Merge branch 'master' into staging-next

Hydra: ?compare=1473892

pkgs/applications/audio/mimic/default.nix

@@ -0,0 +1,35 @@
+{ stdenv, autoreconfHook, fetchFromGitHub, pkgconfig
+, alsaLib, libtool, icu
+, pulseaudioSupport ? true, libpulseaudio }:
+
+stdenv.mkDerivation rec {
+  name = "mimic-${version}";
+  version = "1.2.0.2";
+
+  src = fetchFromGitHub {
+    rev = version;
+    repo = "mimic";
+    owner = "MycroftAI";
+    sha256 = "1wkpbwk88lsahzkc7pzbznmyy0lc02vsp0vkj8f1ags1gh0lc52j";
+  };
+
+  nativeBuildInputs = [ 
+    autoreconfHook
+    pkgconfig
+  ];
+
+  buildInputs = [
+    alsaLib
+    libtool
+    icu 
+  ] ++ stdenv.lib.optional pulseaudioSupport libpulseaudio;
+
+  meta = {
+    description = "Mycroft's TTS engine, based on CMU's Flite (Festival Lite)";
+    homepage = https://mimic.mycroft.ai/; 
+    license = stdenv.lib.licenses.free;
+    platforms = stdenv.lib.platforms.linux;
+    maintainers = [ stdenv.lib.maintainers.noneucat ]; 
+  };
+}
+

pkgs/applications/audio/pulseeffects/default.nix

@@ -29,6 +29,7 @@
 , zam-plugins
 , rubberband
 , mda_lv2
+, hicolor-icon-theme
 }:
 
 let
@@ -42,13 +43,13 @@ let
   ];
 in stdenv.mkDerivation rec {
   name = "pulseeffects-${version}";
-  version = "4.2.6";
+  version = "4.2.8";
 
   src = fetchFromGitHub {
     owner = "wwmm";
     repo = "pulseeffects";
     rev = "v${version}";
-    sha256 = "1b5h760bb1wgn4avirjjri5fcfqvnsr076qnhrdiqcic3vgircsm";
+    sha256 = "0ckl0640n6lhk0gcmnmwngajkf46rrd8bxfh7xy5sq6qmm01dhdd";
   };
 
   nativeBuildInputs = [
@@ -79,6 +80,7 @@ in stdenv.mkDerivation rec {
     boost
     fftwFloat
     zita-convolver
+    hicolor-icon-theme
   ];
 
   postPatch = ''

pkgs/applications/audio/snd/default.nix

@@ -4,11 +4,11 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "snd-18.5";
+  name = "snd-18.6";
 
   src = fetchurl {
     url = "mirror://sourceforge/snd/${name}.tar.gz";
-    sha256 = "1m2rw1p9xr9428p9drd3w5irsi12lz23m605lzgk9gjamq9paywy";
+    sha256 = "1jyqkkz2a6zw0jn9y15xd3027r8glkpw794fjk6hd3al1byjhz2z";
   };
 
   nativeBuildInputs = [ pkgconfig ];

pkgs/applications/display-managers/lightdm/gtk-greeter.nix

@@ -20,7 +20,7 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ lightdm exo intltool makeWrapper ]
+  buildInputs = [ lightdm exo intltool makeWrapper hicolor-icon-theme ]
     ++ (if useGTK2 then [ gtk2 ] else [ gtk3 ]);
 
   configureFlags = [

pkgs/applications/editors/emacs/default.nix

@@ -1,11 +1,12 @@
 { stdenv, lib, fetchurl, ncurses, xlibsWrapper, libXaw, libXpm, Xaw3d
 , pkgconfig, gettext, libXft, dbus, libpng, libjpeg, libungif
 , libtiff, librsvg, gconf, libxml2, imagemagick, gnutls, libselinux
-, alsaLib, cairo, acl, gpm, AppKit, GSS, ImageIO
+, alsaLib, cairo, acl, gpm, AppKit, GSS, ImageIO, m17n_lib, libotf
+, systemd ? null
 , withX ? !stdenv.isDarwin
 , withGTK2 ? false, gtk2 ? null
 , withGTK3 ? true, gtk3 ? null, gsettings-desktop-schemas ? null
-, withXwidgets ? false, webkitgtk24x-gtk3 ? null, wrapGAppsHook ? null, glib-networking ? null
+, withXwidgets ? false, webkitgtk ? null, wrapGAppsHook ? null, glib-networking ? null
 , withCsrc ? true
 , srcRepo ? false, autoconf ? null, automake ? null, texinfo ? null
 }:
@@ -16,7 +17,7 @@ assert withGTK2 -> withX || stdenv.isDarwin;
 assert withGTK3 -> withX || stdenv.isDarwin;
 assert withGTK2 -> !withGTK3 && gtk2 != null;
 assert withGTK3 -> !withGTK2 && gtk3 != null;
-assert withXwidgets -> withGTK3 && webkitgtk24x-gtk3 != null;
+assert withXwidgets -> withGTK3 && webkitgtk != null;
 
 let
   toolkit =
@@ -52,14 +53,14 @@ stdenv.mkDerivation rec {
 
   buildInputs =
     [ ncurses gconf libxml2 gnutls alsaLib acl gpm gettext ]
-    ++ lib.optionals stdenv.isLinux [ dbus libselinux ]
+    ++ lib.optionals stdenv.isLinux [ dbus libselinux systemd ]
     ++ lib.optionals withX
       [ xlibsWrapper libXaw Xaw3d libXpm libpng libjpeg libungif libtiff librsvg libXft
-        imagemagick gconf ]
+        imagemagick gconf m17n_lib libotf ]
     ++ lib.optional (withX && withGTK2) gtk2
     ++ lib.optionals (withX && withGTK3) [ gtk3 gsettings-desktop-schemas ]
     ++ lib.optional (stdenv.isDarwin && withX) cairo
-    ++ lib.optionals (withX && withXwidgets) [ webkitgtk24x-gtk3 glib-networking ];
+    ++ lib.optionals (withX && withXwidgets) [ webkitgtk ];
 
   propagatedBuildInputs = lib.optionals stdenv.isDarwin [ AppKit GSS ImageIO ];
 

pkgs/applications/editors/vscode/default.nix

@@ -2,7 +2,7 @@
   gtk2, makeWrapper, libXScrnSaver, libxkbfile, libsecret }:
 
 let
-  version = "1.25.1";
+  version = "1.26.0";
   channel = "stable";
 
   plat = {
@@ -12,9 +12,9 @@ let
   }.${stdenv.system};
 
   sha256 = {
-    "i686-linux" = "1qljnajk4h9ki5gvydh1b557fvhvcryvkrvypvz0pr804lpdqsmg";
-    "x86_64-linux" = "0f1lpwyxfchmbymzzxv97w9cy1z5pdljhwm49mc5v84aygmvnmjq";
-    "x86_64-darwin" = "1dgda1drij1c114xzv4hs44k7rx4x1vzghlxgii0h2rg641n6pbn";
+    "i686-linux" = "fd150bee8e1be4f5461013b8fee19f855200d046643e4ea5387aad170ad5f12b";
+    "x86_64-linux" = "618ca429e23777ef6b512c0cbd78bc711a7cf6f58752d9f805ced1dc62abb8f0";
+    "x86_64-darwin" = "07c2d678596e4e1f0bdf35b7d72a6d46851bf169d89f134fa73ff4f9007efbc3";
   }.${stdenv.system};
 
   archive_fmt = if stdenv.system == "x86_64-darwin" then "zip" else "tar.gz";

pkgs/applications/graphics/darktable/default.nix

@@ -3,7 +3,7 @@
 , ilmbase, gtk3, intltool, lcms2, lensfun, libX11, libexif, libgphoto2, libjpeg
 , libpng, librsvg, libtiff, openexr, osm-gps-map, pkgconfig, sqlite, libxslt
 , openjpeg, lua, pugixml, colord, colord-gtk, libwebp, libsecret, gnome3
-, ocl-icd
+, ocl-icd, pcre, gtk-mac-integration
 }:
 
 stdenv.mkDerivation rec {
@@ -18,24 +18,32 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake ninja llvm pkgconfig intltool perl desktop-file-utils wrapGAppsHook ];
 
   buildInputs = [
-    cairo curl exiv2 glib gtk3 ilmbase lcms2 lensfun libX11 libexif
+    cairo curl exiv2 glib gtk3 ilmbase lcms2 lensfun libexif
     libgphoto2 libjpeg libpng librsvg libtiff openexr sqlite libxslt
     libsoup graphicsmagick json-glib openjpeg lua pugixml
-    colord colord-gtk libwebp libsecret gnome3.adwaita-icon-theme
-    osm-gps-map ocl-icd
-  ];
-    
+    libwebp libsecret gnome3.adwaita-icon-theme osm-gps-map pcre
+  ] ++ stdenv.lib.optionals stdenv.isLinux [
+    colord colord-gtk libX11 ocl-icd
+  ] ++ stdenv.lib.optional stdenv.isDarwin gtk-mac-integration;
+
   cmakeFlags = [
     "-DBUILD_USERMANUAL=False"
+  ] ++ stdenv.lib.optionals stdenv.isDarwin [
+    "-DUSE_COLORD=OFF"
+    "-DUSE_KWALLET=OFF"
   ];
 
+
   # darktable changed its rpath handling in commit
   # 83c70b876af6484506901e6b381304ae0d073d3c and as a result the
   # binaries can't find libdarktable.so, so change LD_LIBRARY_PATH in
   # the wrappers:
-  preFixup = ''
+  preFixup = let
+    libPathEnvVar = if stdenv.isDarwin then "DYLD_LIBRARY_PATH" else "LD_LIBRARY_PATH";
+    libPathPrefix = "$out/lib/darktable" + stdenv.lib.optionalString stdenv.isLinux ":${ocl-icd}/lib";
+  in ''
     gappsWrapperArgs+=(
-      --prefix LD_LIBRARY_PATH ":" "$out/lib/darktable:${ocl-icd}/lib"
+      --prefix ${libPathEnvVar} ":" "${libPathPrefix}"
     )
   '';
 
@@ -43,7 +51,7 @@ stdenv.mkDerivation rec {
     description = "Virtual lighttable and darkroom for photographers";
     homepage = https://www.darktable.org;
     license = licenses.gpl3Plus;
-    platforms = platforms.linux;
+    platforms = platforms.linux ++ platforms.darwin;
     maintainers = with maintainers; [ goibhniu rickynils flosse mrVanDalo ];
   };
 }

pkgs/applications/graphics/meshlab/default.nix

@@ -1,10 +1,13 @@
-{ stdenv, fetchFromGitHub, libGLU, qtbase, qtscript, qtxmlpatterns }:
+{ fetchFromGitHub, libGLU, llvmPackages, qtbase, qtscript, qtxmlpatterns }:
 
 let
-  meshlabRev = "5700f5474c8f90696a8925e2a209a0a8ab506662";
-  vcglibRev = "a8e87662b63ee9f4ded5d4699b28d74183040803";
+  meshlabRev = "d596d7c086c51fbdfb56050f9c30b55dd0286d4c";
+  vcglibRev = "6c3c940e34327322507c703889f9f1cfa73ab183";
+  # ^ this should be the latest commit in the vcglib devel branch at the time of the meshlab revision
+
+  stdenv = llvmPackages.stdenv; # only building with clang seems to be tested upstream
 in stdenv.mkDerivation {
-  name = "meshlab-2016.12";
+  name = "meshlab-20180627-beta";
 
   srcs =
     [
@@ -12,31 +15,32 @@ in stdenv.mkDerivation {
         owner = "cnr-isti-vclab";
         repo = "meshlab";
         rev = meshlabRev;
-        sha256 = "0srrp7zhi86dsg4zsx1615gr26barz38zdl8s03zq6vm1dgzl3cc";
+        sha256 = "0xi7wiyy0yi545l5qvccbqahlcsf70mhx829gf7bq29640si4rax";
         name = "meshlab-${meshlabRev}";
       })
       (fetchFromGitHub {
         owner = "cnr-isti-vclab";
         repo = "vcglib";
         rev = vcglibRev;
-        sha256 = "0jh8jc8rn7rci8qr3q03q574fk2hsc3rllysck41j8xkr3rmxz2f";
+        sha256 = "0jfgjvf21y9ncmyr7caipy3ardhig7hh9z8miy885c99b925hhwd";
         name = "vcglib-${vcglibRev}";
       })
     ];
 
   sourceRoot = "meshlab-${meshlabRev}";
 
-  patches = [ ./fix-2016.02.patch ];
-
   hardeningDisable = [ "format" ];
   enableParallelBuilding = true;
 
+  patches = [ ./fix-20180627-beta.patch ];
+
   buildPhase = ''
     # MeshLab has ../vcglib hardcoded everywhere, so move the source dir
     mv ../vcglib-${vcglibRev} ../vcglib
 
     cd src
     export NIX_LDFLAGS="-rpath $out/opt/meshlab $NIX_LDFLAGS"
+    export QMAKESPEC="linux-clang"
 
     pushd external
     qmake -recursive external.pro
@@ -53,7 +57,7 @@ in stdenv.mkDerivation {
     ln -s $out/opt/meshlab/meshlabserver $out/bin/meshlabserver
   '';
 
-  buildInputs = [ libGLU qtbase qtscript qtxmlpatterns ];
+  buildInputs = [ libGLU llvmPackages.openmp qtbase qtscript qtxmlpatterns ];
 
   meta = {
     description = "A system for processing and editing 3D triangular meshes.";
@@ -61,6 +65,5 @@ in stdenv.mkDerivation {
     license = stdenv.lib.licenses.gpl3;
     maintainers = with stdenv.lib.maintainers; [viric];
     platforms = with stdenv.lib.platforms; linux;
-    broken = true; # 2018-04-11
   };
 }

pkgs/applications/graphics/meshlab/fix-2016.02.patch

@@ -1,88 +0,0 @@
-From 0fd17cd2b6d57e8a2a981a70115c2565ee076d0f Mon Sep 17 00:00:00 2001
-From: Marco Callieri <callieri@isti.cnr.it>
-Date: Mon, 9 Jan 2017 16:06:14 +0100
-Subject: [PATCH 1/3] resolved ambiguity for abs overloads
-
-
-diff --git a/src/meshlabplugins/edit_quality/eqhandle.cpp b/src/meshlabplugins/edit_quality/eqhandle.cpp
-index 364d53bf..ef3d4a2d 100644
---- a/src/meshlabplugins/edit_quality/eqhandle.cpp
-+++ b/src/meshlabplugins/edit_quality/eqhandle.cpp
-@@ -83,7 +83,7 @@ void EqHandle::mouseMoveEvent(QGraphicsSceneMouseEvent *event)
- 	setCursor(Qt::OpenHandCursor);
- 
- 	QPointF newPos = event->scenePos();
--	qreal handleOffset = abs(newPos.x()-pos().x());
-+	qreal handleOffset = std::fabs(newPos.x()-pos().x());
- 
- 	if (handleOffset >= std::numeric_limits<float>::epsilon())
- 	{
--- 
-2.15.0
-
-
-From 33cfd5801e59b6c9e34360c75112e6dcb88d807b Mon Sep 17 00:00:00 2001
-From: Marco Callieri <callieri@isti.cnr.it>
-Date: Tue, 10 Jan 2017 10:05:05 +0100
-Subject: [PATCH 2/3] again, fabs ambiguity
-
-
-diff --git a/src/meshlabplugins/edit_quality/eqhandle.cpp b/src/meshlabplugins/edit_quality/eqhandle.cpp
-index ef3d4a2d..d29f8c45 100644
---- a/src/meshlabplugins/edit_quality/eqhandle.cpp
-+++ b/src/meshlabplugins/edit_quality/eqhandle.cpp
-@@ -30,6 +30,7 @@ FIRST RELEASE
- #include "eqhandle.h"
- #include <QMouseEvent>
- #include <QGraphicsSceneMouseEvent>
-+#include <math.h>
- 
- EqHandle::EqHandle(CHART_INFO *environment_info, QColor color, QPointF position, 
- 				   EQUALIZER_HANDLE_TYPE type, EqHandle** handles, qreal* midHandlePercentilePosition, QDoubleSpinBox* spinbox,
-@@ -83,7 +84,7 @@ void EqHandle::mouseMoveEvent(QGraphicsSceneMouseEvent *event)
- 	setCursor(Qt::OpenHandCursor);
- 
- 	QPointF newPos = event->scenePos();
--	qreal handleOffset = std::fabs(newPos.x()-pos().x());
-+	qreal handleOffset = fabs(newPos.x()-pos().x());
- 
- 	if (handleOffset >= std::numeric_limits<float>::epsilon())
- 	{
--- 
-2.15.0
-
-
-From d717e44f4134ebee03322a6a2a56fce626084a3c Mon Sep 17 00:00:00 2001
-From: Patrick Chilton <chpatrick@gmail.com>
-Date: Mon, 4 Dec 2017 21:27:23 +0100
-Subject: [PATCH 3/3] io_TXT -> io_txt
-
-
-diff --git a/src/meshlab_full.pro b/src/meshlab_full.pro
-index 6ea7f1db..2a95c127 100644
---- a/src/meshlab_full.pro
-+++ b/src/meshlab_full.pro
-@@ -16,7 +16,7 @@ SUBDIRS       = common \
-                 meshlabplugins/io_x3d \
-                 meshlabplugins/io_expe \
-                 meshlabplugins/io_pdb \
--                plugins_experimental/io_TXT \
-+                plugins_experimental/io_txt \
- # Filter plugins
-                 meshlabplugins/filter_aging \
-                 meshlabplugins/filter_ao \
-diff --git a/src/plugins_experimental/io_TXT/io_txt.cpp b/src/plugins_experimental/io_txt/io_txt.cpp
-similarity index 100%
-rename from src/plugins_experimental/io_TXT/io_txt.cpp
-rename to src/plugins_experimental/io_txt/io_txt.cpp
-diff --git a/src/plugins_experimental/io_TXT/io_txt.h b/src/plugins_experimental/io_txt/io_txt.h
-similarity index 100%
-rename from src/plugins_experimental/io_TXT/io_txt.h
-rename to src/plugins_experimental/io_txt/io_txt.h
-diff --git a/src/plugins_experimental/io_TXT/io_txt.pro b/src/plugins_experimental/io_txt/io_txt.pro
-similarity index 100%
-rename from src/plugins_experimental/io_TXT/io_txt.pro
-rename to src/plugins_experimental/io_txt/io_txt.pro
--- 
-2.15.0
-

pkgs/applications/graphics/meshlab/fix-20180627-beta.patch

@@ -0,0 +1,25 @@
+diff --git a/src/meshlabplugins/edit_paint/paintbox.cpp b/src/meshlabplugins/edit_paint/paintbox.cpp
+index 2097a5b..6bcd1a4 100644
+--- a/src/meshlabplugins/edit_paint/paintbox.cpp
++++ b/src/meshlabplugins/edit_paint/paintbox.cpp
+@@ -23,6 +23,7 @@
+ 
+ #include "paintbox.h"
+ #include <QFileDialog>
++#include <QAction>
+ 
+ Paintbox::Paintbox(QWidget * parent, Qt::WindowFlags flags) : QWidget(parent, flags)
+ {
+diff --git a/src/meshlabplugins/render_gdp/shaderDialog.h b/src/meshlabplugins/render_gdp/shaderDialog.h
+index a62d3b5..7eb1594 100644
+--- a/src/meshlabplugins/render_gdp/shaderDialog.h
++++ b/src/meshlabplugins/render_gdp/shaderDialog.h
+@@ -32,6 +32,8 @@
+ #include "shaderStructs.h"
+ #include "ui_shaderDialog.h"
+ #include <QMap>
++#include <QSlider>
++#include <QLineEdit>
+ 
+ class QGLWidget;
+ 

pkgs/applications/graphics/rapid-photo-downloader/default.nix

@@ -6,11 +6,11 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "rapid-photo-downloader";
-  version = "0.9.9";
+  version = "0.9.10";
 
   src = fetchurl {
     url = "https://launchpad.net/rapid/pyqt/${version}/+download/${pname}-${version}.tar.gz";
-    sha256 = "193l55wdxwxmammyxwzp90sg0qw5r316443la3m9611sdpcmy8w3";
+    sha256 = "1i0lfj9gnfya49gxx59ls364z651fqagd4krnz9jhg9m0l48ljdf";
   };
 
