Merge branch 'master.upstream' into staging.upstream

lib/maintainers.nix

@@ -1,11 +1,15 @@
 /* -*- coding: utf-8; -*- */
 
 {
-  /* Add your name and email address here.  Keep the list
+  /* Add your name and email address here.
-     alphabetically sorted.  */
+     Keep the list alphabetically sorted.
+     Prefer the same attrname as your github username, please,
+     so it's easy to ping a package @maintainer.
+  */
 
   abaldeau = "Andreas Baldeau <andreas@baldeau.net>";
   abbradar = "Nikolay Amiantov <ab@fmap.me>";
+  adev	   = "Adrien Devresse <adev@adev.name>";
   aforemny = "Alexander Foremny <alexanderforemny@googlemail.com>";
   aflatter = "Alexander Flatter <flatter@fastmail.fm>";
   aherrmann = "Andreas Herrmann <andreash87@gmx.ch>";

maintainers/scripts/gnome-latest.sh

@@ -1,4 +1,4 @@
-#!/bin/sh
+#!/usr/bin/env bash
 
 GNOME_FTP="ftp.gnome.org/pub/GNOME/sources"
 

nixos/doc/manual/release-notes/rl-unstable.xml

@@ -153,6 +153,19 @@ nix-env -f "<nixpkgs>" -iA haskellPackages.cabal-install
   </para>
 </listitem>
 
+<listitem>
+  <para>
+    The OpenBLAS library has been updated to version
+    <literal>0.2.14</literal>. Support for the
+    <literal>x86_64-darwin</literal> platform was added. Dynamic
+    architecture detection was enabled; OpenBLAS now selects
+    microarchitecture-optimized routines at runtime, so optimal
+    performance is achieved without the need to rebuild OpenBLAS
+    locally. OpenBLAS has replaced ATLAS in most packages which use an
+    optimized BLAS or LAPACK implementation.
+ </para>
+</listitem>
+
 </itemizedlist>
 </para>
 

nixos/lib/test-driver/Machine.pm

@@ -43,8 +43,6 @@ sub new {
         $startCommand .= "-bios $args->{bios} "
             if defined $args->{bios};
         $startCommand .= $args->{qemuFlags} || "";
-    } else {
-        $startCommand = Cwd::abs_path $startCommand;
     }
 
     my $tmpDir = $ENV{'TMPDIR'} || "/tmp";

nixos/maintainers/scripts/ec2/amazon-base-config.nix

@@ -1,5 +1,5 @@
 { modulesPath, ...}:
 {
-  imports = [ "${modulesPath}/virtualisation/amazon-config.nix" ];
+  imports = [ "${modulesPath}/virtualisation/amazon-init.nix" ];
   services.journald.rateLimitBurst = 0;
 }

nixos/modules/config/pulseaudio.nix

@@ -81,7 +81,10 @@ in {
       support32Bit = mkOption {
         type = types.bool;
         default = false;
-        description = "no";
+        description = ''
+          Whether to include the 32-bit pulseaudio libraries in the systemn or not.
+          This is only useful on 64-bit systems and currently limited to x86_64-linux.
+        '';
       };
 
       configFile = mkOption {

nixos/modules/services/misc/apache-kafka.nix

@@ -116,11 +116,19 @@ in {
       ];
     };
 
+    package = mkOption {
+      description = "The kafka package to use";
+
+      default = pkgs.apacheKafka;
+
+      type = types.package;
+    };
+
   };
 
   config = mkIf cfg.enable {
 
-    environment.systemPackages = [pkgs.apacheKafka];
+    environment.systemPackages = [cfg.package];
 
     users.extraUsers = singleton {
       name = "apache-kafka";
@@ -136,7 +144,7 @@ in {
       serviceConfig = {
         ExecStart = ''
           ${pkgs.jre}/bin/java \
-            -cp "${pkgs.apacheKafka}/libs/*:${configDir}" \
+            -cp "${cfg.package}/libs/*:${configDir}" \
             ${toString cfg.jvmOptions} \
             kafka.Kafka \
             ${configDir}/server.properties

nixos/modules/services/misc/disnix.nix

@@ -67,7 +67,7 @@ in
   ###### implementation
 
   config = mkIf cfg.enable {
-    environment.systemPackages = [ pkgs.disnix ] ++ optional cfg.useWebServiceInterface pkgs.DisnixWebService;
+    environment.systemPackages = [ pkgs.disnix pkgs.dysnomia ] ++ optional cfg.useWebServiceInterface pkgs.DisnixWebService;
 
     services.dbus.enable = true;
     services.dbus.packages = [ pkgs.disnix ];

nixos/modules/services/misc/nix-daemon.nix

@@ -63,7 +63,7 @@ in
 
       package = mkOption {
         type = types.package;
-        default = pkgs.nixUnstable;
+        default = pkgs.nix;
         description = ''
           This option specifies the Nix package instance to use throughout the system.
         '';

nixos/modules/services/monitoring/scollector.nix

@@ -73,7 +73,7 @@ in {
       };
 
       collectors = mkOption {
-        type = types.attrs;
+        type = with types; attrsOf (listOf path);
         default = {};
         example = literalExample "{ 0 = [ \"\${postgresStats}/bin/collect-stats\" ]; }";
         description = ''

nixos/modules/services/x11/xserver.nix

@@ -469,6 +469,11 @@ in
     environment.pathsToLink =
       [ "/etc/xdg" "/share/xdg" "/share/applications" "/share/icons" "/share/pixmaps" ];
 
+    # The default max inotify watches is 8192.
+    # Nowadays most apps require a good number of inotify watches,
+    # the value below is used by default on several other distros.
+    boot.kernel.sysctl."fs.inotify.max_user_watches" = mkDefault 524288;
+
     systemd.defaultUnit = mkIf cfg.autorun "graphical.target";
 
     systemd.services.display-manager =

nixos/modules/system/boot/loader/grub/grub.nix

@@ -27,7 +27,12 @@ let
 
   f = x: if x == null then "" else "" + x;
 
-  grubConfig = args: pkgs.writeText "grub-config.xml" (builtins.toXML
+  grubConfig = args:
+    let
+      efiSysMountPoint = if args.efiSysMountPoint == null then args.path else args.efiSysMountPoint;
+      efiSysMountPoint' = replaceChars [ "/" ] [ "-" ] efiSysMountPoint;
+    in
+    pkgs.writeText "grub-config.xml" (builtins.toXML
     { splashImage = f cfg.splashImage;
       grub = f grub;
       grubTarget = f (grub.grubTarget or "");
@@ -36,7 +41,8 @@ let
       grubEfi = f grubEfi;
       grubTargetEfi = if cfg.efiSupport && (cfg.version == 2) then f (grubEfi.grubTarget or "") else "";
       bootPath = args.path;
-      efiSysMountPoint = if args.efiSysMountPoint == null then args.path else args.efiSysMountPoint;
+      bootloaderId = if args.efiBootloaderId == null then "NixOS${efiSysMountPoint'}" else args.efiBootloaderId;
+      inherit efiSysMountPoint;
       inherit (args) devices;
       inherit (efi) canTouchEfiVariables;
       inherit (cfg)
@@ -141,6 +147,17 @@ in
             '';
           };
 
+          efiBootloaderId = mkOption {
+            default = null;
+            example = "NixOS-fsid";
+            type = types.nullOr types.str;
+            description = ''
+              The id of the bootloader to store in efi nvram.
+              The default is to name it NixOS and append the path or efiSysMountPoint.
+              This is only used if <literal>boot.loader.efi.canTouchEfiVariables</literal> is true.
+            '';
+          };
+
           devices = mkOption {
             default = [ ];
             example = [ "/dev/sda" "/dev/sdb" ];

nixos/modules/system/boot/loader/grub/install-grub.pl

@@ -59,6 +59,7 @@ my $canTouchEfiVariables = get("canTouchEfiVariables");
 my $efiSysMountPoint = get("efiSysMountPoint");
 my $gfxmodeEfi = get("gfxmodeEfi");
 my $gfxmodeBios = get("gfxmodeBios");
+my $bootloaderId = get("bootloaderId");
 $ENV{'PATH'} = get("path");
 
 die "unsupported GRUB version\n" if $grubVersion != 1 && $grubVersion != 2;
@@ -521,7 +522,7 @@ if (($requireNewInstall != 0) && ($efiTarget eq "no" || $efiTarget eq "both")) {
 if (($requireNewInstall != 0) && ($efiTarget eq "only" || $efiTarget eq "both")) {
     print STDERR "installing the GRUB $grubVersion EFI boot loader into $efiSysMountPoint...\n";
     if ($canTouchEfiVariables eq "true") {
-        system("$grubEfi/sbin/grub-install", "--recheck", "--target=$grubTargetEfi", "--boot-directory=$bootPath", "--efi-directory=$efiSysMountPoint") == 0
+        system("$grubEfi/sbin/grub-install", "--recheck", "--target=$grubTargetEfi", "--boot-directory=$bootPath", "--efi-directory=$efiSysMountPoint", "--bootloader-id=$bootloaderId") == 0
                 or die "$0: installation of GRUB EFI into $efiSysMountPoint failed\n";
     } else {
         system("$grubEfi/sbin/grub-install", "--recheck", "--target=$grubTargetEfi", "--boot-directory=$bootPath", "--efi-directory=$efiSysMountPoint", "--no-nvram") == 0

nixos/modules/virtualisation/amazon-init.nix

@@ -0,0 +1,52 @@
+{ config, pkgs, modulesPath, ... }:
+
+# This attempts to pull a nix expression from this EC2 instance's user-data.
+
+let
+  bootScript = pkgs.writeScript "bootscript.sh" ''
+    #!${pkgs.stdenv.shell} -eux
+
+    echo "attempting to fetch configuration from user-data..."
+
+    export PATH=${pkgs.nix}/bin:${pkgs.wget}/bin:${pkgs.systemd}/bin:${pkgs.gnugrep}/bin:${pkgs.gnused}/bin:${config.system.build.nixos-rebuild}/bin:$PATH
+    export NIX_PATH=/nix/var/nix/profiles/per-user/root/channels/nixos:nixos-config=/etc/nixos/configuration.nix:/nix/var/nix/profiles/per-user/root/channels
+
+    userData="$(mktemp)"
+    wget -q --wait=1 --tries=0 --retry-connrefused -O - http://169.254.169.254/2011-01-01/user-data > "$userData"
+
+    if [[ $? -eq 0 ]]; then
+      echo "user-data fetched"
+      # If the user-data looks like it could be a nix expression,
+      # copy it over. Also, look for a magic three-hash comment and set
+      # that as the channel.
+      if sed '/^\(#\|SSH_HOST_.*\)/d' < "$userData" | grep -q '\S'; then
+        channels="$(grep '^###' "$userData" | sed 's|###\s*||')"
+        printf "%s" "$channels" | while read channel; do
+          echo "writing channel: $channel"
+        done
+
+        if [[ -n "$channels" ]]; then
+          printf "%s" "$channels" > /root/.nix-channels
+          nix-channel --update
+        fi
+
+        echo "setting configuration"
+        cp "$userData" /etc/nixos/configuration.nix
+      else
+        echo "user-data does not appear to be a nix expression; ignoring"
+      fi
+    else
+      echo "failed to fetch user-data"
+    fi
+
+    type -f nixos-rebuild
+
+    nixos-rebuild switch
+  '';
+in {
+  imports = [ "${modulesPath}/virtualisation/amazon-image.nix" ];
+  ec2.metadata = true;
+  boot.postBootCommands = ''
+    ${bootScript} &
+  '';
+}

nixos/modules/virtualisation/xen-dom0.nix

@@ -6,7 +6,6 @@ with lib;
 
 let
   cfg = config.virtualisation.xen;
-  xen = pkgs.xen;
 in
 
 {
@@ -88,9 +87,9 @@ in
       message = "Xen currently does not support EFI boot";
     } ];
 
-    virtualisation.xen.stored = mkDefault "${xen}/bin/oxenstored";
+    virtualisation.xen.stored = mkDefault "${pkgs.xen}/bin/oxenstored";
 
-    environment.systemPackages = [ xen ];
+    environment.systemPackages = [ pkgs.xen ];
 
     # Make sure Domain 0 gets the required configuration
     #boot.kernelPackages = pkgs.boot.kernelPackages.override { features={xen_dom0=true;}; };
@@ -122,7 +121,7 @@ in
 
     system.extraSystemBuilderCmds =
       ''
-        ln -s ${xen}/boot/xen.gz $out/xen.gz
+        ln -s ${pkgs.xen}/boot/xen.gz $out/xen.gz
         echo "${toString cfg.bootParams}" > $out/xen-params
       '';
 
@@ -158,13 +157,16 @@ in
 
 
     environment.etc =
-      [ { source = "${xen}/etc/xen/xl.conf";
+      [ { source = "${pkgs.xen}/etc/xen/xl.conf";
           target = "xen/xl.conf";
         }
+        { source = "${pkgs.xen}/etc/xen/scripts";
+          target = "xen/scripts";
+        }
       ];
 
     # Xen provides udev rules.
-    services.udev.packages = [ xen ];
+    services.udev.packages = [ pkgs.xen ];
 
     services.udev.path = [ pkgs.bridge-utils pkgs.iproute ];
 
@@ -260,16 +262,13 @@ in
       wantedBy = [ "multi-user.target" ];
       before = [ "xen-domains.service" ];
       serviceConfig.RemainAfterExit = "yes";
-      serviceConfig.ExecStart = ''
+      serviceConfig.ExecStart = "${pkgs.bridge-utils}/bin/brctl addbr ${cfg.bridge}";
-        ${pkgs.bridge-utils}/bin/brctl addbr ${cfg.bridge}
+      postStart = "${pkgs.inetutils}/bin/ifconfig ${cfg.bridge} up";
-        ${pkgs.inetutils}/bin/ifconfig ${cfg.bridge} up
+      serviceConfig.ExecStop = "${pkgs.inetutils}/bin/ifconfig ${cfg.bridge} down";
-        '';
+      postStop = "${pkgs.bridge-utils}/bin/brctl delbr ${cfg.bridge}";
-      serviceConfig.ExecStop = ''
-        ${pkgs.inetutils}/bin/ifconfig ${cfg.bridge} down
-        ${pkgs.bridge-utils}/bin/brctl delbr ${cfg.bridge}
-        '';
     };
 
+
     systemd.services.xen-domains = {
       description = "Xen domains - automatically starts, saves and restores Xen domains";
       wantedBy = [ "multi-user.target" ];

nixos/release-combined.nix

@@ -52,6 +52,7 @@ in rec {
         (all nixos.tests.firefox)
         (all nixos.tests.firewall)
         (all nixos.tests.gnome3)
+        (all nixos.tests.installer.grub1)
         (all nixos.tests.installer.lvm)
         (all nixos.tests.installer.luksroot)
         (all nixos.tests.installer.separateBoot)

nixos/release.nix

@@ -247,6 +247,8 @@ in rec {
   tests.docker = hydraJob (import tests/docker.nix { system = "x86_64-linux"; });
   tests.dockerRegistry = hydraJob (import tests/docker-registry.nix { system = "x86_64-linux"; });
   tests.etcd = hydraJob (import tests/etcd.nix { system = "x86_64-linux"; });
+  tests.ec2-nixops = hydraJob (import tests/ec2.nix { system = "x86_64-linux"; }).boot-ec2-nixops;
+  tests.ec2-config = hydraJob (import tests/ec2.nix { system = "x86_64-linux"; }).boot-ec2-config;
   tests.firefox = callTest tests/firefox.nix {};
   tests.firewall = callTest tests/firewall.nix {};
   tests.fleet = hydraJob (import tests/fleet.nix { system = "x86_64-linux"; });

nixos/tests/ec2.nix

@@ -0,0 +1,119 @@
+{ system ? builtins.currentSystem }:
+
+with import ../lib/testing.nix { inherit system; };
+with import ../lib/qemu-flags.nix;
+with pkgs.lib;
+
+let
+  image =
+    (import ../lib/eval-config.nix {
+      inherit system;
+      modules = [
+        ../maintainers/scripts/ec2/amazon-hvm-config.nix
+        ../../nixos/modules/testing/test-instrumentation.nix
+        { boot.initrd.kernelModules = [ "virtio" "virtio_blk" "virtio_pci" "virtio_ring" ]; }
+      ];
+    }).config.system.build.amazonImage;
+
+  makeEc2Test = { name, userData, script, hostname ? "ec2-instance", sshPublicKey ? null }:
+    let
+      metaData = pkgs.stdenv.mkDerivation {
+        name = "metadata";
+        buildCommand = ''
+          mkdir -p $out/2011-01-01
+          ln -s ${pkgs.writeText "userData" userData} $out/2011-01-01/user-data
+          mkdir -p $out/1.0/meta-data
+          echo "${hostname}" > $out/1.0/meta-data/hostname
+        '' + optionalString (sshPublicKey != null) ''
+          mkdir -p $out/1.0/meta-data/public-keys/0
+          ln -s ${pkgs.writeText "sshPublicKey" sshPublicKey} $out/1.0/meta-data/public-keys/0/openssh-key
+        '';
+      };
+    in makeTest {
+      name = "ec2-" + name;
+      nodes = {};
+      testScript =
+        ''
+          use File::Temp qw/ tempfile /;
+          my ($fh, $filename) = tempfile();
+
+          `qemu-img create -f qcow2 -o backing_file=${image}/nixos.img $filename`;
+
+          my $startCommand = "qemu-kvm -m 768 -net nic -net 'user,net=169.254.0.0/16,guestfwd=tcp:169.254.169.254:80-cmd:${pkgs.micro-httpd}/bin/micro_httpd ${metaData}'";
+          $startCommand .= " -drive file=" . Cwd::abs_path($filename) . ",if=virtio,werror=report";
+          $startCommand .= " \$QEMU_OPTS";
+
+          my $machine = createMachine({ startCommand => $startCommand });
+          ${script}
+        '';
+    };
+
+  snakeOilPrivateKey = [
+    "-----BEGIN EC PRIVATE KEY-----"
+    "MHcCAQEEIHQf/khLvYrQ8IOika5yqtWvI0oquHlpRLTZiJy5dRJmoAoGCCqGSM49"
+    "AwEHoUQDQgAEKF0DYGbBwbj06tA3fd/+yP44cvmwmHBWXZCKbS+RQlAKvLXMWkpN"
+    "r1lwMyJZoSGgBHoUahoYjTh9/sJL7XLJtA=="
+    "-----END EC PRIVATE KEY-----"
+  ];
+
+  snakeOilPublicKey = pkgs.lib.concatStrings [
+    "ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHA"
+    "yNTYAAABBBChdA2BmwcG49OrQN33f/sj+OHL5sJhwVl2Qim0vkUJQCry1zFpKTa"
+    "9ZcDMiWaEhoAR6FGoaGI04ff7CS+1yybQ= snakeoil"
+  ];
+in {
+  boot-ec2-nixops = makeEc2Test {
+    name         = "nixops-userdata";
+    sshPublicKey = snakeOilPublicKey; # That's right folks! My user's key is also the host key!
+
+    userData = ''
+      SSH_HOST_DSA_KEY_PUB:${snakeOilPublicKey}
+      SSH_HOST_DSA_KEY:${pkgs.lib.concatStringsSep "|" snakeOilPrivateKey}
+    '';
+    script = ''
+      $machine->start;
+      $machine->waitForFile("/root/user-data");
+      $machine->waitForUnit("sshd.service");
+
+      # We have no keys configured on the client side yet, so this should fail
+      $machine->fail("ssh -o BatchMode=yes localhost exit");
+
+      # Let's install our client private key
+      $machine->succeed("mkdir -p ~/.ssh");
+      ${concatMapStrings (s: "$machine->succeed('echo ${s} >> ~/.ssh/id_ecdsa');") snakeOilPrivateKey}
+      $machine->succeed("chmod 600 ~/.ssh/id_ecdsa");
+
+      # We haven't configured the host key yet, so this should still fail
+      $machine->fail("ssh -o BatchMode=yes localhost exit");
+
+      # Add the host key; ssh should finally succeed
+      $machine->succeed("echo localhost,127.0.0.1 ${snakeOilPublicKey} > ~/.ssh/known_hosts");
+      $machine->succeed("ssh -o BatchMode=yes localhost exit");
+
+      $machine->shutdown;
+    '';
+  };
+
+  boot-ec2-config = makeEc2Test {
+    name         = "config-userdata";
+    sshPublicKey = snakeOilPublicKey;
+
+    userData = ''
+      ### http://nixos.org/channels/nixos-unstable nixos
+      {
+        imports = [
+          <nixpkgs/nixos/modules/virtualisation/amazon-image.nix>
+          <nixpkgs/nixos/modules/testing/test-instrumentation.nix>
+        ];
+        environment.etc.testFile = {
+          text = "whoa";
+        };
+      }
+    '';
+    script = ''
+      $machine->start;
+      $machine->waitForFile("/etc/testFile");
+      $machine->succeed("cat /etc/testFile | grep -q 'whoa'");
+    '';
+  };
+}

pkgs/applications/audio/aacgain/default.nix

@@ -0,0 +1,46 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation {
+  name = "aacgain-1.9.0";
+  src = fetchFromGitHub {
+    owner = "mulx";
+    repo = "aacgain";
+    rev = "7c29dccd878ade1301710959aeebe87a8f0828f5";
+    sha256 = "07hl432vsscqg01b6wr99qmsj4gbx0i02x4k565432y6zpfmaxm0";
+  };
+
+  configurePhase = ''
+    cd mp4v2
+    ./configure
+
+    cd ../faad2
+    ./configure
+
+    cd ..
+    ./configure
+  '';
+
+  buildPhase = ''
+    cd mp4v2
+    make libmp4v2.la
+
+    cd ../faad2
+    make LDFLAGS=-static
+
+    cd ..
+    make   
+  '';
+
+  installPhase = ''
+    strip -s aacgain/aacgain
+    install -vD aacgain/aacgain "$out/bin/aacgain"
+  '';
+
+  meta = {
+    description = "ReplayGain for AAC files";
+    homepage = https://github.com/mulx/aacgain;
+    license = stdenv.lib.licenses.gpl2;
+    platforms = stdenv.lib.platforms.linux;
+    maintainers = [ stdenv.lib.maintainers.robbinch ];
+  };
+}

pkgs/applications/audio/gmpc/default.nix

@@ -1,6 +1,6 @@
 { stdenv, fetchurl, libtool, intltool, pkgconfig, glib
 , gtk, curl, mpd_clientlib, libsoup, gob2, vala, libunique
-, libSM, libICE, sqlite
+, libSM, libICE, sqlite, hicolor_icon_theme
 }:
 
 stdenv.mkDerivation rec {
@@ -24,7 +24,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     libtool intltool pkgconfig glib gtk curl mpd_clientlib libsoup
-    libunique libmpd gob2 vala libSM libICE sqlite
+    libunique libmpd gob2 vala libSM libICE sqlite hicolor_icon_theme
   ];
 
   meta = with stdenv.lib; {

pkgs/applications/audio/ladspa-plugins/git.nix

@@ -0,0 +1,32 @@
+{ stdenv, fetchgit, automake, autoreconfHook, fftw, gettext, ladspaH, libxml2, pkgconfig, perl, perlPackages }:
+
+stdenv.mkDerivation {
+  name = "swh-plugins-git-2015-03-04";
+
+  src = fetchgit {
+    url = https://github.com/swh/ladspa.git;
+    rev = "4b8437e8037cace3d5bf8ce6d1d1da0182aba686";
+    sha256 = "7d9aa13a064903b330bd52e35c1f810f1c8a253ea5eb4e5a3a69a051af03150e";
+  };
+
+  buildInputs = [ automake autoreconfHook fftw gettext ladspaH libxml2 pkgconfig perl perlPackages.XMLParser ];
+
+  patchPhase = ''
+    patchShebangs .
+    patchShebangs ./metadata/
+    cp ${automake}/share/automake-*/mkinstalldirs .
+  '';
+
+  configurePhase = ''
+    autoreconf -i
+    ./configure --prefix=$out
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = http://plugin.org.uk/;
+    description = "LADSPA format audio plugins";
+    license = licenses.gpl2;
+    maintainers = [ maintainers.magnetophon ];
+    platforms = platforms.linux;
+  };
+}

pkgs/applications/editors/emacs-modes/monky/default.nix

@@ -0,0 +1,19 @@
+{ stdenv, fetchurl, emacs, unzip }:
+
+stdenv.mkDerivation {
+  name = "emacs-monky-20150404";
+
+  src = fetchurl {
+    url = "https://github.com/ananthakumaran/monky/archive/48c0200910739b6521f26f6423b2bfb8c38b4482.zip";
+    sha256 = "0yp3pzddx7yki9n3qrriqa5p442qyrdivvlc4xbl024vzjyzddrj";
+  };
+
+  buildInputs = [ emacs unzip ];
+
+  buildPhase = "emacs -L . --batch -f batch-byte-compile *.el";
+
+  installPhase = ''
+    install -d $out/share/emacs/site-lisp
+    install *.el *.elc $out/share/emacs/site-lisp
+  '';
+}

pkgs/applications/editors/neovim/default.nix

@@ -1,18 +1,20 @@
-{ stdenv, fetchFromGitHub, cmake, gettext, glib, libmsgpack
+{ stdenv, fetchFromGitHub, cmake, gettext, glib, libmsgpack, libtermkey
-, libtermkey, libtool, libuv, lpeg, lua, luajit, luaMessagePack
+, libtool, libuv, lpeg, lua, luajit, luaMessagePack, luabitop, ncurses, perl
-, luabitop, ncurses, perl, pkgconfig, unibilium
+, pkgconfig, unibilium, makeWrapper, vimUtils
-, withJemalloc ? true, jemalloc }:
 
