Merge remote-tracking branch 'upstream/master' into staging

lib/maintainers.nix

@@ -301,6 +301,7 @@
   johnramsden = "John Ramsden <johnramsden@riseup.net>";
   joko = "Ioannis Koutras <ioannis.koutras@gmail.com>";
   jonafato = "Jon Banafato <jon@jonafato.com>";
+  joncojonathan = "Jonathan Haddock <joncojonathan@gmail.com>";
   jpierre03 = "Jean-Pierre PRUNARET <nix@prunetwork.fr>";
   jpotier = "Martin Potier <jpo.contributes.to.nixos@marvid.fr>";
   jraygauthier = "Raymond Gauthier <jraygauthier@gmail.com>";

nixos/modules/services/continuous-integration/buildkite-agent.nix

@@ -9,9 +9,8 @@ let
       token="${cfg.token}"
       name="${cfg.name}"
       meta-data="${cfg.meta-data}"
-      hooks-path="${pkgs.buildkite-agent}/share/hooks"
+      hooks-path="${cfg.package}/share/hooks"
-      build-path="/var/lib/buildkite-agent/builds"
+      build-path="${cfg.dataDir}"
-      bootstrap-script="${pkgs.buildkite-agent}/share/bootstrap.sh"
     '';
 in
 
@@ -20,6 +19,26 @@ in
     services.buildkite-agent = {
       enable = mkEnableOption "buildkite-agent";
 
+      package = mkOption {
+        default = pkgs.buildkite-agent;
+        defaultText = "pkgs.buildkite-agent";
+        description = "Which buildkite-agent derivation to use";
+        type = types.package;
+      };
+
+      dataDir = mkOption {
+        default = "/var/lib/buildkite-agent";
+        description = "The workdir for the agent";
+        type = types.str;
+      };
+
+      runtimePackages = mkOption {
+        default = [ pkgs.nix ];
+        defaultText = "[ pkgs.nix ]";
+        description = "Add programs to the buildkite-agent environment";
+        type = types.listOf types.package;
+      };
+
       token = mkOption {
         type = types.str;
         description = ''
@@ -62,27 +81,31 @@ in
   config = mkIf config.services.buildkite-agent.enable {
     users.extraUsers.buildkite-agent =
       { name = "buildkite-agent";
-        home = "/var/lib/buildkite-agent";
+        home = cfg.dataDir;
         createHome = true;
         description = "Buildkite agent user";
       };
 
-    environment.systemPackages = [ pkgs.buildkite-agent ];
+    environment.systemPackages = [ cfg.package ];
 
     systemd.services.buildkite-agent =
       { description = "Buildkite Agent";
         wantedBy = [ "multi-user.target" ];
         after = [ "network.target" ];
-        environment.HOME = "/var/lib/buildkite-agent";
+        path = cfg.runtimePackages;
+        environment = config.networking.proxy.envVars // {
+          HOME = cfg.dataDir;
+          NIX_REMOTE = "daemon";
+        };
         preStart = ''
-            ${pkgs.coreutils}/bin/mkdir -m 0700 -p /var/lib/buildkite-agent/.ssh
+          ${pkgs.coreutils}/bin/mkdir -m 0700 -p ${cfg.dataDir}/.ssh
 
-            echo "${cfg.openssh.privateKey}" > /var/lib/buildkite-agent/.ssh/id_rsa
+          echo "${cfg.openssh.privateKey}" > ${cfg.dataDir}/.ssh/id_rsa
-            ${pkgs.coreutils}/bin/chmod 600 /var/lib/buildkite-agent/.ssh/id_rsa
+          ${pkgs.coreutils}/bin/chmod 600 ${cfg.dataDir}/.ssh/id_rsa
 
-            echo "${cfg.openssh.publicKey}" > /var/lib/buildkite-agent/.ssh/id_rsa.pub
+          echo "${cfg.openssh.publicKey}" > ${cfg.dataDir}/.ssh/id_rsa.pub
-            ${pkgs.coreutils}/bin/chmod 600 /var/lib/buildkite-agent/.ssh/id_rsa.pub
+          ${pkgs.coreutils}/bin/chmod 600 ${cfg.dataDir}/.ssh/id_rsa.pub
-          '';
+        '';
 
         serviceConfig =
           { ExecStart = "${pkgs.buildkite-agent}/bin/buildkite-agent start --config ${configFile}";

nixos/modules/services/desktops/geoclue2.nix

@@ -17,7 +17,7 @@ with lib;
         default = false;
         description = ''
           Whether to enable GeoClue 2 daemon, a DBus service
-          that provides location informationfor accessing.
+          that provides location information for accessing.
         '';
       };
 

nixos/modules/services/monitoring/munin.nix

@@ -193,6 +193,9 @@ in
       };
     };
 
