From 8d07ba951353b38092c7c93d4ab072fb731455ab Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Fri, 15 May 2026 15:45:36 +0200
Subject: [PATCH 1/5] Use standard R CMD check workflow

---
 .github/workflows/R-CMD-check.yaml | 50 ++++++++++++++++++++++++++++++
 1 file changed, 50 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..13c2168
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# 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, devel]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - 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")'
+          error-on: '"error"'

From d448934847ed59bbb113a76e0fb37c9bac5ae352 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Mon, 18 May 2026 09:25:27 +0200
Subject: [PATCH 2/5] Test r-universe workflow

---
 .github/workflows/r-universe.yaml | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 .github/workflows/r-universe.yaml

diff --git a/.github/workflows/r-universe.yaml b/.github/workflows/r-universe.yaml
new file mode 100644
index 0000000..bdf08a8
--- /dev/null
+++ b/.github/workflows/r-universe.yaml
@@ -0,0 +1,13 @@
+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: bioc
\ No newline at end of file

From 94d04692203dcdcd046683718b84f3b3e7327e20 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Mon, 18 May 2026 09:25:45 +0200
Subject: [PATCH 3/5] Remove bioc custom workflow

---
 .github/workflows/check-bioc.yml | 339 -------------------------------
 1 file changed, 339 deletions(-)
 delete mode 100644 .github/workflows/check-bioc.yml

diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
deleted file mode 100644
index 1c83649..0000000
--- a/.github/workflows/check-bioc.yml
+++ /dev/null
@@ -1,339 +0,0 @@
-## Read more about GitHub actions the features of this GitHub Actions workflow
-## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
-##
-## For more details, check the biocthis developer notes vignette at
-## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
-##
-## You can add this workflow to other packages using:
-## > biocthis::use_bioc_github_action()
-##
-## Using GitHub Actions exposes you to many details about how R packages are
-## compiled and installed in several operating system.s
-### If you need help, please follow the steps listed at
-## https://github.com/r-lib/actions#where-to-find-help
-##
-## If you found an issue specific to biocthis's GHA workflow, please report it
-## with the information that will make it easier for others to help you.
-## Thank you!
-
-## Acronyms:
-## * GHA: GitHub Action
-## * OS: operating system
-
-on:
-  push:
-    branches:
-      - main
-      - devel
-  pull_request:
-    branches:
-      - main 
-      - devel
-
-name: R-CMD-check-bioc
-
-## These environment variables control whether to run GHA code later on that is
-## specific to testthat, covr, and pkgdown.
-##
-## If you need to clear the cache of packages, update the number inside
-## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
-## Note that you can always run a GHA test without the cache by using the word
-## "/nocache" in the commit message.
-env:
-  has_testthat: 'true'
-  run_covr: 'false'
-  run_pkgdown: 'false'
-  has_RUnit: 'false'
-  cache-version: 'cache-v1'
-  run_docker: 'false'
-
-jobs:
-  build-check:
-    runs-on: ${{ matrix.config.os }}
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-    container: ${{ matrix.config.cont }}
-    ## Environment variables unique to this job.
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          #- { os: ubuntu-latest, r: '4.5', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://p3m.dev/cran/__linux__/noble/latest" }
-          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://p3m.dev/cran/__linux__/noble/latest" }
-          - { os: macOS-latest, r: 'devel', bioc: 'devel'}
-          #- { os: windows-latest, r: 'devel', bioc: 'devel'}
-          ## Check https://github.com/r-lib/actions/tree/master/examples
-          ## for examples using the http-user-agent
-    env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
-      NOT_CRAN: true
-      TZ: UTC
-      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-    steps:
-
-      ## Set the R library to the directory matching the
-      ## R packages cache step further below when running on Docker (Linux).
-      - name: Set R Library home on Linux
-        if: runner.os == 'Linux'
-        run: |
-          mkdir /__w/_temp/Library
-          echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
-
-      ## Most of these steps are the same as the ones in
-      ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
-      ## If they update their steps, we will also need to update ours.
-      - name: Checkout Repository
-        uses: actions/checkout@v3
-
-      ## R is already included in the Bioconductor docker images
-      - name: Setup R from r-lib
-        if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-
-      ## pandoc is already included in the Bioconductor docker images
-      - name: Setup pandoc from r-lib
-        if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-
-
-      - name: Cache R packages on Linux
-        if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v3
-        with:
-          path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.5-
-
-      - name: Install macOS system dependencies
-        if: matrix.config.os == 'macOS-latest'
-        run: |
-          ## Enable installing XML from source if needed
-          brew install libxml2
-          echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
-
-          ## For textshaping, required by ragg, and required by pkgdown
-          brew install harfbuzz fribidi
-
-          ## For installing usethis's dependency gert
-          brew install libgit2
-
-          ## Required for tcltk
-          brew install xquartz --cask
-
-      - name: Install Windows system dependencies
-        if: runner.os == 'Windows'
-        run: |
-          ## Edit below if you have any Windows system dependencies
-        shell: Rscript {0}
-
-      - name: Install BiocManager
-        run: |
-          message(paste('****', Sys.time(), 'installing BiocManager ****'))
-          remotes::install_cran("BiocManager")
-        shell: Rscript {0}
-
-      - name: Set BiocVersion
-        run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE)
-        shell: Rscript {0}
-
-      - name: Install dependencies pass 1
-        run: |
-          ## Try installing the package dependencies in steps. First the local
-          ## dependencies, then any remaining dependencies to avoid the
-          ## issues described at
-          ## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
-          ## https://github.com/r-lib/remotes/issues/296
-          ## Ideally, all dependencies should get installed in the first pass.
-
-          ## For running the checks
-          message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          install.packages(c("rcmdcheck", "BiocCheck", "remotes"), repos = BiocManager::repositories())
-          
-          ## TEMP REMOVE LATER:
-          ## For now install Rarr from github since ZarrArray needs >= 1.11.33
-          # BiocManager::install("Rarr", version = "2.1.8")
-
-          ## Pass #1 at installing dependencies
-          message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
-        continue-on-error: true
-        shell: Rscript {0}
-
-      - name: Install dependencies pass 2
-        run: |
-          ## Pass #2 at installing dependencies
-          message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE, force = TRUE)
-        shell: Rscript {0}
-
-      - name: Install BiocGenerics
-        if:  env.has_RUnit == 'true'
-        run: |
-          ## Install BiocGenerics
-          BiocManager::install("BiocGenerics")
-        shell: Rscript {0}
-
-      - name: Install covr
-        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
-        run: |
-          remotes::install_cran("covr")
-        shell: Rscript {0}
-
-      - name: Install pkgdown
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: |
-          remotes::install_cran("pkgdown")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
-        shell: Rscript {0}
-
-      - name: Run CMD check
-        env:
-          _R_CHECK_CRAN_INCOMING_: false
-          DISPLAY: 99.0
-        run: |
-          options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(
-              args = c("--no-manual", "--no-vignettes", "--timings"),
-              build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
-              error_on = "error",
-              check_dir = "check"
-          )
-        shell: Rscript {0}
-
-      ## Might need an to add this to the if:  && runner.os == 'Linux'
-      - name: Reveal testthat details
-        if:  env.has_testthat == 'true'
-        run: find . -name testthat.Rout -exec cat '{}' ';'
-
-      - name: Run RUnit tests
-        if:  env.has_RUnit == 'true'
-        run: |
-          BiocGenerics:::testPackage()
-        shell: Rscript {0}
-
-      - name: Run BiocCheck
-        env:
-          DISPLAY: 99.0
-        run: |
-          BiocCheck::BiocCheck(
-              dir('check', 'tar.gz$', full.names = TRUE),
-              `quit-with-status` = TRUE,
-              `no-check-R-ver` = TRUE,
-              `no-check-bioc-help` = TRUE,
-              `no-check-remotes` = TRUE
-          )
-        shell: Rscript {0}
-
-      - name: Test coverage
-        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
-        run: |
-          covr::codecov(coverage = covr::package_coverage(type = "all"))
-        shell: Rscript {0}
-
-      - name: Install package
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: R CMD INSTALL .
-
-      - name: Build pkgdown site
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
-        shell: Rscript {0}
-        ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
-        ## at least one locally before this will work. This creates the gh-pages
-        ## branch (erasing anything you haven't version controlled!) and
-        ## makes the git history recognizable by pkgdown.
-
-      - name: Install deploy dependencies
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        run: |
-          apt-get update && apt-get -y install rsync
-
-      - name: Deploy pkgdown site to GitHub pages 🚀
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
-        uses: JamesIves/github-pages-deploy-action@releases/v4
-        with:
-          clean: false
-          branch: gh-pages
-          folder: docs
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@master
-        with:
-          name: ${{ runner.os }}-biocversion-devel-r-4.5-results
-          path: check
-
-
-  ## Code adapted from
-  ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
-  docker-build-and-push:
-    runs-on: ubuntu-latest
-    needs: build-check
-    steps:
-      - name: Checkout Repository
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: actions/checkout@v3
-
-      - name: Register repo name
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        id: reg_repo_name
-        run: |
-          echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
-
-      - name: Set up QEMU
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: docker/setup-qemu-action@v2
-
-      - name: Set up Docker Buildx
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: docker/setup-buildx-action@v2
-
-      - name: Login to Docker Hub
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
-      ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
-      ## account, not your actual dockerhub account password. You can get it
-      ## from https://hub.docker.com/settings/security.
-      ## Check https://github.com/docker/build-push-action/tree/v4.0.0
-      ## for more details.
-      ## Alternatively, try checking
-      ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.
-
-      - name: Build and Push Docker
-        if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
-        uses: docker/build-push-action@v4
-        with:
-          context: .
-          push: true
-          tags: >
-            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
-            ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel

From 01a1e76a578f14a359452fd1103e4b891aae89cc Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Wed, 20 May 2026 13:04:53 +0200
Subject: [PATCH 4/5] Remove R CMD check workflow

---
 .github/workflows/R-CMD-check.yaml | 50 ------------------------------
 1 file changed, 50 deletions(-)
 delete mode 100644 .github/workflows/R-CMD-check.yaml

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
deleted file mode 100644
index 13c2168..0000000
--- a/.github/workflows/R-CMD-check.yaml
+++ /dev/null
@@ -1,50 +0,0 @@
-# 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, devel]
-  pull_request:
-
-name: R-CMD-check.yaml
-
-permissions: read-all
-
-jobs:
-  R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: macos-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      R_KEEP_PKG_SOURCE: yes
-
-    steps:
-      - uses: actions/checkout@v6
-
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
-
-      - 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")'
-          error-on: '"error"'

From f565db1b7dd348d0df34f329ddfd2cea800f1324 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <git@hugogruson.fr>
Date: Wed, 20 May 2026 13:40:51 +0200
Subject: [PATCH 5/5] Try to get r-universe to run bioccheck

---
 .github/workflows/r-universe.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/r-universe.yaml b/.github/workflows/r-universe.yaml
index bdf08a8..67da258 100644
--- a/.github/workflows/r-universe.yaml
+++ b/.github/workflows/r-universe.yaml
@@ -10,4 +10,4 @@ jobs:
     uses: r-universe-org/workflows/.github/workflows/build.yml@v3
     with:
       universe: bioc
-      organization: bioc
\ No newline at end of file
+      organization: bioconductor
\ No newline at end of file