Merge commit '8746c77a383f5c76153c7a181f3616d273acfa2a'

37 files changed, 417 insertions, 141 deletions

diff --git a/nixpkgs/pkgs/applications/science/astronomy/openspace/default.nix b/nixpkgs/pkgs/applications/science/astronomy/openspace/default.nix
index ee3a71cf1813..dc7c7c920a17 100644
--- a/nixpkgs/pkgs/applications/science/astronomy/openspace/default.nix
+++ b/nixpkgs/pkgs/applications/science/astronomy/openspace/default.nix
@@ -5,7 +5,7 @@
 stdenv.mkDerivation rec {
   version = "0.11.1";
   name    = "openspace-${version}";
-  
+
   src = fetchFromGitHub {
     owner  = "OpenSpace";
     repo   = "OpenSpace";
@@ -13,37 +13,37 @@ stdenv.mkDerivation rec {
     sha256 = "0msqixf30r0d41xmfmzkdfw6w9jkx2ph5clq8xiwrg1jc3z9q7nv";
     fetchSubmodules = true;
   };
-  
+
   buildInputs = [
     makeWrapper cmake
     curl boost gdal glew soil
     libX11 libXi libXxf86vm libXcursor libXrandr libXinerama
   ];
-      
+
   glmPlatformH = fetchurl {
     url    = "https://raw.githubusercontent.com/g-truc/glm/dd48b56e44d699a022c69155c8672caacafd9e8a/glm/simd/platform.h";
     sha256 = "0y91hlbgn5va7ijg5mz823gqkq9hqxl00lwmdwnf8q2g086rplzw";
   };
-  
+
   # See <https://github.com/g-truc/glm/issues/726>
   prePatch = ''
     cp ${glmPlatformH} ext/sgct/include/glm/simd/platform.h
     cp ${glmPlatformH} ext/ghoul/ext/glm/glm/simd/platform.h
   '';
-  
+
   patches = [
     # See <https://github.com/opensgct/sgct/issues/13>
     ./vrpn.patch
-    
+
     ./constexpr.patch
     ./config.patch
 
     # WARNING: This patch disables some slow torrents in a very dirty way.
-    ./assets.patch 
+    ./assets.patch
   ];
-  
+
   bundle = "$out/usr/share/openspace";
-  
+
   preConfigure = ''
     cmakeFlagsArray=(
       $cmakeFlagsArray
@@ -51,28 +51,28 @@ stdenv.mkDerivation rec {
       "-DCMAKE_INSTALL_PREFIX=${bundle}"
     )
   '';
-  
+
   preInstall = ''
     mkdir -p $out/bin
     mkdir -p ${bundle}
   '';
-  
+
   postInstall = ''
     cp ext/spice/libSpice.so       ${bundle}/lib
     cp ext/ghoul/ext/lua/libLua.so ${bundle}/lib
   '';
-  
+
   postFixup = ''
     for bin in ${bundle}/bin/*
     do
       rpath=$(patchelf --print-rpath $bin)
       patchelf --set-rpath $rpath:${bundle}/lib $bin
-      
+
       name=$(basename $bin)
       makeWrapper $bin $out/bin/$name --run "cd ${bundle}"
     done
   '';
-  
+
   meta = {
     description     = "Open-source astrovisualization project";
     longDescription = ''
@@ -85,5 +85,6 @@ stdenv.mkDerivation rec {
     homepage  = https://www.openspaceproject.com/;
     license   = stdenv.lib.licenses.mit;
     platforms = stdenv.lib.platforms.linux;
+    broken = true; # fails to build
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix
index 2480b80316eb..e3c66199f11c 100644
--- a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix
+++ b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix
@@ -1,7 +1,7 @@
 { mkDerivation, lib, fetchFromGitHub
 , cmake, freetype, libpng, libGLU_combined, openssl, perl, libiconv
 , qtscript, qtserialport, qttools
-, qtmultimedia, qtlocation, makeWrapper, qtbase
+, qtmultimedia, qtlocation, qtbase, wrapQtAppsHook
 }:
 
 mkDerivation rec {
@@ -15,18 +15,13 @@ mkDerivation rec {
     sha256 = "0hf1wv2bb5j7ny2xh29mj9m4hjblhn02zylay8gl85w7xlqs7s5r";
   };
 
-  nativeBuildInputs = [ cmake perl ];
+  nativeBuildInputs = [ cmake perl wrapQtAppsHook ];
 
   buildInputs = [
     freetype libpng libGLU_combined openssl libiconv qtscript qtserialport qttools
-    qtmultimedia qtlocation qtbase makeWrapper
+    qtmultimedia qtlocation qtbase
   ];
 
-  postInstall = ''
-    wrapProgram $out/bin/stellarium \
-      --prefix QT_PLUGIN_PATH : "${qtbase}/lib/qt-5.${lib.versions.minor qtbase.version}/plugins"
-  '';
-
   meta = with lib; {
     description = "Free open-source planetarium";
     homepage = http://stellarium.org/;
diff --git a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
index 406f42e9ad7b..2cdd7fda38ef 100644
--- a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
@@ -1,17 +1,17 @@
-{stdenv, fetchFromGitHub, zlib, python}:
+{stdenv, fetchFromGitHub, zlib, python, bzip2, lzma}:
 
 stdenv.mkDerivation rec {
   name = "bedtools-${version}";
-  version = "2.27.1";
+  version = "2.28.0";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "bedtools2";
     rev = "v${version}";
-    sha256 = "1pk68y052rm2m24yfmy82ms8p6kd6xcqxxgi7n0a1sbh89wllm6s";
+    sha256 = "1266bcn5hgbvysfi6nr4cqxlbxcx7vn7ng8kb0v3gz37qh2zxxw9";
   };
 