-let version = "2015-06-09"; in
+, withPython ? true, pythonPackages, extraPythonPackages ? []
-stdenv.mkDerivation rec {
+, withPython3 ? true, python3Packages, extraPython3Packages ? []
-  name = "neovim-${version}";
+, withJemalloc ? true, jemalloc
 
-  src = fetchFromGitHub {
+, vimAlias ? false
-    sha256 = "1lycql0lwi7ynrsaln4kxybwvxb9fvganiq3ba4pnpcfgl155k1j";
+, configure ? null
-    rev = "6270d431aaeed71e7a8782411f36409ab8e0ee35";
+}:
-    repo = "neovim";
+
-    owner = "neovim";
+with stdenv.lib;
-  };
+
+let
+
+  version = "2015-06-09";
 
   # Note: this is NOT the libvterm already in nixpkgs, but some NIH silliness:
   neovimLibvterm = let version = "2015-02-23"; in stdenv.mkDerivation rec {
@@ -27,11 +29,12 @@ stdenv.mkDerivation rec {
 
     buildInputs = [ libtool perl ];
 
-    makeFlags = "PREFIX=$(out)";
+    makeFlags = [ "PREFIX=$(out)" ]
+      ++ stdenv.lib.optional stdenv.isDarwin "LIBTOOL=${libtool}/bin/libtool";
 
     enableParallelBuilding = true;
 
-    meta = with stdenv.lib; {
+    meta = {
       description = "VT220/xterm/ECMA-48 terminal emulator library";
       homepage = http://www.leonerd.org.uk/code/libvterm/;
       license = licenses.mit;
@@ -40,9 +43,30 @@ stdenv.mkDerivation rec {
     };
   };
 
+  pythonEnv = pythonPackages.python.buildEnv.override {
+    extraLibs = [ pythonPackages.neovim ] ++ extraPythonPackages;
+    ignoreCollisions = true;
+  };
+
+  python3Env = python3Packages.python.buildEnv.override {
+    extraLibs = [ python3Packages.neovim ] ++ extraPython3Packages;
+    ignoreCollisions = true;
+  };
+
+  neovim = stdenv.mkDerivation rec {
+    name = "neovim-${version}";
+
+    src = fetchFromGitHub {
+      sha256 = "1lycql0lwi7ynrsaln4kxybwvxb9fvganiq3ba4pnpcfgl155k1j";
+      rev = "6270d431aaeed71e7a8782411f36409ab8e0ee35";
+      repo = "neovim";
+      owner = "neovim";
+    };
+
     enableParallelBuilding = true;
 
     buildInputs = [
+      makeWrapper
       cmake
       glib
       libtermkey
@@ -57,7 +81,8 @@ stdenv.mkDerivation rec {
       neovimLibvterm
       pkgconfig
       unibilium
-  ] ++ stdenv.lib.optional withJemalloc jemalloc;
+    ] ++ optional withJemalloc jemalloc;
+
     nativeBuildInputs = [
       gettext
     ];
@@ -65,7 +90,29 @@ stdenv.mkDerivation rec {
     LUA_CPATH="${lpeg}/lib/lua/${lua.luaversion}/?.so;${luabitop}/lib/lua/5.2/?.so";
     LUA_PATH="${luaMessagePack}/share/lua/5.1/?.lua";
 
-  meta = with stdenv.lib; {
+    preConfigure = stdenv.lib.optionalString stdenv.isDarwin ''
+      export DYLD_LIBRARY_PATH=${jemalloc}/lib
+    '';
+
+    postInstall = stdenv.lib.optionalString stdenv.isDarwin ''
+      echo patching $out/bin/nvim
+      install_name_tool -change libjemalloc.1.dylib \
+                ${jemalloc}/lib/libjemalloc.1.dylib \
+                $out/bin/nvim
+    '' + optionalString withPython ''
+      ln -s ${pythonEnv}/bin/python $out/bin/nvim-python
+    '' + optionalString withPython3 ''
+      ln -s ${python3Env}/bin/python $out/bin/nvim-python3
+    '' + optionalString (withPython || withPython3) ''
+        wrapProgram $out/bin/nvim --add-flags "${
+          (optionalString withPython
+            ''--cmd \"let g:python_host_prog='$out/bin/nvim-python'\" '') +
+          (optionalString withPython3
+            ''--cmd \"let g:python3_host_prog='$out/bin/nvim-python3'\" '')
+        }"
+    '';
+
+    meta = {
       description = "Vim text editor fork focused on extensibility and agility";
       longDescription = ''
         Neovim is a project that seeks to aggressively refactor Vim in order to:
@@ -82,7 +129,22 @@ stdenv.mkDerivation rec {
       # those contributions were copied from Vim (identified in the commit logs
       # by the vim-patch token). See LICENSE for details."
       license = with licenses; [ asl20 vim ];
-    maintainers = with maintainers; [ manveru nckx ];
+      maintainers = with maintainers; [ manveru nckx garbas ];
       platforms   = platforms.unix;
     };
+  };
+
+in if (vimAlias == false && configure == null) then neovim else stdenv.mkDerivation rec {
+  name = "neovim-${version}-configured";
+  buildInputs = [ makeWrapper ];
+  buildCommand = ''
+    mkdir -p $out/bin
+    for item in ${neovim}/bin/*; do
+      ln -s $item $out/bin/
+    done
+  '' + optionalString vimAlias ''
+    ln -s $out/bin/nvim $out/bin/vim
+  '' + optionalString (configure != null) ''
+    wrapProgram $out/bin/nvim --add-flags "-u ${vimUtils.vimrcFile configure}"
+  '';
 }

pkgs/applications/graphics/photoqt/default.nix

@@ -1,19 +1,17 @@
 { stdenv, fetchurl, cmake, qt5, exiv2, graphicsmagick }:
 
 let
-  version = "1.1.0.1";
+  version = "1.2";
 in
 stdenv.mkDerivation rec {
   name = "photoqt-${version}";
   src = fetchurl {
     url = "http://photoqt.org/pkgs/photoqt-${version}.tar.gz";
-    sha256 = "1y59ys1dgjppahs7v7kxwva7ik23s0x7j2f6glv6sn23l9cfq9rp";
+    sha256 = "1dnnj2h3j517hcbjxlzk035fis44wdmqq7dvhwpmq1rcr0v32aaa";
   };
 
   buildInputs = [ cmake qt5.base qt5.tools exiv2 graphicsmagick ];
 
-  patches = [ ./graphicsmagick-path.patch ];
-
   preConfigure = ''
     export MAGICK_LOCATION="${graphicsmagick}/include/GraphicsMagick"
   '';

pkgs/applications/graphics/photoqt/graphicsmagick-path.patch

@@ -1,46 +0,0 @@
---- a/CMake/FindMagick.cmake	2014-10-13 19:24:30.000000000 +0200
-+++ b/CMake/FindMagick.cmake	2014-12-27 18:54:19.611759021 +0100
-@@ -19,28 +19,11 @@
- SET(MAGICK++_FOUND "NO" )
- 
- FIND_PATH( MAGICK_INCLUDE_DIR magick/magick.h
--  "$ENV{MAGICK_LOCATION}/magick"
--  "$ENV{MAGICK_LOCATION}/include/magick"
--  "$ENV{MAGICK_HOME}/include/magick"
--  /usr/include/magick
--  /usr/include/
--  /usr/include/GraphicsMagick
--  /opt/local/include/GraphicsMagick/magick
--  /opt/local/include/GraphicsMagick
-+  "$ENV{MAGICK_LOCATION}"
-   )
- 
- FIND_PATH( MAGICK++_INCLUDE_DIR Magick++.h
--  "$ENV{MAGICK++_LOCATION}/Magick++"
--  "$ENV{MAGICK++_LOCATION}/include/"
--  "$ENV{MAGICK_LOCATION}/Magick++"
--  "$ENV{MAGICK_LOCATION}/include/Magick++"
--  "$ENV{MAGICK_LOCATION}/include/"
--  "$ENV{MAGICK_HOME}/include/"
--  /usr/include/Magick++
--  /usr/include/GraphicsMagick
--  /usr/include/
--  /opt/local/include/GraphicsMagick/Magick++
--  /opt/local/include/GraphicsMagick
-+  "$ENV{MAGICK_LOCATION}"
-   )
-   
- FIND_LIBRARY( Magick GraphicsMagick
-@@ -55,12 +38,7 @@
- 
- FIND_LIBRARY( Magick++ GraphicsMagick++
-   PATHS 
--  "$ENV{MAGICK++_LOCATION}/.libs"
--  "$ENV{MAGICK_LOCATION}/.libs"
--  "$ENV{MAGICK++_LOCATION}/lib"
-   "$ENV{MAGICK_LOCATION}/lib"
--  "$ENV{MAGICK_HOME}/lib"
--  /opt/local/lib
-   DOC   "GraphicsMagick Magick++ library"
- )
- 

pkgs/applications/misc/dfilemanager/default.nix

@@ -0,0 +1,25 @@
+{ stdenv, fetchgit, cmake, qt5, file, kde5}:
+
+let
+  version = "git-2015-06-10";
+in
+stdenv.mkDerivation rec {
+  name = "dfilemanager-${version}";
+  src = fetchgit {
+    url = "git://git.code.sf.net/p/dfilemanager/code";
+    rev = "806a28aa8fed30941a2fd6784c7c9c240bca30e3";
+    sha256 = "1k15qzjmqg9ffv4cl809b071dpyckf8jspkhfhpbmfd9wasr0m7i";
+  };
+
+  buildInputs = [ cmake qt5.base qt5.tools qt5.x11extras file kde5.solid];
+
+  cmakeFlags = "-DQT5BUILD=true";
+
+  meta = {
+    homepage = "http://dfilemanager.sourceforge.net/";
+    description = "File manager written in Qt/C++, it does use one library from kdelibs, the solid lib for easy device handling";
+    #license = stdenv.lib.licenses; # license not specified
+    platforms = stdenv.lib.platforms.unix;
+    maintainers = [ stdenv.lib.maintainers.eduarrrd ];
+  };
+}

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

@@ -1,7 +1,7 @@
 { stdenv, fetchurl, ninja, which
 
 # default dependencies
-, bzip2, flac, speex, icu, libopus
+, bzip2, flac, speex, libopus
 , libevent, expat, libjpeg, snappy
 , libpng, libxml2, libxslt, libcap
 , xdg_utils, yasm, minizip, libwebp
@@ -84,7 +84,7 @@ let
   };
 
   defaultDependencies = [
-    bzip2 flac speex icu opusWithCustomModes
+    bzip2 flac speex opusWithCustomModes
     libevent expat libjpeg snappy
     libpng libxml2 libxslt libcap
     xdg_utils yasm minizip libwebp
@@ -113,7 +113,7 @@ let
       glib gtk dbus_glib
       libXScrnSaver libXcursor libXtst mesa
       pciutils protobuf speechd libXdamage
-      pythonPackages.gyp_svn1977 pythonPackages.ply pythonPackages.jinja2
+      pythonPackages.gyp pythonPackages.ply pythonPackages.jinja2
     ] ++ optional gnomeKeyringSupport libgnome_keyring3
       ++ optionals gnomeSupport [ gnome.GConf libgcrypt ]
       ++ optional enableSELinux libselinux
@@ -124,15 +124,10 @@ let
     #      be fixed, then try again to unbundle everything into separate
     #      derivations.
     prePatch = ''
-      cp -dsr --no-preserve=mode "${source.main}"/* .
+      cp -dr --no-preserve=mode "${source.main}"/* .
-      cp -dsr --no-preserve=mode "${source.sandbox}" sandbox
+      cp -dr --no-preserve=mode "${source.sandbox}" sandbox
       cp -dr "${source.bundled}" third_party
       chmod -R u+w third_party
-
-      # Hardcode source tree root in all gyp files
-      find -iname '*.gyp*' \( -type f -o -type l \) \
-        -exec sed -i -e 's|<(DEPTH)|'"$(pwd)"'|g' {} + \
-        -exec chmod u+w {} +
     '';
 
     postPatch = optionalString (versionOlder version "42.0.0.0") ''
@@ -200,7 +195,7 @@ let
       # This is to ensure expansion of $out.
       libExecPath="${libExecPath}"
       python build/linux/unbundle/replace_gyp_files.py ${gypFlags}
-      python build/gyp_chromium -f ninja --depth "$(pwd)" ${gypFlags}
+      python build/gyp_chromium -f ninja --depth . ${gypFlags}
     '';
 
     buildPhase = let

pkgs/applications/networking/browsers/chromium/source/default.nix

@@ -18,7 +18,7 @@ let
     "s,^/,,"
   ]);
 
-  pre42 = versionOlder version "42.0.0.0";
+  pre44 = versionOlder version "44.0.0.0";
 
 in stdenv.mkDerivation {
   name = "chromium-source-${version}";
@@ -47,10 +47,10 @@ in stdenv.mkDerivation {
     done
   '';
 
-  patches = if pre42 then [
+  patches = if pre44 then [
-    ./sandbox_userns_36.patch ./nix_plugin_paths.patch
-  ] else [
     ./nix_plugin_paths_42.patch
+  ] else [
+    ./nix_plugin_paths_44.patch
   ];
 
   patchPhase = let
@@ -73,11 +73,10 @@ in stdenv.mkDerivation {
       -e 's|/bin/echo|echo|' \
       -e "/python_arch/s/: *'[^']*'/: '""'/" \
       "$out/build/common.gypi" "$main/chrome/chrome_tests.gypi"
-  '' + optionalString useOpenSSL ''
-    cat $opensslPatches | patch -p1 -d "$bundled/openssl/openssl"
-  '' + optionalString (!pre42) ''
     sed -i -e '/LOG.*no_suid_error/d' \
       "$main/content/browser/browser_main_loop.cc"
+  '' + optionalString useOpenSSL ''
+    cat $opensslPatches | patch -p1 -d "$bundled/openssl/openssl"
   '';
 
   preferLocalBuild = true;

pkgs/applications/networking/browsers/chromium/source/nix_plugin_paths_44.patch

@@ -55,21 +55,6 @@ index 8a205a6..d5c24e1 100644
          return false;
        cur = cur.Append(kInternalFlashPluginFileName);
        break;
-@@ -295,12 +288,12 @@ bool PathProvider(int key, base::FilePath* result) {
-       cur = cur.Append(chrome::kPepperFlashPluginFilename);
-       break;
-     case chrome::FILE_PDF_PLUGIN:
--      if (!GetInternalPluginsDirectory(&cur))
-+      if (!GetInternalPluginsDirectory(&cur, "PDF"))
-         return false;
-       cur = cur.Append(kInternalPDFPluginFileName);
-       break;
-     case chrome::FILE_EFFECTS_PLUGIN:
--      if (!GetInternalPluginsDirectory(&cur))
-+      if (!GetInternalPluginsDirectory(&cur, "FILE_EFFECTS"))
-         return false;
-       cur = cur.Append(kEffectsPluginFileName);
-       break;
 @@ -308,7 +301,7 @@ bool PathProvider(int key, base::FilePath* result) {
      // We currently need a path here to look up whether the plugin is disabled
      // and what its permissions are.

pkgs/applications/networking/browsers/chromium/source/sources.nix

@@ -1,21 +1,21 @@
 # This file is autogenerated from update.sh in the parent directory.
 {
   dev = {
-    version = "43.0.2327.5";
+    version = "45.0.2421.0";
-    sha256 = "0k9jpzm1n7d3zv6f77vz33jcvmnbxnl6plabvlrf8w83kbzhi76n";
+    sha256 = "1qc80y0mhwnvxrvpc3csskgb536wq34c0fgk19h1qb4xc62lxhsk";
-    sha256bin32 = "1dm4xp0x02kqj82giw45qd2z12wf22h2bs0d3hnlz050innxgcb6";
+    sha256bin32 = "1xqhyrlmh00md6i1q4wr0xihqbvcpshzscnjclrn53dlw5zs2s89";
-    sha256bin64 = "1b13g44y704llsnw68840zmaahj1hwzram50v8fqmff44w1b0bxb";
+    sha256bin64 = "0akdhwwdfcbqfh65a82zigbhsi8sbhhw6904cjprb3bmv4l3c598";
   };
   beta = {
-    version = "42.0.2311.39";
+    version = "44.0.2403.39";
-    sha256 = "0qiyg8bg9f1daf8v2jlrv54lis7156h44ak42jdx96xanvj2rvj0";
+    sha256 = "15c4adg0r9ym3pxya7vv4d148gv2pdwaaymxvvw511fjwffdv71n";
-    sha256bin32 = "0v4dr2a3n51dais2mg0dml0rmqfmalfj0zgp20a4kkarbpih1x0v";
+    sha256bin32 = "1gaypkah10y31gb5f7vnyv0v73z5zjznmsp6vh2m4hfajx7s55jn";
-    sha256bin64 = "19638ik9qgfmxpzdry0qwkwpzvhlbs2h2nn1kwsjja5j49817ksx";
+    sha256bin64 = "1j1ma6asl3ibjv3apyw24vhyi1qy64f586w8jizqzp4h962gj95c";
   };
   stable = {
-    version = "41.0.2272.89";
+    version = "43.0.2357.124";
-    sha256 = "1saxcyqp8pz496qwdgl4dqxll6l9icbljm56w1rrkxgwrrvl4iwk";
+    sha256 = "09m8bb5f17mx6cd3h5irslw07h2s0drda35v17vcr7qfhk8jdh92";
-    sha256bin32 = "19srg0isp1k4fwixwjxm1j88bnqx9sb349n992i038c3h8raa1v4";
+    sha256bin32 = "15n2fla1ixrqzi0in0vyl8n5wkv20fpd96lff65rwr9diylz287p";
-    sha256bin64 = "1fb8ffgbsjsij7bd1qawa03z9pybasfig1cmdzwybmlwg2fdlvfv";
+    sha256bin64 = "0x6igpcf29zmwqgphvy9nm527k9g7na2cvgc5nimw4fs5dakzzjr";
   };
 }

pkgs/applications/networking/browsers/chromium/source/update.nix

@@ -9,7 +9,7 @@ let
             then import ./sources.nix
             else null;
 
-  bucketURL = "http://commondatastorage.googleapis.com/"
+  bucketURL = "https://commondatastorage.googleapis.com/"
             + "chromium-browser-official";
 
   debURL = "https://dl.google.com/linux/chrome/deb/pool/main/g";

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

@@ -1,9 +1,10 @@
-{ lib, stdenv, fetchurl, pkgconfig, gtk, pango, perl, python, zip, libIDL
+{ lib, stdenv, fetchurl, pkgconfig, gtk, gtk3, pango, perl, python, zip, libIDL
 , libjpeg, zlib, dbus, dbus_glib, bzip2, xlibs
 , freetype, fontconfig, file, alsaLib, nspr, nss, libnotify
 , yasm, mesa, sqlite, unzip, makeWrapper, pysqlite
 , hunspell, libevent, libstartup_notification, libvpx
 , cairo, gstreamer, gst_plugins_base, icu
+, enableGTK3 ? false
 , debugBuild ? false
 , # If you want the resulting program to call itself "Firefox" instead
   # of "Shiretoko" or whatever, enable this option.  However, those
@@ -34,7 +35,8 @@ stdenv.mkDerivation rec {
       xlibs.libXext xlibs.xextproto sqlite unzip makeWrapper
       hunspell libevent libstartup_notification libvpx cairo
       gstreamer gst_plugins_base icu
-    ];
+    ]
+    ++ lib.optional enableGTK3 gtk3;
 
   configureFlags =
     [ "--enable-application=browser"
@@ -64,6 +66,7 @@ stdenv.mkDerivation rec {
       "--disable-updater"
       "--disable-pulseaudio"
     ]
+    ++ lib.optional enableGTK3 "--enable-default-toolkit=cairo-gtk3"
     ++ (if debugBuild then [ "--enable-debug" "--enable-profiling"]
                       else [ "--disable-debug" "--enable-release"
                              "--enable-optimize${lib.optionalString (stdenv.system == "i686-linux") "=-O1"}"

pkgs/applications/networking/newsreaders/liferea/default.nix

@@ -6,14 +6,14 @@
 }:
 
 let pname = "liferea";
-    version = "1.10.14";
+    version = "1.10.15";
 in
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "https://github.com/lwindolf/${pname}/releases/download/v${version}/${name}.tar.bz2";
-    sha256 = "0szazfknarw6ivnr4flr928ar309pz2mv6alc6pk6l1i9jchcnfs";
+    sha256 = "0iicw42rf0vhq4xs81awlj5v3v7xfid3h5fh87f3bqbpn9pmifdg";
   };
 
   buildInputs = with gst_all_1; [

pkgs/applications/office/abiword/default.nix

@@ -1,6 +1,6 @@
 { stdenv, fetchurl, pkgconfig, gtk3, libglade, libgnomecanvas, fribidi
 , libpng, popt, libgsf, enchant, wv, librsvg, bzip2, libjpeg, perl
-, boost, libxslt
+, boost, libxslt, goffice, makeWrapper, iconTheme
 }:
 
 stdenv.mkDerivation rec {
@@ -16,9 +16,14 @@ stdenv.mkDerivation rec {
 
   buildInputs =
     [ pkgconfig gtk3 libglade librsvg bzip2 libgnomecanvas fribidi libpng popt
-      libgsf enchant wv libjpeg perl boost libxslt
+      libgsf enchant wv libjpeg perl boost libxslt goffice makeWrapper iconTheme
     ];
 
