From 989d2d2a7093b4dada15ee4cc64802dc04f324bf Mon Sep 17 00:00:00 2001 From: James Eapen Date: Wed, 3 Jul 2024 13:23:34 -0400 Subject: [PATCH] ci(pkgdown): install htslib, manually build iscream without pak; htslib needs to be in the same job as the R CMD INSTALL for R to find it --- .github/workflows/pkgdown.yaml | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 5bd9956..07f846f 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -29,21 +29,25 @@ jobs: with: use-public-rspm: true - - name: Install htslib - run: | - sudo apt-get update && sudo apt-get install -y libhts-dev - echo "-------------------HTSLIB-----------------------" - pkg-config --cflags --libs htslib - echo "------------------------------------------------" - - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::pkgdown, local::. + extra-packages: any::pkgdown needs: website - name: Check dev mode run: echo "$GITHUB_ENV" + - name: Install htslib iscream + run: | + sudo apt-get update + sudo apt-get install -y libhts-dev + echo "-------------------HTSLIB-----------------------" + pkg-config --cflags --libs htslib + echo "------------------------------------------------" + + - name: Install htslib iscream + run: R CMD INSTALL . + - name: Build site run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) shell: Rscript {0}