Merge branch 'master' into staging

There's been a mass rebuild on master due to python2 update.

lib/maintainers.nix

@@ -206,6 +206,7 @@
   jb55 = "William Casarin <bill@casarin.me>";
   jbedo = "Justin Bedő <cu@cua0.org>";
   jcumming = "Jack Cummings <jack@mudshark.org>";
+  jdagilliland = "Jason Gilliland <jdagilliland@gmail.com>";
   jefdaj = "Jeffrey David Johnson <jefdaj@gmail.com>";
   jerith666 = "Matt McHenry <github@matt.mchenryfamily.org>";
   jfb = "James Felix Black <james@yamtime.com>";

nixos/modules/services/misc/plex.nix

@@ -19,6 +19,14 @@ in
         description = "The directory where Plex stores its data files.";
       };
 
+      openFirewall = mkOption {
+        type = types.bool;
+        default = false;
+        description = ''
+          Open ports in the firewall for the media server
+        '';
+      };
+
       user = mkOption {
         type = types.str;
         default = "plex";
@@ -127,7 +135,7 @@ in
         User = cfg.user;
         Group = cfg.group;
         PermissionsStartOnly = "true";
-        ExecStart = "/bin/sh -c '${cfg.package}/usr/lib/plexmediaserver/Plex\\ Media\\ Server'";
+        ExecStart = "/bin/sh -c ${cfg.package}/usr/lib/plexmediaserver/Plex\\ Media\\ Server";
         Restart = "on-failure";
       };
       environment = {
@@ -141,6 +149,11 @@ in
       };
     };
 
+    networking.firewall = mkIf cfg.openFirewall {
+      allowedTCPPorts = [ 32400 3005 8324 32469 ];
+      allowedUDPPorts = [ 1900 5353 32410 32412 32413 32414 ];
+    };
+
     users.extraUsers = mkIf (cfg.user == "plex") {
       plex = {
         group = cfg.group;

nixos/modules/services/monitoring/prometheus/default.nix

@@ -191,6 +191,7 @@ let
       };
       labels = mkOption {
         type = types.attrsOf types.str;
+        default = {};
         description = ''
           Labels assigned to all metrics scraped from the targets.
         '';

nixos/modules/services/web-servers/apache-httpd/default.nix

@@ -16,6 +16,8 @@ let
 
   phpMajorVersion = head (splitString "." php.version);
 
+  mod_perl = pkgs.mod_perl.override { apacheHttpd = httpd; };
+
   defaultListen = cfg: if cfg.enableSSL
     then [{ip = "*"; port = 443;}]
     else [{ip = "*"; port = 80;}];
@@ -76,6 +78,7 @@ let
           robotsEntries = "";
           startupScript = "";
           enablePHP = false;
+          enablePerl = false;
           phpOptions = "";
           options = {};
           documentRoot = null;
@@ -355,6 +358,7 @@ let
           ++ map (name: {inherit name; path = "${httpd}/modules/mod_${name}.so";}) apacheModules
           ++ optional mainCfg.enableMellon { name = "auth_mellon"; path = "${pkgs.apacheHttpdPackages.mod_auth_mellon}/modules/mod_auth_mellon.so"; }
           ++ optional enablePHP { name = "php${phpMajorVersion}"; path = "${php}/modules/libphp${phpMajorVersion}.so"; }
+          ++ optional enablePerl { name = "perl"; path = "${mod_perl}/modules/mod_perl.so"; }
           ++ concatMap (svc: svc.extraModules) allSubservices
           ++ extraForeignModules;
       in concatMapStrings load allModules
@@ -415,6 +419,8 @@ let
 
   enablePHP = mainCfg.enablePHP || any (svc: svc.enablePHP) allSubservices;
 
+  enablePerl = mainCfg.enablePerl || any (svc: svc.enablePerl) allSubservices;
+
 
   # Generate the PHP configuration file.  Should probably be factored
   # out into a separate module.
@@ -579,6 +585,12 @@ in
         '';
       };
 
+      enablePerl = mkOption {
+        type = types.bool;
+        default = false;
+        description = "Whether to enable the Perl module (mod_perl).";
+      };
+
       phpOptions = mkOption {
         type = types.lines;
         default = "";

nixos/modules/services/web-servers/lighttpd/inginious.nix

@@ -191,9 +191,8 @@ in
         virtualisation.docker = {
           enable = true;
           # We need docker to listen on port 2375.
-          extraOptions = "-H tcp://127.0.0.1:2375 -H unix:///var/run/docker.sock";
+          listenOptions = ["127.0.0.1:2375" "/var/run/docker.sock"];
           storageDriver = mkDefault "overlay";
-          socketActivation = false;
         };
 
         users.extraUsers."lighttpd".extraGroups = [ "docker" ];

nixos/modules/services/web-servers/nginx/default.nix

@@ -10,6 +10,7 @@ let
       sslCertificateKey = "/var/lib/acme/${vhostName}/key.pem";
     })
   ) cfg.virtualHosts;
+  enableIPv6 = config.networking.enableIPv6;
 
   configFile = pkgs.writeText "nginx.conf" ''
     user ${cfg.user} ${cfg.group};
@@ -84,7 +85,7 @@ let
       ${optionalString cfg.statusPage ''
         server {
           listen 80;
-          listen [::]:80;
+          ${optionalString enableIPv6 "listen [::]:80;" }
 
           server_name localhost;
 
@@ -92,7 +93,7 @@ let
             stub_status on;
             access_log off;
             allow 127.0.0.1;
-            allow ::1;
+            ${optionalString enableIPv6 "allow ::1;"}
             deny all;
           }
         }
@@ -116,7 +117,7 @@ let
         ssl = vhost.enableSSL || vhost.forceSSL;
         port = if vhost.port != null then vhost.port else (if ssl then 443 else 80);
         listenString = toString port + optionalString ssl " ssl http2"
-          + optionalString vhost.default " default";
+          + optionalString vhost.default " default_server";
         acmeLocation = optionalString vhost.enableACME (''
           location /.well-known/acme-challenge {
             ${optionalString (vhost.acmeFallbackHost != null) "try_files $uri @acme-fallback;"}
@@ -132,8 +133,10 @@ let
       in ''
         ${optionalString vhost.forceSSL ''
           server {
-            listen 80 ${optionalString vhost.default "default"};
+            listen 80 ${optionalString vhost.default "default_server"};
-            listen [::]:80 ${optionalString vhost.default "default"};
+            ${optionalString enableIPv6
+              ''listen [::]:80 ${optionalString vhost.default "default_server"};''
+            }
 
             server_name ${serverName} ${concatStringsSep " " vhost.serverAliases};
             ${acmeLocation}
@@ -145,7 +148,7 @@ let
 
         server {
           listen ${listenString};
-          listen [::]:${listenString};
+          ${optionalString enableIPv6 "listen [::]:${listenString};"}
 
           server_name ${serverName} ${concatStringsSep " " vhost.serverAliases};
           ${acmeLocation}

nixos/modules/virtualisation/docker.nix

@@ -28,16 +28,42 @@ in
             <command>docker</command> command line tool.
           '';
       };
-    socketActivation =
+
+    listenOptions =
+      mkOption {
+        type = types.listOf types.str;
+        default = ["/var/run/docker.sock"];
+        description =
+          ''
+            A list of unix and tcp docker should listen to. The format follows
+            ListenStream as described in systemd.socket(5).
+          '';
+      };
+
+    enableOnBoot =
       mkOption {
         type = types.bool;
         default = true;
         description =
           ''
-            This option enables docker with socket activation. I.e. docker will
+            When enabled dockerd is started on boot. This is required for
-            start when first called by client.
+            container, which are created with the
+            <literal>--restart=always</literal> flag, to work. If this option is
+            disabled, docker might be started on demand by socket activation.
           '';
       };
+
+    liveRestore =
+      mkOption {
+        type = types.bool;
+        default = true;
+        description =
+          ''
+            Allow dockerd to be restarted without affecting running container.
+            This option is incompatible with docker swarm.
+          '';
+      };
+
     storageDriver =
       mkOption {
         type = types.nullOr (types.enum ["aufs" "btrfs" "devicemapper" "overlay" "overlay2" "zfs"]);
@@ -69,69 +95,39 @@ in
             <command>docker</command> daemon.
           '';
       };
-
-    postStart =
-      mkOption {
-        type = types.lines;
-        default = ''
-          while ! [ -e /var/run/docker.sock ]; do
-            sleep 0.1
-          done
-        '';
-        description = ''
-          The postStart phase of the systemd service. You may need to
-          override this if you are passing in flags to docker which
-          don't cause the socket file to be created. This option is ignored
-          if socket activation is used.
-        '';
-      };
-
-
   };
 
   ###### implementation
 
-  config = mkIf cfg.enable (mkMerge [
+  config = mkIf cfg.enable (mkMerge [{
-    { environment.systemPackages = [ pkgs.docker ];
+      environment.systemPackages = [ pkgs.docker ];
       users.extraGroups.docker.gid = config.ids.gids.docker;
+      systemd.packages = [ pkgs.docker ];
+
       systemd.services.docker = {
-        description = "Docker Application Container Engine";
+        wantedBy = optional cfg.enableOnBoot "multi-user.target";
-        wantedBy = optional (!cfg.socketActivation) "multi-user.target";
-        after = [ "network.target" ] ++ (optional cfg.socketActivation "docker.socket") ;
-        requires = optional cfg.socketActivation "docker.socket";
         serviceConfig = {
-          ExecStart = ''${pkgs.docker}/bin/dockerd \
+          ExecStart = [
-            --group=docker --log-driver=${cfg.logDriver} \
+            ""
-            ${optionalString (cfg.storageDriver != null) "--storage-driver=${cfg.storageDriver}"} \
+            ''
-            ${optionalString cfg.socketActivation "--host=fd://"} \
+              ${pkgs.docker}/bin/dockerd \
-            ${cfg.extraOptions}
+                --group=docker \
-          '';
+                --host=fd:// \
-          #  I'm not sure if that limits aren't too high, but it's what
+                --log-driver=${cfg.logDriver} \
-          #  goes in config bundled with docker itself
+                ${optionalString (cfg.storageDriver != null) "--storage-driver=${cfg.storageDriver}"} \
-          LimitNOFILE = 1048576;
+                ${optionalString cfg.liveRestore "--live-restore" } \
-          LimitNPROC = 1048576;
+                ${cfg.extraOptions}
+            ''];
+          ExecReload=[
+            ""
+            "${pkgs.procps}/bin/kill -s HUP $MAINPID"
+          ];
         } // proxy_env;
 
         path = [ pkgs.kmod ] ++ (optional (cfg.storageDriver == "zfs") pkgs.zfs);
-
-        postStart = if cfg.socketActivation then "" else cfg.postStart;
-
-        # Presumably some containers are running we don't want to interrupt
-        restartIfChanged = false;
       };
+      systemd.sockets.docker.socketConfig.ListenStream = cfg.listenOptions;
     }
-    (mkIf cfg.socketActivation {
-      systemd.sockets.docker = {
-        description = "Docker Socket for the API";
-        wantedBy = [ "sockets.target" ];
-        socketConfig = {
-          ListenStream = "/var/run/docker.sock";
-          SocketMode = "0660";
-          SocketUser = "root";
-          SocketGroup = "docker";
-        };
-      };
-    })
   ]);
 
 }

nixos/tests/docker-registry.nix

@@ -16,13 +16,11 @@ import ./make-test.nix ({ pkgs, ...} : {
 
     client1 = { config, pkgs, ...}: {
       virtualisation.docker.enable = true;
-      virtualisation.docker.socketActivation = false;
       virtualisation.docker.extraOptions = "--insecure-registry registry:8080";
     };
 
     client2 = { config, pkgs, ...}: {
       virtualisation.docker.enable = true;
-      virtualisation.docker.socketActivation = false;
       virtualisation.docker.extraOptions = "--insecure-registry registry:8080";
     };
   };

pkgs/applications/audio/qmmp/default.nix

@@ -29,11 +29,11 @@
 # handle that.
 
 stdenv.mkDerivation rec {
-  name = "qmmp-1.1.2";
+  name = "qmmp-1.1.5";
 
   src = fetchurl {
     url = "http://qmmp.ylsoftware.com/files/${name}.tar.bz2";
-    sha256 = "023gvgchk6ybkz3miy0z08j9n5awz5cjvav7fqjdmpix4sivhn5q";
+    sha256 = "1gfx6nm9v6qrx58gxib6grfhb45mnib1n4wdsnjq16br6bs8h4lv";
   };
 
   buildInputs =

pkgs/applications/editors/rstudio/default.nix

@@ -1,11 +1,11 @@
-{ stdenv, fetchurl, cmake, boost155, zlib, openssl, R, qt4, libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper }:
+{ stdenv, fetchurl, makeDesktopItem, cmake, boost155, zlib, openssl, R, qt4, libuuid, hunspellDicts, unzip, ant, jdk, gnumake, makeWrapper }:
 
 let
   version = "0.98.110";
   ginVer = "1.5";
   gwtVer = "2.5.1";
 in
-stdenv.mkDerivation {
+stdenv.mkDerivation rec {
   name = "RStudio-${version}";
 
   buildInputs = [ cmake boost155 zlib openssl R qt4 libuuid unzip ant jdk makeWrapper ];
@@ -31,7 +31,7 @@ stdenv.mkDerivation {
     sha256 = "0fjr2rcr8lnywj54mzhg9i4xz1b6fh8yv12p5i2q5mgfld2xymy4";
   };
 
-  hunspellDicts = builtins.attrValues hunspellDicts;
+  hunspellDictionaries = builtins.attrValues hunspellDicts;
 
   mathJaxSrc = fetchurl {
     url = https://s3.amazonaws.com/rstudio-buildtools/mathjax-20.zip;
@@ -50,7 +50,7 @@ stdenv.mkDerivation {
       mv gwt-$gwtVer $GWT_LIB_DIR/gwt/$gwtVer
 
       mkdir dependencies/common/dictionaries
-      for dict in $hunspellDicts; do
+      for dict in $hunspellDictionaries; do
           for i in "$dict/share/hunspell/"*
 	  do ln -sv $i dependencies/common/dictionaries/
 	  done
@@ -61,8 +61,23 @@ stdenv.mkDerivation {
 
   cmakeFlags = [ "-DRSTUDIO_TARGET=Desktop" ];
 
+  desktopItem = makeDesktopItem {
+    name = name;
+    exec = "rstudio %F";
+    icon = "rstudio";
+    desktopName = "RStudio";
+    genericName = "IDE";
+    comment = meta.description;
+    categories = "Development;";
+    mimeType = "text/x-r-source;text/x-r;text/x-R;text/x-r-doc;text/x-r-sweave;text/x-r-markdown;text/x-r-html;text/x-r-presentation;application/x-r-data;application/x-r-project;text/x-r-history;text/x-r-profile;text/x-tex;text/x-markdown;text/html;text/css;text/javascript;text/x-chdr;text/x-csrc;text/x-c++hdr;text/x-c++src;";
+  };
+
   postInstall = ''
       wrapProgram $out/bin/rstudio --suffix PATH : ${gnumake}/bin
+      mkdir $out/share
+      cp -r ${desktopItem}/share/applications $out/share
+      mkdir $out/share/icons
+      ln $out/rstudio.png $out/share/icons
   '';
 
   meta = with stdenv.lib;

pkgs/applications/graphics/shotwell/default.nix

@@ -7,13 +7,13 @@
 
 stdenv.mkDerivation rec {
   version = "${major}.${minor}";
-  major = "0.23";
+  major = "0.25";
-  minor = "5";
+  minor = "2";
   name = "shotwell-${version}";
 
   src = fetchurl {
     url = "mirror://gnome/sources/shotwell/${major}/${name}.tar.xz";
-    sha256 = "0fgs1rgvkmy79bmpxrsvm5w8rvqml4l1vnwma0xqx5zzm02p8a07";
+    sha256 = "1bih5hr3pvpkx3fck55bnhngn4fl92ryjizc34wb8pwigbkxnaj1";
   };
 
   NIX_CFLAGS_COMPILE = "-I${glib.dev}/include/glib-2.0 -I${glib.out}/lib/glib-2.0/include";
@@ -28,7 +28,7 @@ stdenv.mkDerivation rec {
                   pkgconfig gst_all_1.gstreamer gst_all_1.gst-plugins-base gnome3.libgee
                   which udev libgudev gnome3.gexiv2 hicolor_icon_theme
                   libraw json_glib gettext desktop_file_utils glib lcms2 gdk_pixbuf librsvg
-                  wrapGAppsHook gnome_doc_utils gnome3.rest
+                  wrapGAppsHook gnome_doc_utils gnome3.rest gnome3.gcr
                   gnome3.defaultIconTheme itstool ];
 
   meta = with stdenv.lib; {

pkgs/applications/misc/mediainfo-gui/default.nix

@@ -2,11 +2,11 @@
 , desktop_file_utils, libSM, imagemagick }:
 
 stdenv.mkDerivation rec {
-  version = "0.7.87";
+  version = "0.7.91";
   name = "mediainfo-gui-${version}";
   src = fetchurl {
     url = "http://mediaarea.net/download/source/mediainfo/${version}/mediainfo_${version}.tar.xz";
-    sha256 = "1ws4hyfcw289hax0bq8y3bbw5y321xmh0va1x4zv5rjwfzcd51pv";
+    sha256 = "15jrph9hjza4c87m739s7c9v27gji94ha7rpchb8li0rcdvy40dm";
   };
 
   nativeBuildInputs = [ autoreconfHook pkgconfig ];

pkgs/applications/misc/mediainfo/default.nix

@@ -1,11 +1,11 @@
 { stdenv, fetchurl, autoreconfHook, pkgconfig, libzen, libmediainfo, zlib }:
 
 stdenv.mkDerivation rec {
-  version = "0.7.87";
+  version = "0.7.91";
   name = "mediainfo-${version}";
   src = fetchurl {
     url = "http://mediaarea.net/download/source/mediainfo/${version}/mediainfo_${version}.tar.xz";
-    sha256 = "1ws4hyfcw289hax0bq8y3bbw5y321xmh0va1x4zv5rjwfzcd51pv";
+    sha256 = "15jrph9hjza4c87m739s7c9v27gji94ha7rpchb8li0rcdvy40dm";
   };
 
   nativeBuildInputs = [ autoreconfHook pkgconfig ];

pkgs/applications/misc/slade/default.nix

@@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitHub, cmake, pkgconfig, wxGTK, gtk2, sfml, fluidsynth, curl, freeimage, ftgl, glew, zip }:
+
+stdenv.mkDerivation rec {
+  name = "slade-${version}";
+  version = "3.1.1.4";
+
+  src = fetchFromGitHub {
+    owner = "sirjuddington";
+    repo = "SLADE";
+    rev = version;
+    sha256 = "0c2yjkpcwxkid1wczmc9f16x1p40my8jv61jc93ldgjzcprmrpn8";
+  };
+
+  nativeBuildInputs = [ cmake pkgconfig zip ];
+  buildInputs = [ wxGTK gtk2 sfml fluidsynth curl freeimage ftgl glew ];
+
+  enableParallelBuilding = true;
+
+  meta = with stdenv.lib; {
+    description = "Doom editor";
+    homepage = "http://slade.mancubus.net/";
+    license = licenses.gpl2;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ abbradar ];
+  };
+}

