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Fix use_bioconductor = FALSE still hitting bioconductor.org on R 4.5+ #852

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Merged
gaborcsardi merged 3 commits into from
Mar 20, 2026
Merged

Fix use_bioconductor = FALSE still hitting bioconductor.org on R 4.5+ #852

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295ea38
Bug: `use_bioconductor = FALSE` still contacts bioconductor.org
SermetPekin Mar 17, 2026
eb27623
Revert accidental .gitignore change
SermetPekin Mar 17, 2026
9c0cdf2
Improve NEWS entry
gaborcsardi Mar 20, 2026
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4 changes: 4 additions & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
# pak (development version)

* Setting `use_bioconductor = FALSE` (i.e. the `PKG_USE_BIOCONDUCTOR`
env var, or the `pkg.use_bioconductor` option) now truly prevents
any network contact with Bioconductor.

# pak 0.9.2

* No user visible changes.
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2 changes: 1 addition & 1 deletion src/library/pkgcache/R/metadata-cache.R
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Expand Up @@ -1040,7 +1040,7 @@ extract_revdeps <- function(pkgs, packages, dependencies, recursive) {
cmc__get_repos <- function(repos, bioc, cran_mirror, r_version, auth = TRUE) {
repos[["CRAN"]] <- cran_mirror
repos <- unlist(repos)
bioc_names <- bioconductor$get_repos()
bioc_names <- if (bioc) bioconductor$get_repos() else character(0L)
res <- data_frame(
name = names(repos),
url = unname(repos),
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