Merge master into staging-next

7 files changed, 21 insertions, 55 deletions

diff --git a/pkgs/applications/science/math/colpack/default.nix b/pkgs/applications/science/math/colpack/default.nix
index e62df7f11cc..94e0a44226d 100644
--- a/pkgs/applications/science/math/colpack/default.nix
+++ b/pkgs/applications/science/math/colpack/default.nix
@@ -25,6 +25,7 @@ stdenv.mkDerivation rec {
     vertex coloring and derivative computation";
     homepage = "http://cscapes.cs.purdue.edu/coloringpage/software.htm#functionalities";
     license = licenses.lgpl3;
+    platforms = platforms.linux;
     maintainers = with maintainers; [ edwtjo ];
   };
 
diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix
index 6a0b686602f..2823165d022 100644
--- a/pkgs/applications/science/math/giac/default.nix
+++ b/pkgs/applications/science/math/giac/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, fetchpatch, texlive, bison, flex, liblapackWithoutAtlas
+{ stdenv, fetchurl, fetchpatch, texlive, bison, flex, liblapack
 , gmp, mpfr, pari, ntl, gsl, blas, mpfi
 , readline, gettext, libpng, libao, gfortran, perl
 , enableGUI ? false, libGLU_combined ? null, xorg ? null, fltk ? null
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
     # gfortran.cc default output contains static libraries compiled without -fPIC
     # we want libgfortran.so.3 instead
     (stdenv.lib.getLib gfortran.cc)
-    liblapackWithoutAtlas
+    liblapack
   ] ++ stdenv.lib.optionals enableGUI [
     libGLU_combined fltk xorg.libX11
   ];
diff --git a/pkgs/applications/science/math/gmsh/CMakeLists.txt.patch b/pkgs/applications/science/math/gmsh/CMakeLists.txt.patch
deleted file mode 100644
index 0326a8d296a..00000000000
--- a/pkgs/applications/science/math/gmsh/CMakeLists.txt.patch
+++ /dev/null
@@ -1,37 +0,0 @@
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -324,25 +324,16 @@
-         set_config_option(HAVE_BLAS "Blas(IntelMKL)")
-         set_config_option(HAVE_LAPACK "Lapack(IntelMKL)")
-       else(LAPACK_LIBRARIES)
--        # on Linux also try to find ATLAS without a Fortran compiler, because
--        # cmake ships with a buggy FindBLAS e.g. on Ubuntu Lucid Lynx
--        set(ATLAS_LIBS_REQUIRED lapack f77blas cblas atlas)
--        find_all_libraries(LAPACK_LIBRARIES ATLAS_LIBS_REQUIRED "" "")
-+        # try with generic names
-+        set(GENERIC_LIBS_REQUIRED lapack blas pthread)
-+        find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "")
-         if(LAPACK_LIBRARIES)
--          set_config_option(HAVE_BLAS "Blas(ATLAS)")
--          set_config_option(HAVE_LAPACK "Lapack(ATLAS)")
--        else(LAPACK_LIBRARIES)
--          # try with generic names
--          set(GENERIC_LIBS_REQUIRED lapack blas pthread)
--          find_all_libraries(LAPACK_LIBRARIES GENERIC_LIBS_REQUIRED "" "")
--          if(LAPACK_LIBRARIES)
--            set_config_option(HAVE_BLAS "Blas(Generic)")
--            set_config_option(HAVE_LAPACK "Lapack(Generic)")
--            find_library(GFORTRAN_LIB gfortran)
--            if(GFORTRAN_LIB)
--              list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB})
--            endif(GFORTRAN_LIB)
--          endif(LAPACK_LIBRARIES)
-+          set_config_option(HAVE_BLAS "Blas(Generic)")
-+          set_config_option(HAVE_LAPACK "Lapack(Generic)")
-+          find_library(GFORTRAN_LIB gfortran)
-+          if(GFORTRAN_LIB)
-+            list(APPEND LAPACK_LIBRARIES ${GFORTRAN_LIB})
-+          endif(GFORTRAN_LIB)
-         endif(LAPACK_LIBRARIES)
-       endif(LAPACK_LIBRARIES)
-     elseif(${CMAKE_SYSTEM_NAME} MATCHES "SunOS")
diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix
index 525fc5f1dc2..7c8e62cc97c 100644
--- a/pkgs/applications/science/math/gmsh/default.nix
+++ b/pkgs/applications/science/math/gmsh/default.nix
@@ -1,21 +1,17 @@
-{ stdenv, fetchurl, cmake, blas, liblapack, gfortran, gmm, fltk, libjpeg
+{ stdenv, fetchurl, cmake, openblasCompat, gfortran, gmm, fltk, libjpeg
 , zlib, libGLU_combined, libGLU, xorg }:
 