-  buildInputs = [ zlib python ];
+  buildInputs = [ zlib python bzip2 lzma ];
   cc = if stdenv.cc.isClang then "clang++" else "g++";
   buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} -j $NIX_BUILD_CORES";
   installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} install";
diff --git a/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix b/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix
new file mode 100644
index 000000000000..dcc725233551
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix
@@ -0,0 +1,28 @@
+{ stdenv, fetchurl, gsl }:
+
+stdenv.mkDerivation rec {
+  pname = "est-sfs";
+  version = "2.03";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/est-usfs/${pname}-release-${version}.tar.gz";
+    sha256 = "1hvamrgagz0xi89w8qafyd9mjrdpyika8zm22drddnjkp4sdj65n";
+  };
+
+  buildInputs = [ gsl ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    mkdir -p $out/share/doc/${pname}
+    cp est-sfs $out/bin
+    cp est-sfs-documentation.pdf $out/share/doc/${pname}
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://sourceforge.net/projects/est-usfs;
+    description = "Estimate the unfolded site frequency spectrum and ancestral states";
+    license = licenses.gpl3;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.all;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix b/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix
index 9ccf54a81133..9d41fed06911 100644
--- a/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix
@@ -1,4 +1,4 @@
-{stdenv, fetchurl, unzip, which, python}:
+{stdenv, fetchurl, unzip, which, python, perl}:
 
 stdenv.mkDerivation rec {
   name = "hisat2-${version}";
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9";
   };
 
-  buildInputs = [ unzip  which python ];
+  nativeBuildInputs = [ unzip which ];
+  buildInputs = [ python perl ];
 
   installPhase = ''
     mkdir -p $out/bin
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
index 5fc222bb2993..70c72779c52a 100644
--- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "picard-tools-${version}";
-  version = "2.20.2";
+  version = "2.20.4";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "0qpc6pi3fmzv8rs5cmk3dd4clrkzbrngsl384b5g0y7471lhavbi";
+    sha256 = "1z2zpwqhk8i7l9awajdrzxwij0vcmkwq7rajzjil7n65apj2hz9i";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
index d188ca02b183..e778c3bd52cc 100644
--- a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
@@ -2,10 +2,10 @@
     
 stdenv.mkDerivation rec {
   pname = "stacks";
-  version = "2.4";
+  version = "2.41";
   src = fetchurl {
     url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz";
-    sha256 = "1ha1avkh6rqqvsy4k42336a2gj14y1jq19a2x8cjmiidi9l3s29h";
+    sha256 = "0q420rzjb05jfchcls3pysm4hxfgs6xj2jw246isx0il10g93gkq";
   };
 
   buildInputs = [ zlib ];
diff --git a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix
index 1527f5d3ddad..e7f5eab8bfaf 100644
--- a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix
@@ -2,16 +2,17 @@
 
 stdenv.mkDerivation rec {
   name = "strelka-${version}";
-  version = "2.9.5";
+  version = "2.9.10";
 
   src = fetchFromGitHub {
     owner = "Illumina";
     repo = "strelka";
     rev = "v${version}";
-    sha256 = "0x4a6nkx1jnyag9svghsdjz1fz6q7qx5pn77wphdfnk81f9yspf8";
+    sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
   };
 
-  buildInputs = [ cmake zlib python2 ];
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib python2 ];
 
   preConfigure = ''
     sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py
diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
index 84c01cbfd673..00231113d2cf 100644
--- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix
@@ -17,14 +17,14 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "14.29.46";
+  version = "14.29.49";
   pname = "jmol";
 
   src = let
     baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
   in fetchurl {
     url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    sha256 = "00ig1f1fz5qbkam0h06vs1gsb95hdqa0iyhsp4qbyjjfxir7m59l";
+    sha256 = "19fyr4ldvbd5rbw19hslg9fpwc42wxmyx7r3z78k6dw653vb1ml5";
   };
 
   patchPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/electronics/bitscope/common.nix b/nixpkgs/pkgs/applications/science/electronics/bitscope/common.nix
index 64777b5a0ac8..9101f1fdbe5e 100644
--- a/nixpkgs/pkgs/applications/science/electronics/bitscope/common.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/bitscope/common.nix
@@ -2,7 +2,7 @@
 , buildFHSUserEnv
 , cairo
 , dpkg
-, gdk_pixbuf
+, gdk-pixbuf
 , glib
 , gtk2-x11
 , makeWrapper
@@ -39,7 +39,7 @@ let
     libs = attrs.libs or [
       atk
       cairo
-      gdk_pixbuf
+      gdk-pixbuf
       glib
       gtk2-x11
       pango
diff --git a/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix b/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix
index ecbbeff108d2..55e8a7b4ffe9 100644
--- a/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/dsview/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, pkgconfig, cmake,
 libzip, boost, fftw, qtbase,
-libusb, makeWrapper, libsigrok4dsl, libsigrokdecode4dsl
+libusb, wrapQtAppsHook, libsigrok4dsl, libsigrokdecode4dsl
 }:
 
 stdenv.mkDerivation rec {
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
     ./install.patch
   ];
 
-  nativeBuildInputs = [ cmake pkgconfig makeWrapper ];
+  nativeBuildInputs = [ cmake pkgconfig wrapQtAppsHook ];
 
   buildInputs = [
    boost fftw qtbase libusb libzip libsigrokdecode4dsl libsigrok4dsl
@@ -32,11 +32,6 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
-  postFixup = ''
-    wrapProgram $out/bin/DSView --suffix QT_PLUGIN_PATH : \
-      ${qtbase.bin}/${qtbase.qtPluginPrefix}
-  '';
-
   meta = with stdenv.lib; {
     description = "A GUI program for supporting various instruments from DreamSourceLab, including logic analyzer, oscilloscope, etc";
     homepage = https://www.dreamsourcelab.com/;
diff --git a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
index 90b7db4b545c..ba1b9e174bea 100644
--- a/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/eagle/eagle.nix
@@ -13,11 +13,11 @@ let
   in
   stdenv.mkDerivation rec {
     name = "eagle-${version}";
-    version = "9.4.1";
+    version = "9.4.2";
 
