Fix pkgBiocRevDeps(recursive = TRUE) leaking forward dependencies

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: BiocPkgTools
 Type: Package
 Title: Collection of simple tools for learning about Bioconductor Packages
-Version: 1.31.7
-Date: 2026-05-14
+Version: 1.31.8
+Date: 2026-06-25
 Authors@R: c( 
     person("Shian", "Su", role=c("aut", "ctb"), email = "su.s@wehi.edu.au"),
     person("Lori", "Shepherd", role="ctb", email = "Lori.Shepherd@roswellpark.org"),

NEWS

@@ -12,6 +12,10 @@ SIGNIFICANT USER-VISIBLE CHANGES
 
 BUG FIXES AND MINOR IMPROVEMENTS
 
+    o `pkgBiocRevDeps(recursive = TRUE)` no longer returns forward
+      (non-reverse) dependencies. Recursion now follows only strong
+      dependencies, avoiding the `Suggests` / `Enhances` explosion that pulled
+      in nearly the entire repository (#81).
     o Switch `generateBiocPkgDOI` to use `httr2` instead of `httr`
     o Switch `repositoryStats` to use `httr2` instead of `httr`
     o Support `match.arg` for `event` argument in `generateBiocPkgDOI`

R/pkgBiocDeps.R

@@ -98,8 +98,12 @@ pkgBiocRevDeps <- function(
     biocdb <- utils::available.packages(repos = repo)
 
     if (recursive)
+        ## Only recurse over strong dependencies. Recursing reverse
+        ## dependencies over 'Suggests' / 'Enhances' explodes to nearly the
+        ## entire repository (e.g. thousands of packages 'Suggests' knitr),
+        ## which pulls in forward (non-reverse) dependencies. See issue #81.
         res <- tools::package_dependencies(
-            pkg, all_db, reverse = TRUE, which = which, recursive = recursive
+            pkg, all_db, reverse = TRUE, which = which, recursive = "strong"
         )[[pkg]]
     else
         res <- lapply(which, function(ofwhich) {

tests/testthat/test-pkgBiocDeps.R

@@ -0,0 +1,26 @@
+test_that("pkgBiocRevDeps(recursive = TRUE) returns only reverse deps", {
+    ## Regression test for issue #81: recursive reverse dependencies must not
+    ## leak forward (non-reverse) dependencies. Recursing reverse dependencies
+    ## over 'Suggests' / 'Enhances' previously exploded to nearly the entire
+    ## repository, pulling in forward dependencies of the queried package.
+    pkg <- "Rarr"
+
+    db <- utils::available.packages(repos = BiocManager::repositories())
+    skip_if_not(pkg %in% rownames(db), "Rarr not available in repositories")
+
+    ## Forward dependencies that are not themselves reverse dependencies should
+    ## never appear in the recursive reverse-dependency result.
+    fwd <- tools::package_dependencies(pkg, db, which = "all")[[pkg]]
+    rev1 <- tools::package_dependencies(
+        pkg, db, reverse = TRUE, which = "all"
+    )[[pkg]]
+    fwd_only <- setdiff(fwd, rev1)
+
+    res <- pkgBiocRevDeps(pkg, recursive = TRUE, only.bioc = FALSE)
+    rec <- as.character(res)
+
+    expect_false(any(fwd_only %in% rec))
+    ## The explosion produced tens of thousands of packages; a sane recursive
+    ## reverse-dependency set is a small fraction of the repository.
+    expect_lt(length(rec), nrow(db) / 2)
+})