pkgs/applications/networking/browsers/mozilla-plugins/flashplayer-11/default.nix

@@ -1,134 +0,0 @@
-{ stdenv
-, lib
-, fetchurl
-, zlib
-, alsaLib
-, curl
-, nspr
-, fontconfig
-, freetype
-, expat
-, libX11
-, libXext
-, libXrender
-, libXcursor
-, libXt
-, libvdpau
-, gtk2
-, glib
-, pango
-, cairo
-, atk
-, gdk_pixbuf
-, nss
-, unzip
-, debug ? false
-
-/* you have to add ~/mm.cfg :
-
-    TraceOutputFileEnable=1
-    ErrorReportingEnable=1
-    MaxWarnings=1
-
-  in order to read the flash trace at ~/.macromedia/Flash_Player/Logs/flashlog.txt
-  Then FlashBug (a FireFox plugin) shows the log as well
-*/
-
-}:
-
-/* When updating this package, test that the following derivations build:
-
-   * flashplayer
-   * flashplayer-standalone
-   * flashplayer-standalone-debugger
-*/
-
-let
-  arch =
-    if      stdenv.system == "x86_64-linux" then
-      if    debug then throw "no x86_64 debugging version available"
-      else  "64bit"
-    else if stdenv.system == "i686-linux"   then
-      if    debug then "32bit_debug"
-      else             "32bit"
-    else throw "Flash Player is not supported on this platform";
-
-  suffix =
-    if      stdenv.system == "x86_64-linux" then
-      if    debug then throw "no x86_64 debugging version available"
-      else             "_linux.x86_64"
-    else if stdenv.system == "i686-linux"   then
-      if    debug then "_linux_debug.i386"
-      else             "_linux.i386"
-    else throw "Flash Player is not supported on this platform";
-
-  saname =
-    if debug then "flashplayerdebugger"
-    else          "flashplayer";
-
-  is-i686 = (stdenv.system == "i686-linux");
-in
-stdenv.mkDerivation rec {
-  name = "flashplayer-${version}";
-  version = "11.2.202.644";
-
-  src = fetchurl {
-    url = "https://fpdownload.macromedia.com/pub/flashplayer/installers/archive/fp_${version}_archive.zip";
-    sha256 = "0hf0hwg4kvz99g9d2arg5dwm3nx0hjnpngz9ay1mihhgjksy585b";
-  };
-
-  nativeBuildInputs = [ unzip ];
-
-  sourceRoot = ".";
-
-  postUnpack = ''
-    cd *${arch}
-
-    tar -xvzf *${suffix}.tar.gz
-
-    ${lib.optionalString is-i686 ''
-       tar -xvzf *_sa[_.]*.tar.gz
-    ''}
-  '';
-
-  dontStrip = true;
-  dontPatchELF = true;
-
-  preferLocalBuild = true;
-
-  outputs = [ "out" ] ++ lib.optional is-i686 "sa";
-
-  installPhase = ''
-    mkdir -p $out/lib/mozilla/plugins
-    cp -pv libflashplayer.so $out/lib/mozilla/plugins
-
-    patchelf --set-rpath "$rpath" $out/lib/mozilla/plugins/libflashplayer.so
-
-    ${lib.optionalString is-i686 ''
-      install -Dm755 ${saname} $sa/bin/flashplayer
-
-      patchelf \
-        --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \
-        --set-rpath "$rpath" \
-        $sa/bin/flashplayer
-    ''}
-  '';
-
-  passthru = {
-    mozillaPlugin = "/lib/mozilla/plugins";
-  };
-
-  rpath = lib.makeLibraryPath
-    [ zlib alsaLib curl nspr fontconfig freetype expat libX11
-      libXext libXrender libXcursor libXt gtk2 glib pango atk cairo gdk_pixbuf
-      libvdpau nss
-    ];
-
-  meta = {
-    description = "Adobe Flash Player browser plugin";
-    homepage = http://www.adobe.com/products/flashplayer/;
-    license = stdenv.lib.licenses.unfree;
-    maintainers = [];
-    platforms = [ "x86_64-linux" "i686-linux" ];
-  };
-}

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

@@ -0,0 +1,146 @@
+{ stdenv
+, lib
+, fetchurl
+, alsaLib
+, atk
+, bzip2
+, cairo
+, curl
+, expat
+, fontconfig
+, freetype
+, gdk_pixbuf
+, glib
+, glibc
+, graphite2
+, gtk2
+, harfbuzz
+, libICE
+, libSM
+, libX11
+, libXau
+, libXcomposite
+, libXcursor
+, libXdamage
+, libXdmcp
+, libXext
+, libXfixes
+, libXi
+, libXinerama
+, libXrandr
+, libXrender
+, libXt
+, libXxf86vm
+, libdrm
+, libffi
+, libpng
+, libvdpau
+, libxcb
+, libxshmfence
+, nspr
+, nss
+, pango
+, pcre
+, pixman
+, zlib
+, unzip
+, debug ? false
+
+/* you have to add ~/mm.cfg :
+
+    TraceOutputFileEnable=1
+    ErrorReportingEnable=1
+    MaxWarnings=1
+
+  in order to read the flash trace at ~/.macromedia/Flash_Player/Logs/flashlog.txt
+  Then FlashBug (a FireFox plugin) shows the log as well
+*/
+
+}:
+
+let
+  arch =
+    if      stdenv.system == "x86_64-linux" then
+      "x86_64"
+    else if stdenv.system == "i686-linux"   then
+      "i386"
+    else throw "Flash Player is not supported on this platform";
+  lib_suffix =
+      if stdenv.system == "x86_64-linux" then
+      "64"
+    else
+      "";
+in
+stdenv.mkDerivation rec {
+  name = "flashplayer-${version}";
+  version = "24.0.0.186";
+
+  src = fetchurl {
+    url =
+      if debug then
+        "https://fpdownload.macromedia.com/pub/flashplayer/updaters/24/flash_player_npapi_linux_debug.${arch}.tar.gz"
+      else
+        "https://fpdownload.adobe.com/get/flashplayer/pdc/${version}/flash_player_npapi_linux.${arch}.tar.gz";
+    sha256 =
+      if debug then
+        if arch == "x86_64" then
+          "0i7c861n42vb2zd9hnp26lxjakkv0fxp53smcwzc9xhdbjr14ail"
+        else
+          "0gj59iinh8gbjm5bn24qi3niyvi8x6byyc1sa6qvqkvjwh1ckdi3"
+      else
+        if arch == "x86_64" then
+          "0qs6hx31p1q2zqsr8jcf7niwsp6nncpqs3igb6l9f9fi0a8va8f7"
+        else
+          "1zcinq7629bgbashx25krby8r91sag2v8382q620951iiww06n1v";
+  };
+
+  nativeBuildInputs = [ unzip ];
+
+  sourceRoot = ".";
+
+  dontStrip = true;
+  dontPatchELF = true;
+
+  preferLocalBuild = true;
+
+  installPhase = ''
+    mkdir -p $out/lib/mozilla/plugins
+    cp -pv libflashplayer.so $out/lib/mozilla/plugins
+
+    mkdir -p $out/bin
+    cp -pv usr/bin/flash-player-properties $out/bin
+
+    mkdir -p $out/lib${lib_suffix}/kde4
+    cp -pv usr/lib${lib_suffix}/kde4/kcm_adobe_flash_player.so $out/lib${lib_suffix}/kde4
+
+    patchelf --set-rpath "$rpath" \
+      $out/lib/mozilla/plugins/libflashplayer.so \
+      $out/lib${lib_suffix}/kde4/kcm_adobe_flash_player.so
+
+    patchelf \
+      --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \
+      --set-rpath "$rpath" \
+      $out/bin/flash-player-properties
+  '';
+
+  passthru = {
+    mozillaPlugin = "/lib/mozilla/plugins";
+  };
+
+  rpath = lib.makeLibraryPath
+    [ stdenv.cc.cc
+      alsaLib atk bzip2 cairo curl expat fontconfig freetype gdk_pixbuf glib
+      glibc graphite2 gtk2 harfbuzz libICE libSM libX11 libXau libXcomposite
+      libXcursor libXdamage libXdmcp libXext libXfixes libXi libXinerama
+      libXrandr libXrender libXt libXxf86vm libdrm libffi libpng libvdpau
+      libxcb libxshmfence nspr nss pango pcre pixman zlib
+    ];
+
+  meta = {
+    description = "Adobe Flash Player browser plugin";
+    homepage = http://www.adobe.com/products/flashplayer/;
+    license = stdenv.lib.licenses.unfree;
+    maintainers = [];
+    platforms = [ "x86_64-linux" "i686-linux" ];
+  };
+}

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

@@ -0,0 +1,110 @@
+{ stdenv
+, lib
+, fetchurl
+, alsaLib
+, atk
+, bzip2
+, cairo
+, curl
+, expat
+, fontconfig
+, freetype
+, gdk_pixbuf
+, glib
+, glibc
+, graphite2
+, gtk2
+, harfbuzz
+, libICE
+, libSM
+, libX11
+, libXau
+, libXcomposite
+, libXcursor
+, libXdamage
+, libXdmcp
+, libXext
+, libXfixes
+, libXi
+, libXinerama
+, libXrandr
+, libXrender
+, libXt
+, libXxf86vm
+, libdrm
+, libffi
+, libpng
+, libvdpau
+, libxcb
+, libxshmfence
+, nspr
+, nss
+, pango
+, pcre
+, pixman
+, zlib
+, unzip
+, debug ? false
+}:
+
+let
+  arch =
+    if      stdenv.system == "x86_64-linux" then
+      "x86_64"
+    else if stdenv.system == "i686-linux"   then
+      "i386"
+    else throw "Flash Player is not supported on this platform";
+in
+stdenv.mkDerivation rec {
+  name = "flashplayer-standalone-${version}";
+  version = "24.0.0.186";
+
+  src = fetchurl {
+    url =
+      if debug then
+        "https://fpdownload.macromedia.com/pub/flashplayer/updaters/24/flash_player_sa_linux_debug.x86_64.tar.gz"
+      else
+        "https://fpdownload.macromedia.com/pub/flashplayer/updaters/24/flash_player_sa_linux.x86_64.tar.gz";
+    sha256 =
+      if debug then
+        "09653jphzijk3w3dcd05f4pya1ciaymna31qqrmcwhxa0ginxhz2"
+      else
+        "0q0wc2lgjzi1v4lpcr5x5nszigli3vsryfq2zk4qq4pqy3i6aq7q";
+  };
+
+  nativeBuildInputs = [ unzip ];
+
+  sourceRoot = ".";
+
+  dontStrip = true;
+  dontPatchELF = true;
+
+  preferLocalBuild = true;
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp -pv flashplayer${lib.optionalString debug "debugger"} $out/bin
+
+    patchelf \
+      --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \
+      --set-rpath "$rpath" \
+      $out/bin/flashplayer${lib.optionalString debug "debugger"}
+  '';
+
+  rpath = lib.makeLibraryPath
+    [ stdenv.cc.cc
+      alsaLib atk bzip2 cairo curl expat fontconfig freetype gdk_pixbuf glib
+      glibc graphite2 gtk2 harfbuzz libICE libSM libX11 libXau libXcomposite
+      libXcursor libXdamage libXdmcp libXext libXfixes libXi libXinerama
+      libXrandr libXrender libXt libXxf86vm libdrm libffi libpng libvdpau
+      libxcb libxshmfence nspr nss pango pcre pixman zlib
+    ];
+
+  meta = {
+    description = "Adobe Flash Player standalone executable";
+    homepage = https://www.adobe.com/support/flashplayer/debug_downloads.html;
+    license = stdenv.lib.licenses.unfree;
+    maintainers = [];
+    platforms = [ "x86_64-linux" ];
+  };
+}

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

@@ -4,12 +4,12 @@ let
          then "linux-amd64"
          else "darwin-amd64";
   checksum = if stdenv.isLinux
-             then "dad3791fb07e6cf34f4cf611728cb8ae109a75234498a888529a68ac6923f200"
+             then "1797ab74720f122432eace591fb415e5e5f5db97f4b6608ca8dbe59bae988374"
-             else "d27bd7e40e12c0a5f08782a8a883166008565b28e0b82126d2089300ff3f8465";
+             else "2b522dcfe27e987138f7826c79fb26a187075dd9be5c5a4c76fd6846bf109014";
 in
 stdenv.mkDerivation rec {
   pname = "helm";
-  version = "2.0.2";
+  version = "2.1.2";
   name = "${pname}-${version}";
 
   src = fetchurl {

pkgs/applications/networking/remote/remmina/default.nix

@@ -4,7 +4,10 @@
 , pcre, webkitgtk, libdbusmenu-gtk3, libappindicator-gtk3
 , libvncserver, libpthreadstubs, libXdmcp, libxkbcommon
 , libsecret, spice_protocol, spice_gtk, epoxy, at_spi2_core
-, openssl }:
+, openssl
+# The themes here are soft dependencies; only icons are missing without them.
+, hicolor_icon_theme, adwaita-icon-theme
+}:
 
 let
   version = "1.2.0-rcgit.15";
@@ -51,7 +54,7 @@ stdenv.mkDerivation {
                   pcre webkitgtk libdbusmenu-gtk3 libappindicator-gtk3
                   libvncserver libpthreadstubs libXdmcp libxkbcommon
                   libsecret spice_protocol spice_gtk epoxy at_spi2_core
-                  openssl ];
+                  openssl hicolor_icon_theme adwaita-icon-theme ];
 
   cmakeFlags = "-DWITH_VTE=OFF -DWITH_TELEPATHY=OFF -DWITH_AVAHI=OFF -DWINPR_INCLUDE_DIR=${freerdp_git}/include/winpr2";
 

pkgs/applications/office/libreoffice/default-primary-src.nix

@@ -3,8 +3,8 @@
 rec {
   major = "5";
   minor = "2";
-  patch = "3";
+  patch = "4";
-  tweak = "3";
+  tweak = "2";
 
   subdir = "${major}.${minor}.${patch}";
 
@@ -12,6 +12,6 @@ rec {
 
   src = fetchurl {
     url = "http://download.documentfoundation.org/libreoffice/src/${subdir}/libreoffice-${version}.tar.xz";
-    sha256 = "1h9j3j7drhr49nw2p6by5vvrr8nc8rpldn3yp724mwkb2rfkdwd8";
+    sha256 = "047byvyg13baws1bycaq1s6wqhkcr2pk27xbag0npzx1lspx2wwb";
   };
 }

pkgs/applications/office/libreoffice/default.nix

@@ -42,14 +42,14 @@ let
 
     translations = fetchSrc {
       name = "translations";
-      sha256 = "0j0ajli1cbfwbgzrcqkx3db174jv1fgm22ds0gqlgkci9cffa0c4";
+      sha256 = "075f7jpp8qi6piwrw4n8inynvsgp0270pdd9jmc2fqv6j5gsn332";
     };
 
     # TODO: dictionaries
 
     help = fetchSrc {
       name = "help";
-      sha256 = "0fndi6cv8rw426c3l071z130ks9sqf6ca5yas7am9d666mmy4fs4";
+      sha256 = "10p1xd077278gm3syd3lc54fzjsvrvzm0zr6csn9iq90kmlsgwzy";
     };
 
   };

pkgs/applications/office/libreoffice/libreoffice-srcs.nix

@@ -112,11 +112,11 @@
     md5name = "1f467e5bb703f12cbbb09d5cf67ecf4a-converttexttonumber-1-5-0.oxt";
   }
   {
-    name = "curl-7.43.0.tar.bz2";
+    name = "curl-7.51.0.tar.gz";
-    url = "http://dev-www.libreoffice.org/src/curl-7.43.0.tar.bz2";
+    url = "http://dev-www.libreoffice.org/src/curl-7.51.0.tar.gz";
-    sha256 = "baa654a1122530483ccc1c58cc112fec3724a82c11c6a389f1e6a37dc8858df9";
+    sha256 = "65b5216a6fbfa72f547eb7706ca5902d7400db9868269017a8888aa91d87977c";
-    md5 = "11bddbb452a8b766b932f859aaeeed39";
+    md5 = "490e19a8ccd1f4a244b50338a0eb9456";
-    md5name = "11bddbb452a8b766b932f859aaeeed39-curl-7.43.0.tar.bz2";
+    md5name = "490e19a8ccd1f4a244b50338a0eb9456-curl-7.51.0.tar.gz";
   }
   {
     name = "libe-book-0.1.2.tar.bz2";
@@ -224,11 +224,11 @@
     md5name = "c3c1a8ba7452950636e871d25020ce0d-pt-serif-font-1.0000W.tar.gz";
   }
   {
-    name = "source-code-font-1.009.tar.gz";
+    name = "source-code-pro-2.030R-ro-1.050R-it.tar.gz";
-    url = "http://dev-www.libreoffice.org/src/0279a21fab6f245e85a6f85fea54f511-source-code-font-1.009.tar.gz";
+    url = "http://dev-www.libreoffice.org/src/907d6e99f241876695c19ff3db0b8923-source-code-pro-2.030R-ro-1.050R-it.tar.gz";
-    sha256 = "9b295127164c81bcf28c7ebb687f1555b71796108b443a04d40202b7364e4cce";
+    sha256 = "09466dce87653333f189acd8358c60c6736dcd95f042dee0b644bdcf65b6ae2f";
-    md5 = "0279a21fab6f245e85a6f85fea54f511";
+    md5 = "907d6e99f241876695c19ff3db0b8923";
-    md5name = "0279a21fab6f245e85a6f85fea54f511-source-code-font-1.009.tar.gz";
+    md5name = "907d6e99f241876695c19ff3db0b8923-source-code-pro-2.030R-ro-1.050R-it.tar.gz";
   }
   {
     name = "source-sans-pro-2.010R-ro-1.065R-it.tar.gz";
@@ -497,11 +497,11 @@
     md5name = "a233181e03d3c307668b4c722d881661-mariadb_client-2.0.0-src.tar.gz";
   }
   {
-    name = "mdds-1.2.0.tar.bz2";
+    name = "mdds-1.2.2.tar.bz2";
-    url = "http://dev-www.libreoffice.org/src/mdds-1.2.0.tar.bz2";
+    url = "http://dev-www.libreoffice.org/src/mdds-1.2.2.tar.bz2";
-    sha256 = "f44fd0635de94c7d490f9a65f74b5e55860d7bdd507951428294f9690fda45b6";
+    sha256 = "141e730b39110434b02cd844c5ad3442103f7c35f7e9a4d6a9f8af813594cc9d";
-    md5 = "9f3383fb7bae825eab69f3a6ec1d74b2";
+    md5 = "8855cf852a6088cfdc792c6f7ceb0243";
-    md5name = "9f3383fb7bae825eab69f3a6ec1d74b2-mdds-1.2.0.tar.bz2";
+    md5name = "8855cf852a6088cfdc792c6f7ceb0243-mdds-1.2.2.tar.bz2";
   }
   {
     name = "mDNSResponder-576.30.4.tar.gz";
@@ -546,11 +546,11 @@
     md5name = "231adebe5c2f78fded3e3df6e958878e-neon-0.30.1.tar.gz";
   }
   {
-    name = "nss-3.22.2-with-nspr-4.12.tar.gz";
+    name = "nss-3.27-with-nspr-4.13.tar.gz";
-    url = "http://dev-www.libreoffice.org/src/6b254cf2f8cb4b27a3f0b8b7b9966ea7-nss-3.22.2-with-nspr-4.12.tar.gz";
+    url = "http://dev-www.libreoffice.org/src/0e3eee39402386cf16fd7aaa7399ebef-nss-3.27-with-nspr-4.13.tar.gz";
-    sha256 = "7bc7e5483fc90071be5facd3043f94c69b153055a369c8f0b751ad374c5ae09e";
+    sha256 = "c74ad468ed5da0304b58ec56fa627fa388b256451b1a44fd184145c6d8203820";
-    md5 = "6b254cf2f8cb4b27a3f0b8b7b9966ea7";
+    md5 = "0e3eee39402386cf16fd7aaa7399ebef";
-    md5name = "6b254cf2f8cb4b27a3f0b8b7b9966ea7-nss-3.22.2-with-nspr-4.12.tar.gz";
+    md5name = "0e3eee39402386cf16fd7aaa7399ebef-nss-3.27-with-nspr-4.13.tar.gz";
   }
   {
     name = "libodfgen-0.1.6.tar.bz2";