   # Disable version check and fix install tests

pkgs/applications/misc/eureka-editor/default.nix

@@ -0,0 +1,39 @@
+{ stdenv, fetchzip, fltk, zlib, xdg_utils, xorg, libjpeg, libGL }:
+
+stdenv.mkDerivation rec {
+  name = "eureka-editor-${version}";
+  version = "1.21";
+  shortver = "121";
+
+  src = fetchzip {
+    url = "mirror://sourceforge/eureka-editor/Eureka/${version}/eureka-${shortver}-source.tar.gz";
+    sha256 = "0fpj13aq4wh3f7473cdc5jkf1c71jiiqmjc0ihqa0nm3hic1d4yv";
+  };
+
+  buildInputs = [ fltk zlib xdg_utils libjpeg xorg.libXinerama libGL ];
+
+  enableParallelBuilding = true;
+
+  preBuild = ''
+    substituteInPlace src/main.cc \
+      --replace /usr/local $out
+    substituteInPlace Makefile \
+      --replace /usr/local $out \
+      --replace "-o root " ""
+  '';
+
+  preInstall = ''
+    mkdir -p $out/bin $out/share/applications $out/share/icons $out/man/man6
+    cp misc/eureka.desktop $out/share/applications
+    cp misc/eureka.ico $out/share/icons
+    cp misc/eureka.6 $out/man/man6
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = http://eureka-editor.sourceforge.net;
+    description = "A map editor for the classic DOOM games, and a few related games such as Heretic and Hexen";
+    license = licenses.gpl2;
+    platforms = platforms.all;
+    maintainers = with maintainers; [ neonfuz ];
+  };
+}

pkgs/applications/misc/evilvte/default.nix

@@ -31,5 +31,8 @@ stdenv.mkDerivation rec {
     license = licenses.gpl2;
     maintainers = [ maintainers.bodil ];
     platforms = platforms.linux;
+    knownVulnerabilities = [
+      "https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=854585"
+    ];
   };
 }

pkgs/applications/misc/gxmessage/default.nix

@@ -1,4 +1,4 @@
-{stdenv, fetchurl, gnome3, intltool, pkgconfig, texinfo}:
+{ stdenv, fetchurl, gnome3, intltool, pkgconfig, texinfo, hicolor-icon-theme }:
 
 stdenv.mkDerivation rec {
   name = "gxmessage-${version}";
@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ intltool gnome3.gtk texinfo ];
+  buildInputs = [ intltool gnome3.gtk texinfo hicolor-icon-theme ];
+
   meta = {
     description = "A GTK enabled dropin replacement for xmessage";
     homepage = "http://homepages.ihug.co.nz/~trmusson/programs.html#gxmessage";

pkgs/applications/misc/nnn/default.nix

@@ -4,13 +4,13 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "nnn-${version}";
-  version = "1.8";
+  version = "1.9";
 
   src = fetchFromGitHub {
     owner = "jarun";
     repo = "nnn";
     rev = "v${version}";
-    sha256 = "0sd8djig56163k0b0y4a7kg3malxlg08gayjw4zmvqaihvbbkc6v";
+    sha256 = "0z7mr9lql5hz0518wzkj8fdsdp8yh17fr418arjxjn66md4kwgpg";
   };
 
   configFile = optionalString (conf!=null) (builtins.toFile "nnn.h" conf);

pkgs/applications/misc/overmind/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, buildGoPackage, fetchFromGitHub, tmux, makeWrapper }:
+{ stdenv, buildGoPackage, fetchFromGitHub, tmux, which, makeWrapper }:
 
 buildGoPackage rec {
   name = "overmind-${version}";
@@ -8,7 +8,7 @@ buildGoPackage rec {
   nativeBuildInputs = [ makeWrapper ];
 
   postInstall = ''
-    wrapProgram "$bin/bin/overmind" --prefix PATH : "${stdenv.lib.makeBinPath [ tmux ]}"
+    wrapProgram "$bin/bin/overmind" --prefix PATH : "${stdenv.lib.makeBinPath [ tmux which ]}"
   '';
 
   src = fetchFromGitHub {

pkgs/applications/misc/ptask/default.nix

@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ pkgconfig makeWrapper ];
 
-  patches = [ ./tw-version.patch ];
+  patches = [ ./tw-version.patch ./json_c_is_error.patch ];
 
   preFixup = ''
     wrapProgram "$out/bin/ptask" \
@@ -25,5 +25,6 @@ stdenv.mkDerivation rec {
     description = "GTK-based GUI for taskwarrior";
     license = licenses.gpl2;
     maintainers = [ maintainers.spacefrogg ];
+    platforms = platforms.linux;
   };
 }

pkgs/applications/misc/ptask/json_c_is_error.patch

@@ -0,0 +1,13 @@
+diff --git a/src/tw.c b/src/tw.c
+index 602f7b3..ca601cd 100644
+--- a/src/tw.c
++++ b/src/tw.c
+@@ -163,7 +163,7 @@ static struct json_object *task_exec_json(const char *opts)
+ 
+ 	free(cmd);
+ 
+-	if (o && is_error(o))
++	if (!o)
+ 		return NULL;
+ 
+ 	return o;

pkgs/applications/misc/qradiolink/default.nix

@@ -0,0 +1,57 @@
+{ stdenv, fetchFromGitHub, alsaLib, boost
+, qt4, libpulseaudio, codec2, libconfig
+, gnuradio, gnuradio-osmosdr, gsm
+, libopus, libjpeg, protobuf, qwt, speex
+} :
+
+let
+  version = "0.5.0";
+
+in stdenv.mkDerivation {
+  name = "qradiolink-${version}";
+
+  src = fetchFromGitHub {
+    owner = "kantooon";
+    repo = "qradiolink";
+    rev = "${version}";
+    sha256 = "0xhg5zhjznmls5m3rhpk1qx0dipxmca12s85w15d0i7qwva2f1gi";
+  };
+
+  preBuild = ''
+    cd ext
+    protoc --cpp_out=. Mumble.proto
+    protoc --cpp_out=. QRadioLink.proto
+    cd ..
+    qmake
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp qradiolink $out/bin
+  '';
+
+  buildInputs = [
+    qt4
+    alsaLib
+    boost
+    libpulseaudio
+    codec2
+    libconfig
+    gsm
+    gnuradio
+    gnuradio-osmosdr
+    libopus
+    libjpeg
+    protobuf
+    speex
+    qwt
+  ];
+
+  meta = with stdenv.lib; {
+    description = "SDR transceiver application for analog and digital modes";
+    homepage = http://qradiolink.org/;
+    license = licenses.agpl3;
+    maintainers = [ maintainers.markuskowa ];
+    platforms = platforms.linux;
+  };
+}

pkgs/applications/misc/redshift/default.nix

@@ -61,6 +61,15 @@ stdenv.mkDerivation rec {
 
   postFixup = "wrapPythonPrograms";
 
+  # the geoclue agent may inspect these paths and expect them to be
+  # valid without having the correct $PATH set
+  postInstall = ''
+    substituteInPlace $out/share/applications/redshift.desktop \
+      --replace 'Exec=redshift' "Exec=$out/bin/redshift"
+    substituteInPlace $out/share/applications/redshift.desktop \
+      --replace 'Exec=redshift-gtk' "Exec=$out/bin/redshift-gtk"
+  '';
+
   enableParallelBuilding = true;
 
   meta = with stdenv.lib; {

pkgs/applications/misc/rtv/default.nix

@@ -2,14 +2,14 @@
 
 with python3Packages;
 buildPythonApplication rec {
-  version = "1.23.0";
+  version = "1.24.0";
   pname = "rtv";
 
   src = fetchFromGitHub {
     owner = "michael-lazar";
     repo = "rtv";
     rev = "v${version}";
-    sha256 = "0i6iqj3ly1bgsfa9403m5190mfl9yk1x4ific3v31wqfja985nsr";
+    sha256 = "0vzhnqys8nr6ymsi1mnv092z3i7nwyhgnj4jv6mjifak9j3164fw";
   };
 
   # Tests try to access network

pkgs/applications/misc/translate-shell/default.nix

@@ -3,13 +3,13 @@
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "translate-shell";
-  version = "0.9.6.7";
+  version = "0.9.6.8";
 
   src = fetchFromGitHub {
     owner = "soimort";
     repo = "translate-shell";
     rev = "v${version}";
-    sha256 = "0krcidjh32xwybr1v4nykgf0jjnffjqx125bvn3jh2a44cikyq3n";
+    sha256 = "17fc5nlc594lvmihx39h4ddmi8ja3qqsyswzxadbaz7l3zm356b8";
   };
 
   buildInputs = [ makeWrapper ];

pkgs/applications/misc/urlscan/default.nix

@@ -2,13 +2,13 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "urlscan";
-  version = "0.8.7";
+  version = "0.8.9";
 
   src = fetchFromGitHub {
     owner = "firecat53";
     repo = pname;
     rev = version;
-    sha256 = "1jxjcq869jimsq1ihk2fbjhp5lj7yga0hbp0msskxyz92afl1kz8";
+    sha256 = "18wvfayib79lylv3g9ay3f85qanhrljvnfarwl9snfzklj4gkf2v";
   };
 
   propagatedBuildInputs = [ python3Packages.urwid ];

pkgs/applications/misc/viking/default.nix

@@ -1,6 +1,6 @@
 { fetchurl, stdenv, makeWrapper, pkgconfig, intltool, gettext, gtk2, expat, curl
 , gpsd, bc, file, gnome-doc-utils, libexif, libxml2, libxslt, scrollkeeper
-, docbook_xml_dtd_412, gexiv2, sqlite, gpsbabel, expect }:
+, docbook_xml_dtd_412, gexiv2, sqlite, gpsbabel, expect, hicolor-icon-theme }:
 
 stdenv.mkDerivation rec {
   name = "viking-${version}";
@@ -13,7 +13,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ makeWrapper intltool gettext gtk2 expat curl gpsd bc file gnome-doc-utils
-    libexif libxml2 libxslt scrollkeeper docbook_xml_dtd_412 gexiv2 sqlite
+    libexif libxml2 libxslt scrollkeeper docbook_xml_dtd_412 gexiv2 sqlite hicolor-icon-theme
   ];
 
   configureFlags = [ "--disable-scrollkeeper --disable-mapnik" ];

pkgs/applications/misc/xterm/default.nix

@@ -3,14 +3,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "xterm-333";
+  name = "xterm-335";
 
   src = fetchurl {
     urls = [
      "ftp://ftp.invisible-island.net/xterm/${name}.tgz"
      "https://invisible-mirror.net/archives/xterm/${name}.tgz"
    ];
-    sha256 = "0y7gl26mxw6kwqx9j9mi6lx1lp1v3nrlga19ddn07j2m9q0l479g";
+    sha256 = "15nbgys4s2idhx6jzzc24g9bb1s6yps5fyg2bafvs0gkkcm1ggz0";
   };
 
   buildInputs =

pkgs/applications/networking/browsers/chromium/plugins.nix

@@ -98,11 +98,11 @@ let
 
   flash = stdenv.mkDerivation rec {
     name = "flashplayer-ppapi-${version}";
-    version = "30.0.0.134";
+    version = "30.0.0.154";
 
     src = fetchzip {
       url = "https://fpdownload.adobe.com/pub/flashplayer/pdc/${version}/flash_player_ppapi_linux.x86_64.tar.gz";
-      sha256 = "1g6695w1ijqs8jbkbrb403ca1vvrf298ayvxslrvk70x6l7lp2ys";
+      sha256 = "0bi9b6syx7x2avixgjwanrvynzanf89xm2g3nxazw9qgxxc1cp48";
       stripRoot = false;
     };
 

pkgs/applications/networking/browsers/firefox/wrapper.nix

@@ -43,6 +43,9 @@ let
 
       plugins =
         assert !(jre && icedtea);
+        if builtins.hasAttr "enableVLC" cfg
+        then throw "The option \"${browserName}.enableVLC\" has been removed since Firefox no longer supports npapi plugins"
+        else
         ([ ]
           ++ lib.optional enableAdobeFlash flashplayer
           ++ lib.optional (cfg.enableDjvu or false) (djview4)

pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/default.nix

@@ -73,7 +73,7 @@ let
 in
 stdenv.mkDerivation rec {
   name = "flashplayer-${version}";
-  version = "30.0.0.134";
+  version = "30.0.0.154";
 
   src = fetchurl {
     url =
@@ -84,14 +84,14 @@ stdenv.mkDerivation rec {
     sha256 =
       if debug then
         if arch == "x86_64" then
-          "1xa2mcbcxpfrqdf37a98nvvsvyp0bm3lsv21ky3ps9cba8a13z80"
+          "04hfh0vn1n70gdpfydq0sj94d6rkbk80h4pmy3rsfvhg0x540wx8"
         else
-          "1jgl57ggcszdim51dcr0gsjmrdb2kdvxl0lv5zl83cvxcyz0z4p6"
+          "073327sszbvkglh5b18axmwv40sy2vyacdhcd1fx82qskv44sfda"
       else
         if arch == "x86_64" then
-          "0331r5af4zrvwc4h7dp5qyy91dfam5z03yjggls3x04i10nz5myw"
+          "03ypgzy88ck5rn1q971v0km9yw3p10ly1zkxh239v6nx0hs35w84"
         else
-          "011cf0kycs4ih45l23bp6rr2vm7w7jaj4pjvmqwjax4xrb5pzkic";
+          "0rld7i659ccp4gvcvdkqkc1lajvlss5d4qndzf9aqiksvdknv62x";
   };
 
   nativeBuildInputs = [ unzip ];

pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/standalone.nix

@@ -49,7 +49,7 @@
 
 stdenv.mkDerivation rec {
   name = "flashplayer-standalone-${version}";
-  version = "30.0.0.134";
+  version = "30.0.0.154";
 
   src = fetchurl {
     url =
@@ -59,9 +59,9 @@ stdenv.mkDerivation rec {
         "https://fpdownload.macromedia.com/pub/flashplayer/updaters/30/flash_player_sa_linux.x86_64.tar.gz";
     sha256 =
       if debug then
-        "1plmhv1799j0habmyxy7zhvilh823djmg4i387s6qifr5iv66pax"
+        "133zhgc5fh6s0xr93lv70xcrgvaj7lhjxk5w7xz79h3mp185p3g4"
       else
-        "13cb7sca5mw5b1iiimyxbfxwpmdh7aya8rnlhkv3fgk5a1jwrxqr";
+        "1xz1l5q0zahalh0l4mkrwhmfrmcli3sckg3rcfnllizq9rbfzcmr";
   };
 
   nativeBuildInputs = [ unzip ];

pkgs/applications/networking/cluster/hadoop/default.nix

@@ -11,10 +11,15 @@ let
           inherit sha256;
         };
 
+        postUnpack = stdenv.lib.optionalString (tomcat != null) ''
+          install -D ${tomcat.src} $sourceRoot/hadoop-hdfs-project/hadoop-hdfs-httpfs/downloads/apache-tomcat-${tomcat.version}.tar.gz
+          install -D ${tomcat.src} $sourceRoot/hadoop-common-project/hadoop-kms/downloads/apache-tomcat-${tomcat.version}.tar.gz
+        '';
+
         # perform fake build to make a fixed-output derivation of dependencies downloaded from maven central (~100Mb in ~3000 files)
         fetched-maven-deps = stdenv.mkDerivation {
           name = "hadoop-${version}-maven-deps";
-          inherit src nativeBuildInputs buildInputs configurePhase;
+          inherit src postUnpack nativeBuildInputs buildInputs configurePhase;
           buildPhase = ''
             while mvn package -Dmaven.repo.local=$out/.m2 ${mavenFlags} -Dmaven.wagon.rto=5000; [ $? = 1 ]; do
               echo "timeout, restart maven to continue downloading"
@@ -48,11 +53,6 @@ let
         '';
         configurePhase = "true"; # do not trigger cmake hook
         mavenFlags = "-Drequire.snappy -Drequire.bzip2 -DskipTests -Pdist,native -e";
-        # prevent downloading tomcat during the build
-        preBuild = stdenv.lib.optionalString (tomcat != null) ''
-          install -D ${tomcat.src} hadoop-hdfs-project/hadoop-hdfs-httpfs/downloads/apache-tomcat-${tomcat.version}.tar.gz
-          install -D ${tomcat.src} hadoop-common-project/hadoop-kms/downloads/apache-tomcat-${tomcat.version}.tar.gz
-        '';
         buildPhase = ''
           # 'maven.repo.local' must be writable
           mvn package --offline -Dmaven.repo.local=$(cp -dpR ${fetched-maven-deps}/.m2 ./ && chmod +w -R .m2 && pwd)/.m2 ${mavenFlags}
@@ -123,8 +123,8 @@ let
 
 in {
   hadoop_2_7 = common {
-    version = "2.7.6";
-    sha256 = "0wmg0iy0qxrf43fzajzmx03gxp4yx197vxacqwkxaj45clqwl010";
+    version = "2.7.7";
+    sha256 = "1ahv67f3lwak3kbjvnk1gncq56z6dksbajj872iqd0awdsj3p5rf";
     dependencies-sha256 = "1lsr9nvrynzspxqcamb10d596zlnmnfpxhkd884gdiva0frm0b1r";
     tomcat = tomcat_6_0_48;
   };
@@ -147,9 +147,9 @@ in {
     tomcat = null;
   };
   hadoop_3_1 = common {
-    version = "3.1.0";
-    sha256 = "0lig25jkffkzc2bfgyrnm3wymapgyw9fkai8sk9fnmp7cljia314";
-    dependencies-sha256 = "1ri6a7lrijh538vy7v0fzgvkw603pf8jkh3ldl1kl7l0dvszd70d";
+    version = "3.1.1";
+    sha256 = "04hhdbyd4x1hy0fpy537f8mi0864hww97zap29x7dk1smrffwabd";
+    dependencies-sha256 = "1q63jsxg3d31x0p8hvhpvbly2b07almyzsbhwphbczl3fhlqgiwn";
     tomcat = null;
   };
 }

pkgs/applications/networking/cluster/kontemplate/default.nix

@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name          = "kontemplate-${version}";
-  version       = "1.6.0";
+  version       = "1.7.0";
   goPackagePath = "github.com/tazjin/kontemplate";
   goDeps        = ./deps.nix;
 