+  postFixup = ''
+    wrapProgram "$out/bin/abiword" \
+      --prefix XDG_DATA_DIRS : "$XDG_ICON_DIRS:$GSETTINGS_SCHEMAS_PATH"
+  '';
+
   meta = with stdenv.lib; {
     description = "Word processing program, similar to Microsoft Word";
     homepage = http://www.abisource.com/;

pkgs/applications/office/gnumeric/default.nix

@@ -1,5 +1,5 @@
 { stdenv, fetchurl, pkgconfig, intltool, perl, perlXMLParser
-, gnome3, makeWrapper, gtk3
+, goffice, gnome3, makeWrapper, gtk3
 }:
 
 stdenv.mkDerivation rec {
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
   # ToDo: optional libgda, python, introspection?
   buildInputs = [
     pkgconfig intltool perl perlXMLParser
-    gnome3.goffice gtk3 makeWrapper gnome3.defaultIconTheme
+    goffice gtk3 makeWrapper gnome3.defaultIconTheme
   ];
 
   enableParallelBuilding = true;

pkgs/applications/science/logic/z3/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "z3-${version}";
-  version = "4.3.2";
+  version = "4.4.0";
 
   src = fetchFromGitHub {
     owner  = "Z3Prover";
     repo   = "z3";
-    rev    = "ac21ffebdf1512da2a77dc46c47bde87cc3850f3";
+    rev    = "7f6ef0b6c0813f2e9e8f993d45722c0e5b99e152";
-    sha256 = "1y86akhpy41wx3gx7r8gvf7xbax7dj36ikj6gqh5a7p6r6maz9ci";
+    sha256 = "1xllvq9fcj4cz34biq2a9dn2sj33bdgrzyzkj26hqw70wkzv1kzx";
   };
 
   buildInputs = [ python ];

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

@@ -1,7 +1,7 @@
-{ stdenv, fetchurl, blas, bzip2, gfortran, liblapack, libX11, libXmu, libXt
+{ stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt
 , libjpeg, libpng, libtiff, ncurses, pango, pcre, perl, readline, tcl
 , texLive, tk, xz, zlib, less, texinfo, graphviz, icu, pkgconfig, bison
-, imake, which, jdk, atlas
+, imake, which, jdk, openblas
 , withRecommendedPackages ? true
 }:
 
@@ -13,10 +13,10 @@ stdenv.mkDerivation rec {
     sha256 = "0dagyqgvi8i3nw158qi2zpwm04s4ffzvnmk5niaksvxs30zrbbpm";
   };
 
-  buildInputs = [ blas bzip2 gfortran liblapack libX11 libXmu libXt
+  buildInputs = [ bzip2 gfortran libX11 libXmu libXt
     libXt libjpeg libpng libtiff ncurses pango pcre perl readline tcl
     texLive tk xz zlib less texinfo graphviz icu pkgconfig bison imake
-    which jdk atlas
+    which jdk openblas
   ];
 
   patches = [ ./no-usr-local-search-paths.patch ];
@@ -25,8 +25,8 @@ stdenv.mkDerivation rec {
     configureFlagsArray=(
       --disable-lto
       --with${stdenv.lib.optionalString (!withRecommendedPackages) "out"}-recommended-packages
-      --with-blas="-L${atlas}/lib -lf77blas -latlas"
+      --with-blas="-L${openblas}/lib -lopenblas"
-      --with-lapack="-L${liblapack}/lib -llapack"
+      --with-lapack="-L${openblas}/lib -lopenblas"
       --with-readline
       --with-tcltk --with-tcl-config="${tcl}/lib/tclConfig.sh" --with-tk-config="${tk}/lib/tkConfig.sh"
       --with-cairo

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

@@ -1,4 +1,4 @@
-{stdenv, fetchurl, gfortran, liblapack, blas}:
+{stdenv, fetchurl, gfortran, openblas}:
 
 stdenv.mkDerivation rec {
   name = "JAGS-3.4.0";
@@ -6,7 +6,8 @@ stdenv.mkDerivation rec {
     url = "mirror://sourceforge/mcmc-jags/${name}.tar.gz";
     sha256 = "0ayqsz9kkmbss7mxlwr34ch2z1vsb65lryjzqpprab1ccyiaksib";
   };
-  buildInputs = [gfortran liblapack blas];
+  buildInputs = [gfortran openblas];
+  configureFlags = [ "--with-blas=-lopenblas" "--with-lapack=-lopenblas" ];
 
   meta = {
     description = "Just Another Gibbs Sampler";

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

@@ -51,6 +51,9 @@ stdenv.mkDerivation {
       mkdir -p $out/share/cgi-bin
       cp -v hgweb.cgi contrib/hgweb.wsgi $out/share/cgi-bin
       chmod u+x $out/share/cgi-bin/hgweb.cgi
+
+      # install bash completion
+      install -D -v contrib/bash_completion $out/share/bash-completion/completions/mercurial
     '';
 
   meta = {

pkgs/build-support/fetchnuget/default.nix

@@ -18,7 +18,7 @@ attrs @
 
     buildInputs = [ unzip ];
 
-    phases = [ "unpackPhase" "installPhase" ];
+    dontBuild = true;
 
     preInstall = ''
       function traverseRename () {

pkgs/build-support/fetchurl/mirrors.nix

@@ -14,8 +14,6 @@ rec {
     http://heanet.dl.sourceforge.net/sourceforge/
     http://surfnet.dl.sourceforge.net/sourceforge/
     http://dfn.dl.sourceforge.net/sourceforge/
-    http://mesh.dl.sourceforge.net/sourceforge/
-    http://ovh.dl.sourceforge.net/sourceforge/
     http://osdn.dl.sourceforge.net/sourceforge/
     http://kent.dl.sourceforge.net/sourceforge/
   ];

pkgs/build-support/vm/default.nix

@@ -1710,22 +1710,22 @@ rec {
     };
 
     debian8i386 = {
-      name = "debian-8.0-jessie-i386";
+      name = "debian-8.1-jessie-i386";
-      fullName = "Debian 8.0 Jessie (i386)";
+      fullName = "Debian 8.1 Jessie (i386)";
       packagesList = fetchurl {
         url = mirror://debian/dists/jessie/main/binary-i386/Packages.xz;
-        sha256 = "0lrv1lnd595c346ci7z8ja2b0rm2gx5r4hwp0wbp9lzxi8k5nk1d";
+        sha256 = "e658c2aebc3c0bc529e89de3ad916a71372f0a80161111d86a7dab1026644507";
       };
       urlPrefix = mirror://debian;
       packages = commonDebianPackages;
     };
 
     debian8x86_64 = {
-      name = "debian-8.0-jessie-amd64";
+      name = "debian-8.1-jessie-amd64";
-      fullName = "Debian 8.0 Jessie (amd64)";
+      fullName = "Debian 8.1 Jessie (amd64)";
       packagesList = fetchurl {
         url = mirror://debian/dists/jessie/main/binary-amd64/Packages.xz;
-        sha256 = "0hhagvybciy89wr1cy9dgdfki668dvcywgbz4w01qwivyd6dsia4";
+        sha256 = "265907f3cb05aff5f653907e9babd4704902f78cd5e355d4cd4ae590e4d5b043";
       };
       urlPrefix = mirror://debian;
       packages = commonDebianPackages;

pkgs/data/fonts/fira-mono/default.nix

@@ -1,16 +1,16 @@
 { stdenv, fetchurl, unzip }:
 
 stdenv.mkDerivation rec {
-  name = "fira-mono-3.2";
+  name = "fira-mono-3.203";
 
   src = fetchurl {
-    url = http://www.carrois.com/downloads/fira_mono_3_2/FiraMonoFonts3200.zip;
+    url = http://www.carrois.com/downloads/fira_mono_3_2/FiraMonoFonts3203.zip;
-    sha256 = "0g3i54q8czf3vylgasj62w2n7l1a2yrbyibjlx1qk3awh7fr1r7p";
+    sha256 = "0qaplpmsqys42a49x8d15ca2gqw1v6a6k2d56ja1j38dmr2qmpv4";
   };
 
   buildInputs = [ unzip ];
   phases = [ "unpackPhase" "installPhase" ];
-  sourceRoot = "FiraMonoFonts3200";
+  sourceRoot = "FiraMonoFonts3203";
 
   installPhase = ''
     mkdir -p $out/share/fonts/opentype

pkgs/data/fonts/fira/default.nix

@@ -1,16 +1,16 @@
 { stdenv, fetchurl, unzip }:
 
 stdenv.mkDerivation rec {
-  name = "fira-4.1";
+  name = "fira-4.103";
 
   src = fetchurl {
-    url = "http://www.carrois.com/downloads/fira_4_1/FiraFonts4100.zip";
+    url = http://www.carrois.com/downloads/fira_4_1/FiraFonts4103.zip;
-    sha256 = "0mqmmq1m2p0hb0x4mr74gghqr75iglilah7psfb3vdc80fc9h6yk";
+    sha256 = "1nw5icg3134qq2qfspvj2kclsv3965szby2lfcr65imf7lj4k52z";
   };
 
   buildInputs = [unzip];
   phases = [ "unpackPhase" "installPhase" ];
-  sourceRoot = "FiraFonts4100";
+  sourceRoot = "FiraFonts4103";
 
   installPhase = ''
     mkdir -p $out/share/fonts/opentype

pkgs/data/misc/nixos-artwork/default.nix

@@ -1,24 +1,23 @@
-{ stdenv, fetchFromGitHub }:
+{ stdenv, fetchurl }:
 
 stdenv.mkDerivation {
   name = "nixos-artwork-2015-02-27";
   # Remember to check the default lightdm wallpaper when updating
 
-  src = fetchFromGitHub {
+  GnomeDark = fetchurl {
-    owner = "NixOS";
+    url = https://raw.githubusercontent.com/NixOS/nixos-artwork/7ece5356398db14b5513392be4b31f8aedbb85a2/gnome/Gnome_Dark.png;
-    repo = "nixos-artwork";
+    sha256 = "0c7sl9k4zdjwvdz3nhlm8i4qv4cjr0qagalaa1a438jigixx27l7";
-    rev = "e71b6846023919136795ede22b16d73b2cf1693d";
-    sha256 = "167yvhm2qy7qgyrqqs4hv98mmlarhgxpcsyv0r8a9g3vkblfdczb";
   };
 
+  unpackPhase = "true";
+
   installPhase = ''
-    mkdir -p $out/share/artwork
+    mkdir -p $out/share/artwork/gnome
-    cp -r * $out/share/artwork
+    ln -s $GnomeDark $out/share/artwork/gnome/Gnome_Dark.png
-    find $out -name \*.xcf -exec rm {} \;
   '';
   
   meta = with stdenv.lib; {
-    homepage = "https://github.com/NixOS/nixos-artwork";
+    homepage = https://github.com/NixOS/nixos-artwork;
     platforms = platforms.all;
   };
 }

pkgs/desktops/gnome-3/3.16/apps/evolution/default.nix

@@ -7,11 +7,11 @@
 let
   majVer = gnome3.version;
 in stdenv.mkDerivation rec {
-  name = "evolution-${majVer}.1";
+  name = "evolution-${majVer}.3";
 
   src = fetchurl {
     url = "mirror://gnome/sources/evolution/${majVer}/${name}.tar.xz";
-    sha256 = "1lm877rrcfy98mpp4iq7m9p8r1nr9kir916n4qin2ygas9zx0qlb";
+    sha256 = "1mh769adz40r22x0jw5z4carkcbhx36qy2j8kl2djjbp1jf5vhnd";
   };
 
   doCheck = true;

pkgs/desktops/gnome-3/3.16/apps/pomodoro/default.nix

@@ -38,9 +38,11 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     homepage = https://github.com/codito/gnome-shell-pomodoro;
-    description =
+    description = "A time management utility for GNOME based on the pomodoro technique";
-      "Personal information management application that provides integrated " + 
+    longDescription = ''
-      "mail, calendaring and address book functionality";
+      This GNOME utility helps to manage time according to Pomodoro Technique.
+      It intends to improve productivity and focus by taking short breaks.
+    '';
     maintainers = with maintainers; [ DamienCassou jgeerds ];
     license = licenses.gpl3;
     platforms = platforms.linux;

pkgs/desktops/gnome-3/3.16/core/evolution-data-server/default.nix

@@ -4,11 +4,11 @@
 
 
 stdenv.mkDerivation rec {
-  name = "evolution-data-server-${gnome3.version}.1";
+  name = "evolution-data-server-${gnome3.version}.3";
 
   src = fetchurl {
     url = "mirror://gnome/sources/evolution-data-server/${gnome3.version}/${name}.tar.xz";
-    sha256 = "0lgb8jvn8kx50692gg1m9klvwm7msvk4f7wm0yl7rj880wbxzvh4";
+    sha256 = "19dcvhlqh25pkkd29hhm9yik8xxfy01hcakikrai0x1a04aa2s7f";
   };
 
   buildInputs = with gnome3;

pkgs/desktops/gnome-3/3.16/default.nix

@@ -273,14 +273,6 @@ rec {
 
   gfbgraph = callPackage ./misc/gfbgraph { };
 
-  goffice = callPackage ./misc/goffice { };
-
-  goffice_0_8 = callPackage ./misc/goffice/0.8.nix { 
-    inherit (pkgs.gnome2) libglade libgnomeui;
-    gconf = pkgs.gnome2.GConf;
-    libart = pkgs.gnome2.libart_lgpl;
-  };
-
   gitg = callPackage ./misc/gitg { 
     webkitgtk = webkitgtk24x;
   };

pkgs/development/compilers/julia/0.2.nix

@@ -1,6 +1,6 @@
 { stdenv, fetchgit, gfortran, perl, m4, llvm, gmp, pcre, zlib
  , readline, fftwSinglePrec, fftw, libunwind, suitesparse, glpk, fetchurl
- , ncurses, libunistring, lighttpd, patchelf, openblas, liblapack
+ , ncurses, libunistring, lighttpd, patchelf, openblas
  , tcl, tk, xproto, libX11, git, mpfr
  } :
 let
@@ -71,7 +71,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [ gfortran perl m4 gmp pcre llvm readline zlib
     fftw fftwSinglePrec libunwind suitesparse glpk ncurses libunistring patchelf
-    openblas liblapack tcl tk xproto libX11 git mpfr
+    openblas tcl tk xproto libX11 git mpfr
     ];
 
   configurePhase = ''
@@ -91,14 +91,13 @@ stdenv.mkDerivation rec {
     copy_kill_hash "${dsfmt_src}" deps/random
 
     ${if realGcc ==null then "" else 
-    ''export NIX_LDFLAGS="$NIX_LDFLAGS -L${realGcc}/lib -L${realGcc}/lib64 -lpcre -llapack -lm -lfftw3f -lfftw3 -lglpk -lunistring -lz -lgmp -lmpfr"''}
+    ''export NIX_LDFLAGS="$NIX_LDFLAGS -L${realGcc}/lib -L${realGcc}/lib64 -lpcre -lopenblas -lm -lfftw3f -lfftw3 -lglpk -lunistring -lz -lgmp -lmpfr"''}
     export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE -fPIC "
 
     export LDFLAGS="-L${suitesparse}/lib -L$out/lib/julia -Wl,-rpath,$out/lib/julia"
 
     export GLPK_PREFIX="${glpk}/include"
 
-    mkdir -p "$out/lib"
     sed -e "s@/usr/local/lib@$out/lib@g" -i deps/Makefile
     sed -e "s@/usr/lib@$out/lib@g" -i deps/Makefile
 
@@ -112,8 +111,11 @@ stdenv.mkDerivation rec {
   preBuild = ''
     mkdir -p usr/lib
 
-    echo "$out"
     mkdir -p "$out/lib"
+    ln -s "${openblas}/lib/libopenblas.so" "$out/lib/libblas.so"
+    ln -s "${openblas}/lib/libopenblas.so" "$out/lib/liblapack.so"
+
+    echo "$out"
     (
     cd "$(mktemp -d)"
     for i in "${suitesparse}"/lib/lib*.a; do

pkgs/development/compilers/julia/0.3.nix

@@ -1,142 +1,138 @@
-{ stdenv, fetchgit, gfortran, perl, m4, llvm, gmp, pcre, zlib
+{ stdenv, fetchgit, fetchurl
- , readline, fftwSinglePrec, fftw, libunwind, suitesparse, glpk, fetchurl
+# build tools
- , ncurses, libunistring, patchelf, openblas, liblapack
+, gfortran, git, m4, patchelf, perl, which
- , tcl, tk, xproto, libX11, git, mpfr, which, wget
+# libjulia dependencies
- } :
+, libunwind, llvm, readline, utf8proc, zlib
+# standard library dependencies
+, double_conversion, fftwSinglePrec, fftw, glpk, gmp, mpfr, pcre
+, openblas, arpack, suitesparse
+}:
 
-assert stdenv.isLinux; 
+with stdenv.lib;
 
-let
-  realGcc = stdenv.cc.cc;
-in
 stdenv.mkDerivation rec {
   pname = "julia";
-  version = "0.3.6";
+  version = "0.3.9";
   name = "${pname}-${version}";
 
+  src = fetchgit {
+    url = "git://github.com/JuliaLang/julia.git";
+    rev = "refs/tags/v${version}";
+    sha256 = "ad0820affefd04eb6fba7deb2603756974711846a251900a9202b8d2665a37cf";
+    name = "julia-git-v${version}";
+  };
+
+  patches = [ ./0001-work-around-buggy-wcwidth.patch ];
+
+  extraSrcs =
+    let
       dsfmt_ver = "2.2";
-  grisu_ver = "1.1.1";
-  openblas_ver = "v0.2.13";
-  lapack_ver = "3.5.0";
-  arpack_ver = "3.1.5";
-  patchelf_ver = "0.8";
-  pcre_ver = "8.36";
-  utf8proc_ver = "1.1.6";
 
       dsfmt_src = fetchurl {
         url = "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-${dsfmt_ver}.tar.gz";
         name = "dsfmt-${dsfmt_ver}.tar.gz";
         md5 = "cb61be3be7254eae39684612c524740d";
       };
-  grisu_src = fetchurl {
+    in [ dsfmt_src ];
-    url = "http://double-conversion.googlecode.com/files/double-conversion-${grisu_ver}.tar.gz";
-    md5 = "29b533ed4311161267bff1a9a97e2953";
-  };
-  openblas_src = fetchurl {
-    url = "https://github.com/xianyi/OpenBLAS/tarball/${openblas_ver}";
-    name = "openblas-${openblas_ver}.tar.gz";
-    md5 = "74adf4c0d0d82bff4774be5bf2134183";
-  };
-  arpack_src = fetchurl rec {
-    url = "https://github.com/opencollab/arpack-ng/archive/${arpack_ver}.tar.gz";
-    md5 = "d84e1b6108d9ee67c0d21aba7099e953";
-    name = "arpack-ng-${arpack_ver}.tar.gz";
-  };
-  lapack_src = fetchurl {
-    url = "http://www.netlib.org/lapack/lapack-${lapack_ver}.tgz";
-    name = "lapack-${lapack_ver}.tgz";
-    md5 = "b1d3e3e425b2e44a06760ff173104bdf";
-  };
-  patchelf_src = fetchurl {
-    url = "http://hydra.nixos.org/build/1524660/download/2/patchelf-${patchelf_ver}.tar.bz2";
-    md5 = "5087261514b4b5814a39c3d3a36eb6ef";
-  };
-  pcre_src = fetchurl {
-    url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-${pcre_ver}.tar.bz2";
-    md5 = "b767bc9af0c20bc9c1fe403b0d41ad97";
-  };
-  utf8proc_src = fetchurl {
-    url = "http://www.public-software-group.org/pub/projects/utf8proc/v${utf8proc_ver}/utf8proc-v${utf8proc_ver}.tar.gz";
-    md5 = "2462346301fac2994c34f5574d6c3ca7";
-  };
-
-  src = fetchgit {
-    url = "git://github.com/JuliaLang/julia.git";
-    rev = "refs/tags/v${version}";
-    md5 = "d28e8f428485219f756d80c011d5dd32";
-    name = "julia-git-v${version}";
-  };
-
-  buildInputs = [ gfortran perl m4 gmp pcre llvm readline zlib
-    fftw fftwSinglePrec libunwind suitesparse glpk ncurses libunistring patchelf
-    openblas liblapack tcl tk xproto libX11 git mpfr which wget
-    ];
-
-  configurePhase = ''
-    for i in GMP LLVM PCRE READLINE FFTW LIBUNWIND SUITESPARSE GLPK ZLIB MPFR;
-    do
-      makeFlags="$makeFlags USE_SYSTEM_$i=1 "
-    done
-	makeFlags="$makeFlags JULIA_CPU_TARGET=core2";
 
+  prePatch = ''
     copy_kill_hash(){
       cp "$1" "$2/$(basename "$1" | sed -e 's/^[a-z0-9]*-//')"
     }
 
-    for i in "${grisu_src}" "${dsfmt_src}" "${arpack_src}" "${patchelf_src}" \
+    for i in $extraSrcs; do
-        "${pcre_src}" "${utf8proc_src}" "${lapack_src}" "${openblas_src}"; do
       copy_kill_hash "$i" deps
     done
+  '';
 
-    ${if realGcc ==null then "" else 
+  postPatch = ''
-    ''export NIX_LDFLAGS="$NIX_LDFLAGS -L${realGcc}/lib -L${realGcc}/lib64 -lpcre -llapack -lm -lfftw3f -lfftw3 -lglpk -lunistring -lz -lgmp -lmpfr -lblas -lopenblas -L$out/lib"''}
+    sed -i deps/Makefile \
-    export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE -fPIC "
+        -e "s@/usr/local/lib@$out/lib@g" \
-
+        -e "s@/usr/lib@$out/lib@g" \
-    export LDFLAGS="-L${suitesparse}/lib -L$out/lib/julia -Wl,-rpath,$out/lib/julia"
+        -e "s@/usr/include/double-conversion@${double_conversion}/include/double-conversion@g"
-
-    export GLPK_PREFIX="${glpk}/include"
-
-    mkdir -p "$out/lib"
-    sed -e "s@/usr/local/lib@$out/lib@g" -i deps/Makefile
-    sed -e "s@/usr/lib@$out/lib@g" -i deps/Makefile
-
-    export makeFlags="$makeFlags PREFIX=$out SHELL=${stdenv.shell} prefix=$out"
-
-    export dontPatchELF=1
-
-    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PWD/usr/lib:$PWD/usr/lib/julia"
 
     patchShebangs . contrib
 
-    export PATH="$PATH:${stdenv.cc.libc}/sbin"
-
     # ldconfig doesn't seem to ever work on NixOS; system-wide ldconfig cache
     # is probably not what we want anyway on non-NixOS
     sed -e "s@/sbin/ldconfig@true@" -i src/ccall.*
-
-    ln -s "${openblas}/lib/libopenblas.so" "$out/lib/libblas.so"
   '';
 
