From dc7d529414790fe6d1e01a91a1fcf508f0f584a8 Mon Sep 17 00:00:00 2001 From: LiNk-NY Date: Sun, 12 Apr 2026 20:34:44 -0400 Subject: [PATCH 1/6] add noble link --- .github/workflows/basic_checks.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index ac3e545..89a6d73 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -13,7 +13,7 @@ jobs: env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: TRUE GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest + CRAN: https://packagemanager.posit.co/cran/__linux__/noble/latest steps: - name: Checkout Repository From 725893c11906d83f2314d51dcec8ea27570193cf Mon Sep 17 00:00:00 2001 From: LiNk-NY Date: Sun, 12 Apr 2026 20:35:34 -0400 Subject: [PATCH 2/6] update repos and install deps --- .github/workflows/basic_checks.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index 89a6d73..b90cd15 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -21,7 +21,8 @@ jobs: - name: Query dependencies and update old packages run: | - BiocManager::install(ask=FALSE) + options(repos = c(CRAN = Sys.getenv("CRAN"))) + BiocManager::install(c("remotes", "rcmdcheck"), ask = FALSE) saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) shell: Rscript {0} @@ -35,9 +36,9 @@ jobs: - name: Install dependencies run: | - BiocManager::repositories() + options(repos = c(CRAN = Sys.getenv("CRAN"))) remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) - remotes::install_cran("rcmdcheck") + BiocManager::install(ask = FALSE, update = TRUE) shell: Rscript {0} - name: Check From a3e939d8180a3c32f41a50985921b5a8673c2eca Mon Sep 17 00:00:00 2001 From: LiNk-NY Date: Sun, 12 Apr 2026 20:36:11 -0400 Subject: [PATCH 3/6] upload docs to pages via GHA --- .github/workflows/basic_checks.yaml | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index b90cd15..b132f13 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -51,18 +51,10 @@ jobs: run: | PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")' - # deploy needs rsync? Seems so. - - name: Install deploy dependencies - run: | - apt-get update - apt-get -y install rsync - - - name: Deploy 🚀 - uses: JamesIves/github-pages-deploy-action@v4 + - name: Upload pkgdown artifact + uses: actions/upload-pages-artifact@v3 with: - TOKEN: ${{ secrets.GITHUB_TOKEN }} - BRANCH: gh-pages # The branch the action should deploy to. - FOLDER: docs # The folder the action should deploy. + path: docs docker-build-and-push: #needs: r-build-and-check @@ -129,3 +121,15 @@ jobs: tags: | ${{ env.IMAGE }}:latest ${{ env.IMAGE }}:${{ env.GIT_SHA }} + + deploy: + permissions: + contents: write + pages: write + id-token: write + runs-on: ubuntu-24.04 + steps: + - name: Deploy to GitHub Pages + id: deployment + uses: actions/deploy-pages@v4 + From 0388adb3dcc62ae28244fc3a8e2713e77f22995e Mon Sep 17 00:00:00 2001 From: LiNk-NY Date: Sun, 12 Apr 2026 20:36:27 -0400 Subject: [PATCH 4/6] update docker build-push-action --- .github/workflows/basic_checks.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index b132f13..be573a1 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -114,7 +114,7 @@ jobs: # https://github.com/docker/build-push-action - name: Build and push Docker image id: build-and-push - uses: docker/build-push-action@v5 + uses: docker/build-push-action@v6 with: context: . push: ${{ github.event_name != 'pull_request' }} From 696f2bb70092d73daf3d81755dc43b80cd8d0ef5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marcel=20Ramos=20P=C3=A9rez?= Date: Sun, 12 Apr 2026 20:41:39 -0400 Subject: [PATCH 5/6] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- .github/workflows/basic_checks.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index be573a1..7deb3a9 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -123,6 +123,7 @@ jobs: ${{ env.IMAGE }}:${{ env.GIT_SHA }} deploy: + needs: r-build-and-check permissions: contents: write pages: write From 40643ed6effa86437c98af471fa7667bb76eeae3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marcel=20Ramos=20P=C3=A9rez?= Date: Sun, 12 Apr 2026 20:42:04 -0400 Subject: [PATCH 6/6] Potential fix for pull request finding Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- .github/workflows/basic_checks.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/basic_checks.yaml b/.github/workflows/basic_checks.yaml index 7deb3a9..902a13e 100644 --- a/.github/workflows/basic_checks.yaml +++ b/.github/workflows/basic_checks.yaml @@ -125,7 +125,6 @@ jobs: deploy: needs: r-build-and-check permissions: - contents: write pages: write id-token: write runs-on: ubuntu-24.04