@@ -10,7 +10,7 @@ buildGoPackage rec {
     owner  = "tazjin";
     repo   = "kontemplate";
     rev    = "v${version}";
-    sha256 = "06qcf2cxs686kd7iqccmqd5chdzxgbkav95byjim7sgvq9qjajfi";
+    sha256 = "0vzircajhrfq1nykwpl52cqgzyhy51w4ff7ldpgi95w3a4fz1hzz";
   };
 
   meta = with lib; {

pkgs/applications/networking/cluster/kontemplate/deps.nix

@@ -5,8 +5,8 @@
     fetch = {
       type   = "git";
       url    = "https://github.com/Masterminds/semver";
-      rev    = "517734cc7d6470c0d07130e40fd40bdeb9bcd3fd";
-      sha256 = "1625b5sxpmlz60jw67j1ljfcc09d4lhxg3z6gc4am8s2rrdgwij6";
+      rev    = "c84ddcca87bf5a941b138dde832a7e20b0159ad8";
+      sha256 = "1dcfdr018a0yszjpvr3wshvq9cc3kvy95l55si556p617wsn1wan";
     };
   }
   {
@@ -14,8 +14,8 @@
     fetch = {
       type   = "git";
       url    = "https://github.com/Masterminds/sprig";
-      rev    = "e039e20e500c2c025d9145be375e27cf42a94174";
-      sha256 = "1yhpyzq6ghwl0242phjpbc9358fcw63pxrcxsyv9n4dm0w15va3m";
+      rev    = "77bb58b7f5e10889a1195c21b9e7a96ee166f199";
+      sha256 = "0q4g12f3nvda1skz33qzbbdd2vj3gjfwf361hyzlx20s71brk3bk";
     };
   }
   {
@@ -50,8 +50,17 @@
     fetch = {
       type   = "git";
       url    = "https://github.com/ghodss/yaml";
-      rev    = "0ca9ea5df5451ffdf184b4428c902747c2c11cd7";
-      sha256 = "0skwmimpy7hlh7pva2slpcplnm912rp3igs98xnqmn859kwa5v8g";
+      rev    = "e9ed3c6dfb39bb1a32197cb10d527906fe4da4b6";
+      sha256 = "07cf0j3wbsl1gmn175mdgljcarfz4xbqd6pgc7b08a5lcn7zwhjz";
+    };
+  }
+  {
+    goPackagePath = "github.com/google/uuid";
+    fetch = {
+      type   = "git";
+      url    = "https://github.com/google/uuid";
+      rev    = "dec09d789f3dba190787f8b4454c7d3c936fed9e";
+      sha256 = "1hc4w67p6zkh2qk7wm1yrl69jjrjjk615mly5ll4iidn1m4mzi4i";
     };
   }
   {
@@ -59,8 +68,8 @@
     fetch = {
       type   = "git";
       url    = "https://github.com/huandu/xstrings";
-      rev    = "3959339b333561bf62a38b424fd41517c2c90f40";
-      sha256 = "0f1jyd80grpr88gwhljx2x0xgsyzw07807n4z4axxxlybh5f0nh1";
+      rev    = "7bb0250b58e5c15670406e6f93ffda43281305b1";
+      sha256 = "1fc8q65xvsxpa12p8hcjqap2pf72zqlwpm165js9kwbgm2sf977c";
     };
   }
   {
@@ -68,17 +77,8 @@
     fetch = {
       type   = "git";
       url    = "https://github.com/imdario/mergo";
-      rev    = "d806ba8c21777d504a2090a2ca4913c750dd3a33";
-      sha256 = "12n3lfbfxvnag916c6dpxl48j29s482zwsqjc6wk4vb68qbz2nl3";
-    };
-  }
-  {
-    goPackagePath = "github.com/satori/go.uuid";
-    fetch = {
-      type   = "git";
-      url    = "https://github.com/satori/go.uuid";
-      rev    = "5bf94b69c6b68ee1b541973bb8e1144db23a194b";
-      sha256 = "0l782l4srv36pj8pfgn61996d0vjifld4a569rbjwq5h14pd0c07";
+      rev    = "9f23e2d6bd2a77f959b2bf6acdbefd708a83a4a4";
+      sha256 = "1lbzy8p8wv439sqgf0n21q52flf2wbamp6qa1jkyv6an0nc952q7";
     };
   }
   {
@@ -86,8 +86,8 @@
     fetch = {
       type   = "git";
       url    = "https://go.googlesource.com/crypto";
-      rev    = "ab89591268e0c8b748cbe4047b00197516011af5";
-      sha256 = "1cbg8wlv1hmdps9ksa4kym5zy0mb2yjykw4ns7yqv7nmz4s5xajr";
+      rev    = "de0752318171da717af4ce24d0a2e8626afaeb11";
+      sha256 = "1ps1dl2a5lwr3vbwcy8n4i1v73m567y024sk961fk281phrzp13i";
     };
   }
   {
@@ -95,8 +95,8 @@
     fetch = {
       type   = "git";
       url    = "https://gopkg.in/alecthomas/kingpin.v2";
-      rev    = "1087e65c9441605df944fb12c33f0fe7072d18ca";
-      sha256 = "18llqzkdqf62qbqcv2fd3j0igl6cwwn4dissf5skkvxrcxjcmmj0";
+      rev    = "947dcec5ba9c011838740e680966fd7087a71d0d";
+      sha256 = "0mndnv3hdngr3bxp7yxfd47cas4prv98sqw534mx7vp38gd88n5r";
     };
   }
   {
@@ -104,8 +104,8 @@
     fetch = {
       type   = "git";
       url    = "https://gopkg.in/yaml.v2";
-      rev    = "eb3733d160e74a9c7e442f435eb3bea458e1d19f";
-      sha256 = "1srhvcaa9db3a6xj29mkjr5kg33y71pclrlx4vcwz5m1lgb5c7q6";
+      rev    = "5420a8b6744d3b0345ab293f6fcba19c978f1183";
+      sha256 = "0dwjrs2lp2gdlscs7bsrmyc5yf6mm4fvgw71bzr9mv2qrd2q73s1";
     };
   }
 ]

pkgs/applications/networking/cluster/terraform/default.nix

@@ -104,8 +104,8 @@ in rec {
   terraform_0_10-full = terraform_0_10.withPlugins lib.attrValues;
 
   terraform_0_11 = pluggable (generic {
-    version = "0.11.7";
-    sha256 = "0q5gl8yn1f8fas1v68lz081k88gbmlk7f2xqlwqmh01qpqjxd42q";
+    version = "0.11.8";
+    sha256 = "1kdmx21l32vj5kvkimkx0s5mxgmgkdwlgbin4f3iqjflzip0cddh";
     patches = [ ./provider-path.patch ];
     passthru = { inherit plugins; };
   });

pkgs/applications/networking/cluster/terragrunt/default.nix

@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "terragrunt-${version}";
-  version = "0.14.6";
+  version = "0.16.6";
 
   goPackagePath = "github.com/gruntwork-io/terragrunt";
 
@@ -10,7 +10,7 @@ buildGoPackage rec {
     owner  = "gruntwork-io";
     repo   = "terragrunt";
     rev    = "v${version}";
-    sha256 = "14zg1h76wfg6aa78llcnza7kapnl5ks6m2vg73b90azfi49fmkwz";
+    sha256 = "0fzn2ymk8x0lzwfqlvnry8s6wf3q0sqn76lfardjyz6wgxl8011i";
   };
 
   goDeps = ./deps.nix;

pkgs/applications/networking/dropbox/default.nix

@@ -7,7 +7,7 @@ assert lib.elem stdenv.system platforms;
 # Dropbox client to bootstrap installation.
 # The client is self-updating, so the actual version may be newer.
 let
-  version = "52.3.56";
+  version = "55.4.171";
 
   arch = {
     "x86_64-linux" = "x86_64";

pkgs/applications/networking/instant-messengers/signal-desktop/default.nix

@@ -55,11 +55,11 @@ let
 
 in stdenv.mkDerivation rec {
   name = "signal-desktop-${version}";
-  version = "1.15.4";
+  version = "1.15.5";
 
   src = fetchurl {
     url = "https://updates.signal.org/desktop/apt/pool/main/s/signal-desktop/signal-desktop_${version}_amd64.deb";
-    sha256 = "02k64hnfzq8d5g805n4bjm2x8xazskp8fwbmcbl2s2rshdwil1jz";
+    sha256 = "1a63kyxbhdaz6izprg8wryvscmvfjii50xi1v5pxlf74x2pkxs8k";
   };
 
   phases = [ "unpackPhase" "installPhase" ];

pkgs/applications/networking/instant-messengers/wavebox/default.nix

@@ -0,0 +1,66 @@
+{ stdenv, fetchurl, makeDesktopItem, makeWrapper, autoPatchelfHook
+, xorg, gtk2, gtk3 , gnome2, gnome3, nss, alsaLib, udev, libnotify, xdg_utils }:
+
+with stdenv.lib;
+
+let
+  bits = "x86_64";
+
+  version = "3.14.10";
+
+  desktopItem = makeDesktopItem rec {
+    name = "Wavebox";
+    exec = name;
+    icon = "wavebox";
+    desktopName = name;
+    genericName = name;
+    categories = "Network;";
+  };
+
+  tarball = "Wavebox_${replaceStrings ["."] ["_"] (toString version)}_linux_${bits}.tar.gz";
+
+in stdenv.mkDerivation rec {
+  name = "wavebox-${version}";
+  src = fetchurl {
+    url = "https://github.com/wavebox/waveboxapp/releases/download/v${version}/${tarball}";
+    sha256 = "06ce349f561c6122b2d326e9a1363fb358e263c81a7d1d08723ec567235bbd74";
+  };
+
+  # don't remove runtime deps
+  dontPatchELF = true;
+
+  nativeBuildInputs = [ autoPatchelfHook makeWrapper ];
+
+  buildInputs = with xorg; [
+    libXScrnSaver libXtst
+  ] ++ [
+    gtk3 nss gtk2 alsaLib gnome2.GConf
+  ];
+
+  runtimeDependencies = [ udev.lib libnotify ];
+
+  installPhase = ''
+    mkdir -p $out/bin $out/opt/wavebox
+    cp -r * $out/opt/wavebox
+
+    # provide desktop item and icon
+    mkdir -p $out/share/applications $out/share/pixmaps
+    ln -s ${desktopItem}/share/applications/* $out/share/applications
+    ln -s $out/opt/wavebox/Wavebox-linux-x64/wavebox_icon.png $out/share/pixmaps/wavebox.png
+  '';
+
+  postFixup = ''
+    paxmark m $out/opt/wavebox/Wavebox
+    makeWrapper $out/opt/wavebox/Wavebox $out/bin/wavebox \
+      --prefix PATH : ${xdg_utils}/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Wavebox messaging application";
+    homepage = https://wavebox.io;
+    license = licenses.mpl20;
+    maintainers = with maintainers; [ rawkode ];
+    platforms = ["x86_64-linux"];
+    hydraPlatforms = [];
+  };
+}

pkgs/applications/networking/instant-messengers/weechat-xmpp/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, xmpppy }:
+{ stdenv, fetchFromGitHub, xmpppy, pydns, substituteAll, buildEnv }:
 
 stdenv.mkDerivation {
   name = "weechat-jabber-2017-08-30";
@@ -15,15 +15,14 @@ stdenv.mkDerivation {
     cp jabber.py $out/share/jabber.py
   '';
 
-  buildInputs = [ xmpppy ];
-
-  postPatch = ''
-    substituteInPlace jabber.py \
-      --replace "__NIX_OUTPUT__" "${xmpppy}/lib/python2.7/site-packages"
-  '';
-
   patches = [
-    ./libpath.patch
+    (substituteAll {
+      src = ./libpath.patch;
+      env = "${buildEnv {
+        name = "weechat-xmpp-env";
+        paths = [ pydns xmpppy ];
+      }}/lib/python2.7/site-packages";
+    })
   ];
 
   meta = with stdenv.lib; {

pkgs/applications/networking/instant-messengers/weechat-xmpp/libpath.patch

@@ -8,7 +8,7 @@ index 27006a3..e53c2c0 100644
  
 +import sys
 +
-+sys.path.append('__NIX_OUTPUT__')
++sys.path.append('@env@')
 +
 +
  import_ok = True

pkgs/applications/networking/instant-messengers/zoom-us/default.nix

@@ -13,11 +13,11 @@ assert pulseaudioSupport -> libpulseaudio != null;
 let
   inherit (stdenv.lib) concatStringsSep makeBinPath optional;
 
-  version = "2.2.128200.0702";
+  version = "2.3.128305.0716";
   srcs = {
     x86_64-linux = fetchurl {
       url = "https://zoom.us/client/${version}/zoom_x86_64.tar.xz";
-      sha256 = "0n9kyj94bj35gbpwiz4kq7hc8pwfqwnfqf003g4c8gx5pda3g56w";
+      sha256 = "1jpw5sclr5bhif559hmnyiggjh6gkm1smiw34y3ad4k8xhag9dkh";
     };
   };
 

pkgs/applications/networking/msmtp/default.nix

@@ -10,11 +10,11 @@ let
 in stdenv.mkDerivation rec {
   pname = "msmtp";
   name = "${pname}-${version}";
-  version = "1.6.6";
+  version = "1.6.8";
 
   src = fetchurl {
-    url = "mirror://sourceforge/msmtp/${name}.tar.xz";
-    sha256 = "0ppvww0sb09bnsrpqnvlrn8vx231r24xn2iiwpy020mxc8gxn5fs";
+    url = "https://marlam.de/msmtp/releases/${name}.tar.xz";
+    sha256 = "1ysrnshvwhzwmvb2walw5i9jdzlvmckj7inr0xnvb26q0jirbzsm";
   };
 
   patches = [
@@ -52,7 +52,7 @@ in stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Simple and easy to use SMTP client with excellent sendmail compatibility";
-    homepage = http://msmtp.sourceforge.net/;
+    homepage = https://marlam.de/msmtp/;
     license = licenses.gpl3;
     maintainers = with maintainers; [ garbas peterhoeg ];
     platforms = platforms.unix;

pkgs/applications/networking/p2p/qbittorrent/default.nix

@@ -10,13 +10,13 @@ with stdenv.lib;
 
 stdenv.mkDerivation rec {
   name = "qbittorrent-${version}";
-  version = "4.1.1";
+  version = "4.1.2";
 
   src = fetchFromGitHub {
     owner = "qbittorrent";
     repo = "qbittorrent";
     rev = "release-${version}";
-    sha256 = "09bf1jr2sfdps8cb154gjw7zhdcpsamhnfbgacdmkfyd7qgcbykf";
+    sha256 = "1756hr92rvh4xlf6bk2wl24ypczhwf1rv1pdq05flk118jciqb05";
   };
 
   # NOTE: 2018-05-31: CMake is working but it is not officially supported

pkgs/applications/networking/protonmail-bridge/default.nix

@@ -6,7 +6,9 @@ let
 
   description = ''
     An application that runs on your computer in the background and seamlessly encrypts
-    and decrypts your mail as it enters and leaves your computer
+    and decrypts your mail as it enters and leaves your computer.
+
+    To work, gnome-keyring service must be enabled.
   '';
 
   desktopItem = makeDesktopItem {

pkgs/applications/science/astronomy/gildas/default.nix

@@ -7,13 +7,13 @@ let
 in
 
 stdenv.mkDerivation rec {
-  srcVersion = "jul18a";
-  version = "20180701_a";
+  srcVersion = "aug18a";
+  version = "20180801_a";
   name = "gildas-${version}";
 
   src = fetchurl {
-    url = "http://www.iram.fr/~gildas/dist/archive/gildas/gildas-src-${srcVersion}.tar.gz";
-    sha256 = "0kl3zf6b1kv8hgsfrarsnm2gnrdax3vi8f856249y4nxsa7lbv2i";
+    url = "http://www.iram.fr/~gildas/dist/gildas-src-${srcVersion}.tar.gz";
+    sha256 = "0mg3wijrj8x1p912vkgrhxbypjx7aj9b1492yxvq2y3fxban6bj1";
   };
 
   enableParallelBuilding = true;
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ gtk2-x11 lesstif cfitsio python27Env ];
 
-  patches = [ ./wrapper.patch ./return-error-code.patch ./clang.patch ./mod.patch ./aarch64.patch ];
+  patches = [ ./wrapper.patch ./return-error-code.patch ./clang.patch ./aarch64.patch ];
 
   configurePhase=''
     substituteInPlace admin/wrapper.sh --replace '%%OUT%%' $out

pkgs/applications/science/astronomy/gildas/mod.patch

@@ -1,17 +0,0 @@
-diff -ruN gildas-src-jul18a/admin/Makefile.build gildas-src-jul18a.mod/admin/Makefile.build
---- gildas-src-jul18a/admin/Makefile.build	2018-06-14 14:36:54.000000000 +0200
-+++ gildas-src-jul18a.mod/admin/Makefile.build	2018-07-06 13:31:46.000000000 +0200
-@@ -291,6 +291,13 @@
- 	win-$(LIB_IDENTITY)-und.def -o $@ $(FLDLIBS) $(LIB_DEPENDS) $(ADD_LIBS) $(SYS_LIBS))
- endif
- 
-+# Dummy rules for modules just so that make consider the module a
-+# valid dependency when first parsing the makefiles. This rule should
-+# never be applied as the modules are a by-product of the compilation
-+# of the object
-+$(builddir)/%.mod:
-+	echo "dummy" > /dev/null
-+
- # Fortran executables
- $(bindir)/% : $(builddir)/%.o | $(bindir)
- 	$(FC) $(ALL_FLDFLAGS) $< $(OBJECTS) -o $@ \

pkgs/applications/science/biology/picard-tools/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "picard-tools-${version}";
-  version = "2.18.10";
+  version = "2.18.11";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "1px5ar6iizm4czpc66hyyafandw6g9x9s1abj8klc78alvihciw4";
+    sha256 = "03wkyz3bjx3n8bwambhz9lr09271r1wxycmx4p7m2naqs4afxb89";
   };
 
   buildInputs = [ jre makeWrapper ];

pkgs/applications/science/logic/aiger/default.nix

@@ -13,18 +13,15 @@ stdenv.mkDerivation rec {
 
   configurePhase = ''
     # Set up picosat, so we can build 'aigbmc'
-    echo $(pwd)
-    ls ..
     mkdir ../picosat
     ln -s ${picosat}/include/picosat/picosat.h ../picosat/picosat.h
     ln -s ${picosat}/lib/picosat.o             ../picosat/picosat.o
     ln -s ${picosat}/share/picosat.version     ../picosat/VERSION
-    ls ..
     ./configure.sh
   '';
 
   installPhase = ''
-    mkdir -p $out/bin
+    mkdir -p $out/bin $dev/include $lib/lib
 
     # Do the installation manually, as the Makefile has odd
     # cyrillic characters, and this is easier than adding
@@ -41,8 +38,13 @@ stdenv.mkDerivation rec {
     for x in ''${BINS[*]}; do
       install -m 755 -s $x $out/bin/$x
     done
+
+    cp -v aiger.o $lib/lib
+    cp -v aiger.h $dev/include
   '';
 
