From f6b75799995e6a4e5d3e4ed385dff304cf9f954a Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Fri, 29 Sep 2023 15:51:30 -0700 Subject: [PATCH 1/8] CLEANUP: No longer a need for 'Additional_repositories' in DESCRIPTION --- DESCRIPTION | 2 -- 1 file changed, 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9973a5cc..63c8451c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -145,8 +145,6 @@ Suggests: visNetwork, vroom, xgboost -Additional_repositories: - https://rpolars.r-universe.dev Encoding: UTF-8 Config/testthat/edition: 3 Roxygen: list(markdown = TRUE) From 5873d582f79e0b332bdcef807ef8810d3cc36401 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Fri, 29 Sep 2023 15:58:04 -0700 Subject: [PATCH 2/8] GitHub Actions: First step towards R CMD check --- .Rbuildignore | 2 ++ .github/.gitignore | 1 + .github/workflows/R-CMD-check.yaml | 29 +++++++++++++++++++++++++++++ .travis.yml | 17 ----------------- 4 files changed, 32 insertions(+), 17 deletions(-) create mode 100644 .github/.gitignore create mode 100644 .github/workflows/R-CMD-check.yaml delete mode 100644 .travis.yml diff --git a/.Rbuildignore b/.Rbuildignore index 8b384df2..0d513518 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -12,3 +12,5 @@ spark-warehouse ^_pkgdown\.yml$ ^docs$ ^pkgdown$ +^\.github$ +^codecov\.yml$ diff --git a/.github/.gitignore b/.github/.gitignore new file mode 100644 index 00000000..2d19fc76 --- /dev/null +++ b/.github/.gitignore @@ -0,0 +1 @@ +*.html diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 00000000..132aa773 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,29 @@ +on: + push: + branches: main + pull_request: + branches: main + +name: R-CMD-check + +jobs: + R-CMD-check: + runs-on: ubuntu-latest + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v3 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + +# - uses: r-lib/actions/check-r-package@v2 diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 632fbccb..00000000 --- a/.travis.yml +++ /dev/null @@ -1,17 +0,0 @@ -language: r -r: - - release - - devel -sudo: false -warnings_are_errors: false -cache: packages - -env: - global: - - _R_CHECK_FORCE_SUGGESTS_=FALSE - -before_install: - - R -e 'install.packages(c("remotes", "knitr", "rmarkdown", "fansi", "NMF", "flexclust", "pbapply", "matrixStats", "mlbench", "ranger"))' - -install: - - R -e 'remotes::install_deps(dep = NA)' From 3b45495172b7a0f32bca09ac556fd1c90b54c1cc Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Fri, 29 Sep 2023 15:59:58 -0700 Subject: [PATCH 3/8] ping --- .github/workflows/R-CMD-check.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 132aa773..e32cbf68 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -27,3 +27,4 @@ jobs: needs: check # - uses: r-lib/actions/check-r-package@v2 + From a7053fd8a297ad70b094ecc170cfef7b2afda2c8 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Fri, 29 Sep 2023 16:01:52 -0700 Subject: [PATCH 4/8] ping 2 --- .github/workflows/R-CMD-check.yaml | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index e32cbf68..c803ed16 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,8 +1,4 @@ -on: - push: - branches: main - pull_request: - branches: main +on: [push, pull_request] name: R-CMD-check @@ -27,4 +23,3 @@ jobs: needs: check # - uses: r-lib/actions/check-r-package@v2 - From 733f39870962366828cf6ef5ed0e736b829efad2 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Fri, 29 Sep 2023 16:18:26 -0700 Subject: [PATCH 5/8] GA: Step 2 - run R CMD check --- .github/workflows/R-CMD-check.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index c803ed16..40eb240f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -22,4 +22,6 @@ jobs: extra-packages: any::rcmdcheck needs: check -# - uses: r-lib/actions/check-r-package@v2 + - uses: r-lib/actions/check-r-package@v2 + with: + error-on: '"error"' From 988e071728b39f0c1524aa88220c97e3b6e28186 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Fri, 29 Sep 2023 16:29:12 -0700 Subject: [PATCH 6/8] GitHub Actions: Give error on 'R CMD check' WARNINGS + add badge --- .github/workflows/R-CMD-check.yaml | 2 +- README.md | 4 +++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 40eb240f..80d32e05 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -24,4 +24,4 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: - error-on: '"error"' + error-on: '"warning"' diff --git a/README.md b/README.md index 590d8f71..6a38d888 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,5 @@ +[![R-CMD-check](https://github.com/egenn/rtemis/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/egenn/rtemis/actions/workflows/R-CMD-check.yaml) + # **_rtemis_** Machine Learning and Visualization A platform for advanced Machine Learning research and applications. @@ -18,7 +20,7 @@ R version 4.1 or higher ## Installation -Install `rtemis` usikg `pak`, `remotes`, or `devtools`: +Install `rtemis` using `pak`, `remotes`, or `devtools`: ```r pak::pkg_install("egenn/rtemis") From 725431f894c035350a323d902094bff2fdb4b761 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Fri, 29 Sep 2023 16:30:10 -0700 Subject: [PATCH 7/8] Bump version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 63c8451c..fd991ab0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: rtemis -Version: 0.95.7 +Version: 0.95.8 Title: Machine Learning and Visualization Date: 2023-09-29 Authors@R: person(given = "E.D.", family = "Gennatas", role = c("aut", "cre"), email = "gennatas@lambdamd.org", comment = c(ORCID = "0000-0001-9280-3609")) From abe7b08ab34afdb69e2d901fcfac5f3b455eaad5 Mon Sep 17 00:00:00 2001 From: Henrik Bengtsson Date: Fri, 29 Sep 2023 16:38:43 -0700 Subject: [PATCH 8/8] GitHub Actions: Allow WARNINGS from 'R CMD check', because help pages are still incomplete --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 80d32e05..40eb240f 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -24,4 +24,4 @@ jobs: - uses: r-lib/actions/check-r-package@v2 with: - error-on: '"warning"' + error-on: '"error"'