diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml deleted file mode 100644 index e453784..0000000 --- a/.github/workflows/R-CMD-check.yaml +++ /dev/null @@ -1,103 +0,0 @@ -# NOTE: This workflow is overkill for most R packages -# check-standard.yaml is likely a better choice -# usethis::use_github_action("check-standard") will install it. -# -# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. -# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions -on: - push: - branches: - - main - - master - pull_request: - branches: - - main - - master - -name: R-CMD-check - -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-18.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest", http-user-agent: "R/4.0.0 (ubuntu-18.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" } - - {os: ubuntu-18.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v1 - with: - r-version: ${{ matrix.config.r }} - http-user-agent: ${{ matrix.config.http-user-agent }} - - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Restore R package cache - if: runner.os != 'Windows' - uses: actions/cache@v2 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies - if: runner.os == 'Linux' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "18.04"))') - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - 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: Check - env: - _R_CHECK_CRAN_INCOMING_: false - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} - - - name: Show testthat output - if: always() - run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true - shell: bash - - - name: Upload check results - if: failure() - uses: actions/upload-artifact@main - with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml deleted file mode 100644 index eeb5ec2..0000000 --- a/.github/workflows/pkgdown.yaml +++ /dev/null @@ -1,48 +0,0 @@ -on: - push: - branches: - - main - - master - -name: pkgdown - -jobs: - pkgdown: - runs-on: macos-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@v1 - - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Restore R package cache - uses: actions/cache@v2 - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - install.packages("pkgdown", type = "binary") - shell: Rscript {0} - - - name: Install package - run: R CMD INSTALL . - - - name: Deploy package - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)' diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml deleted file mode 100644 index e5edf9f..0000000 --- a/.github/workflows/pr-commands.yaml +++ /dev/null @@ -1,55 +0,0 @@ -on: - issue_comment: - types: [created] -name: Commands -jobs: - document: - if: startsWith(github.event.comment.body, '/document') - name: document - runs-on: macOS-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - steps: - - uses: actions/checkout@v2 - - uses: r-lib/actions/pr-fetch@v1 - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} - - uses: r-lib/actions/setup-r@v1 - - name: Install dependencies - run: Rscript -e 'install.packages(c("remotes", "roxygen2"))' -e 'remotes::install_deps(dependencies = TRUE)' - - name: Document - run: Rscript -e 'roxygen2::roxygenise()' - - name: commit - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - git add man/\* NAMESPACE - git commit -m 'Document' - - uses: r-lib/actions/pr-push@v1 - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} - style: - if: startsWith(github.event.comment.body, '/style') - name: style - runs-on: macOS-latest - env: - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - steps: - - uses: actions/checkout@v2 - - uses: r-lib/actions/pr-fetch@v1 - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} - - uses: r-lib/actions/setup-r@v1 - - name: Install dependencies - run: Rscript -e 'install.packages("styler")' - - name: Style - run: Rscript -e 'styler::style_pkg()' - - name: commit - run: | - git config --local user.email "actions@github.com" - git config --local user.name "GitHub Actions" - git add \*.R - git commit -m 'Style' - - uses: r-lib/actions/pr-push@v1 - with: - repo-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml new file mode 100644 index 0000000..5524630 --- /dev/null +++ b/.github/workflows/rworkflows.yml @@ -0,0 +1,62 @@ +name: rworkflows +'on': + push: + branches: + - master + - main + - devel + - RELEASE_** + pull_request: + branches: + - master + - main + - devel + - RELEASE_** +jobs: + rworkflows: + permissions: write-all + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + container: ${{ matrix.config.cont }} + strategy: + fail-fast: ${{ false }} + matrix: + config: + - os: ubuntu-latest + bioc: devel + r: auto + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: ~ + - os: ubuntu-latest + bioc: release + r: auto + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: ~ + - os: macOS-latest + bioc: release + r: auto + cont: ~ + rspm: ~ + - os: windows-latest + bioc: release + 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