+    # munin_stats plugin breaks as of 2.0.33 when this doesn't exist
+    systemd.tmpfiles.rules = [ "d /var/run/munin 0755 munin munin -" ];
+
   }) (mkIf cronCfg.enable {
 
     systemd.timers.munin-cron = {
@@ -212,9 +215,11 @@ in
       };
     };
 
-    system.activationScripts.munin-cron = stringAfter [ "users" "groups" ] ''
+    systemd.tmpfiles.rules = [
-      mkdir -p /var/{run,log,www,lib}/munin
+      "d /var/run/munin 0755 munin munin -"
-      chown -R munin:munin /var/{run,log,www,lib}/munin
+      "d /var/log/munin 0755 munin munin -"
-    '';
+      "d /var/www/munin 0755 munin munin -"
+      "d /var/lib/munin 0755 munin munin -"
+    ];
   })];
 }

nixos/modules/services/x11/desktop-managers/plasma5.nix

@@ -175,7 +175,7 @@ in
         serif = [ "Noto Serif" ];
       };
 
-      programs.ssh.askPassword = "${plasma5.ksshaskpass.out}/bin/ksshaskpass";
+      programs.ssh.askPassword = mkDefault "${plasma5.ksshaskpass.out}/bin/ksshaskpass";
 
       # Enable helpful DBus services.
       services.udisks2.enable = true;
@@ -190,7 +190,7 @@ in
       ];
 
       services.xserver.displayManager.sddm = {
-        theme = "breeze";
+        theme = mkDefault "breeze";
       };
 
       security.pam.services.kde = { allowNullPassword = true; };

nixos/modules/services/x11/redshift.nix

@@ -19,18 +19,31 @@ in {
     };
 
     latitude = mkOption {
-      type = types.str;
+      type = types.nullOr types.str;
+      default = null;
       description = ''
         Your current latitude, between
-        <literal>-90.0</literal> and <literal>90.0</literal>.
+        <literal>-90.0</literal> and <literal>90.0</literal>. Must be provided
+        along with longitude.
       '';
     };
 
     longitude = mkOption {
-      type = types.str;
+      type = types.nullOr types.str;
+      default = null;
       description = ''
         Your current longitude, between
-        between <literal>-180.0</literal> and <literal>180.0</literal>.
+        between <literal>-180.0</literal> and <literal>180.0</literal>. Must be
+        provided along with latitude.
+      '';
+    };
+
+    provider = mkOption {
+      type = types.enum [ "manual" "geoclue2" ];
+      default = "manual";
+      description = ''
+        The location provider to use for determining your location. If set to
+        <literal>manual</literal> you must also provide latitude/longitude.
       '';
     };
 
@@ -93,14 +106,33 @@ in {
   };
 
   config = mkIf cfg.enable {
-    systemd.user.services.redshift = {
+    assertions = [ 
+      {
+        assertion = 
+          if cfg.provider == "manual"
+          then (cfg.latitude != null && cfg.longitude != null) 
+          else (cfg.latitude == null && cfg.longitude == null);
+        message = "Latitude and longitude must be provided together, and with provider set to null.";
+      }
+    ];
+
+    services.geoclue2.enable = mkIf (cfg.provider == "geoclue2") true;
+
+    systemd.user.services.redshift = 
+    let
+      providerString = 
+        if cfg.provider == "manual"
+        then "${cfg.latitude}:${cfg.longitude}"
+        else cfg.provider;
+    in
+    {
       description = "Redshift colour temperature adjuster";
       wantedBy = [ "graphical-session.target" ];
       partOf = [ "graphical-session.target" ];
       serviceConfig = {
         ExecStart = ''
           ${cfg.package}/bin/redshift \
-            -l ${cfg.latitude}:${cfg.longitude} \
+            -l ${providerString} \
             -t ${toString cfg.temperature.day}:${toString cfg.temperature.night} \
             -b ${toString cfg.brightness.day}:${toString cfg.brightness.night} \
             ${lib.strings.concatStringsSep " " cfg.extraOptions}

nixos/release.nix

@@ -256,7 +256,7 @@ in rec {
   tests.gocd-server = callTest tests/gocd-server.nix {};
   tests.gnome3 = callTest tests/gnome3.nix {};
   tests.gnome3-gdm = callTest tests/gnome3-gdm.nix {};
-  tests.grafama = callTest tests/grafana.nix {};
+  tests.grafana = callTest tests/grafana.nix {};
   tests.graphite = callTest tests/graphite.nix {};
   tests.hardened = callTest tests/hardened.nix { };
   tests.hibernate = callTest tests/hibernate.nix {};

nixos/tests/gitolite.nix

@@ -11,7 +11,7 @@ let
     -----END OPENSSH PRIVATE KEY-----
   '';
 
-  adminPublicKey = pkgs.writeText "id_ed25519.pub" ''
+  adminPublicKey = ''
     ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIO7urFhAA90BTpGuEHeWWTY3W/g9PBxXNxfWhfbrm4Le root@client
   '';
 