+  outputs = [ "out" "dev" "lib" ];
+
   meta = {
     description = "And-Inverter Graph (AIG) utilities";
     homepage    = http://fmv.jku.at/aiger/;

pkgs/applications/science/logic/boolector/default.nix

@@ -1,41 +1,50 @@
-{ stdenv, fetchurl, writeShellScriptBin }:
+{ stdenv, fetchFromGitHub
+, cmake, lingeling, btor2tools
+}:
 
 stdenv.mkDerivation rec {
   name    = "boolector-${version}";
-  version = "2.4.1";
-  src = fetchurl {
-    url    = "http://fmv.jku.at/boolector/boolector-${version}-with-lingeling-bbc.tar.bz2";
-    sha256 = "0mdf7hwix237pvknvrpazcx6s3ininj5k7vhysqjqgxa7lxgq045";
+  version = "3.0.0";
+
+  src = fetchFromGitHub {
+    owner  = "boolector";
+    repo   = "boolector";
+    rev    = "refs/tags/${version}";
+    sha256 = "15i3ni5klss423m57wcy1gx0m5wfrjmglapwg85pm7fb3jj1y7sz";
   };
 
-  prePatch =
-    let
-      lingelingPatch = writeShellScriptBin "lingeling-patch" ''
-        sed -i -e "1i#include <stdint.h>" lingeling/lglib.h
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ lingeling btor2tools ];
 
-        ${crossFix}/bin/crossFix lingeling
-      '';
-      crossFix = writeShellScriptBin "crossFix" ''
-        # substituteInPlace not available here
-        sed -i $1/makefile.in \
-          -e 's@ar rc@$(AR) rc@' \
-          -e 's@ranlib@$(RANLIB)@'
-      '';
-    in ''
-    sed -i -e 's@mv lingeling\* lingeling@\0 \&\& ${lingelingPatch}/bin/lingeling-patch@' makefile
-    sed -i -e 's@mv boolector\* boolector@\0 \&\& ${crossFix}/bin/crossFix boolector@' makefile
-  '';
+  cmakeFlags =
+    [ "-DSHARED=ON"
+      "-DUSE_LINGELING=YES"
+      "-DBTOR2_INCLUDE_DIR=${btor2tools.dev}/include"
+      "-DBTOR2_LIBRARIES=${btor2tools.lib}/lib/libbtor2parser.so"
+      "-DLINGELING_INCLUDE_DIR=${lingeling.dev}/include"
+      "-DLINGELING_LIBRARIES=${lingeling.lib}/lib/liblgl.a"
+    ];
 
   installPhase = ''
-    mkdir $out
-    mv boolector/bin $out
+    mkdir -p $out/bin $lib/lib $dev/include
+
+    cp -vr bin/* $out/bin
+    cp -vr lib/* $lib/lib
+
+    rm -rf $out/bin/{examples,test}
+
+    cd ../src
+    find . -iname '*.h' -exec cp --parents '{}' $dev/include \;
+    rm -rf $dev/include/tests
   '';
 
-  meta = {
-    license = stdenv.lib.licenses.unfreeRedistributable;
+  outputs = [ "out" "dev" "lib" ];
+
+  meta = with stdenv.lib; {
     description = "An extremely fast SMT solver for bit-vectors and arrays";
-    homepage    = "http://fmv.jku.at/boolector";
-    platforms   = stdenv.lib.platforms.linux;
-    maintainers = [ stdenv.lib.maintainers.thoughtpolice ];
+    homepage    = https://boolector.github.io;
+    license     = licenses.mit;
+    platforms   = platforms.linux;
+    maintainers = with maintainers; [ thoughtpolice ];
   };
 }

pkgs/applications/science/logic/btor2tools/default.nix

@@ -0,0 +1,33 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  name = "btor2tools-${version}";
+  version = "pre55_8c150b39";
+
+  src = fetchFromGitHub {
+    owner  = "boolector";
+    repo   = "btor2tools";
+    rev    = "8c150b39cdbcdef4247344acf465d75ef642365d";
+    sha256 = "1r5pid4x567nms02ajjrz3v0zj18k0fi5pansrmc2907rnx2acxx";
+  };
+
+  configurePhase = "./configure.sh -shared";
+
+  installPhase = ''
+    mkdir -p $out $dev/include/btor2parser/ $lib/lib
+
+    cp -vr bin $out
+    cp -v  src/btor2parser/btor2parser.h $dev/include/btor2parser
+    cp -v  build/libbtor2parser.* $lib/lib
+  '';
+
+  outputs = [ "out" "dev" "lib" ];
+
+  meta = with stdenv.lib; {
+    description = "Fast SAT solver";
+    homepage    = http://fmv.jku.at/lingeling/;
+    license     = licenses.mit;
+    platforms   = platforms.linux;
+    maintainers = with maintainers; [ thoughtpolice ];
+  };
+}

pkgs/applications/science/logic/lingeling/default.nix

@@ -0,0 +1,49 @@
+{ stdenv, fetchFromGitHub
+, aiger
+}:
+
+stdenv.mkDerivation rec {
+  name = "lingeling-${version}";
+  # This is the version used in satcomp2018, which was
+  # relicensed, and also known as version 'bcj'
+  version = "pre1_03b4860d";
+
+  src = fetchFromGitHub {
+    owner  = "arminbiere";
+    repo   = "lingeling";
+    rev    = "03b4860d14016f42213ea271014f2f13d181f504";
+    sha256 = "1lw1yfy219p7rrk88sbq4zl24b70040zapbjdrpv5a6i0jsblksx";
+  };
+
+  configurePhase = ''
+    ./configure.sh
+
+    # Rather than patch ./configure, just sneak in use of aiger here, since it
+    # doesn't handle real build products very well (it works on a build-time
+    # dir, not installed copy)... This is so we can build 'blimc'
+    substituteInPlace ./makefile \
+      --replace 'targets: liblgl.a' 'targets: liblgl.a blimc'      \
+      --replace '$(AIGER)/aiger.o'  '${aiger.lib}/lib/aiger.o'     \
+      --replace '$(AIGER)/aiger.h'  '${aiger.dev}/include/aiger.h' \
+      --replace '-I$(AIGER)'        '-I${aiger.dev}/include'
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin $lib/lib $dev/include
+
+    cp lglib.h  $dev/include
+    cp liblgl.a $lib/lib
+
+    cp lingeling plingeling treengeling ilingeling blimc $out/bin
+  '';
+
+  outputs = [ "out" "dev" "lib" ];
+
+  meta = with stdenv.lib; {
+    description = "Fast SAT solver";
+    homepage    = http://fmv.jku.at/lingeling/;
+    license     = licenses.mit;
+    platforms   = platforms.linux;
+    maintainers = with maintainers; [ thoughtpolice ];
+  };
+}

pkgs/applications/science/math/caffe/darwin.patch

@@ -0,0 +1,47 @@
+diff --git a/Makefile b/Makefile
+index c823f66e..65b90c5e 100644
+--- a/Makefile
++++ b/Makefile
+@@ -32,9 +32,9 @@ SRC_DIRS := $(shell find * -type d -exec bash -c "find {} -maxdepth 1 \
+ LIBRARY_NAME := $(PROJECT)
+ LIB_BUILD_DIR := $(BUILD_DIR)/lib
+ STATIC_NAME := $(LIB_BUILD_DIR)/lib$(LIBRARY_NAME).a
+-DYNAMIC_VERSION_MAJOR 		:= 1
+-DYNAMIC_VERSION_MINOR 		:= 0
+-DYNAMIC_VERSION_REVISION 	:= 0
++DYNAMIC_VERSION_MAJOR		:= 1
++DYNAMIC_VERSION_MINOR		:= 0
++DYNAMIC_VERSION_REVISION	:= 0
+ DYNAMIC_NAME_SHORT := lib$(LIBRARY_NAME).so
+ #DYNAMIC_SONAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR)
+ DYNAMIC_VERSIONED_NAME_SHORT := $(DYNAMIC_NAME_SHORT).$(DYNAMIC_VERSION_MAJOR).$(DYNAMIC_VERSION_MINOR).$(DYNAMIC_VERSION_REVISION)
+diff --git a/cmake/Dependencies.cmake b/cmake/Dependencies.cmake
+index c48255c8..cf4c580e 100644
+--- a/cmake/Dependencies.cmake
++++ b/cmake/Dependencies.cmake
+@@ -105,7 +105,6 @@ if(USE_OPENCV)
+ endif()
+ 
+ # ---[ BLAS
+-if(NOT APPLE)
+   set(BLAS "Atlas" CACHE STRING "Selected BLAS library")
+   set_property(CACHE BLAS PROPERTY STRINGS "Atlas;Open;MKL")
+ 
+@@ -123,17 +122,6 @@ if(NOT APPLE)
+     list(APPEND Caffe_LINKER_LIBS PUBLIC ${MKL_LIBRARIES})
+     list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_MKL)
+   endif()
+-elseif(APPLE)
+-  find_package(vecLib REQUIRED)
+-  list(APPEND Caffe_INCLUDE_DIRS PUBLIC ${vecLib_INCLUDE_DIR})
+-  list(APPEND Caffe_LINKER_LIBS PUBLIC ${vecLib_LINKER_LIBS})
+-
+-  if(VECLIB_FOUND)
+-    if(NOT vecLib_INCLUDE_DIR MATCHES "^/System/Library/Frameworks/vecLib.framework.*")
+-      list(APPEND Caffe_DEFINITIONS PUBLIC -DUSE_ACCELERATE)
+-    endif()
+-  endif()
+-endif()
+ 
+ # ---[ Python
+ if(BUILD_python)

pkgs/applications/science/math/caffe/default.nix

@@ -1,27 +1,39 @@
-{ stdenv, lib
+{ stdenv, lib, runCommand
 , fetchFromGitHub
+, fetchurl
 , cmake
 , boost
 , google-gflags
 , glog
 , hdf5-cpp
-, leveldb
-, lmdb
 , opencv3
 , protobuf
-, snappy
 , doxygen
 , openblas
-, cudaSupport ? true, cudatoolkit
+, Accelerate, CoreGraphics, CoreVideo
+, lmdbSupport ? true, lmdb
+, leveldbSupport ? true, leveldb, snappy
+, cudaSupport ? stdenv.isLinux, cudatoolkit
 , cudnnSupport ? false, cudnn ? null
 , ncclSupport ? false, nccl ? null
 , pythonSupport ? false, python ? null, numpy ? null
 }:
 
+assert leveldbSupport -> (leveldb != null && snappy != null);
 assert cudnnSupport -> cudaSupport;
 assert ncclSupport -> cudaSupport;
 assert pythonSupport -> (python != null && numpy != null);
 
+let
+  toggle = bool: if bool then "ON" else "OFF";
+
+  test_model_weights = fetchurl {
+    url = "http://dl.caffe.berkeleyvision.org/bvlc_reference_caffenet.caffemodel";
+    sha256 = "472d4a06035497b180636d8a82667129960371375bd10fcb6df5c6c7631f25e0";
+  };
+
+in
+
 stdenv.mkDerivation rec {
   name = "caffe-${version}";
   version = "1.0";
@@ -44,19 +56,27 @@ stdenv.mkDerivation rec {
            "-DCUDA_ARCH_NAME=All"
            "-DCUDA_HOST_COMPILER=${cudatoolkit.cc}/bin/cc"
          ] else [ "-DCPU_ONLY=ON" ])
-      ++ lib.optional ncclSupport "-DUSE_NCCL=ON";
+      ++ ["-DUSE_NCCL=${toggle ncclSupport}"]
+      ++ ["-DUSE_LEVELDB=${toggle leveldbSupport}"]
+      ++ ["-DUSE_LMDB=${toggle lmdbSupport}"];
 
-  buildInputs = [ boost google-gflags glog protobuf hdf5-cpp lmdb leveldb snappy opencv3 openblas ]
+  buildInputs = [ boost google-gflags glog protobuf hdf5-cpp opencv3 openblas ]
                 ++ lib.optional cudaSupport cudatoolkit
                 ++ lib.optional cudnnSupport cudnn
+                ++ lib.optional lmdbSupport lmdb
                 ++ lib.optional ncclSupport nccl
-                ++ lib.optionals pythonSupport [ python numpy ];
+                ++ lib.optionals leveldbSupport [ leveldb snappy ]
+                ++ lib.optionals pythonSupport [ python numpy ]
+                ++ lib.optionals stdenv.isDarwin [ Accelerate CoreGraphics CoreVideo ]
+                ;
 
   propagatedBuildInputs = lib.optional pythonSupport python.pkgs.protobuf;
 
   outputs = [ "bin" "out"];
   propagatedBuildOutputs = []; # otherwise propagates out -> bin cycle
 
+  patches = [ ./darwin.patch ];
+
   preConfigure = lib.optionalString (cudaSupport && lib.versionAtLeast cudatoolkit.version "9.0") ''
     # CUDA 9.0 doesn't support sm_20
     sed -i 's,20 21(20) ,,' cmake/Cuda.cmake
@@ -71,6 +91,9 @@ stdenv.mkDerivation rec {
     # Internal static library.
     rm $out/lib/libproto.a
 
+    # Install models
+    cp -a ../models $out/share/Caffe/models
+
     moveToOutput "bin" "$bin"
   '' + lib.optionalString pythonSupport ''
     mkdir -p $out/${python.sitePackages}
@@ -78,6 +101,16 @@ stdenv.mkDerivation rec {
     rm -rf $out/python
   '';
 
+  doInstallCheck = false; # build takes more than 30 min otherwise
+  installCheckPhase = ''
+    model=bvlc_reference_caffenet
+    m_path="$out/share/Caffe/models/$model"
+    $bin/bin/caffe test \
+      -model "$m_path/deploy.prototxt" \
+      -solver "$m_path/solver.prototxt" \
+      -weights "${test_model_weights}"
+  '';
+
   meta = with stdenv.lib; {
     description = "Deep learning framework";
     longDescription = ''
@@ -88,6 +121,6 @@ stdenv.mkDerivation rec {
     homepage = http://caffe.berkeleyvision.org/;
     maintainers = with maintainers; [ jb55 ];
     license = licenses.bsd2;
-    platforms = platforms.linux;
+    platforms = platforms.linux ++ platforms.darwin;
   };
 }

pkgs/applications/science/math/cplex/default.nix

@@ -0,0 +1,82 @@
+{ stdenv, makeWrapper, openjdk, gtk2, xorg, glibcLocales, releasePath }:
+
+# To use this package, you need to download your own cplex installer from IBM
+# and override the releasePath attribute to point to the location of the file.  
+#
+# Note: cplex creates an individual build for each license which screws
+# somewhat with the use of functions like requireFile as the hash will be
+# different for every user.
+
+stdenv.mkDerivation rec {
+  name = "cplex-${version}";
+  version = "128";
+  
+  src =
+    if builtins.isNull releasePath then
+      throw ''
+        This nix expression requires that the cplex installer is already
+        downloaded to your machine. Get it from IBM: 
+        https://developer.ibm.com/docloud/blog/2017/12/20/cplex-optimization-studio-12-8-now-available/ 
+
+        Set `cplex.releasePath = /path/to/download;` in your
+        ~/.config/nixpkgs/config.nix for `nix-*` commands, or
+        `config.cplex.releasePath = /path/to/download;` in your
+        `configuration.nix` for NixOS.
+      ''
+    else
+      releasePath;
+
+  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = [ openjdk gtk2 xorg.libXtst glibcLocales ];
+
+  unpackPhase = "cp $src $name";
+
+  patchPhase = ''
+    sed -i -e 's|/usr/bin/tr"|tr"         |' $name
+  '';
+
+  buildPhase = ''
+    sh $name -i silent -DLICENSE_ACCEPTED=TRUE -DUSER_INSTALL_DIR=$out
+  '';
+
+  installPhase = ''
+    mkdir -p $out/bin
+    ln -s $out/opl/bin/x86-64_linux/oplrun\
+      $out/opl/bin/x86-64_linux/oplrunjava\
+      $out/opl/oplide/oplide\
+      $out/cplex/bin/x86-64_linux/cplex\
+      $out/cpoptimizer/bin/x86-64_linux/cpoptimizer\
+      $out/bin
+  '';
+
+  fixupPhase = 
+  let 
+    libraryPath = stdenv.lib.makeLibraryPath [ stdenv.cc.cc gtk2 xorg.libXtst ];
+  in ''
+    interpreter=${stdenv.glibc}/lib/ld-linux-x86-64.so.2
+
+    for pgm in $out/opl/bin/x86-64_linux/oplrun $out/opl/bin/x86-64_linux/oplrunjava $out/opl/oplide/oplide;
+    do
+      patchelf --set-interpreter "$interpreter" $pgm;
+      wrapProgram $pgm \
+        --prefix LD_LIBRARY_PATH : $out/opl/bin/x86-64_linux:${libraryPath} \
+        --set LOCALE_ARCHIVE ${glibcLocales}/lib/locale/locale-archive;
+    done
+
+    for pgm in $out/cplex/bin/x86-64_linux/cplex $out/cpoptimizer/bin/x86-64_linux/cpoptimizer $out/opl/oplide/jre/bin/*; 
+    do
+      if grep ELF $pgm > /dev/null;
+      then
+        patchelf --set-interpreter "$interpreter" $pgm;
+      fi
+    done
+  '';
+  
+  meta = with stdenv.lib; {
+    description = "Optimization solver for mathematical programming";
+    homepage = "https://www.ibm.com/be-en/marketplace/ibm-ilog-cplex";
+    license = licenses.unfree;
+    platforms = [ "x86_64-linux" ];
+    maintainers = with maintainers; [ bfortz ];
+  };
+}

pkgs/applications/science/math/gfan/default.nix

@@ -9,15 +9,20 @@ stdenv.mkDerivation rec {
     sha256 = "02pihqb1lb76a0xbfwjzs1cd6ay3ldfxsm8dvsbl6qs3vkjxax56";
   };
 
