neuron: fix on clang 3.8 and above

This is in preparation for upgrading Darwin stdenv to LLVM 4
NixOS · Mar 21, 2017 · 7ad3fd7 · 7ad3fd7 · copumpkin · Mar 21, 2017
1 parent 93005b8
commit 7ad3fd7
Showing 1 changed file with 25 additions and 16 deletions.
diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix
@@ -1,20 +1,20 @@
-{ stdenv 
-, fetchurl 
+{ stdenv
+, fetchurl
 , pkgconfig
 , automake
 , autoconf
 , libtool
 , ncurses
 , readline
 , which
-, python ? null 
+, python ? null
 , mpi ? null
 }:
 
 stdenv.mkDerivation rec {
   name = "neuron-${version}";
   version = "7.4";
-  
+
   nativeBuildInputs = [ which pkgconfig automake autoconf libtool ];
   buildInputs = [ ncurses readline python mpi  ];
 
@@ -25,46 +25,55 @@ stdenv.mkDerivation rec {
 
   patches = (stdenv.lib.optional (stdenv.isDarwin) [ ./neuron-carbon-disable.patch ]);
 
+  # With LLVM 3.8 and above, clang (really libc++) gets upset if you attempt to redefine these...
+  postPatch = stdenv.lib.optionalString stdenv.cc.isClang ''
+    substituteInPlace src/gnu/neuron_gnu_builtin.h \
+      --replace 'double abs(double arg);' "" \
+      --replace 'float abs(float arg);' "" \
+      --replace 'short abs(short arg);' "" \
+      --replace 'long abs(long arg);' ""
+  '';
+
   enableParallelBuilding = true;
 
   ## neuron install by default everything under prefix/${host_arch}/*
-  ## override this to support nix standard file hierarchy 
+  ## override this to support nix standard file hierarchy
   ## without issues: install everything under prefix/
   preConfigure = ''
     ./build.sh
-    export prefix="''${prefix} --exec-prefix=''${out}" 
+    export prefix="''${prefix} --exec-prefix=''${out}"
   '';
 
   configureFlags = with stdenv.lib;
                     [ "--without-x" "--with-readline=${readline}" ]
                     ++  optionals (python != null)  [ "--with-nrnpython=${python.interpreter}" ]
-                    ++ (if mpi != null then ["--with-mpi" "--with-paranrn"] 
+                    ++ (if mpi != null then ["--with-mpi" "--with-paranrn"]
                         else ["--without-mpi"]);
-                        
-                        
+
+
   postInstall = stdenv.lib.optionals (python != null) [ ''
     ## standardise python neuron install dir if any
     if [[ -d $out/lib/python ]]; then
         mkdir -p ''${out}/${python.sitePackages}
         mv ''${out}/lib/python/*  ''${out}/${python.sitePackages}/
     fi
   ''];
-  
-  propagatedBuildInputs = [ readline ncurses which libtool ];  
+
+  propagatedBuildInputs = [ readline ncurses which libtool ];
 
   meta = with stdenv.lib; {
     description = "Simulation environment for empirically-based simulations of neurons and networks of neurons";
 
-    longDescription = "NEURON is a simulation environment for developing and exercising models of 
-                neurons and networks of neurons. It is particularly well-suited to problems where 
-                cable properties of cells play an important role, possibly including extracellular 
-                potential close to the membrane), and where cell membrane properties are complex, 
+    longDescription = "NEURON is a simulation environment for developing and exercising models of
+                neurons and networks of neurons. It is particularly well-suited to problems where
+                cable properties of cells play an important role, possibly including extracellular
+                potential close to the membrane), and where cell membrane properties are complex,
                 involving many ion-specific channels, ion accumulation, and second messengers";
 
     license     = licenses.bsd3;
     homepage    = http://www.neuron.yale.edu/neuron;
     maintainers = [ maintainers.adev ];
     platforms   = platforms.all;
-  };  
+  };
 }