@@ -62,7 +62,7 @@ in
       {
         services.gitolite = {
           enable = true;
-          adminPubkey = builtins.readFile adminPublicKey;
+          adminPubkey = adminPublicKey;
         };
         services.openssh.enable = true;
       };

pkgs/applications/backup/deja-dup/default.nix

@@ -7,11 +7,11 @@
 
 stdenv.mkDerivation rec {
   name = "deja-dup-${version}";
-  version = "36.1";
+  version = "36.3";
 
   src = fetchurl {
     url = "https://launchpad.net/deja-dup/36/${version}/+download/deja-dup-${version}.tar.xz";
-    sha256 = "1s48k2sxrpwkzp37s4x7934lyg5194c47nv9ks15rksd5s0alnld";
+    sha256 = "08pwybzp7ynfcf0vqxfc3p8ir4gnzcv4v4cq5bwidbff9crklhrc";
   };
 
   patches = [
@@ -77,7 +77,7 @@ stdenv.mkDerivation rec {
     '';
     homepage = https://launchpad.net/deja-dup;
     license = with licenses; gpl3;
-    maintainers = with maintainers; [ jtojnar ];
+    maintainers = with maintainers; [ jtojnar joncojonathan ];
     platforms = with platforms; linux;
   };
 }

pkgs/applications/misc/et/default.nix

@@ -2,23 +2,18 @@
 
 stdenv.mkDerivation rec {
   name = "et-${version}";
-  version = "2017-03-04";
+  version = "0.1";
 
   src = fetchFromGitHub {
     owner = "geistesk";
     repo = "et";
-    rev = "151e9b6bc0d2d4f45bda8ced740ee99d0f2012f6";
+    rev = "${version}";
-    sha256 = "1a1jdnzmal05k506bbvzlwsj2f3kql6l5xc1gdabm79y6vaf4r7s";
+    sha256 = "1d2hq6p1y2ynk0a3l35lwbm1fcl9kg7rpjcin8bx4xcdpbw42y94";
   };
 
   buildInputs = [ libnotify gdk_pixbuf ];
   nativeBuildInputs = [ pkgconfig ];
 
-  prePatch = ''
-    substituteInPlace Makefile \
-        --replace ' = gcc' ' ?= gcc'
-  '';
-
   installPhase = ''
     mkdir -p $out/bin
     cp et $out/bin
@@ -26,7 +21,7 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with stdenv.lib; {
-    description = "Minimal libnotify-based (egg) timer for GNU/Linux";
+    description = "Minimal libnotify-based (egg) timer";
     homepage = https://github.com/geistesk/et;
     license = licenses.gpl3;
     platforms = platforms.unix;

pkgs/applications/misc/keepass/default.nix

@@ -8,11 +8,11 @@
 # plugin derivations in the Nix store and nowhere else.
 with builtins; buildDotnetPackage rec {
   baseName = "keepass";
-  version = "2.36";
+  version = "2.37";
 
   src = fetchurl {
     url = "mirror://sourceforge/keepass/KeePass-${version}-Source.zip";
-    sha256 = "1j6qhy8h3z6higbpq3q9v04amvgbn90yj3kbsvj17azdkffkwzny";
+    sha256 = "1wfbpfjng1blzkbjnxsdnny544297bm9869ianbr6l0hrvcgv3qx";
   };
 
   sourceRoot = ".";
@@ -98,7 +98,7 @@ with builtins; buildDotnetPackage rec {
   meta = {
     description = "GUI password manager with strong cryptography";
     homepage = http://www.keepass.info/;
-    maintainers = with stdenv.lib.maintainers; [ amorsillo obadz jraygauthier ];
+    maintainers = with stdenv.lib.maintainers; [ amorsillo obadz joncojonathan jraygauthier ];
     platforms = with stdenv.lib.platforms; all;
     license = stdenv.lib.licenses.gpl2;
   };

pkgs/applications/misc/pell/default.nix

@@ -2,14 +2,14 @@
 
 stdenv.mkDerivation rec {
   pname = "pell";
-  version = "0.0.1";
+  version = "0.0.2";
   name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "ebzzry";
     repo = pname;
-    rev = "3f95341eb9439c7a6be1f3c6366c0552ab8208f0";
+    rev = "ec14de0a9b666433954184167bf3b82cf21193f8";
-    sha256 = "183aj3ys080g2kahl8x8rkhzlsb6h5ls9xm1v2kasfbn1pi5i6nn";
+    sha256 = "0r2gbb4l9rr5x99m62zicknsp1gf9fr124xpyd8ak9izr5hvskn9";
   };
 