     src = fetchurl {
       url = "https://eagle-updates.circuits.io/downloads/${builtins.replaceStrings ["."] ["_"] version}/Autodesk_EAGLE_${version}_English_Linux_64bit.tar.gz";
-      sha256 = "0p3kxryvk853rx24phcadvmqn6f37rnnql8sf6cqn9cqhrrkbvlq";
+      sha256 = "0lrwrvqcb91mcggmicvwjrngccsdy0f06l7a8nfgp9ckn4d9vmg2";
     };
 
     desktopItem = makeDesktopItem {
diff --git a/nixpkgs/pkgs/applications/science/electronics/verilog/default.nix b/nixpkgs/pkgs/applications/science/electronics/verilog/default.nix
index 83352df18e6e..f850a1bf94df 100644
--- a/nixpkgs/pkgs/applications/science/electronics/verilog/default.nix
+++ b/nixpkgs/pkgs/applications/science/electronics/verilog/default.nix
@@ -1,31 +1,40 @@
-{ stdenv, fetchFromGitHub, autoconf, gperf, flex, bison }:
+{ stdenv, fetchFromGitHub, autoconf, gperf, flex, bison, readline, ncurses
+, bzip2, zlib
+}:
 
 stdenv.mkDerivation rec {
-  name = "iverilog-${version}";
-  version = "2019.03.27";
+  pname = "iverilog";
+  version = "unstable-2019-08-01";
 
   src = fetchFromGitHub {
     owner  = "steveicarus";
-    repo   = "iverilog";
-    rev    = "a9388a895eb85a9d7f2924b89f839f94e1b6d7c4";
-    sha256 = "01d48sy3pzg9x1xpczqrsii2ckrvgnrfj720wiz22jdn90nirhhr";
+    repo = pname;
+    rev    = "c383d2048c0bd15f5db083f14736400546fb6215";
+    sha256 = "1zs0gyhws0qa315magz3w5m45v97knczdgbf2zn4d7bdb7cv417c";
   };
 
   enableParallelBuilding = true;
 
-  patchPhase = ''
+  prePatch = ''
+    substituteInPlace configure.in \
+      --replace "AC_CHECK_LIB(termcap, tputs)" "AC_CHECK_LIB(termcap, tputs)"
+  '';
+
+  preConfigure = ''
     chmod +x $PWD/autoconf.sh
     $PWD/autoconf.sh
   '';
 
-  buildInputs = [ autoconf gperf flex bison ];
+  nativeBuildInputs = [ autoconf gperf flex bison ];
+
+  buildInputs = [ readline ncurses bzip2 zlib ];
 
-  meta = {
+  meta = with stdenv.lib; {
     description = "Icarus Verilog compiler";
     repositories.git = https://github.com/steveicarus/iverilog.git;
-    homepage = http://www.icarus.com;
-    license = stdenv.lib.licenses.gpl2Plus;
-    maintainers = with stdenv.lib.maintainers; [winden];
-    platforms = with stdenv.lib.platforms; linux;
+    homepage = "http://iverilog.icarus.com/";
+    license = licenses.lgpl21;
+    maintainers = with maintainers; [ winden ];
+    platforms = platforms.linux;
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/logic/coq/default.nix b/nixpkgs/pkgs/applications/science/logic/coq/default.nix
index 2373ae43e76e..10fe722d7e9a 100644
--- a/nixpkgs/pkgs/applications/science/logic/coq/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/coq/default.nix
@@ -28,7 +28,7 @@ let
    "8.8.2" = "1lip3xja924dm6qblisk1bk0x8ai24s5xxqxphbdxj6djglj68fd";
    "8.9.0" = "1dkgdjc4n1m15m1p724hhi5cyxpqbjw6rxc5na6fl3v4qjjfnizh";
    "8.9.1" = "1xrq6mkhpq994bncmnijf8jwmwn961kkpl4mwwlv7j3dgnysrcv2";
-   "8.10+beta1" = "19wf39i0ap2vakglgdlqxpjd3l1h5w7dp460w8y7nc1y06b2153h";
+   "8.10+beta2" = "0jk7pwydhd17ab7ii69zvi4sgrr630q2lsxhckaj3sz55cpjlhal";
   }."${version}";
   coq-version = stdenv.lib.versions.majorMinor version;
   versionAtLeast = stdenv.lib.versionAtLeast coq-version;
diff --git a/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix b/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix
index cd8a3747bea1..09801f54e7ee 100644
--- a/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/cryptoverif/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "cryptoverif-${version}";
-  version = "2.01";
+  version = "2.01pl1";
 
   src = fetchurl {
     url    = "http://prosecco.gforge.inria.fr/personal/bblanche/cryptoverif/cryptoverif${version}.tar.gz";
-    sha256 = "122pryci8rsdzv9qszw11g3izh78r2lvd1raahv2j7qmvgi76nab";
+    sha256 = "1bkmrv3wsy8mwhrxd3z3br9zgv37c2w6443rm4s9jl0aphcgnbiw";
   };
 
   buildInputs = [ ocaml ];
diff --git a/nixpkgs/pkgs/applications/science/logic/verifast/default.nix b/nixpkgs/pkgs/applications/science/logic/verifast/default.nix
index 22eb5d07f1c1..360f75cc6f07 100644
--- a/nixpkgs/pkgs/applications/science/logic/verifast/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/verifast/default.nix
@@ -1,10 +1,10 @@
-{ stdenv, fetchurl, gtk2, gdk_pixbuf, atk, pango, glib, cairo, freetype
+{ stdenv, fetchurl, gtk2, gdk-pixbuf, atk, pango, glib, cairo, freetype
 , fontconfig, libxml2, gnome2 }:
 
 let
 
   libPath = stdenv.lib.makeLibraryPath
-    [ stdenv.cc.libc stdenv.cc.cc gtk2 gdk_pixbuf atk pango glib cairo
+    [ stdenv.cc.libc stdenv.cc.cc gtk2 gdk-pixbuf atk pango glib cairo
       freetype fontconfig libxml2 gnome2.gtksourceview
     ] + ":${stdenv.cc.cc.lib}/lib64:$out/libexec";
 
