diff --git a/pkgs/applications/science/machine-learning/shogun/default.nix b/pkgs/applications/science/machine-learning/shogun/default.nix
index e1e7c4d8a0ae..fae5f8a00782 100644
--- a/pkgs/applications/science/machine-learning/shogun/default.nix
+++ b/pkgs/applications/science/machine-learning/shogun/default.nix
@@ -191,7 +191,7 @@ stdenv.mkDerivation (finalAttrs: {
       (lib.cmakeBool "USE_SVMLIGHT" withSvmLight)
     ];
 
-  CXXFLAGS = "-faligned-new";
+  env.CXXFLAGS = "-faligned-new";
 
   doCheck = true;