From b753d3ec7874991bae707361cdae613fb63b90a0 Mon Sep 17 00:00:00 2001 From: bailliem Date: Sat, 11 Apr 2026 12:06:13 +0200 Subject: [PATCH 1/6] chore: add .gitignore for R package --- .gitignore | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 .gitignore diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..6255bde --- /dev/null +++ b/.gitignore @@ -0,0 +1,15 @@ +# R session files +.Rhistory +.Rdata +.RData +.Ruserdata +.Rproj.user + +# Built vignettes +inst/doc + +# macOS +.DS_Store + +# pkgdown site +docs/ From 9a2c6be9528684a51e6984e8946e51eb7c0150d6 Mon Sep 17 00:00:00 2001 From: bailliem Date: Sat, 11 Apr 2026 12:06:15 +0200 Subject: [PATCH 2/6] chore: add .Rbuildignore to exclude non-package files --- .Rbuildignore | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 .Rbuildignore diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..bf2e3f7 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,7 @@ +^\.github$ +^docs$ +^_pkgdown\.yml$ +^\.gitignore$ +^knockofftools\.Rproj$ +^LICENSE$ +^README\.md$ From f5b04f8bf17df2a5553d71ea3a41631bdc4d4893 Mon Sep 17 00:00:00 2001 From: bailliem Date: Sat, 11 Apr 2026 12:07:16 +0200 Subject: [PATCH 3/6] ci: add R-CMD-check workflow with Ubuntu and macOS matrix --- .github/workflows/R-CMD-check.yaml | 48 ++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 .github/workflows/R-CMD-check.yaml diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml new file mode 100644 index 0000000..6f8e219 --- /dev/null +++ b/.github/workflows/R-CMD-check.yaml @@ -0,0 +1,48 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main] + pull_request: + branches: [main] + +name: R-CMD-check + +permissions: read-all + +jobs: + R-CMD-check: + runs-on: ${{ matrix.config.os }} + name: R-CMD-check (${{ matrix.config.os }}, ${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + - {os: macos-latest, r: 'release'} + + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes + + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + use-public-rspm: true + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' From 3cd742a47f730afbda223b633d3d555a65ace80d Mon Sep 17 00:00:00 2001 From: bailliem Date: Sat, 11 Apr 2026 12:07:19 +0200 Subject: [PATCH 4/6] ci: add pkgdown build and GitHub Pages deployment workflow --- .github/workflows/pkgdown.yaml | 45 ++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 .github/workflows/pkgdown.yaml diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml new file mode 100644 index 0000000..aaa01e1 --- /dev/null +++ b/.github/workflows/pkgdown.yaml @@ -0,0 +1,45 @@ +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +on: + push: + branches: [main] + workflow_dispatch: + +name: pkgdown + +permissions: + contents: write + +jobs: + pkgdown: + runs-on: ubuntu-latest + # Only restrict concurrency for non-PR jobs + concurrency: + group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + steps: + - uses: actions/checkout@v4 + + - uses: r-lib/actions/setup-r@v2 + with: + use-public-rspm: true + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::pkgdown, local::. + needs: website + + - name: Build site + run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) + shell: Rscript {0} + + - name: Deploy to GitHub Pages + if: github.event_name != 'pull_request' + uses: JamesIves/github-pages-deploy-action@v4 + with: + clean: false + branch: gh-pages + folder: docs From 1e1f936200f024ae03af3c886c65d7e559b54ab1 Mon Sep 17 00:00:00 2001 From: bailliem Date: Sat, 11 Apr 2026 12:08:24 +0200 Subject: [PATCH 5/6] chore: update pkgdown URL to GitHub Pages --- _pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 7456055..2b859b8 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: http://opensource.nibr.com/knockofftools/ +url: https://openpharma.github.io/knockofftools/ template: bootstrap: 5 From 01b5c53a278b8b7e2db5fef900be1c9ee2070175 Mon Sep 17 00:00:00 2001 From: bailliem Date: Sat, 11 Apr 2026 12:08:24 +0200 Subject: [PATCH 6/6] docs: add R-CMD-check badge to README --- README.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/README.md b/README.md index 417d88f..7825441 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,7 @@ + +[![R-CMD-check](https://github.com/openpharma/knockofftools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/openpharma/knockofftools/actions/workflows/R-CMD-check.yaml) + + The `knockofftools` package ====================