Only add BiocManager as dep when used (#1408)

Includes new `renv_tests_scope_system_cache()` to make it easier to install packages from the system cache to speed up performance in tests.

Fixes #1356

R/status.R

@@ -160,11 +160,11 @@ renv_status_check_synchronized <- function(project,
                                            library,
                                            packages)
 {
-  # projects will implicitly depend on BiocManager if any Bioconductor
-  # packages are in use
-  sources <- extract_chr(library, "Source")
+  # projects will implicitly depend on BiocManager & BiocVersion if any
+  # Bioconductor packages are in use
+  sources <- extract_chr(keep(library, packages), "Source")
   if ("Bioconductor" %in% sources)
-    packages <- unique(c(packages, "BiocManager"))
+    packages <- union(packages, "BiocManager")
 
   # missing dependencies -------------------------------------------------------
   # Must return early because `packages` will be incomplete making later

tests/testthat/_snaps/bioconductor.md

@@ -0,0 +1,20 @@
+# Bioconductor packages add BiocManager as a dependency
+
+    Code
+      status()
+    Output
+      The following package(s) are installed, but not recorded in the lockfile:
+      
+      - BiocGenerics [<version>]
+      - BiocManager  [<version>]
+      
+      Use `renv::snapshot()` to add these packages to the lockfile.
+      
+
+---
+
+    Code
+      status()
+    Output
+      * The project is already synchronized with the lockfile.
+

tests/testthat/helper-scope.R

@@ -57,3 +57,10 @@ renv_tests_scope_repos <- function(envir = parent.frame()) {
   )
 
 }
+
+renv_tests_scope_system_cache <- function(envir = parent.frame()) {
+  skip_on_cran()
+
+  renv_scope_options(repos = c(CRAN = "https://cloud.r-project.org"), envir = envir)
+  renv_scope_envvars(RENV_PATHS_ROOT = renv_paths_root_default_impl(), envir = envir)
+}

tests/testthat/helper-snapshot.R

@@ -1,7 +1,7 @@
-expect_snapshot <- function(...) {
+expect_snapshot <- function(..., transform = strip_dirs) {
   renv_scope_options(renv.verbose = TRUE)
 
-  testthat::expect_snapshot(..., transform = strip_dirs)
+  testthat::expect_snapshot(..., transform = transform)
 }
 
 strip_dirs <- function(x) {

tests/testthat/test-bioconductor.R

@@ -9,7 +9,10 @@ test_that("packages can be installed, restored from Bioconductor", {
   renv_tests_scope("Biobase")
   renv_scope_options(repos = c(CRAN = "https://cloud.r-project.org"))
 
-  install.packages("BiocManager", quiet = TRUE)
+  local({
+    renv_tests_scope_system_cache()
+    install("BiocManager")
+  })
   suppressMessages(BiocManager::install("Biobase", quiet = TRUE, update = FALSE, ask = FALSE))
 
   expect_true(renv_package_installed("BiocManager"))
@@ -87,3 +90,31 @@ test_that("we can restore a lockfile using multiple Bioconductor releases", {
   expect_true(renv_package_version("BiocGenerics") == "0.38.0")
 
 })
+
+test_that("Bioconductor packages add BiocManager as a dependency", {
+
+  renv_tests_scope()
+  init()
+  local({
+    renv_tests_scope_system_cache()
+    install("BiocManager")
+    install("bioc::BiocGenerics")
+  })
+
+  snapshot()
+  writeLines("library(BiocGenerics)", "dependencies.R")
+
+  expect_snapshot(
+    status(),
+    transform = function(x) gsub("\\[.*\\]", "[<version>]", x)
+  )
+  snap <- snapshot()
+  expect_setequal(names(snap$Packages), c("BiocManager", "BiocGenerics"))
+
+  # And it goes away when we remove the dependency
+  unlink("dependencies.R")
+  snap <- snapshot()
+  expect_named(snap$Packages, character())
+  expect_snapshot(status())
+
+})