-  preBuild = ''
+  buildInputs =
-    mkdir -p usr/lib
+    [ libunwind llvm readline utf8proc zlib
+      double_conversion fftw fftwSinglePrec glpk gmp mpfr pcre
+      openblas arpack suitesparse
+    ];
 
-    echo "$out"
+  nativeBuildInputs = [ gfortran git m4 patchelf perl which ];
-    mkdir -p "$out/lib"
+
-    (
+  makeFlags =
-    cd "$(mktemp -d)"
+    let
-    for i in "${suitesparse}"/lib/lib*.a; do
+      arch = head (splitString "-" stdenv.system);
-      ar -x $i
+      march =
-    done
+        { "x86_64-linux" = "x86-64";
-    gcc *.o --shared -o "$out/lib/libsuitesparse.so"
+          "x86_64-darwin" = "x86-64";
-    )
+          "i686-linux" = "i686";
-    cp "$out/lib/libsuitesparse.so" usr/lib
+        }."${stdenv.system}" or (throw "unsupported system: ${stdenv.system}");
-    for i in umfpack cholmod amd camd colamd spqr; do
+    in [
-      ln -s libsuitesparse.so "$out"/lib/lib$i.so;
+      "ARCH=${arch}"
-      ln -s libsuitesparse.so "usr"/lib/lib$i.so;
+      "MARCH=${march}"
-    done
+      "JULIA_CPU_TARGET=${march}"
+      "PREFIX=$(out)"
+      "prefix=$(out)"
+      "SHELL=${stdenv.shell}"
+
+      "USE_SYSTEM_BLAS=1"
+      "LIBBLAS=-lopenblas"
+      "LIBBLASNAME=libopenblas"
+
+      "USE_SYSTEM_LAPACK=1"
+      "LIBLAPACK=-lopenblas"
+      "LIBLAPACKNAME=libopenblas"
+
+      "USE_SYSTEM_ARPACK=1"
+      "USE_SYSTEM_FFTW=1"
+      "USE_SYSTEM_GLPK=1"
+      "USE_SYSTEM_GMP=1"
+      "USE_SYSTEM_GRISU=1"
+      "USE_SYSTEM_LIBUNWIND=1"
+      "USE_SYSTEM_LLVM=1"
+      "USE_SYSTEM_MPFR=1"
+      "USE_SYSTEM_PATCHELF=1"
+      "USE_SYSTEM_PCRE=1"
+      "USE_SYSTEM_READLINE=1"
+      "USE_SYSTEM_SUITESPARSE=1"
+      "USE_SYSTEM_UTF8PROC=1"
+      "USE_SYSTEM_ZLIB=1"
+    ];
+
+  GLPK_PREFIX = "${glpk}/include";
+
+  NIX_CFLAGS_COMPILE = [ "-fPIC" ];
+
+  # Julia tries to load these libraries dynamically at runtime, but they can't be found.
+  # Easier by far to link against them as usual.
+  # These go in LDFLAGS, where they affect only Julia itself, and not NIX_LDFLAGS,
+  # where they would also be used for all the private libraries Julia builds.
+  LDFLAGS = [
+    "-larpack"
+    "-lfftw3_threads"
+    "-lfftw3f_threads"
+    "-lglpk"
+    "-lgmp"
+    "-lmpfr"
+    "-lopenblas"
+    "-lpcre"
+    "-lsuitesparse"
+    "-lz"
+  ];
+
+  preConfigure = ''
+    export PATH="$PATH:${stdenv.cc.libc}/sbin"
   '';
 
   dontStrip = true;
+  dontPatchELF = true;
 
   enableParallelBuilding = true;
 
@@ -147,8 +143,8 @@ stdenv.mkDerivation rec {
     description = "High-level performance-oriented dynamical language for technical computing";
     homepage = "http://julialang.org/";
     license = stdenv.lib.licenses.mit;
-    maintainers = [ stdenv.lib.maintainers.raskin ];
+    maintainers = with stdenv.lib.maintainers; [ raskin ttuegel ];
-    platforms = with stdenv.lib.platforms; linux;
+    platforms = [ "i686-linux" "x86_64-linux" "x86_64-darwin" ];
     broken = false;
   };
 }

pkgs/development/compilers/julia/0001-work-around-buggy-wcwidth.patch

@@ -0,0 +1,24 @@
+From b9070aeab0ab672ffe321089631f9afe263b0caa Mon Sep 17 00:00:00 2001
+From: Thomas Tuegel <ttuegel@gmail.com>
+Date: Thu, 4 Jun 2015 12:03:32 -0500
+Subject: [PATCH] work around buggy wcwidth
+
+---
+ test/unicode.jl | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/test/unicode.jl b/test/unicode.jl
+index 52c3e6a..f1ef698 100644
+--- a/test/unicode.jl
++++ b/test/unicode.jl
+@@ -103,5 +103,6 @@ end
+ 
+ # handling of embedded NUL chars (#10958)
+ @test length("\0w") == length("\0α") == 2
+-@test strwidth("\0w") == strwidth("\0α") == 1
++@test strwidth("\0w") == charwidth('\0') + charwidth('w')
++@test strwidth("\0α") == charwidth('\0') + charwidth('α')
+ @test normalize_string("\0W", casefold=true) == "\0w"
+-- 
+2.4.1
+

pkgs/development/compilers/llvm/3.4/llvm.nix

@@ -44,6 +44,7 @@ in stdenv.mkDerivation rec {
     "-DCMAKE_BUILD_TYPE=Release"
     "-DLLVM_BUILD_TESTS=ON"
     "-DLLVM_ENABLE_FFI=ON"
+    "-DLLVM_REQUIRES_RTTI=1"
     "-DLLVM_BINUTILS_INCDIR=${binutils}/include"
     "-DCMAKE_CXX_FLAGS=-std=c++11"
   ] ++ stdenv.lib.optional (!isDarwin) "-DBUILD_SHARED_LIBS=ON";

pkgs/development/compilers/uhc/default.nix

@@ -2,13 +2,13 @@
 
 let wrappedGhc = ghcWithPackages (hpkgs: with hpkgs; [shuffle hashable mtl network uhc-util uulib] );
 in stdenv.mkDerivation rec {
-  version = "1.1.9.0";
+  version = "1.1.9.1";
   name = "uhc-${version}";
 
   src = fetchgit {
     url = "https://github.com/UU-ComputerScience/uhc.git";
-    rev = "0363bbcf4cf8c47d30c3a188e3e53b3f8454bbe4";
+    rev = "c4955d01089485cdcfec785fe2bbcdf2253bee4b";
-    sha256 = "0sa9b341mm5ggmbydc33ja3h7k9w65qnki9gsaagb06gkvvqc7c2";
+    sha256 = "1n2bfbzni2hwv90z3mgn0x3l3jwc7sy8ryk81p5mlvlis1wzxnq3";
   };
 
   postUnpack = "sourceRoot=\${sourceRoot}/EHC";

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

@@ -119,6 +119,22 @@ self: super: {
   # Help libconfig find it's C language counterpart.
   libconfig = (dontCheck super.libconfig).override { config = pkgs.libconfig; };
 
+  hmatrix = overrideCabal super.hmatrix (drv: {
+    configureFlags = (drv.configureFlags or []) ++ [ "-fopenblas" ];
+    extraLibraries = [ pkgs.openblasCompat ];
+    preConfigure = ''
+      sed -i hmatrix.cabal -e 's@/usr/lib/openblas/lib@${pkgs.openblasCompat}/lib@'
+    '';
+  });
+
+  bindings-levmar = overrideCabal super.bindings-levmar (drv: {
+    preConfigure = ''
+      sed -i bindings-levmar.cabal \
+          -e 's,extra-libraries: lapack blas,extra-libraries: openblas,'
+    '';
+    extraLibraries = [ pkgs.openblas ];
+  });
+
   # The Haddock phase fails for one reason or another.
   attoparsec-conduit = dontHaddock super.attoparsec-conduit;
   base-noprelude = dontHaddock super.base-noprelude;
@@ -293,6 +309,7 @@ self: super: {
   amqp-conduit = dontCheck super.amqp-conduit;
   bitcoin-api = dontCheck super.bitcoin-api;
   bitcoin-api-extra = dontCheck super.bitcoin-api-extra;
+  bitx-bitcoin = dontCheck super.bitx-bitcoin;          # http://hydra.cryp.to/build/926187/log/raw
   concurrent-dns-cache = dontCheck super.concurrent-dns-cache;
   dbus = dontCheck super.dbus;                          # http://hydra.cryp.to/build/498404/log/raw
   hadoop-rpc = dontCheck super.hadoop-rpc;              # http://hydra.cryp.to/build/527461/nixlog/2/raw
@@ -305,6 +322,7 @@ self: super: {
   marmalade-upload = dontCheck super.marmalade-upload;  # http://hydra.cryp.to/build/501904/nixlog/1/raw
   network-transport-tcp = dontCheck super.network-transport-tcp;
   network-transport-zeromq = dontCheck super.network-transport-zeromq; # https://github.com/tweag/network-transport-zeromq/issues/30
+  pipes-mongodb = dontCheck super.pipes-mongodb;        # http://hydra.cryp.to/build/926195/log/raw
   raven-haskell = dontCheck super.raven-haskell;        # http://hydra.cryp.to/build/502053/log/raw
   riak = dontCheck super.riak;                          # http://hydra.cryp.to/build/498763/log/raw
   scotty-binding-play = dontCheck super.scotty-binding-play;
@@ -758,7 +776,7 @@ self: super: {
   dyre = appendPatch super.dyre ./dyre-nix.patch;
 
   # https://github.com/gwern/mueval/issues/9
-  mueval = markBrokenVersion "0.9.1.1" super.mueval;
+  mueval = appendPatch (appendPatch super.mueval ./mueval-fix.patch) ./mueval-nix.patch;
 
   # Test suite won't compile against tasty-hunit 0.9.x.
   zlib = dontCheck super.zlib;
@@ -847,4 +865,11 @@ self: super: {
   # Avoid spurious test suite failures.
   fft = dontCheck super.fft;
 
+  # This package can't be built on non-Windows systems.
+  Win32 = overrideCabal super.Win32 (drv: { broken = !pkgs.stdenv.isCygwin; });
+  inline-c-win32 = dontDistribute super.inline-c-win32;
+
+  # Doesn't work with recent versions of mtl.
+  cron-compat = markBroken super.cron-compat;
+
 }

pkgs/development/haskell-modules/configuration-ghc-7.10.x.nix

@@ -116,11 +116,6 @@ self: super: {
   # https://github.com/kazu-yamamoto/unix-time/issues/30
   unix-time = dontCheck super.unix-time;
 
-  # Until the changes have been pushed to Hackage
-  mueval = appendPatch super.mueval (pkgs.fetchpatch {
-    url = "https://github.com/gwern/mueval/commit/c41aa40ed63b74c069d1e4e3caa8c8d890cde960.patch";
-    sha256 = "0h1lx4z15imq009k0qmwkn5l3hmigw463ahvwffdnszi2n618kpg";
-  });
   present = appendPatch super.present (pkgs.fetchpatch {
     url = "https://github.com/chrisdone/present/commit/6a61f099bf01e2127d0c68f1abe438cd3eaa15f7.patch";
     sha256 = "1vn3xm38v2f4lzyzkadvq322f3s2yf8c88v56wpdpzfxmvlzaqr8";

pkgs/development/haskell-modules/hackage-packages.nix

@@ -10657,9 +10657,9 @@ self: {
      }:
      mkDerivation {
        pname = "Neks";
-       version = "0.3.0.0";
+       version = "0.4.0.0";
-       sha256 = "1nqww81d9hdm4d2kgv5k4vhp3wavlpa39vym4x7bddcxg1g5drmv";
+       sha256 = "0xi5d9wvk2xzsn500d61b6mmvwd36fs2n92l5qy4hzhww5lmkrrb";
-       isLibrary = false;
+       isLibrary = true;
        isExecutable = true;
        buildDepends = [
          base bytestring cereal containers directory hashable messagepack
@@ -14442,6 +14442,24 @@ self: {
        license = stdenv.lib.licenses.bsd3;
      }) {};
 
+  "TestExplode" = callPackage
+    ({ mkDerivation, base, containers, directory, fgl, graphviz
+     , interpolatedstring-perl6, mtl, process, text
+     }:
+     mkDerivation {
+       pname = "TestExplode";
+       version = "0.1.0.0";
+       sha256 = "0r4nwzwdila9p05g5y99rp06dbh1k2yl5jsc6yn6dwvxkvvdjcs1";
+       buildDepends = [
+         base containers directory fgl graphviz interpolatedstring-perl6 mtl
+         process text
+       ];
+       jailbreak = true;
+       homepage = "https://github.com/testexplode/testexplode";
+       description = "Generates testcases from program-snippets";
+       license = stdenv.lib.licenses.gpl3;
+     }) {};
+
   "Theora" = callPackage
     ({ mkDerivation, base, ogg, theora }:
      mkDerivation {
@@ -25018,6 +25036,19 @@ self: {
        license = stdenv.lib.licenses.bsd3;
      }) {};
 
+  "bindings-potrace" = callPackage
+    ({ mkDerivation, base, bindings-DSL, potrace }:
+     mkDerivation {
+       pname = "bindings-potrace";
+       version = "0.1";
+       sha256 = "0vb889f49li0lwy3zsji0f1cwzriizh9x6kg3r8676q5j08p7znd";
+       buildDepends = [ base bindings-DSL ];
+       extraLibraries = [ potrace ];
+       homepage = "https://github.com/rwbarton/bindings-potrace";
+       description = "Low-level bindings to the potrace bitmap tracing library";
+       license = stdenv.lib.licenses.gpl2;
+     }) { inherit (pkgs) potrace;};
+
   "bindings-ppdev" = callPackage
     ({ mkDerivation, base, bindings-DSL, ioctl }:
      mkDerivation {
@@ -25797,18 +25828,19 @@ self: {
      }) {};
 
   "bitx-bitcoin" = callPackage
-    ({ mkDerivation, aeson, base, bytestring, Decimal, hspec
+    ({ mkDerivation, aeson, base, bytestring, hspec, http-conduit
-     , http-conduit, network, record, split, text, time
+     , network, record, scientific, split, text, time
      }:
      mkDerivation {
        pname = "bitx-bitcoin";
-       version = "0.1.0.0";
+       version = "0.2.0.0";
-       sha256 = "05k2cwkd9y327c75fhjqwyxhwrwxhalsx724xa0ng5dw3d30icc2";
+       sha256 = "1n0hp16rpddm74q2rfldga7vpvvsqfn099qdp8qd5pqh8swkmwq8";
        buildDepends = [
-         aeson base bytestring Decimal http-conduit network record split
+         aeson base bytestring http-conduit network record scientific split
          text time
        ];
        testDepends = [ aeson base bytestring hspec record time ];
+       homepage = "https://github.com/tebello-thejane/bitx-haskell";
        description = "A Haskell library for working with the BitX bitcoin exchange";
        license = stdenv.lib.licenses.publicDomain;
      }) {};
@@ -30565,31 +30597,29 @@ self: {
 
   "chatter" = callPackage
     ({ mkDerivation, array, base, bytestring, cereal, containers
-     , deepseq, directory, filepath, fullstop, ghc-prim, HUnit, mbox
+     , deepseq, directory, filepath, fullstop, HUnit, mbox, MonadRandom
-     , MonadRandom, parsec, QuickCheck, quickcheck-instances
+     , parsec, QuickCheck, quickcheck-instances, random-shuffle
-     , random-shuffle, regex-base, regex-tdfa, regex-tdfa-text, safe
+     , regex-tdfa, regex-tdfa-text, test-framework, test-framework-hunit
-     , split, test-framework, test-framework-hunit
      , test-framework-quickcheck2, test-framework-skip, text, tokenize
      , transformers, zlib
      }:
      mkDerivation {
        pname = "chatter";
-       version = "0.5.0.1";
+       version = "0.5.0.2";
-       sha256 = "0saavfnxd6l6w3ybvdmi14ia06ssc4lndb0ba8hhyqb3qzz7l7zs";
+       sha256 = "1nbdc4np4hmvnsh1rfpldi2j1wm1klmfm9szi2kz9fa8g8n3kxxl";
        isLibrary = true;
        isExecutable = true;
        buildDepends = [
          array base bytestring cereal containers deepseq directory filepath
-         fullstop ghc-prim mbox MonadRandom parsec QuickCheck
+         fullstop mbox MonadRandom parsec QuickCheck quickcheck-instances
-         quickcheck-instances random-shuffle regex-base regex-tdfa
+         random-shuffle regex-tdfa regex-tdfa-text text tokenize
-         regex-tdfa-text safe split text tokenize transformers zlib
+         transformers zlib
        ];
        testDepends = [
          base cereal containers filepath HUnit parsec QuickCheck
          quickcheck-instances test-framework test-framework-hunit
          test-framework-quickcheck2 test-framework-skip text tokenize
        ];
-       jailbreak = true;
        homepage = "http://github.com/creswick/chatter";
        description = "A library of simple NLP algorithms";
        license = stdenv.lib.licenses.bsd3;
@@ -32800,8 +32830,8 @@ self: {
      }:
      mkDerivation {
        pname = "coinbase-exchange";
-       version = "0.1.0.0";
+       version = "0.2.0.0";
-       sha256 = "0l09gjn0lk7v51s1gw52p0m9i8amhci93qpi98p1r1nlxx09xj3v";
+       sha256 = "1x9cgdj38z1zhrx464rj3qhh8rxqs98mfpqfsnn5yill037p1ig8";
        isLibrary = true;
        isExecutable = true;
        buildDepends = [
@@ -32815,7 +32845,6 @@ self: {
          base bytestring http-client-tls http-conduit old-locale tasty
          tasty-hunit tasty-quickcheck tasty-th time transformers uuid
        ];
-       jailbreak = true;
        description = "Connector library for the coinbase exchange";
        license = stdenv.lib.licenses.mit;
        hydraPlatforms = stdenv.lib.platforms.none;
@@ -43508,8 +43537,8 @@ self: {
      }:
      mkDerivation {
        pname = "dsh-sql";
-       version = "0.2.0.1";
+       version = "0.2.0.2";
-       sha256 = "0vr9wsad74735py2i2kqwqi4phf49ksw3d4w89jlcgi6xpsc02s1";
+       sha256 = "00r1wbgbkpnza1jjd14vqr4hwgfkhnz7yivkx4bla5frfdlv5q58";
        isLibrary = true;
        isExecutable = true;
        buildDepends = [
@@ -44398,8 +44427,8 @@ self: {
     ({ mkDerivation, base, edenmodules, parallel }:
      mkDerivation {
        pname = "edenskel";
-       version = "2.0.0.2";
+       version = "2.1.0.0";
-       sha256 = "0dkvbdy04w4zbbc3q11hzzg3h5d8azka11yiiz3rvy1nkhp9wv5l";
+       sha256 = "1bf5zw1x4f6a801ig2b8b84kbnmp0asn804gkm18v9fjcchz3j9q";
        buildDepends = [ base edenmodules parallel ];
        description = "Semi-explicit parallel programming skeleton library";
        license = stdenv.lib.licenses.bsd3;
@@ -47805,6 +47834,18 @@ self: {
        license = stdenv.lib.licenses.bsd3;
      }) {};
 
+  "fay-geoposition" = callPackage
+    ({ mkDerivation, fay-base, fay-text }:
+     mkDerivation {
+       pname = "fay-geoposition";
+       version = "0.1.0.1";
+       sha256 = "1qmkwfqgvj6a8fan1l3i18ggpl00vrfd2mhqj13g0gh9yhvgxv1q";
+       buildDepends = [ fay-base fay-text ];
+       homepage = "https://github.com/victoredwardocallaghan/fay-geoposition";
+       description = "W3C compliant implementation of GeoPosition API";
+       license = stdenv.lib.licenses.bsd3;
+     }) {};
+
   "fay-hsx" = callPackage
     ({ mkDerivation, fay-base, fay-jquery }:
      mkDerivation {
@@ -52808,6 +52849,18 @@ self: {
        hydraPlatforms = stdenv.lib.platforms.none;
      }) {};
 
+  "ghc-simple" = callPackage
+    ({ mkDerivation, base, data-default, ghc, ghc-paths }:
+     mkDerivation {
+       pname = "ghc-simple";
+       version = "0.1.0.0";
+       sha256 = "0a8xla80al1glxpf0dsbzdgwbzwxmk9cr6xwfmmz237q7dv4pjhf";
+       buildDepends = [ base data-default ghc ghc-paths ];
+       homepage = "https://github.com/valderman/ghc-simple";
+       description = "Simplified interface to the GHC API";
+       license = stdenv.lib.licenses.mit;
+     }) {};
+
   "ghc-srcspan-plugin" = callPackage
     ({ mkDerivation, array, base, containers, ghc, hpc }:
      mkDerivation {
@@ -52996,8 +53049,8 @@ self: {
      }:
      mkDerivation {
        pname = "ghcid";
-       version = "0.4";
+       version = "0.4.2";
-       sha256 = "0z54444ygxc3irnqjkd9cdzg2b6df9d87lkkazj1cl2qy1x5kbv0";
+       sha256 = "094ffwwlxg7qgrcgw35rmzincfrwyhxkh6iw9bqdib5l8w9gcr6d";
        isLibrary = true;
        isExecutable = true;
        buildDepends = [
@@ -74970,6 +75023,20 @@ self: {
        license = stdenv.lib.licenses.mit;
      }) {};
 
+  "inline-c-win32" = callPackage
+    ({ mkDerivation, base, containers, inline-c, template-haskell
+     , Win32
+     }:
+     mkDerivation {
+       pname = "inline-c-win32";
+       version = "0.1";
+       sha256 = "14255dn7smmm1rpnjifn7gn2amcncnf3j45ah22bblyb4h27iikm";
+       buildDepends = [ base containers inline-c template-haskell Win32 ];
+       homepage = "https://github.com/anton-dessiatov/inline-c-win32";
+       description = "Win32 API Context for the inline-c library";
+       license = stdenv.lib.licenses.mit;
+     }) {};
+
   "inquire" = callPackage
     ({ mkDerivation, aether, base, text }:
      mkDerivation {
@@ -75598,6 +75665,23 @@ self: {
        hydraPlatforms = stdenv.lib.platforms.none;
      }) {};
 