-  makeFlags = ''PREFIX=$(out) CC=cc CXX=c++ cddnoprefix=1'';
-  buildInputs = [gmp mpir cddlib];
+  patchPhase = stdenv.lib.optionalString stdenv.isDarwin ''
+    substituteInPlace Makefile --replace "-fno-guess-branch-probability" ""
+  '';
+
+  buildFlags = [ "CC=cc" "CXX=c++" "cddnoprefix=1" ];
+  installFlags = [ ''PREFIX=$(out)'' ];
+  buildInputs = [ gmp mpir cddlib ];
 
   meta = {
     inherit version;
     description = ''A software package for computing Gröbner fans and tropical varieties'';
     license = stdenv.lib.licenses.gpl2 ;
     maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = stdenv.lib.platforms.unix;
     homepage = http://home.math.au.dk/jensen/software/gfan/gfan.html;
   };
 }

pkgs/applications/science/math/qalculate-gtk/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "qalculate-gtk-${version}";
-  version = "2.6.1";
+  version = "2.6.2";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "19jw1w29x0r1qq5r8gmqrqr00ml2pfi2w433723vjzxpfg2pp70r";
+    sha256 = "1yzw6avhka7bbi071z9d8cipcghyjq2bg9x3arv1cf395xlnrmb9";
   };
 
   patchPhase = ''

pkgs/applications/science/math/ratpoints/default.nix

@@ -1,20 +1,36 @@
-{stdenv, fetchurl, gmp}:
+{ stdenv, fetchurl, fetchpatch, gmp }:
 stdenv.mkDerivation rec {
   name = "ratpoints-${version}";
-  version = "2.1.3";
+  version = "2.1.3.p4";
+
   src = fetchurl {
     url = "http://www.mathe2.uni-bayreuth.de/stoll/programs/ratpoints-${version}.tar.gz";
     sha256 = "0zhad84sfds7izyksbqjmwpfw4rvyqk63yzdjd3ysd32zss5bgf4";
   };
-  buildInputs = [gmp];
-  makeFlags = "INSTALL_DIR=$(out)";
+
+  enableParallelBuilding = true;
+
+  patches = [
+    (fetchpatch {
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/ratpoints/patches/sturm_and_rp_private.patch?id=1615f58890e8f9881c4228c78a6b39b9aab1303a";
+      sha256 = "0q3wajncyfr3gahd8gwk9x7g56zw54lpywrl63lqk7drkf60mrcl";
+    })
+  ];
+
+  buildInputs = [ gmp ];
+
+  makeFlags = [ "CC=cc" ];
+  buildFlags = stdenv.lib.optional stdenv.isDarwin ["CCFLAGS2=-lgmp -lc -lm" "CCFLAGS=-UUSE_SSE"];
+  installFlags = [ "INSTALL_DIR=$(out)" ];
+
   preInstall = ''mkdir -p "$out"/{bin,share,lib,include}'';
+
   meta = {
     inherit version;
     description = ''A program to find rational points on hyperelliptic curves'';
     license = stdenv.lib.licenses.gpl2Plus;
     maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = stdenv.lib.platforms.unix;
     homepage = http://www.mathe2.uni-bayreuth.de/stoll/programs/;
     updateWalker = true;
   };

pkgs/applications/science/math/symmetrica/default.nix

@@ -5,20 +5,15 @@
 stdenv.mkDerivation rec {
   name = "symmetrica-${version}";
   version = "2.0";
+
   src = fetchurl {
     url = "http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/SYM2_0_tar.gz";
     sha256 = "1qhfrbd5ybb0sinl9pad64rscr08qvlfzrzmi4p4hk61xn6phlmz";
     name = "symmetrica-2.0.tar.gz";
   };
+
   sourceRoot = ".";
-  installPhase = ''
-    mkdir -p "$out"/{lib,share/doc/symmetrica,include/symmetrica}
-    ar crs libsymmetrica.a *.o
-    ranlib libsymmetrica.a
-    cp libsymmetrica.a "$out/lib"
-    cp *.h "$out/include/symmetrica"
-    cp README *.doc "$out/share/doc/symmetrica"
-  '';
+
   patches = [
       # don't show banner ("SYMMETRICA VERSION X - STARTING)
       # it doesn't contain very much helpful information and a banner is not ideal for a library
@@ -34,13 +29,34 @@ stdenv.mkDerivation rec {
         url = "https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/int32.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
         sha256 = "0p33c85ck4kd453z687ni4bdcqr1pqx2756j7aq11bf63vjz4cyz";
       })
+
+      (fetchpatch {
+        url = "https://git.sagemath.org/sage.git/plain/build/pkgs/symmetrica/patches/return_values.patch?id=1615f58890e8f9881c4228c78a6b39b9aab1303a";
+        sha256 = "0dmczkicwl50sivc07w3wm3jpfk78wm576dr25999jdj2ipsb7nk";
+      })
   ];
+
+  postPatch = ''
+    substituteInPlace makefile --replace gcc cc
+  '';
+
+  enableParallelBuilding = true;
+
+  installPhase = ''
+    mkdir -p "$out"/{lib,share/doc/symmetrica,include/symmetrica}
+    ar crs libsymmetrica.a *.o
+    ranlib libsymmetrica.a
+    cp libsymmetrica.a "$out/lib"
+    cp *.h "$out/include/symmetrica"
+    cp README *.doc "$out/share/doc/symmetrica"
+  '';
+
   meta = {
     inherit version;
     description = ''A collection of routines for representation theory and combinatorics'';
     license = stdenv.lib.licenses.publicDomain;
     maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = stdenv.lib.platforms.unix;
     homepage = http://www.symmetrica.de/;
   };
 }

pkgs/applications/science/misc/simgrid/default.nix

@@ -1,11 +1,11 @@
-{ stdenv, fetchFromGitHub, cmake, elfutils, perl, python3, boost, valgrind
+{ stdenv, fetchFromGitHub, cmake, perl, python3, boost, valgrind
 # Optional requirements
 # Lua 5.3 needed and not available now
 #, luaSupport ? false, lua5
 , fortranSupport ? false, gfortran
 , buildDocumentation ? false, transfig, ghostscript, doxygen
 , buildJavaBindings ? false, openjdk
-, modelCheckingSupport ? false, libunwind, libevent # Inside elfutils - , libelf, libevent, libdw
+, modelCheckingSupport ? false, libunwind, libevent, elfutils # Inside elfutils: libelf and libdw
 , debug ? false
 , moreTests ? false
 }:
@@ -18,20 +18,20 @@ in
 
 stdenv.mkDerivation rec {
   name = "simgrid-${version}";
-  version = "3.19.1";
+  version = "3.20";
 
   src = fetchFromGitHub {
     owner = "simgrid";
     repo = "simgrid";
     rev = "v${version}";
-    sha256 = "0vpgcp40xv20hcpslx5wz2mf2phaq41f7x8yr0bm7mknqd3zwxih";
+    sha256 = "0xb20qhvsah2dz2hvn850i3w9a5ghsbcx8vka2ap6xsdkxf593gy";
   };
 
-  nativeBuildInputs = [ cmake perl elfutils python3 boost valgrind ]
+  nativeBuildInputs = [ cmake perl python3 boost valgrind ]
       ++ optionals fortranSupport [ gfortran ]
       ++ optionals buildJavaBindings [ openjdk ]
       ++ optionals buildDocumentation [ transfig ghostscript doxygen ]
-      ++ optionals modelCheckingSupport [ libunwind libevent ];
+      ++ optionals modelCheckingSupport [ libunwind libevent elfutils ];
 
   #buildInputs = optional luaSupport lua5;
 
@@ -83,13 +83,15 @@ stdenv.mkDerivation rec {
   '';
 
   doCheck = true;
-  
+
   checkPhase = ''
     runHook preCheck
-    ctest --output-on-failure -E smpi-replay-multiple
+
+    ctest -j $NIX_BUILD_CORES --output-on-failure -E smpi-replay-multiple
+
     runHook postCheck
   '';
-    
+
   enableParallelBuilding = true;
 
   meta = {

pkgs/applications/version-management/cvs/default.nix

@@ -32,9 +32,10 @@ stdenv.mkDerivation {
 
   doCheck = false; # fails 1 of 1 tests
 
-  meta = {
+  meta = with stdenv.lib; {
     homepage = http://cvs.nongnu.org;
     description = "Concurrent Versions System - a source control system";
-    platforms = stdenv.lib.platforms.all;
+    license = licenses.gpl2; # library is GPLv2, main is GPLv1
+    platforms = platforms.all;
   };
 }

pkgs/applications/version-management/git-and-tools/tig/default.nix

@@ -4,14 +4,14 @@
 
 stdenv.mkDerivation rec {
   pname = "tig";
-  version = "2.4.0";
+  version = "2.4.1";
   name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "jonas";
     repo = pname;
     rev = name;
-    sha256 = "1d5clkdgj0ip1j0k335pr4dabcnap6jr016q90i49p1jxixy96pb";
+    sha256 = "0i26yfn2vjgsg1kdvhhv55jwzds7ih7cnad1xqvilqm83zh47ksd";
   };
 
   nativeBuildInputs = [ makeWrapper autoreconfHook asciidoc xmlto docbook_xsl docbook_xml_dtd_45 findXMLCatalogs pkgconfig ];

pkgs/applications/version-management/gitkraken/default.nix

@@ -12,11 +12,11 @@ let
 in
 stdenv.mkDerivation rec {
   name = "gitkraken-${version}";
-  version = "3.6.6";
+  version = "4.0.1";
 
   src = fetchurl {
     url = "https://release.gitkraken.com/linux/v${version}.deb";
-    sha256 = "01ir325ls1fb6ml79c02c7dyi910lxw0avlwc0nzv8fy4aqavl6p";
+    sha256 = "0y4r5d21mxwnwla9ggy9c4pm3zbz67yi9z06znkdz9x2chv1ci3n";
   };
 
   libPath = makeLibraryPath [

pkgs/applications/video/mpv/scripts/mpris.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "mpv-mpris-${version}.so";
-  version = "0.1";
+  version = "0.2";
 
   src = fetchFromGitHub {
     owner = "hoyon";
     repo = "mpv-mpris";
-    rev = "v${version}";
-    sha256 = "0rsbrbv5q7vki59wdlx4cdkd0vvd79qgbjvdb3fn3li7aznvjwiy";
+    rev = version;
+    sha256 = "06hq3j1jjlaaz9ss5l7illxz8vm5bng86jl24kawglwkqayhdnjx";
   };
 
   nativeBuildInputs = [ pkgconfig ];

pkgs/applications/video/obs-studio/linuxbrowser.nix

@@ -10,12 +10,12 @@
 
 stdenv.mkDerivation rec {
   name = "obs-linuxbrowser-${version}";
-  version = "0.4.0";
+  version = "0.5.0";
   src = fetchFromGitHub {
     owner = "bazukas";
     repo = "obs-linuxbrowser";
     rev = version;
-    sha256 = "1nqi04ici9n1xjliy1gaqy2bq8zj1z32dffk890x2hi7ml688y9h";
+    sha256 = "0jgh377yv69wbcqg7m7axi22x2p9jmcirws1pgrz22vaw7zbbdzl";
   };
   nativeBuildInputs = [ cmake ];
   buildInputs = [ obs-studio ];

pkgs/applications/virtualization/qemu/default.nix

@@ -22,8 +22,8 @@
 
 with stdenv.lib;
 let
-  version = "2.12.0";
-  sha256 = "17377xxbmwbrnh895a108z944pqi39hzrbw4jzgj8pcipi3s3x69";
+  version = "2.12.1";
+  sha256 = "1jp5y56682bgpfjapagxjfrjdvqkal34pj9qzn6kj8fqaad80l21";
   audio = optionalString (hasSuffix "linux" stdenv.system) "alsa,"
     + optionalString pulseSupport "pa,"
     + optionalString sdlSupport "sdl,";
@@ -71,8 +71,10 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "ga" ];
 
-  patches = [ ./no-etc-install.patch ]
-    ++ optional nixosTestRunner ./force-uid0-on-9p.patch
+  patches = [
+    ./no-etc-install.patch
+    ./fix-qemu-ga.patch
+  ] ++ optional nixosTestRunner ./force-uid0-on-9p.patch
     ++ optional pulseSupport ./fix-hda-recording.patch
     ++ optionals stdenv.hostPlatform.isMusl [
     (fetchpatch {

pkgs/applications/virtualization/qemu/fix-qemu-ga.patch

@@ -0,0 +1,22 @@
+diff --git a/qga/commands-posix.c b/qga/commands-posix.c
+index 0dc219d..9d020d3 100644
+--- a/qga/commands-posix.c
++++ b/qga/commands-posix.c
+@@ -102,6 +102,8 @@ void qmp_guest_shutdown(bool has_mode, const char *mode, Error **errp)
+         reopen_fd_to_null(1);
+         reopen_fd_to_null(2);
+
++        execle("/run/current-system/sw/bin/shutdown", "shutdown", "-h", shutdown_flag, "+0",
++               "hypervisor initiated shutdown", (char*)NULL, environ);
+         execle("/sbin/shutdown", "shutdown", "-h", shutdown_flag, "+0",
+                "hypervisor initiated shutdown", (char*)NULL, environ);
+         _exit(EXIT_FAILURE);
+@@ -189,6 +191,8 @@ void qmp_guest_set_time(bool has_time, int64_t time_ns, Error **errp)
+
+         /* Use '/sbin/hwclock -w' to set RTC from the system time,
+          * or '/sbin/hwclock -s' to set the system time from RTC. */
++        execle("/run/current-system/sw/bin/hwclock", "hwclock", has_time ? "-w" : "-s",
++               NULL, environ);
+         execle("/sbin/hwclock", "hwclock", has_time ? "-w" : "-s",
+                NULL, environ);
+         _exit(EXIT_FAILURE);

pkgs/applications/virtualization/singularity/default.nix

@@ -19,7 +19,7 @@
 
 stdenv.mkDerivation rec {
   name = "singularity-${version}";
-  version = "2.5.2";
+  version = "2.6.0";
 
   enableParallelBuilding = true;
 
@@ -47,7 +47,7 @@ stdenv.mkDerivation rec {
     owner = "singularityware";
     repo = "singularity";
     rev = version;
-    sha256 = "09wv8xagr5fjfhra5vyig0f1frfp97g99baqkh4avbzpg296q933";
+    sha256 = "0bi7acgppbkfbra8r29s1ldq02lazdww0z2h1rfvv8spr8dzzi94";
   };
 
   nativeBuildInputs = [ autoreconfHook makeWrapper ];

pkgs/applications/virtualization/virtualbox/default.nix

@@ -6,7 +6,7 @@
 , xorriso, makeself, perl
 , javaBindings ? false, jdk ? null
 , pythonBindings ? false, python2 ? null
-, enableExtensionPack ? false, requireFile ? null, fakeroot ? null
+, extensionPack ? null, fakeroot ? null
 , pulseSupport ? false, libpulseaudio ? null
 , enableHardening ? false
 , headless ? false
@@ -19,30 +19,9 @@ with stdenv.lib;
 let
   python = python2;
   buildType = "release";
-  # Manually sha256sum the extensionPack file, must be hex!
-  # Do not forget to update the hash in ./guest-additions/default.nix!
-  extpack = "d90c1b0c89de19010f7c7fe7a675ac744067baf29a9966b034e97b5b2053b37e";
-  extpackRev = "123301";
+  # Remember to change the extpackRev and version in extpack.nix as well.
   main = "ee3af129a581ec4c1a3e777e98247f8943e976ce6edd24962bcaa5c53ed1f644";
   version = "5.2.14";
-
-  # See https://github.com/NixOS/nixpkgs/issues/672 for details
-  extensionPack = requireFile rec {
-    name = "Oracle_VM_VirtualBox_Extension_Pack-${version}-${toString extpackRev}.vbox-extpack";
-    sha256 = extpack;
-    message = ''
-      In order to use the extension pack, you need to comply with the VirtualBox Personal Use
-      and Evaluation License (PUEL) available at:
-
-      https://www.virtualbox.org/wiki/VirtualBox_PUEL
-
-      Once you have read and if you agree with the license, please use the
-      following command and re-run the installation:
-
-      nix-prefetch-url http://download.virtualbox.org/virtualbox/${version}/${name}
-    '';
-  };
-
 in stdenv.mkDerivation {
   name = "virtualbox-${version}";
 
@@ -174,7 +153,7 @@ in stdenv.mkDerivation {
         ln -s "$libexec/$file" $out/bin/$file
     done
 
-    ${optionalString enableExtensionPack ''
+    ${optionalString (extensionPack != null) ''
       mkdir -p "$share"
       "${fakeroot}/bin/fakeroot" "${stdenv.shell}" <<EXTHELPER
       "$libexec/VBoxExtPackHelperApp" install \

pkgs/applications/virtualization/virtualbox/extpack.nix

@@ -0,0 +1,20 @@
+{stdenv, fetchurl, lib}:
+
+with lib;
+
+let extpackRev = "123301";
+    version = "5.2.14";
+in
+fetchurl rec {
+  name = "Oracle_VM_VirtualBox_Extension_Pack-${version}-${toString extpackRev}.vbox-extpack";
+  url = "http://download.virtualbox.org/virtualbox/${version}/${name}";
+  sha256 = "d90c1b0c89de19010f7c7fe7a675ac744067baf29a9966b034e97b5b2053b37e";
+
+  meta = {
+    description = "Oracle Extension pack for VirtualBox";
+    license = licenses.virtualbox-puel;
+    homepage = https://www.virtualbox.org/;
+    maintainers = with maintainers; [ flokli sander cdepillabout ];
+    platforms = [ "x86_64-linux" "i686-linux" ];
+  };
+}

pkgs/build-support/rust/default-crate-overrides.nix

@@ -1,6 +1,6 @@
 { stdenv, pkgconfig, curl, darwin, libiconv, libgit2, libssh2,
   openssl, sqlite, zlib, dbus, dbus-glib, gdk_pixbuf, cairo, python3,
-  libsodium, postgresql, ... }:
+  libsodium, postgresql, gmp, ... }:
 
 let
   inherit (darwin.apple_sdk.frameworks) CoreFoundation Security;
@@ -58,6 +58,10 @@ in
   gdk-pixbuf = attrs: {
     buildInputs = [ gdk_pixbuf ];
   };
+  rink = attrs: {
+    buildInputs = [ gmp ];
+    crateBin = [ {  name = "rink"; path = "src/bin/rink.rs"; } ];
+  };
   cairo-rs = attrs: {
     buildInputs = [ cairo ];
   };

pkgs/build-support/rust/default.nix

@@ -7,6 +7,8 @@ in
 { name, cargoSha256 ? "unset"
 , src ? null
 , srcs ? null
+, cargoPatches ? []
+, patches ? []
 , sourceRoot ? null
 , logLevel ? ""
 , buildInputs ? []
@@ -23,6 +25,7 @@ let
   cargoDeps = if cargoVendorDir == null
     then fetchcargo {
         inherit name src srcs sourceRoot cargoUpdateHook;
+        patches = cargoPatches;
         sha256 = cargoSha256;
       }
     else null;
@@ -44,6 +47,8 @@ in stdenv.mkDerivation (args // {
 
   buildInputs = [ cacert git rust.cargo rust.rustc ] ++ buildInputs;
 
+  patches = cargoPatches ++ patches;
+
   configurePhase = args.configurePhase or ''
     runHook preConfigure
     # noop

pkgs/build-support/rust/fetchcargo.nix

@@ -1,11 +1,11 @@
 { stdenv, cacert, git, rust, cargo-vendor }:
-{ name ? "cargo-deps", src, srcs, sourceRoot, sha256, cargoUpdateHook ? "" }:
+{ name ? "cargo-deps", src, srcs, patches, sourceRoot, sha256, cargoUpdateHook ? "" }:
 stdenv.mkDerivation {
   name = "${name}-vendor";
   nativeBuildInputs = [ cacert cargo-vendor git rust.cargo ];
-  inherit src srcs sourceRoot;
+  inherit src srcs patches sourceRoot;
 