diff --git a/nixpkgs/pkgs/applications/science/logic/why3/configure.patch b/nixpkgs/pkgs/applications/science/logic/why3/configure.patch
new file mode 100644
index 000000000000..3eebf3cf165d
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/logic/why3/configure.patch
@@ -0,0 +1,11 @@
+diff --git a/configure b/configure
+--- a/configure
++++ b/configure
+@@ -4029,7 +4029,6 @@ fi
+ 
+ if test "$USEOCAMLFIND" = yes; then
+    OCAMLFINDLIB=$(ocamlfind printconf stdlib)
+-   OCAMLFIND=$(which ocamlfind)
+    if test "$OCAMLFINDLIB" != "$OCAMLLIB"; then
+    USEOCAMLFIND=no;
+    echo "but your ocamlfind is not compatible with your ocamlc:"
diff --git a/nixpkgs/pkgs/applications/science/logic/why3/default.nix b/nixpkgs/pkgs/applications/science/logic/why3/default.nix
index a3b369ad54a3..bd538dc6c757 100644
--- a/nixpkgs/pkgs/applications/science/logic/why3/default.nix
+++ b/nixpkgs/pkgs/applications/science/logic/why3/default.nix
@@ -1,4 +1,5 @@
-{ fetchurl, stdenv, ocamlPackages, coq }:
+{ callPackage, fetchurl, stdenv
+, ocamlPackages, coqPackages, rubber, hevea, emacs }:
 
 stdenv.mkDerivation rec {
   name    = "why3-${version}";
@@ -9,14 +10,34 @@ stdenv.mkDerivation rec {
     sha256 = "0xz001jhi71ja8vqrjz27v63bidrzj4qvg1yqarq6p4dmpxhk348";
   };
 
-  buildInputs = (with ocamlPackages; [
-      ocaml findlib num lablgtk ocamlgraph zarith menhir ]) ++
-    stdenv.lib.optionals (ocamlPackages.ocaml == coq.ocamlPackages.ocaml ) [
-      coq ocamlPackages.camlp5
-    ];
+  buildInputs = with ocamlPackages; [
+    ocaml findlib ocamlgraph zarith menhir
+    # Compressed Sessions
+    # Emacs compilation of why3.el
+    emacs
+    # Documentation
+    rubber hevea
+    # GUI
+    lablgtk
+    # WebIDE
+    js_of_ocaml js_of_ocaml-ppx
+    # Coq Support
+    coqPackages.coq coqPackages.flocq ocamlPackages.camlp5
+  ];
+
+  propagatedBuildInputs = with ocamlPackages; [ camlzip num ];
+
+  enableParallelBuilding = true;
+
+  # Remove unnecessary call to which
+  patches = [ ./configure.patch ];
+
+  configureFlags = [ "--enable-verbose-make" ];
 
   installTargets = [ "install" "install-lib" ];
 
+  passthru.withProvers = callPackage ./with-provers.nix {};
+
   meta = with stdenv.lib; {
     description = "A platform for deductive program verification";
     homepage    = "http://why3.lri.fr/";
diff --git a/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix b/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix
new file mode 100644
index 000000000000..3528dbd3a647
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix
@@ -0,0 +1,30 @@
+{ stdenv, makeWrapper, runCommand, symlinkJoin, why3 }:
+provers:
+let configAwkScript = runCommand "why3-conf.awk" { inherit provers; }
+    ''
+      for p in $provers; do
+        for b in $p/bin/*; do
+          BASENAME=$(basename $b)
+          echo "/^command =/{ gsub(\"$BASENAME\", \"$b\") }" >> $out
+        done
+      done
+      echo '{ print }' >> $out
+    '';
+in stdenv.mkDerivation {
+  name = "${why3.name}-with-provers";
+
+  phases = [ "buildPhase" "installPhase" ];
+
+  buildInputs = [ why3 makeWrapper ] ++ provers;
+
+  buildPhase = ''
+      mkdir -p $out/share/why3/
+      why3 config --detect-provers -C $out/share/why3/why3.conf
+      awk -i inplace -f ${configAwkScript} $out/share/why3/why3.conf
+  '';
+
+  installPhase = ''
+      mkdir -p $out/bin
+      makeWrapper ${why3}/bin/why3 $out/bin/why3 --add-flags "--extra-config $out/share/why3/why3.conf"
+  '';
+}
diff --git a/nixpkgs/pkgs/applications/science/machine-learning/fasttext/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/fasttext/default.nix
index 0ae9a74d0d0a..0de54572862b 100644
--- a/nixpkgs/pkgs/applications/science/machine-learning/fasttext/default.nix
+++ b/nixpkgs/pkgs/applications/science/machine-learning/fasttext/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "fasttext";
-  version = "0.2.0";
+  version = "0.9.1";
 
   src = fetchFromGitHub {
     owner = "facebookresearch";
     repo = "fastText";
-    rev = version;
-    sha256 = "1fcrz648r2s80bf7vc0l371xillz5jk3ldaiv9jb7wnsyri831b4";
+    rev = "v${version}";
+    sha256 = "1cbzz98qn8aypp4r5kwwwc9wiq5bwzv51kcsb15xjfs9lz8h3rii";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/nixpkgs/pkgs/applications/science/math/caffe/default.nix b/nixpkgs/pkgs/applications/science/math/caffe/default.nix
index 3367fa87422b..e8171bcb256a 100644
--- a/nixpkgs/pkgs/applications/science/math/caffe/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/caffe/default.nix
@@ -3,7 +3,7 @@
 , fetchurl
 , cmake
 , boost
-, google-gflags
+, gflags
 , glog
 , hdf5-cpp
 , opencv3
@@ -53,7 +53,7 @@ stdenv.mkDerivation rec {
   cmakeFlags =
     # It's important that caffe is passed the major and minor version only because that's what
     # boost_python expects
-    [ (if pythonSupport then "-Dpython_version=3${python.pythonVersion}" else "-DBUILD_python=OFF")
+    [ (if pythonSupport then "-Dpython_version=${python.pythonVersion}" else "-DBUILD_python=OFF")
       "-DBLAS=open"
     ] ++ (if cudaSupport then [
            "-DCUDA_ARCH_NAME=All"
@@ -63,7 +63,7 @@ stdenv.mkDerivation rec {
       ++ ["-DUSE_LEVELDB=${toggle leveldbSupport}"]
       ++ ["-DUSE_LMDB=${toggle lmdbSupport}"];
 