   installPhase = ''
@@ -29,7 +29,7 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     homepage = https://github.com/ebzzry/pell;
-    description = "A simple periodic host monitor using ping";
+    description = "A simple host availability monitor";
     license = licenses.mit;
     maintainers = [ maintainers.ebzzry ];
     platforms = platforms.unix;

pkgs/applications/misc/rofi/default.nix

@@ -4,12 +4,12 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.4.1";
+  version = "1.4.2";
   name = "rofi-${version}";
 
   src = fetchurl {
     url = "https://github.com/DaveDavenport/rofi/releases/download/${version}/${name}.tar.gz";
-    sha256 = "19x11s71q24gjdnsjf1ar6raq1drav7qp3nzjkw8qajpgvjrxwcn";
+    sha256 = "0ys7grazqz5hw3nx2393df54ykcd5gw0zn66kik5fvzijpg3qfcx";
   };
 
   preConfigure = ''

pkgs/applications/misc/sent/default.nix

@@ -1,15 +1,18 @@
-{ stdenv, fetchurl, libpng, libX11, libXft
+{ stdenv, fetchurl, farbfeld, libX11, libXft
 , patches ? [] }:
 
 stdenv.mkDerivation rec {
-  name = "sent-0.2";
+  name = "sent-1";
 
   src = fetchurl {
-    url = "http://dl.suckless.org/tools/${name}.tar.gz";
+    url = "https://dl.suckless.org/tools/${name}.tar.gz";
-    sha256 = "0xhh752hwaa26k4q6wvrb9jnpbnylss2aw6z11j7l9rav7wn3fak";
+    sha256 = "0cxysz5lp25mgww73jl0mgip68x7iyvialyzdbriyaff269xxwvv";
   };
 
-  buildInputs = [ libpng libX11 libXft ];
+  buildInputs = [ farbfeld libX11 libXft ];
+
+  # unpacking doesn't create a directory
+  sourceRoot = ".";
 
   inherit patches;
 
@@ -17,8 +20,8 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "A simple plaintext presentation tool";
-    homepage = http://tools.suckless.org/sent/;
+    homepage = https://tools.suckless.org/sent/;
-    license = licenses.mit;
+    license = licenses.isc;
     platforms = platforms.linux;
     maintainers = with maintainers; [ pSub ];
   };

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

@@ -133,22 +133,14 @@ let
       # https://gitweb.gentoo.org/repo/gentoo.git/plain/www-client/chromium/
       # https://git.archlinux.org/svntogit/packages.git/tree/trunk?h=packages/chromium
       # for updated patches and hints about build flags
-      ++ optionals (versionRange "61" "62") [
-      ./patches/chromium-gn-bootstrap-r14.patch
-      ./patches/chromium-gcc-r1.patch
-      ./patches/chromium-atk-r1.patch
-      ./patches/chromium-gcc5-r1.patch
-    ]
       ++ optionals (versionRange "62" "63") [
       ./patches/chromium-gn-bootstrap-r17.patch
-      ./patches/chromium-gcc5-r2.patch
+      ./patches/chromium-gcc5-r3.patch
       ./patches/chromium-glibc2.26-r1.patch
     ]
       ++ optionals (versionAtLeast version "63") [
-      ./patches/chromium-gn-bootstrap-r19.patch
+      ./patches/chromium-gcc5-r4.patch
-      ./patches/chromium-gcc5-r2.patch
+      ./patches/constexpr-fix.patch
-      ./patches/chromium-glibc2.26-r1.patch
-      ./patches/chromium-sysroot-r1.patch
     ]
       ++ optional enableWideVine ./patches/widevine.patch;
 

pkgs/applications/networking/browsers/chromium/patches/chromium-atk-r1.patch

@@ -1,11 +0,0 @@
---- a/content/browser/accessibility/browser_accessibility_auralinux.cc.orig	2017-07-27 06:28:01.090257874 +0000
-+++ b/content/browser/accessibility/browser_accessibility_auralinux.cc	2017-07-27 06:28:21.174653680 +0000
-@@ -571,7 +571,7 @@
- // it's best to leave this out rather than break people's builds:
- #if defined(ATK_CHECK_VERSION)
- #if ATK_CHECK_VERSION(2, 16, 0)
--      atk_state_set_add_state(atk_state_set, ATK_STATE_READ_ONLY);
-+      atk_state_set_add_state(state_set, ATK_STATE_READ_ONLY);
- #endif
- #endif
-       break;