pkgs/applications/science/biology/freebayes/builder.sh

@@ -0,0 +1,11 @@
+source $stdenv/setup
+
+unpackPhase
+
+cd freebayes-*
+
+make
+
+mkdir -p $out/bin
+cp bin/freebayes bin/bamleftalign $out/bin
+cp scripts/* $out/bin

pkgs/applications/science/biology/freebayes/default.nix

@@ -0,0 +1,27 @@
+{ stdenv, fetchFromGitHub, cmake, gcc, zlib}:
+
+stdenv.mkDerivation rec {
+  name    = "freebayes-${version}";
+  version = "1.1.0";
+
+  src = fetchFromGitHub {
+    name = "freebayes-${version}-src";
+    owner  = "ekg";
+    repo   = "freebayes";
+    rev    = "refs/tags/v${version}";
+    sha256 = "0xb8aicb36w9mfs1gq1x7mcp3p82kl7i61d162hfncqzg2npg8rr";
+    fetchSubmodules = true;
+  };
+
+  buildInputs = [ cmake gcc zlib ];
+
+  builder = ./builder.sh;
+
+  meta = with stdenv.lib; {
+    description = "Bayesian haplotype-based polymorphism discovery and genotyping";
+    license     = licenses.mit;
+    homepage    = https://github.com/ekg/freebayes;
+    maintainers = with maintainers; [ jdagilliland ];
+    platforms = [ "x86_64-linux" ];
+  };
+}

pkgs/applications/science/biology/igv/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "igv-${version}";
-  version = "2.3.77";
+  version = "2.3.89";
 
   src = fetchurl {
     url = "http://data.broadinstitute.org/igv/projects/downloads/IGV_${version}.zip";
-    sha256 = "9d8c622649f9f02026e92fa44006bb57e897baad4359c8708ca9cdbb71f94bb5";
+    sha256 = "06bmj9jsnk5010ipv0w4qlcvgw67dy8hsvgcx9l74v3s0zp5di3y";
   };
 
   buildInputs = [ unzip jre ];

pkgs/applications/window-managers/bspwm/default.nix

@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   name = "bspwm-${version}";
-  version = "0.9.1";
+  version = "0.9.2";
 
 
   src = fetchurl {
     url = "https://github.com/baskerville/bspwm/archive/${version}.tar.gz";
-    sha256 = "11dvfcvr8bc116yb3pvl0k1h2gfm9rv652jbxd1c5pmc0yimifq2";
+    sha256 = "1w6wxwgyb14w664xafp3b2ps6zzf9yw7cfhbh9229x2hil9rss1k";
   };
 
   buildInputs = [ libxcb libXinerama xcbutil xcbutilkeysyms xcbutilwm ];

pkgs/data/fonts/unifont/default.nix

@@ -2,16 +2,16 @@
 
 stdenv.mkDerivation rec {
   name = "unifont-${version}";
-  version = "9.0.04";
+  version = "9.0.06";
 
   ttf = fetchurl {
     url = "mirror://gnu/unifont/${name}/${name}.ttf";
-    sha256 = "052waajjdry67jjl7vy984padyzdrkhf5gylgbnvj90q6d52j02z";
+    sha256 = "0r96giih04din07wlmw8538izwr7dh5v6dyriq13zfn19brgn5z2";
   };
 
   pcf = fetchurl {
     url = "mirror://gnu/unifont/${name}/${name}.pcf.gz";
-    sha256 = "0736qmlzsf4xlipj4vzihafkigc3xjisxnwcqhl9dzkhxfjq9612";
+    sha256 = "11ivfzpyz54rbz0cvd437abs6qlv28q0qp37kn27jggxlcpfh8vd";
   };
 
   buildInputs = [ mkfontscale mkfontdir ];

pkgs/desktops/gnome-3/3.22/misc/gexiv2/default.nix

@@ -5,11 +5,11 @@ let
 in
 stdenv.mkDerivation rec {
   name = "gexiv2-${version}";
-  version = "${majorVersion}.3";
+  version = "${majorVersion}.4";
 
   src = fetchurl {
     url = "mirror://gnome/sources/gexiv2/${majorVersion}/${name}.tar.xz";
-    sha256 = "390cfb966197fa9f3f32200bc578d7c7f3560358c235e6419657206a362d3988";
+    sha256 = "190www3b61spfgwx42jw8h5hsz2996jcxky48k63468avjpk33dd";
   };
 
   preConfigure = ''

pkgs/development/compilers/ats2/default.nix

@@ -3,11 +3,11 @@
 , withContrib ? true }:
 
 let
-  versionPkg = "0.2.12" ;
+  versionPkg = "0.2.13" ;
 
   contrib = fetchurl {
     url = "mirror://sourceforge/ats2-lang/ATS2-Postiats-contrib-${versionPkg}.tgz" ;
-    sha256 = "16jzabmwq5yz72dzlkc2hmvf2lan83gayn21gbl65jgpwdsbh170" ;
+    sha256 = "1hsqvdwiydks46sfjmm04rmjcx5v25xpjgnq0b96psrdbd0ky2kf" ;
   };
 
   postInstallContrib = stdenv.lib.optionalString withContrib
@@ -31,7 +31,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "mirror://sourceforge/ats2-lang/ATS2-Postiats-${version}.tgz";
-    sha256 = "0m8gmm1pnklixxw76yjjqqqixm2cyp91rnq4sj1k29qp4k9zxpl4";
+    sha256 = "01rkybkwgbpx6blv72n46ml9ii3p6kpxbpczsrpbjkqmf22b4vii";
   };
 
   buildInputs = [ gmp ];
@@ -45,8 +45,6 @@ stdenv.mkDerivation rec {
       builtins.toFile "setupHook.sh"
       (concatMapStringsSep "\n" builtins.readFile hookFiles);
 
-  patches = [ ./installed-lib-directory-version.patch ];
-
   postInstall = postInstallContrib + postInstallEmacs;
 
   meta = with stdenv.lib; {

pkgs/development/compilers/ats2/installed-lib-directory-version.patch

@@ -1,99 +0,0 @@
-Change the name of the library directory to match the version of the package.
-
-diff -Naur ATS2-Postiats-0.2.12/configure postiats-new/configure
---- ATS2-Postiats-0.2.12/configure	2016-10-13 12:03:20.000000000 -0400
-+++ postiats-new/configure	2016-10-23 20:17:29.912579618 -0400
-@@ -1,6 +1,6 @@
- #! /bin/sh
- # Guess values for system-dependent variables and create Makefiles.
--# Generated by GNU Autoconf 2.69 for ATS2/Postiats 0.2.10.
-+# Generated by GNU Autoconf 2.69 for ATS2/Postiats 0.2.12.
- #
- # Report bugs to <gmpostiats@gmail.com>.
- #
-@@ -580,8 +580,8 @@
- # Identity of this package.
- PACKAGE_NAME='ATS2/Postiats'
- PACKAGE_TARNAME='ats2-postiats'
--PACKAGE_VERSION='0.2.10'
--PACKAGE_STRING='ATS2/Postiats 0.2.10'
-+PACKAGE_VERSION='0.2.12'
-+PACKAGE_STRING='ATS2/Postiats 0.2.12'
- PACKAGE_BUGREPORT='gmpostiats@gmail.com'
- PACKAGE_URL=''
- 
-@@ -1242,7 +1242,7 @@
-   # Omit some internal or obsolete options to make the list less imposing.
-   # This message is too long to be a string in the A/UX 3.1 sh.
-   cat <<_ACEOF
--\`configure' configures ATS2/Postiats 0.2.10 to adapt to many kinds of systems.
-+\`configure' configures ATS2/Postiats 0.2.12 to adapt to many kinds of systems.
- 
- Usage: $0 [OPTION]... [VAR=VALUE]...
- 
-@@ -1304,7 +1304,7 @@
- 
- if test -n "$ac_init_help"; then
-   case $ac_init_help in
--     short | recursive ) echo "Configuration of ATS2/Postiats 0.2.10:";;
-+     short | recursive ) echo "Configuration of ATS2/Postiats 0.2.12:";;
-    esac
-   cat <<\_ACEOF
- 
-@@ -1384,7 +1384,7 @@
- test -n "$ac_init_help" && exit $ac_status
- if $ac_init_version; then
-   cat <<\_ACEOF
--ATS2/Postiats configure 0.2.10
-+ATS2/Postiats configure 0.2.12
- generated by GNU Autoconf 2.69
- 
- Copyright (C) 2012 Free Software Foundation, Inc.
-@@ -1936,7 +1936,7 @@
- This file contains any messages produced by compilers while
- running configure, to aid debugging if configure makes a mistake.
- 
--It was created by ATS2/Postiats $as_me 0.2.10, which was
-+It was created by ATS2/Postiats $as_me 0.2.12, which was
- generated by GNU Autoconf 2.69.  Invocation command line was
- 
-   $ $0 $@
-@@ -4226,7 +4226,7 @@
- # report actual input values of CONFIG_FILES etc. instead of their
- # values after options handling.
- ac_log="
--This file was extended by ATS2/Postiats $as_me 0.2.10, which was
-+This file was extended by ATS2/Postiats $as_me 0.2.12, which was
- generated by GNU Autoconf 2.69.  Invocation command line was
- 
-   CONFIG_FILES    = $CONFIG_FILES
-@@ -4288,7 +4288,7 @@
- cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
- ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
- ac_cs_version="\\
--ATS2/Postiats config.status 0.2.10
-+ATS2/Postiats config.status 0.2.12
- configured by $0, generated by GNU Autoconf 2.69,
-   with options \\"\$ac_cs_config\\"
- 
-diff -Naur ATS2-Postiats-0.2.12/src/CBOOT/config.h postiats-new/src/CBOOT/config.h
---- ATS2-Postiats-0.2.12/src/CBOOT/config.h	2016-10-13 12:03:20.000000000 -0400
-+++ postiats-new/src/CBOOT/config.h	2016-10-23 20:16:34.613836556 -0400
-@@ -44,7 +44,7 @@
- #define PACKAGE_NAME "ATS2/Postiats"
- 
- /* Define to the full name and version of this package. */
--#define PACKAGE_STRING "ATS2/Postiats 0.2.10"
-+#define PACKAGE_STRING "ATS2/Postiats 0.2.12"
- 
- /* Define to the one symbol short name of this package. */
- #define PACKAGE_TARNAME "ats2-postiats"
-@@ -53,7 +53,7 @@
- #define PACKAGE_URL ""
- 
- /* Define to the version of this package. */
--#define PACKAGE_VERSION "0.2.10"
-+#define PACKAGE_VERSION "0.2.12"
- 
- /* The size of `void*', as computed by sizeof. */
- #define SIZEOF_VOIDP 8

pkgs/development/compilers/crystal/default.nix

@@ -0,0 +1,96 @@
+{ stdenv, fetchurl, boehmgc, libatomic_ops, pcre, libevent, libiconv, llvm_39, makeWrapper }:
+
+stdenv.mkDerivation rec {
+  version = "0.20.3";
+  name = "crystal-${version}-1";
+  arch =
+    {
+      "x86_64-linux" = "linux-x86_64";
+      "i686-linux" = "linux-i686";
+      "x86_64-darwin" = "darwin-x86_64";
+    }."${stdenv.system}" or (throw "system ${stdenv.system} not supported");
+
+  prebuiltBinary = fetchurl {
+    url = "https://github.com/crystal-lang/crystal/releases/download/${version}/crystal-${version}-1-${arch}.tar.gz";
+    sha256 =
+      {
+        "x86_64-linux" = "c656dc8092a6161262f527df441aaab4ea9dd9a836a013f7155c6378b26b8cd7";
+        "i686-linux" = "85edfa1dda5e712341869bab87f6de0f7c6860e2a04dec2f00e8dc6aa1418611";
+        "x86_64-darwin" = "0088972c5cad9543f262976ae6c8ee1dbcbefdee3a8bedae851998bfa7098637";
+      }."${stdenv.system}" or (throw "system ${stdenv.system} not supported");
+  };
+
+  src = fetchurl {
+    url = "https://github.com/crystal-lang/crystal/archive/${version}.tar.gz";
+    sha256 = "5372ba2a35d885345207047a51b9389f9190fd12389847e7f7298618bcf59ad6";
+  };
+
+  # crystal on Darwin needs libiconv to build
+  buildInputs = [
+    boehmgc libatomic_ops pcre libevent llvm_39 makeWrapper
+  ] ++ stdenv.lib.optionals stdenv.isDarwin [
+    libiconv
+  ];
+
+  libPath = stdenv.lib.makeLibraryPath ([
+    boehmgc libatomic_ops pcre libevent
+  ] ++ stdenv.lib.optionals stdenv.isDarwin [
+    libiconv
+  ]);
+
+  unpackPhase = ''
+    tar zxf ${src}
+    tar zxf ${prebuiltBinary}
+  '';
+
+  sourceRoot = ".";
+
+  fixPrebuiltBinary = if stdenv.isDarwin then ''
+    wrapProgram $(pwd)/crystal-${version}-1/embedded/bin/crystal \
+        --suffix DYLD_LIBRARY_PATH : $libPath
+  ''
+  else ''
+    patchelf --set-interpreter $(cat $NIX_CC/nix-support/dynamic-linker) \
+      crystal-${version}-1/embedded/bin/crystal
+    patchelf --set-rpath ${ stdenv.lib.makeLibraryPath [ stdenv.cc.cc ] } \
+      crystal-${version}-1/embedded/bin/crystal
+  '';
+
+  buildPhase = ''
+    ${fixPrebuiltBinary}
+
+    cd crystal-${version}
+    make release=1 PATH="../crystal-${version}-1/bin:$PATH"
+    make doc
+  '';
+
+  installPhase = ''
+    install -Dm755 .build/crystal $out/bin/crystal
+    wrapProgram $out/bin/crystal \
+        --suffix CRYSTAL_PATH : $out/lib/crystal \
+        --suffix LIBRARY_PATH : $libPath
+
+    install -dm755 $out/lib/crystal
+    cp -r src/* $out/lib/crystal/
+
+    install -dm755 $out/share/doc/crystal/api
+    cp -r doc/* $out/share/doc/crystal/api/
+    cp -r samples $out/share/doc/crystal/
+
+    install -Dm644 etc/completion.bash $out/share/bash-completion/completions/crystal
+    install -Dm644 etc/completion.zsh $out/share/zsh/site-functions/_crystal
+
+    install -Dm644 LICENSE $out/share/licenses/crystal/LICENSE
+  '';
+
+  dontStrip = true;
+
+  meta = {
+    description = "A compiled language with Ruby like syntax and type inference";
+    homepage = "https://crystal-lang.org/";
+    license = stdenv.lib.licenses.asl20;
+    maintainers = with stdenv.lib.maintainers; [ mingchuan ];
+    platforms = [ "x86_64-linux" "i686-linux" "x86_64-darwin" ];
+  };
+}
+

pkgs/development/compilers/dmd/default.nix

@@ -20,10 +20,6 @@ stdenv.mkDerivation rec {
       substituteInPlace src/dmd/posix.mak \
           --replace g++ clang++ \
           --replace MACOSX_DEPLOYMENT_TARGET MACOSX_DEPLOYMENT_TARGET_
-
-      # Was not able to compile on darwin due to "__inline_isnanl"
-      # being undefined.
-      substituteInPlace src/dmd/root/port.c --replace __inline_isnanl __inline_isnan
   '';
 
   # Buid and install are based on http://wiki.dlang.org/Building_DMD

pkgs/development/compilers/ghc/8.0.2.nix

@@ -13,21 +13,15 @@ let
   });
 in
 stdenv.mkDerivation rec {
-  version = "8.0.1.20161117";
+  version = "8.0.1.20161213";
   name = "ghc-${version}";
 
   src = fetchurl {
-    url = "https://downloads.haskell.org/~ghc/8.0.2-rc1/${name}-src.tar.xz";
+    url = "https://downloads.haskell.org/~ghc/8.0.2-rc2/${name}-src.tar.xz";
-    sha256 = "08hpzvg059ha0knmlngd0winfkplkkb7dk88zfz3s177z38kd874";
+    sha256 = "0l1arhbh3rbs011f0y4pgc35yn07x3hz6lfqlvqbwn96f8ff5529";
   };
 
-  patches = [
+  patches = [] ++ stdenv.lib.optional stdenv.isLinux ./ghc-no-madv-free.patch;
-    # Already applied?
-    # ./relocation.patch
-    # Fix https://ghc.haskell.org/trac/ghc/ticket/12130
-    # (fetchFilteredPatch { url = https://git.haskell.org/ghc.git/patch/4d71cc89b4e9648f3fbb29c8fcd25d725616e265; sha256 = "0syaxb4y4s2dc440qmrggb4vagvqqhb55m6mx12rip4i9qhxl8k0"; })
-    (fetchFilteredPatch { url = https://git.haskell.org/ghc.git/patch/2f8cd14fe909a377b3e084a4f2ded83a0e6d44dd; sha256 = "06zvlgcf50ab58bw6yw3krn45dsmhg4cmlz4nqff8k4z1f1bj01v"; })
-  ] ++ stdenv.lib.optional stdenv.isLinux ./ghc-no-madv-free.patch;
 
   buildInputs = [ ghc perl hscolour ];
 

pkgs/development/compilers/ghcjs/base.nix

@@ -183,4 +183,5 @@ in mkDerivation (rec {
   license = stdenv.lib.licenses.bsd3;
   platforms = ghc.meta.platforms;
   maintainers = with stdenv.lib.maintainers; [ jwiegley cstrahan ];
+  broken = true;  # http://hydra.nixos.org/build/45110274
 })

pkgs/development/compilers/haxe/default.nix

@@ -1,17 +1,17 @@
 { stdenv, fetchgit, ocaml, zlib, neko, camlp4 }:
 
 stdenv.mkDerivation {
-  name = "haxe-3.1.3";
+  name = "haxe-3.2.1";
 
   buildInputs = [ocaml zlib neko camlp4];
 
   src = fetchgit {
     url = "https://github.com/HaxeFoundation/haxe.git";
-    sha256 = "0d8s9yqsqcbr2lfw4xnmg7vzgb6k1jq6hlwwaf1kmn9wxpvcc6x9";
+    sha256 = "1x9ay5a2llq46fww3k07jxx8h1vfpyxb522snc6702a050ki5vz3";
     fetchSubmodules = true;
 