+  "ip-quoter" = callPackage
+    ({ mkDerivation, base, network, split, tasty, tasty-hunit
+     , template-haskell
+     }:
+     mkDerivation {
+       pname = "ip-quoter";
+       version = "1.0.0.0";
+       revision = "1";
+       sha256 = "1idi03f6l9nwnsfp2mvkxz4sgwqlpa8ag3h5drb3i4hwgx0mkhfg";
+       editedCabalFile = "5cd6b449c4acd24b27d27a839acdab85f65b5556dd7bc8be115b7e2f6dc5df11";
+       buildDepends = [ base network split template-haskell ];
+       testDepends = [ base network tasty tasty-hunit ];
+       homepage = "https://github.com/shlevy/ip-quoter";
+       description = "Quasiquoter for IP addresses";
+       license = stdenv.lib.licenses.mit;
+     }) {};
+
   "ip6addr" = callPackage
     ({ mkDerivation, base, cmdargs, IPv6Addr, text }:
      mkDerivation {
@@ -81116,14 +81200,14 @@ self: {
 
   "lens-simple" = callPackage
     ({ mkDerivation, base, lens-family, lens-family-core
-     , lens-family-th
+     , lens-family-th, transformers
      }:
      mkDerivation {
        pname = "lens-simple";
-       version = "0.1.0.3";
+       version = "0.1.0.4";
-       sha256 = "17s7fjggajlamqi2lc2lrhswykbyba6zv5rf0kr24hn3mv8a6yrk";
+       sha256 = "0cr1jghg8dnyclih21zlm9190j2dyl6mwc0gw216l5yj67c5aly3";
        buildDepends = [
-         base lens-family lens-family-core lens-family-th
+         base lens-family lens-family-core lens-family-th transformers
        ];
        homepage = "https://github.com/michaelt/lens-simple";
        description = "simplified import of elementary lens-family combinators";
@@ -82370,6 +82454,18 @@ self: {
        hydraPlatforms = stdenv.lib.platforms.none;
      }) {};
 
+  "linear-grammar" = callPackage
+    ({ mkDerivation, base, hspec, QuickCheck, quickcheck-instances }:
+     mkDerivation {
+       pname = "linear-grammar";
+       version = "0.0.0.5";
+       sha256 = "0cw0w1fz3m2kwnbff543h5as9zvl66y1ry1q3ppvy9lc409570ry";
+       buildDepends = [ base ];
+       testDepends = [ base hspec QuickCheck quickcheck-instances ];
+       description = "A simple grammar for building linear equations and inclusive inequalities";
+       license = stdenv.lib.licenses.bsd3;
+     }) {};
+
   "linear-maps" = callPackage
     ({ mkDerivation, base, containers, HUnit }:
      mkDerivation {
@@ -84756,9 +84852,12 @@ self: {
      mkDerivation {
        pname = "machinecell";
        version = "1.3.1";
+       revision = "1";
        sha256 = "1v4rrjszh6sm2x1nwq33f4xwa41bnls0awhy9qfkap62bpad8fxg";
+       editedCabalFile = "5a7ee43c327694ac753228da8f16d681a60d23b4926132726e2a093ecacb4725";
        buildDepends = [ arrows base free mtl profunctors semigroups ];
        testDepends = [ base hspec mtl profunctors QuickCheck ];
+       jailbreak = true;
        homepage = "http://github.com/as-capabl/machinecell";
        description = "Arrow based stream transducers";
        license = stdenv.lib.licenses.bsd3;
@@ -90266,16 +90365,17 @@ self: {
      }) {};
 
   "multistate" = callPackage
-    ({ mkDerivation, base, mtl, transformers }:
+    ({ mkDerivation, base, hspec, mtl, tagged, transformers }:
      mkDerivation {
        pname = "multistate";
-       version = "0.3.0.0";
+       version = "0.6.0.0";
-       sha256 = "1sqaxvvs94max8gw1sz3kkgnp8y9zwrjdclnzv1kkkhciix9a1d1";
+       sha256 = "17b54qy4dgacj0lwy61nf3hbppd950xk9c1yphjn6i6jcr8z66li";
        isLibrary = true;
        isExecutable = true;
-       buildDepends = [ base mtl transformers ];
+       buildDepends = [ base mtl tagged transformers ];
+       testDepends = [ base hspec transformers ];
        homepage = "https://github.com/lspitzner/multistate";
-       description = "like mtl's ReaderT/WriterT/StateT, but more than one contained value/type";
+       description = "like mtl's ReaderT / WriterT / StateT, but more than one contained value/type";
        license = stdenv.lib.licenses.bsd3;
      }) {};
 
@@ -95856,8 +95956,8 @@ self: {
      }:
      mkDerivation {
        pname = "pandoc-citeproc";
-       version = "0.7.1.1";
+       version = "0.7.2";
-       sha256 = "1n96g7l16cn1qcp9xsbdmp844078lpcjsz3lg1x81drnzax9fpa1";
+       sha256 = "0dpr74alkz9vy5yc09bnqb968hcrqys2xlydjda1g3qsarjg7p9y";
        isLibrary = true;
        isExecutable = true;
        buildDepends = [
@@ -95870,7 +95970,6 @@ self: {
          aeson base bytestring directory filepath pandoc pandoc-types
          process temporary text yaml
        ];
-       jailbreak = true;
        description = "Supports using pandoc with citeproc";
        license = stdenv.lib.licenses.bsd3;
      }) {};
@@ -95881,8 +95980,8 @@ self: {
      }:
      mkDerivation {
        pname = "pandoc-crossref";
-       version = "0.1.2.0";
+       version = "0.1.2.1";
-       sha256 = "0q9ia1nzmzv1q8hplrmxszwk49mlp4v8skbfv4ggsl8s0vxc1c6f";
+       sha256 = "1hr2jfbzanpqbkvsfcbzvlfsnzba11hdrmvc3j63fwqk931qi2jm";
        isLibrary = false;
        isExecutable = true;
        buildDepends = [
@@ -98829,6 +98928,19 @@ self: {
        license = stdenv.lib.licenses.bsd3;
      }) {};
 
+  "pipes-mongodb" = callPackage
+    ({ mkDerivation, base, monad-control, mongoDB, pipes, text }:
+     mkDerivation {
+       pname = "pipes-mongodb";
+       version = "0.1.0.0";
+       sha256 = "0h4334fajrza7r8jrr78nqhs522kxnbzdj0gnbp7ndvzvx5ij888";
+       buildDepends = [ base monad-control mongoDB pipes ];
+       testDepends = [ base monad-control mongoDB pipes text ];
+       homepage = "http://github.com/jb55/pipes-mongodb";
+       description = "Stream results from MongoDB";
+       license = stdenv.lib.licenses.mit;
+     }) {};
+
   "pipes-network" = callPackage
     ({ mkDerivation, base, bytestring, network, network-simple, pipes
      , pipes-safe, transformers
@@ -100642,6 +100754,34 @@ self: {
        hydraPlatforms = stdenv.lib.platforms.none;
      }) { inherit (pkgs) adns;  inherit (pkgs) openssl;};
 
+  "potrace" = callPackage
+    ({ mkDerivation, base, bindings-potrace, bytestring, containers
+     , data-default, JuicyPixels, vector
+     }:
+     mkDerivation {
+       pname = "potrace";
+       version = "0.1.0.0";
+       sha256 = "1frxf3jzjyyp3bfj6b2mi29fxwcml4bya6sn4c5aizg741dhphng";
+       buildDepends = [
+         base bindings-potrace bytestring containers data-default
+         JuicyPixels vector
+       ];
+       description = "Trace bitmap images to paths using potrace";
+       license = stdenv.lib.licenses.gpl2;
+     }) {};
+
+  "potrace-diagrams" = callPackage
+    ({ mkDerivation, base, diagrams-lib, JuicyPixels, potrace }:
+     mkDerivation {
+       pname = "potrace-diagrams";
+       version = "0.1.0.0";
+       sha256 = "0ys70a5k384czz0c6bpyy0cqrk35wa1yg6ph19smhm3ag9d8161v";
+       buildDepends = [ base diagrams-lib JuicyPixels potrace ];
+       homepage = "http://projects.haskell.org/diagrams/";
+       description = "Potrace bindings for the diagrams library";
+       license = stdenv.lib.licenses.gpl2;
+     }) {};
+
   "powermate" = callPackage
     ({ mkDerivation, base, directory, network, unix }:
      mkDerivation {
@@ -108719,6 +108859,24 @@ self: {
        hydraPlatforms = stdenv.lib.platforms.none;
      }) {};
 
+  "safe-printf" = callPackage
+    ({ mkDerivation, base, doctest, haskell-src-meta, hspec, QuickCheck
+     , template-haskell, th-lift
+     }:
+     mkDerivation {
+       pname = "safe-printf";
+       version = "0.1.0.0";
+       sha256 = "19nw306q7xlj6s132qxlfskg67x6rx3zhsk2n6lbz2kryr7v99g6";
+       buildDepends = [ base haskell-src-meta template-haskell th-lift ];
+       testDepends = [
+         base doctest haskell-src-meta hspec QuickCheck template-haskell
+         th-lift
+       ];
+       homepage = "https://github.com/konn/safe-printf";
+       description = "Well-typed, flexible and variadic printf for Haskell";
+       license = stdenv.lib.licenses.bsd3;
+     }) {};
+
   "safecopy" = callPackage
     ({ mkDerivation, array, base, bytestring, cereal, containers, lens
      , lens-action, old-time, quickcheck-instances, tasty
@@ -109533,8 +109691,8 @@ self: {
      }:
      mkDerivation {
        pname = "schedule-planner";
-       version = "1.0.0.1";
+       version = "1.0.1.0";
-       sha256 = "0p2k67g281f08njhann4yv0vhfbjh4m6rr2x58smxhwqxgpjg399";
+       sha256 = "0vlr4wwazpr7xf5pym2f42gwniy017h02wwymn0zn80wypiv6dz1";
        isLibrary = false;
        isExecutable = true;
        buildDepends = [
@@ -118894,8 +119052,8 @@ test/package-dump/ghc-7.10.txt";
      }:
      mkDerivation {
        pname = "structural-induction";
-       version = "0.2";
+       version = "0.2.0.1";
-       sha256 = "1lr91wc1m655pi3ljw3n89svfazrb16785s9mfx361jgn335m8rd";
+       sha256 = "0ac5yhx6cbxzcdqy74lp791xwgammsnd8jazx0xy3ngxn4wwf23r";
        buildDepends = [ base containers genifunctors mtl pretty safe ];
        testDepends = [
          base geniplate language-haskell-extract mtl pretty QuickCheck safe
@@ -124568,6 +124726,46 @@ test/package-dump/ghc-7.10.txt";
        license = stdenv.lib.licenses.mit;
      }) {};
 
+  "tip-haskell-frontend" = callPackage
+    ({ mkDerivation, base, bytestring, containers, directory, filepath
+     , geniplate-mirror, ghc, ghc-paths, mtl, pretty, pretty-show
+     , QuickCheck, split, tip-lib
+     }:
+     mkDerivation {
+       pname = "tip-haskell-frontend";
+       version = "0.1.1";
+       sha256 = "0za8ls980f98qj3k6pgmzaidmnrlk0nzg1r7skif6jmhh1snqc5h";
+       isLibrary = true;
+       isExecutable = true;
+       buildDepends = [
+         base bytestring containers directory filepath geniplate-mirror ghc
+         ghc-paths mtl pretty pretty-show QuickCheck split tip-lib
+       ];
+       homepage = "http://tip-org.github.io";
+       description = "Convert from Haskell to Tip";
+       license = stdenv.lib.licenses.bsd3;
+     }) {};
+
+  "tip-lib" = callPackage
+    ({ mkDerivation, alex, array, base, containers, geniplate-mirror
+     , happy, mtl, optparse-applicative, pretty, pretty-show, split
+     }:
+     mkDerivation {
+       pname = "tip-lib";
+       version = "0.1.1";
+       sha256 = "0xvsr6hh7r6y82linkpvbby6jkxw744y3mh82kma4cbpwc84gxhi";
+       isLibrary = true;
+       isExecutable = true;
+       buildDepends = [
+         array base containers geniplate-mirror mtl optparse-applicative
+         pretty pretty-show split
+       ];
+       buildTools = [ alex happy ];
+       homepage = "http://tip-org.github.io";
+       description = "tons of inductive problems - support library and tools";
+       license = stdenv.lib.licenses.bsd3;
+     }) {};
+
   "titlecase" = callPackage
     ({ mkDerivation, base, blaze-markup, semigroups, tasty, tasty-hunit
      , tasty-quickcheck, text
@@ -125699,6 +125897,28 @@ test/package-dump/ghc-7.10.txt";
        license = stdenv.lib.licenses.bsd3;
      }) {};
 
+  "trurl" = callPackage
+    ({ mkDerivation, aeson, base, bytestring, directory, hastache
+     , http-conduit, MissingH, scientific, tar, tasty, tasty-hunit, text
+     , unordered-containers
+     }:
+     mkDerivation {
+       pname = "trurl";
+       version = "0.1.0.0";
+       sha256 = "0lq4x3vkif6sldcw07llmhwixgk1x2bfyzi0zq32jardp7ah0rc5";
+       isLibrary = true;
+       isExecutable = true;
+       buildDepends = [
+         aeson base bytestring directory hastache http-conduit MissingH
+         scientific tar text unordered-containers
+       ];
+       testDepends = [ base hastache tasty tasty-hunit ];
+       jailbreak = true;
+       homepage = "http://github.com/dbushenko/trurl";
+       description = "Haskell template code generator";
+       license = stdenv.lib.licenses.bsd3;
+     }) {};
+
   "tsession" = callPackage
     ({ mkDerivation, base, containers, mtl, time, transformers }:
      mkDerivation {
@@ -127361,6 +127581,7 @@ test/package-dump/ghc-7.10.txt";
          hashable mtl network old-locale primitive process syb transformers
          uhc-util uulib vector
        ];
+       jailbreak = true;
        homepage = "https://github.com/UU-ComputerScience/uhc";
        description = "Part of UHC packaged as cabal/hackage installable library";
        license = stdenv.lib.licenses.bsd3;
@@ -127373,8 +127594,8 @@ test/package-dump/ghc-7.10.txt";
      }:
      mkDerivation {
        pname = "uhc-util";
-       version = "0.1.5.5";
+       version = "0.1.5.6";
-       sha256 = "00b1ycdnm0gm01izs96qwsx3c3p1mrcimzamscaimyr1y14jvfc1";
+       sha256 = "1axg2apkvg3xk1cq78shbnc68i0h6fqcpjg8z3l4nc49kl5dywwz";
        buildDepends = [
          array base binary bytestring containers directory fclabels fgl
          hashable ListLike mtl process syb time time-compat uulib

pkgs/development/haskell-modules/mueval-fix.patch

@@ -0,0 +1,90 @@
+diff --git a/Mueval/ArgsParse.hs b/Mueval/ArgsParse.hs
+index 05c8fd9..0c32e27 100644
+--- a/Mueval/ArgsParse.hs
++++ b/Mueval/ArgsParse.hs
+@@ -1,10 +1,9 @@
++{-# LANGUAGE CPP #-}
+ module Mueval.ArgsParse (Options(..), interpreterOpts, getOptions) where
+ 
+ import Control.Monad (liftM)
+ import System.Console.GetOpt
+ 
+-import qualified Codec.Binary.UTF8.String as Codec (decodeString)
+-
+ import Mueval.Context (defaultModules, defaultPackages)
+ 
+ -- | See the results of --help for information on what each option means.
+@@ -98,4 +97,11 @@ header = "Usage: mueval [OPTION...] --expression EXPRESSION..."
+ -- | Just give us the end result options; this parsing for
+ --   us. Bonus points for handling UTF.
+ getOptions :: [String] -> Either (Bool, String) Options
+-getOptions = interpreterOpts . map Codec.decodeString
+\ No newline at end of file
++getOptions = interpreterOpts . map decodeString
++
++decodeString :: String -> String
++#if __GLASGOW_HASKELL__ >= 702
++decodeString = id
++#else
++decodeString = Codec.decodeString
++#endif
+diff --git a/Mueval/Context.hs b/Mueval/Context.hs
+index 78925cf..548514c 100644
+--- a/Mueval/Context.hs
++++ b/Mueval/Context.hs
+@@ -1,3 +1,4 @@
++{-# LANGUAGE CPP #-}
+ module Mueval.Context (
+   cleanModules,
+   defaultModules,
+@@ -32,7 +33,9 @@ defaultModules = ["Prelude",
+                   "Control.Monad.Error",
+                   "Control.Monad.Fix",
+                   "Control.Monad.Identity",
++#if !MIN_VERSION_base(4,7,0)
+                   "Control.Monad.Instances",
++#endif
+                   "Control.Monad.RWS",
+                   "Control.Monad.Reader",
+                   "Control.Monad.State",
+diff --git a/Mueval/Interpreter.hs b/Mueval/Interpreter.hs
+index 29b771f..6c39482 100644
+--- a/Mueval/Interpreter.hs
++++ b/Mueval/Interpreter.hs
+@@ -1,4 +1,5 @@
+ {-# LANGUAGE PatternGuards #-}
++{-# LANGUAGE FlexibleContexts #-}
+ -- TODO: suggest the convenience functions be put into Hint proper?
+ module Mueval.Interpreter where
+ 
+@@ -12,8 +13,6 @@ import System.Exit (exitFailure)
+ import System.FilePath.Posix (takeFileName)
+ import qualified Control.Exception.Extensible as E (evaluate,catch,SomeException(..))
+ 
+-import qualified System.IO.UTF8 as UTF (putStrLn)
+-
+ import Language.Haskell.Interpreter (eval, set, reset, setImportsQ, loadModules, liftIO,
+                                      installedModulesInScope, languageExtensions,
+                                      typeOf, setTopLevelModules, runInterpreter, glasgowExtensions,
+@@ -100,7 +99,7 @@ mvload lfl = do canonfile <- makeRelativeToCurrentDirectory lfl
+ -- flooding. Lambdabot has a similar limit.
+ sayIO :: String -> IO ()
+ sayIO str = do (out,b) <- render 1024 str
+-               UTF.putStrLn out
++               putStrLn out
+                when b exitFailure
+ 
+ -- | Oh no, something has gone wrong. If it's a compilation error pretty print
+diff --git a/mueval.cabal b/mueval.cabal
+index 3f9406d..b86d796 100644
+--- a/mueval.cabal
++++ b/mueval.cabal
+@@ -32,7 +32,7 @@ library
+         exposed-modules:     Mueval.Parallel, Mueval.Context, Mueval.Interpreter,
+                              Mueval.ArgsParse, Mueval.Resources
+         build-depends:       base>=4 && < 5, containers, directory, mtl>2, filepath, unix, process,
+-                             hint>=0.3.1, show>=0.3, utf8-string, Cabal, extensible-exceptions, simple-reflect
++                             hint>=0.3.1, show>=0.3, Cabal, extensible-exceptions, simple-reflect
+         ghc-options:         -Wall -static
+ 
+ executable mueval-core

pkgs/development/interpreters/gnu-apl/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, liblapack, readline, gettext, ncurses }:
+{ stdenv, fetchurl, readline, gettext, ncurses }:
 
 stdenv.mkDerivation rec {
   name = "gnu-apl-${version}";
@@ -9,7 +9,7 @@ stdenv.mkDerivation rec {
     sha256 = "0h4diq3wfbdwxp5nm0z4b0p1zq13lwip0y7v28r9v0mbbk8xsfh1";
   };
 
-  buildInputs = [ liblapack readline gettext ncurses ];
+  buildInputs = [ readline gettext ncurses ];
 
   postInstall = ''
     cp -r support-files/ $out/share/doc/

pkgs/development/interpreters/octave/default.nix

@@ -1,10 +1,22 @@
 { stdenv, fetchurl, gfortran, readline, ncurses, perl, flex, texinfo, qhull
-, libX11, graphicsmagick, pcre, liblapack, pkgconfig, mesa, fltk
+, libX11, graphicsmagick, pcre, pkgconfig, mesa, fltk
-, fftw, fftwSinglePrec, zlib, curl, qrupdate
+, fftw, fftwSinglePrec, zlib, curl, qrupdate, openblas
 , qt ? null, qscintilla ? null, ghostscript ? null, llvm ? null, hdf5 ? null,glpk ? null
 , suitesparse ? null, gnuplot ? null, jdk ? null, python ? null
 }:
 
+let
+  suitesparseOrig = suitesparse;
+  qrupdateOrig = qrupdate;
+in
+# integer width is determined by openblas, so all dependencies must be built
+# with exactly the same openblas
+let
+  suitesparse =
+    if suitesparseOrig != null then suitesparseOrig.override { inherit openblas; } else null;
+  qrupdate = if qrupdateOrig != null then qrupdateOrig.override { inherit openblas; } else null;
+in
+
 stdenv.mkDerivation rec {
   version = "4.0.0";
   name = "octave-${version}";
@@ -14,7 +26,7 @@ stdenv.mkDerivation rec {
   };
 
   buildInputs = [ gfortran readline ncurses perl flex texinfo qhull libX11
-    graphicsmagick pcre liblapack pkgconfig mesa fltk zlib curl
+    graphicsmagick pcre pkgconfig mesa fltk zlib curl openblas
     fftw fftwSinglePrec qrupdate ]
     ++ (stdenv.lib.optional (qt != null) qt)
     ++ (stdenv.lib.optional (qscintilla != null) qscintilla)
@@ -34,7 +46,13 @@ stdenv.mkDerivation rec {
   # problems on Hydra
   enableParallelBuilding = false;
 
-  configureFlags = [ "--enable-readline" "--enable-dl" ];
+  configureFlags =
+    [ "--enable-readline"
+      "--enable-dl"
+      "--with-blas=openblas"
+      "--with-lapack=openblas"
+    ]
+    ++ stdenv.lib.optional openblas.blas64 "--enable-64";
 
   # Keep a copy of the octave tests detailed results in the output
   # derivation, because someone may care

pkgs/development/interpreters/php/5.4.nix

@@ -1,6 +1,6 @@
 { callPackage, apacheHttpd }:
 callPackage ./generic.nix {
-  phpVersion = "5.4.41";
+  phpVersion = "5.4.42";
-  sha = "0wl27f5z6vymajm2bzfp440zsp1jdxqn71avryiq1zw029db9i2v";
+  sha = "1yg03b6a88i7hg593m9zmmcm4kr59wdrhz9xk1frx9ps9gkb51b2";
   apacheHttpd = apacheHttpd;
 }

pkgs/development/interpreters/php/5.6.nix

@@ -1,6 +1,6 @@
 { callPackage, apacheHttpd  }:
 callPackage ./generic.nix {
-  phpVersion = "5.6.9";
+  phpVersion = "5.6.10";
-  sha = "1fdwk8g509gxd5ad3y1s3j49hfkjdg8mgmzn9ki3pflbgdxvilqr";
+  sha = "0iccgibmbc659z6dh6c58l1b7vnqly7al37fbs0l3si4qy0rqmqa";
   apacheHttpd = apacheHttpd;
 }

pkgs/development/interpreters/pypy/default.nix

@@ -6,8 +6,8 @@ assert zlibSupport -> zlib != null;
 
 let
 
-  majorVersion = "2.5";
+  majorVersion = "2.6";
-  version = "${majorVersion}.1";
+  version = "${majorVersion}.0";
   libPrefix = "pypy${majorVersion}";
 
   pypy = stdenv.mkDerivation rec {
@@ -18,7 +18,7 @@ let
 
     src = fetchurl {
       url = "https://bitbucket.org/pypy/pypy/get/release-${version}.tar.bz2";
-      sha256 = "0gzhgc0rh5ywpkvzishpvkninl41r5k207y8afa8vxwpfx03vcrj";
+      sha256 = "0xympj874cnjpxj68xm5gllq2f8bbvz8hr0md8mh1yd6fgzzxibh";
     };
 
     buildInputs = [ bzip2 openssl pkgconfig pythonFull libffi ncurses expat sqlite tk tcl x11 libX11 makeWrapper ]

