1","title":"rdev 0.3.1","text":"maintenance release, updated R 4.1.0","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-030","dir":"Changelog","previous_headings":"","what":"rdev 0.3.0","title":"rdev 0.3.0","text":"build_analysis_site(), new function migrated rtraining: wrapper pkgdown::build_site() adds ‘Analysis’ menu containing rendered versions .Rmd files analysis/. still considered Experimental, due lack test coverage features implemented, work projects limited pkgdown customization. update also includes function convert notebooks html_document, to_document().","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-022","dir":"Changelog","previous_headings":"","what":"rdev 0.2.2","title":"rdev 0.2.2","text":"minor updates, maintenance","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-021","dir":"Changelog","previous_headings":"","what":"rdev 0.2.1","title":"rdev 0.2.1","text":"bug fixes","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-020","dir":"Changelog","previous_headings":"","what":"rdev 0.2.0","title":"rdev 0.2.0","text":"installing rdev now automatically install preferred development tools ‘meta-package’ (like tidyverse), including: styler, lintr, rcmdcheck, renv, miniUI (RStudio Addin support), devtools, rmarkdown","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-012","dir":"Changelog","previous_headings":"","what":"rdev 0.1.2","title":"rdev 0.1.2","text":"minor updates package site (https://jabenninghoff.github.io/rdev/)","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-011","dir":"Changelog","previous_headings":"","what":"rdev 0.1.1","title":"rdev 0.1.1","text":"maintenance release","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"updates-0-1-1","dir":"Changelog","previous_headings":"","what":"Updates","title":"rdev 0.1.1","text":"ci(): updated match preferred GitHub workflow: use_github_action_check_standard() ---cran removed documentation updates functions (style, links)","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"rdev-010","dir":"Changelog","previous_headings":"","what":"rdev 0.1.0","title":"rdev 0.1.0","text":"Initial GitHub release","code":""},{"path":"https://jabenninghoff.github.io/rdev/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"rdev 0.1.0","text":"./tools/setup-r: shell script install development packages site repository macOS + Homebrew check_renv(): convenience function runs renv status(), clean(), optionally update() (default). style_all(): style .R .Rmd files project using styler lint_all(): lint .R .Rmd files project using lintr sort_file(): sort file using R sort(), similar unix sort command sort_rbuildignore(): sort .Rbuildignore file using sort_file(), unsorted annoying ci(): run continuous integration tests locally: lint, R CMD check, style (default).","code":""}] diff --git a/inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd index e333a7c6..4f84922c 100644 --- a/inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd +++ b/inst/rmarkdown/templates/analysis/skeleton/skeleton.Rmd @@ -1,8 +1,8 @@ --- title: "TEMPLATE Analysis" author: "" -date: '2025-00-00' -date-modified: '2025-00-00' +date: '2026-00-00' +date-modified: '2026-00-00' categories: [] order: output: diff --git a/inst/templates/analysis.qmd b/inst/templates/analysis.qmd index 8fb2628f..fd51e98f 100644 --- a/inst/templates/analysis.qmd +++ b/inst/templates/analysis.qmd @@ -1,8 +1,8 @@ --- title: "TEMPLATE Analysis" author: "" -date: '2025-00-00' -date-modified: '2025-00-00' +date: '2026-00-00' +date-modified: '2026-00-00' categories: [] order: format: diff --git a/renv.lock b/renv.lock index e2f8c537..83ac1c3a 100644 --- a/renv.lock +++ b/renv.lock @@ -1690,7 +1690,7 @@ }, "httr2": { "Package": "httr2", - "Version": "1.2.1", + "Version": "1.2.2", "Source": "Repository", "Title": "Perform HTTP Requests and Process the Responses", "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"Maximilian\", \"Girlich\", role = \"ctb\") )", @@ -1726,7 +1726,9 @@ "knitr", "later (>= 1.4.0)", "nanonext", - "paws.common", + "otel (>= 0.2.0)", + "otelsdk (>= 0.2.0)", + "paws.common (>= 0.8.0)", "promises", "rmarkdown", "testthat (>= 3.1.8)", @@ -1740,7 +1742,7 @@ "Config/testthat/parallel": "true", "Config/testthat/start-first": "resp-stream, req-perform", "Encoding": "UTF-8", - "RoxygenNote": "7.3.2", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Author": "Hadley Wickham [aut, cre], Posit Software, PBC [cph, fnd], Maximilian Girlich [ctb]", "Maintainer": "Hadley Wickham ", @@ -1857,7 +1859,7 @@ }, "knitr": { "Package": "knitr", - "Version": "1.50", + "Version": "1.51", "Source": "Repository", "Type": "Package", "Title": "A General-Purpose Package for Dynamic Report Generation in R", @@ -1871,12 +1873,11 @@ "highr (>= 0.11)", "methods", "tools", - "xfun (>= 0.51)", + "xfun (>= 0.52)", "yaml (>= 2.1.19)" ], "Suggests": [ "bslib", - "codetools", "DBI (>= 0.4-1)", "digest", "formatR", @@ -1888,6 +1889,8 @@ "magick", "litedown", "markdown (>= 1.3)", + "otel", + "otelsdk", "png", "ragg", "reticulate (>= 1.4)", @@ -1912,10 +1915,10 @@ "Encoding": "UTF-8", "VignetteBuilder": "litedown, knitr", "SystemRequirements": "Package vignettes based on R Markdown v2 or reStructuredText require Pandoc (http://pandoc.org). The function rst2pdf() requires rst2pdf (https://github.com/rst2pdf/rst2pdf).", - "Collate": "'block.R' 'cache.R' 'citation.R' 'hooks-html.R' 'plot.R' 'utils.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", - "RoxygenNote": "7.3.2", + "Collate": "'block.R' 'cache.R' 'citation.R' 'hooks-html.R' 'plot.R' 'utils.R' 'defaults.R' 'concordance.R' 'engine.R' 'highlight.R' 'themes.R' 'header.R' 'hooks-asciidoc.R' 'hooks-chunk.R' 'hooks-extra.R' 'hooks-latex.R' 'hooks-md.R' 'hooks-rst.R' 'hooks-textile.R' 'hooks.R' 'otel.R' 'output.R' 'package.R' 'pandoc.R' 'params.R' 'parser.R' 'pattern.R' 'rocco.R' 'spin.R' 'table.R' 'template.R' 'utils-conversion.R' 'utils-rd2html.R' 'utils-string.R' 'utils-sweave.R' 'utils-upload.R' 'utils-vignettes.R' 'zzz.R'", + "RoxygenNote": "7.3.3", "NeedsCompilation": "no", - "Author": "Yihui Xie [aut, cre] (, https://yihui.org), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (), Posit Software, PBC [cph, fnd]", + "Author": "Yihui Xie [aut, cre] (ORCID: , URL: https://yihui.org), Abhraneel Sarma [ctb], Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Amar Al-Zubaidi [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Atsushi Yasumoto [ctb] (ORCID: ), Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Bulat Yapparov [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hall [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Ellis Hughes [ctb], Emily Riederer [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jacob Bien [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Marius Hofert [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Miller Patrick [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Niels Richard Hansen [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Pavel N. Krivitsky [ctb] (ORCID: ), Pedro Faria [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Rodrigo Copetti [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Sagiru Mati [ctb] (ORCID: ), Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb], Zhian N. Kamvar [ctb] (ORCID: ), Posit Software, PBC [cph, fnd]", "Maintainer": "Yihui Xie ", "Repository": "CRAN" }, @@ -3455,7 +3458,7 @@ }, "shiny": { "Package": "shiny", - "Version": "1.12.0", + "Version": "1.12.1", "Source": "Repository", "Type": "Package", "Title": "Web Application Framework for R", @@ -3519,7 +3522,7 @@ "Config/testthat/edition": "3", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", - "Collate": "'globals.R' 'app-state.R' 'app_template.R' 'bind-cache.R' 'bind-event.R' 'bookmark-state-local.R' 'bookmark-state.R' 'bootstrap-deprecated.R' 'bootstrap-layout.R' 'conditions.R' 'map.R' 'utils.R' 'bootstrap.R' 'busy-indicators-spinners.R' 'busy-indicators.R' 'cache-utils.R' 'deprecated.R' 'devmode.R' 'diagnose.R' 'extended-task.R' 'fileupload.R' 'graph.R' 'reactives.R' 'reactive-domains.R' 'history.R' 'hooks.R' 'html-deps.R' 'image-interact-opts.R' 'image-interact.R' 'imageutils.R' 'input-action.R' 'input-checkbox.R' 'input-checkboxgroup.R' 'input-date.R' 'input-daterange.R' 'input-file.R' 'input-numeric.R' 'input-password.R' 'input-radiobuttons.R' 'input-select.R' 'input-slider.R' 'input-submit.R' 'input-text.R' 'input-textarea.R' 'input-utils.R' 'insert-tab.R' 'insert-ui.R' 'jqueryui.R' 'knitr.R' 'middleware-shiny.R' 'middleware.R' 'timer.R' 'shiny.R' 'mock-session.R' 'modal.R' 'modules.R' 'notifications.R' 'otel-attr-srcref.R' 'otel-collect.R' 'otel-enable.R' 'otel-error.R' 'otel-label.R' 'otel-reactive-update.R' 'otel-session.R' 'otel-shiny.R' 'priorityqueue.R' 'progress.R' 'react.R' 'reexports.R' 'render-cached-plot.R' 'render-plot.R' 'render-table.R' 'run-url.R' 'runapp.R' 'serializers.R' 'server-input-handlers.R' 'server-resource-paths.R' 'server.R' 'shiny-options.R' 'shiny-package.R' 'shinyapp.R' 'shinyui.R' 'shinywrappers.R' 'showcase.R' 'snapshot.R' 'staticimports.R' 'tar.R' 'test-export.R' 'test-server.R' 'test.R' 'update-input.R' 'utils-lang.R' 'utils-tags.R' 'version_bs_date_picker.R' 'version_ion_range_slider.R' 'version_jquery.R' 'version_jqueryui.R' 'version_selectize.R' 'version_strftime.R' 'viewer.R'", + "Collate": "'globals.R' 'app-state.R' 'app_template.R' 'bind-cache.R' 'bind-event.R' 'bookmark-state-local.R' 'bookmark-state.R' 'bootstrap-deprecated.R' 'bootstrap-layout.R' 'conditions.R' 'map.R' 'utils.R' 'bootstrap.R' 'busy-indicators-spinners.R' 'busy-indicators.R' 'cache-utils.R' 'deprecated.R' 'devmode.R' 'diagnose.R' 'extended-task.R' 'fileupload.R' 'graph.R' 'reactives.R' 'reactive-domains.R' 'history.R' 'hooks.R' 'html-deps.R' 'image-interact-opts.R' 'image-interact.R' 'imageutils.R' 'input-action.R' 'input-checkbox.R' 'input-checkboxgroup.R' 'input-date.R' 'input-daterange.R' 'input-file.R' 'input-numeric.R' 'input-password.R' 'input-radiobuttons.R' 'input-select.R' 'input-slider.R' 'input-submit.R' 'input-text.R' 'input-textarea.R' 'input-utils.R' 'insert-tab.R' 'insert-ui.R' 'jqueryui.R' 'knitr.R' 'middleware-shiny.R' 'middleware.R' 'timer.R' 'shiny.R' 'mock-session.R' 'modal.R' 'modules.R' 'notifications.R' 'otel-attr-srcref.R' 'otel-collect.R' 'otel-enable.R' 'otel-error.R' 'otel-label.R' 'otel-reactive-update.R' 'otel-session.R' 'otel-shiny.R' 'otel-with.R' 'priorityqueue.R' 'progress.R' 'react.R' 'reexports.R' 'render-cached-plot.R' 'render-plot.R' 'render-table.R' 'run-url.R' 'runapp.R' 'serializers.R' 'server-input-handlers.R' 'server-resource-paths.R' 'server.R' 'shiny-options.R' 'shiny-package.R' 'shinyapp.R' 'shinyui.R' 'shinywrappers.R' 'showcase.R' 'snapshot.R' 'staticimports.R' 'tar.R' 'test-export.R' 'test-server.R' 'test.R' 'update-input.R' 'utils-lang.R' 'utils-tags.R' 'version_bs_date_picker.R' 'version_ion_range_slider.R' 'version_jquery.R' 'version_jqueryui.R' 'version_selectize.R' 'version_strftime.R' 'viewer.R'", "NeedsCompilation": "no", "Author": "Winston