sage: preload openblasCompat

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

@@ -32,8 +32,9 @@ let
 
       # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
       sagelib = self.callPackage ./sagelib.nix {
-        inherit flint ecl arb;
-        inherit sage-src pynac singular;
+        inherit ecl;
+        inherit sage-src;
+        pynac = pkgs.pynac; # *not* python.pkgs.pynac
         linbox = pkgs.linbox.override { withSage = true; };
       };
     };
@@ -59,7 +60,6 @@ let
   # the files its looking fore are located. Also see `sage-env`.
   env-locations = callPackage ./env-locations.nix {
     inherit pari_data ecl;
-    inherit singular;
     cysignals = python.pkgs.cysignals;
     three = nodePackages.three;
     mathjax = nodePackages.mathjax;
@@ -70,7 +70,7 @@ let
   sage-env = callPackage ./sage-env.nix {
     sagelib = python.pkgs.sagelib;
     inherit env-locations;
-    inherit python ecl singular palp flint pynac pythonEnv;
+    inherit python ecl palp pythonEnv;
     pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
   };
 
@@ -84,7 +84,6 @@ let
   sage-with-env = callPackage ./sage-with-env.nix {
     inherit pythonEnv;
     inherit sage-env;
-    inherit pynac singular;
     pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
     three = nodePackages.three;
   };
@@ -124,19 +123,6 @@ let
     ignoreCollisions = true;
   } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
 
-  arb = pkgs.arb.override { inherit flint; };
-
-  singular = pkgs.singular.override { inherit flint; };
-
-  # *not* to confuse with the python package "pynac"
-  pynac = pkgs.pynac.override { inherit singular flint; };
-
-  # With openblas (64 bit), the tests fail the same way as when sage is build with
-  # openblas instead of openblasCompat. Apparently other packages somehow use flints
-  # blas when it is available. Alternative would be to override flint to use
-  # openblasCompat.
-  flint = pkgs.flint.override { withBlas = false; };
-
   # Multiple palp dimensions need to be available and sage expects them all to be
   # in the same folder.
   palp = symlinkJoin {

pkgs/applications/science/math/sage/sage-env.nix

@@ -163,6 +163,17 @@ writeTextFile rec {
 
   # for find_library
     export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}:$DYLD_LIBRARY_PATH"
+
+    # Make sure the correct openblas library is picked up. Without this, sage
+    # can either end up using flints openblas (which is not openblasCopmat, thus
+    # leading to the issues described in https://trac.sagemath.org/ticket/26000)
+    # or R's blas, leading to the issues described in
+    # https://bitbucket.org/rpy2/rpy2/issues/491.
+    # The first issue could alternatively be solved by overriding flint's
+    # openblas dependency and the second one is effectively solved by loading
+    # rpy2 lazily in sage. Preloading explicitly makes all the headaches go
+    # away much easier and more future proof though.
+    export LD_PRELOAD="${openblasCompat}/lib/libopenblas.so:$LD_PRELOAD"
   '';
 } // {
   lib = sagelib; # equivalent of `passthru`, which `writeTextFile` doesn't support