Merge pull request #171597 from NixOS/r-updates

R 4.2.0

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

@@ -14,11 +14,11 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "R";
-  version = "4.1.3";
+  version = "4.2.0";
 
   src = fetchurl {
     url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz";
-    sha256 = "sha256-Ff9bMzxhCUBgsqUunB2OxVzELdAp45yiKr2qkJUm/tY=";
+    sha256 = "sha256-OOq3cZt60JU4jwaqCQxaKyAnkZRd5g0+K7DqsfUJdIg=";
   };
 
   dontUseImakeConfigure = true;
@@ -31,6 +31,7 @@ stdenv.mkDerivation rec {
 
   patches = [
     ./no-usr-local-search-paths.patch
+    ./test-reg-packages.patch
   ];
 
   # Test of the examples for package 'tcltk' fails in Darwin sandbox. See:
@@ -90,7 +91,7 @@ stdenv.mkDerivation rec {
   postFixup = "echo ${which} > $out/nix-support/undetected-runtime-dependencies";
 
   doCheck = true;
-  preCheck = "export TZ=CET; bin/Rscript -e 'sessionInfo()'";
+  preCheck = "export HOME=$TMPDIR; export TZ=CET; bin/Rscript -e 'sessionInfo()'";
 
   enableParallelBuilding = true;
 

pkgs/applications/science/math/R/test-reg-packages.patch

@@ -0,0 +1,15 @@
+Upper bounds shifts due to extra warnings re. internet connectivity.
+
+diff --git a/tests/reg-packages.R b/tests/reg-packages.R
+index c9962ce..a40b0fa 100644
+--- a/tests/reg-packages.R
++++ b/tests/reg-packages.R
+@@ -260,7 +260,7 @@ stopifnot(exprs = {
+     (lenN <- length(print(iN <- grep("^[1-9][0-9]:", tlines)))) >= 2
+     iN - iw == seq_len(lenN) # these (3) lines come immediately after 'Warning',
+     ## and "related" to the some 'missing .. paren' above:
+-    8 <= print(iw - i) & iw - i <= 20 # see ~14
++    8 <= print(iw - i) & iw - i <= 22 # see ~14
+ }) ## failed in R <= 4.1.1
+
+

pkgs/development/r-modules/default.nix

@@ -389,7 +389,7 @@ let
     Rglpk = [ pkgs.glpk ];
     RGtk2 = [ pkgs.gtk2.dev ];
     rhdf5 = [ pkgs.zlib ];
-    Rhdf5lib = [ pkgs.zlib.dev ];
+    Rhdf5lib = with pkgs; [ zlib.dev hdf5.dev ];
     Rhpc = with pkgs; [ zlib bzip2.dev icu xz.dev mpi pcre.dev ];
     Rhtslib = with pkgs; [ zlib.dev automake autoconf bzip2.dev xz.dev curl.dev ];
     rjags = [ pkgs.jags ];
@@ -997,10 +997,6 @@ let
       patchPhase = "patchShebangs configure";
     });
 
-    Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
-      patches = [ ./patches/Rhdf5lib.patch ];
-    });
-
     rJava = old.rJava.overrideDerivation (attrs: {
       preConfigure = ''
         export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
@@ -1300,6 +1296,10 @@ let
       RGL_USE_NULL = "true";
     });
 
+    Rhdf5lib = old.Rhdf5lib.overrideDerivation (attrs: {
+      propagatedBuildInputs = attrs.propagatedBuildInputs ++ [ pkgs.hdf5.dev ];
+    });
+
     RNifti = old.RNifti.overrideDerivation (attrs: {
       patches = [ ./patches/RNifti.patch ];
     });

pkgs/top-level/all-packages.nix

@@ -21482,7 +21482,6 @@ with pkgs;
     withRecommendedPackages = false;
     inherit (darwin.apple_sdk.frameworks) Cocoa Foundation;
     inherit (darwin) libobjc;
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
   };
 
   rWrapper = callPackage ../development/r-modules/wrapper.nix {