From 80d523ae1e6581598bdd7f5ed0fad9f76feed54c Mon Sep 17 00:00:00 2001 From: PopeRaj <51174148+PopeRaj@users.noreply.github.com> Date: Wed, 24 May 2023 16:46:53 -0400 Subject: [PATCH 1/3] Edited workflow yaml files to change versions --- .github/workflows/BioC-check.yaml | 10 +++++----- .github/workflows/R-CMD-check.yaml | 24 +++++++++++------------- .github/workflows/lint.yaml | 10 +++++----- 3 files changed, 21 insertions(+), 23 deletions(-) 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 From 6b4db2cb024c49c47abb1c7b375844b7962163c3 Mon Sep 17 00:00:00 2001 From: PopeRaj <51174148+PopeRaj@users.noreply.github.com> Date: Wed, 24 May 2023 16:52:33 -0400 Subject: [PATCH 2/3] Reverted BioC yaml due to permission access for pushing to origin --- .github/workflows/BioC-check.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/BioC-check.yaml b/.github/workflows/BioC-check.yaml index 70ad09e..cd13eff 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@v3 + - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-pandoc@v2 + - uses: r-lib/actions/setup-pandoc@v1 - - uses: r-lib/actions/setup-r@v2 + - uses: r-lib/actions/setup-r@v1 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@v2 + - uses: r-lib/actions/setup-r-dependencies@v1 with: extra-packages: rcmdcheck, BiocManager @@ -49,4 +49,4 @@ jobs: `no-check-bioc-help` = TRUE ) shell: Rscript {0} - \ No newline at end of file + From 3d781a80178b8f0a7e15e3128305dcdbf7dfbfbc Mon Sep 17 00:00:00 2001 From: PopeRaj <51174148+PopeRaj@users.noreply.github.com> Date: Wed, 24 May 2023 17:02:24 -0400 Subject: [PATCH 3/3] updated token access and reverted BioC yaml --- .github/workflows/BioC-check.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) 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