-let version = "4.0.2"; in
+let version = "4.0.4"; in
 
 stdenv.mkDerivation {
   name = "gmsh-${version}";
 
   src = fetchurl {
     url = "http://gmsh.info/src/gmsh-${version}-source.tgz";
-    sha256 = "03aw3sbz4x998rk29az7mgm0mrdb6614aqnppg81p5jkh5097jgk";
+    sha256 = "1hvrls3xyxvn69kwicpvndrs0zhifcfkhfsxr8zkmhmn6fhnjhha";
   };
 
-  # The original CMakeLists tries to use some version of the Lapack lib
-  # that is supposed to work without Fortran but didn't for me.
-  patches = [ ./CMakeLists.txt.patch ];
-
-  buildInputs = [ cmake blas liblapack gmm fltk libjpeg zlib libGLU_combined
+  buildInputs = [ cmake openblasCompat gmm fltk libjpeg zlib libGLU_combined
     libGLU xorg.libXrender xorg.libXcursor xorg.libXfixes xorg.libXext
     xorg.libXft xorg.libXinerama xorg.libX11 xorg.libSM xorg.libICE
   ];
@@ -27,7 +23,7 @@ stdenv.mkDerivation {
   meta = {
     description = "A three-dimensional finite element mesh generator";
     homepage = http://gmsh.info/;
-    platforms = stdenv.lib.platforms.all;
+    platforms = [ "x86_64-linux" ];
     license = stdenv.lib.licenses.gpl2Plus;
   };
 }
diff --git a/pkgs/applications/science/math/gurobi/default.nix b/pkgs/applications/science/math/gurobi/default.nix
index 06d448f6252..d4a4133d06e 100644
--- a/pkgs/applications/science/math/gurobi/default.nix
+++ b/pkgs/applications/science/math/gurobi/default.nix
@@ -33,9 +33,15 @@ stdenv.mkDerivation rec {
     cp include/gurobi*.h $out/include/
 
     mkdir -p $out/lib
+    cp lib/*.jar $out/lib/
+    cp lib/libGurobiJni*.so $out/lib/
     cp lib/libgurobi*.so* $out/lib/
     cp lib/libgurobi*.a $out/lib/
     cp src/build/*.a $out/lib/
+
+    mkdir -p $out/share/java
+    ln -s $out/lib/gurobi.jar $out/share/java/
+    ln -s $out/lib/gurobi-javadoc.jar $out/share/java/
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/science/math/pari/gp2c.nix b/pkgs/applications/science/math/pari/gp2c.nix
index 42f35edb256..4915e42025b 100644
--- a/pkgs/applications/science/math/pari/gp2c.nix
+++ b/pkgs/applications/science/math/pari/gp2c.nix
@@ -4,11 +4,11 @@
 stdenv.mkDerivation rec {
 
   name = "gp2c-${version}";
-  version = "0.0.11";
+  version = "0.0.11pl1";
 
   src = fetchurl {
     url = "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/${name}.tar.gz";
-    sha256 = "1z69xj2dpd8yyi8108rz26c50xpv0k2j8qnk0bzy1c5lw3pd1adm";
+    sha256 = "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s";
   };
 
   buildInputs = [ pari perl ];
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
index 7e62f0cf75e..cf8515283cd 100644
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@@ -3,7 +3,7 @@
 }:
 
 let
-  inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages_8_x;
+  inherit (nixpkgs) fetchpatch fetchurl symlinkJoin callPackage nodePackages;
 
   # https://trac.sagemath.org/ticket/15980 for tracking of python3 support
   python = nixpkgs.python2.override {
@@ -26,7 +26,7 @@ let
       };
 
       sagenb = self.callPackage ./sagenb.nix {
-        mathjax = nodePackages_8_x.mathjax;
+        mathjax = nodePackages.mathjax;
       };
 
       sagedoc = self.callPackage ./sagedoc.nix {
@@ -36,8 +36,8 @@ let
       env-locations = self.callPackage ./env-locations.nix {
         inherit pari_data ecl;
         inherit singular;
-        three = nodePackages_8_x.three;
-        mathjax = nodePackages_8_x.mathjax;
+        three = nodePackages.three;
+        mathjax = nodePackages.mathjax;
       };
 
       sage-env = self.callPackage ./sage-env.nix {
@@ -49,7 +49,7 @@ let
         inherit pythonEnv;
         inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular;
         pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
-        three = nodePackages_8_x.three;
+        three = nodePackages.three;
       };
 
       sage = self.callPackage ./sage.nix { };