From c2b96a1c0d53c55afa36702a9d1b8a8e20fdd135 Mon Sep 17 00:00:00 2001 From: Sarah Kelley Date: Mon, 14 Sep 2026 08:57:26 -0400 Subject: [PATCH 1/5] Add initial R-universe Github action --- .github/workflows/devel-build.yml | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/.github/workflows/devel-build.yml b/.github/workflows/devel-build.yml index 43f4a0d..748b304 100644 --- a/.github/workflows/devel-build.yml +++ b/.github/workflows/devel-build.yml @@ -1,13 +1,11 @@ name: Cardinal CI workflow run-name: Cardinal CI workflow run on: - - push + - push: + - pull_request: jobs: build: - # TODO confirm the base image we should use. "latest" - # leaves us open to unexpected breakage if there's a - # breaking change in the base image; we should control - # when we update the base. - runs-on: ubuntu-latest - steps: - - run: echo "Running the Cardinal CI workflow. Triggered by ${{ github.event_name }}" + runs-on: R-universe testing + uses: r-universe-org/workflows/.github/workflows/build.yml@v3 + with: + universe: ${{ github.repository_owner }} From 2619c7cea3ec11e24836931e5fd5e1ebdfdaa1cd Mon Sep 17 00:00:00 2001 From: Sarah Kelley Date: Mon, 14 Sep 2026 09:03:57 -0400 Subject: [PATCH 2/5] take two? --- .github/workflows/devel-build.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/devel-build.yml b/.github/workflows/devel-build.yml index 748b304..6da9530 100644 --- a/.github/workflows/devel-build.yml +++ b/.github/workflows/devel-build.yml @@ -1,8 +1,7 @@ -name: Cardinal CI workflow -run-name: Cardinal CI workflow run +name: Test R-universe on: - - push: - - pull_request: + - push + - pull_request jobs: build: runs-on: R-universe testing From 320296fffef9bc620315ca6b4401ab3e8a278024 Mon Sep 17 00:00:00 2001 From: Sarah Kelley Date: Mon, 14 Sep 2026 09:06:10 -0400 Subject: [PATCH 3/5] Use correct field name: instead of runs-on: --- .github/workflows/devel-build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/devel-build.yml b/.github/workflows/devel-build.yml index 6da9530..7be3f4d 100644 --- a/.github/workflows/devel-build.yml +++ b/.github/workflows/devel-build.yml @@ -4,7 +4,7 @@ on: - pull_request jobs: build: - runs-on: R-universe testing + name: R-universe testing uses: r-universe-org/workflows/.github/workflows/build.yml@v3 with: universe: ${{ github.repository_owner }} From ce80733f2a9a2fd947a257b952b52086808dbd77 Mon Sep 17 00:00:00 2001 From: Sarah Kelley Date: Mon, 14 Sep 2026 09:21:58 -0400 Subject: [PATCH 4/5] Add bioconductor checks --- .github/workflows/r-universe.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 .github/workflows/r-universe.yml diff --git a/.github/workflows/r-universe.yml b/.github/workflows/r-universe.yml new file mode 100644 index 0000000..d6d07be --- /dev/null +++ b/.github/workflows/r-universe.yml @@ -0,0 +1,15 @@ +# This workflow is directly ripped off from # the Bioconductor docs: +# https://docs.r-universe.dev/bioconductor/#debugging-the-ci +name: Test R-universe + +on: + push: + pull_request: + +jobs: + build: + name: R-universe testing + uses: r-universe-org/workflows/.github/workflows/build.yml@v3 + with: + universe: bioc + organization: bioconductor # for BiocCheck checks From d17bb98ca7b16af3b5218a468ed1f02053e19ffe Mon Sep 17 00:00:00 2001 From: Sarah Kelley Date: Tue, 15 Sep 2026 19:13:37 -0400 Subject: [PATCH 5/5] Attempt skipping bioc-specific checks --- .github/workflows/r-universe.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/r-universe.yml b/.github/workflows/r-universe.yml index d6d07be..523fbfa 100644 --- a/.github/workflows/r-universe.yml +++ b/.github/workflows/r-universe.yml @@ -12,4 +12,5 @@ jobs: uses: r-universe-org/workflows/.github/workflows/build.yml@v3 with: universe: bioc - organization: bioconductor # for BiocCheck checks +# Trying this out - does omitting the organization skip the BiocCheck task? + # organization: bioconductor # for BiocCheck checks