-  buildInputs = [ boost google-gflags glog protobuf hdf5-cpp opencv3 openblas ]
+  buildInputs = [ boost gflags glog protobuf hdf5-cpp opencv3 openblas ]
                 ++ lib.optional cudaSupport cudatoolkit
                 ++ lib.optional cudnnSupport cudnn
                 ++ lib.optional lmdbSupport lmdb
@@ -73,9 +73,17 @@ stdenv.mkDerivation rec {
                 ++ lib.optionals stdenv.isDarwin [ Accelerate CoreGraphics CoreVideo ]
                 ;
 
-  propagatedBuildInputs = lib.optional pythonSupport python.pkgs.protobuf;
-
-  outputs = [ "bin" "out"];
+  propagatedBuildInputs = lib.optionals pythonSupport (
+    # requirements.txt
+    let pp = python.pkgs; in ([
+      pp.numpy pp.scipy pp.scikitimage pp.h5py
+      pp.matplotlib pp.ipython pp.networkx pp.nose
+      pp.pandas pp.dateutil pp.protobuf pp.gflags
+      pp.pyyaml pp.pillow pp.six
+    ] ++ lib.optional leveldbSupport pp.leveldb)
+  );
+
+  outputs = [ "bin" "out" ];
   propagatedBuildOutputs = []; # otherwise propagates out -> bin cycle
 
   patches = [
diff --git a/nixpkgs/pkgs/applications/science/math/caffe/python.patch b/nixpkgs/pkgs/applications/science/math/caffe/python.patch
index b1bed6c174b8..dac5071aa08c 100644
--- a/nixpkgs/pkgs/applications/science/math/caffe/python.patch
+++ b/nixpkgs/pkgs/applications/science/math/caffe/python.patch
@@ -64,7 +64,7 @@ index 4a5bac47..be026d43 100644
 -  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON_FOUND)
 +  find_package(NumPy 1.7.1)
 +  find_package(Boost 1.46 REQUIRED COMPONENTS python@major@@minor@)
-+  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND BOOST_PYTHON@major@@minor@_FOUND)
++  if(PYTHONLIBS_FOUND AND NUMPY_FOUND AND Boost_PYTHON@major@@minor@_FOUND)
      set(HAVE_PYTHON TRUE)
      if(BUILD_python_layer)
        list(APPEND Caffe_DEFINITIONS PRIVATE -DWITH_PYTHON_LAYER)
diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
index 1a3ba8096e29..fbdbac003dcd 100644
--- a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix
@@ -1,14 +1,14 @@
 { stdenv, fetchurl, cmake, openblasCompat, gfortran, gmm, fltk, libjpeg
 , zlib, libGLU_combined, libGLU, xorg }:
 
-let version = "4.4.0"; in
+let version = "4.4.1"; in
 
 stdenv.mkDerivation {
   name = "gmsh-${version}";
 
   src = fetchurl {
     url = "http://gmsh.info/src/gmsh-${version}-source.tgz";
-    sha256 = "0b0h15cmi6zy31cii7r9jmfm9xksljff255dn6l9frhdjymkmx7l";
+    sha256 = "1p7hibmsgv961lfkzdxlgcvmcb0q155m2sp60r97cjsfzhw68g45";
   };
 