pkgs/applications/networking/browsers/chromium/patches/chromium-gcc-r1.patch

@@ -1,14 +0,0 @@
-diff --git a/base/numerics/safe_math_shared_impl.h b/base/numerics/safe_math_shared_impl.h
-index 99f230ce7e9a..de2415d402f5 100644
---- a/base/numerics/safe_math_shared_impl.h
-+++ b/base/numerics/safe_math_shared_impl.h
-@@ -21,8 +21,7 @@
- #if !defined(__native_client__) &&                         \
-     ((defined(__clang__) &&                                \
-       ((__clang_major__ > 3) ||                            \
--       (__clang_major__ == 3 && __clang_minor__ >= 4))) || \
--     (defined(__GNUC__) && __GNUC__ >= 5))
-+       (__clang_major__ == 3 && __clang_minor__ >= 4))))
- #include "base/numerics/safe_math_clang_gcc_impl.h"
- #define BASE_HAS_OPTIMIZED_SAFE_MATH (1)
- #else

pkgs/applications/networking/browsers/chromium/patches/chromium-gcc5-r1.patch

@@ -1,66 +0,0 @@
---- a/chrome/browser/devtools/devtools_file_system_indexer.cc
-+++ b/chrome/browser/devtools/devtools_file_system_indexer.cc
-@@ -34,7 +34,6 @@ using base::TimeDelta;
- using base::TimeTicks;
- using content::BrowserThread;
- using std::map;
--using std::set;
- using std::string;
- using std::vector;
- 
-@@ -191,7 +190,7 @@ vector<FilePath> Index::Search(const string& query) {
-     if (trigram != kUndefinedTrigram)
-       trigrams.push_back(trigram);
-   }
--  set<FileId> file_ids;
-+  std::set<FileId> file_ids;
-   bool first = true;
-   vector<Trigram>::const_iterator it = trigrams.begin();
-   for (; it != trigrams.end(); ++it) {
-@@ -203,7 +202,7 @@ vector<FilePath> Index::Search(const string& query) {
-       first = false;
-       continue;
-     }
--    set<FileId> intersection = base::STLSetIntersection<set<FileId> >(
-+    std::set<FileId> intersection = base::STLSetIntersection<std::set<FileId> >(
-         file_ids, index_[trigram]);
-     file_ids.swap(intersection);
-   }
-diff --git a/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h b/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h
-index 94bb9161ec85..e40c6387f72e 100644
---- a/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h
-+++ b/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h
-@@ -63,7 +63,7 @@ class WTF_EXPORT ArrayBufferContents {
-           allocation_length_(0),
-           data_(data),
-           data_length_(0),
--          kind_(AllocationKind::kNormal),
-+          kind_(WTF::ArrayBufferContents::AllocationKind::kNormal),
-           deleter_(deleter) {}
-     DataHandle(void* allocation_base,
-                size_t allocation_length,
-@@ -94,11 +94,11 @@ class WTF_EXPORT ArrayBufferContents {
-              reinterpret_cast<uintptr_t>(allocation_base_) +
-                  allocation_length_);
-       switch (kind_) {
--        case AllocationKind::kNormal:
-+        case WTF::ArrayBufferContents::AllocationKind::kNormal:
-           DCHECK(deleter_);
-           deleter_(data_);
-           return;
--        case AllocationKind::kReservation:
-+        case WTF::ArrayBufferContents::AllocationKind::kReservation:
-           ReleaseReservedMemory(allocation_base_, allocation_length_);
-           return;
-       }
---- a/third_party/webrtc/modules/audio_processing/aec3/aec_state.cc.orig	2017-08-15 12:45:59.433532111 +0000
-+++ b/third_party/webrtc/modules/audio_processing/aec3/aec_state.cc	2017-08-15 17:52:59.691328825 +0000
-@@ -10,7 +10,7 @@
- 
- #include "webrtc/modules/audio_processing/aec3/aec_state.h"
- 
--#include <math.h>
-+#include <cmath>
- #include <numeric>
- #include <vector>
- 

pkgs/applications/networking/browsers/chromium/patches/chromium-gcc5-r2.patch

@@ -1,36 +0,0 @@
---- a/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h
-+++ b/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h
-@@ -63,7 +63,7 @@ class WTF_EXPORT ArrayBufferContents {
-           allocation_length_(0),
-           data_(data),
-           data_length_(0),
--          kind_(AllocationKind::kNormal),
-+          kind_(WTF::ArrayBufferContents::AllocationKind::kNormal),
-           deleter_(deleter) {}
-     DataHandle(void* allocation_base,
-                size_t allocation_length,
-@@ -94,11 +94,11 @@ class WTF_EXPORT ArrayBufferContents {
-              reinterpret_cast<uintptr_t>(allocation_base_) +
-                  allocation_length_);
-       switch (kind_) {
--        case AllocationKind::kNormal:
-+        case WTF::ArrayBufferContents::AllocationKind::kNormal:
-           DCHECK(deleter_);
-           deleter_(data_);
-           return;
--        case AllocationKind::kReservation:
-+        case WTF::ArrayBufferContents::AllocationKind::kReservation:
-           ReleaseReservedMemory(allocation_base_, allocation_length_);
-           return;
-       }
---- a/third_party/webrtc/modules/audio_processing/aec3/aec_state.cc.orig	2017-08-15 12:45:59.433532111 +0000
-+++ b/third_party/webrtc/modules/audio_processing/aec3/aec_state.cc	2017-08-15 17:52:59.691328825 +0000
-@@ -10,7 +10,7 @@
- 
- #include "webrtc/modules/audio_processing/aec3/aec_state.h"
- 
--#include <math.h>
-+#include <cmath>
- #include <numeric>
- #include <vector>
- 

