Fix pkgBiocRevDeps(recursive = TRUE) leaking forward dependencies#82
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Recursing reverse dependencies over 'Suggests' / 'Enhances' edges explodes to nearly the entire repository (e.g. thousands of packages 'Suggests' knitr), which pulled in the queried package's own forward (non-reverse) dependencies. Restrict the recursion to strong dependencies so only genuine reverse dependencies are returned. For Rarr this reduces the recursive result from 25,613 packages to 4. Adds a regression test and bumps the version with a NEWS entry. Fixes #81 Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…ve-revdeps # Conflicts: # DESCRIPTION # NEWS
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Problem
pkgBiocRevDeps("Rarr", recursive = TRUE)returned 25,613 packages — essentially the entire CRAN+Bioconductor repository — including "Suggests" and "Enhances" dependencies of the queried package such ascurl,jsonlite,knitr, andrmarkdown.Fixes #81.
Root cause
The recursive branch passed
recursive = TRUEtotools::package_dependencies(). With the defaultwhich = "all", the reverse recursion followsSuggests/Enhancesedges. Those edges form a near-fully-connected graph (thousands of packagesSuggestsknitr/testthat/rmarkdown), so recursing reverse over them closes over almost the whole repository.Fix
Restrict the recursion to strong dependencies (
recursive = "strong"). Level-1 reverse deps still honor the user'swhich(a package that merelySuggeststhe target still counts), but recursion only propagates throughDepends/Imports/LinkingTo— the standard "what would break if this package broke" semantics.Test
Adds
tests/testthat/test-pkgBiocDeps.R, a regression test asserting the result is a small fraction of the repository.