From 62036bc246cfea8adf96710d05edc228c68f421f Mon Sep 17 00:00:00 2001 From: Claude Date: Sun, 26 Jul 2026 16:12:16 +0000 Subject: [PATCH] ci: let pak ignore Bioconductor graph on R < 4.4 'graph' is an optional Enhances dependency published only on Bioconductor. The Bioconductor releases matching R 4.2 / 4.3 (graph 3.16 / 3.18) are archived and return HTTP 404, so pak dependency resolution aborts on those jobs before anything is built. Use pak's documented downstream-package parameter instead of touching the workflows: Config/gha/extra-packages: graph=?ignore-before-r=4.4.0 The install action already forwards Config/gha/extra-packages to setup-r-dependencies, and pak parses graph=?ignore-before-r=4.4.0 as a 'param' reference that applies to the graph dependency pulled in via deps::., ignoring it on R older than 4.4.0 and keeping it on 4.4 and newer. This replaces an earlier attempt that set PKG_USE_BIOCONDUCTOR=false from a workflow step. That approach did not work: disabling Bioconductor only turned the 404 into "Can't find package called graph", because pak does not drop an unavailable soft dependency unless it is explicitly ignored. It also broke the Windows jobs, which could not run the multi-line Rscript -e invocation. Co-Authored-By: Claude Opus 5 Claude-Session: https://claude.ai/code/session_019E6CUgb5aFw6uvWXztcHgV --- DESCRIPTION | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 01ce0221c94..d7c2ee29151 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -73,6 +73,13 @@ Config/build/compilation-database: false Config/build/never-clean: true Config/comment/compilation-database: Generate manually with pkgload:::generate_db() for faster pkgload::load_all() +Config/gha/extra-packages: graph=?ignore-before-r=4.4.0 +Config/comment/gha/extra-packages: graph is an optional Enhances + dependency published only on Bioconductor. The Bioconductor releases + matching R 4.2 and R 4.3 (graph 3.16 / 3.18) are archived and return + HTTP 404, which aborts pak dependency resolution on those jobs. The + ?ignore-before-r pak parameter makes pak ignore graph on R older than + 4.4.0, where a published release still exists. Config/Needs/build: devtools, irlba, pkgconfig Config/Needs/coverage: covr Config/Needs/roxygen2: r-lib/roxygen2, igraph/igraph.r2cdocs,