From 83a01c36f242228ea05a0f017c1593fb82f28f8e Mon Sep 17 00:00:00 2001 From: Ilia Kats Date: Mon, 11 Sep 2023 16:17:23 +0200 Subject: [PATCH] CI: install SeuratData after setup-r-dependencies setup-r-dependencies installs pre-built binary packages even on Linux --- .github/workflows/R-CMD-check.yaml | 8 ++++---- .github/workflows/pkgdown.yaml | 10 +++++----- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index caeed1e..f8bc480 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -37,14 +37,14 @@ jobs: if: runner.os == 'macOS' run: brew install hdf5 + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: rcmdcheck + - name: Install SeuratData if: always() run: Rscript -e "install.packages(c('remotes', 'Seurat'), repos = 'http://cran.us.r-project.org'); remotes:::install_github('satijalab/seurat-data')" shell: bash - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: rcmdcheck - uses: r-lib/actions/check-r-package@v2 diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index dfeaadd..d168452 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -8,7 +8,7 @@ name: pkgdown jobs: pkgdown: - runs-on: macOS-latest + runs-on: ubuntu-latest env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: @@ -20,14 +20,14 @@ jobs: with: use-public-rspm: true + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::pkgdown, local::. + - name: Install SeuratData if: always() run: Rscript -e "install.packages(c('remotes', 'Seurat'), repos = 'http://cran.us.r-project.org'); remotes:::install_github('satijalab/seurat-data')" shell: bash - - - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: any::pkgdown - name: Build site run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)