   buildInputs = [ openblasCompat gmm fltk libjpeg zlib libGLU_combined
diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/11.nix b/nixpkgs/pkgs/applications/science/math/mathematica/11.nix
new file mode 100644
index 000000000000..521cb70099b9
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/math/mathematica/11.nix
@@ -0,0 +1,150 @@
+{ stdenv
+, coreutils
+, patchelf
+, requireFile
+, callPackage
+, alsaLib
+, dbus
+, fontconfig
+, freetype
+, gcc
+, glib
+, ncurses
+, opencv
+, openssl
+, unixODBC
+, xkeyboard_config
+, xorg
+, zlib
+, libxml2
+, libuuid
+, lang ? "en"
+, libGL
+, libGLU
+}:
+
+let
+  l10n =
+    import ./l10ns.nix {
+      lib = stdenv.lib;
+      inherit requireFile lang;
+      majorVersion = "11";
+    };
+in
+stdenv.mkDerivation rec {
+  inherit (l10n) version name src;
+
+  buildInputs = [
+    coreutils
+    patchelf
+    alsaLib
+    coreutils
+    dbus
+    fontconfig
+    freetype
+    gcc.cc
+    gcc.libc
+    glib
+    ncurses
+    opencv
+    openssl
+    unixODBC
+    xkeyboard_config
+    libxml2
+    libuuid
+    zlib
+    libGL
+    libGLU
+  ] ++ (with xorg; [
+    libX11
+    libXext
+    libXtst
+    libXi
+    libXmu
+    libXrender
+    libxcb
+    libXcursor
+    libXfixes
+    libXrandr
+    libICE
+    libSM
+  ]);
+
+  ldpath = stdenv.lib.makeLibraryPath buildInputs
+    + stdenv.lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux")
+      (":" + stdenv.lib.makeSearchPathOutput "lib" "lib64" buildInputs);
+
+  phases = "unpackPhase installPhase fixupPhase";
+
+  unpackPhase = ''
+    echo "=== Extracting makeself archive ==="
+    # find offset from file
+    offset=$(${stdenv.shell} -c "$(grep -axm1 -e 'offset=.*' $src); echo \$offset" $src)
+    dd if="$src" ibs=$offset skip=1 | tar -xf -
+    cd Unix
+  '';
+
+  installPhase = ''
+    cd Installer
+    # don't restrict PATH, that has already been done
+    sed -i -e 's/^PATH=/# PATH=/' MathInstaller
+    sed -i -e 's/\/bin\/bash/\/bin\/sh/' MathInstaller
+
+    echo "=== Running MathInstaller ==="
+    ./MathInstaller -auto -createdir=y -execdir=$out/bin -targetdir=$out/libexec/Mathematica -silent
+
+    # Fix library paths
+    cd $out/libexec/Mathematica/Executables
+    for path in mathematica MathKernel Mathematica WolframKernel wolfram math; do
+      sed -i -e 's#export LD_LIBRARY_PATH$#export LD_LIBRARY_PATH=${zlib}/lib:\''${LD_LIBRARY_PATH}#' $path
+    done
+
+    # Fix xkeyboard config path for Qt
+    for path in mathematica Mathematica; do
+      line=$(grep -n QT_PLUGIN_PATH $path | sed 's/:.*//')
+      sed -i -e "$line iexport QT_XKB_CONFIG_ROOT=\"${xkeyboard_config}/share/X11/xkb\"" $path
+    done
+  '';
+
+  preFixup = ''
+    echo "=== PatchElfing away ==="
+    # This code should be a bit forgiving of errors, unfortunately
+    set +e
+    find $out/libexec/Mathematica/SystemFiles -type f -perm -0100 | while read f; do
+      type=$(readelf -h "$f" 2>/dev/null | grep 'Type:' | sed -e 's/ *Type: *\([A-Z]*\) (.*/\1/')
+      if [ -z "$type" ]; then
+        :
+      elif [ "$type" == "EXEC" ]; then
+        echo "patching $f executable <<"
+        patchelf --shrink-rpath "$f"
+        patchelf \
+	  --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \
+          --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \
+          "$f" \
+          && patchelf --shrink-rpath "$f" \
+          || echo unable to patch ... ignoring 1>&2
+      elif [ "$type" == "DYN" ]; then
+        echo "patching $f library <<"
+        patchelf \
+          --set-rpath "$(patchelf --print-rpath "$f"):${ldpath}" \
+          "$f" \
+          && patchelf --shrink-rpath "$f" \
+          || echo unable to patch ... ignoring 1>&2
+      else
+        echo "not patching $f <<: unknown elf type"
+      fi
+    done
+  '';
+
+  # all binaries are already stripped
+  dontStrip = true;
+
+  # we did this in prefixup already
+  dontPatchELF = true;
+
+  meta = {
+    description = "Wolfram Mathematica computational software system";
+    homepage = http://www.wolfram.com/mathematica/;
+    license = stdenv.lib.licenses.unfree;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/default.nix b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix
index 165a56605579..ca9a87abe13b 100644
--- a/nixpkgs/pkgs/applications/science/math/mathematica/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/mathematica/default.nix
@@ -1,6 +1,7 @@
 { stdenv
 , coreutils
 , patchelf
+, requireFile
 , callPackage
 , alsaLib
 , dbus
@@ -24,10 +25,10 @@
 
 let
   l10n =
-    with stdenv.lib;
-    with callPackage ./l10ns.nix {};
-    flip (findFirst (l: l.lang == lang)) l10ns
-      (throw "Language '${lang}' not supported");
+    import ./l10ns.nix {
+      lib = stdenv.lib;
+      inherit requireFile lang;
+    };
 in
 stdenv.mkDerivation rec {
   inherit (l10n) version name src;
@@ -72,8 +73,6 @@ stdenv.mkDerivation rec {
     + stdenv.lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux")
       (":" + stdenv.lib.makeSearchPathOutput "lib" "lib64" buildInputs);
 
-  phases = "unpackPhase installPhase fixupPhase";
-
   unpackPhase = ''
     echo "=== Extracting makeself archive ==="
     # find offset from file
@@ -99,8 +98,7 @@ stdenv.mkDerivation rec {
 
     # Fix xkeyboard config path for Qt
     for path in mathematica Mathematica; do
-      line=$(grep -n QT_PLUGIN_PATH $path | sed 's/:.*//')
-      sed -i -e "$line iexport QT_XKB_CONFIG_ROOT=\"${xkeyboard_config}/share/X11/xkb\"" $path
+      sed -i -e "2iexport QT_XKB_CONFIG_ROOT=\"${xkeyboard_config}/share/X11/xkb\"\n" $path
     done
   '';
 
@@ -134,15 +132,19 @@ stdenv.mkDerivation rec {
     done
   '';
 
+  dontBuild = true;
+
   # all binaries are already stripped
   dontStrip = true;
 
   # we did this in prefixup already
   dontPatchELF = true;
 
-  meta = {
+  meta = with stdenv.lib; {
     description = "Wolfram Mathematica computational software system";
     homepage = http://www.wolfram.com/mathematica/;
-    license = stdenv.lib.licenses.unfree;
+    license = licenses.unfree;
+    maintainers = with maintainers; [ herberteuler ];
+    platforms = [ "x86_64-linux" ];
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix b/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix
index 065360a112d8..51fb489be7ec 100644
--- a/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix
+++ b/nixpkgs/pkgs/applications/science/math/mathematica/l10ns.nix
@@ -1,10 +1,19 @@
-{ lib, requireFile }:
+{ lib
+, requireFile
+, lang
+, majorVersion ? null
+}:
 