pkgs/applications/networking/browsers/chromium/patches/chromium-gcc5-r3.patch

@@ -0,0 +1,98 @@
+--- a/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h
++++ b/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h
+@@ -63,7 +63,7 @@ class WTF_EXPORT ArrayBufferContents {
+           allocation_length_(0),
+           data_(data),
+           data_length_(0),
+-          kind_(AllocationKind::kNormal),
++          kind_(WTF::ArrayBufferContents::AllocationKind::kNormal),
+           deleter_(deleter) {}
+     DataHandle(void* allocation_base,
+                size_t allocation_length,
+@@ -94,11 +94,11 @@ class WTF_EXPORT ArrayBufferContents {
+              reinterpret_cast<uintptr_t>(allocation_base_) +
+                  allocation_length_);
+       switch (kind_) {
+-        case AllocationKind::kNormal:
++        case WTF::ArrayBufferContents::AllocationKind::kNormal:
+           DCHECK(deleter_);
+           deleter_(data_);
+           return;
+-        case AllocationKind::kReservation:
++        case WTF::ArrayBufferContents::AllocationKind::kReservation:
+           ReleaseReservedMemory(allocation_base_, allocation_length_);
+           return;
+       }
+--- a/third_party/webrtc/modules/audio_processing/aec3/aec_state.cc.orig	2017-08-15 12:45:59.433532111 +0000
++++ b/third_party/webrtc/modules/audio_processing/aec3/aec_state.cc	2017-08-15 17:52:59.691328825 +0000
+@@ -10,7 +10,7 @@
+ 
+ #include "webrtc/modules/audio_processing/aec3/aec_state.h"
+ 
+-#include <math.h>
++#include <cmath>
+ #include <numeric>
+ #include <vector>
+ 
+--- a/gpu/ipc/common/mailbox_struct_traits.h
++++ b/gpu/ipc/common/mailbox_struct_traits.h
+@@ -15,7 +15,7 @@ namespace mojo {
+ template <>
+ struct StructTraits<gpu::mojom::MailboxDataView, gpu::Mailbox> {
+   static base::span<const int8_t> name(const gpu::Mailbox& mailbox) {
+-    return mailbox.name;
++    return base::make_span(mailbox.name);
+   }
+   static bool Read(gpu::mojom::MailboxDataView data, gpu::Mailbox* out);
+ };
+--- a/services/viz/public/cpp/compositing/filter_operation_struct_traits.h
++++ b/services/viz/public/cpp/compositing/filter_operation_struct_traits.h
+@@ -134,7 +134,7 @@ struct StructTraits<viz::mojom::FilterOperationDataView, cc::FilterOperation> {
+   static base::span<const float> matrix(const cc::FilterOperation& operation) {
+     if (operation.type() != cc::FilterOperation::COLOR_MATRIX)
+       return base::span<const float>();
+-    return operation.matrix();
++    return base::make_span(operation.matrix());
+   }
+ 
+   static base::span<const gfx::Rect> shape(
+--- a/services/viz/public/cpp/compositing/quads_struct_traits.h
++++ b/services/viz/public/cpp/compositing/quads_struct_traits.h
+@@ -284,7 +284,7 @@
+ 
+   static base::span<const float> vertex_opacity(const cc::DrawQuad& input) {
+     const cc::TextureDrawQuad* quad = cc::TextureDrawQuad::MaterialCast(&input);
+-    return quad->vertex_opacity;
++    return base::make_span(quad->vertex_opacity);
+   }
+ 
+   static bool y_flipped(const cc::DrawQuad& input) {
+--- a/third_party/WebKit/Source/platform/exported/WebCORS.cpp
++++ b/third_party/WebKit/Source/platform/exported/WebCORS.cpp
+@@ -480,7 +480,7 @@ WebString AccessControlErrorString(
+     }
+     default:
+       NOTREACHED();
+-      return "";
++      return WebString();
+   }
+ }
+ 
+@@ -512,7 +512,7 @@ WebString PreflightErrorString(const PreflightStatus status,
+     }
+     default:
+       NOTREACHED();
+-      return "";
++      return WebString();
+   }
+ }
+ 
+@@ -533,7 +533,7 @@ WebString RedirectErrorString(const RedirectStatus status,
+     }
+     default:
+       NOTREACHED();
+-      return "";
++      return WebString();
+   }
+ }
+ 

