From 4104bf9fd384c97a14b236500260033088cacc39 Mon Sep 17 00:00:00 2001 From: Levi Waldron Date: Tue, 6 Oct 2026 13:15:15 -0400 Subject: [PATCH] Drop --as-cran from R CMD check Bioconductor packages are checked against Bioconductor policy, not CRAN policy, so --as-cran produces NOTEs that are irrelevant here (and can fail the job under error_on: warning). BiocCheck already covers the Bioconductor-specific requirements. Also removes _R_CHECK_CRAN_INCOMING_REMOTE_, which only existed to suppress the remote incoming checks that --as-cran turns on. Co-Authored-By: Claude Opus 5 --- .github/workflows/bioccheck.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/bioccheck.yml b/.github/workflows/bioccheck.yml index 3a1d461..f28b72f 100644 --- a/.github/workflows/bioccheck.yml +++ b/.github/workflows/bioccheck.yml @@ -94,7 +94,6 @@ jobs: env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: 'true' GITHUB_PAT: ${{ github.token }} - _R_CHECK_CRAN_INCOMING_REMOTE_: 'false' CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} steps: - name: Checkout Repository @@ -134,7 +133,7 @@ jobs: allowed <- c("never", "note", "warning", "error") error_on <- Sys.getenv("RCMDCHECK_ERROR_ON", unset = "warning") if (!error_on %in% allowed) stop("Invalid error_on value: '", error_on, "'. Must be one of: ", paste(allowed, collapse = ", ")) - res <- rcmdcheck::rcmdcheck(".", args = c("--no-manual", "--as-cran"), error_on = error_on, check_dir = "check") + res <- rcmdcheck::rcmdcheck(".", args = "--no-manual", error_on = error_on, check_dir = "check") print(res) - name: Run BiocCheck