Merge pull request #127790 from PhDyellow/r_bioc_updater_revised

r-modules: R bioc updater revised

3 files changed, 28 insertions, 8 deletions

diff --git a/pkgs/development/r-modules/default.nix b/pkgs/development/r-modules/default.nix
index b1b1cd7d605..ed39d1c653a 100644
--- a/pkgs/development/r-modules/default.nix
+++ b/pkgs/development/r-modules/default.nix
@@ -43,21 +43,29 @@ let
   #
   deriveBioc = mkDerive {
     mkHomepage = {name, biocVersion, ...}: "https://bioconductor.org/packages/${biocVersion}/bioc/html/${name}.html";
-    mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz"
-                                             "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}/${name}_${version}.tar.gz"
-                                             "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz" ];
+    mkUrls = {name, version, biocVersion}: [
+      "mirror://bioc/${biocVersion}/bioc/src/contrib/${name}_${version}.tar.gz"
+      "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}/${name}_${version}.tar.gz"
+      "mirror://bioc/${biocVersion}/bioc/src/contrib/Archive/${name}_${version}.tar.gz"
+    ];
   };
   deriveBiocAnn = mkDerive {
     mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
-    mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz" ];
+    mkUrls = {name, version, biocVersion}: [
+      "mirror://bioc/${biocVersion}/data/annotation/src/contrib/${name}_${version}.tar.gz"
+    ];
   };
   deriveBiocExp = mkDerive {
     mkHomepage = {name, ...}: "http://www.bioconductor.org/packages/${name}.html";
-    mkUrls = {name, version, biocVersion}: [ "mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz" ];
+    mkUrls = {name, version, biocVersion}: [
+      "mirror://bioc/${biocVersion}/data/experiment/src/contrib/${name}_${version}.tar.gz"
+    ];
   };
   deriveCran = mkDerive {
     mkHomepage = {name, snapshot, ...}: "http://mran.revolutionanalytics.com/snapshot/${snapshot}/web/packages/${name}/";
-    mkUrls = {name, version, snapshot}: [ "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz" ];
+    mkUrls = {name, version, snapshot}: [
+      "http://mran.revolutionanalytics.com/snapshot/${snapshot}/src/contrib/${name}_${version}.tar.gz"
+    ];
   };
 
   # Overrides package definitions with nativeBuildInputs.
diff --git a/pkgs/development/r-modules/generate-r-packages.R b/pkgs/development/r-modules/generate-r-packages.R
index 1ac15ef79e7..f656fdca092 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 beb37827508..1c96cf05cb5 100644
--- a/pkgs/development/r-modules/generate-shell.nix
+++ b/pkgs/development/r-modules/generate-shell.nix
@@ -5,13 +5,18 @@ stdenv.mkDerivation {
 
   buildCommand = "exit 1";
 
-  buildInputs = [ wget ];
+  buildInputs = [
+    wget
+    cacert
+    nix
+  ];
 
   nativeBuildInputs = [
     (rWrapper.override {
       packages = with rPackages; [
         data_table
         parallel
+        BiocManager
       ];
     })
   ];