-with lib;
-{
-  l10ns = flip map
+let allVersions = with lib; flip map
+  # N.B. Versions in this list should be ordered from newest to oldest.
   [
     {
+      version = "12.0.0";
+      lang = "en";
+      language = "English";
+      sha256 = "b9fb71e1afcc1d72c200196ffa434512d208fa2920e207878433f504e58ae9d7";
+    }
+    {
       version = "11.3.0";
       lang = "en";
       language = "English";
@@ -30,4 +39,16 @@ with lib;
       inherit sha256;
     };
   });
-}
+minVersion =
+  with lib;
+  if majorVersion == null
+  then elemAt (builtins.splitVersion (elemAt allVersions 0).version) 0
+  else majorVersion;
+maxVersion = toString (1 + builtins.fromJSON minVersion);
+in
+with lib;
+findFirst (l: (l.lang == lang
+               && l.version >= minVersion
+               && l.version < maxVersion))
+          (throw "Version ${minVersion} in language ${lang} not supported")
+          allVersions
diff --git a/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix b/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix
index 4915e42025b5..86bd2e843678 100644
--- a/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix
+++ b/nixpkgs/pkgs/applications/science/math/pari/gp2c.nix
@@ -4,11 +4,11 @@
 stdenv.mkDerivation rec {
 
   name = "gp2c-${version}";
-  version = "0.0.11pl1";
+  version = "0.0.11pl2";
 
   src = fetchurl {
     url = "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/${name}.tar.gz";
-    sha256 = "1c6f6vmncw032kfzrfyr8bynw6yd3faxpy2285r009fmr0zxfs5s";
+    sha256 = "0wqsf05wgkqvmmsx7jinvzdqav6rl56sr8haibgs31nzz4x9xz9g";
   };
 
   buildInputs = [ pari perl ];
diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
index 4da3a3f3d7bc..b4d82b9583c4 100644
--- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "qalculate-gtk";
-  version = "3.2.0";
+  version = "3.3.0";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "1yhhfqcxi1b7dfrl8qh16l9iwgzvw1p0hhl7nnjpxhdwxz880sv0";
+    sha256 = "1z2d32dcvdd66114j3km58xfk80hc5rd0zrh2fgz1azv8r4cqq1b";
   };
 
   patchPhase = ''
diff --git a/nixpkgs/pkgs/applications/science/math/sage/patches/sympow-cache.patch b/nixpkgs/pkgs/applications/science/math/sage/patches/sympow-cache.patch
new file mode 100644
index 000000000000..20020d610f80
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/math/sage/patches/sympow-cache.patch
@@ -0,0 +1,21 @@
+diff --git a/src/sage/lfunctions/sympow.py b/src/sage/lfunctions/sympow.py
+index 1640ac4f6a..03578be7b8 100644
+--- a/src/sage/lfunctions/sympow.py
++++ b/src/sage/lfunctions/sympow.py
+@@ -50,6 +50,7 @@ from __future__ import print_function, absolute_import
+ 
+ import os
+ 
++from sage.env import DOT_SAGE
+ from sage.structure.sage_object import SageObject
+ from sage.misc.all import pager, verbose
+ import sage.rings.all
+@@ -76,7 +77,7 @@ class Sympow(SageObject):
+         """
+         Used to call sympow with given args
+         """
+-        cmd = 'sympow %s'%args
++        cmd = 'env SYMPOW_CACHEDIR="%s/sympow///" sympow %s' % (DOT_SAGE, args)
+         v = os.popen(cmd).read().strip()
+         verbose(v, level=2)
+         return v
diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
index 51460154c5de..04a2cde9ba99 100644
--- a/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
+++ b/nixpkgs/pkgs/applications/science/math/sage/sage-src.nix
@@ -100,6 +100,11 @@ stdenv.mkDerivation rec {
       rev = "c11d9cfa23ff9f77681a8f12742f68143eed4504";
       sha256 = "0xzra7mbgqvahk9v45bjwir2mqz73hrhhy314jq5nxrb35ysdxyi";
     })
+
+    # After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
+    # now set the cache dir to be withing the .sage directory. This is not
+    # strictly necessary, but keeps us from littering in the user's HOME.
+    ./patches/sympow-cache.patch
   ];
 
   patches = nixPatches ++ bugfixPatches ++ packageUpgradePatches;
diff --git a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix
index 262ee7d0d5da..21ce53e70c51 100644
--- a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix
+++ b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix
@@ -3,7 +3,7 @@
 let
   name = "scilab-bin-${ver}";
 
-  ver = "6.0.1";
+  ver = "6.0.2";
 
   badArch = throw "${name} requires i686-linux or x86_64-linux";
 
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
       if stdenv.hostPlatform.system == "i686-linux" then
         "0fgjc2ak3b2qi6yin3fy50qwk2bcj0zbz1h4lyyic9n1n1qcliib"
       else if stdenv.hostPlatform.system == "x86_64-linux" then
-        "1scswlznc14vyzg0gqa1q9gcpwx05kz1sbn563463mzkdp7nd35d"
+        "05clcdgry90drirl3swbxn5q36fmgknnhs6h5pr7mmrzfr6r818w"
       else
         badArch;
   };
diff --git a/nixpkgs/pkgs/applications/science/misc/motu-client/default.nix b/nixpkgs/pkgs/applications/science/misc/motu-client/default.nix
deleted file mode 100644
index d4367ef7e2d3..000000000000
--- a/nixpkgs/pkgs/applications/science/misc/motu-client/default.nix
+++ /dev/null
@@ -1,23 +0,0 @@
-{ python27Packages, fetchurl, lib } :
-python27Packages.buildPythonApplication rec {
-  pname = "motu-client";
-  version = "1.5.00";
-
-  src = fetchurl {
-    url = "https://github.com/quiet-oceans/motuclient-setuptools/archive/${version}.tar.gz";
-    sha256 = "1iqsws3wa2gpb36ms21xmaxfi83i8p8cdya4cxpn4r47c8mz74x8";
-  };
-
-  meta = with lib; {
-    homepage = https://github.com/quiet-oceans/motuclient-setuptools;
-    description = "CLI to query oceanographic data to Motu servers";
-    longDescription = ''
-      Access data from (motu)[https://sourceforge.net/projects/cls-motu/] servers.
-      This is a refactored fork of the original release in order to simplify integration,
-      deployment and packaging. Upstream code can be found at
-      https://sourceforge.net/projects/cls-motu/ .
-    '';
-    license = licenses.lgpl3Plus;
-    maintainers = [ maintainers.lsix ];
-  };
-}
diff --git a/nixpkgs/pkgs/applications/science/misc/openmvs/default.nix b/nixpkgs/pkgs/applications/science/misc/openmvs/default.nix
index f44d07d36db8..43d57feab71b 100644
--- a/nixpkgs/pkgs/applications/science/misc/openmvs/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/openmvs/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, pkgconfig, cmake
 , eigen, opencv, ceres-solver, cgal, boost, vcg
-, gmp, mpfr, glog, google-gflags, libjpeg_turbo }:
+, gmp, mpfr, glog, gflags, libjpeg_turbo }:
 