Chang [aut] (ORCID: ), Joe Cheng [aut], JJ Allaire [aut], Carson Sievert [aut, cre] (ORCID: ), Barret Schloerke [aut] (ORCID: ), Garrick Aden-Buie [aut] (ORCID: ), Yihui Xie [aut], Jeff Allen [aut], Jonathan McPherson [aut], Alan Dipert [aut], Barbara Borges [aut], Posit Software, PBC [cph, fnd] (ROR: ), jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in inst/www/shared/jqueryui/AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Prem Nawaz Khan [ctb] (Bootstrap accessibility plugin), Victor Tsaran [ctb] (Bootstrap accessibility plugin), Dennis Lembree [ctb] (Bootstrap accessibility plugin), Srinivasu Chakravarthula [ctb] (Bootstrap accessibility plugin), Cathy O'Connor [ctb] (Bootstrap accessibility plugin), PayPal, Inc [cph] (Bootstrap accessibility plugin), Stefan Petre [ctb, cph] (Bootstrap-datepicker library), Andrew Rowls [ctb, cph] (Bootstrap-datepicker library), Brian Reavis [ctb, cph] (selectize.js library), Salmen Bejaoui [ctb, cph] (selectize-plugin-a11y library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library), SpryMedia Limited [ctb, cph] (DataTables library), Ivan Sagalaev [ctb, cph] (highlight.js library), R Core Team [ctb, cph] (tar implementation from R)", "Maintainer": "Carson Sievert ", @@ -4277,7 +4280,7 @@ }, "xfun": { "Package": "xfun", - "Version": "0.54", + "Version": "0.55", "Source": "Repository", "Type": "Package", "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", @@ -4310,6 +4313,7 @@ "magick", "yaml", "data.table", + "qs2", "qs" ], "License": "MIT + file LICENSE", @@ -4448,22 +4452,28 @@ }, "yaml": { "Package": "yaml", - "Version": "2.3.11", + "Version": "2.3.12", "Source": "Repository", "Type": "Package", "Title": "Methods to Convert R Data to YAML and Back", - "Date": "2025-11-06", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"cre\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Shawn\", \"Garbett\", , \"shawn.garbett@vumc.org\", role = \"ctb\", comment = c(ORCID = \"0000-0003-4079-5621\")), person(\"Jeremy\", \"Stephens\", role = c(\"aut\", \"ctb\")), person(\"Kirill\", \"Simonov\", role = \"aut\"), person(\"Yihui\", \"Xie\", role = \"ctb\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Zhuoer\", \"Dong\", role = \"ctb\"), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"reikoch\", role = \"ctb\"), person(\"Will\", \"Beasley\", role = \"ctb\", comment = c(ORCID = \"0000-0002-5613-5006\")), person(\"Brendan\", \"O'Connor\", role = \"ctb\"), person(\"Michael\", \"Quinn\", role = \"ctb\"), person(\"Charlie\", \"Gao\", role = \"ctb\"), person(c(\"Gregory\", \"R.\"), \"Warnes\", role = \"ctb\"), person(c(\"Zhian\", \"N.\"), \"Kamvar\", role = \"ctb\") )", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://yaml.r-lib.org, https://github.com/r-lib/yaml/", + "BugReports": "https://github.com/r-lib/yaml/issues", "Suggests": [ - "RUnit" + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" ], - "Authors@R": "c( person(\"Shawn\", \"Garbett\", role = c(\"cre\",\"ctb\"), email = \"shawn.garbett@vumc.org\", comment = c(ORCID=\"0000-0003-4079-5621\") ), person(\"Jeremy\", \"Stephens\", role = c(\"aut\", \"ctb\")), person(\"Kirill\", \"Simonov\", role = \"aut\"), person(\"Yihui\", \"Xie\", role = \"ctb\", comment = c(ORCID=\"0000-0003-0645-5666\")), person(\"Zhuoer\", \"Dong\", role = \"ctb\"), person(\"Hadley\", \"Wickham\", role = \"ctb\", comment = c(ORCID=\"0000-0003-4757-117X\")), person(\"Jeffrey\", \"Horner\", role = \"ctb\"), person(\"reikoch\", role = \"ctb\"), person(\"Will\", \"Beasley\", role = \"ctb\", comment = c(ORCID=\"0000-0002-5613-5006\")), person(\"Brendan\", \"O'Connor\", role = \"ctb\"), person(\"Michael\", \"Quinn\", role = \"ctb\"), person(\"Charlie\", \"Gao\", role = \"ctb\"), person(c(\"Gregory\", \"R.