From 29fdc0ce2d98641fc1ae0ce3057dbc7fd1bdd3d6 Mon Sep 17 00:00:00 2001
From: Phil Dyer <phildyer@protonmail.com>
Date: Wed, 15 Sep 2021 11:09:17 +1000
Subject: [PATCH] rPackages: autoset bioconductor ver to match R ver

BioConductor releases are tied to specific R releases.

Updating the package set now automatically selects the
correct version of bioconductor to match the current version of
R.
---
 pkgs/development/r-modules/generate-r-packages.R | 9 ++++++++-
 pkgs/development/r-modules/generate-shell.nix    | 1 +
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/pkgs/development/r-modules/generate-r-packages.R b/pkgs/development/r-modules/generate-r-packages.R
index da9e0970b0f4..50b2d3b5f9ec 100755
--- a/pkgs/development/r-modules/generate-r-packages.R
+++ b/pkgs/development/r-modules/generate-r-packages.R
@@ -1,9 +1,16 @@
 #!/usr/bin/env Rscript
 library(data.table)
 library(parallel)
+library(BiocManager)
 cl <- makeCluster(10)
 
-biocVersion <- 3.12
+biocVersion <- BiocManager:::.version_map()
+biocVersion <- biocVersion[biocVersion$R == getRversion()[, 1:2],c("Bioc", "BiocStatus")]
+if ("release" %in% biocVersion$BiocStatus) {
+  biocVersion <-  as.numeric(as.character(biocVersion[biocVersion$BiocStatus == "release", "Bioc"]))
+} else {
+  biocVersion <-  max(as.numeric(as.character(biocVersion$Bioc)))
+}
 snapshotDate <- Sys.Date()-1
 
 mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/bioc/src/contrib/")
diff --git a/pkgs/development/r-modules/generate-shell.nix b/pkgs/development/r-modules/generate-shell.nix
index beb378275087..9719a61f4427 100644
--- a/pkgs/development/r-modules/generate-shell.nix
+++ b/pkgs/development/r-modules/generate-shell.nix
@@ -12,6 +12,7 @@ stdenv.mkDerivation {
       packages = with rPackages; [
         data_table
         parallel
+        BiocManager
       ];
     })
   ];