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neuron: fix on clang 3.8 and above

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This is in preparation for upgrading Darwin stdenv to LLVM 4
This commit is contained in:
Dan Peebles 2017-03-21 01:00:18 -04:00
parent 93005b82dc
commit 7ad3fd7ca7
1 changed files with 25 additions and 16 deletions
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41
pkgs/applications/science/biology/neuron/default.nix
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@ -1,5 +1,5 @@
{ stdenv
, fetchurl
{ stdenv
, fetchurl
, pkgconfig
, automake
, autoconf
@ -7,14 +7,14 @@
, ncurses
, readline
, which
, python ? null
, python ? null
, mpi ? null
}:
stdenv.mkDerivation rec {
name = "neuron-${version}";
version = "7.4";
nativeBuildInputs = [ which pkgconfig automake autoconf libtool ];
buildInputs = [ ncurses readline python mpi ];
@ -25,23 +25,32 @@ stdenv.mkDerivation rec {
patches = (stdenv.lib.optional (stdenv.isDarwin) [ ./neuron-carbon-disable.patch ]);
# With LLVM 3.8 and above, clang (really libc++) gets upset if you attempt to redefine these...
postPatch = stdenv.lib.optionalString stdenv.cc.isClang ''
substituteInPlace src/gnu/neuron_gnu_builtin.h \
--replace 'double abs(double arg);' "" \
--replace 'float abs(float arg);' "" \
--replace 'short abs(short arg);' "" \
--replace 'long abs(long arg);' ""
'';
enableParallelBuilding = true;
## neuron install by default everything under prefix/${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 $out/lib/python ]]; then
@ -49,22 +58,22 @@ stdenv.mkDerivation rec {
mv ''${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;
};
};
}