pkgs/applications/networking/browsers/chromium/patches/chromium-gcc5-r4.patch

@@ -0,0 +1,98 @@
+--- a/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h
++++ b/third_party/WebKit/Source/platform/wtf/typed_arrays/ArrayBufferContents.h
+@@ -63,7 +63,7 @@ class WTF_EXPORT ArrayBufferContents {
+           allocation_length_(0),
+           data_(data),
+           data_length_(0),
+-          kind_(AllocationKind::kNormal),
++          kind_(WTF::ArrayBufferContents::AllocationKind::kNormal),
+           deleter_(deleter) {}
+     DataHandle(void* allocation_base,
+                size_t allocation_length,
+@@ -94,11 +94,11 @@ class WTF_EXPORT ArrayBufferContents {
+              reinterpret_cast<uintptr_t>(allocation_base_) +
+                  allocation_length_);
+       switch (kind_) {
+-        case AllocationKind::kNormal:
++        case WTF::ArrayBufferContents::AllocationKind::kNormal:
+           DCHECK(deleter_);
+           deleter_(data_);
+           return;
+-        case AllocationKind::kReservation:
++        case WTF::ArrayBufferContents::AllocationKind::kReservation:
+           ReleaseReservedMemory(allocation_base_, allocation_length_);
+           return;
+       }
+--- a/third_party/webrtc/modules/audio_processing/aec3/aec_state.cc.orig	2017-08-15 12:45:59.433532111 +0000
++++ b/third_party/webrtc/modules/audio_processing/aec3/aec_state.cc	2017-08-15 17:52:59.691328825 +0000
+@@ -10,7 +10,7 @@
+ 
+ #include "webrtc/modules/audio_processing/aec3/aec_state.h"
+ 
+-#include <math.h>
++#include <cmath>
+ #include <numeric>
+ #include <vector>
+ 
+--- a/gpu/ipc/common/mailbox_struct_traits.h
++++ b/gpu/ipc/common/mailbox_struct_traits.h
+@@ -15,7 +15,7 @@ namespace mojo {
+ template <>
+ struct StructTraits<gpu::mojom::MailboxDataView, gpu::Mailbox> {
+   static base::span<const int8_t> name(const gpu::Mailbox& mailbox) {
+-    return mailbox.name;
++    return base::make_span(mailbox.name);
+   }
+   static bool Read(gpu::mojom::MailboxDataView data, gpu::Mailbox* out);
+ };
+--- a/services/viz/public/cpp/compositing/filter_operation_struct_traits.h
++++ b/services/viz/public/cpp/compositing/filter_operation_struct_traits.h
+@@ -134,7 +134,7 @@ struct StructTraits<viz::mojom::FilterOperationDataView, cc::FilterOperation> {
+   static base::span<const float> matrix(const cc::FilterOperation& operation) {
+     if (operation.type() != cc::FilterOperation::COLOR_MATRIX)
+       return base::span<const float>();
+-    return operation.matrix();
++    return base::make_span(operation.matrix());
+   }
+ 
+   static base::span<const gfx::Rect> shape(
+--- a/services/viz/public/cpp/compositing/quads_struct_traits.h
++++ b/services/viz/public/cpp/compositing/quads_struct_traits.h
+@@ -303,7 +303,7 @@ struct StructTraits<viz::mojom::TextureQuadStateDataView, viz::DrawQuad> {
+   static base::span<const float> vertex_opacity(const viz::DrawQuad& input) {
+     const viz::TextureDrawQuad* quad =
+         viz::TextureDrawQuad::MaterialCast(&input);
+-    return quad->vertex_opacity;
++    return base::make_span(quad->vertex_opacity);
+   }
+
+   static bool y_flipped(const viz::DrawQuad& input) {
+--- a/third_party/WebKit/Source/platform/exported/WebCORS.cpp
++++ b/third_party/WebKit/Source/platform/exported/WebCORS.cpp
+@@ -480,7 +480,7 @@ WebString AccessControlErrorString(
+     }
+     default:
+       NOTREACHED();
+-      return "";
++      return WebString();
+   }
+ }
+ 
+@@ -512,7 +512,7 @@ WebString PreflightErrorString(const PreflightStatus status,
+     }
+     default:
+       NOTREACHED();
+-      return "";
++      return WebString();
+   }
+ }
+ 
+@@ -533,7 +533,7 @@ WebString RedirectErrorString(const RedirectStatus status,
+     }
+     default:
+       NOTREACHED();
+-      return "";
++      return WebString();
+   }
+ }
+ 

pkgs/applications/networking/browsers/chromium/patches/chromium-gn-bootstrap-r14.patch