\"), \"Warnes\", role = \"ctb\"), person(c(\"Zhian\", \"N.\"), \"Kamvar\", role = \"ctb\") )", - "Maintainer": "Shawn Garbett ", - "License": "BSD_3_clause + file LICENSE", - "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", - "URL": "https://github.com/vubiostat/r-yaml/", - "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.3", + "VignetteBuilder": "knitr", "NeedsCompilation": "yes", - "Author": "Shawn Garbett [cre, ctb] (ORCID: ), Jeremy Stephens [aut, ctb], Kirill Simonov [aut], Yihui Xie [ctb] (ORCID: ), Zhuoer Dong [ctb], Hadley Wickham [ctb] (ORCID: ), Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb] (ORCID: ), Brendan O'Connor [ctb], Michael Quinn [ctb], Charlie Gao [ctb], Gregory R. Warnes [ctb], Zhian N. Kamvar [ctb]", + "Author": "Hadley Wickham [cre] (ORCID: ), Shawn Garbett [ctb] (ORCID: ), Jeremy Stephens [aut, ctb], Kirill Simonov [aut], Yihui Xie [ctb] (ORCID: ), Zhuoer Dong [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb] (ORCID: ), Brendan O'Connor [ctb], Michael Quinn [ctb], Charlie Gao [ctb], Gregory R. Warnes [ctb], Zhian N. Kamvar [ctb]", + "Maintainer": "Hadley Wickham ", "Repository": "CRAN" }, "zip": { diff --git a/tests/manual/setup.Rmd b/tests/manual/setup.Rmd index 3380c7cf..ed8197ce 100644 --- a/tests/manual/setup.Rmd +++ b/tests/manual/setup.Rmd @@ -18,7 +18,10 @@ Test script to manually validate creating a new rdev package or R analysis packa Load devtools. Load package manually using `devtools::load_all(".")` (command-shift-l). -```{r setup, message = FALSE, warning = FALSE} +```{r} +#| label: setup +#| message: false +#| warning: false # devtools already loaded htmltools::tagList( xaringanExtra::use_clipboard( diff --git a/tests/testthat/test-to_document/document.Rmd b/tests/testthat/test-to_document/document.Rmd index b269f450..965ecd27 100644 --- a/tests/testthat/test-to_document/document.Rmd +++ b/tests/testthat/test-to_document/document.Rmd @@ -15,7 +15,10 @@ Valid Document from 'Analysis Notebook' template - [ ] Questions/TODO list here -```{r setup, message = FALSE, warning = FALSE} +```{r} +#| label: setup +#| message: false +#| warning: false # setup code here ``` diff --git a/tests/testthat/test-to_document/extra-spaces.Rmd b/tests/testthat/test-to_document/extra-spaces.Rmd index b996972e..6a5418d1 100644 --- a/tests/testthat/test-to_document/extra-spaces.Rmd +++ b/tests/testthat/test-to_document/extra-spaces.Rmd @@ -19,7 +19,10 @@ Valid Notebook from 'Analysis Notebook' template with extra spaces before the de - [ ] Questions/TODO list here -```{r setup, message = FALSE, warning = FALSE} +```{r} +#| label: setup +#| message: false +#| warning: false # setup code here ``` diff --git a/tests/testthat/test-to_document/minimal-document.Rmd b/tests/testthat/test-to_document/minimal-document.Rmd index 3b8d645d..8c6a0724 100644 --- a/tests/testthat/test-to_document/minimal-document.Rmd +++ b/tests/testthat/test-to_document/minimal-document.Rmd @@ -10,7 +10,10 @@ Valid Notebook with minimal `html_notebook` output - [ ] Questions/TODO list here -```{r setup, message = FALSE, warning = FALSE} +```{r} +#| label: setup +#| message: false +#| warning: false # setup code here ``` diff --git a/tests/testthat/test-to_document/minimal.Rmd b/tests/testthat/test-to_document/minimal.Rmd index e4913bf4..0c760b61 100644 --- a/tests/testthat/test-to_document/minimal.Rmd +++ b/tests/testthat/test-to_document/minimal.Rmd @@ -10,7 +10,10 @@ Valid Notebook with minimal `html_notebook` output - [ ] Questions/TODO list here -```{r setup, message = FALSE, warning = FALSE} +```{r} +#| label: setup +#| message: false +#| warning: false # setup code here ``` diff --git a/tests/testthat/test-to_document/multiple.Rmd b/tests/testthat/test-to_document/multiple.Rmd index bcb83ff0..3cb8f98d 100644 --- a/tests/testthat/test-to_document/multiple.Rmd +++ b/tests/testthat/test-to_document/multiple.Rmd @@ -26,7 +26,10 @@ Valid Notebook from 'Analysis Notebook' template with multiple output types. - [ ] Questions/TODO list here -```{r setup, message = FALSE, warning = FALSE} +```{r} +#| label: setup +#| message: false +#| warning: false # setup code here ``` diff --git a/tests/testthat/test-to_document/no-output.Rmd b/tests/testthat/test-to_document/no-output.Rmd index 341a3bf0..c1a68208 100644 --- a/tests/testthat/test-to_document/no-output.Rmd +++ b/tests/testthat/test-to_document/no-output.Rmd @@ -9,7 +9,10 @@ Invalid Notebook without `output` in front matter. - [ ] Questions/TODO list here -```{r setup, message = FALSE, warning = FALSE} +```{r} +#| label: setup +#| message: false +#| warning: false # setup code here ``` diff --git a/tests/testthat/test-to_document/valid.Rmd b/tests/testthat/test-to_document/valid.Rmd index 216f4425..38e4a76b 100644 --- a/tests/testthat/test-to_document/valid.Rmd +++ b/tests/testthat/test-to_document/valid.Rmd @@ -17,7 +17,10 @@ Valid Notebook from 'Analysis Notebook' template. - [ ] Questions/TODO list here -```{r setup, message = FALSE, warning = FALSE} +```{r} +#| label: setup +#| message: false +#| warning: false # setup code here ``` diff --git a/tests/testthat/test-to_document/with-code.Rmd b/tests/testthat/test-to_document/with-code.Rmd index 5f15a2c4..2298ae8e 100644 --- a/tests/testthat/test-to_document/with-code.Rmd +++ b/tests/testthat/test-to_document/with-code.Rmd @@ -17,7 +17,10 @@ Valid Notebook from 'Analysis Notebook' template that creates a cars plot. - [ ] Questions/TODO list here -```{r setup, message = FALSE, warning = FALSE} +```{r} +#| label: setup +#| message: false +#| warning: false # setup code here ``` @@ -35,7 +38,8 @@ Graph and model data to ask and answer questions. Plot the speed and stopping distances from the `cars` dataset (circa 1920). -```{r cars} +```{r} +#| label: cars plot(cars) ``` diff --git a/tests/testthat/test-upkeep.R b/tests/testthat/test-upkeep.R index c47b3487..0faddafd 100644 --- a/tests/testthat/test-upkeep.R +++ b/tests/testthat/test-upkeep.R @@ -18,7 +18,7 @@ test_that("use_upkeep_issue validates arguments", { # upkeep_checklist -base_length <- 37 +base_length <- 43 test_that("upkeep_checklist is expected length for first upkeep", { usethis::ui_silence(local_temppkg(type = "rdev")) @@ -75,5 +75,5 @@ test_that("upkeep_checklist is expected length for last upkeep year", { expect_length(upkeep_checklist(2023), base_length - 11) expect_length(upkeep_checklist(2024), base_length - 16) expect_length(upkeep_checklist(2025), base_length - 16) - expect_length(upkeep_checklist(2026), base_length - 24) + expect_length(upkeep_checklist(2026), base_length - 30) })
YEAR: 2025 +YEAR: 2026 COPYRIGHT HOLDER: John Benninghoff diff --git a/docs/LICENSE.html b/docs/LICENSE.html index e0b51245..5b4bd80e 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 @@ -45,7 +45,7 @@ -Copyright (c) 2025 John Benninghoff +Copyright (c) 2026 John Benninghoff Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/docs/TODO.html b/docs/TODO.html index 54531c5c..c7d6aaed 100644 --- a/docs/TODO.html +++ b/docs/TODO.