From 84af7caecb5f60e1706f83d1d2a40a871344e9b5 Mon Sep 17 00:00:00 2001 From: Stefanie Peschel Date: Thu, 7 Nov 2024 15:56:23 +0100 Subject: [PATCH] docs: update pkgdown.yaml --- .github/workflows/pkgdown.yaml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 4bbce75..121f6ba 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -1,5 +1,9 @@ # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +# By Stefanie Peschel: Adapted to install Bioconductor packages in advance + +name: pkgdown.yaml + on: push: branches: [main, master] @@ -9,8 +13,6 @@ on: types: [published] workflow_dispatch: -name: pkgdown.yaml - permissions: read-all jobs: @@ -34,9 +36,14 @@ jobs: - uses: r-lib/actions/setup-r-dependencies@v2 with: - extra-packages: any::pkgdown, local::. + extra-packages: any::pkgdown, any::BiocManager, local::. needs: website + - name: Install Bioconductor dependencies + run: | + Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' + Rscript -e 'BiocManager::install(c("metagenomeSeq", "Biobase", "phyloseq"))' + - name: Build site run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) shell: Rscript {0}