-  phases = "unpackPhase installPhase";
+  phases = "unpackPhase patchPhase installPhase";
 
   installPhase = ''
     if [[ ! -f Cargo.lock ]]; then

pkgs/data/fonts/twemoji-color-font/default.nix

@@ -6,7 +6,7 @@ stdenv.mkDerivation rec {
     owner = "eosrei";
     repo = "twemoji-color-font";
     rev = "v${meta.version}";
-    sha256 = "0i7krmg99nrrj7mbjjd2cw6dx24aja63571mcyp6d7q1z09asz9k";
+    sha256 = "0z8r7z2r0r2wng4a7hvqvkcpd43l0d57yl402r7ci5bnmb02yvsa";
   };
 
   nativeBuildInputs = [ inkscape imagemagick potrace svgo scfbuild ];
@@ -21,7 +21,7 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with stdenv.lib; {
-    version = "1.3";
+    version = "1.4";
     description = "Color emoji SVGinOT font using Twitter Unicode 10 emoji with diversity and country flags";
     longDescription = ''
       A color and B&W emoji SVGinOT font built from the Twitter Emoji for
@@ -38,6 +38,6 @@ stdenv.mkDerivation rec {
     downloadPage = "https://github.com/eosrei/twemoji-color-font/releases";
     license = with licenses; [ cc-by-40 mit ];
     maintainers = [ maintainers.fgaz ];
-    platforms = platforms.all;
+    platforms = platforms.linux;
   };
 }

pkgs/desktops/gnome-3/default.nix

@@ -34,7 +34,7 @@ lib.makeScope pkgs.newScope (self: with self; {
   ];
 
   gamesPackages = with gnome3; [ swell-foop lightsoff iagno
-    tali quadrapassel gnome-sudoku aisleriot five-or-more
+    tali quadrapassel gnome-sudoku atomix aisleriot five-or-more
     four-in-a-row gnome-chess gnome-klotski gnome-mahjongg
     gnome-mines gnome-nibbles gnome-robots gnome-tetravex
     hitori gnome-taquin
@@ -319,6 +319,8 @@ lib.makeScope pkgs.newScope (self: with self; {
 
   aisleriot = callPackage ./games/aisleriot { };
 
+  atomix = callPackage ./games/atomix { };
+
   five-or-more = callPackage ./games/five-or-more { };
 
   four-in-a-row = callPackage ./games/four-in-a-row { };

pkgs/desktops/gnome-3/games/atomix/default.nix

@@ -0,0 +1,37 @@
+{ stdenv, fetchurl, meson, ninja, pkgconfig, wrapGAppsHook
+, gettext, gnome3, glib, gtk3, libgnome-games-support, gdk_pixbuf }:
+
+let
+  pname = "atomix";
+  version = "3.29.3";
+in stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${name}.tar.xz";
+    sha256 = "1k8bvwywpvw5f13pw40brk6c3rz2mdz9cd4zhcawg7qdm77dvcvb";
+  };
+
+  nativeBuildInputs = [ meson ninja pkgconfig gettext wrapGAppsHook ];
+  buildInputs = [ glib gtk3 gdk_pixbuf libgnome-games-support gnome3.defaultIconTheme ];
+
+  postPatch = ''
+    chmod +x meson_post_install.py
+    patchShebangs meson_post_install.py
+  '';
+
+  passthru = {
+    updateScript = gnome3.updateScript {
+      packageName = pname;
+      attrPath = "gnome3.${pname}";
+    };
+  };
+
+  meta = with stdenv.lib; {
+    description = "Puzzle game where you move atoms to build a molecule";
+    homepage = https://wiki.gnome.org/Apps/Atomix;
+    license = licenses.gpl2Plus;
+    maintainers = gnome3.maintainers;
+    platforms = platforms.linux;
+  };
+}

pkgs/desktops/gnome-3/misc/libgnome-games-support/default.nix

@@ -13,7 +13,11 @@ in stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ pkgconfig intltool ];
-  buildInputs = [ glib gtk3 libgee libintl ];
+  buildInputs = [ libintl ];
+  propagatedBuildInputs = [
+    # Required by libgnome-games-support-1.pc
+    glib gtk3 libgee
+  ];
 
   passthru = {
     updateScript = gnome3.updateScript {

pkgs/development/compilers/dmd/default.nix

@@ -1,34 +1,15 @@
-{ stdenv, fetchFromGitHub, overrideCC, gcc5
+{ stdenv, fetchFromGitHub
 , makeWrapper, unzip, which
 , curl, tzdata, gdb, darwin
-, callPackage, targetPackages
-, bootstrapVersion ? false
-, version ? "2.079.1"
-, dmdSha256 ? "0mlk095aw94d940qkymfp85daggiz3f0xv598nlc7acgp6408kyj"
-, druntimeSha256 ? "18r8gwvb54ar80j5155wx0qbqq4w56hqmbf6wap20xwijg2rw90g"
-, phobosSha256 ? "1x5v1ln51nr8x2vyki864160bakdyq0acmvbfv7jcipaj2w3m9bb"
+, callPackage, targetPackages, ldc
+, version ? "2.081.1"
+, dmdSha256 ? "1xdz7p0pdzwkn57ai93mavgdkd8xb1sr2brlc6y3c12x84h43s8z"
+, druntimeSha256 ? "1vl8ag6rjvqqmc5bn5jk3yfynjb9ggy3hw1awwl7c76bq4f7nbif"
+, phobosSha256 ? "0h1jdc3yai1l42bxjdlyi9hf9qadh76v925rjk2q4ibv2fzl56b7"
 }:
 
 let
 
-  bootstrapDmd = if !bootstrapVersion then
-    # Versions 2.070.2 and up require a working dmd compiler to build so we just
-    # use the last dmd without any D code to bootstrap the actual build.
-    callPackage ./default.nix {
-      stdenv = if stdenv.hostPlatform.isDarwin then
-                 stdenv
-               else
-                 # Doesn't build with gcc6 on linux
-                 overrideCC stdenv gcc5;
-      bootstrapVersion = true;
-      version = "2.067.1";
-      dmdSha256 = "0fm29lg8axfmzdaj0y6vg70lhwb5d9rv4aavnvdd15xjschinlcz";
-      druntimeSha256 = "1n2qfw9kmnql0fk2nxikispqs7vh85nhvyyr00fk227n9lgnqf02";
-      phobosSha256 = "0fywgds9xvjcgnqxmpwr67p3wi2m535619pvj159cgwv5y0nr3p1";
-    }
-  else
-    "";
-
   dmdBuild = stdenv.mkDerivation rec {
     name = "dmdBuild-${version}";
     inherit version;
@@ -74,11 +55,6 @@ let
     usePIC = "-fPIC";
     ROOT_HOME_DIR = "$(echo ~root)";
 
-    datetimePath = if bootstrapVersion then
-      "phobos/std/datetime.d"
-    else
-      "phobos/std/datetime/timezone.d";
-
     phobosPatches = ''
         # Ugly hack so the dlopen call has a chance to succeed.
         # https://issues.dlang.org/show_bug.cgi?id=15391
@@ -89,77 +65,24 @@ let
         substituteInPlace phobos/posix.mak \
             --replace "-soname=libcurl.so.4" "-soname=${curl.out}/lib/libcurl.so.4"
 
-    ''
-
-    + stdenv.lib.optionalString (!bootstrapVersion) ''
-	# Can be removed when https://github.com/dlang/phobos/pull/6224 is included.
-        substituteInPlace ${datetimePath} \
-            --replace "foreach (DirEntry de; dirEntries(tzDatabaseDir, SpanMode.depth))" "import std.path : baseName; foreach (DirEntry de; dirEntries(tzDatabaseDir, SpanMode.depth))"
-
-        substituteInPlace ${datetimePath} \
-            --replace "tzName == \"leapseconds\"" "baseName(tzName) == \"leapseconds\""
-    ''
-
-    + stdenv.lib.optionalString (bootstrapVersion) ''
-        substituteInPlace ${datetimePath} \
-            --replace "import std.traits;" "import std.traits;import std.path;"
-
-        substituteInPlace ${datetimePath} \
-            --replace "tzName == \"+VERSION\"" "baseName(tzName) == \"leapseconds\" || tzName == \"+VERSION\""
-
-        # Ugly hack to fix the hardcoded path to zoneinfo in the source file.
-        # https://issues.dlang.org/show_bug.cgi?id=15391
-        substituteInPlace ${datetimePath} \
-            --replace /usr/share/zoneinfo/ ${tzdata}/share/zoneinfo/
-    ''
-
-    + stdenv.lib.optionalString (bootstrapVersion && stdenv.hostPlatform.isLinux) ''
-        # See https://github.com/dlang/phobos/pull/5960
-        substituteInPlace phobos/std/path.d \
-            --replace "\"/root" "\"${ROOT_HOME_DIR}"
     '';
 
-    dmdPath = if bootstrapVersion then
-      "dmd/src"
-    else
-      "dmd";
-
     postPatch = ''
-    ''
-
-    + stdenv.lib.optionalString (!bootstrapVersion) ''
         substituteInPlace druntime/test/common.mak \
             --replace "DFLAGS:=" "DFLAGS:=${usePIC} "
-    ''
 
-    + stdenv.lib.optionalString (bootstrapVersion) ''
-        # Use proper C++ compiler
-        substituteInPlace ${dmdPath}/posix.mak \
-            --replace g++ $CXX
+        substituteInPlace dmd/src/posix.mak \
+            --replace "DFLAGS :=" "DFLAGS += -link-defaultlib-shared=false"
     ''
 
     + phobosPatches
 
-    + stdenv.lib.optionalString (stdenv.hostPlatform.isLinux && bootstrapVersion) ''
-      substituteInPlace ${dmdPath}/root/port.c \
-        --replace "#include <bits/mathdef.h>" "#include <complex.h>"
-
-      substituteInPlace ${dmdPath}/root/port.c \
-        --replace "#include <bits/nan.h>" "#include <math.h>"
-    ''
-
     + stdenv.lib.optionalString stdenv.hostPlatform.isDarwin ''
-        substituteInPlace ${dmdPath}/posix.mak \
+        substituteInPlace dmd/posix.mak \
             --replace MACOSX_DEPLOYMENT_TARGET MACOSX_DEPLOYMENT_TARGET_
-    ''
-
-    + stdenv.lib.optionalString (stdenv.hostPlatform.isDarwin && bootstrapVersion) ''
-	    # Was not able to compile on darwin due to "__inline_isnanl"
-	    # being undefined.
-	    substituteInPlace ${dmdPath}/root/port.c --replace __inline_isnanl __inline_isnan
     '';
 
-    nativeBuildInputs = [ bootstrapDmd makeWrapper unzip which gdb ]
+    nativeBuildInputs = [ ldc makeWrapper unzip which gdb ]
 
     ++ stdenv.lib.optional stdenv.hostPlatform.isDarwin (with darwin.apple_sdk.frameworks; [
       Foundation
@@ -173,23 +96,22 @@ let
     else
       stdenv.hostPlatform.parsed.kernel.name;
     top = "$(echo $NIX_BUILD_TOP)";
-    pathToDmd = if bootstrapVersion then
-      "${top}/dmd/src/dmd"
-    else
-      "${top}/dmd/generated/${osname}/release/${bits}/dmd";
+    pathToDmd = "${top}/dmd/generated/${osname}/release/${bits}/dmd";
 
     # Buid and install are based on http://wiki.dlang.org/Building_DMD
     buildPhase = ''
         cd dmd
-        make -j$NIX_BUILD_CORES -f posix.mak INSTALL_DIR=$out
+        make -j$NIX_BUILD_CORES -f posix.mak INSTALL_DIR=$out BUILD=release ENABLE_RELEASE=1 PIC=1 HOST_DMD=ldmd2
         cd ../druntime
-        make -j$NIX_BUILD_CORES -f posix.mak PIC=1 INSTALL_DIR=$out DMD=${pathToDmd}
+        make -j$NIX_BUILD_CORES -f posix.mak BUILD=release ENABLE_RELEASE=1 PIC=1 INSTALL_DIR=$out DMD=${pathToDmd}
         cd ../phobos
-        make -j$NIX_BUILD_CORES -f posix.mak PIC=1 INSTALL_DIR=$out DMD=${pathToDmd} TZ_DATABASE_DIR=${tzdata}/share/zoneinfo/
+        make -j$NIX_BUILD_CORES -f posix.mak BUILD=release ENABLE_RELEASE=1 PIC=1 INSTALL_DIR=$out DMD=${pathToDmd} TZ_DATABASE_DIR=${tzdata}/share/zoneinfo/
         cd ..
     '';
 
-    doCheck = !bootstrapVersion;
+    # Disable tests on Darwin for now because of
+    # https://github.com/NixOS/nixpkgs/issues/41099
+    doCheck = !stdenv.hostPlatform.isDarwin;
 
     checkPhase = ''
         cd dmd
@@ -198,9 +120,9 @@ let
         make -j$NIX_BUILD_CORES -f posix.mak unittest PIC=1 DMD=${pathToDmd} BUILD=release
         cd ..
     '';
-    
-    extension = if stdenv.hostPlatform.isDarwin then "a" else "{a,so}";
 
+    extension = if stdenv.hostPlatform.isDarwin then "a" else "{a,so}";
+    
     dontStrip = true;
 
     installPhase = ''
@@ -250,34 +172,40 @@ let
 
   # Need to test Phobos in a fixed-output derivation, otherwise the
   # network stuff in Phobos would fail if sandbox mode is enabled.
-  phobosUnittests = stdenv.mkDerivation rec {
-    name = "phobosUnittests-${version}";
-    version = dmdBuild.version;
+  #
+  # Disable tests on Darwin for now because of
+  # https://github.com/NixOS/nixpkgs/issues/41099
+  phobosUnittests = if !stdenv.hostPlatform.isDarwin then
+    stdenv.mkDerivation rec {
+      name = "phobosUnittests-${version}";
+      version = dmdBuild.version;
 
-    enableParallelBuilding = dmdBuild.enableParallelBuilding;
-    preferLocalBuild = true;
-    inputString = dmdBuild.outPath;
-    outputHashAlgo = "sha256";
-    outputHash = builtins.hashString "sha256" inputString;
+      enableParallelBuilding = dmdBuild.enableParallelBuilding;
+      preferLocalBuild = true;
+      inputString = dmdBuild.outPath;
+      outputHashAlgo = "sha256";
+      outputHash = builtins.hashString "sha256" inputString;
 
-    srcs = dmdBuild.srcs;
+      srcs = dmdBuild.srcs;
 
-    sourceRoot = ".";
+      sourceRoot = ".";
 
-    postPatch = dmdBuild.phobosPatches;
+      postPatch = dmdBuild.phobosPatches;
 
-    nativeBuildInputs = dmdBuild.nativeBuildInputs;
-    buildInputs = dmdBuild.buildInputs;
+      nativeBuildInputs = dmdBuild.nativeBuildInputs;
+      buildInputs = dmdBuild.buildInputs;
 
-    buildPhase = ''
-        cd phobos
-        make -j$NIX_BUILD_CORES -f posix.mak unittest PIC=1 DMD=${dmdBuild}/bin/dmd BUILD=release TZ_DATABASE_DIR=${tzdata}/share/zoneinfo/
-    '';
+      buildPhase = ''
+          cd phobos
+          make -j$NIX_BUILD_CORES -f posix.mak unittest BUILD=release ENABLE_RELEASE=1 PIC=1 DMD=${dmdBuild}/bin/dmd TZ_DATABASE_DIR=${tzdata}/share/zoneinfo/
+      '';
 
-    installPhase = ''
-        echo -n $inputString > $out
-    '';
-  };
+      installPhase = ''
+          echo -n $inputString > $out
+      '';
+    }
+  else
+    "";
 
 in
 

pkgs/development/compilers/ghc/8.4.3.nix

@@ -30,6 +30,10 @@
 , # What flavour to build. An empty string indicates no
   # specific flavour and falls back to ghc default values.
   ghcFlavour ? stdenv.lib.optionalString (targetPlatform != hostPlatform) "perf-cross"
+, # Whether to backport https://phabricator.haskell.org/D4388 for
+  # deterministic profiling symbol names, at the cost of a slightly
+  # non-standard GHC API
+  deterministicProfiling ? false
 }:
 
 assert !enableIntegerSimple -> gmp != null;
@@ -94,7 +98,11 @@ stdenv.mkDerivation (rec {
     sha256 = "0plzsbfaq6vb1023lsarrjglwgr9chld4q3m99rcfzx0yx5mibp3";
     extraPrefix = "utils/hsc2hs/";
     stripLen = 1;
-  })]
+  })] ++ stdenv.lib.optional deterministicProfiling
+    (fetchpatch {
+      url = "https://phabricator-files.haskell.org/file/data/yd2fclrwulila2quki5q/PHID-FILE-lr2j63hkglwauprxycrt/D4388.diff";
+      sha256 = "0w6sdcvnqjlnlzpvnzw20b80v150ijjyjvs9548ildc1928j0w7s";
+    })
     ++ stdenv.lib.optional stdenv.isDarwin ./backport-dylib-command-size-limit.patch;
 
   postPatch = "patchShebangs .";

pkgs/development/compilers/javacard-devkit/default.nix

@@ -0,0 +1,67 @@
+{ stdenv, requireFile, unzip, makeWrapper, oraclejdk8, autoPatchelfHook
+, pcsclite
+}:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "javacard-devkit";
+  version = "2.2.2";
+  uscoreVersion = builtins.replaceStrings ["."] ["_"] version;
+
+  src = requireFile {
+    name = "java_card_kit-${uscoreVersion}-linux.zip";
+    url = "http://www.oracle.com/technetwork/java/javasebusiness/downloads/"
+        + "java-archive-downloads-javame-419430.html#java_card_kit-2.2.2-oth-JPR";
+    sha256 = "1rzkw8izqq73ifvyp937wnjjc40a40drc4zsm0l1s6jyv3d7agb2";
+  };
+
+  nativeBuildInputs = [ unzip oraclejdk8 makeWrapper autoPatchelfHook ];
+  buildInputs = [ pcsclite ];
+
+  zipPrefix = "java_card_kit-${uscoreVersion}";
+
+  sourceRoot = ".";
+  unpackCmd = ''
+    unzip -p "$curSrc" "$zipPrefix/$zipPrefix-rr-bin-linux-do.zip" | jar x
+  '';
+
+  installPhase = ''
+    mkdir -p "$out/share/$pname"
+    cp -rt "$out/share/$pname" api_export_files
+    cp -rt "$out" lib
+
+    for i in bin/*; do
+      case "$i" in
+        *.so) install -vD "$i" "$out/libexec/$pname/$(basename "$i")";;
+        *) target="$out/bin/$(basename "$i")"
+           install -vD "$i" "$target"
+           wrapProgram "$target" \
+             --set JAVA_HOME "$JAVA_HOME" \
+             --prefix CLASSPATH : "$out/share/$pname/api_export_files"
+           ;;
+      esac
+    done
+
+    makeWrapper "$JAVA_HOME/bin/javac" "$out/bin/javacardc" \
+      --prefix CLASSPATH : "$out/lib/api.jar"
+  '';
+
+  meta = {
+    description = "Official development kit by Oracle for programming for the Java Card platform";
+    longDescription = ''
+      This Java Card SDK is the official SDK made available by Oracle for programming for the Java Card platform.
+
+      Instructions for usage:
+
+      First, compile your '.java' (NixOS-specific: you should not need to set the class path -- if you need, it's a bug):
+          javacardc -source 1.5 -target 1.5 [MyJavaFile].java
+      Then, convert the '.class' file into a '.cap':
+          converter -applet [AppletAID] [MyApplet] [myPackage] [PackageAID] [Version]
+      For more details, please refer to the documentation by Oracle
+    '';
+    homepage = http://www.oracle.com/technetwork/java/embedded/javacard/overview/index.html;
+    license = stdenv.lib.licenses.unfree;
+    maintainers = [ stdenv.lib.maintainers.ekleog ];
+    platforms = [ "i686-linux" "x86_64-linux" ];
+  };
+}

pkgs/development/compilers/ldc/default.nix

@@ -2,8 +2,8 @@
 , python, libconfig, lit, gdb, unzip, darwin, bash
 , callPackage, makeWrapper, targetPackages
 , bootstrapVersion ? false
-, version ? "1.8.0"
-, ldcSha256 ? "0zswjlibj8zcdj06nn09jjhbd99chsa5f4kps8xifzgrpgsa28g4"
+, version ? "1.10.0"
+, ldcSha256 ? "0wc3vlblsz4qdwa9ay9plv9nvfd07zj2byqqffaa4a5gvjwf5dlr"
 }:
 
 let
@@ -155,7 +155,10 @@ let
 
     makeFlags = [ "DMD=$DMD" ];
 