-    # Tag 3.1.3
+    # Tag 3.2.1
-    rev = "7be30670b2f1f9b6082499c8fb9e23c0a6df6c28";
+    rev = "deab4424399b520750671e51e5f5c2684e942c17";
   };
 
   prePatch = ''

pkgs/development/compilers/haxe/haxelib-nix.patch

@@ -1,10 +1,10 @@
-diff --git a/extra/haxelib_src/src/tools/haxelib/Main.hx b/extra/haxelib_src/src/tools/haxelib/Main.hx
+diff --git a/src/tools/haxelib/Main.hx b/src/tools/haxelib/Main.hx
-index a44a785..0eb811a 100644
+index dc18815..def5231 100644
 --- a/extra/haxelib_src/src/tools/haxelib/Main.hx
 +++ b/extra/haxelib_src/src/tools/haxelib/Main.hx
-@@ -996,21 +996,26 @@ class Main {
+@@ -1301,21 +1301,26 @@ class Main {
  	}
- 
+
  	function checkRec( prj : String, version : String, l : List<{ project : String, version : String, info : Infos }> ) {
 -		var pdir = getRepository() + Data.safe(prj);
 -		if( !FileSystem.exists(pdir) )
@@ -44,7 +44,7 @@ index a44a785..0eb811a 100644
  		var json = try File.getContent(vdir+"/"+Data.JSON) catch( e : Dynamic ) null;
  		var inf = Data.readData(json,false);
  		l.add({ project : prj, version : version, info: inf });
-@@ -1025,15 +1030,21 @@ class Main {
+@@ -1330,15 +1335,21 @@ class Main {
  			var a = args[argcur++].split(":");
  			checkRec(a[0],a[1],list);
  		}
@@ -73,10 +73,10 @@ index a44a785..0eb811a 100644
  			var ndir = dir + "ndll";
  			if( FileSystem.exists(ndir) ) {
  				var sysdir = ndir+"/"+Sys.systemName();
-@@ -1153,21 +1164,39 @@ class Main {
+@@ -1491,23 +1502,43 @@ class Main {
- 		print('  Path: $devPath');
+ 			);
  	}
- 
+
 +	function getNixLib(project:String):Null<String>
 +	{
 +		var hlibPath = Sys.getEnv("HAXELIB_PATH");
@@ -91,7 +91,7 @@ index a44a785..0eb811a 100644
 +		}
 +		return null;
 +	}
-+
+
  	function run() {
 -		var rep = getRepository();
  		var project = param("Library");
@@ -103,10 +103,10 @@ index a44a785..0eb811a 100644
 -		pdir += "/";
 -		var version = temp[1] != null ? temp[1] : getCurrent(pdir);
 -		var dev = try getDev(pdir) catch ( e : Dynamic ) null;
--		var vdir = dev!=null ? dev : pdir + Data.safe(version);
+-		var vdir = dev != null ? dev : pdir + Data.safe(version);
--		var rdir = vdir + "/run.n";
+
--		if( !FileSystem.exists(rdir) )
+ 		args.push(cli.cwd);
--			throw "Library "+project+" version "+version+" does not have a run script";
++
 +		var vdir = this.getNixLib(project);
 +		if (vdir == null) {
 +			var rep = getRepository();
@@ -121,6 +121,8 @@ index a44a785..0eb811a 100644
 +			if( !FileSystem.exists(rdir) )
 +				throw "Library "+project+" version "+version+" does not have a run script";
 +		}
- 		args.push(Sys.getCwd());
+ 		cli.cwd = vdir;
- 		Sys.setCwd(vdir);
+-
- 		var cmd = "neko run.n";
+ 		var callArgs =
+ 			switch try [Data.readData(File.getContent(vdir + '/haxelib.json'), false), null] catch (e:Dynamic) [null, e] {
+ 				case [null, e]:

pkgs/development/coq-modules/mathcomp/default.nix

@@ -1,24 +1,39 @@
-{ callPackage, coq, fetchurl }:
+{ callPackage, fetchurl, coq }:
 
-let src = 
+if coq.coq-version == "8.4" then
-  if coq.coq-version == "8.4" then
-
-    fetchurl {
-      url = http://ssr.msr-inria.inria.fr/FTP/mathcomp-1.6.tar.gz;
-      sha256 = "0adr556032r1jkvphbpfvrrv041qk0yqb7a1xnbam52ji0mdl2w8";
-    }
-
-  else if coq.coq-version == "8.5" then
-
-    fetchurl {
-      url = http://ssr.msr-inria.inria.fr/FTP/mathcomp-1.6.tar.gz;
-      sha256 = "0adr556032r1jkvphbpfvrrv041qk0yqb7a1xnbam52ji0mdl2w8";
-    }
-
-  else throw "No mathcomp package for Coq version ${coq.coq-version}";
-
-in
 
 callPackage ./generic.nix {
-  inherit src;
+
+  name = "coq-mathcomp-1.6-${coq.coq-version}";
+  src = fetchurl {
+    url = http://ssr.msr-inria.inria.fr/FTP/mathcomp-1.6.tar.gz;
+    sha256 = "0adr556032r1jkvphbpfvrrv041qk0yqb7a1xnbam52ji0mdl2w8";
+  };
+
 }
+
+else if coq.coq-version == "8.5" then
+
+callPackage ./generic.nix {
+
+  name = "coq-mathcomp-1.6-${coq.coq-version}";
+  src = fetchurl {
+    url = http://ssr.msr-inria.inria.fr/FTP/mathcomp-1.6.tar.gz;
+    sha256 = "0adr556032r1jkvphbpfvrrv041qk0yqb7a1xnbam52ji0mdl2w8";
+  };
+
+}
+
+else if coq.coq-version == "8.6" then
+
+callPackage ./generic.nix {
+
+  name = "coq-mathcomp-1.6.1-${coq.coq-version}";
+  src = fetchurl {
+    url = https://github.com/math-comp/math-comp/archive/mathcomp-1.6.1.tar.gz;
+    sha256 = "1j9ylggjzrxz1i2hdl2yhsvmvy5z6l4rprwx7604401080p5sgjw";
+  };
+
+}
+
+else throw "No ssreflect package for Coq version ${coq.coq-version}"

pkgs/development/coq-modules/mathcomp/generic.nix

@@ -1,12 +1,11 @@
 { stdenv, fetchurl, coq, ssreflect, ncurses, which
 , graphviz, ocamlPackages, withDoc ? false
-, src
+, src, name
 }:
 
 stdenv.mkDerivation {
 
-  name = "coq-mathcomp-1.6-${coq.coq-version}";
+  inherit name;
-
   inherit src;
 
   nativeBuildInputs = stdenv.lib.optionals withDoc [ graphviz ];

pkgs/development/coq-modules/ssreflect/default.nix

@@ -4,6 +4,7 @@ if coq.coq-version == "8.4" then
 
 callPackage ./generic.nix {
 
+  name = "coq-ssreflect-1.6-${coq.coq-version}";
   src = fetchurl {
     url = http://ssr.msr-inria.inria.fr/FTP/mathcomp-1.6.tar.gz;
     sha256 = "0adr556032r1jkvphbpfvrrv041qk0yqb7a1xnbam52ji0mdl2w8";
@@ -15,6 +16,7 @@ else if coq.coq-version == "8.5" then
 
 callPackage ./generic.nix {
 
+  name = "coq-ssreflect-1.6-${coq.coq-version}";
   src = fetchurl {
     url = http://ssr.msr-inria.inria.fr/FTP/mathcomp-1.6.tar.gz;
     sha256 = "0adr556032r1jkvphbpfvrrv041qk0yqb7a1xnbam52ji0mdl2w8";
@@ -22,4 +24,16 @@ callPackage ./generic.nix {
 
 }
 
+else if coq.coq-version == "8.6" then
+
+callPackage ./generic.nix {
+
+  name = "coq-ssreflect-1.6.1-${coq.coq-version}";
+  src = fetchurl {
+    url = https://github.com/math-comp/math-comp/archive/mathcomp-1.6.1.tar.gz;
+    sha256 = "1j9ylggjzrxz1i2hdl2yhsvmvy5z6l4rprwx7604401080p5sgjw";
+  };
+
+}
+
 else throw "No ssreflect package for Coq version ${coq.coq-version}"

pkgs/development/coq-modules/ssreflect/generic.nix

@@ -1,12 +1,11 @@
 { stdenv, fetchurl, coq, ncurses, which
 , graphviz, withDoc ? false
-, src, patches ? []
+, src, name, patches ? []
 }:
 
 stdenv.mkDerivation {
 
-  name = "coq-ssreflect-1.6-${coq.coq-version}";
+  inherit name;
-
   inherit src;
 
   nativeBuildInputs = stdenv.lib.optionals withDoc [ graphviz ];

pkgs/development/haskell-modules/configuration-hackage2nix.yaml

@@ -3829,6 +3829,7 @@ dont-distribute-packages:
   git-date:                                     [ i686-linux, x86_64-linux, x86_64-darwin ]
   git-gpush:                                    [ i686-linux, x86_64-linux, x86_64-darwin ]
   git-jump:                                     [ i686-linux, x86_64-linux, x86_64-darwin ]
+  git-mediate:                                  [ i686-linux, x86_64-linux, x86_64-darwin ]
   git-object:                                   [ i686-linux, x86_64-linux, x86_64-darwin ]
   git-repair:                                   [ i686-linux, x86_64-linux, x86_64-darwin ]
   git-sanity:                                   [ i686-linux, x86_64-linux, x86_64-darwin ]
@@ -5440,6 +5441,7 @@ dont-distribute-packages:
   lzma-enumerator:                              [ i686-linux, x86_64-linux, x86_64-darwin ]
   maam:                                         [ i686-linux, x86_64-linux, x86_64-darwin ]
   macbeth-lib:                                  [ i686-linux, x86_64-linux, x86_64-darwin ]
+  machinecell:                                  [ i686-linux, x86_64-linux, x86_64-darwin ]
   machines-zlib:                                [ i686-linux, x86_64-linux, x86_64-darwin ]
   macosx-make-standalone:                       [ i686-linux, x86_64-linux, x86_64-darwin ]
   mage:                                         [ i686-linux, x86_64-linux, x86_64-darwin ]
@@ -5826,6 +5828,7 @@ dont-distribute-packages:
   newtype-generics:                             [ i686-linux, x86_64-linux, x86_64-darwin ]
   newtype-th:                                   [ i686-linux, x86_64-linux, x86_64-darwin ]
   next-ref:                                     [ i686-linux, x86_64-linux, x86_64-darwin ]
+  nfc:                                          [ i686-linux, x86_64-linux, x86_64-darwin ]
   ngrams-loader:                                [ i686-linux, x86_64-linux, x86_64-darwin ]
   NGrams:                                       [ i686-linux, x86_64-linux, x86_64-darwin ]
   niagra:                                       [ i686-linux, x86_64-linux, x86_64-darwin ]
@@ -6209,6 +6212,7 @@ dont-distribute-packages:
   press:                                        [ i686-linux, x86_64-linux, x86_64-darwin ]
   presto-hdbc:                                  [ i686-linux, x86_64-linux, x86_64-darwin ]
   pretty-error:                                 [ i686-linux, x86_64-linux, x86_64-darwin ]
+  pretty-simple:                                [ i686-linux, x86_64-linux, x86_64-darwin ]
   primitive-simd:                               [ i686-linux, x86_64-linux, x86_64-darwin ]
   PrimitiveArray-Pretty:                        [ i686-linux, x86_64-linux, x86_64-darwin ]
   primula-board:                                [ i686-linux, x86_64-linux, x86_64-darwin ]
@@ -7217,6 +7221,7 @@ dont-distribute-packages:
   texrunner:                                    [ i686-linux, x86_64-linux, x86_64-darwin ]
   text-all:                                     [ i686-linux, x86_64-linux, x86_64-darwin ]
   text-and-plots:                               [ i686-linux, x86_64-linux, x86_64-darwin ]
+  text-icu-normalized:                          [ i686-linux, x86_64-linux, x86_64-darwin ]
   text-json-qq:                                 [ i686-linux, x86_64-linux, x86_64-darwin ]
   text-normal:                                  [ i686-linux, x86_64-linux, x86_64-darwin ]
   text-position:                                [ i686-linux, x86_64-linux, x86_64-darwin ]
@@ -7705,6 +7710,7 @@ dont-distribute-packages:
   wxFruit:                                      [ i686-linux, x86_64-linux, x86_64-darwin ]
   WxGeneric:                                    [ i686-linux, x86_64-linux, x86_64-darwin ]
   wxhnotepad:                                   [ i686-linux, x86_64-linux, x86_64-darwin ]
+  wxSimpleCanvas:                               [ i686-linux, x86_64-linux, x86_64-darwin ]
   wxturtle:                                     [ i686-linux, x86_64-linux, x86_64-darwin ]
   wyvern:                                       [ i686-linux, x86_64-linux, x86_64-darwin ]
   x-dsp:                                        [ i686-linux, x86_64-linux, x86_64-darwin ]

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

@@ -245,9 +245,41 @@ stdenv.mkDerivation ({
     runHook postConfigure
   '';
 
+  # The darwin pre/post build sections are a workaround https://github.com/haskell/cabal/issues/4183
+  # It seems like --extra-lib-dirs from the previous steps is not detected properly,
+  # to work around this we build using a DYLD_LIBRARY_PATH and fixup the build afterwards.
   buildPhase = ''
     runHook preBuild
+    ${optionalString stdenv.isDarwin ''
+      local inputClosure=""
+      for i in $propagatedNativeBuildInputs $nativeBuildInputs; do
+        findInputs $i inputClosure propagated-native-build-inputs
+      done
+      local -a inputLibs=()
+      for p in $inputClosure; do
+        if [ -d "$p/lib/${ghc.name}/package.conf.d" ]; then
+          continue
+        fi
+        if [ -d "$p/lib" ]; then
+          inputLibs+="$p/lib"
+        fi
+      done
+
+      for lib in $inputLibs; do
+        export DYLD_LIBRARY_PATH="$lib:''${DYLD_LIBRARY_PATH:+:$DYLD_LIBRARY_PATH}"
+      done
+    ''}
     ${setupCommand} build ${buildTarget}${crossCabalFlagsString}
+    ${optionalString stdenv.isDarwin ''
+      unset DYLD_LIBRARY_PATH
+
+      local outputLib=dist/build/*-ghc${ghc.version}.dylib
+      for lib in $inputLib/*.dylib; do
+        for name in $(otool -L $outputLib | awk '$1 ~ /^'$(basename lib)'/ {print $1}' | cat); do
+          install_name_tool -change $name $lib $outputLib
+        done
+      done
+    ''}
     runHook postBuild
   '';
 

pkgs/development/interpreters/maude/default.nix

@@ -1,26 +1,34 @@
-{ stdenv, fetchurl, flex, bison, ncurses, buddy, tecla, libsigsegv, gmpxx, makeWrapper }:
+{ stdenv, fetchurl, unzip, makeWrapper
+, flex, bison, ncurses, buddy, tecla, libsigsegv, gmpxx,
+}:
 
-stdenv.mkDerivation rec {
+let
-  name = "maude-2.6";
 
-  src = fetchurl {
+  version = "2.7";
-    url = "http://maude.cs.uiuc.edu/download/current/Maude-2.6.tar.gz";
-    sha256 = "182abzhvjvlaa21aqv7802v3bs57a4dm7cw09s3mqmih7nzpkfm5";
-  };
 
   fullMaude = fetchurl {
-    url = "https://full-maude.googlecode.com/git/full-maude261h.maude";
+    url = "https://raw.githubusercontent.com/maude-team/full-maude/master/full-maude27c.maude";
-    sha256 = "0xx8bfn6arsa75m5vhp5lmpazgfw230ssq33h9vifswlvzzc81ha";
+    sha256 = "08bg3gn1vyjy5k69hnynpzc9s1hnrbkyv6z08y1h2j37rlc4c18y";
   };
 
-  buildInputs = [flex bison ncurses buddy tecla gmpxx libsigsegv makeWrapper];
+in
+
+stdenv.mkDerivation rec {
+  name = "maude-${version}";
+
+  src = fetchurl {
+    url = "https://github.com/maude-team/maude/archive/v${version}-ext-hooks.tar.gz";
+    sha256 = "02p0snxm69rs8pvm93r91p881dw6p3bxmazr3cfw5pnxpgz0vjl0";
+  };
+
+  buildInputs = [flex bison ncurses buddy tecla gmpxx libsigsegv makeWrapper unzip];
 
   hardeningDisable = [ "stackprotector" ] ++
     stdenv.lib.optionals stdenv.isi686 [ "pic" "fortify" ];
 
   preConfigure = ''
     configureFlagsArray=(
-      --datadir=$out/share/maude
+      --datadir="$out/share/maude"
       TECLA_LIBS="-ltecla -lncursesw"
       CFLAGS="-O3" CXXFLAGS="-O3"
     )
@@ -30,8 +38,7 @@ stdenv.mkDerivation rec {
 
   postInstall = ''
     for n in "$out/bin/"*; do wrapProgram "$n" --suffix MAUDE_LIB ':' "$out/share/maude"; done
-    mkdir -p $out/share/maude
+    install -D -m 444 ${fullMaude} $out/share/maude/full-maude.maude
-    cp ${fullMaude} -d $out/share/maude/full-maude.maude
   '';
 
   meta = {

pkgs/development/interpreters/python/cpython/2.7/default.nix

@@ -28,7 +28,7 @@ with stdenv.lib;
 
 let
   majorVersion = "2.7";
-  minorVersion = "12";
+  minorVersion = "13";
   minorVersionSuffix = "";
   pythonVersion = majorVersion;
   version = "${majorVersion}.${minorVersion}${minorVersionSuffix}";
@@ -37,7 +37,7 @@ let
 
   src = fetchurl {
     url = "https://www.python.org/ftp/python/${majorVersion}.${minorVersion}/Python-${version}.tar.xz";
-    sha256 = "0y7rl603vmwlxm6ilkhc51rx2mfj14ckcz40xxgs0ljnvlhp30yp";
+    sha256 = "0cgpk3zk0fgpji59pb4zy9nzljr70qzgv1vpz5hq5xw2d2c47m9m";
   };
 
   hasDistutilsCxxPatch = !(stdenv.cc.isGNU or false);
@@ -57,13 +57,6 @@ let
 
       ./properly-detect-curses.patch
 
-      # FIXME: get rid of this after the next release, when the commit referenced here makes
-      # it in. We need it until then because it breaks compilation of programs that use
-      # locale with clang 3.8 and higher.
-      (fetchpatch {
-        url    = "https://hg.python.org/cpython/raw-rev/e0ec3471cb09";
-        sha256 = "1jdgb70jw942r4kmr01qll7mk1di8jx0qiabmp20jhnmha246ivq";
-      })
     ] ++ optionals stdenv.isLinux [
 
