R: don't install the "recommended packages"

These packages come with R, but if we install them as part of this build, then
we cannot update them without re-building R as well. Instead, we add those
packages to the R environment through the r-wrapper. This means that
recommended packages can be updated in cran-packgaes.nix, and those updates
have an effect on the installation without re-building R itself.

pkgs/applications/science/math/R/default.nix

@@ -2,6 +2,7 @@
 , libjpeg, libpng, libtiff, ncurses, pango, pcre, perl, readline, tcl
 , texLive, tk, xz, zlib, less, texinfo, graphviz, icu, pkgconfig, bison
 , imake, which, jdk, atlas
+, withRecommendedPackages ? true
 }:
 
 stdenv.mkDerivation rec {
@@ -23,6 +24,7 @@ stdenv.mkDerivation rec {
   preConfigure = ''
     configureFlagsArray=(
       --disable-lto
+      --with${stdenv.lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages
       --with-blas="-L${atlas}/lib -lf77blas -latlas"
       --with-lapack="-L${liblapack}/lib -llapack"
       --with-readline

pkgs/development/r-modules/wrapper/default.nix

@@ -1,9 +1,9 @@
-{ stdenv, R, packages, makeWrapper }:
+{ stdenv, R, makeWrapper, recommendedPackages, packages }:
 
 stdenv.mkDerivation {
   name = R.name + "-wrapper";
 
-  buildInputs = [makeWrapper R] ++ packages;
+  buildInputs = [makeWrapper R] ++ recommendedPackages ++ packages;
 
   unpackPhase = ":";
 

pkgs/top-level/all-packages.nix

@@ -6431,9 +6431,15 @@ let
   R = callPackage ../applications/science/math/R {
     inherit (xlibs) libX11 libXt;
     texLive = texLiveAggregationFun { paths = [ texLive texLiveExtra ]; };
+    withRecommendedPackages = false;
   };
 
-  rWrapper = callPackage ../development/r-modules/generic/wrapper.nix {
+  rWrapper = callPackage ../development/r-modules/wrapper {
+    # Those packages are usually installed as part of the R build.
+    recommendedPackages = with rPackages; [ MASS lattice Matrix nlme
+      survival boot cluster codetools foreign KernSmooth rpart class
+      nnet spatial mgcv ];
+    # Override this attribute to register additional libraries.
     packages = [];
   };