From c0861f4756fb0d24dd36655fa3f61c39f0e1f998 Mon Sep 17 00:00:00 2001 From: Levi Waldron Date: Sat, 3 Oct 2026 12:21:04 -0700 Subject: [PATCH 1/2] Install pkgdown before pkgdown::build_site() The reusable workflow installs remotes/rcmdcheck/BiocCheck/covr plus the package's declared dependencies, but nothing installs pkgdown, so the Build pkgdown step (release-branch pushes with enable_pkgdown) fails unless a calling package happens to Suggest it. Install it just before use. Flagged by Copilot review on waldronlab/curatedCRCData#5. Co-Authored-By: Claude Fable 5 --- .github/workflows/bioc-pr-cmdcheck-pkgdown.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml b/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml index ebecb49..c8cb256 100644 --- a/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml +++ b/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml @@ -182,6 +182,7 @@ jobs: && needs.set-matrix.outputs.is_release_branch == 'true' }} run: | + Rscript -e 'if (!requireNamespace("pkgdown", quietly = TRUE)) BiocManager::install("pkgdown", ask = FALSE)' PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site()' - name: Upload pkgdown artifact From 287523711d615ffd4d7126ad39aa00d7e0b0c3b4 Mon Sep 17 00:00:00 2001 From: Levi Waldron Date: Sat, 3 Oct 2026 12:25:36 -0700 Subject: [PATCH 2/2] Honor the CRAN input when installing pkgdown Set options(repos) from the CRAN env var before BiocManager::install, matching the workflow's other install steps. Flagged by Copilot. Co-Authored-By: Claude Fable 5 --- .github/workflows/bioc-pr-cmdcheck-pkgdown.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml b/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml index c8cb256..079cd9a 100644 --- a/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml +++ b/.github/workflows/bioc-pr-cmdcheck-pkgdown.yml @@ -182,7 +182,7 @@ jobs: && needs.set-matrix.outputs.is_release_branch == 'true' }} run: | - Rscript -e 'if (!requireNamespace("pkgdown", quietly = TRUE)) BiocManager::install("pkgdown", ask = FALSE)' + Rscript -e 'options(repos = c(CRAN = Sys.getenv("CRAN"))); if (!requireNamespace("pkgdown", quietly = TRUE)) BiocManager::install("pkgdown", ask = FALSE)' PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site()' - name: Upload pkgdown artifact