       # Disable the use of ldconfig in ctypes.util.find_library (since

pkgs/development/interpreters/python/cpython/2.7/no-ldconfig.patch

@@ -1,8 +1,18 @@
+From 6b0f329a9f37110020ca02b35c8125391ef282b7 Mon Sep 17 00:00:00 2001
+From: Frederik Rietdijk <fridh@fridh.nl>
+Date: Sat, 24 Dec 2016 15:56:10 +0100
+Subject: [PATCH] no ldconfig
+
+---
+ Lib/ctypes/util.py | 35 +----------------------------------
+ Lib/uuid.py        | 47 -----------------------------------------------
+ 2 files changed, 1 insertion(+), 81 deletions(-)
+
 diff --git a/Lib/ctypes/util.py b/Lib/ctypes/util.py
-index b2c514d..a6eca81 100644
+index ab10ec5..f253e34 100644
 --- a/Lib/ctypes/util.py
 +++ b/Lib/ctypes/util.py
-@@ -207,31 +207,7 @@ elif os.name == "posix":
+@@ -235,40 +235,7 @@ elif os.name == "posix":
      else:
  
          def _findSoname_ldconfig(name):
@@ -22,11 +32,20 @@ index b2c514d..a6eca81 100644
 -
 -            # XXX assuming GLIBC's ldconfig (with option -p)
 -            expr = r'\s+(lib%s\.[^\s]+)\s+\(%s' % (re.escape(name), abi_type)
--            f = os.popen('LC_ALL=C LANG=C /sbin/ldconfig -p 2>/dev/null')
+-
+-            env = dict(os.environ)
+-            env['LC_ALL'] = 'C'
+-            env['LANG'] = 'C'
+-            null = open(os.devnull, 'wb')
 -            try:
--                data = f.read()
+-                with null:
--            finally:
+-                    p = subprocess.Popen(['/sbin/ldconfig', '-p'],
--                f.close()
+-                                          stderr=null,
+-                                          stdout=subprocess.PIPE,
+-                                          env=env)
+-            except OSError:  # E.g. command not found
+-                return None
+-            [data, _] = p.communicate()
 -            res = re.search(expr, data)
 -            if not res:
 -                return None
@@ -36,16 +55,12 @@ index b2c514d..a6eca81 100644
          def find_library(name):
              return _findSoname_ldconfig(name) or _get_soname(_findLib_gcc(name))
 diff --git a/Lib/uuid.py b/Lib/uuid.py
-index 7432032..9829d18 100644
+index 7432032..05eeee5 100644
 --- a/Lib/uuid.py
 +++ b/Lib/uuid.py
-@@ -437,57 +437,7 @@ def _netbios_getnode():
+@@ -441,53 +441,6 @@ def _netbios_getnode():
-         return ((bytes[0]<<40L) + (bytes[1]<<32L) + (bytes[2]<<24L) +
-                 (bytes[3]<<16L) + (bytes[4]<<8L) + bytes[5])
  
--# Thanks to Thomas Heller for ctypes and for his help with its use here.
+ # If ctypes is available, use it to find system routines for UUID generation.
--
--# If ctypes is available, use it to find system routines for UUID generation.
  _uuid_generate_time = _UuidCreate = None
 -try:
 -    import ctypes, ctypes.util
@@ -97,3 +112,6 @@ index 7432032..9829d18 100644
  
  def _unixdll_getnode():
      """Get the hardware address on Unix using ctypes."""
+-- 
+2.11.0
+

pkgs/development/interpreters/python/cpython/3.6/default.nix

@@ -25,7 +25,7 @@ with stdenv.lib;
 let
   majorVersion = "3.6";
   minorVersion = "0";
-  minorVersionSuffix = "rc1";
+  minorVersionSuffix = "";
   pythonVersion = majorVersion;
   version = "${majorVersion}.${minorVersion}${minorVersionSuffix}";
   libPrefix = "python${majorVersion}";
@@ -45,7 +45,7 @@ in stdenv.mkDerivation {
 
   src = fetchurl {
     url = "https://www.python.org/ftp/python/${majorVersion}.${minorVersion}/Python-${version}.tar.xz";
-    sha256 = "01sqzz5iq7law93zgdxkb8sv98a493a2wzslynz64cl3hhdqr1pw";
+    sha256 = "08inlbb2vb8lahw6wfq654lqk6l1x7ncpggp6a92vqw5yq2gkidh";
   };
 
   NIX_LDFLAGS = optionalString stdenv.isLinux "-lgcc_s";

pkgs/development/libraries/SDL2/default.nix

@@ -31,6 +31,8 @@ stdenv.mkDerivation rec {
     sha256 = "0jqp46mxxbh9lhpx1ih6sp93k752j2smhpc0ad0q4cb3px0famfs";
   };
 
+  outputs = [ "out" "dev" ];
+
   patches = [ ./find-headers.patch ];
 
   nativeBuildInputs = [ pkgconfig ];
@@ -61,6 +63,7 @@ stdenv.mkDerivation rec {
 
   postInstall = ''
     rm $out/lib/*.a
+    moveToOutput bin/sdl2-config "$dev"
   '';
 
   setupHook = ./setup-hook.sh;

pkgs/development/libraries/aws-sdk-cpp/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchFromGitHub, cmake, curl, libuuid, openssl, zlib
+{ lib, stdenv, fetchFromGitHub, cmake, curl, openssl, zlib
 , # Allow building a limited set of APIs, e.g. ["s3" "ec2"].
   apis ? ["*"]
 , # Whether to enable AWS' custom memory management.
@@ -7,20 +7,22 @@
 
 stdenv.mkDerivation rec {
   name = "aws-sdk-cpp-${version}";
-  version = "1.0.34";
+  version = "1.0.43";
 
   src = fetchFromGitHub {
     owner = "awslabs";
     repo = "aws-sdk-cpp";
     rev = version;
-    sha256 = "09vag1ybfqvw37djmd9g740iqjvg8nwr4p0xb21rfj06vazrdg4b";
+    sha256 = "0sa0pkkbxxfn3h7b19yf296r5g5nqm4aqpwrkij0rq7jix9lxqj6";
   };
 
+  patches = [ ./s3-encryption-headers.patch ];
+
   # FIXME: might be nice to put different APIs in different outputs
   # (e.g. libaws-cpp-sdk-s3.so in output "s3").
   outputs = [ "out" "dev" ];
 
-  buildInputs = [ cmake curl libuuid ];
+  buildInputs = [ cmake curl ];
 
   cmakeFlags =
     lib.optional (!customMemoryManagement) "-DCUSTOM_MEMORY_MANAGEMENT=0"
@@ -39,13 +41,13 @@ stdenv.mkDerivation rec {
 
   NIX_LDFLAGS = lib.concatStringsSep " " (
     (map (pkg: "-rpath ${lib.getOutput "lib" pkg}/lib"))
-      [ libuuid curl openssl zlib stdenv.cc.cc ]);
+      [ curl openssl zlib stdenv.cc.cc ]);
 
   meta = {
     description = "A C++ interface for Amazon Web Services";
     homepage = https://github.com/awslabs/aws-sdk-cpp;
     license = lib.licenses.asl20;
-    platforms = lib.platforms.linux;
+    platforms = lib.platforms.linux ++ lib.platforms.darwin;
     maintainers = [ lib.maintainers.eelco ];
   };
 }

pkgs/development/libraries/aws-sdk-cpp/s3-encryption-headers.patch

@@ -0,0 +1,18 @@
+diff --git a/aws-cpp-sdk-s3-encryption/CMakeLists.txt b/aws-cpp-sdk-s3-encryption/CMakeLists.txt
+index 0a1a907..cf9ce0e 100644
+--- a/aws-cpp-sdk-s3-encryption/CMakeLists.txt
++++ b/aws-cpp-sdk-s3-encryption/CMakeLists.txt
+@@ -69,9 +69,9 @@ target_link_libraries(${PROJECT_NAME} ${PROJECT_LIBS})
+ 
+ setup_install()
+ 
+-install (FILES ${S3ENCRYPTION_HEADERS} DESTINATION include/aws/s3-encryption)
+-install (FILES ${S3ENCRYPTION_MATERIALS_HEADERS} DESTINATION include/aws/s3-encryption/materials)
+-install (FILES ${S3ENCRYPTION_HANDLERS_HEADERS} DESTINATION include/aws/s3-encryption/handlers)
+-install (FILES ${S3ENCRYPTION_MODULES_HEADERS} DESTINATION include/aws/s3-encryption/modules)
++install (FILES ${S3ENCRYPTION_HEADERS} DESTINATION ${INCLUDE_DIRECTORY}/aws/s3-encryption)
++install (FILES ${S3ENCRYPTION_MATERIALS_HEADERS} DESTINATION ${INCLUDE_DIRECTORY}/aws/s3-encryption/materials)
++install (FILES ${S3ENCRYPTION_HANDLERS_HEADERS} DESTINATION ${INCLUDE_DIRECTORY}/aws/s3-encryption/handlers)
++install (FILES ${S3ENCRYPTION_MODULES_HEADERS} DESTINATION ${INCLUDE_DIRECTORY}/aws/s3-encryption/modules)
+ 
+ do_packaging()

pkgs/development/libraries/kde-frameworks/default.nix

@@ -57,7 +57,7 @@ let
       });
 
     kdeWrapper = import ./kde-wrapper.nix {
-      inherit (pkgs) stdenv lib makeWrapper;
+      inherit (pkgs) stdenv lib makeWrapper buildEnv;
     };
 
     attica = callPackage ./attica.nix {};

pkgs/development/libraries/kde-frameworks/kde-wrapper.nix

@@ -1,53 +1,40 @@
-{ stdenv, lib, makeWrapper }:
+{ stdenv, lib, makeWrapper, buildEnv }:
 
 drv:
 
 { targets, paths ? [] }:
 
+let
+  env = buildEnv {
+    inherit (drv) name meta;
+    paths = builtins.map lib.getBin ([drv] ++ paths);
+    pathsToLink = [ "/bin" "/share" "/lib/qt5" "/etc/xdg" ];
+  };
+in
+
 stdenv.mkDerivation {
   inherit (drv) name meta;
+  preferLocalBuild = true;
 
   paths = builtins.map lib.getBin ([drv] ++ paths);
-  inherit drv targets;
+  inherit drv env targets;
   passthru = { unwrapped = drv; };
 
   nativeBuildInputs = [ makeWrapper ];
 
-  unpackPhase = "true";
+  builder = builtins.toFile "builder.sh" ''
-  configurePhase = "runHook preConfigure; runHook postConfigure";
+    . $stdenv/setup
-  buildPhase = "true";
-
-  installPhase = ''
-    propagated=
-    for p in $drv $paths; do
-        findInputs $p propagated propagated-user-env-packages
-    done
-
-    wrap_PATH="$out/bin"
-    wrap_XDG_DATA_DIRS=
-    wrap_XDG_CONFIG_DIRS=
-    wrap_QML_IMPORT_PATH=
-    wrap_QML2_IMPORT_PATH=
-    wrap_QT_PLUGIN_PATH=
-    for p in $propagated; do
-        addToSearchPath wrap_PATH "$p/bin"
-        addToSearchPath wrap_XDG_DATA_DIRS "$p/share"
-        addToSearchPath wrap_XDG_CONFIG_DIRS "$p/etc/xdg"
-        addToSearchPath wrap_QML_IMPORT_PATH "$p/lib/qt5/imports"
-        addToSearchPath wrap_QML2_IMPORT_PATH "$p/lib/qt5/qml"
-        addToSearchPath wrap_QT_PLUGIN_PATH "$p/lib/qt5/plugins"
-    done
 
     for t in $targets; do
         if [ -a "$drv/$t" ]; then
             makeWrapper "$drv/$t" "$out/$t" \
                 --argv0 '"$0"' \
-                --suffix PATH : "$wrap_PATH" \
+                --suffix PATH : "$env/bin" \
-                --prefix XDG_CONFIG_DIRS : "$wrap_XDG_CONFIG_DIRS" \
+                --prefix XDG_CONFIG_DIRS : "$env/share" \
-                --prefix XDG_DATA_DIRS : "$wrap_XDG_DATA_DIRS" \
+                --prefix XDG_DATA_DIRS : "$env/etc/xdg" \
-                --set QML_IMPORT_PATH "$wrap_QML_IMPORT_PATH" \
+                --set QML_IMPORT_PATH "$env/lib/qt5/imports" \
-                --set QML2_IMPORT_PATH "$wrap_QML2_IMPORT_PATH" \
+                --set QML2_IMPORT_PATH "$env/lib/qt5/qml" \
-                --set QT_PLUGIN_PATH "$wrap_QT_PLUGIN_PATH"
+                --set QT_PLUGIN_PATH "$env/lib/qt5/plugins"
         else
             echo "no such file or directory: $drv/$t"
             exit 1

pkgs/development/libraries/libgcrypt/default.nix

@@ -4,11 +4,11 @@ assert enableCapabilities -> stdenv.isLinux;
 
 stdenv.mkDerivation rec {
   name = "libgcrypt-${version}";
-  version = "1.7.3";
+  version = "1.7.5";
 
   src = fetchurl {
     url = "mirror://gnupg/libgcrypt/${name}.tar.bz2";
-    sha256 = "0wbh6fq5zi9wg2xcfvfpwh7dv52jihivx1vm4h91c2kx0w8n3b6x";
+    sha256 = "0078pbzm6nlgvnwlylshsg707ifcmfpnpbvhlhqbpwpfic9a9zni";
   };
 
   outputs = [ "out" "dev" "info" ];

pkgs/development/libraries/libmediainfo/default.nix

@@ -1,11 +1,11 @@
 { stdenv, fetchurl, autoreconfHook, pkgconfig, libzen, zlib }:
 
 stdenv.mkDerivation rec {
-  version = "0.7.87";
+  version = "0.7.91";
   name = "libmediainfo-${version}";
   src = fetchurl {
     url = "http://mediaarea.net/download/source/libmediainfo/${version}/libmediainfo_${version}.tar.xz";
-    sha256 = "1gvjvc809mrhpcqr62cihhc6jnwml197xjbgydnzvsghih8dq8s9";
+    sha256 = "1h39cwd85rgidr0hbwab9dwbjv25xhvjv8y2nv35p3fwrs48p098";
   };
 
   nativeBuildInputs = [ autoreconfHook pkgconfig ];

pkgs/development/libraries/libwacom/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "libwacom-${version}";
-  version = "0.19";
+  version = "0.22";
 
   src = fetchurl {
     url = "mirror://sourceforge/linuxwacom/libwacom/${name}.tar.bz2";
-    sha256 = "1zsmp2l53fbfy6jykh4c0i127baf503lq2fvd5y1066ihp6qh3b2";
+    sha256 = "1h10awwapj5v8nik220ga0raggv3lgaq0kzwlma2qjmzdhhrrhcp";
   };
 
   nativeBuildInputs = [ pkgconfig ];

pkgs/development/libraries/libzen/default.nix

@@ -1,11 +1,11 @@
 { stdenv, fetchurl, autoreconfHook }:
 
 stdenv.mkDerivation rec {
-  version = "0.4.33";
+  version = "0.4.34";
   name = "libzen-${version}";
   src = fetchurl {
     url = "https://mediaarea.net/download/source/libzen/${version}/libzen_${version}.tar.bz2";
-    sha256 = "0py5iagajz6m5zh26svkjyy85k1dmyhi6cdbmc3cb56a4ix1k2d2";
+    sha256 = "02krmhl6dplidz6h251ajpzzdhzzm0hp0lwwv9rgn55xjgh4yxw3";
   };
 
   nativeBuildInputs = [ autoreconfHook ];

pkgs/development/libraries/science/biology/htslib/default.nix

@@ -3,11 +3,11 @@
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "htslib";
-  version = "1.3.1";
+  version = "1.3.2";
 
   src = fetchurl {
     url = "https://github.com/samtools/${pname}/releases/download/${version}/${name}.tar.bz2";
-    sha256 = "49d53a2395b8cef7d1d11270a09de888df8ba06f70fe68282e8235ee04124ae6";
+    sha256 = "0iq3blw23s55vkr1z88p9y2dqrb2dybzhl6hz2nlk53ncihrxcdr";
   };
 
   buildInputs = [ zlib ];

pkgs/development/libraries/simgear/default.nix

@@ -1,20 +1,22 @@
 { stdenv, fetchurl, plib, freeglut, xproto, libX11, libXext, xextproto, libXi
 , inputproto, libICE, libSM, libXt, libXmu, mesa, boost, zlib, libjpeg, freealut
 , openscenegraph, openal, expat, cmake, apr
+, curl
 }:
 
 stdenv.mkDerivation rec {
   name = "simgear-${version}";
-  version = "3.4.0";
+  version = "2016.4.3";
+  shortVersion = "2016.4";
 
   src = fetchurl {
-    url = "http://mirrors.ibiblio.org/pub/mirrors/simgear/ftp/Source/${name}.tar.bz2";
+    url = "mirror://sourceforge/flightgear/release-${shortVersion}/${name}.tar.bz2";
-    sha256 = "152q3aqlrg3631ppvl6kr1mp5iszplq68l6lrsn9vjxafbz6czcj";
+    sha256 = "1gfj0d03jbi0p08baj46ihhyzbgpymmipw2dp11j13412l15acv9";
   };
 
   buildInputs = [ plib freeglut xproto libX11 libXext xextproto libXi inputproto
                   libICE libSM libXt libXmu mesa boost zlib libjpeg freealut
-                  openscenegraph openal expat cmake apr ];
+                  openscenegraph openal expat cmake apr curl ];
 
   meta = with stdenv.lib; {
     description = "Simulation construction toolkit";

pkgs/development/libraries/tecla/default.nix

@@ -1,15 +1,13 @@
 { stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
-  name = "tecla-1.6.2";
+  name = "tecla-1.6.3";
 
   src = fetchurl {
     url = "http://www.astro.caltech.edu/~mcs/tecla/lib${name}.tar.gz";
-    sha256 = "1f5p1v9ac5r1f6pjzwacb4yf8m6z19rv77p76j7fix34hd9dnqcc";
+    sha256 = "06pfq5wa8d25i9bdjkp4xhms5101dsrbg82riz7rz1a0a32pqxgj";
   };
 