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

@@ -1,11 +1,11 @@
 { stdenv, fetchurl, self, callPackage
-, bzip2, openssl
+, bzip2, openssl, gettext
 
 , includeModules ? false
 
 , db, gdbm, ncurses, sqlite, readline
 
-, tcl ? null, tk ? null, x11 ? null, libX11 ? null, x11Support ? true
+, tcl ? null, tk ? null, x11 ? null, libX11 ? null, x11Support ? !stdenv.isCygwin
 , zlib ? null, zlibSupport ? true
 , expat, libffi
 }:
@@ -224,7 +224,7 @@ let
     gdbm = buildInternalPythonModule {
       moduleName = "gdbm";
       internalName = "gdbm";
-      deps = [ gdbm ];
+      deps = [ gdbm ] ++ stdenv.lib.optional stdenv.isCygwin gettext;
     };
 
     sqlite3 = buildInternalPythonModule {

pkgs/development/libraries/apr-util/default.nix

@@ -1,7 +1,7 @@
 { stdenv, fetchurl, makeWrapper, apr, expat, gnused
 , sslSupport ? true, openssl
 , bdbSupport ? false, db
-, ldapSupport ? true, openldap
+, ldapSupport ? !stdenv.isCygwin, openldap
 , libiconv
 }:
 
@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
 
   configureFlags = ''
     --with-apr=${apr} --with-expat=${expat}
-    --with-crypto
+    ${if !stdenv.isCygwin then "--with-crypto" else "--without-pgsql --without-sqlite2 --without-sqlite3 --without-freetds --without-berkeley-db --without-crypto"}
     ${stdenv.lib.optionalString sslSupport "--with-openssl=${openssl}"}
     ${stdenv.lib.optionalString bdbSupport "--with-berkeley-db=${db}"}
     ${stdenv.lib.optionalString ldapSupport "--with-ldap"}

pkgs/development/libraries/ffmpeg/0.11.nix

@@ -1,7 +0,0 @@
-{ callPackage, ... } @ args:
-
-callPackage ./generic.nix (args // rec {
-  version = "${branch}.5";
-  branch = "0.11";
-  sha256 = "1h5qwn4h7sppqw36hri5p6zlv2387vwaxh2pyj070xfn8hgrk4ll";
-})

pkgs/development/libraries/goffice/0.8.nix

@@ -1,6 +1,6 @@
 { fetchurl, stdenv, pkgconfig, glib, gtk, libglade, bzip2
 , pango, libgsf, libxml2, libart, intltool, gettext
-, cairo, gconf, libgnomeui, pcre, gnome3/*just meta*/ }:
+, cairo, gconf, libgnomeui, pcre, goffice/*just meta*/ }:
 
 stdenv.mkDerivation rec {
   name = "goffice-0.8.17";
@@ -31,7 +31,7 @@ stdenv.mkDerivation rec {
 
   doCheck = true;
 
-  meta = gnome3.goffice.meta // {
+  meta = goffice.meta // {
     maintainers = [ ];
   };
 }

pkgs/development/libraries/libedit/01-cygwin.patch

@@ -0,0 +1,25 @@
+--- libedit-20120311-3.0/src/chartype.h	2012-03-11 10:54:58.000000000 +0100
++++ libedit-20120311-3.0/src/chartype.h	2012-05-03 19:00:20.651847423 +0200
+@@ -56,9 +56,11 @@
+ /* Oh for a <uchar.h> with char32_t and __STDC_UTF_32__ in it...
+  * ref: ISO/IEC DTR 19769
+  */
++#ifndef __CYGWIN__
+ #if WCHAR_MAX < INT32_MAX
+ #warning Build environment does not support non-BMP characters
+ #endif
++#endif
+ 
+ #ifndef HAVE_WCSDUP
+ wchar_t *wcsdup(const wchar_t *s);
+--- libedit-20120311-3.0/src/editline/readline.h	2011-02-26 23:42:59.000000000 +0100
++++ libedit-20120311-3.0/src/editline/readline.h	2012-05-03 19:00:49.211244803 +0200
+@@ -75,7 +75,7 @@ typedef KEYMAP_ENTRY *Keymap;
+ 
+ #ifndef CTRL
+ #include <sys/ioctl.h>
+-#if !defined(__sun) && !defined(__hpux) && !defined(_AIX)
++#if !defined(__sun) && !defined(__hpux) && !defined(_AIX) && !defined(__CYGWIN__)
+ #include <sys/ttydefaults.h>
+ #endif
+ #ifndef CTRL

pkgs/development/libraries/libedit/default.nix

@@ -11,6 +11,10 @@ stdenv.mkDerivation rec {
   # Have `configure' avoid `/usr/bin/nroff' in non-chroot builds.
   NROFF = "${groff}/bin/nroff";
 
+  patches = if stdenv.isCygwin then [
+    ./01-cygwin.patch
+  ] else null;
+
   postInstall = ''
     sed -i ${stdenv.lib.optionalString (stdenv.isDarwin && stdenv.cc.nativeTools) "''"} s/-lncurses/-lncursesw/g $out/lib/pkgconfig/libedit.pc
   '';

pkgs/development/libraries/libevent/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, autoreconfHook, python }:
+{ stdenv, fetchFromGitHub, autoreconfHook, python, findutils }:
 
 let version = "2.0.22"; in
 stdenv.mkDerivation {
@@ -12,7 +12,7 @@ stdenv.mkDerivation {
   };
 
   nativeBuildInputs = [ autoreconfHook ];
-  buildInputs = [ python ];
+  buildInputs = [ python ] ++ stdenv.lib.optional stdenv.isCygwin findutils;
 
   patchPhase = ''
     patchShebangs event_rpcgen.py

pkgs/development/libraries/libical/respect-env-tzdir.patch

@@ -1,28 +1,25 @@
-diff --git a/src/libical/icaltz-util.c b/src/libical/icaltz-util.c
+--- a/src/libical/icaltz-util.c	2015-06-11 15:40:58.843138630 +0200
-index fe984c9..22ba0a1 100644
++++ b/src/libical/icaltz-util.c	2015-06-11 15:43:12.722046252 +0200
---- a/src/libical/icaltz-util.c
+@@ -107,7 +107,7 @@
-+++ b/src/libical/icaltz-util.c
-@@ -107,7 +107,7 @@ typedef struct
  	char	charcnt[4];			
  } tzinfo; 
  
 -static char *search_paths [] = {"/usr/share/zoneinfo","/usr/lib/zoneinfo","/etc/zoneinfo","/usr/share/lib/zoneinfo"};
-+static char *search_paths [] = {"/etc/zoneinfo"};
++static char *search_paths [] = {"/etc/zoneinfo","/usr/share/zoneinfo","/usr/lib/zoneinfo","/usr/share/lib/zoneinfo"};
  static char *zdir = NULL;
  
  #define NUM_SEARCH_PATHS (sizeof (search_paths)/ sizeof (search_paths [0]))
-@@ -194,6 +194,16 @@ set_zonedir (void)
+@@ -194,6 +194,15 @@
  	const char *fname = ZONES_TAB_SYSTEM_FILENAME;
  	unsigned int i;
  
-+	const char *env_tzdir = strdup (getenv ("TZDIR"));
++	const char *env_tzdir = getenv ("TZDIR");
 +	if (env_tzdir) {
 +		sprintf (file_path, "%s/%s", env_tzdir, fname);
 +		if (!access (file_path, F_OK|R_OK)) {
 +			zdir = env_tzdir;
 +			return;
 +		}
-+		free (env_tzdir);
 +	}
 +
  	for (i = 0; i < NUM_SEARCH_PATHS; i++) {

pkgs/development/libraries/libtermkey/default.nix

@@ -10,7 +10,8 @@ stdenv.mkDerivation rec {
     sha256 = "085mdshgqsn76gfnnzfns7awv6lals9mgv5a6bybd9f9aj7lvrm5";
   };
 
-  makeFlags = [ "PREFIX=$(out)" ];
+  makeFlags = [ "PREFIX=$(out)" ]
+    ++ stdenv.lib.optional stdenv.isDarwin "LIBTOOL=${libtool}/bin/libtool";
 
   buildInputs = [ libtool pkgconfig ncurses ];
 

pkgs/development/libraries/qrupdate/default.nix

@@ -1,7 +1,7 @@
 { stdenv
 , fetchurl
 , gfortran
-, liblapack
+, openblas
 }:
 stdenv.mkDerivation {
   name = "qrupdate-1.1.2";
@@ -10,20 +10,25 @@ stdenv.mkDerivation {
     sha256 = "024f601685phcm1pg8lhif3lpy5j9j0k6n0r46743g4fvh8wg8g2";
   };
 
-  configurePhase = ''
+  configurePhase =
+    ''
       export PREFIX=$out
-    sed -i -e 's,^BLAS=.*,BLAS=-L${liblapack}/lib -L${liblapack.blas} -lcblas -lf77blas -latlas,' \
+      sed -i -e 's,^BLAS=.*,BLAS=-L${openblas}/lib -lopenblas,' \
-      -e 's,^LAPACK=.*,LAPACK=-L${liblapack}/lib -llapack -lcblas -lf77blas -latlas,' \
+          -e 's,^LAPACK=.*,LAPACK=-L${openblas}/lib -lopenblas,' \
           Makeconf
+    ''
+    + stdenv.lib.optionalString openblas.blas64
+    ''
+      sed -i Makeconf -e '/^FFLAGS=.*/ s/$/-fdefault-integer-8/'
     '';
 
   doCheck = true;
 
   checkTarget = "test";
 
-  buildTarget = "lib";
+  buildFlags = [ "lib" "solib" ];
 
-  installTarget = "install-staticlib";
+  installTargets = "install";
 
-  buildInputs = [ gfortran liblapack ];
+  buildInputs = [ gfortran openblas ];
 }

pkgs/development/libraries/qt-5/5.4/0100-ssl.patch

@@ -0,0 +1,13 @@
+diff --git a/qtbase/src/network/ssl/qsslsocket_openssl.cpp b/qtbase/src/network/ssl/qsslsocket_openssl.cpp
+index 8833e3f..c56d381 100644
+--- a/qtbase/src/network/ssl/qsslsocket_openssl.cpp
++++ b/qtbase/src/network/ssl/qsslsocket_openssl.cpp
+@@ -47,7 +47,7 @@
+ ****************************************************************************/
+ 
+ //#define QSSLSOCKET_DEBUG
+-//#define QT_DECRYPT_SSL_TRAFFIC
++#define QT_DECRYPT_SSL_TRAFFIC
+ 
+ #include "qssl_p.h"
+ #include "qsslsocket_openssl_p.h"

pkgs/development/libraries/qt-5/5.4/default.nix

@@ -20,6 +20,7 @@
 
 # options
 , developerBuild ? false
+, decryptSslTraffic ? false
 }:
 
 with autonix;
@@ -61,7 +62,7 @@ let
         # GNOME dependencies are not used unless gtkStyle == true
         inherit (gnome) libgnomeui GConf gnome_vfs;
         bison = bison2; # error: too few arguments to function 'int yylex(...
-        inherit developerBuild srcs version;
+        inherit developerBuild srcs version decryptSslTraffic;
       };
 
       connectivity = callPackage

pkgs/development/libraries/qt-5/5.4/qtbase.nix

@@ -20,6 +20,7 @@
 , buildTests ? false
 , developerBuild ? false
 , gtkStyle ? false, libgnomeui, GConf, gnome_vfs, gtk
+, decryptSslTraffic ? false
 }:
 
 with stdenv.lib;
@@ -68,7 +69,8 @@ stdenv.mkDerivation {
       (substituteAll { src = ./0011-dlopen-openssl.patch; inherit openssl; })
       (substituteAll { src = ./0012-dlopen-dbus.patch; dbus_libs = dbus; })
       ./0013-xdg_config_dirs.patch
-    ];
+    ]
+    ++ (optional decryptSslTraffic ./0100-ssl.patch);
 
   preConfigure = ''
     export LD_LIBRARY_PATH="$PWD/qtbase/lib:$PWD/qtbase/plugins/platforms:$PWD/qttools/lib:$LD_LIBRARY_PATH"

pkgs/development/libraries/science/math/arpack/default.nix

@@ -1,4 +1,6 @@
-{ stdenv, fetchurl, gfortran, atlasWithLapack }:
+{ stdenv, fetchurl, gfortran, openblas }:
+
+with stdenv.lib;
 
 let
   version = "3.2.0";
@@ -10,10 +12,15 @@ stdenv.mkDerivation {
     sha256 = "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff";
   };
 
-  buildInputs = [ gfortran atlasWithLapack ];
+  buildInputs = [ gfortran openblas ];
 
   # Auto-detection fails because gfortran brings in BLAS by default
-  configureFlags="--with-blas=-latlas --with-lapack=-latlas";
+  configureFlags = [
+    "--with-blas=-lopenblas"
+    "--with-lapack=-lopenblas"
+  ];
+
+  FFLAGS = optional openblas.blas64 "-fdefault-integer-8";
 
   meta = {
     homepage = "http://forge.scilab.org/index.php/p/arpack-ng/";

pkgs/development/libraries/science/math/ipopt/default.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, unzip, blas, liblapack, gfortran }:
+{ stdenv, fetchurl, unzip, openblas, gfortran }:
 
 stdenv.mkDerivation rec {
   version = "3.12.3";
@@ -13,9 +13,14 @@ stdenv.mkDerivation rec {
      export CXXDEFS="-DHAVE_RAND -DHAVE_CSTRING -DHAVE_CSTDIO"
   '';
 
+  configureFlags = [
+    "--with-blas-lib=-lopenblas"
+    "--with-lapack-lib=-lopenblas"
+  ];
+
   nativeBuildInputs = [ unzip ];
 
-  buildInputs = [ gfortran blas liblapack ];
+  buildInputs = [ gfortran openblas ];
 
   enableParallelBuilding = true;
 

pkgs/development/libraries/science/math/openblas/0.2.10.nix

@@ -1,37 +0,0 @@
-{ stdenv, fetchurl, gfortran, perl, liblapack, config }:
-
-let local = config.openblas.preferLocalBuild or false;
-    localTarget = config.openblas.target or "";
-in
-stdenv.mkDerivation rec {
-  version = "0.2.10";
-
-  name = "openblas-${version}";
-  src = fetchurl {
-    url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}";
-    sha256 = "06i0q4qnd5q5xljzrgvda0gjsczc6l2pl9hw6dn2qjpw38al73za";
-    name = "openblas-${version}.tar.gz";
-  };
-
-  preBuild = "cp ${liblapack.src} lapack-${liblapack.meta.version}.tgz";
-
-  buildInputs = [gfortran perl];
-
-  cpu = builtins.head (stdenv.lib.splitString "-" stdenv.system);
-
-  target = if local then localTarget else
-    if cpu == "i686" then "P2" else
-    if cpu == "x86_64" then "CORE2" else
-     # allow autodetect
-      "";
-
-  makeFlags = "${if target != "" then "TARGET=" else ""}${target} FC=gfortran CC=cc PREFIX=\"\$(out)\" INTERFACE64=1";
-
-  meta = with stdenv.lib; {
-    description = "Basic Linear Algebra Subprograms";
-    license = licenses.bsd3;
-    homepage = "https://github.com/xianyi/OpenBLAS";
-    platforms = [ "x86_64-linux" ];
-    maintainers = with maintainers; [ ttuegel ];
-  };
-}

pkgs/development/libraries/science/math/openblas/0.2.2.nix

@@ -1,37 +0,0 @@
-{ stdenv, fetchurl, gfortran, perl, liblapack, config }:
-
-let local = config.openblas.preferLocalBuild or false;
-    localTarget = config.openblas.target or "";
-in
-stdenv.mkDerivation rec {
-  version = "0.2.2";
-
-  name = "openblas-${version}";
-  src = fetchurl {
-    url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}";
-    sha256 = "13kdx3knff5ajnmgn419g0dnh83plin07p7akwamr3v7z5qfrzqr";
-    name = "openblas-${version}.tar.gz";
-  };
-
-  preBuild = "cp ${liblapack.src} lapack-${liblapack.meta.version}.tgz";
-
-  buildInputs = [gfortran perl];
-
-  cpu = builtins.head (stdenv.lib.splitString "-" stdenv.system);
-
-  target = if local then localTarget else
-    if cpu == "i686" then "P2" else
-    if cpu == "x86_64" then "CORE2" else
-     # allow autodetect
-      "";
-
-  makeFlags = "${if target != "" then "TARGET=" else ""}${target} FC=gfortran CC=cc PREFIX=\"\$(out)\"";
-
-  meta = with stdenv.lib; {
-    description = "Basic Linear Algebra Subprograms";
-    license = licenses.bsd3;
-    homepage = "https://github.com/xianyi/OpenBLAS";
-    platforms = [ "x86_64-linux" ];
-    maintainers = with maintainers; [ ttuegel ];
-  };
-}

pkgs/development/libraries/science/math/openblas/default.nix

@@ -1,22 +1,24 @@
-{ stdenv, fetchurl, gfortran, perl, liblapack, config, coreutils }:
+{ stdenv, fetchurl, gfortran, perl, liblapack, config, coreutils
+# Most packages depending on openblas expect integer width to match pointer width,
+# but some expect to use 32-bit integers always (for compatibility with reference BLAS).
+, blas64 ? null
+}:
 
 with stdenv.lib;
 
 let local = config.openblas.preferLocalBuild or false;
     binary =
-      {
+      { i686-linux = "32";
-        i686-linux = "32";
         x86_64-linux = "64";
         x86_64-darwin = "64";
       }."${stdenv.system}" or (throw "unsupported system: ${stdenv.system}");
     genericFlags =
-      [
+      [ "DYNAMIC_ARCH=1"
-        "DYNAMIC_ARCH=1"
         "NUM_THREADS=64"
-        "BINARY=${binary}"
       ];
     localFlags = config.openblas.flags or
       optionals (hasAttr "target" config.openblas) [ "TARGET=${config.openblas.target}" ];
+    blas64Orig = blas64;
 in
 stdenv.mkDerivation rec {
   version = "0.2.14";
@@ -43,9 +45,13 @@ stdenv.mkDerivation rec {
       # thus is not an explicit dependency.
       "CC=${if stdenv.isDarwin then "clang" else "gcc"}"
       ''PREFIX="''$(out)"''
-      "INTERFACE64=1"
+      "BINARY=${binary}"
+      "USE_OPENMP=${if stdenv.isDarwin then "0" else "1"}"
+      "INTERFACE64=${if blas64 then "1" else "0"}"
     ];
 
+  blas64 = if blas64Orig != null then blas64Orig else hasPrefix "x86_64" stdenv.system;
+
   meta = with stdenv.lib; {
     description = "Basic Linear Algebra Subprograms";
     license = licenses.bsd3;

pkgs/development/libraries/science/math/suitesparse/0001-disable-metis.patch

@@ -1,36 +0,0 @@
-From 456b26d0c9101adaa5876954baac0ca0e872dab6 Mon Sep 17 00:00:00 2001
-From: Thomas Tuegel <ttuegel@gmail.com>
-Date: Mon, 15 Dec 2014 10:18:01 -0600
-Subject: [PATCH 1/3] disable metis
-
----
- SuiteSparse_config/SuiteSparse_config.mk | 6 +++---
- 1 file changed, 3 insertions(+), 3 deletions(-)
-
-diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
-index ba2da23..e1514bf 100644
---- a/SuiteSparse_config/SuiteSparse_config.mk
-+++ b/SuiteSparse_config/SuiteSparse_config.mk
-@@ -212,8 +212,8 @@ XERBLA =
- # The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
- # You may wish to use an absolute path.  METIS is optional.  Compile
- # CHOLMOD with -DNPARTITION if you do not wish to use METIS.
--METIS_PATH = ../../metis-4.0
--METIS = ../../metis-4.0/libmetis.a
-+# METIS_PATH = ../../metis-4.0
-+# METIS = ../../metis-4.0/libmetis.a
- 
- #------------------------------------------------------------------------------
- # UMFPACK configuration:
-@@ -273,7 +273,7 @@ UMFPACK_CONFIG =
- # -DNSUNPERF        for Solaris only.  If defined, do not use the Sun
- #                   Performance Library
- 
--CHOLMOD_CONFIG = $(GPU_CONFIG)
-+CHOLMOD_CONFIG = $(GPU_CONFIG) -DNPARTITION
- 
- # uncomment this line to compile CHOLMOD without METIS:
- # CHOLMOD_CONFIG = -DNPARTITION
--- 
-2.1.3
-

pkgs/development/libraries/science/math/suitesparse/0002-set-install-dir.patch

@@ -1,27 +0,0 @@
-From e0fee492a315ce1ef8697b056af210beb1465334 Mon Sep 17 00:00:00 2001
-From: Thomas Tuegel <ttuegel@gmail.com>
-Date: Mon, 15 Dec 2014 10:18:12 -0600
-Subject: [PATCH 2/3] set install dir
-
----
- SuiteSparse_config/SuiteSparse_config.mk | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
-index e1514bf..f1046a6 100644
---- a/SuiteSparse_config/SuiteSparse_config.mk
-+++ b/SuiteSparse_config/SuiteSparse_config.mk
-@@ -95,8 +95,8 @@ F77LIB =
- # LIB = -lm
- 
- # For "make install"
--INSTALL_LIB = /usr/local/lib
--INSTALL_INCLUDE = /usr/local/include
-+INSTALL_LIB = @out@/lib
-+INSTALL_INCLUDE = @out@/include
- 
- # Which version of MAKE you are using (default is "make")
- # MAKE = make
--- 
-2.1.3
-

pkgs/development/libraries/science/math/suitesparse/0003-blas-lapack-flags.patch

@@ -1,27 +0,0 @@
-From a99cca30cfd965683564ae024e8ecc615c61697a Mon Sep 17 00:00:00 2001
-From: Thomas Tuegel <ttuegel@gmail.com>
-Date: Mon, 15 Dec 2014 10:24:08 -0600
-Subject: [PATCH 3/3] blas lapack flags
-
----
- SuiteSparse_config/SuiteSparse_config.mk | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
-index f1046a6..1710162 100644
---- a/SuiteSparse_config/SuiteSparse_config.mk
-+++ b/SuiteSparse_config/SuiteSparse_config.mk
-@@ -119,8 +119,8 @@ INSTALL_INCLUDE = @out@/include
- # naming the BLAS and LAPACK library (*.a or *.so) files.
- 
- # This is probably slow ... it might connect to the Standard Reference BLAS:
--  BLAS = -lblas -lgfortran
--  LAPACK = -llapack
-+  BLAS = @blasFlags@
-+  LAPACK = @lapackFlags@
- 
- # MKL 
- # BLAS = -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -lpthread -lm
--- 
-2.1.3
-

pkgs/development/libraries/science/math/suitesparse/4.2.nix

@@ -1,4 +1,8 @@
-{ stdenv, fetchurl, blas, liblapack, gfortran } :
+{ stdenv, fetchurl, gfortran, openblas }:
+
+let
+  int_t = if openblas.blas64 then "int64_t" else "int32_t";
+in
 stdenv.mkDerivation rec {
   version = "4.2.1";
   name = "suitesparse-${version}";
@@ -6,17 +10,35 @@ stdenv.mkDerivation rec {
     url = "http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-${version}.tar.gz" ;
     sha256 = "1ga69637x7kdkiy3w3lq9dvva7220bdangv2lch2wx1hpi83h0p8";
   };
-  buildInputs = [blas liblapack gfortran] ;
+
-  patches = [./disable-metis.patch];
+  nativeBuildInputs = [ gfortran ];
+  buildInputs = [ openblas ];
 
   preConfigure = ''
-    export PREFIX=$out
     mkdir -p $out/lib
     mkdir -p $out/include
+
+    sed -i "SuiteSparse_config/SuiteSparse_config.mk" \
+        -e 's/METIS .*$/METIS =/' \
+        -e 's/METIS_PATH .*$/METIS_PATH =/' \
+        -e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION -DLONGBLAS=${int_t}/' \
+        -e '/UMFPACK_CONFIG/ s/$/-DLONGBLAS=${int_t}/'
   '';
 
