diff --git a/.github/workflows/BioC-check.yaml b/.github/workflows/BioC-check.yaml index cd13eff..70ad09e 100644 --- a/.github/workflows/BioC-check.yaml +++ b/.github/workflows/BioC-check.yaml @@ -25,17 +25,17 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: rcmdcheck, BiocManager @@ -49,4 +49,4 @@ jobs: `no-check-bioc-help` = TRUE ) shell: Rscript {0} - + \ No newline at end of file diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index d9de82f..f3e835d 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -29,33 +29,31 @@ jobs: - {os: windows-latest, r: '3.6'} # Use older ubuntu to maximise backward compatibility - - {os: ubuntu-18.04, r: 'devel', http-user-agent: 'release'} - - {os: ubuntu-18.04, r: 'release'} - - {os: ubuntu-18.04, r: 'oldrel-1'} - - {os: ubuntu-18.04, r: 'oldrel-2'} - - {os: ubuntu-18.04, r: 'oldrel-3'} - - {os: ubuntu-18.04, r: 'oldrel-4'} + - {os: ubuntu-20.04, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-20.04, r: 'release'} + - {os: ubuntu-20.04, r: 'oldrel-1'} + - {os: ubuntu-20.04, r: 'oldrel-2'} env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-pandoc@v1 + - uses: r-lib/actions/setup-pandoc@v2 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} http-user-agent: ${{ matrix.config.http-user-agent }} use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: rcmdcheck + extra-packages: rcmdcheck, knitr - - uses: r-lib/actions/check-r-package@v1 + - uses: r-lib/actions/check-r-package@v2 - name: Show testthat output if: always() @@ -67,4 +65,4 @@ jobs: uses: actions/upload-artifact@main with: name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + path: check \ No newline at end of file diff --git a/.github/workflows/lint.yaml b/.github/workflows/lint.yaml index 6388f75..7f8955e 100644 --- a/.github/workflows/lint.yaml +++ b/.github/workflows/lint.yaml @@ -14,16 +14,16 @@ jobs: env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-r@v2 with: use-public-rspm: true - - uses: r-lib/actions/setup-r-dependencies@v1 + - uses: r-lib/actions/setup-r-dependencies@v2 with: extra-packages: lintr - name: Lint - run: lintr::lint_package() - shell: Rscript {0} + run: lintr::lint_package(linters = lintr::linters_with_defaults(object_name_linter = lintr::object_name_linter("camelCase"))) + shell: Rscript {0} \ No newline at end of file