From 1cee9657f320eda70ae780ca7e587620674128c2 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 30 Jul 2026 22:18:44 +0000 Subject: [PATCH 1/2] Initial plan From 68f72937f40e55c5692d0fc7466103012a201c70 Mon Sep 17 00:00:00 2001 From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com> Date: Thu, 30 Jul 2026 22:20:30 +0000 Subject: [PATCH 2/2] Change jammy to noble in workflow CRAN repository URLs --- .github/workflows/bioccheck.yml | 4 ++-- workflow_comparison.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/bioccheck.yml b/.github/workflows/bioccheck.yml index eec45b8..3a1d461 100644 --- a/.github/workflows/bioccheck.yml +++ b/.github/workflows/bioccheck.yml @@ -106,7 +106,7 @@ jobs: id: get-deps shell: Rscript {0} run: | - options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest", BiocManager::repositories())) + options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/noble/latest", BiocManager::repositories())) if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") deps <- remotes::dev_package_deps(".", dependencies = TRUE) saveRDS(deps, ".github/depends.Rds") @@ -122,7 +122,7 @@ jobs: - name: Install Package Dependencies shell: Rscript {0} run: | - options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest", BiocManager::repositories())) + options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/noble/latest", BiocManager::repositories())) remotes::install_local(".", dependencies = TRUE, Ncpus = parallel::detectCores()) BiocManager::install(c("rcmdcheck", "BiocCheck", "covr", "pkgdown", "cyclocomp"), Ncpus = parallel::detectCores()) diff --git a/workflow_comparison.md b/workflow_comparison.md index 7623b7e..0a2eaca 100644 --- a/workflow_comparison.md +++ b/workflow_comparison.md @@ -184,7 +184,7 @@ Below is the complete unified diff comparing `waldronlab/bioc-pr-cmdcheck-pkgdow + id: get-deps shell: Rscript {0} + run: | -+ options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest", BiocManager::repositories())) ++ options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/noble/latest", BiocManager::repositories())) + if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") + deps <- remotes::dev_package_deps(".", dependencies = TRUE) + saveRDS(deps, ".github/depends.Rds") @@ -213,7 +213,7 @@ Below is the complete unified diff comparing `waldronlab/bioc-pr-cmdcheck-pkgdow + - name: Install Package Dependencies shell: Rscript {0} + run: | -+ options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/latest", BiocManager::repositories())) ++ options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/noble/latest", BiocManager::repositories())) + remotes::install_local(".", dependencies = TRUE, Ncpus = parallel::detectCores()) + BiocManager::install(c("rcmdcheck", "BiocCheck", "covr", "pkgdown"), Ncpus = parallel::detectCores())