 stdenv.mkDerivation rec {
   name = "openmvs-unstable-2018-05-26";
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
     sha256 = "12dgkwwfdp24581y3i41gsd1k9hq0aw917q0ja5s0if4qbmc8pni";
   };
 
-  buildInputs = [ eigen opencv ceres-solver cgal boost vcg gmp mpfr glog google-gflags libjpeg_turbo ];
+  buildInputs = [ eigen opencv ceres-solver cgal boost vcg gmp mpfr glog gflags libjpeg_turbo ];
 
   nativeBuildInputs = [ cmake pkgconfig ];
 
@@ -28,7 +28,7 @@ stdenv.mkDerivation rec {
       "-DCERES_DIR=${ceres-solver}/lib/cmake/Ceres/"
     )
   '';
-  
+
   postFixup = ''
     rp=$(patchelf --print-rpath $out/bin/DensifyPointCloud)
     patchelf --set-rpath $rp:$out/lib/OpenMVS $out/bin/DensifyPointCloud
@@ -45,7 +45,7 @@ stdenv.mkDerivation rec {
     rp=$(patchelf --print-rpath $out/bin/TextureMesh)
     patchelf --set-rpath $rp:$out/lib/OpenMVS $out/bin/TextureMesh
   '';
-  
+
   cmakeDir = "./";
 
   dontUseCmakeBuildDir = true;
diff --git a/nixpkgs/pkgs/applications/science/misc/root/5.nix b/nixpkgs/pkgs/applications/science/misc/root/5.nix
index 871f5ece9cfe..0199373b082c 100644
--- a/nixpkgs/pkgs/applications/science/misc/root/5.nix
+++ b/nixpkgs/pkgs/applications/science/misc/root/5.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, fetchpatch, cmake, pcre, pkgconfig, python2
 , libX11, libXpm, libXft, libXext, libGLU_combined, zlib, libxml2, lzma, gsl_1
-, Cocoa, OpenGL, cf-private, noSplash ? false }:
+, Cocoa, OpenGL, noSplash ? false }:
 
 stdenv.mkDerivation rec {
   name = "root-${version}";
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ cmake pcre python2 zlib libxml2 lzma gsl_1 ]
     ++ stdenv.lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU_combined ]
-    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL cf-private ]
+    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
     ;
 
   patches = [
diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix
index 8b9573ce4e8b..2ec1ded68a26 100644
--- a/nixpkgs/pkgs/applications/science/misc/root/default.nix
+++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, cmake, pcre, pkgconfig, python2
 , libX11, libXpm, libXft, libXext, libGLU_combined, zlib, libxml2, lz4, lzma, gsl, xxHash
-, Cocoa, OpenGL, cf-private, noSplash ? false }:
+, Cocoa, OpenGL, noSplash ? false }:
 
 stdenv.mkDerivation rec {
   name = "root-${version}";
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ cmake pcre python2 zlib libxml2 lz4 lzma gsl xxHash ]
     ++ stdenv.lib.optionals (!stdenv.isDarwin) [ libX11 libXpm libXft libXext libGLU_combined ]
-    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL cf-private ]
+    ++ stdenv.lib.optionals (stdenv.isDarwin) [ Cocoa OpenGL ]
     ;
 
   patches = [
diff --git a/nixpkgs/pkgs/applications/science/physics/sacrifice/default.nix b/nixpkgs/pkgs/applications/science/physics/sacrifice/default.nix
index 64b88dcc3d4f..d43a05f1c616 100644
--- a/nixpkgs/pkgs/applications/science/physics/sacrifice/default.nix
+++ b/nixpkgs/pkgs/applications/science/physics/sacrifice/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, boost, hepmc, lhapdf, pythia, makeWrapper }:
+{ stdenv, fetchurl, boost, hepmc2, lhapdf, pythia, makeWrapper }:
 
 stdenv.mkDerivation rec {
   name = "sacrifice-${version}";
@@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
     sha256 = "10bvpq63kmszy1habydwncm0j1dgvam0fkrmvkgbkvf804dcjp6g";
   };
 
-  buildInputs = [ boost hepmc lhapdf pythia ];
+  buildInputs = [ boost hepmc2 lhapdf pythia ];
   nativeBuildInputs = [ makeWrapper ];
 
   patches = [
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
   '';
 
   configureFlags = [
-    "--with-HepMC=${hepmc}"
+    "--with-HepMC=${hepmc2}"
     "--with-pythia=${pythia}"
   ];
 
diff --git a/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix b/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix
index 7cb3e8881caf..1d61c612563f 100644
--- a/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix
+++ b/nixpkgs/pkgs/applications/science/physics/sherpa/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, gfortran, hepmc, fastjet, lhapdf, rivet, sqlite }:
+{ stdenv, fetchurl, gfortran, hepmc2, fastjet, lhapdf, rivet, sqlite }:
 
 stdenv.mkDerivation rec {
   name = "sherpa-${version}";
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
 
   configureFlags = [
     "--with-sqlite3=${sqlite.dev}"
-    "--enable-hepmc2=${hepmc}"
+    "--enable-hepmc2=${hepmc2}"
     "--enable-fastjet=${fastjet}"
     "--enable-lhapdf=${lhapdf}"
     "--enable-rivet=${rivet}"