Merge branch 'master' into staging

* master: (271 commits)
  pysmbc: clarify license
  pysmbc: fix license
  bazel: 0.5.4 -> 0.6.0 (#29990)
  googler: init at 3.3
  go: declare support for aarch64
  firefox-beta-bin: 56.0b5 -> 57.0b4
  spotify: 1.0.64.401.g9d720389-21 -> 1.0.64.407.g9bd02c2d-26
  gogs: 0.11.19 -> 0.11.29
  grafana: 4.5.1 -> 4.5.2
  mopidy-iris: 3.4.1 -> 3.4.9
  nextcloud: 12.0.2 -> 12.0.3
  haskell-json-autotype: jailbreak to fix build within LTS 9.x
  kore: fix up
  kore: init at 2.0.0
  glusterfs service: fix issues with useRpcbind
  tig: 2.2.2 -> 2.3.0
  haskell-hspec-core: enable test suite again
  hackage-packages.nix: automatic Haskell package set update
  librsvg: fix thumbnailer path
  awscli: 1.11.108 -> 1.11.162
  ...

4 files changed, 100 insertions, 6 deletions

diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix
index 5adece31370e..fd0ff24d58b3 100644
--- a/pkgs/applications/science/math/R/default.nix
+++ b/pkgs/applications/science/math/R/default.nix
@@ -7,11 +7,11 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "R-3.4.1";
+  name = "R-3.4.2";
 
   src = fetchurl {
     url = "http://cran.r-project.org/src/base/R-3/${name}.tar.gz";
-    sha256 = "0y7wlfk3cn1dxn2mpnxwvsk31s0599crbsyah8srm5pa2mfi7c82";
+    sha256 = "0r0cv2kc3x5z9xycpnxx6fbvv22psw2m342jhpslbxkc8g1307lp";
   };
 
   buildInputs = [
diff --git a/pkgs/applications/science/math/clp/default.nix b/pkgs/applications/science/math/clp/default.nix
new file mode 100644
index 000000000000..daa9a53c59a1
--- /dev/null
+++ b/pkgs/applications/science/math/clp/default.nix
@@ -0,0 +1,24 @@
+{ stdenv, fetchurl, zlib }:
+
+stdenv.mkDerivation rec {
+	version = "1.16.11";
+	name = "clp-${version}";
+	src = fetchurl {
+		url = "https://www.coin-or.org/download/source/Clp/Clp-${version}.tgz";
+		sha256 = "0fazlqpp845186nmixa9f1xfxqqkdr1xj4va7q29m8594ca4a9dm";
+	};
+
+	propagatedBuildInputs = [ zlib ];
+
+	doCheck = true;
+
+	checkTarget = "test";
+
+	meta = {
+		license = stdenv.lib.licenses.epl10;
+		homepage = https://projects.coin-or.org/Clp;
+		description = "An open-source linear programming solver written in C++";
+		platforms = stdenv.lib.platforms.all;
+		maintainers = [ stdenv.lib.maintainers.vbgl ];
+	};
+}
diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix
new file mode 100644
index 000000000000..4ef00d56f182
--- /dev/null
+++ b/pkgs/applications/science/math/giac/default.nix
@@ -0,0 +1,68 @@
+{ stdenv, fetchurl, texlive, bison, flex
+, gmp, mpfr, pari, ntl, gsl, blas, mpfi, liblapackWithAtlas
+, readline, gettext, libpng, libao, gfortran, perl
+, enableGUI ? false, mesa ? null, xorg ? null, fltk ? null
+}:
+
+assert enableGUI -> mesa != null && xorg != null && fltk != null;
+
+stdenv.mkDerivation rec {
+  name = "${attr}-${version}";
+  attr = if enableGUI then "giac-with-xcas" else "giac";
+  version = "1.4.9";
+
+  src = fetchurl {
+    url = "https://www-fourier.ujf-grenoble.fr/~parisse/giac/giac-${version}.tar.bz2";
+    sha256 = "1n7xxgpqrsq7cv5wgcmgag6jvxw5wijkf1yv1r5aizlf1rc7dhai";
+  };
+
+  postPatch = ''
+    for i in doc/*/Makefile*; do
+      substituteInPlace "$i" --replace "/bin/cp" "cp";
+    done;
+  '';
+
+  nativeBuildInputs = [
+    texlive.combined.scheme-small bison flex
+  ];
+
+  # perl is only needed for patchShebangs fixup.
+  buildInputs = [
+    gmp mpfr pari ntl gsl blas mpfi liblapackWithAtlas
+    readline gettext libpng libao gfortran perl
+  ] ++ stdenv.lib.optionals enableGUI [
+    mesa fltk xorg.libX11
+  ];
+
+  outputs = [ "out" ];
+
+  enableParallelBuilding = true;
+  hardeningDisable = [ "format" "bindnow" "relro" ];
+
+  configureFlags = [
+    "--enable-gc" "--enable-png" "--enable-gsl" "--enable-lapack"
+    "--enable-pari" "--enable-ntl" "--enable-gmpxx" # "--enable-cocoa"
+    "--enable-ao"
+  ] ++ stdenv.lib.optionals enableGUI [
+    "--enable-gui" "--with-x"
+  ];
+
+  postInstall = ''
+    # example Makefiles contain the full path to some commands
+    # notably texlive, and we don't want texlive to become a runtime
+    # dependency
+    for file in $(find $out -name Makefile) ; do
+      sed -i "s@/nix/store/[^/]*/bin/@@" "$file" ;
+    done;
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A free computer algebra system (CAS)";
+    homepage = "https://www-fourier.ujf-grenoble.fr/~parisse/giac.html";
+    license = licenses.gpl3Plus;
+    ## xcas is buildable on darwin but there are specific instructions I could
+    ## not test
+    platforms = platforms.linux;
+    maintainers = [ maintainers.symphorien ];
+  };
+}
diff --git a/pkgs/applications/science/math/gmsh/default.nix b/pkgs/applications/science/math/gmsh/default.nix
index b55961205922..bb24ac9bd499 100644
--- a/pkgs/applications/science/math/gmsh/default.nix
+++ b/pkgs/applications/science/math/gmsh/default.nix
@@ -1,25 +1,27 @@
-{ stdenv, fetchurl, cmake, blas, liblapack, gfortran, fltk, libjpeg
+{ stdenv, fetchurl, cmake, blas, liblapack, gfortran, gmm, fltk, libjpeg
 , zlib, mesa, mesa_glu, xorg }:
 
-let version = "2.12.0"; in
+let version = "3.0.5"; in
 
 stdenv.mkDerivation {
   name = "gmsh-${version}";
 
   src = fetchurl {
     url = "http://gmsh.info/src/gmsh-${version}-source.tgz";
-    sha256 = "02cx2mfbxx6m18s54z4yzbk4ybch3v9489z7cr974y8y0z42xgbz";
+    sha256 = "ae39ed81178d94b76990b8c89b69a5ded8910fd8f7426b800044d00373d12a93";
   };
 
   # 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 gfortran fltk libjpeg zlib mesa
+  buildInputs = [ cmake blas liblapack gfortran gmm fltk libjpeg zlib mesa
     mesa_glu xorg.libXrender xorg.libXcursor xorg.libXfixes xorg.libXext
     xorg.libXft xorg.libXinerama xorg.libX11 xorg.libSM xorg.libICE
   ];
 
+  enableParallelBuilding = true;
+
   meta = {
     description = "A three-dimensional finite element mesh generator";
     homepage = http://gmsh.info/;