-  makeFlags = ''PREFIX=\"$(out)\" INSTALL_LIB=$(out)/lib INSTALL_INCLUDE=$(out)/include'';
+  makeFlags = [
+    "PREFIX=\"$(out)\""
+    "INSTALL_LIB=$(out)/lib"
+    "INSTALL_INCLUDE=$(out)/include"
+    "BLAS=-lopenblas"
+    "LAPACK="
+  ];
 
   NIX_CFLAGS = "-fPIC";
 
+  meta = with stdenv.lib; {
+    homepage = http://faculty.cse.tamu.edu/davis/suitesparse.html;
+    description = "A suite of sparse matrix algorithms";
+    license = with licenses; [ bsd2 gpl2Plus lgpl21Plus ];
+    maintainers = with maintainers; [ ttuegel ];
+  };
 }

pkgs/development/libraries/science/math/suitesparse/SuiteSparse_config.mk

@@ -1,452 +0,0 @@
-#===============================================================================
-# SuiteSparse_config.mk:  common configuration file for the SuiteSparse
-#===============================================================================
-
-# This file contains all configuration settings for all packages authored or
-# co-authored by Tim Davis:
-#
-# Package Version       Description
-# ------- -------       -----------
-# AMD     1.2 or later  approximate minimum degree ordering
-# COLAMD  2.4 or later  column approximate minimum degree ordering
-# CCOLAMD 1.0 or later  constrained column approximate minimum degree ordering
-# CAMD    any           constrained approximate minimum degree ordering
-# UMFPACK 4.5 or later  sparse LU factorization, with the BLAS
-# CHOLMOD any           sparse Cholesky factorization, update/downdate
-# KLU     0.8 or later  sparse LU factorization, BLAS-free
-# BTF     0.8 or later  permutation to block triangular form
-# LDL     1.2 or later  concise sparse LDL'
-# CXSparse any          extended version of CSparse (int/long, real/complex)
-# SuiteSparseQR any     sparse QR factorization
-# RBio    2.0 or later  read/write sparse matrices in Rutherford-Boeing format
-#
-# By design, this file is NOT included in the CSparse makefile.
-# That package is fully stand-alone.  CSparse is primarily for teaching;
-# production code should use CXSparse.
-#
-# The SuiteSparse_config directory and the above packages should all appear in
-# a single directory, in order for the Makefile's within each package to find
-# this file.
-#
-# To enable an option of the form "# OPTION = ...", edit this file and
-# delete the "#" in the first column of the option you wish to use.
-#
-# The use of METIS 4.0.1 is optional.  To exclude METIS, you must compile with
-# CHOLMOD_CONFIG set to -DNPARTITION.  See below for details.  However, if you
-# do not have a metis-4.0 directory inside the SuiteSparse directory, the
-# */Makefile's that optionally rely on METIS will automatically detect this
-# and compile without METIS.
-
-#------------------------------------------------------------------------------
-# Generic configuration
-#------------------------------------------------------------------------------
-
-# Using standard definitions from the make environment, typically:
-#
-#   CC              cc      C compiler
-#   CXX             g++     C++ compiler
-#   CFLAGS          [ ]     flags for C and C++ compiler
-#   CPPFLAGS        [ ]     flags for C and C++ compiler
-#   TARGET_ARCH     [ ]     target architecture
-#   FFLAGS          [ ]     flags for Fortran compiler
-#   RM              rm -f   delete a file
-#   AR              ar      create a static *.a library archive
-#   ARFLAGS         rv      flags for ar
-#   MAKE            make    make itself (sometimes called gmake)
-#
-# You can redefine them here, but by default they are used from the
-# default make environment.
-
-# To use OpenMP add -openmp to the CFLAGS
-# If OpenMP is used, it is recommended to define CHOLMOD_OMP_NUM_THREADS
-# as the number of cores per socket on the machine being used to maximize
-# memory performance
-  CFLAGS = 
-# CFLAGS = -g
-# for the icc compiler and OpenMP:
-# CFLAGS = -openmp
-
-# C and C++ compiler flags.  The first three are standard for *.c and *.cpp
-# Add -DNTIMER if you do use any timing routines (otherwise -lrt is required).
-# CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O3 -fexceptions -fPIC -DNTIMER
-  CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O3 -fexceptions -fPIC
-# for the MKL BLAS:
-# CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O3 -fexceptions -fPIC -I$(MKLROOT)/include -D_GNU_SOURCE
-# with no optimization:
-# CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH)     -fexceptions -fPIC
-
-# ranlib, and ar, for generating libraries.  If you don't need ranlib,
-# just change it to RANLAB = echo
-RANLIB = ranlib
-ARCHIVE = $(AR) $(ARFLAGS)
-
-# copy and delete a file
-CP = cp -f
-MV = mv -f
-
-# Fortran compiler (not required for 'make' or 'make library')
-F77 = gfortran
-F77FLAGS = $(FFLAGS) -O
-F77LIB =
-
-# C and Fortran libraries.  Remove -lrt if you don't have it.
-  LIB = -lm -lrt
-# Using the following requires CF = ... -DNTIMER on POSIX C systems.
-# LIB = -lm
-
-# For "make install"
-INSTALL_LIB = @out@/lib
-INSTALL_INCLUDE = @out@/include
-
-# Which version of MAKE you are using (default is "make")
-# MAKE = make
-# MAKE = gmake
-
-#------------------------------------------------------------------------------
-# BLAS and LAPACK configuration:
-#------------------------------------------------------------------------------
-
-# UMFPACK and CHOLMOD both require the BLAS.  CHOLMOD also requires LAPACK.
-# See Kazushige Goto's BLAS at http://www.cs.utexas.edu/users/flame/goto/ or
-# http://www.tacc.utexas.edu/~kgoto/ for the best BLAS to use with CHOLMOD.
-# LAPACK is at http://www.netlib.org/lapack/ .  You can use the standard
-# Fortran LAPACK along with Goto's BLAS to obtain very good performance.
-# CHOLMOD gets a peak numeric factorization rate of 3.6 Gflops on a 3.2 GHz
-# Pentium 4 (512K cache, 4GB main memory) with the Goto BLAS, and 6 Gflops
-# on a 2.5Ghz dual-core AMD Opteron.
-
-# These settings will probably not work, since there is no fixed convention for
-# naming the BLAS and LAPACK library (*.a or *.so) files.
-
-# This is probably slow ... it might connect to the Standard Reference BLAS:
-  BLAS = -lf77blas -latlas -lcblas -lgfortran
-  LAPACK = -llapack -latlas -lcblas
-
-# MKL 
-# BLAS = -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a $(MKLROOT)/lib/intel64/libmkl_core.a $(MKLROOT)/lib/intel64/libmkl_intel_thread.a -Wl,--end-group -lpthread -lm
-# LAPACK = 
-
-# ACML
-# BLAS = -lacml -lgfortran
-# LAPACK =
-
-# OpenBLAS
-# BLAS = -lopenblas
-# LAPACK = 
-
-# NOTE: this next option for the "Goto BLAS" has nothing to do with a "goto"
-# statement.  Rather, the Goto BLAS is written by Dr. Kazushige Goto.
-# Using the Goto BLAS:
-# BLAS = -lgoto -lgfortran -lgfortranbegin
-# BLAS = -lgoto2 -lgfortran -lgfortranbegin -lpthread
-
-# Using non-optimized versions:
-# BLAS = -lblas_plain -lgfortran -lgfortranbegin
-# LAPACK = -llapack_plain
-
-# BLAS = -lblas_plain -lgfortran -lgfortranbegin
-# LAPACK = -llapack
-
-# The BLAS might not contain xerbla, an error-handling routine for LAPACK and
-# the BLAS.  Also, the standard xerbla requires the Fortran I/O library, and
-# stops the application program if an error occurs.  A C version of xerbla
-# distributed with this software (SuiteSparse_config/xerbla/libcerbla.a)
-# includes a Fortran-callable xerbla routine that prints nothing and does not
-# stop the application program.  This is optional.
-
-# XERBLA = ../../SuiteSparse_config/xerbla/libcerbla.a 
-
-# If you wish to use the XERBLA in LAPACK and/or the BLAS instead,
-# use this option:
-XERBLA = 
-
-# If you wish to use the Fortran SuiteSparse_config/xerbla/xerbla.f instead,
-# use this:
-
-# XERBLA = ../../SuiteSparse_config/xerbla/libxerbla.a 
-
-#------------------------------------------------------------------------------
-# GPU configuration for CHOLMOD and SPQR
-#------------------------------------------------------------------------------
-
-# no cuda
-  CUDA_ROOT     =
-  GPU_BLAS_PATH =
-  GPU_CONFIG    =
-  CUDA_PATH     =
-  CUDART_LIB    =
-  CUBLAS_LIB    =
-  CUDA_INC_PATH =
-  NV20          =
-  NV30          =
-  NV35          =
-  NVCC          = echo
-  NVCCFLAGS     =
-
-# with cuda for CHOLMOD
-# CUDA_ROOT     = /usr/local/cuda
-# GPU_BLAS_PATH = $(CUDA_ROOT)
-# with 4 cores (default):
-# GPU_CONFIG    = -I$(CUDA_ROOT)/include -DGPU_BLAS
-# with 10 cores:
-# GPU_CONFIG    = -I$(CUDA_ROOT)/include -DGPU_BLAS -DCHOLMOD_OMP_NUM_THREADS=10
-# CUDA_PATH     = $(CUDA_ROOT)
-# CUDART_LIB    = $(CUDA_ROOT)/lib64/libcudart.so
-# CUBLAS_LIB    = $(CUDA_ROOT)/lib64/libcublas.so
-# CUDA_INC_PATH = $(CUDA_ROOT)/include/
-# NV20          = -arch=sm_20 -Xcompiler -fPIC
-# NV30          = -arch=sm_30 -Xcompiler -fPIC
-# NV35          = -arch=sm_35 -Xcompiler -fPIC
-# NVCC          = $(CUDA_ROOT)/bin/nvcc
-# NVCCFLAGS     = $(NV20) -O3 -gencode=arch=compute_20,code=sm_20 -gencode=arch=compute_30,code=sm_30 -gencode=arch=compute_35,code=sm_35
-
-# was NVCC      = $(CUDA_ROOT)/bin/nvcc $(NV35) $(NV30) $(NV20)
-
-#------------------------------------------------------------------------------
-# METIS, optionally used by CHOLMOD
-#------------------------------------------------------------------------------
-
-# If you do not have METIS, or do not wish to use it in CHOLMOD, you must
-# compile CHOLMOD with the -DNPARTITION flag.
-
-# The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
-# You may wish to use an absolute path.  METIS is optional.  Compile
-# CHOLMOD with -DNPARTITION if you do not wish to use METIS.
-# METIS_PATH = ../../metis-4.0
-# METIS = ../../metis-4.0/libmetis.a
-
-#------------------------------------------------------------------------------
-# UMFPACK configuration:
-#------------------------------------------------------------------------------
-
-# Configuration flags for UMFPACK.  See UMFPACK/Source/umf_config.h for details.
-#
-# -DNBLAS       do not use the BLAS.  UMFPACK will be very slow.
-# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
-#               LAPACK and the BLAS (defaults to 'int')
-# -DNSUNPERF    do not use the Sun Perf. Library (default is use it on Solaris)
-# -DNRECIPROCAL do not multiply by the reciprocal
-# -DNO_DIVIDE_BY_ZERO   do not divide by zero
-# -DNCHOLMOD    do not use CHOLMOD as a ordering method.  If -DNCHOLMOD is
-#               included in UMFPACK_CONFIG, then UMFPACK  does not rely on
-#               CHOLMOD, CAMD, CCOLAMD, COLAMD, and METIS.
-
-UMFPACK_CONFIG =
-
-# uncomment this line to compile UMFPACK without CHOLMOD:
-# UMFPACK_CONFIG = -DNCHOLMOD
-
-#------------------------------------------------------------------------------
-# CHOLMOD configuration
-#------------------------------------------------------------------------------
-
-# CHOLMOD Library Modules, which appear in libcholmod.a:
-# Core          requires: none
-# Check         requires: Core
-# Cholesky      requires: Core, AMD, COLAMD.  optional: Partition, Supernodal
-# MatrixOps     requires: Core
-# Modify        requires: Core
-# Partition     requires: Core, CCOLAMD, METIS.  optional: Cholesky
-# Supernodal    requires: Core, BLAS, LAPACK
-#
-# CHOLMOD test/demo Modules (all are GNU GPL, do not appear in libcholmod.a):
-# Tcov          requires: Core, Check, Cholesky, MatrixOps, Modify, Supernodal
-#               optional: Partition
-# Valgrind      same as Tcov
-# Demo          requires: Core, Check, Cholesky, MatrixOps, Supernodal
-#               optional: Partition
-#
-# Configuration flags:
-# -DNCHECK          do not include the Check module.       License GNU LGPL
-# -DNCHOLESKY       do not include the Cholesky module.    License GNU LGPL
-# -DNPARTITION      do not include the Partition module.   License GNU LGPL
-#                   also do not include METIS.
-# -DNCAMD           do not use CAMD, etc from Partition module.    GNU LGPL
-# -DNGPL            do not include any GNU GPL Modules in the CHOLMOD library:
-# -DNMATRIXOPS      do not include the MatrixOps module.   License GNU GPL
-# -DNMODIFY         do not include the Modify module.      License GNU GPL
-# -DNSUPERNODAL     do not include the Supernodal module.  License GNU GPL
-#
-# -DNPRINT          do not print anything.
-# -D'LONGBLAS=long' or -DLONGBLAS='long long' defines the integers used by
-#                   LAPACK and the BLAS (defaults to 'int')
-# -DNSUNPERF        for Solaris only.  If defined, do not use the Sun
-#                   Performance Library
-
-CHOLMOD_CONFIG = $(GPU_CONFIG) -DNPARTITION
-
-# uncomment this line to compile CHOLMOD without METIS:
-# CHOLMOD_CONFIG = -DNPARTITION
-
-#------------------------------------------------------------------------------
-# SuiteSparseQR configuration:
-#------------------------------------------------------------------------------
-
-# The SuiteSparseQR library can be compiled with the following options:
-#
-# -DNPARTITION      do not include the CHOLMOD partition module
-# -DNEXPERT         do not include the functions in SuiteSparseQR_expert.cpp
-# -DHAVE_TBB        enable the use of Intel's Threading Building Blocks (TBB)
-
-# default, without timing, without TBB:
-SPQR_CONFIG = $(GPU_CONFIG)
-# with TBB:
-# SPQR_CONFIG = -DHAVE_TBB
-
-# This is needed for IBM AIX: (but not for and C codes, just C++)
-# SPQR_CONFIG = -DBLAS_NO_UNDERSCORE
-
-# with TBB, you must select this:
-# TBB = -ltbb
-# without TBB:
-TBB =
-
-#------------------------------------------------------------------------------
-# code formatting
-#------------------------------------------------------------------------------
-
-# Use "grep" only, if you do not have "indent"  
-# PRETTY = grep -v "^\#"
-# PRETTY = grep -v "^\#" | indent -bl -nce -ss -bli0 -i4 -sob -l120
-  PRETTY = grep -v "^\#" | indent -bl -nce -bli0 -i4 -sob -l120
-
-#------------------------------------------------------------------------------
-# Linux
-#------------------------------------------------------------------------------
-
-# Using default compilers:
-# CC = gcc
-# CF = $(CFLAGS) -O3 -fexceptions
-
-# alternatives:
-# CF = $(CFLAGS) -g -fexceptions \
-#       -Wall -W -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
-#       -Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi \
-#       -funit-at-a-time
-# CF = $(CFLAGS) -O3 -fexceptions \
-#       -Wall -W -Werror -Wshadow -Wmissing-prototypes -Wstrict-prototypes \
-#       -Wredundant-decls -Wnested-externs -Wdisabled-optimization -ansi
-# CF = $(CFLAGS) -O3 -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
-# CF = $(CFLAGS) -O3
-# CF = $(CFLAGS) -O3 -g -fexceptions
-# CF = $(CFLAGS) -g -fexceptions \
-#       -Wall -W -Wshadow \
-#       -Wredundant-decls -Wdisabled-optimization -ansi
-
-# consider:
-# -fforce-addr -fmove-all-movables -freduce-all-givs -ftsp-ordering
-# -frename-registers -ffast-math -funroll-loops
-
-# Using the Goto BLAS:
-# BLAS = -lgoto -lfrtbegin -lg2c $(XERBLA) -lpthread
-
-# Using Intel's icc and ifort compilers:
-#   (does not work for mexFunctions unless you add a mexopts.sh file)
-# F77 = ifort
-# CC = icc
-# CF = $(CFLAGS) -O3 -xN -vec_report=0
-# CF = $(CFLAGS) -g
-
-# 64bit:
-# F77FLAGS = -O -m64
-# CF = $(CFLAGS) -O3 -fexceptions -m64
-# BLAS = -lgoto64 -lfrtbegin -lg2c -lpthread $(XERBLA)
-# LAPACK = -llapack64
-
-# SUSE Linux 10.1, AMD Opteron, with GOTO Blas
-# F77 = gfortran
-# BLAS = -lgoto_opteron64 -lgfortran
-
-# SUSE Linux 10.1, Intel Pentium, with GOTO Blas
-# F77 = gfortran
-# BLAS = -lgoto -lgfortran
-
-#------------------------------------------------------------------------------
-# Mac
-#------------------------------------------------------------------------------
-
-# As recommended by macports, http://suitesparse.darwinports.com/
-# I've tested them myself on Mac OSX 10.6.1 and 10.6.8 (Snow Leopard),
-# on my MacBook Air, and they work fine.
-
-# F77 = gfortran
-# CF = $(CFLAGS) -O3 -fno-common -fexceptions -DNTIMER
-# BLAS = -framework Accelerate
-# LAPACK = -framework Accelerate
-# LIB = -lm
-
-#------------------------------------------------------------------------------
-# Solaris
-#------------------------------------------------------------------------------
-
-# 32-bit
-# CF = $(CFLAGS) -KPIC -dalign -xc99=%none -Xc -xlibmieee -xO5 -xlibmil -m32
-
-# 64-bit
-# CF = $(CFLAGS) -fast -KPIC -xc99=%none -xlibmieee -xlibmil -m64 -Xc
-
-# FFLAGS = -fast -KPIC -dalign -xlibmil -m64
-
-# The Sun Performance Library includes both LAPACK and the BLAS:
-# BLAS = -xlic_lib=sunperf
-# LAPACK =
-
-
-#------------------------------------------------------------------------------
-# Compaq Alpha
-#------------------------------------------------------------------------------
-
-# 64-bit mode only
-# CF = $(CFLAGS) -O2 -std1
-# BLAS = -ldxml
-# LAPACK =
-
-#------------------------------------------------------------------------------
-# IBM RS 6000
-#------------------------------------------------------------------------------
-
-# BLAS = -lessl
-# LAPACK =
-
-# 32-bit mode:
-# CF = $(CFLAGS) -O4 -qipa -qmaxmem=16384 -qproto
-# F77FLAGS = -O4 -qipa -qmaxmem=16384
-
-# 64-bit mode:
-# CF = $(CFLAGS) -O4 -qipa -qmaxmem=16384 -q64 -qproto
-# F77FLAGS = -O4 -qipa -qmaxmem=16384 -q64
-
-#------------------------------------------------------------------------------
-# SGI IRIX
-#------------------------------------------------------------------------------
-
-# BLAS = -lscsl
-# LAPACK =
-
-# 32-bit mode
-# CF = $(CFLAGS) -O
-
-# 64-bit mode (32 bit int's and 64-bit long's):
-# CF = $(CFLAGS) -64
-# F77FLAGS = -64
-
-# SGI doesn't have ranlib
-# RANLIB = echo
-
-#------------------------------------------------------------------------------
-# AMD Opteron (64 bit)
-#------------------------------------------------------------------------------
-
-# BLAS = -lgoto_opteron64 -lg2c
-# LAPACK = -llapack_opteron64
-
-# SUSE Linux 10.1, AMD Opteron
-# F77 = gfortran
-# BLAS = -lgoto_opteron64 -lgfortran
-# LAPACK = -llapack_opteron64
-
-#------------------------------------------------------------------------------
-# remove object files and profile output
-#------------------------------------------------------------------------------
-
-CLEAN = *.o *.obj *.ln *.bb *.bbg *.da *.tcov *.gcov gmon.out *.bak *.d *.gcda *.gcno

pkgs/development/libraries/science/math/suitesparse/default.nix

@@ -1,34 +1,53 @@
-{ stdenv, fetchurl, substituteAll
+{ stdenv, fetchurl, gfortran, openblas }:
-, atlasWithLapack, gfortran }:
 
 let
-  name = "suitesparse-4.4.1";
+  version = "4.4.4";
+  name = "suitesparse-${version}";
+
+  int_t = if openblas.blas64 then "int64_t" else "int32_t";
 in
 stdenv.mkDerivation {
   inherit name;
 
   src = fetchurl {
-    url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.1.tar.gz";
+    url = "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-${version}.tar.gz";
-    sha256 = "0y8i6dizrr556xggpjyc7wijjv4jbizhssmjj4jv8n1s7zxy2z0n";
+    sha256 = "1zdn1y0ij6amj7smmcslkqgbqv9yy5cwmbyzqc9v6drzdzllgbpj";
   };
 