-    doCheck = true;
+    # Disable tests on Darwin for now because of
+    # https://github.com/NixOS/nixpkgs/issues/41099
+    # https://github.com/NixOS/nixpkgs/pull/36378#issuecomment-385034818
+    doCheck = !bootstrapVersion && !stdenv.hostPlatform.isDarwin;
 
     checkPhase = ''
       # Build and run LDC D unittests.
@@ -184,65 +187,72 @@ let
 
   # Need to test Phobos in a fixed-output derivation, otherwise the
   # network stuff in Phobos would fail if sandbox mode is enabled.
-  ldcUnittests = stdenv.mkDerivation rec {
-    name = "ldcUnittests-${version}";
+  #
+  # Disable tests on Darwin for now because of
+  # https://github.com/NixOS/nixpkgs/issues/41099
+  # https://github.com/NixOS/nixpkgs/pull/36378#issuecomment-385034818
+  ldcUnittests = if (!bootstrapVersion && !stdenv.hostPlatform.isDarwin) then
+    stdenv.mkDerivation rec {
+      name = "ldcUnittests-${version}";
 
-    enableParallelBuilding = ldcBuild.enableParallelBuilding;
-    preferLocalBuild = true;
-    inputString = ldcBuild.outPath;
-    outputHashAlgo = "sha256";
-    outputHash = builtins.hashString "sha256" inputString;
+      enableParallelBuilding = ldcBuild.enableParallelBuilding;
+      preferLocalBuild = true;
+      inputString = ldcBuild.outPath;
+      outputHashAlgo = "sha256";
+      outputHash = builtins.hashString "sha256" inputString;
 
-    src = ldcBuild.src;
+      src = ldcBuild.src;
 
-    postUnpack = ldcBuild.postUnpack;
+      postUnpack = ldcBuild.postUnpack;
 
-    postPatch = ldcBuild.postPatch;
+      postPatch = ldcBuild.postPatch;
 
-    nativeBuildInputs = ldcBuild.nativeBuildInputs
+      nativeBuildInputs = ldcBuild.nativeBuildInputs
 
-    ++ [
-      ldcBuild
-    ];
+      ++ [
+        ldcBuild
+      ];
 
-    buildInputs = ldcBuild.buildInputs;
+      buildInputs = ldcBuild.buildInputs;
 
-    preConfigure = ''
-      cmakeFlagsArray=( "-DINCLUDE_INSTALL_DIR=$out/include/dlang/ldc"
-                        "-DCMAKE_BUILD_TYPE=Release"
-                        "-DCMAKE_SKIP_RPATH=ON"
-                        "-DBUILD_SHARED_LIBS=OFF"
-                        "-DLDC_WITH_LLD=OFF"
-                        # Xcode 9.0.1 fixes that bug according to ldc release notes
-                        "-DRT_ARCHIVE_WITH_LDC=OFF"
-                        "-DD_COMPILER=${ldcBuild.out}/bin/ldmd2"
-                      )
-    '';
+      preConfigure = ''
+        cmakeFlagsArray=( "-DINCLUDE_INSTALL_DIR=$out/include/dlang/ldc"
+                          "-DCMAKE_BUILD_TYPE=Release"
+                          "-DCMAKE_SKIP_RPATH=ON"
+                          "-DBUILD_SHARED_LIBS=OFF"
+                          "-DLDC_WITH_LLD=OFF"
+                          # Xcode 9.0.1 fixes that bug according to ldc release notes
+                          "-DRT_ARCHIVE_WITH_LDC=OFF"
+                          "-DD_COMPILER=${ldcBuild.out}/bin/ldmd2"
+                        )
+      '';
 
-    postConfigure = ldcBuild.postConfigure;
+      postConfigure = ldcBuild.postConfigure;
 
-    makeFlags = ldcBuild.makeFlags;
+      makeFlags = ldcBuild.makeFlags;
 
-    buildCmd = if bootstrapVersion then
-      "ctest -V -R \"build-druntime-ldc-unittest|build-phobos2-ldc-unittest\""
-    else
-      "make -j$NIX_BUILD_CORES DMD=${ldcBuild.out}/bin/ldc2 phobos2-test-runner phobos2-test-runner-debug";
+      buildCmd = if bootstrapVersion then
+        "ctest -V -R \"build-druntime-ldc-unittest|build-phobos2-ldc-unittest\""
+      else
+        "make -j$NIX_BUILD_CORES DMD=${ldcBuild.out}/bin/ldc2 phobos2-test-runner phobos2-test-runner-debug";
 
-    testCmd = if bootstrapVersion then
-      "ctest -j$NIX_BUILD_CORES --output-on-failure -E \"dmd-testsuite|lit-tests|ldc2-unittest|llvm-ir-testsuite\""
-    else
-      "ctest -j$NIX_BUILD_CORES --output-on-failure -E \"dmd-testsuite|lit-tests|ldc2-unittest\"";
+      testCmd = if bootstrapVersion then
+        "ctest -j$NIX_BUILD_CORES --output-on-failure -E \"dmd-testsuite|lit-tests|ldc2-unittest|llvm-ir-testsuite\""
+      else
+        "ctest -j$NIX_BUILD_CORES --output-on-failure -E \"dmd-testsuite|lit-tests|ldc2-unittest\"";
 
-    buildPhase = ''
-        ${buildCmd}
-        ln -s ${ldcBuild.out}/bin/ldmd2 $PWD/bin/ldmd2
-        ${testCmd}
-    '';
+      buildPhase = ''
+          ${buildCmd}
+          ln -s ${ldcBuild.out}/bin/ldmd2 $PWD/bin/ldmd2
+          ${testCmd}
+      '';
 
-    installPhase = ''
-        echo -n $inputString > $out
-    '';
-  };
+      installPhase = ''
+          echo -n $inputString > $out
+      '';
+    }
+  else
+    "";
 
 in
 

pkgs/development/compilers/nextpnr/default.nix

@@ -0,0 +1,35 @@
+{ stdenv, fetchFromGitHub, cmake
+, icestorm, python3, boost, qtbase
+}:
+
+let
+  boostPython = boost.override { python = python3; enablePython = true; };
+in
+stdenv.mkDerivation rec {
+  name = "nextpnr-${version}";
+  version = "2018.08.09";
+
+  src = fetchFromGitHub {
+    owner  = "yosyshq";
+    repo   = "nextpnr";
+    rev    = "2e02f2d6166c75b1fcec73d268e97e407071a372";
+    sha256 = "1f98mkailn75gz5fvhjhnyr0gwa0r8mm3f2sbvgl0yvys8qi08wr";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ boostPython python3 qtbase ];
+
+  enableParallelBuilding = true;
+  cmakeFlags =
+    [ "-DARCH=generic;ice40"
+      "-DICEBOX_ROOT=${icestorm}/share/icebox"
+    ];
+
+  meta = with stdenv.lib; {
+    description = "Place and route tool for FPGAs";
+    homepage    = https://github.com/yosyshq/nextpnr;
+    license     = licenses.isc;
+    platforms   = platforms.linux;
+    maintainers = with maintainers; [ thoughtpolice ];
+  };
+}

pkgs/development/compilers/pakcs/default.nix

@@ -8,7 +8,7 @@ let
 
   src = fetchurl {
     url = "https://www.informatik.uni-kiel.de/~pakcs/download/${name}-src.tar.gz";
-    sha256 = "0fdzw2zz5vs6z20jn6a8jfvpr6dp7fs1rr01cy0xjnzg2mgmn42a";
+    sha256 = "086nbsfv363cwrfxzhs54ggdwwkh1ms0pn0v1a4lvqlksjm7jdhv";
   };
 
   curry-frontend = (haskellPackages.override {

pkgs/development/compilers/rust/cargo.nix

@@ -19,8 +19,8 @@ rustPlatform.buildRustPackage rec {
 
   passthru.rustc = rustc;
 
-  # changes hash of vendor directory otherwise on aarch64
-  dontUpdateAutotoolsGnuConfigScripts = if stdenv.isAarch64 then "1" else null;
+  # changes hash of vendor directory otherwise
+  dontUpdateAutotoolsGnuConfigScripts = true;
 
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ cacert file curl python openssl cmake zlib makeWrapper libgit2 ]

pkgs/development/compilers/rust/rustc.nix

@@ -32,8 +32,8 @@ stdenv.mkDerivation {
 
   __darwinAllowLocalNetworking = true;
 
-  # The build will fail at the very end on AArch64 without this.
-  dontUpdateAutotoolsGnuConfigScripts = if stdenv.isAarch64 then true else null;
+  # rustc complains about modified source files otherwise
+  dontUpdateAutotoolsGnuConfigScripts = true;
 
   # Running the default `strip -S` command on Darwin corrupts the
   # .rlib files in "lib/".

pkgs/development/haskell-modules/configuration-common.nix

@@ -858,9 +858,6 @@ self: super: {
   fluid-idl-http-client = markBroken super.fluid-idl-http-client;
   fluid-idl-scotty = markBroken super.fluid-idl-scotty;
 
-  # missing dependencies: Glob >=0.7.14 && <0.8, data-fix ==0.0.4
-  stack2nix = doJailbreak super.stack2nix;
-
   # Work around https://github.com/haskell/c2hs/issues/192.
   c2hs = dontCheck super.c2hs;
 
@@ -954,12 +951,6 @@ self: super: {
   # https://github.com/yesodweb/Shelly.hs/issues/162
   shelly = dontCheck super.shelly;
 
-  # Support ansi-terminal 0.7.x.
-  cabal-plan = appendPatch super.cabal-plan (pkgs.fetchpatch {
-    url = "https://github.com/haskell-hvr/cabal-plan/pull/16.patch";
-    sha256 = "0i889zs46wn09d7iqdy99201zaqxb175cfs8jz2zi3mv4ywx3a0l";
-  });
-
   # https://github.com/simonmichael/hledger/issues/852
   hledger-lib = appendPatch super.hledger-lib (pkgs.fetchpatch {
     url = "https://github.com/simonmichael/hledger/commit/007b9f8caaf699852511634752a7d7c86f6adc67.patch";
@@ -1080,19 +1071,18 @@ self: super: {
   haddock-library = doJailbreak (dontCheck super.haddock-library);
   haddock-library_1_6_0 = doJailbreak (dontCheck super.haddock-library_1_6_0);
 
+  # cabal2nix requires hpack >= 0.29.6 but the LTS has hpack-0.28.2.
+  # Lets remove this once the LTS has upraded to 0.29.6.
+  hpack = super.hpack_0_29_6;
+
   cabal2nix =
-    let
-      # The test suite does not know how to find the 'cabal2nix' binary.
-      drv1 = overrideCabal super.cabal2nix (drv: {
-               preCheck = ''
-                 export PATH="$PWD/dist/build/cabal2nix:$PATH"
-                 export HOME="$TMPDIR/home"
-               '';
-             });
-       # cabal2nix requires hpack >= 0.29.6 but the LTS has hpack-0.28.2.
-       # Lets remove this once the LTS has upraded to 0.29.6.
-       drv2 = drv1.override { hpack = self.hpack_0_29_6; };
-    in drv2;
+    # The test suite does not know how to find the 'cabal2nix' binary.
+    overrideCabal super.cabal2nix (drv: {
+      preCheck = ''
+        export PATH="$PWD/dist/build/cabal2nix:$PATH"
+        export HOME="$TMPDIR/home"
+      '';
+    });
 
   # Break out of "aeson <1.3, temporary <1.3".
   stack = doJailbreak super.stack;
@@ -1129,4 +1119,7 @@ self: super: {
 
   # Can be removed once yi-language >= 0.18 is in the LTS
   yi-core = super.yi-core.override { yi-language = self.yi-language_0_18_0; };
-}
+
+  # https://github.com/MarcWeber/hasktags/issues/52
+  hasktags = dontCheck super.hasktags;
+} // import ./configuration-tensorflow.nix {inherit pkgs haskellLib;} self super

pkgs/development/haskell-modules/configuration-ghc-8.0.x.nix

@@ -19,6 +19,7 @@ self: super: {
   filepath = null;
   ghc-boot = null;
   ghc-boot-th = null;
+  ghc-compact = null;
   ghc-prim = null;
   ghci = null;
   haskeline = null;

pkgs/development/haskell-modules/configuration-ghc-8.2.x.nix

@@ -96,4 +96,4 @@ self: super: {
     haddock-library = dontHaddock (dontCheck self.haddock-library_1_5_0_1);
   }));
 
-} // import ./configuration-tensorflow-ghc-8.2.x.nix {inherit pkgs haskellLib;} self super
+}

pkgs/development/haskell-modules/configuration-tensorflow-ghc-8.2.x.nix

@@ -1,292 +0,0 @@
-{ pkgs, haskellLib }:
-
-with haskellLib;
-
-self: super:
-let
-  tensorflow-haskell = pkgs.fetchFromGitHub {
-    owner = "tensorflow";
-    repo = "haskell";
-    rev = "e40d2c44f0a861701cc90ec73c2bcee669ab5ba7";
-    sha256 = "05pda34jfrlqmb8y9l8g87n4iq87v1z820vnd3cy41v5c5nrdpa8";
-    fetchSubmodules = true;
-  };
-
-  setSourceRoot = dir: drv: drv.overrideAttrs (_oldAttrs: {sourceRoot = "source/${dir}";});
-
-  proto-lens = self.proto-lens_0_2_2_0;
-  proto-lens-protoc = self.proto-lens-protoc_0_2_2_3;
-  proto-lens-protobuf-types = self.proto-lens-protobuf-types_0_2_2_0;
-  mainland-pretty = self.mainland-pretty_0_6_2;
-  lens-labels = self.lens-labels_0_1_0_2;
-  haskell-src-exts = self.haskell-src-exts_1_19_1;
-in
-{
-  proto-lens-descriptors = super.proto-lens-descriptors.override {
-    inherit proto-lens lens-labels;
-  };
-  proto-lens-protoc_0_2_2_3 = super.proto-lens-protoc_0_2_2_3.override {
-    inherit proto-lens haskell-src-exts;
-  };
-  proto-lens-protobuf-types_0_2_2_0 = super.proto-lens-protobuf-types_0_2_2_0.override {
-    inherit proto-lens proto-lens-protoc;
-  };
-  tensorflow-proto = setSourceRoot "tensorflow-proto" (super.callPackage (
-    { mkDerivation, base, Cabal, proto-lens, proto-lens-protobuf-types
-    , proto-lens-protoc, stdenv
-    }:
-    mkDerivation {
-      pname = "tensorflow-proto";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      setupHaskellDepends = [ base Cabal proto-lens-protoc ];
-      libraryHaskellDepends = [
-        base proto-lens proto-lens-protobuf-types proto-lens-protoc
-      ];
-      libraryToolDepends = [ pkgs.protobuf ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "TensorFlow protocol buffers";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {
-    inherit proto-lens proto-lens-protoc proto-lens-protobuf-types;
-  });
-  tensorflow = setSourceRoot "tensorflow" (super.callPackage (
-    { mkDerivation, async, attoparsec, base, bytestring, c2hs
-    , containers, data-default, exceptions, fgl, HUnit, lens-family
-    , mainland-pretty, mtl, proto-lens, semigroups, split, stdenv
-    , temporary, libtensorflow, tensorflow-proto, test-framework
-    , test-framework-hunit, test-framework-quickcheck2, text
-    , transformers, vector
-    }:
-    mkDerivation {
-      pname = "tensorflow";
-      version = "0.1.0.2";
-      src = tensorflow-haskell;
-      libraryHaskellDepends = [
-        async attoparsec base bytestring containers data-default exceptions
-        fgl lens-family mainland-pretty mtl proto-lens semigroups split
-        temporary tensorflow-proto text transformers vector
-      ];
-      librarySystemDepends = [ libtensorflow ];
-      libraryToolDepends = [ c2hs ];
-      testHaskellDepends = [
-        attoparsec base bytestring HUnit lens-family proto-lens
-        tensorflow-proto test-framework test-framework-hunit
-        test-framework-quickcheck2
-      ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "TensorFlow bindings";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {
-    inherit mainland-pretty proto-lens;
-  });
-  tensorflow-core-ops = setSourceRoot "tensorflow-core-ops" (super.callPackage (
-    { mkDerivation, base, bytestring, Cabal, directory, filepath
-    , lens-family, mainland-pretty, proto-lens, stdenv, tensorflow
-    , tensorflow-opgen, text
-    }:
-    mkDerivation {
-      pname = "tensorflow-core-ops";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      setupHaskellDepends = [
-        base bytestring Cabal directory filepath mainland-pretty proto-lens
-        tensorflow tensorflow-opgen text
-      ];
-      libraryHaskellDepends = [
-        base bytestring lens-family proto-lens tensorflow text
-      ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "Haskell wrappers for Core Tensorflow Ops";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {
-    inherit mainland-pretty proto-lens;
-  });
-  tensorflow-logging = setSourceRoot "tensorflow-logging" (super.callPackage (
-    { mkDerivation, base, bytestring, conduit, data-default, directory
-    , exceptions, filepath, hostname, HUnit, lens-family, proto-lens
-    , resourcet, stdenv, stm, stm-chans, stm-conduit, temporary
-    , tensorflow, tensorflow-core-ops, tensorflow-ops, tensorflow-proto
-    , tensorflow-records-conduit, test-framework, test-framework-hunit
-    , text, time, transformers
-    }:
-    mkDerivation {
-      pname = "tensorflow-logging";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      libraryHaskellDepends = [
-        base bytestring conduit data-default directory exceptions filepath
-        hostname lens-family proto-lens resourcet stm stm-chans stm-conduit
-        tensorflow tensorflow-core-ops tensorflow-ops tensorflow-proto
-        tensorflow-records-conduit text time transformers
-      ];
-      testHaskellDepends = [
-        base bytestring conduit data-default directory filepath HUnit
-        lens-family proto-lens resourcet temporary tensorflow
-        tensorflow-proto tensorflow-records-conduit test-framework
-        test-framework-hunit text
-      ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "TensorBoard related functionality";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {
-    inherit proto-lens;
-  });
-  tensorflow-mnist = setSourceRoot "tensorflow-mnist" (super.callPackage (
-    { mkDerivation, base, binary, bytestring, containers, filepath
-    , HUnit, lens-family, proto-lens, split, stdenv, tensorflow
-    , tensorflow-core-ops, tensorflow-mnist-input-data, tensorflow-ops
-    , tensorflow-proto, test-framework, test-framework-hunit, text
-    , transformers, vector, zlib
-    }:
-    mkDerivation {
-      pname = "tensorflow-mnist";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      isLibrary = true;
-      isExecutable = true;
-      enableSeparateDataOutput = true;
-      libraryHaskellDepends = [
-        base binary bytestring containers filepath lens-family proto-lens
-        split tensorflow tensorflow-core-ops tensorflow-proto text vector
-        zlib
-      ];
-      executableHaskellDepends = [
-        base bytestring filepath lens-family proto-lens tensorflow
-        tensorflow-mnist-input-data tensorflow-ops tensorflow-proto text
-        transformers vector
-      ];
-      testHaskellDepends = [
-        base bytestring HUnit lens-family proto-lens tensorflow
-        tensorflow-mnist-input-data tensorflow-ops tensorflow-proto
-        test-framework test-framework-hunit text transformers vector
-      ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "TensorFlow demo application for learning MNIST model";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {
-    inherit proto-lens;
-  });
-  tensorflow-mnist-input-data = setSourceRoot "tensorflow-mnist-input-data" (super.callPackage (
-    { mkDerivation, base, bytestring, Cabal, cryptonite, directory
-    , filepath, HTTP, network-uri, stdenv
-    }:
-    mkDerivation {
-      pname = "tensorflow-mnist-input-data";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      enableSeparateDataOutput = true;
-      setupHaskellDepends = [
-        base bytestring Cabal cryptonite directory filepath HTTP
-        network-uri
-      ];
-      libraryHaskellDepends = [ base ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "Downloader of input data for training MNIST";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {});
-  tensorflow-opgen = setSourceRoot "tensorflow-opgen" (super.callPackage (
-    { mkDerivation, base, bytestring, containers, filepath, lens-family
-    , mainland-pretty, optparse-applicative, proto-lens, semigroups
-    , stdenv, tensorflow-proto, text
-    }:
-    mkDerivation {
-      pname = "tensorflow-opgen";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      libraryHaskellDepends = [
-        base bytestring containers filepath lens-family mainland-pretty
-        optparse-applicative proto-lens semigroups tensorflow-proto text
-      ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "Code generation for TensorFlow operations";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {
-    inherit mainland-pretty proto-lens;
-  });
-  tensorflow-ops = setSourceRoot "tensorflow-ops" (super.callPackage (
-    { mkDerivation, base, bytestring, containers, criterion
-    , data-default, deepseq, fgl, HUnit, lens-family, mtl, proto-lens
-    , QuickCheck, random, stdenv, temporary, tensorflow
-    , tensorflow-core-ops, tensorflow-proto, tensorflow-test
-    , test-framework, test-framework-hunit, test-framework-quickcheck2
-    , text, transformers, vector
-    }:
-    mkDerivation {
-      pname = "tensorflow-ops";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      libraryHaskellDepends = [
-        base bytestring containers data-default fgl lens-family mtl
-        proto-lens tensorflow tensorflow-core-ops tensorflow-proto text
-      ];
-      testHaskellDepends = [
-        base bytestring data-default HUnit lens-family proto-lens
-        QuickCheck random temporary tensorflow tensorflow-core-ops
-        tensorflow-proto tensorflow-test test-framework
-        test-framework-hunit test-framework-quickcheck2 transformers vector
-      ];
-      benchmarkHaskellDepends = [
-        base criterion deepseq tensorflow transformers vector
-      ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "Friendly layer around TensorFlow bindings";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {
-    inherit proto-lens;
-  });
-  tensorflow-records = setSourceRoot "tensorflow-records" (super.callPackage (
-    { mkDerivation, base, bytestring, cereal, snappy-framing, stdenv
-    , test-framework, test-framework-quickcheck2
-    }:
-    mkDerivation {
-      pname = "tensorflow-records";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      libraryHaskellDepends = [ base bytestring cereal snappy-framing ];
-      testHaskellDepends = [
-        base bytestring cereal test-framework test-framework-quickcheck2
-      ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "Encoder and decoder for the TensorFlow \"TFRecords\" format";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {});
-  tensorflow-records-conduit = setSourceRoot "tensorflow-records-conduit" (super.callPackage (
-    { mkDerivation, base, bytestring, cereal-conduit, conduit
-    , conduit-extra, exceptions, resourcet, stdenv, tensorflow-records
-    }:
-    mkDerivation {
-      pname = "tensorflow-records-conduit";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      libraryHaskellDepends = [
-        base bytestring cereal-conduit conduit conduit-extra exceptions
-        resourcet tensorflow-records
-      ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "Conduit wrappers for TensorFlow.Records.";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {});
-  tensorflow-test = setSourceRoot "tensorflow-test" (super.callPackage (
-    { mkDerivation, base, HUnit, stdenv, vector }:
-    mkDerivation {
-      pname = "tensorflow-test";
-      version = "0.1.0.0";
-      src = tensorflow-haskell;
-      libraryHaskellDepends = [ base HUnit vector ];
-      homepage = "https://github.com/tensorflow/haskell#readme";
-      description = "Some common functions for test suites";
-      license = stdenv.lib.licenses.asl20;
-    }
-  ) {});
-}