-  configureFlags = "CFLAGS=-O3 CXXFLAGS=-O3";
-
   meta = {
     homepage = "http://www.astro.caltech.edu/~mcs/tecla/";
     description = "Command-line editing library";

pkgs/development/python-modules/pandas/default.nix

@@ -0,0 +1,91 @@
+{ buildPythonPackage
+, python
+, stdenv
+, fetchurl
+, nose
+, glibcLocales
+, cython
+, dateutil
+, scipy
+, numexpr
+, pytz
+, xlrd
+, bottleneck
+, sqlalchemy
+, lxml
+, html5lib
+, beautifulsoup4
+, openpyxl
+, tables
+, xlwt
+, darwin ? {}
+, libcxx ? null
+}:
+
+let
+  inherit (stdenv.lib) optional optionalString concatStringsSep;
+  inherit (stdenv) isDarwin;
+in buildPythonPackage rec {
+  pname = "pandas";
+  version = "0.19.2";
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${name}.tar.gz";
+    sha256 = "6f0f4f598c2b16746803c8bafef7c721c57e4844da752d36240c0acf97658014";
+  };
+
+  LC_ALL = "en_US.UTF-8";
+  buildInputs = [ nose glibcLocales ] ++ optional isDarwin libcxx;
+  propagatedBuildInputs = [
+    cython
+    dateutil
+    scipy
+    numexpr
+    pytz
+    xlrd
+    bottleneck
+    sqlalchemy
+    lxml
+    html5lib
+    beautifulsoup4
+    openpyxl
+    tables
+    xlwt
+  ] ++ optional isDarwin darwin.locale; # provides the locale command
+
+  # For OSX, we need to add a dependency on libcxx, which provides
+  # `complex.h` and other libraries that pandas depends on to build.
+  patchPhase = optionalString isDarwin ''
+    cpp_sdk="${libcxx}/include/c++/v1";
+    echo "Adding $cpp_sdk to the setup.py common_include variable"
+    substituteInPlace setup.py \
+      --replace "['pandas/src/klib', 'pandas/src']" \
+                "['pandas/src/klib', 'pandas/src', '$cpp_sdk']"
+
+  # disable clipboard tests since pbcopy/pbpaste are not open source
+    substituteInPlace pandas/io/tests/test_clipboard.py \
+      --replace pandas.util.clipboard no_such_module \
+      --replace OSError ImportError
+  '';
+
+  # The flag `-A 'not network'` will disable tests that use internet.
+  # The `-e` flag disables a few problematic tests.
+
+  checkPhase = ''
+    runHook preCheck
+    # The flag `-w` provides the initial directory to search for tests.
+    # The flag `-A 'not network'` will disable tests that use internet.
+    nosetests -w $out/${python.sitePackages}/pandas --no-path-adjustment -A 'not slow and not network' --stop \
+      --verbosity=3
+     runHook postCheck
+  '';
+
+  meta = {
+    homepage = "http://pandas.pydata.org/";
+    description = "Python Data Analysis Library";
+    license = stdenv.lib.licenses.bsd3;
+    maintainers = with stdenv.lib.maintainers; [ raskin fridh ];
+    platforms = stdenv.lib.platforms.unix;
+  };
+}

pkgs/development/python-modules/pytest-expect/default.nix

@@ -0,0 +1,31 @@
+{ buildPythonPackage
+, lib
+, fetchurl
+, pytest
+, u-msgpack-python
+, six
+}:
+
+let
+  pname = "pytest-expect";
+  version = "1.1.0";
+in buildPythonPackage rec {
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${name}.tar.gz";
+    sha256 = "36b4462704450798197d090809a05f4e13649d9cba9acdc557ce9517da1fd847";
+  };
+
+  buildInputs = [ pytest ];
+  propagatedBuildInputs = [ u-msgpack-python six ];
+
+  # Tests in neither the archive nor the repo
+  doCheck = false;
+
+  meta = {
+    description = "py.test plugin to store test expectations and mark tests based on them";
+    homepage = https://github.com/gsnedders/pytest-expect;
+    license = lib.licenses.mit;
+  };
+}

pkgs/development/python-modules/u-msgpack-python/default.nix

@@ -0,0 +1,33 @@
+{ buildPythonPackage
+, lib
+, fetchurl
+, glibcLocales
+, python
+}:
+
+let
+  pname = "u-msgpack-python";
+  version = "2.3.0";
+in buildPythonPackage rec {
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${name}.tar.gz";
+    sha256 = "d8df6bb0e2a838aa227c39cfd14aa147ab32b3df6871001874e9b9da9ce1760c";
+  };
+
+  LC_ALL="en_US.UTF-8";
+
+  buildInputs = [ glibcLocales ];
+
+  checkPhase = ''
+    ${python.interpreter} -m unittest discover
+  '';
+
+  meta = {
+    description = "A portable, lightweight MessagePack serializer and deserializer written in pure Python";
+    homepage = https://github.com/vsergeev/u-msgpack-python;
+    license = lib.licenses.mit;
+  };
+
+}

pkgs/development/python-modules/webencodings/default.nix

@@ -0,0 +1,29 @@
+{ buildPythonPackage
+, lib
+, fetchurl
+, pytest
+}:
+
+let
+  pname = "webencodings";
+  version = "0.5";
+in buildPythonPackage rec {
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${name}.tar.gz";
+    sha256 = "a5c55ee93b24e740fe951c37b5c228dccc1f171450e188555a775261cce1b904";
+  };
+
+  buildInputs = [ pytest ];
+
+  checkPhase = ''
+    py.test webencodings/tests.py
+  '';
+
+  meta = {
+    description = "Character encoding aliases for legacy web content";
+    homepage = https://github.com/SimonSapin/python-webencodings;
+    license = lib.licenses.bsd3;
+  };
+}

pkgs/development/python-modules/xlwt/default.nix

@@ -0,0 +1,36 @@
+{ buildPythonPackage
+, fetchurl
+, fetchpatch
+, nose
+, lib
+}:
+
+buildPythonPackage rec {
+  pname = "xlwt";
+  name = "${pname}-${version}";
+  version = "1.1.2";
+
+  src = fetchurl {
+    url = "mirror://pypi/${builtins.substring 0 1 pname}/${pname}/${name}.tar.gz";
+    sha256 = "aed648c17731f40f84550dd2a1aaa53569f0cbcaf5610ba895cd2632587b723c";
+  };
+
+  # re.LOCALE was removed in Python 3.6
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/python-excel/xlwt/commit/86564ef26341020316cd8a27c704ef1dc5a6129b.patch";
+      sha256 = "0ifavfld3rrqjb0iyriy4c0drw31gszvlg3nmnn9dmfsh91vxhs6";
+    })
+  ];
+
+  buildInputs = [ nose ];
+  checkPhase = ''
+    nosetests -v
+  '';
+
+  meta = {
+    description = "Library to create spreadsheet files compatible with MS";
+    homepage = https://github.com/python-excel/xlwt;
+    license = with lib.licenses; [ bsdOriginal bsd3 lgpl21 ];
+  };
+}

pkgs/development/tools/build-managers/shards/default.nix

@@ -0,0 +1,28 @@
+{ stdenv, fetchurl, crystal, libyaml, which }:
+
+stdenv.mkDerivation rec {
+  name = "shards-${version}";
+  version = "0.7.1";
+
+  src = fetchurl {
+    url = "https://github.com/crystal-lang/shards/archive/v${version}.tar.gz";
+    sha256 = "31de819c66518479682ec781a39ef42c157a1a8e6e865544194534e2567cb110";
+  };
+
+  buildInputs = [ crystal libyaml which ];
+
+  buildFlags = [ "CRFLAGS=" "release" ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp bin/shards $out/bin/
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://crystal-lang.org/";
+    license = licenses.asl20;
+    description = "Dependency manager for the Crystal language";
+    maintainers = with maintainers; [ mingchuan ];
+    platforms = [ "x86_64-linux" "i686-linux" "x86_64-darwin" ];
+  };
+}

pkgs/development/tools/continuous-integration/gitlab-runner/default.nix

@@ -1,16 +1,16 @@
 { lib, buildGoPackage, fetchFromGitLab, fetchurl, go-bindata }:
 
 let
-  version = "1.8.0";
+  version = "1.9.0";
   # Gitlab runner embeds some docker images these are prebuilt for arm and x86_64
   docker_x86_64 = fetchurl {
     url = "https://gitlab-ci-multi-runner-downloads.s3.amazonaws.com/v${version}/docker/prebuilt-x86_64.tar.xz";
-    sha256 = "0fa8hfdxg903n1dqrqbm4069sr8rq6zx7zzybfyj7qz4mmayp24m";
+    sha256 = "12hcpvc0j6g200qhz12gfsslngbqx4sifrikr05vh2av17hba25s";
   };
 
   docker_arm = fetchurl {
     url = "https://gitlab-ci-multi-runner-downloads.s3.amazonaws.com/v${version}/docker/prebuilt-arm.tar.xz";
-    sha256 = "1rvvz34rsjxrgg59rda6v4k8zw16slwprnh4h5b16yhyp7lcx93q";
+    sha256 = "1hqwhg94g514g0ad4h0h7wh7k5clm9i7whzr6c30i8yb00ga628s";
   };
 in
 buildGoPackage rec {
@@ -29,7 +29,7 @@ buildGoPackage rec {
     owner = "gitlab-org";
     repo = "gitlab-ci-multi-runner";
     rev = "v${version}";
-    sha256 = "0svmy2dc4h6jll80y8j2ml7k0a9krknsp9d0zpsfkw3wcz1wfipl";
+    sha256 = "1b30daxnpn1psy3vds1m4mnbl2hmvr2bc0zrd3nn9xm3xacm3dqj";
   };
 
   buildInputs = [ go-bindata ];
@@ -57,7 +57,7 @@ buildGoPackage rec {
   '';
 
   meta = with lib; {
-    description = "GitLab Runner the continous integration executor of GitLab";
+    description = "GitLab Runner the continuous integration executor of GitLab";
     license = licenses.mit;
     homepage = "https://about.gitlab.com/gitlab-ci/";
     platforms = platforms.unix;

pkgs/development/tools/pypi2nix/default.nix

@@ -1,13 +1,13 @@
-{ stdenv, fetchurl, python, zip, makeWrapper
+{ stdenv, fetchurl, python, zip, makeWrapper, nix, nix-prefetch-scripts
 }:
 
 let
 
-  version = "1.5.0";
+  version = "1.6.0";
 
   src = fetchurl {
     url = "https://github.com/garbas/pypi2nix/archive/v${version}.tar.gz";
-    sha256 = "0s79pp7gkgyk7discnv94m6z81fd67p66rdbd4cwk1ma0qljlh2k";
+    sha256 = "08iad1ad2gnvsnd66ddw3lff19ms2yly4iq63c8800j603d0pdhn";
   };
 
   click = fetchurl {
@@ -16,8 +16,8 @@ let
   };
 
   requests = fetchurl {
-    url = "https://pypi.python.org/packages/2e/ad/e627446492cc374c284e82381215dcd9a0a87c4f6e90e9789afefe6da0ad/requests-2.11.1.tar.gz";
+    url = "https://pypi.python.org/packages/5b/0b/34be574b1ec997247796e5d516f3a6b6509c4e064f2885a96ed885ce7579/requests-2.12.4.tar.gz";
-    sha256 = "0cx1w7m4cpslxz9jljxv0l9892ygrrckkiwpp2hangr8b01rikss";
+    sha256 = "0d5fwxmw4ibynk3imph3n4n84m0n3ib1vj339fxhkqri0qd4767d";
   };
 
 in stdenv.mkDerivation rec {
@@ -27,7 +27,7 @@ in stdenv.mkDerivation rec {
     click
     requests
   ];
-  buildInputs = [ python zip makeWrapper ];
+  buildInputs = [ python zip makeWrapper nix.out nix-prefetch-scripts ];
   sourceRoot = ".";
 
   postUnpack = ''
@@ -45,6 +45,11 @@ in stdenv.mkDerivation rec {
     fi
   '';
 
+  patchPhase = ''
+    sed -i -e "s|default='nix-shell',|default='${nix.out}/bin/nix-shell',|" $out/pkgs/pypi2nix/cli.py
+    sed -i -e "s|nix-prefetch-git|${nix-prefetch-scripts}/bin/nix-prefetch-git|" $out/pkgs/pypi2nix/stage2.py
+  '';
+
   commonPhase = ''
     mkdir -p $out/bin
 

pkgs/games/flightgear/default.nix

@@ -1,22 +1,36 @@
-{ stdenv, fetchurl
+{ stdenv, fetchurl, makeWrapper
 , freeglut, freealut, mesa, libICE, libjpeg, openal, openscenegraph, plib
 , libSM, libunwind, libX11, xproto, libXext, xextproto, libXi, inputproto
 , libXmu, libXt, simgear, zlib, boost, cmake, libpng, udev, fltk13, apr
 , makeDesktopItem, qtbase
 }:
 
+let
+  version = "2016.4.3";
+  shortVersion = "2016.4";
+  data = stdenv.mkDerivation rec {
+    name = "flightgear-base-${version}";
+
+    src = fetchurl {
+      url = "mirror://sourceforge/flightgear/release-${shortVersion}/FlightGear-${version}-data.tar.bz2";
+      sha256 = "1wy4fg6r79a635rrjy2a2a6jkz2p5zzahxs0hz7scgxg4ikb5xp4";
+    };
+
+    phases = [ "installPhase" ];
+
+    installPhase = ''
+      mkdir -p "$out/share/FlightGear"
+      tar xf "${src}" -C "$out/share/FlightGear/" --strip-components=1
+    '';
+  };
+in
 stdenv.mkDerivation rec {
-  version = "3.4.0";
   name = "flightgear-${version}";
+  inherit version;
 
   src = fetchurl {
-    url = "http://ftp.igh.cnrs.fr/pub/flightgear/ftp/Source/${name}.tar.bz2";
+    url = "mirror://sourceforge/flightgear/release-${shortVersion}/${name}.tar.bz2";
-    sha256 = "102pg7mahgxzypvyp76x363qy3a4gxavr4hj16gsha07nl2msr5m";
+    sha256 = "08i8dlia3aral2wwf72n5q5ji4vxj51bnn24g6prqjjy4qww9a9m";
-  };
-
-  datasrc = fetchurl {
-    url = "http://ftp.igh.cnrs.fr/pub/flightgear/ftp/Shared/FlightGear-data-${version}.tar.bz2";
-    sha256 = "12qjvycizg693g5jj5qyp1jiwwywg6p9fg6j3zjxhx6r4g1sgvwc";
   };
 
   # Of all the files in the source and data archives, there doesn't seem to be
@@ -37,21 +51,22 @@ stdenv.mkDerivation rec {
   };
 
   buildInputs = [
+    makeWrapper
     freeglut freealut mesa libICE libjpeg openal openscenegraph plib
     libSM libunwind libX11 xproto libXext xextproto libXi inputproto
     libXmu libXt simgear zlib boost cmake libpng udev fltk13 apr qtbase
   ];
 
-  preConfigure = ''
-    export cmakeFlagsArray=(-DFG_DATA_DIR="$out/share/FlightGear/")
-  '';
-
   postInstall = ''
     mkdir -p "$out/share/applications/"
-    cp "${desktopItem}"/share/applications/* "$out/share/applications/"
+    cp "${desktopItem}"/share/applications/* "$out/share/applications/" #*/
+
+    for f in $out/bin/* #*/
+    do
+      wrapProgram $f --set FG_ROOT "${data}/share/FlightGear"
+    done
+
 
-    mkdir -p "$out/share/FlightGear"
-    tar xvf "${datasrc}" -C "$out/share/FlightGear/" --strip-components=1
   '';
 
   meta = with stdenv.lib; {

pkgs/games/gnuchess/default.nix

@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
     inherit (s) version;
     description = "GNU Chess engine";
     maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = stdenv.lib.platforms.unix;
     license = stdenv.lib.licenses.gpl3Plus;
   };
 }

pkgs/games/xboard/default.nix

@@ -28,7 +28,7 @@ stdenv.mkDerivation {
     inherit (s) version;
     description = ''GUI for chess engines'';
     maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = stdenv.lib.platforms.unix;
     license = stdenv.lib.licenses.gpl3Plus;
   };
 }

pkgs/misc/emulators/wine/sources.nix

@@ -30,9 +30,9 @@ in rec {
   };
 
   unstable = fetchurl rec {
-    version = "1.9.23";
+    version = "2.0-rc2";
-    url = "https://dl.winehq.org/wine/source/1.9/wine-${version}.tar.bz2";
+    url = "https://dl.winehq.org/wine/source/2.0/wine-${version}.tar.bz2";
-    sha256 = "131nqkwlss24r8la84s3v1qx376wq0016d2i2767bpxkyqkagvz3";
+    sha256 = "0pjkrvslfksx7m2w52pnd3dfxb82l082cz9dr57x58s9al2jpwb6";
     inherit (stable) mono;
     gecko32 = fetchurl rec {
       version = "2.47";
@@ -48,7 +48,7 @@ in rec {
 
   staging = fetchFromGitHub rec {
     inherit (unstable) version;
-    sha256 = "188svpmaba2x5a7g8rk68cl2mqrv1vhf1si2g5j5lps9r6pgq1c0";
+    sha256 = "1xx9bfirij12l278f5f7vpxxay1zacnrsaib6yfzrybm517ynfw3";
     owner = "wine-compholio";
     repo = "wine-staging";
     rev = "v${version}";

pkgs/os-specific/linux/alsa-lib/default.nix

@@ -27,12 +27,6 @@ stdenv.mkDerivation rec {
 
   outputs = [ "out" "dev" ];
 
-  crossAttrs = {
-    patchPhase = ''
-      sed -i s/extern/static/g include/iatomic.h
-    '';
-  };
-
   meta = with stdenv.lib; {
     homepage = http://www.alsa-project.org/;
     description = "ALSA, the Advanced Linux Sound Architecture libraries";

pkgs/os-specific/linux/nvidia-x11/default.nix

@@ -12,7 +12,7 @@ assert (!libsOnly) -> kernel != null;
 
 let
 
-  versionNumber = "375.20";
+  versionNumber = "375.26";
 
   # Policy: use the highest stable version as the default (on our master).
   inherit (stdenv.lib) makeLibraryPath;
@@ -30,12 +30,12 @@ stdenv.mkDerivation {
     if stdenv.system == "i686-linux" then
       fetchurl {
         url = "http://download.nvidia.com/XFree86/Linux-x86/${versionNumber}/NVIDIA-Linux-x86-${versionNumber}.run";
-        sha256 = "0da3mgfmkhs576wfkdmk8pbmvsksalkwz8a75vnhk0385fnd6yfc";
+        sha256 = "0yv19rkz2wzzj0fygfjb1mh21iy769kff3yg2kzk8bsiwnmcyybw";
       }
     else if stdenv.system == "x86_64-linux" then
       fetchurl {
         url = "http://download.nvidia.com/XFree86/Linux-x86_64/${versionNumber}/NVIDIA-Linux-x86_64-${versionNumber}.run";
-        sha256 = "02v20xns8w4flpllibc684g5yghi5dy28avsarccjyn5knhl03ni";
+        sha256 = "1kqy9ayja3g5znj2hzx8pklz8qi0b0l9da7c3ldg3hlxf31v4hjg";
       }
     else throw "nvidia-x11 does not support platform ${stdenv.system}";
 

pkgs/os-specific/linux/thin-provisioning-tools/default.nix

@@ -1,30 +0,0 @@
-{ stdenv, fetchFromGitHub, autoconf, pkgconfig, utillinux, coreutils, expat, libaio, boost}:
-
-let
-  version = "0.6.1";
-in
-
-stdenv.mkDerivation {
-  name = "thin-provisioning-tools-${version}";
-
-  src = fetchFromGitHub {
-    owner = "jthornber";
-    repo = "thin-provisioning-tools";
-    rev = "e46bdfd4cc6cdb13852de8aba4e3019425ab0a89";
-    sha256 = "061rw33nw16g71ij05axl713wimawx54h2ggpqxvzy7iyi6lhdcm";
-  };
-
-  nativeBuildInputs = [ autoconf pkgconfig expat libaio boost ];
-
-  preConfigure =
-    ''
-      autoconf
-    '';
-
-  meta = {
-    homepage = https://github.com/jthornber/thin-provisioning-tools;
-    descriptions = "Tools for manipulating the metadata of the device-mapper targets (dm-thin-pool, dm-cache, dm-era)";
-    platforms = stdenv.lib.platforms.linux;
-    inherit version;
-  };
-}

pkgs/os-specific/linux/wireguard/default.nix

@@ -6,11 +6,11 @@ assert kernel != null -> stdenv.lib.versionAtLeast kernel.version "4.1";
 let
   name = "wireguard-${version}";
 