-  patches = [
-    ./0001-disable-metis.patch
-    ./0002-set-install-dir.patch
-    (substituteAll {
-      src = ./0003-blas-lapack-flags.patch;
-      blasFlags = "-lf77blas -latlas -lcblas -lgfortran";
-      lapackFlags= "-llapack -latlas -lcblas";
-    })
-  ];
-
   preConfigure = ''
-    substituteAllInPlace SuiteSparse_config/SuiteSparse_config.mk
     mkdir -p $out/lib
     mkdir -p $out/include
+
+    sed -i "SuiteSparse_config/SuiteSparse_config.mk" \
+        -e 's/METIS .*$/METIS =/' \
+        -e 's/METIS_PATH .*$/METIS_PATH =/' \
+        -e '/CHOLMOD_CONFIG/ s/$/-DNPARTITION -DLONGBLAS=${int_t}/' \
+        -e '/UMFPACK_CONFIG/ s/$/-DLONGBLAS=${int_t}/'
   '';
 
+  makeFlags = [
+    "PREFIX=\"$(out)\""
+    "INSTALL_LIB=$(out)/lib"
+    "INSTALL_INCLUDE=$(out)/include"
+    "BLAS=-lopenblas"
+    "LAPACK="
+  ];
+
+  NIX_CFLAGS = "-fPIC";
+
   postInstall = ''
+    # Build and install shared library
+    (
+        cd "$(mktemp -d)"
+        for i in "$out"/lib/lib*.a; do
+          ar -x $i
+        done
+        gcc *.o --shared -o "$out/lib/libsuitesparse.so"
+    )
+    for i in umfpack cholmod amd camd colamd spqr; do
+      ln -s libsuitesparse.so "$out"/lib/lib$i.so;
+    done
+
     # Install documentation
     outdoc=$out/share/doc/${name}
     mkdir -p $outdoc
@@ -47,7 +66,7 @@ stdenv.mkDerivation {
   '';
 
   nativeBuildInputs = [ gfortran ];
-  buildInputs = [ atlasWithLapack ];
+  buildInputs = [ openblas ];
 
   meta = with stdenv.lib; {
     homepage = http://faculty.cse.tamu.edu/davis/suitesparse.html;

pkgs/development/libraries/science/math/suitesparse/disable-metis.patch

@@ -1,18 +0,0 @@
-diff -Nrc SuiteSparse/UMFPACK/Demo/Makefile SuiteSparse-new/UMFPACK/Demo/Makefile
-*** SuiteSparse/UMFPACK/Demo/Makefile	2009-11-11 21:09:45.000000000 +0100
---- SuiteSparse-new/UMFPACK/Demo/Makefile	2010-08-02 12:53:16.000000000 +0200
-***************
-*** 40,46 ****
-  ../../CAMD/Lib/libcamd.a:
-  	( cd ../../CAMD ; $(MAKE) library )
-  
-- $(METIS):
-- 	( cd $(METIS_PATH) && $(MAKE) )
-  
-  UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \
---- 40,44 ----
-  ../../CAMD/Lib/libcamd.a:
-  	( cd ../../CAMD ; $(MAKE) library )
-  
-  
-  UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \

pkgs/development/libraries/serf/default.nix

@@ -8,7 +8,9 @@ stdenv.mkDerivation rec {
     sha256 = "1bphz616dv1svc50kkm8xbgyszhg3ni2dqbij99sfvjycr7bgk7c";
   };
 
-  buildInputs = [ apr scons openssl aprutil zlib kerberos pkgconfig ];
+  buildInputs = [ apr scons openssl aprutil zlib ]
+    ++ stdenv.lib.optional (!stdenv.isCygwin) kerberos
+    ++ [ pkgconfig ];
 
   configurePhase = ''
     ${gnused}/bin/sed -e '/^env[.]Append(BUILDERS/ienv.Append(ENV={"PATH":os.environ["PATH"]})' -i SConstruct
@@ -21,7 +23,7 @@ stdenv.mkDerivation rec {
         APU="$(echo "${aprutil}"/bin/*-config)" CC="${
           if stdenv.isDarwin then "clang" else "${stdenv.cc}/bin/gcc"
         }" ${
-          if stdenv.isDarwin then "" else "GSSAPI=\"${kerberos}\""
+          if (stdenv.isDarwin || stdenv.isCygwin) then "" else "GSSAPI=\"${kerberos}\""
         }
   '';
 

pkgs/development/libraries/sqlite/default.nix

@@ -3,11 +3,11 @@
 assert interactive -> readline != null && ncurses != null;
 
 stdenv.mkDerivation {
-  name = "sqlite-3.8.10.1";
+  name = "sqlite-3.8.10.2";
 
   src = fetchurl {
-    url = "http://sqlite.org/2015/sqlite-autoconf-3081001.tar.gz";
+    url = "http://sqlite.org/2015/sqlite-autoconf-3081002.tar.gz";
-    sha1 = "86bfed5752783fb24c051f3efac5972ce11023f0";
+    sha1 = "c2f2c17d3dc4c4e179d35cc04e4420636d48a152";
   };
 
   buildInputs = lib.optionals interactive [ readline ncurses ];

pkgs/development/libraries/unibilium/default.nix

@@ -12,7 +12,8 @@ stdenv.mkDerivation rec {
     sha256 = "143j7qrqjxxmdf3yzhn6av2qwiyjjk4cnskkgz6ir2scjfd5gvja";
   };
 
-  makeFlags = [ "PREFIX=$(out)" ];
+  makeFlags = [ "PREFIX=$(out)" ]
+    ++ stdenv.lib.optional stdenv.isDarwin "LIBTOOL=${libtool}/bin/libtool";
 
   buildInputs = [ libtool pkgconfig ];
 

pkgs/development/libraries/utf8proc/default.nix

@@ -11,9 +11,7 @@ stdenv.mkDerivation rec {
     sha256 = "1ryjlcnpfm7fpkq6444ybi576hbnh2l0w7kjhbqady5lxwjyg3pf";
   };
 
-  installPhase = ''
+  makeFlags = [ "prefix=$(out)" ];
-    make install prefix=$out
-  '';
 
   meta = with stdenv.lib; {
     description = "A clean C library for processing UTF-8 Unicode data";

pkgs/development/libraries/wavpack/default.nix

@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   name = "wavpack-${version}";
-  version = "4.70.0";
+  version = "4.75.0";
 
   enableParallelBuilding = true;
 
@@ -12,7 +12,7 @@ stdenv.mkDerivation rec {
 
   src = fetchurl {
     url = "http://www.wavpack.com/${name}.tar.bz2";
-    sha256 = "191h8hv8qk72hfh1crg429i9yq3cminwqb249sy9zadbn1wy7b9c";
+    sha256 = "0bmgwcvch3cjcivk7pyasqysj0s81wkg40j3zfrcd7bl0qhmqgn6";
   };
 
   meta = with stdenv.lib; {

pkgs/development/python-modules/numpy-scipy-support.nix

@@ -3,14 +3,14 @@
   python,
   # Name of package (e.g. numpy or scipy)
   pkgName,
-  # Atlas math library
+  # OpenBLAS math library
-  atlas
+  openblas
 }:
 
 {
-  # Re-export atlas here so that it can be sure that the same one will be used
+  # Re-export openblas here so that it can be sure that the same one will be used
   # in the propagatedBuildInputs.
-  inherit atlas;
+  inherit openblas;
 
   # First "install" the package, then import what was installed, and call the
   # .test() function, which will run the test suite.
@@ -48,9 +48,9 @@
   preBuild = ''
     echo "Creating site.cfg file..."
     cat << EOF > site.cfg
-    [atlas]
+    [openblas]
-    include_dirs = ${atlas}/include
+    include_dirs = ${openblas}/include
-    library_dirs = ${atlas}/lib
+    library_dirs = ${openblas}/lib
     EOF
   '';
 }

pkgs/development/r-modules/default.nix

@@ -997,7 +997,7 @@ let
     });
 
     Mposterior = old.Mposterior.overrideDerivation (attrs: {
-      PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
+      PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
     });
 
     qtbase = old.qtbase.overrideDerivation (attrs: {
@@ -1037,11 +1037,11 @@ let
     });
 
     slfm = old.slfm.overrideDerivation (attrs: {
-      PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
+      PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
     });
 
     SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
-      PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
+      PKG_LIBS = "-L${pkgs.openblasCompat}/lib -lopenblas";
     });
 
     gputools = old.gputools.overrideDerivation (attrs: {
@@ -1087,6 +1087,7 @@ let
 
     BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
       patches = [ ./patches/BayesLogit.patch ];
+      buildInputs = (attrs.buildInputs or []) ++ [ pkgs.openblasCompat ];
     });
 
     BayesBridge = old.BayesBridge.overrideDerivation (attrs: {

pkgs/development/r-modules/patches/BayesLogit_cblas.patch

@@ -6,7 +6,7 @@ diff -ru -x '*~' BayesLogit_orig/src/Makevars BayesLogit/src/Makevars
  OBJECTS = Matrix.o MatrixFrame.o RRNG.o RNG.o FSF_nmix.o LogitWrapper.o \
  	PolyaGamma.o PolyaGammaAlt.o PolyaGammaSP.o InvertY.o
 -PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) 
-+PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -llapack -lf77blas -lcblas -latlas -lgfortran
++PKG_LIBS = $(BLAS_LIBS) $(FLIBS) $(LAPACK_LIBS) -lopenblas
  # PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -Wall -pedantic -Wextra
  PKG_CPPFLAGS = -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW 
  

pkgs/development/tools/analysis/include-what-you-use/default.nix

@@ -1,11 +1,13 @@
-{ stdenv, fetchurl, cmake, llvmPackages_35 }:
+{ stdenv, fetchurl, cmake, llvmPackages_36 }:
 
-let version = "3.5"; in with llvmPackages_35;
+let
-stdenv.mkDerivation rec {
+  version = "0.4";
+  llvmPackages = llvmPackages_36;
+in stdenv.mkDerivation rec {
   name = "include-what-you-use-${version}";
 
   src = fetchurl {
-    sha256 = "1wfl78wkg8m2ssjnkb2rwcqy35nhc8fa63mk3sa60jrshpy7b15w";
+    sha256 = "19pwhgwvfr86n8ks099p9r02v7zh8d3qs7g7snzkhpdgq1azww85";
     url = "${meta.homepage}/downloads/${name}.src.tar.gz";
   };
 
@@ -19,14 +21,16 @@ stdenv.mkDerivation rec {
       actually needed for this file (for both .cc and .h files), and by
       replacing #includes with forward-declares when possible.
     '';
-    homepage = http://include-what-you-use.com;
+    homepage = http://include-what-you-use.org;
     license = licenses.bsd3;
     platforms = with platforms; linux;
     maintainers = with maintainers; [ nckx ];
   };
 
-  buildInputs = [ clang cmake llvm ];
+  buildInputs = with llvmPackages; [ clang llvm ];
+  nativeBuildInputs = [ cmake ];
+
+  cmakeFlags = "-DIWYU_LLVM_ROOT_PATH=${llvmPackages.clang-unwrapped}";
 
-  cmakeFlags = [ "-DLLVM_PATH=${llvm}" ];
   enableParallelBuilding = true;
 }

pkgs/development/tools/build-managers/cmake/3.2.2-cygwin.patch

@@ -0,0 +1,274 @@
+--- cmake-3.2.2/Source/cmFileCommand.cxx	2015-04-13 19:09:00.000000000 +0200
++++ cmake-3.2.2/Source/ccmFileCommand.cxx	2015-06-10 11:02:27.345598700 +0200
+@@ -1179,7 +1179,7 @@
+   MatchProperties CollectMatchProperties(const char* file)
+     {
+     // Match rules are case-insensitive on some platforms.
+-#if defined(_WIN32) || defined(__APPLE__) || defined(__CYGWIN__)
++#if defined(_WIN32) || defined(__APPLE__)
+     std::string lower = cmSystemTools::LowerCase(file);
+     const char* file_to_match = lower.c_str();
+ #else
+--- cmake-3.2.2/Source/cmInstallCommand.cxx	2015-04-13 19:09:00.000000000 +0200
++++ cmake-3.2.2/Source/cmInstallCommand.cxx	2015-06-10 11:04:19.257935200 +0200
+@@ -1138,7 +1138,7 @@
+       {
+       literal_args += " REGEX \"";
+     // Match rules are case-insensitive on some platforms.
+-#if defined(_WIN32) || defined(__APPLE__) || defined(__CYGWIN__)
++#if defined(_WIN32) || defined(__APPLE__)
+       std::string regex = cmSystemTools::LowerCase(args[i]);
+ #else
+       std::string regex = args[i];
+--- cmake-3.2.2/Source/kwsys/Glob.cxx	2015-04-13 19:09:00.000000000 +0200
++++ cmake-3.2.2/Source/kwsys/Glob.cxx	2015-06-10 11:05:51.602674000 +0200
+@@ -37,7 +37,7 @@
+ #include <string.h>
+ namespace KWSYS_NAMESPACE
+ {
+-#if defined(_WIN32) || defined(__APPLE__) || defined(__CYGWIN__)
++#if defined(_WIN32) || defined(__APPLE__)
+ // On Windows and apple, no difference between lower and upper case
+ # define KWSYS_GLOB_CASE_INDEPENDENT
+ #endif
+--- cmake-3.2.2/Source/kwsys/SystemInformation.cxx	2015-04-13 19:09:00.000000000 +0200
++++ cmake-3.2.2/Source/kwsys/SystemInformation.cxx	2015-06-10 11:13:00.308303500 +0200
+@@ -911,7 +911,7 @@
+ // Hide implementation details in an anonymous namespace.
+ namespace {
+ // *****************************************************************************
+-#if defined(__linux) || defined(__APPLE__)
++#if defined(__linux) || defined(__APPLE__) || defined(__CYGWIN__)
+ int LoadLines(
+       FILE *file,
+       kwsys_stl::vector<kwsys_stl::string> &lines)
+@@ -947,7 +947,7 @@
+   return nRead;
+ }
+ 
+-# if defined(__linux)
++# if defined(__linux) || defined(__CYGWIN__)
+ // *****************************************************************************
+ int LoadLines(
+       const char *fileName,
+@@ -986,7 +986,7 @@
+ }
+ #endif
+ 
+-#if defined(__linux)
++#if defined(__linux) || defined(__CYGWIN__)
+ // ****************************************************************************
+ template<typename T>
+ int GetFieldsFromFile(
+@@ -3132,7 +3132,6 @@
+     pos = buffer.find("processor\t",pos+1);
+     }
+ 
+-#ifdef __linux
+   // Find the largest physical id.
+   int maxId = -1;
+   kwsys_stl::string idc =
+@@ -3165,14 +3164,6 @@
+             atoi(this->ExtractValueFromCpuInfoFile(buffer,"ncpus active").c_str());
+     }
+ 
+-#else // __CYGWIN__
+-  // does not have "physical id" entries, neither "cpu cores"
+-  // this has to be fixed for hyper-threading.
+-  kwsys_stl::string cpucount =
+-    this->ExtractValueFromCpuInfoFile(buffer,"cpu count");
+-  this->NumberOfPhysicalCPU=
+-    this->NumberOfLogicalCPU = atoi(cpucount.c_str());
+-#endif
+   // gotta have one, and if this is 0 then we get a / by 0n
+   // better to have a bad answer than a crash
+   if(this->NumberOfPhysicalCPU <= 0)
+@@ -3370,7 +3361,7 @@
+   GlobalMemoryStatusEx(&statex);
+   return statex.ullTotalPhys/1024;
+ # endif
+-#elif defined(__linux)
++#elif defined(__linux) || defined(__CYGWIN__)
+   SystemInformation::LongLong memTotal=0;
+   int ierr=GetFieldFromFile("/proc/meminfo","MemTotal:",memTotal);
+   if (ierr)
+@@ -3501,7 +3492,7 @@
+   GlobalMemoryStatusEx(&statex);
+   return (statex.ullTotalPhys - statex.ullAvailPhys)/1024;
+ # endif
+-#elif defined(__linux)
++#elif defined(__linux) || defined(__CYGWIN__)
+   const char *names[3]={"MemTotal:","MemFree:",NULL};
+   SystemInformation::LongLong values[2]={SystemInformation::LongLong(0)};
+   int ierr=GetFieldsFromFile("/proc/meminfo",names,values);
+@@ -3560,7 +3551,7 @@
+     return -2;
+     }
+   return pmc.WorkingSetSize/1024;
+-#elif defined(__linux)
++#elif defined(__linux) || defined(__CYGWIN__)
+   SystemInformation::LongLong memUsed=0;
+   int ierr=GetFieldFromFile("/proc/self/status","VmRSS:",memUsed);
+   if (ierr)
+@@ -3612,7 +3603,7 @@
+ {
+ #if defined(_WIN32)
+   return GetCurrentProcessId();
+-#elif defined(__linux) || defined(__APPLE__)
++#elif defined(__linux) || defined(__APPLE__) || defined(__CYGWIN__)
+   return getpid();
+ #else
+   return -1;
+--- cmake-3.2.2/Source/kwsys/SystemTools.cxx	2015-04-13 19:09:00.000000000 +0200
++++ cmake-3.2.2/Source/kwsys/SystemTools.cxx	2015-06-10 11:21:58.980443200 +0200
+@@ -93,19 +93,12 @@
+ # if defined(_MSC_VER) && _MSC_VER >= 1800
+ #  define KWSYS_WINDOWS_DEPRECATED_GetVersionEx
+ # endif
+-#elif defined (__CYGWIN__)
+-# include <windows.h>
+-# undef _WIN32
+ #endif
+ 
+ #if !KWSYS_CXX_HAS_ENVIRON_IN_STDLIB_H
+ extern char **environ;
+ #endif
+ 
+-#ifdef __CYGWIN__
+-# include <sys/cygwin.h>
+-#endif
+-
+ // getpwnam doesn't exist on Windows and Cray Xt3/Catamount
+ // same for TIOCGWINSZ
+ #if defined(_WIN32) || defined (__LIBCATAMOUNT__)
+@@ -1148,15 +1141,7 @@
+     {
+     return false;
+     }
+-#if defined(__CYGWIN__)
+-  // Convert filename to native windows path if possible.
+-  char winpath[MAX_PATH];
+-  if(SystemTools::PathCygwinToWin32(filename.c_str(), winpath))
+-    {
+-    return (GetFileAttributesA(winpath) != INVALID_FILE_ATTRIBUTES);
+-    }
+-  return access(filename.c_str(), R_OK) == 0;
+-#elif defined(_WIN32)
++#if defined(_WIN32)
+   return (GetFileAttributesW(
+             SystemTools::ConvertToWindowsExtendedPath(filename).c_str())
+           != INVALID_FILE_ATTRIBUTES);
+@@ -1190,28 +1175,6 @@
+ }
+ 
+ //----------------------------------------------------------------------------
+-#ifdef __CYGWIN__
+-bool SystemTools::PathCygwinToWin32(const char *path, char *win32_path)
+-{
+-  SystemToolsTranslationMap::iterator i =
+-    SystemTools::Cyg2Win32Map->find(path);
+-
+-  if (i != SystemTools::Cyg2Win32Map->end())
+-    {
+-    strncpy(win32_path, i->second.c_str(), MAX_PATH);
+-    }
+-  else
+-    {
+-    if(cygwin_conv_path(CCP_POSIX_TO_WIN_A, path, win32_path, MAX_PATH) != 0)
+-      {
+-      win32_path[0] = 0;
+-      }
+-    SystemToolsTranslationMap::value_type entry(path, win32_path);
+-    SystemTools::Cyg2Win32Map->insert(entry);
+-    }
+-  return win32_path[0] != 0;
+-}
+-#endif
+ 
+ bool SystemTools::Touch(const kwsys_stl::string& filename, bool create)
+ {
+@@ -4307,7 +4270,7 @@
+ 
+ bool SystemTools::FileIsFullPath(const char* in_name, size_t len)
+ {
+-#if defined(_WIN32) || defined(__CYGWIN__)
++#if defined(_WIN32)
+   // On Windows, the name must be at least two characters long.
+   if(len < 2)
+     {
+@@ -5078,9 +5041,6 @@
+ static unsigned int SystemToolsManagerCount;
+ SystemToolsTranslationMap *SystemTools::TranslationMap;
+ SystemToolsTranslationMap *SystemTools::LongPathMap;
+-#ifdef __CYGWIN__
+-SystemToolsTranslationMap *SystemTools::Cyg2Win32Map;
+-#endif
+ 
+ // SystemToolsManager manages the SystemTools singleton.
+ // SystemToolsManager should be included in any translation unit
+@@ -5126,9 +5086,6 @@
+   // Allocate the translation map first.
+   SystemTools::TranslationMap = new SystemToolsTranslationMap;
+   SystemTools::LongPathMap = new SystemToolsTranslationMap;
+-#ifdef __CYGWIN__
+-  SystemTools::Cyg2Win32Map = new SystemToolsTranslationMap;
+-#endif
+ 
+   // Add some special translation paths for unix.  These are not added
+   // for windows because drive letters need to be maintained.  Also,
+@@ -5183,9 +5140,6 @@
+ {
+   delete SystemTools::TranslationMap;
+   delete SystemTools::LongPathMap;
+-#ifdef __CYGWIN__
+-  delete SystemTools::Cyg2Win32Map;
+-#endif
+ }
+ 
+ 
+--- cmake-3.2.2/Source/kwsys/SystemTools.hxx.in	2015-04-13 19:09:00.000000000 +0200
++++ cmake-3.2.2/Source/kwsys/SystemTools.hxx.in	2015-06-10 11:24:24.271286600 +0200
+@@ -298,15 +298,6 @@
+   static bool FileExists(const kwsys_stl::string& filename);
+ 
+   /**
+-   * Converts Cygwin path to Win32 path. Uses dictionary container for
+-   * caching and calls to cygwin_conv_to_win32_path from Cygwin dll
+-   * for actual translation.  Returns true on success, else false.
+-   */
+-#ifdef __CYGWIN__
+-  static bool PathCygwinToWin32(const char *path, char *win32_path);
+-#endif
+-
+-  /**
+    * Return file length
+    */
+   static unsigned long FileLength(const kwsys_stl::string& filename);
+@@ -942,9 +933,6 @@
+    */
+   static SystemToolsTranslationMap *TranslationMap;
+   static SystemToolsTranslationMap *LongPathMap;
+-#ifdef __CYGWIN__
+-  static SystemToolsTranslationMap *Cyg2Win32Map;
+-#endif
+   friend class SystemToolsManager;
+ };
+ 
+--- cmake-3.2.2/Modules/FindCurses.cmake	2015-04-13 19:09:00.000000000 +0200
++++ cmake-3.2.2/Modules/FindCurses.cmake	2015-06-10 12:10:19.682030300 +0200
+@@ -60,15 +60,6 @@
+ if(CURSES_NCURSES_LIBRARY  AND ((NOT CURSES_CURSES_LIBRARY) OR CURSES_NEED_NCURSES))
+   set(CURSES_USE_NCURSES TRUE)
+ endif()
+-# http://cygwin.com/ml/cygwin-announce/2010-01/msg00002.html
+-# cygwin ncurses stopped providing curses.h symlinks see above
+-# message.  Cygwin is an ncurses package, so force ncurses on
+-# cygwin if the curses.h is missing
+-if(CYGWIN)
+-  if(NOT EXISTS /usr/include/curses.h)
+-    set(CURSES_USE_NCURSES TRUE)
+-  endif()
+-endif()
+ 
+ 
+ # Not sure the logic is correct here.