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/articles/analysis-package-layout.html b/docs/articles/analysis-package-layout.html index e4cf9fc7..1b2a7ae6 100644 --- a/docs/articles/analysis-package-layout.html +++ b/docs/articles/analysis-package-layout.html @@ -26,7 +26,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/articles/index.html b/docs/articles/index.html index d8c5f629..529459e5 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/articles/rdev.html b/docs/articles/rdev.html index fc067e9c..0593987f 100644 --- a/docs/articles/rdev.html +++ b/docs/articles/rdev.html @@ -26,7 +26,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/articles/style-guide.html b/docs/articles/style-guide.html index 6aa8477f..2f58d77f 100644 --- a/docs/articles/style-guide.html +++ b/docs/articles/style-guide.html @@ -26,7 +26,7 @@ rdev - 1.15.5 + 1.15.6 diff --git a/docs/authors.html b/docs/authors.html index 8087f6ae..2531cdba 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -7,7 +7,7 @@ rdev - 1.15.5 + 1.15.6 @@ -55,15 +55,15 @@ Authors Citation Source: DESCRIPTION - Benninghoff J (2025). + Benninghoff J (2026). rdev: R Development Tools. -R package version 1.15.5, https://jabenninghoff.github.io/rdev/. +R package version 1.15.6, https://jabenninghoff.github.io/rdev/. @Manual{, title = {rdev: R Development Tools}, author = {John Benninghoff}, - year = {2025}, - note = {R package version 1.15.5}, + year = {2026}, + note = {R package version 1.15.6}, url = {https://jabenninghoff.github.io/rdev/}, } diff --git a/docs/index.html b/docs/index.html index 4aa17d3a..6c94b20a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -29,7 +29,7 @@ rdev - 1.15.5 + 1.15.6 @@ -279,20 +279,20 @@ Workflow#> * creating vignettes ... OK #> * checking for LF line-endings in source and make files and shell scripts #> * checking for empty or unneeded directories -#> * building ‘rdev_1.15.5.tar.gz’ +#> * building ‘rdev_1.15.6.tar.gz’ #> #> ── R CMD check ───────────────────────────────────────────────────────────────── -#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/Rtmpqk420B/file11cd6e62afeb/rdev.Rcheck’ +#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpqNxoSE/file820a21bb3a1a/rdev.Rcheck’ #> * using R version 4.5.2 (2025-10-31) #> * using platform: aarch64-apple-darwin20 #> * R was compiled by #> Apple clang version 16.0.0 (clang-1600.0.26.6) #> GNU Fortran (GCC) 14.2.0 -#> * running under: macOS Sequoia 15.7.2 +#> * running under: macOS Sequoia 15.7.3 #> * using session charset: UTF-8 #> * using option ‘--no-manual’ #> * checking for file ‘rdev/DESCRIPTION’ ... OK -#> * this is package ‘rdev’ version ‘1.15.5’ +#> * this is package ‘rdev’ version ‘1.15.6’ #> * package encoding: UTF-8 #> * checking package namespace information ... OK #> * checking package dependencies ... OK @@ -347,8 +347,8 @@ Workflow#> * DONE #> #> Status: OK -#> ── R CMD check results ──────────────────────────────────────── rdev 1.15.5 ──── -#> Duration: 28.9s +#> ── R CMD check results ──────────────────────────────────────── rdev 1.15.6 ──── +#> Duration: 26.8s #> #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
YEAR: 2026 COPYRIGHT HOLDER: John Benninghoff
Copyright (c) 2025 John Benninghoff
Copyright (c) 2026 John Benninghoff
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Source: DESCRIPTION
DESCRIPTION
Benninghoff J (2025). +
Benninghoff J (2026). rdev: R Development Tools. -R package version 1.15.5, https://jabenninghoff.github.io/rdev/. +R package version 1.15.6, https://jabenninghoff.github.io/rdev/.
@Manual{, title = {rdev: R Development Tools}, author = {John Benninghoff}, - year = {2025}, - note = {R package version 1.15.5}, + year = {2026}, + note = {R package version 1.15.6}, url = {https://jabenninghoff.github.io/rdev/}, }
NEWS.md
Added instructions for YAML chunk syntax update to upkeep_checklist()
upkeep_checklist()
2026 Upkeep