-  version = "0.0.20161218";
+  version = "0.0.20161223";
 
   src = fetchurl {
     url    = "https://git.zx2c4.com/WireGuard/snapshot/WireGuard-${version}.tar.xz";
-    sha256 = "d805035d3e99768e69d8cdeb8fb5250a59b994ce127fceb71a078582c30f5597";
+    sha256 = "0wmrsap34nd1x4gvz80isgsjjxbplvkrxnw56qlaqxkycvv8zndv";
   };
 
   meta = with stdenv.lib; {

pkgs/os-specific/linux/xf86-input-wacom/default.nix

@@ -3,11 +3,11 @@
 , ncurses, pkgconfig, randrproto, xorgserver, xproto, udev, libXinerama, pixman }:
 
 stdenv.mkDerivation rec {
-  name = "xf86-input-wacom-0.32.0";
+  name = "xf86-input-wacom-0.34.0";
 
   src = fetchurl {
     url = "mirror://sourceforge/linuxwacom/${name}.tar.bz2";
-    sha256 = "03c73vi5rrcr92442k82f4kbabp21yqcrqi6ak2afl41zjdar5wc";
+    sha256 = "0idhkigl0pnyp08sqm6bqfb4h20v6rjrb71z1gdv59gk7d7qwpgi";
   };
 
   buildInputs = [ inputproto libX11 libXext libXi libXrandr libXrender

pkgs/servers/bird/default.nix

@@ -2,11 +2,11 @@
 , enableIPv6 ? false }:
 
 stdenv.mkDerivation rec {
-  name = "bird-1.6.2";
+  name = "bird-1.6.3";
 
   src = fetchurl {
     url = "ftp://bird.network.cz/pub/bird/${name}.tar.gz";
-    sha256 = "1xlq78mgfyh9yvg9zld9mx75bxg9ajbn4cjjchnf0msh0ibzhlw8";
+    sha256 = "0z3yrxqb0p7f8b7r2gk4mvrwfzk45zx7yr9aifbvba1vgksiri9r";
   };
 
   buildInputs = [ flex bison readline ];

pkgs/servers/http/apache-modules/mod_perl/default.nix

@@ -0,0 +1,25 @@
+{ stdenv, fetchurl, apacheHttpd, perl }:
+
+stdenv.mkDerivation rec {
+  name = "mod_perl-2.0.10";
+
+  src = fetchurl {
+    url = "mirror://apache/perl/${name}.tar.gz";
+    sha256 = "0r1bhzwl5gr0202r6448943hjxsickzn55kdmb7dzad39vnq7kyi";
+  };
+
+  buildInputs = [ apacheHttpd perl ];
+  buildPhase = ''
+    perl Makefile.PL \
+      MP_APXS=${apacheHttpd.dev}/bin/apxs
+    make
+  '';
+  installPhase = ''
+    mkdir -p $out
+    make install DESTDIR=$out
+    mv $out${apacheHttpd}/* $out
+    mv $out${apacheHttpd.dev}/* $out
+    mv $out${perl}/* $out
+    rm $out/nix -rf
+  '';
+}

pkgs/servers/mail/exim/default.nix

@@ -1,11 +1,11 @@
 { coreutils, fetchurl, db, openssl, pcre, perl, pkgconfig, stdenv }:
 
 stdenv.mkDerivation rec {
-  name = "exim-4.87";
+  name = "exim-4.88";
 
   src = fetchurl {
-    url = "http://mirror.switch.ch/ftp/mirror/exim/exim/exim4/${name}.tar.bz2";
+    url = "http://ftp.exim.org/pub/exim/exim4/${name}.tar.bz2";
-    sha256 = "1jbxn13shq90kpn0s73qpjnx5xm8jrpwhcwwgqw5s6sdzw6iwsbl";
+    sha256 = "0bca3wb45hl7h8m8bpvsmrmqa07jhbhqyigs9pl29hhzwgbmz78i";
   };
 
   buildInputs = [ coreutils db openssl pcre perl pkgconfig ];

pkgs/servers/monitoring/grafana/default.nix

@@ -1,8 +1,8 @@
 { lib, buildGoPackage, fetchurl, fetchFromGitHub, phantomjs2 }:
 
 buildGoPackage rec {
-  version = "4.0.0";
+  version = "4.0.2";
-  ts = "1480439068";
+  ts = "1481203731";
   name = "grafana-v${version}";
   goPackagePath = "github.com/grafana/grafana";
 
@@ -10,12 +10,12 @@ buildGoPackage rec {
     rev = "v${version}";
     owner = "grafana";
     repo = "grafana";
-    sha256 = "0ps9bi4mnb3k6g2824crhyb804srk2b4d2j9k306vg0cizirn75c";
+    sha256 = "1z71nb4qmp1qavsc101k86hc4yyis3mlqb1csrymkhgl94qpiiqm";
   };
 
   srcStatic = fetchurl {
     url = "https://grafanarel.s3.amazonaws.com/builds/grafana-${version}-${ts}.linux-x64.tar.gz";
-    sha256 = "10n3vmmyr1rvq29r5cz1rwz60smavj6fahz4vaqldh1v0qyqzjlm";
+    sha256 = "1jnh2hn95r1ik0z31b4p0niq7apykppf8jcjjhsbqf8yp8i2b737";
   };
 
   preBuild = "export GOPATH=$GOPATH:$NIX_BUILD_TOP/go/src/${goPackagePath}/Godeps/_workspace";

pkgs/servers/plex/default.nix

@@ -6,9 +6,9 @@
 let
   plexPass = throw "Plex pass has been removed at upstream's request; please unset nixpkgs.config.plex.pass";
   plexpkg = if enablePlexPass then plexPass else {
-    version = "1.2.7.2987";
+    version = "1.3.3.3148";
-    vsnHash = "1bef33a";
+    vsnHash = "b38628e";
-    sha256 = "17d1yisbikcp25mgn71rf8w76zhy015f33hxjj93swfm1qrq55hq";
+    sha256 = "1dx8z27l1dwigr3ipcdzn25hnj0206255ihxh9rnh2qchrcqmb5y";
   };
 
 in stdenv.mkDerivation rec {

pkgs/servers/sonarr/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "sonarr-${version}";
-  version = "2.0.0.4409";
+  version = "2.0.0.4427";
 
   src = fetchurl {
     url = "http://download.sonarr.tv/v2/master/mono/NzbDrone.master.${version}.mono.tar.gz";
-    sha256 = "1kaj1m4ifby8liks8i7fsbgwbajaqwd96yindqp5maf2n6px2nw2";
+    sha256 = "066jhvz57hxrcgn902z25a21sj87wiqz224fjzpk1lpxrylv4ac2";
   };
 
   buildInputs = [

pkgs/tools/admin/salt/fix-libcrypto-loading.patch

@@ -2,10 +2,10 @@ diff --git a/salt/utils/rsax931.py b/salt/utils/rsax931.py
 index 9eb1f4a..d764f7a 100644
 --- a/salt/utils/rsax931.py
 +++ b/salt/utils/rsax931.py
-@@ -36,7 +36,7 @@ def _load_libcrypto():
+@@ -36,7 +36,6 @@ def _load_libcrypto():
                  'libcrypto.so*'))
              lib = lib[0] if len(lib) > 0 else None
-         if lib:
+-        if lib:
 -            return cdll.LoadLibrary(lib)
-+            return cdll.LoadLibrary('@libcrypto@')
++        return cdll.LoadLibrary('@libcrypto@')
          raise OSError('Cannot locate OpenSSL libcrypto')

pkgs/tools/backup/borg/default.nix

@@ -2,18 +2,18 @@
 
 python3Packages.buildPythonApplication rec {
   name = "borgbackup-${version}";
-  version = "1.0.8";
+  version = "1.0.9";
   namePrefix = "";
 
   src = fetchurl {
     url = "https://github.com/borgbackup/borg/releases/download/"
       + "${version}/${name}.tar.gz";
-    sha256 = "1fdfi0yzzdrrlml6780n4fh61sqm7pw6fcd1y67kfkvw8hy5c0k9";
+    sha256 = "1ciwp9yilcibk0x82y5nn8ps95jrm8rxvff8mjrlp7a2w100i1im";
   };
 
   nativeBuildInputs = with python3Packages; [
     # For building documentation:
-    sphinx
+    sphinx sphinx_rtd_theme
   ];
   propagatedBuildInputs = [
     acl lz4 openssl

pkgs/tools/misc/coreutils/default.nix

@@ -54,13 +54,13 @@ let
         ++ optional (stdenv.ccCross.libc ? libiconv)
           stdenv.ccCross.libc.libiconv.crossDrv;
 
-      buildPhase = ''
+      # Prevents attempts of running 'help2man' on cross-built binaries.
-        make || (
+      PERL = "missing";
-          pushd man
+
-          for a in *.x; do
+      # Works around a bug with 8.26:
-            touch `basename $a .x`.1
+      # Makefile:3440: *** Recursive variable 'INSTALL' references itself (eventually).  Stop.
-          done
+      preInstall = ''
-          popd; make )
+        sed -i Makefile -e 's|^INSTALL =.*|INSTALL = ${self}/bin/install -c|'
       '';
 
       postInstall = ''

pkgs/tools/misc/os-prober/default.nix

@@ -0,0 +1,77 @@
+{ stdenv, fetchurl, makeWrapper, 
+systemd, # udevadm
+busybox, 
+coreutils, # os-prober desn't seem to work with pure busybox
+devicemapper, # lvs
+# optional dependencies
+cryptsetup ? null,
+libuuid ? null, # blkid and blockdev
+dmraid ? null,
+ntfs3g ? null
+}:
+
+stdenv.mkDerivation rec {
+  version = "1.65";
+  name = "os-prober-${version}";
+  src = fetchurl {
+    url = "mirror://debian/pool/main/o/os-prober/os-prober_${version}.tar.xz";
+    sha256 = "c4a7661a52edae722f7e6bacb3f107cf7086cbe768275fadf5398d04360bfc84";
+  };
+
+  buildInputs = [ makeWrapper ];
+  installPhase = ''
+    # executables
+    mkdir -p $out/bin
+    mkdir -p $out/lib
+    mkdir -p $out/share
+    cp os-prober linux-boot-prober $out/bin
+    cp newns $out/lib
+    cp common.sh $out/share
+
+    # probes
+    case "${stdenv.system}" in
+        i686*|x86_64*) ARCH=x86;;
+        powerpc*) ARCH=powerpc;;
+        arm*) ARCH=arm;;
+        *) ARCH=other;;
+    esac;
+    for probes in os-probes os-probes/mounted os-probes/init linux-boot-probes linux-boot-probes/mounted; do
+      mkdir -p $out/lib/$probes;
+      cp $probes/common/* $out/lib/$probes;
+      if [ -e "$probes/$ARCH" ]; then
+        mkdir -p $out/lib/$probes
+        cp -r $probes/$ARCH/* $out/lib/$probes;
+      fi;
+    done
+    if [ $ARCH = "x86" ]; then
+        cp -r os-probes/mounted/powerpc/20macosx $out/lib/os-probes/mounted;
+    fi;
+  '';
+  postFixup = ''
+    for file in $(find $out  -type f ! -name newns) ; do
+      substituteInPlace $file \
+        --replace /usr/share/os-prober/ $out/share/ \
+        --replace /usr/lib/os-probes/ $out/lib/os-probes/ \
+        --replace /usr/lib/linux-boot-probes/ $out/lib/linux-boot-probes/ \
+        --replace /usr/lib/os-prober/ $out/lib/
+    done;
+    for file in $out/bin/*; do
+      wrapProgram $file \
+        --set LVM_SYSTEM_DIR ${devicemapper} \
+        --suffix PATH : "$out/bin${builtins.foldl' (x: y: x + ":" + y) "" (
+          map (x: (toString x) + "/bin") (
+            builtins.filter (x: x!=null)
+              [ devicemapper systemd coreutils cryptsetup libuuid dmraid ntfs3g busybox ]
+            )
+          )
+        }" \
+        --run "[ -d /var/lib/os-prober ] || mkdir /var/lib/os-prober"
+    done;
+  '';
+
+  meta = {
+    description = "Utility to detect other OSs on a set of drives";
+    homepage = http://packages.debian.org/source/sid/os-prober;
+    license = stdenv.lib.licenses.gpl2Plus;
+  };
+}

pkgs/tools/misc/parallel/default.nix

@@ -1,11 +1,11 @@
 { fetchurl, stdenv, perl, makeWrapper, procps }:
 
 stdenv.mkDerivation rec {
-  name = "parallel-20161122";
+  name = "parallel-20161222";
 
   src = fetchurl {
     url = "mirror://gnu/parallel/${name}.tar.bz2";
-    sha256 = "0z5c4r35d926ac04ilaivx67cmflr1rsvmjb2ci7hmab948m0ng2";
+    sha256 = "1chgr3csyc7hbq2wq4jnwnbsr3ix8rzsk2lf4vdnvkjpd6dvw517";
   };
 
   nativeBuildInputs = [ makeWrapper ];

pkgs/tools/networking/strongswan/default.nix

@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   name = "strongswan-${version}";
-  version = "5.5.0";
+  version = "5.5.1";
 
   src = fetchurl {
     url = "http://download.strongswan.org/${name}.tar.bz2";
-    sha256 = "0m449i5s51ikqh36s1sp4rvw60wqyv0j12kyd31yl9b7mjc3jijq";
+    sha256 = "1drahhmwz1jg14rfh67cl231dlg2a9pra6jmipfxwyzpj4ck02vj";
   };
 
   dontPatchELF = true;

pkgs/tools/security/gnupg/21.nix

@@ -15,11 +15,11 @@ assert guiSupport -> pinentry != null;
 stdenv.mkDerivation rec {
   name = "gnupg-${version}";
 
-  version = "2.1.16";
+  version = "2.1.17";
 
   src = fetchurl {
     url = "mirror://gnupg/gnupg/${name}.tar.bz2";
-    sha256 = "0i483m9q032a0s50f1izb213g4h5i7pcgn395m6hvl3sg2kadfa9";
+    sha256 = "1js308b46ifx1gim0c9nivr5yxhans7iq1yvkf7zl2928gdm9p65";
   };
 
   buildInputs = [

pkgs/tools/security/sudo/default.nix

@@ -4,14 +4,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "sudo-1.8.18p1";
+  name = "sudo-1.8.19p1";
 
   src = fetchurl {
     urls =
       [ "ftp://ftp.sudo.ws/pub/sudo/${name}.tar.gz"
         "ftp://ftp.sudo.ws/pub/sudo/OLD/${name}.tar.gz"
       ];
-    sha256 = "0d4l6y03khmzdd8vhfnq8lrb8gcxplzf7gav0a9sd08jf8f4g875";
+    sha256 = "14pwdwl03kdbbyjkvxrfx409x3c1fjqz8aqz2wgwddinhz7v3bxq";
   };
 
   configureFlags = [

pkgs/top-level/all-packages.nix

@@ -1476,6 +1476,10 @@ in
 
   doomseeker = callPackage ../applications/misc/doomseeker { };
 
+  slade = callPackage ../applications/misc/slade {
+    wxGTK = wxGTK30;
+  };
+
   drive = callPackage ../applications/networking/drive { };
 
   driftnet = callPackage ../tools/networking/driftnet {};
@@ -1804,16 +1808,16 @@ in
 
   gawp = callPackage ../tools/misc/gawp { };
 
-  gazeboSimulator = recurseIntoAttrs {
+  gazeboSimulator = recurseIntoAttrs rec {
     sdformat = gazeboSimulator.sdformat4;
 
     sdformat3 = callPackage ../development/libraries/sdformat/3.nix { };
 
     sdformat4 = callPackage ../development/libraries/sdformat { };
 
-    gazebo6 = callPackage ../applications/science/robotics/gazebo/6.nix { };
+    gazebo6 = callPackage ../applications/science/robotics/gazebo/6.nix { boost = boost160; };
 
-    gazebo6-headless = callPackage ../applications/science/robotics/gazebo/6.nix { withHeadless = true;  };
+    gazebo6-headless = gazebo6.override { withHeadless = true;  };
 
     gazebo7 = callPackage ../applications/science/robotics/gazebo { };
 
@@ -2253,7 +2257,7 @@ in
   ioping = callPackage ../tools/system/ioping { };
 
   iops = callPackage ../tools/system/iops { };
-  
+
   ior = callPackage ../tools/system/ior { };
 
   iodine = callPackage ../tools/networking/iodine { };
@@ -2606,7 +2610,7 @@ in
   libmbim = callPackage ../development/libraries/libmbim { };
 
   libmongo-client = callPackage ../development/libraries/libmongo-client { };
-  
+
   libmesode = callPackage ../development/libraries/libmesode { };
 
   libnabo = callPackage ../development/libraries/libnabo { };
@@ -3129,6 +3133,8 @@ in
 
   olsrd = callPackage ../tools/networking/olsrd { };
 
+  os-prober = callPackage ../tools/misc/os-prober {};
+
   ossec = callPackage ../tools/security/ossec {};
 
   ostree = callPackage ../tools/misc/ostree { };
@@ -3539,7 +3545,7 @@ in
 
   remind = callPackage ../tools/misc/remind { };
 
-  remmina = callPackage ../applications/networking/remote/remmina {};
+  remmina = callPackage ../applications/networking/remote/remmina { adwaita-icon-theme = gnome3.adwaita-icon-theme; };
 
   renameutils = callPackage ../tools/misc/renameutils { };
 
@@ -4649,6 +4655,8 @@ in
     '';
   });
 
+  crystal = callPackage ../development/compilers/crystal { };
+
   devpi-client = callPackage ../development/tools/devpi-client {};
 
   drumstick = callPackage ../development/libraries/drumstick { };
@@ -4959,7 +4967,9 @@ in
 
   hxcpp = callPackage ../development/compilers/haxe/hxcpp.nix { };
 
-  hhvm = callPackage ../development/compilers/hhvm { };
+  hhvm = callPackage ../development/compilers/hhvm {
+    boost = boost160;
+  };
 
   hop = callPackage ../development/compilers/hop { };
 
@@ -6499,6 +6509,8 @@ in
   sbt = callPackage ../development/tools/build-managers/sbt { };
   simpleBuildTool = sbt;
 
+  shards = callPackage ../development/tools/build-managers/shards { };
+
   shellcheck = self.haskellPackages.ShellCheck;
 
   shncpd = callPackage ../tools/networking/shncpd { };
@@ -6605,7 +6617,9 @@ in
 
   valkyrie = callPackage ../development/tools/analysis/valkyrie { };
 