pkgs/development/haskell-modules/configuration-tensorflow.nix

@@ -0,0 +1,86 @@
+{ pkgs, haskellLib }:
+
+with haskellLib;
+
+self: super:
+let
+  tensorflow-haskell = pkgs.fetchFromGitHub {
+    owner = "tensorflow";
+    repo = "haskell";
+    rev = "85bf0bb12cecfcdfcf31dea43b67cbe44576f685";
+    sha256 = "1xbwc8y4a7n2163g746dpyh1q86rbxaw3d41kcy1mbhvmfqq56x7";
+    fetchSubmodules = true;
+  };
+
+  setSourceRoot = dir: drv: drv.overrideAttrs (_oldAttrs: {sourceRoot = "source/${dir}";});
+
+  proto-lens = self.proto-lens_0_2_2_0;
+  proto-lens-protoc = self.proto-lens-protoc_0_2_2_3;
+  proto-lens-protobuf-types = self.proto-lens-protobuf-types_0_2_2_0;
+  mainland-pretty = self.mainland-pretty_0_6_2;
+in
+{
+  proto-lens_0_2_2_0 = appendPatch super.proto-lens_0_2_2_0 ./patches/proto-lens-0.2.2.0.patch;
+  proto-lens-descriptors = doJailbreak (super.proto-lens-descriptors.override {
+    inherit proto-lens;
+    lens-labels = self.lens-labels_0_1_0_2;
+  });
+  proto-lens-protoc_0_2_2_3 = appendPatch (addBuildDepend (super.proto-lens-protoc_0_2_2_3.override {
+    inherit proto-lens;
+    haskell-src-exts = self.haskell-src-exts_1_19_1;
+  }) self.semigroups) ./patches/proto-lens-protoc-0.2.2.3.patch;
+  proto-lens-protobuf-types_0_2_2_0 = doJailbreak (super.proto-lens-protobuf-types_0_2_2_0.override {
+    inherit proto-lens proto-lens-protoc;
+  });
+
+  lens-labels_0_1_0_2 = doJailbreak super.lens-labels_0_1_0_2;
+
+  haskell-src-exts_1_19_1 = appendPatch (doJailbreak super.haskell-src-exts_1_19_1) (
+    # Adapt to the Semigroup–Monoid Proposal (enables building on GHC >= 8.4)
+    pkgs.fetchpatch {
+      url = https://github.com/haskell-suite/haskell-src-exts/commit/258e072fe9e37f94360b7488b58ea2832843bbb8.patch;
+      sha256 = "0ja6ai41v9plinlhjwja282m6ahn6mw4xi79np0jxqk83cg0z1ff";
+    }
+  );
+
+  tensorflow-proto = super.tensorflow-proto.override {
+    inherit proto-lens proto-lens-protoc proto-lens-protobuf-types;
+  };
+  tensorflow = super.tensorflow.override {
+    inherit mainland-pretty proto-lens;
+  };
+  tensorflow-core-ops = super.tensorflow-core-ops.override {
+    inherit mainland-pretty proto-lens;
+  };
+  tensorflow-logging = super.tensorflow-logging.override {
+    inherit proto-lens;
+  };
+  tensorflow-mnist = super.tensorflow-mnist.override {
+    inherit proto-lens;
+  };
+  tensorflow-mnist-input-data = setSourceRoot "tensorflow-mnist-input-data" (super.callPackage (
+    { mkDerivation, base, bytestring, Cabal, cryptonite, directory
+    , filepath, HTTP, network-uri, stdenv
+    }:
+    mkDerivation {
+      pname = "tensorflow-mnist-input-data";
+      version = "0.1.0.0";
+      src = tensorflow-haskell;
+      enableSeparateDataOutput = true;
+      setupHaskellDepends = [
+        base bytestring Cabal cryptonite directory filepath HTTP
+        network-uri
+      ];
+      libraryHaskellDepends = [ base ];
+      homepage = "https://github.com/tensorflow/haskell#readme";
+      description = "Downloader of input data for training MNIST";
+      license = stdenv.lib.licenses.asl20;
+    }
+  ) {});
+  tensorflow-opgen = super.tensorflow-opgen.override {
+    inherit mainland-pretty proto-lens;
+  };
+  tensorflow-ops = super.tensorflow-ops.override {
+    inherit proto-lens;
+  };
+}

pkgs/development/haskell-modules/generic-stack-builder.nix

@@ -33,7 +33,7 @@ in stdenv.mkDerivation (args // {
   STACK_PLATFORM_VARIANT="nix";
   STACK_IN_NIX_SHELL=1;
   STACK_IN_NIX_EXTRA_ARGS = extraArgs;
-  shellHook = addStackArgsHook;
+  shellHook = addStackArgsHook + args.shellHook or "";
 
 
   # XXX: workaround for https://ghc.haskell.org/trac/ghc/ticket/11042.

pkgs/development/haskell-modules/lib.nix

@@ -301,7 +301,7 @@ rec {
   getHaskellBuildInputs = p:
     (overrideCabal p (args: {
       passthru = (args.passthru or {}) // {
-        _getHaskellBuildInputs = extractBuildInputs p.compiler args;
+        _getHaskellBuildInputs = (extractBuildInputs p.compiler args).haskellBuildInputs;
       };
     }))._getHaskellBuildInputs;
 

pkgs/development/haskell-modules/patches/proto-lens-0.2.2.0.patch

@@ -0,0 +1,23 @@
+diff -Naur proto-lens-0.2.2.0/proto-lens.cabal proto-lens-0.2.2.0-patched/proto-lens.cabal
+--- proto-lens-0.2.2.0/proto-lens.cabal	2018-08-13 18:05:41.704823370 +0200
++++ proto-lens-0.2.2.0-patched/proto-lens.cabal	2018-08-13 18:07:42.352372300 +0200
+@@ -33,7 +33,7 @@
+                        Data.ProtoLens.Encoding.Wire
+                        Data.ProtoLens.TextFormat.Parser
+   build-depends:  attoparsec == 0.13.*
+-                , base >= 4.8 && < 4.11
++                , base >= 4.8
+                 , bytestring == 0.10.*
+                 , containers == 0.5.*
+                 , data-default-class >= 0.0 && < 0.2
+diff -Naur proto-lens-0.2.2.0/src/Data/ProtoLens/TextFormat.hs proto-lens-0.2.2.0-patched/src/Data/ProtoLens/TextFormat.hs
+--- proto-lens-0.2.2.0/src/Data/ProtoLens/TextFormat.hs	2017-04-28 02:16:46.000000000 +0200
++++ proto-lens-0.2.2.0-patched/src/Data/ProtoLens/TextFormat.hs	2018-08-13 18:08:06.371486594 +0200
+@@ -17,6 +17,7 @@
+     readMessageOrDie,
+     ) where
+ 
++import Prelude hiding ((<>))
+ import Lens.Family2 ((&),(^.),(.~), set, over)
+ import Control.Arrow (left)
+ import qualified Data.ByteString

pkgs/development/haskell-modules/patches/proto-lens-protoc-0.2.2.3.patch

@@ -0,0 +1,51 @@
+diff -Naur proto-lens-protoc-0.2.2.3/proto-lens-protoc.cabal proto-lens-protoc-0.2.2.3-patched/proto-lens-protoc.cabal
+--- proto-lens-protoc-0.2.2.3/proto-lens-protoc.cabal	2018-07-21 22:55:12.041698876 +0200
++++ proto-lens-protoc-0.2.2.3-patched/proto-lens-protoc.cabal	2018-08-13 19:44:44.993147985 +0200
+@@ -37,8 +37,8 @@
+     default-language:  Haskell2010
+     hs-source-dirs:    src
+     build-depends:
+-          Cabal >= 1.22 && < 2.1
+-        , base >= 4.8 && < 4.11
++          Cabal >= 1.22
++        , base >= 4.8
+         , bytestring == 0.10.*
+         , containers == 0.5.*
+         , data-default-class >= 0.0 && < 0.2
+@@ -53,6 +53,7 @@
+         , proto-lens == 0.2.2.*
+         , proto-lens-descriptors == 0.2.2.*
+         , text == 1.2.*
++        , semigroups
+     reexported-modules:
+         -- Modules that are needed by the generated Haskell files.
+         -- For forwards compatibility, reexport them as new module names so that
+@@ -76,7 +77,7 @@
+   main-is:  protoc-gen-haskell.hs
+ 
+   build-depends:
+-        base >= 4.8 && < 4.11
++        base >= 4.8
+       , bytestring == 0.10.*
+       , containers == 0.5.*
+       , data-default-class >= 0.0 && < 0.2
+diff -Naur proto-lens-protoc-0.2.2.3/src/Data/ProtoLens/Compiler/Definitions.hs proto-lens-protoc-0.2.2.3-patched/src/Data/ProtoLens/Compiler/Definitions.hs
+--- proto-lens-protoc-0.2.2.3/src/Data/ProtoLens/Compiler/Definitions.hs	2017-08-07 06:52:21.000000000 +0200
++++ proto-lens-protoc-0.2.2.3-patched/src/Data/ProtoLens/Compiler/Definitions.hs	2018-08-13 19:14:07.240505220 +0200
+@@ -35,6 +35,7 @@
+ import qualified Data.Map as Map
+ import Data.Maybe (fromMaybe)
+ import Data.Monoid
++import qualified Data.Semigroup as Semigroup
+ import qualified Data.Set as Set
+ import Data.String (IsString(..))
+ import Data.Text (Text, cons, splitOn, toLower, uncons, unpack)
+@@ -139,7 +140,7 @@
+ -- a 'Symbol' is used to construct both the type-level argument to
+ -- @HasLens@ and the name of the function @foo@.
+ newtype Symbol = Symbol String
+-    deriving (Eq, Ord, IsString, Monoid)
++    deriving (Eq, Ord, IsString, Semigroup.Semigroup, Monoid)
+ 
+ nameFromSymbol :: Symbol -> Name
+ nameFromSymbol (Symbol s) = fromString s

pkgs/development/libraries/cddlib/default.nix

@@ -27,7 +27,7 @@ stdenv.mkDerivation rec {
     description = ''An implementation of the Double Description Method for generating all vertices of a convex polyhedron'';
     license = licenses.gpl2Plus;
     maintainers = with maintainers; [raskin timokau];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
     homepage = https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html;
   };
 }

pkgs/development/libraries/codec2/default.nix

@@ -0,0 +1,25 @@
+{ stdenv, fetchsvn, cmake } :
+
+let
+  version = "0.8";
+
+in stdenv.mkDerivation {
+  name = "codec2-${version}";
+
+  src = fetchsvn {
+    url = "https://svn.code.sf.net/p/freetel/code/codec2/branches/${version}";
+    sha256 = "0qbyaqdn37253s30n6m2ric8nfdsxhkslb9h572kdx18j2yjccki";
+  };
+
+  enableParallelBuilding = true;
+
+  nativeBuildInputs = [ cmake ];
+
+  meta = with stdenv.lib; {
+    description = "Speech codec designed for communications quality speech at low data rates";
+    homepage = http://www.rowetel.com/blog/?page_id=452;
+    license = licenses.lgpl21;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ markuskowa ];
+  };
+}

pkgs/development/libraries/cppunit/default.nix

@@ -9,9 +9,10 @@ stdenv.mkDerivation rec {
     sha256 = "1027cyfx5gsjkdkaf6c2wnjh68882grw8n672018cj3vs9lrhmix";
   };
 
-  meta = {
+  meta = with stdenv.lib; {
     homepage = https://freedesktop.org/wiki/Software/cppunit/;
     description = "C++ unit testing framework";
-    platforms = stdenv.lib.platforms.linux ++ stdenv.lib.platforms.darwin;
+    license = licenses.lgpl21;
+    platforms = platforms.linux ++ platforms.darwin;
   };
 }

pkgs/development/libraries/cracklib/default.nix

@@ -13,6 +13,7 @@ stdenv.mkDerivation rec {
   meta = with stdenv.lib; {
     homepage    = https://github.com/cracklib/cracklib;
     description = "A library for checking the strength of passwords";
+    license = licenses.lgpl21; # Different license for the wordlist: http://www.openwall.com/wordlists
     maintainers = with maintainers; [ lovek323 ];
     platforms   = platforms.unix;
   };

pkgs/development/libraries/eclib/default.nix

@@ -16,7 +16,7 @@ assert withFlint -> flint != null;
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "eclib";
-  version = "20180710"; # upgrade might break the sage interface
+  version = "20180815"; # upgrade might break the sage interface
   # sage tests to run:
   # src/sage/interfaces/mwrank.py
   # src/sage/libs/eclib
@@ -25,16 +25,8 @@ stdenv.mkDerivation rec {
     owner = "JohnCremona";
     repo = "${pname}";
     rev = "v${version}";
-    sha256 = "1kmwpw971sipb4499c9b35q5pz6sms5qndqrvq7396d8hhwjg1i2";
+    sha256 = "12syn83lnzx0xc4r1v3glfimbzndyilkpdmx50xrihbjz1hzczif";
   };
-  patches = [
-    # One of the headers doesn't get installed.
-    # See https://github.com/NixOS/nixpkgs/pull/43476.
-    (fetchpatch {
-      url = "https://github.com/JohnCremona/eclib/pull/42/commits/c9b96429815e31a6e3372c106e31eef2a96431f9.patch";
-      sha256 = "0cw26h94m66rbh8jjsfnb1bvc6z7ybh8zcp8xl5nhxjxiawhcl73";
-    })
-  ];
   buildInputs = [
     pari
     ntl

pkgs/development/libraries/flint/default.nix

@@ -39,7 +39,7 @@ stdenv.mkDerivation rec {
   ];
 
   # issues with ntl -- https://github.com/wbhart/flint2/issues/487
-  NIX_CFLAGS_COMPILE = [ "-std=c++11" ];
+  NIX_CXXSTDLIB_COMPILE = [ "-std=c++11" ];
 
   patches = [
     (fetchpatch {
@@ -55,7 +55,7 @@ stdenv.mkDerivation rec {
     description = ''Fast Library for Number Theory'';
     license = stdenv.lib.licenses.gpl2Plus;
     maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = stdenv.lib.platforms.unix;
     homepage = http://www.flintlib.org/;
     downloadPage = "http://www.flintlib.org/downloads.html";
     updateWalker = true;