From f899bfd02145b33858550d829dcbfaa88df46837 Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Tue, 24 Jun 2025 06:36:15 +0300 Subject: [PATCH 1/8] Update rworkflows.yml --- .github/workflows/rworkflows.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index ebc5a11..93db5e8 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -29,7 +29,7 @@ jobs: rspm: ~ - os: macOS-latest bioc: devel - r: auto + r: latest cont: ~ rspm: ~ - os: windows-latest From 775be76b1cd2040f26737a55acd5fe893c849f46 Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Thu, 17 Jul 2025 20:02:00 +0300 Subject: [PATCH 2/8] Update rworkflows.yml --- .github/workflows/rworkflows.yml | 99 +++++++++++++++++++------------- 1 file changed, 58 insertions(+), 41 deletions(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 93db5e8..d187bb7 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -2,16 +2,17 @@ name: rworkflows 'on': push: branches: - - master - - main - - devel - - RELEASE_** + - master + - main + - devel + - RELEASE_** pull_request: branches: - - master - - main - - devel - - RELEASE_** + - master + - main + - devel + - RELEASE_** + jobs: rworkflows: permissions: write-all @@ -19,39 +20,55 @@ jobs: name: ${{ matrix.config.os }} (${{ matrix.config.r }}) container: ${{ matrix.config.cont }} strategy: - fail-fast: ${{ false }} + fail-fast: false matrix: config: - - os: ubuntu-latest - bioc: devel - r: auto - cont: ghcr.io/bioconductor/bioconductor_docker:devel - rspm: ~ - - os: macOS-latest - bioc: devel - r: latest - cont: ~ - rspm: ~ - - os: windows-latest - bioc: devel - r: auto - cont: ~ - rspm: ~ + - os: ubuntu-latest + bioc: devel + r: auto + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: ~ + - os: macOS-latest + bioc: devel + r: auto + cont: ~ + rspm: ~ + - os: windows-latest + bioc: devel + r: auto + cont: ~ + rspm: ~ steps: - - uses: neurogenomics/rworkflows@master - with: - run_bioccheck: ${{ false }} - run_rcmdcheck: ${{ true }} - as_cran: ${{ true }} - run_vignettes: ${{ true }} - has_testthat: ${{ true }} - run_covr: ${{ true }} - run_pkgdown: ${{ true }} - has_runit: ${{ false }} - has_latex: ${{ false }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run_docker: ${{ false }} - DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} - runner_os: ${{ runner.os }} - cache_version: cache-v1 - docker_registry: ghcr.io + - uses: actions/checkout@v4 + - name: Set up R + uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + # Update package repositories to devel + - name: Set BiocManager Repos + run: | + echo 'options(repos = BiocManager::repositories())' >> ~/.Rprofile + - name: Install BiocManager + run: | + Rscript -e "if (!requireNamespace('BiocManager', quietly=TRUE)) install.packages('BiocManager')" + # Ensure all Bioconductor and key packages are latest + - name: Update Packages + run: | + Rscript -e "BiocManager::install(ask=FALSE, update=TRUE)" + - uses: neurogenomics/rworkflows@master + with: + run_bioccheck: false + run_rcmdcheck: true + as_cran: true + run_vignettes: true + has_testthat: true + run_covr: true + run_pkgdown: true + has_runit: false + has_latex: false + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run_docker: false + DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} + runner_os: ${{ runner.os }} + cache_version: cache-v2 + docker_registry: ghcr.io From 33465d8ec7554bdd8971287cb794134678dbde52 Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Thu, 17 Jul 2025 20:04:06 +0300 Subject: [PATCH 3/8] Update rworkflows.yml --- .github/workflows/rworkflows.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index d187bb7..738a954 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -3,6 +3,7 @@ name: rworkflows push: branches: - master + - rw - main - devel - RELEASE_** From 5d9b4bce8129f33bf2b15642a764d8e03855c1ad Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Thu, 17 Jul 2025 20:07:28 +0300 Subject: [PATCH 4/8] Update rworkflows.yml --- .github/workflows/rworkflows.yml | 101 +++++++++++++------------------ 1 file changed, 42 insertions(+), 59 deletions(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 738a954..b986001 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -2,18 +2,17 @@ name: rworkflows 'on': push: branches: - - master - - rw - - main - - devel - - RELEASE_** + - master + - rw + - main + - devel + - RELEASE_** pull_request: branches: - - master - - main - - devel - - RELEASE_** - + - master + - main + - devel + - RELEASE_** jobs: rworkflows: permissions: write-all @@ -21,55 +20,39 @@ jobs: name: ${{ matrix.config.os }} (${{ matrix.config.r }}) container: ${{ matrix.config.cont }} strategy: - fail-fast: false + fail-fast: ${{ false }} matrix: config: - - os: ubuntu-latest - bioc: devel - r: auto - cont: ghcr.io/bioconductor/bioconductor_docker:devel - rspm: ~ - - os: macOS-latest - bioc: devel - r: auto - cont: ~ - rspm: ~ - - os: windows-latest - bioc: devel - r: auto - cont: ~ - rspm: ~ + - os: ubuntu-latest + bioc: devel + r: auto + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: ~ + - os: macOS-latest + bioc: devel + r: auto + cont: ~ + rspm: ~ + - os: windows-latest + bioc: devel + r: auto + cont: ~ + rspm: ~ steps: - - uses: actions/checkout@v4 - - name: Set up R - uses: r-lib/actions/setup-r@v2 - with: - r-version: ${{ matrix.config.r }} - # Update package repositories to devel - - name: Set BiocManager Repos - run: | - echo 'options(repos = BiocManager::repositories())' >> ~/.Rprofile - - name: Install BiocManager - run: | - Rscript -e "if (!requireNamespace('BiocManager', quietly=TRUE)) install.packages('BiocManager')" - # Ensure all Bioconductor and key packages are latest - - name: Update Packages - run: | - Rscript -e "BiocManager::install(ask=FALSE, update=TRUE)" - - uses: neurogenomics/rworkflows@master - with: - run_bioccheck: false - run_rcmdcheck: true - as_cran: true - run_vignettes: true - has_testthat: true - run_covr: true - run_pkgdown: true - has_runit: false - has_latex: false - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - run_docker: false - DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} - runner_os: ${{ runner.os }} - cache_version: cache-v2 - docker_registry: ghcr.io + - uses: neurogenomics/rworkflows@master + with: + run_bioccheck: ${{ false }} + run_rcmdcheck: ${{ true }} + as_cran: ${{ true }} + run_vignettes: ${{ true }} + has_testthat: ${{ true }} + run_covr: ${{ true }} + run_pkgdown: ${{ true }} + has_runit: ${{ false }} + has_latex: ${{ false }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run_docker: ${{ false }} + DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} + runner_os: ${{ runner.os }} + cache_version: cache-v1 + docker_registry: ghcr.io From d79e707cba6d35957b621554e05dbd32c4d3150e Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Thu, 17 Jul 2025 20:26:21 +0300 Subject: [PATCH 5/8] Update rworkflows.yml --- .github/workflows/rworkflows.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index b986001..fb5fb41 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -26,8 +26,8 @@ jobs: - os: ubuntu-latest bioc: devel r: auto - cont: ghcr.io/bioconductor/bioconductor_docker:devel - rspm: ~ + cont: ghcr.io/bioconductor/bioconductor:devel + rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release - os: macOS-latest bioc: devel r: auto From f0070deef9202ec52fd851c8945b8c4dd0e2b1a1 Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Thu, 17 Jul 2025 20:45:44 +0300 Subject: [PATCH 6/8] Update rworkflows.yml --- .github/workflows/rworkflows.yml | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index fb5fb41..385b346 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -3,16 +3,19 @@ name: rworkflows push: branches: - master - - rw - main - devel - RELEASE_** + - '*' + - '!gh-pages' pull_request: branches: - master - main - devel - RELEASE_** + - '*' + - '!gh-pages' jobs: rworkflows: permissions: write-all @@ -26,15 +29,15 @@ jobs: - os: ubuntu-latest bioc: devel r: auto - cont: ghcr.io/bioconductor/bioconductor:devel - rspm: https://packagemanager.rstudio.com/cran/__linux__/focal/release + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: ~ - os: macOS-latest - bioc: devel + bioc: release r: auto cont: ~ rspm: ~ - os: windows-latest - bioc: devel + bioc: release r: auto cont: ~ rspm: ~ @@ -54,5 +57,6 @@ jobs: run_docker: ${{ false }} DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} runner_os: ${{ runner.os }} - cache_version: cache-v1 + cache_version: cache-v2 docker_registry: ghcr.io + force_install: ${{ true }} From 0cf7fe50802eebcd96c1edc67bf399e287911ea7 Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Thu, 17 Jul 2025 20:57:55 +0300 Subject: [PATCH 7/8] Update rworkflows.yml --- .github/workflows/rworkflows.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 385b346..42d1b51 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -27,7 +27,7 @@ jobs: matrix: config: - os: ubuntu-latest - bioc: devel + bioc: release r: auto cont: ghcr.io/bioconductor/bioconductor_docker:devel rspm: ~ From 033a86a20b697d1f553314683c59107e10f1cde6 Mon Sep 17 00:00:00 2001 From: Muluh <127390183+Daenarys8@users.noreply.github.com> Date: Thu, 17 Jul 2025 21:39:46 +0300 Subject: [PATCH 8/8] Update rworkflows.yml --- .github/workflows/rworkflows.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml index 42d1b51..b30549b 100644 --- a/.github/workflows/rworkflows.yml +++ b/.github/workflows/rworkflows.yml @@ -29,7 +29,7 @@ jobs: - os: ubuntu-latest bioc: release r: auto - cont: ghcr.io/bioconductor/bioconductor_docker:devel + cont: ghcr.io/bioconductor/bioconductor_docker:RELEASE_3_21 rspm: ~ - os: macOS-latest bioc: release