-  inherit (ocaml-ng.ocamlPackages_4_02) verasco;
+  verasco = ocaml-ng.ocamlPackages_4_02.verasco.override {
+    coq = coq_8_4;
+  };
 
   visualvm = callPackage ../development/tools/java/visualvm { };
 
@@ -10007,6 +10021,8 @@ in
 
     mod_evasive = callPackage ../servers/http/apache-modules/mod_evasive { };
 
+    mod_perl = callPackage ../servers/http/apache-modules/mod_perl { };
+
     mod_fastcgi = callPackage ../servers/http/apache-modules/mod_fastcgi { };
 
     mod_python = callPackage ../servers/http/apache-modules/mod_python { };
@@ -11004,8 +11020,6 @@ in
   linux_3_12 = callPackage ../os-specific/linux/kernel/linux-3.12.nix {
     kernelPatches = with kernelPatches;
       [ bridge_stp_helper
-        crc_regression
-        packet_fix_race_condition_CVE_2016_8655
       ]
       ++ lib.optionals ((platform.kernelArch or null) == "mips")
       [ kernelPatches.mips_fpureg_emu
@@ -11362,8 +11376,6 @@ in
 
   lvm2 = callPackage ../os-specific/linux/lvm2 { };
 
-  thin_provisioning_tools = callPackage ../os-specific/linux/thin-provisioning-tools { };
-
   mbpfan = callPackage ../os-specific/linux/mbpfan { };
 
   mdadm = callPackage ../os-specific/linux/mdadm { };
@@ -12994,6 +13006,8 @@ in
 
   fossil = callPackage ../applications/version-management/fossil { };
 
+  freebayes = callPackage ../applications/science/biology/freebayes { };
+
   freewheeling = callPackage ../applications/audio/freewheeling { };
 
   fribid = callPackage ../applications/networking/browsers/mozilla-plugins/fribid { };
@@ -13139,13 +13153,17 @@ in
 
   flac = callPackage ../applications/audio/flac { };
 
-  flashplayer = callPackage ../applications/networking/browsers/mozilla-plugins/flashplayer-11 {
+  flashplayer = callPackage ../applications/networking/browsers/mozilla-plugins/flashplayer {
-    debug = config.flashplayer.debug or false;
+      debug = config.flashplayer.debug or false;
   };
 
-  flashplayer-standalone = pkgsi686Linux.flashplayer.sa;
+  flashplayer-standalone = callPackage ../applications/networking/browsers/mozilla-plugins/flashplayer/standalone.nix {
+      debug = config.flashplayer.debug or false;
+  };
 
-  flashplayer-standalone-debugger = (pkgsi686Linux.flashplayer.override { debug = true; }).sa;
+  flashplayer-standalone-debugger = flashplayer-standalone.override {
+      debug = true;
+  };
 
   fluxbox = callPackage ../applications/window-managers/fluxbox { };
 
@@ -16720,38 +16738,34 @@ in
 
   aspino = callPackage ../applications/science/logic/aspino {};
 
-  coq = callPackage ../applications/science/logic/coq {
-    inherit (ocamlPackages_4_01_0) ocaml findlib lablgtk;
-    camlp5 = ocamlPackages_4_01_0.camlp5_transitional;
-  };
-
-  coq_HEAD = callPackage ../applications/science/logic/coq/HEAD.nix {
-    inherit (ocamlPackages) ocaml findlib lablgtk;
-    camlp5 = ocamlPackages.camlp5_transitional;
-  };
-
-  coq_8_6 = callPackage ../applications/science/logic/coq/8.6.nix {
-    inherit (ocamlPackages) ocaml findlib lablgtk;
-    camlp5 = ocamlPackages.camlp5_transitional;
-  };
-
-  coq_8_5 = callPackage ../applications/science/logic/coq/8.5.nix {
-    inherit (ocamlPackages) ocaml findlib lablgtk;
-    camlp5 = ocamlPackages.camlp5_transitional;
-  };
-
   coq_8_3 = callPackage ../applications/science/logic/coq/8.3.nix {
     make = pkgs.gnumake3;
     inherit (ocamlPackages_3_12_1) ocaml findlib;
     camlp5 = ocamlPackages_3_12_1.camlp5_transitional;
     lablgtk = ocamlPackages_3_12_1.lablgtk_2_14;
   };
+  coq_8_4 = callPackage ../applications/science/logic/coq/8.4.nix {
+    inherit (ocamlPackages_4_01_0) ocaml findlib lablgtk;
+    camlp5 = ocamlPackages_4_01_0.camlp5_transitional;
+  };
+  coq_8_5 = callPackage ../applications/science/logic/coq/8.5.nix {
+    inherit (ocamlPackages) ocaml findlib lablgtk;
+    camlp5 = ocamlPackages.camlp5_transitional;
+  };
+  coq_8_6 = callPackage ../applications/science/logic/coq/8.6.nix {
+    inherit (ocamlPackages) ocaml findlib lablgtk;
+    camlp5 = ocamlPackages.camlp5_transitional;
+  };
+  coq_HEAD = callPackage ../applications/science/logic/coq/HEAD.nix {
+    inherit (ocamlPackages) ocaml findlib lablgtk;
+    camlp5 = ocamlPackages.camlp5_transitional;
+  };
+  coq = coq_8_4;
 
   mkCoqPackages_8_4 = self: let callPackage = newScope self; in {
-
     inherit callPackage;
-
+    coq = coq_8_4;
-    bedrock = callPackage ../development/coq-modules/bedrock {};
+    coqPackages = coqPackages_8_4;
 
     contribs =
       let contribs =
@@ -16761,86 +16775,59 @@ in
       in
         recurseIntoAttrs contribs;
 
+    bedrock = callPackage ../development/coq-modules/bedrock {};
     coqExtLib = callPackage ../development/coq-modules/coq-ext-lib {};
-
     coqeal = callPackage ../development/coq-modules/coqeal {};
-
     coquelicot = callPackage ../development/coq-modules/coquelicot {};
-
     domains = callPackage ../development/coq-modules/domains {};
-
     fiat = callPackage ../development/coq-modules/fiat {};
     fiat_HEAD = callPackage ../development/coq-modules/fiat/HEAD.nix {};
-
     flocq = callPackage ../development/coq-modules/flocq {};
-
     heq = callPackage ../development/coq-modules/heq {};
-
     interval = callPackage ../development/coq-modules/interval {};
-
     mathcomp = callPackage ../development/coq-modules/mathcomp {};
-
     paco = callPackage ../development/coq-modules/paco {};
-
     QuickChick = callPackage ../development/coq-modules/QuickChick {};
-
     ssreflect = callPackage ../development/coq-modules/ssreflect {};
-
     tlc = callPackage ../development/coq-modules/tlc {};
-
     unimath = callPackage ../development/coq-modules/unimath {};
-
     ynot = callPackage ../development/coq-modules/ynot {};
-
   };
 
   mkCoqPackages_8_5 = self: let callPackage = newScope self; in rec {
-
     inherit callPackage;
-
     coq = coq_8_5;
+    coqPackages = coqPackages_8_5;
 
     coq-ext-lib = callPackage ../development/coq-modules/coq-ext-lib {};
-
     coquelicot = callPackage ../development/coq-modules/coquelicot {};
-
     dpdgraph = callPackage ../development/coq-modules/dpdgraph {};
-
     flocq = callPackage ../development/coq-modules/flocq {};
-
     interval = callPackage ../development/coq-modules/interval {};
-
     mathcomp = callPackage ../development/coq-modules/mathcomp { };
-
     ssreflect = callPackage ../development/coq-modules/ssreflect { };
-
     fiat_HEAD = callPackage ../development/coq-modules/fiat/HEAD.nix {};
-
   };
 
   mkCoqPackages_8_6 = self: let callPackage = newScope self; in rec {
-
     inherit callPackage;
-
     coq = coq_8_6;
+    coqPackages = coqPackages_8_6;
 
     coq-ext-lib = callPackage ../development/coq-modules/coq-ext-lib {};
-
     coquelicot = callPackage ../development/coq-modules/coquelicot {};
-
     dpdgraph = callPackage ../development/coq-modules/dpdgraph {};
-
     flocq = callPackage ../development/coq-modules/flocq {};
-
     interval = callPackage ../development/coq-modules/interval {};
-
+    mathcomp = callPackage ../development/coq-modules/mathcomp { };
+    ssreflect = callPackage ../development/coq-modules/ssreflect { };
     fiat_HEAD = callPackage ../development/coq-modules/fiat/HEAD.nix {};
-
   };
 
-  coqPackages = mkCoqPackages_8_4 coqPackages;
+  coqPackages_8_4 = mkCoqPackages_8_4 coqPackages_8_4;
   coqPackages_8_5 = mkCoqPackages_8_5 coqPackages_8_5;
   coqPackages_8_6 = mkCoqPackages_8_6 coqPackages_8_6;
+  coqPackages = coqPackages_8_4;
 
   cryptoverif = callPackage ../applications/science/logic/cryptoverif { };
 
@@ -16965,6 +16952,7 @@ in
 
   kicad = callPackage ../applications/science/electronics/kicad {
     wxGTK = wxGTK30;
+    boost = boost160;
   };
 
   ngspice = callPackage ../applications/science/electronics/ngspice { };

pkgs/top-level/python-packages.nix

@@ -2229,6 +2229,9 @@ in {
       url = "mirror://pypi/b/buttersink/${name}.tar.gz";
     };
 
+    # Python 2 syntax
+    disabled = isPy3k;
+
     meta = {
       description = "Synchronise btrfs snapshots";
       longDescription = ''
@@ -5247,6 +5250,8 @@ in {
     };
   });
 
+  pytest-expect = callPackage ../development/python-modules/pytest-expect { };
+
   pytest-virtualenv = buildPythonPackage rec {
     name = "${pname}-${version}";
     pname = "pytest-virtualenv";
@@ -5452,6 +5457,8 @@ in {
       url = "mirror://pypi/d/datrie/datrie-${version}.tar.gz";
       sha256 = "08r0if7dry2q7p34gf7ffyrlnf4bdvnprxgydlfxgfnvq8f3f4bs";
     };
+
+    buildInputs = with self; [ pytest pytestrunner hypothesis ];
     meta = {
       description = "Super-fast, efficiently stored Trie for Python";
       homepage = "https://github.com/kmike/datrie";
@@ -12504,20 +12511,22 @@ in {
 
 
   html5lib = buildPythonPackage (rec {
-    version = "0.999";
+    version = "0.999999999";
     name = "html5lib-${version}";
 
     src = pkgs.fetchurl {
       url = "http://github.com/html5lib/html5lib-python/archive/${version}.tar.gz";
-      sha256 = "1kxl36p0csssaf37zbbc9p4h8l1s7yb1qnfv3d4nixplvrxqkybp";
+      sha256 = "09j6194f5mlnd5xwbavwvnndwl1x91jw74shxl6hcxjp4fxg3h05";
     };
 
-    buildInputs = with self; [ nose flake8 ];
+    buildInputs = with self; [ flake8 pytest pytest-expect mock ];
     propagatedBuildInputs = with self; [
-      six
+      six webencodings
     ] ++ optionals isPy26 [ ordereddict ];
 
-    checkPhase = "nosetests";
+    checkPhase = ''
+      py.test
+    '';
 
     meta = {
       homepage = https://github.com/html5lib/html5lib-python;
@@ -14055,6 +14064,7 @@ in {
     meta = {
       description = "A Python wrapper around libmagic";
       homepage = http://www.darwinsys.com/file/;
+      broken = true;
     };
   };
 
@@ -14140,12 +14150,12 @@ in {
   };
 
   markdown = buildPythonPackage rec {
-    version = "2.6.4";
+    version = "2.6.7";
     name = "markdown-${version}";
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/M/Markdown/Markdown-${version}.tar.gz";
-      sha256 = "1kll5b35wqkhvniwm2kh6rqc43wakv9ls0qm6g5318pjmbkywdp4";
+      sha256 = "1h055llfd0ps0ig7qb3v1j9068xv90dc9s7xkhkgz9zg8r4g5sys";
     };
 
     # error: invalid command 'test'
@@ -15074,18 +15084,20 @@ in {
   };
 
   mwclient = buildPythonPackage rec {
-    version = "0.8.1";
+    version = "0.8.3";
-    basename = "mwclient";
+    pname = "mwclient";
-    name = "${basename}-${version}";
+    name = "${pname}-${version}";
 
-    src = pkgs.fetchurl {
+    src = pkgs.fetchFromGitHub {
-      url = "mirror://pypi/m/${basename}/${name}.tar.gz";
+      owner = "mwclient";
-      sha256 = "1r322v6i6xps9xh861rbr4ggshydcgp8cycbdlmgy8qbrh8jg2az";
+      repo = "mwclient";
+      rev = "v${version}";
+      sha256 = "0kl1yp9z5f1wl6lkm0vix87zkrbl9wcmkrrj1x5c35xvf95laf53";
     };
 
     buildInputs = with self; [ mock responses pytestcov pytest pytestcache pytestpep8 coverage ];
 
-    propagatedBuildInputs = with self; [ six requests2 ];
+    propagatedBuildInputs = with self; [ six requests2 requests_oauthlib ];
 
     checkPhase = ''
       py.test
@@ -15095,6 +15107,7 @@ in {
       description = "Python client library to the MediaWiki API";
       maintainers = with maintainers; [ DamienCassou ];
       license = licenses.mit;
+      homepage = https://github.com/mwclient/mwclient;
     };
   };
 
@@ -17879,77 +17892,7 @@ in {
     };
   };
 
-  pandas = let
+  pandas = callPackage ../development/python-modules/pandas { };
-    inherit (pkgs.stdenv.lib) optional optionalString;
-    inherit (pkgs.stdenv) isDarwin;
-  in buildPythonPackage rec {
-    name = "pandas-${version}";
-    version = "0.19.1";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/p/pandas/${name}.tar.gz";
-      sha256 = "2509feaeda72fce03675e2eccd2284bb1cadb6a0737008a5e741fe2431d47421";
-    };
-
-    LC_ALL = "en_US.UTF-8";
-    buildInputs = with self; [ nose pkgs.glibcLocales ] ++ optional isDarwin pkgs.libcxx;
-    propagatedBuildInputs = with self; [
-      cython
-      dateutil
-      scipy
-      numexpr
-      pytz
-      xlrd
-      bottleneck
-      sqlalchemy
-      lxml
-      html5lib
-      beautifulsoup4
-      openpyxl
-      tables
-      xlwt
-    ] ++ optional isDarwin pkgs.darwin.locale; # provides the locale command
-
-    # For OSX, we need to add a dependency on libcxx, which provides
-    # `complex.h` and other libraries that pandas depends on to build.
-    patchPhase = optionalString isDarwin ''
-      cpp_sdk="${pkgs.libcxx}/include/c++/v1";
-      echo "Adding $cpp_sdk to the setup.py common_include variable"
-      substituteInPlace setup.py \
-        --replace "['pandas/src/klib', 'pandas/src']" \
-                  "['pandas/src/klib', 'pandas/src', '$cpp_sdk']"
-
-      # disable clipboard tests since pbcopy/pbpaste are not open source
-      substituteInPlace pandas/io/tests/test_clipboard.py \
-        --replace pandas.util.clipboard no_such_module \
-        --replace OSError ImportError
-    '';
-
-    # The flag `-A 'not network'` will disable tests that use internet.
-    # The `-e` flag disables a few problematic tests.
-
-    # Disable two tests that are broken since numpy 1.11. Fixed upstream.
-
-    checkPhase = let
-      testsToSkip = [ "test_range_slice_day" "test_range_slice_seconds" ];
-    in ''
-      runHook preCheck
-      # The flag `-A 'not network'` will disable tests that use internet.
-      # The `-e` flag disables a few problematic tests.
-      ${python.executable} setup.py nosetests -A 'not slow and not network' --stop \
-        -e '${concatStringsSep "|" testsToSkip}' --verbosity=3
-
-      runHook postCheck
-    '';
-
-    meta = {
-      homepage = "http://pandas.pydata.org/";
-      description = "Python Data Analysis Library";
-      license = licenses.bsd3;
-      maintainers = with maintainers; [ raskin fridh ];
-      platforms = platforms.unix;
-    };
-  };
 
   xlrd = buildPythonPackage rec {
     name = "xlrd-${version}";
@@ -25933,6 +25876,8 @@ in {
     };
   };
 
+  u-msgpack-python = callPackage ../development/python-modules/u-msgpack-python { };
+
   umalqurra = buildPythonPackage rec {
     name = "umalqurra-${version}";
     version = "0.2";
@@ -26487,6 +26432,8 @@ EOF
     };
   };
 
+  webencodings = callPackage ../development/python-modules/webencodings { };
+
   websockets = callPackage ../development/python-modules/websockets { };
 
   wand = buildPythonPackage rec {
@@ -26862,26 +26809,7 @@ EOF
     };
   };
 
-  xlwt = buildPythonPackage rec {
+  xlwt = callPackage ../development/python-modules/xlwt { };
-    name = "xlwt-${version}";
-    version = "1.0.0";
-
-    src = pkgs.fetchurl {
-      url = "mirror://pypi/x/xlwt/${name}.tar.gz";
-      sha256 = "1y8w5imsicp01gn749qhw6j0grh9y19zz57ribwaknn8xqwjjhxc";
-    };
-
-    buildInputs = with self; [ nose ];
-    checkPhase = ''
-      nosetests -v
-    '';
-
-    meta = {
-      description = "Library to create spreadsheet files compatible with MS";
-      homepage = https://github.com/python-excel/xlwt;
-      license = with licenses; [ bsdOriginal bsd3 lgpl21 ];
-    };
-  };
 
   youtube-dl = callPackage ../tools/misc/youtube-dl {};
 
@@ -30214,6 +30142,9 @@ EOF
     propagatedBuildInputs = with self; [ scipy ];
     buildInputs = with self; [ nose ];
 
+    # Cannot be installed with Python 2.x, most likely due to the patch below.
+    disabled = !isPy3k;
+
     postPatch = ''
       cd python-package
 
@@ -31456,7 +31387,7 @@ EOF
   txaio = buildPythonPackage rec {
     name = "${pname}-${version}";
     pname = "txaio";
-    version = "2.5.1";
+    version = "2.5.2";
 
     meta = {
       description = "Utilities to support code that runs unmodified on Twisted and asyncio.";
@@ -31475,7 +31406,7 @@ EOF
 
     src = pkgs.fetchurl {
       url = "mirror://pypi/t/${pname}/${name}.tar.gz";
-      sha256 = "1pni1m66mlmbybmaf3py4h7cpkmkssqb5l3rigkxvql2f53pcl32";
+      sha256 = "321d441b336447b72dbe81a4d73470414454baf0543ec701fcfecbf4dcbda0fe";
     };
   };
 
@@ -31758,6 +31689,10 @@ EOF
       ${python.interpreter} -m unittest test_zipfile.py
     '';
 
+    # Only works with Python 3.x.
+    # Not supposed to be used with 3.6 and up.
+    disabled = !(isPy3k && (pythonOlder "3.6"));
+
     meta = {
       description = "Read and write ZIP files - backport of the zipfile module from Python 3.6";
       homepage = https://gitlab.com/takluyver/zipfile36;