@@ -1,27 +0,0 @@
-commit 96c271f8ab2be7ea4199078ea65ac50c6ada4685
-Author: Pawel Hajdan, Jr <phajdan.jr@chromium.org>
-Date:   Wed Jul 26 21:51:54 2017 +0000
-
-    wip
-
-diff --git a/tools/gn/bootstrap/bootstrap.py b/tools/gn/bootstrap/bootstrap.py
-index 1390560f8e37..ff2ae57c46b0 100755
---- a/tools/gn/bootstrap/bootstrap.py
-+++ b/tools/gn/bootstrap/bootstrap.py
-@@ -449,6 +449,7 @@ def write_gn_ninja(path, root_gen_dir, options):
-       'base/metrics/histogram_base.cc',
-       'base/metrics/histogram_functions.cc',
-       'base/metrics/histogram_samples.cc',
-+      'base/metrics/histogram_snapshot_manager.cc',
-       'base/metrics/metrics_hashes.cc',
-       'base/metrics/persistent_histogram_allocator.cc',
-       'base/metrics/persistent_memory_allocator.cc',
-@@ -534,7 +535,7 @@ def write_gn_ninja(path, root_gen_dir, options):
-       'base/trace_event/heap_profiler_allocation_context_tracker.cc',
-       'base/trace_event/heap_profiler_allocation_register.cc',
-       'base/trace_event/heap_profiler_event_filter.cc',
--      'base/trace_event/heap_profiler_event_writer.cc',
-+      'base/trace_event/heap_profiler_heap_dump_writer.cc',
-       'base/trace_event/heap_profiler_serialization_state.cc',
-       'base/trace_event/heap_profiler_stack_frame_deduplicator.cc',
-       'base/trace_event/heap_profiler_type_name_deduplicator.cc',

pkgs/applications/networking/browsers/chromium/patches/chromium-gn-bootstrap-r19.patch

@@ -1,10 +0,0 @@
---- a/tools/gn/bootstrap/bootstrap.py
-+++ b/tools/gn/bootstrap/bootstrap.py
-@@ -576,7 +576,6 @@ def write_gn_ninja(path, root_gen_dir, options):
-       'base/trace_event/trace_log.cc',
-       'base/trace_event/trace_log_constants.cc',
-       'base/trace_event/tracing_agent.cc',
--      'base/tracked_objects.cc',
-       'base/unguessable_token.cc',
-       'base/value_iterators.cc',
-       'base/values.cc',

pkgs/applications/networking/browsers/chromium/patches/chromium-sysroot-r1.patch

@@ -1,14 +0,0 @@
---- a/chrome/installer/BUILD.gn
-+++ b/chrome/installer/BUILD.gn
-@@ -3,9 +3,10 @@
- # found in the LICENSE file.
- 
- import("//build/config/chrome_build.gni")
-+import("//build/config/sysroot.gni")
- 
- declare_args() {
--  enable_linux_installer = is_linux && !is_component_build
-+  enable_linux_installer = is_linux && !is_component_build && use_sysroot
- }
- 
- # Meta-target that forwards to the installer of the correct type (if any).

pkgs/applications/networking/browsers/chromium/patches/constexpr-fix.patch

@@ -0,0 +1,98 @@
+From aab2cc3a20af9ebe9ddb8dfd15089f131f95817f Mon Sep 17 00:00:00 2001
+From: Tomas Popela <tomas.popela@gmail.com>
+Date: Fri, 20 Oct 2017 14:06:42 +0200
+Subject: [PATCH] Fix the build of base/numerics with GCC
+
+Initialize the uninitialized variables where the build is failing.
+
+BUG=776705
+
+Change-Id: I5782e18086a752b3676f8738930bf0553f3f97ad
+---
+ base/numerics/checked_math_impl.h |  6 +++---
+ base/numerics/clamped_math_impl.h | 10 +++++-----
+ 2 files changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/base/numerics/checked_math_impl.h b/base/numerics/checked_math_impl.h
+index 2926b37b5e..e083389ebf 100644
+--- a/base/numerics/checked_math_impl.h
++++ b/base/numerics/checked_math_impl.h
+@@ -67,7 +67,7 @@ struct CheckedAddOp<T,
+       return false;
+     }
+ 
+-    Promotion presult;
++    Promotion presult = {};
+     bool is_valid = true;
+     if (IsIntegerArithmeticSafe<Promotion, T, U>::value) {
+       presult = static_cast<Promotion>(x) + static_cast<Promotion>(y);
+@@ -127,7 +127,7 @@ struct CheckedSubOp<T,
+       return false;
+     }
+ 
+-    Promotion presult;
++    Promotion presult = {};
+     bool is_valid = true;
+     if (IsIntegerArithmeticSafe<Promotion, T, U>::value) {
+       presult = static_cast<Promotion>(x) - static_cast<Promotion>(y);
+@@ -183,7 +183,7 @@ struct CheckedMulOp<T,
+       return false;
+     }
+ 
+-    Promotion presult;
++    Promotion presult = {};
+     bool is_valid = true;
+     if (CheckedMulFastOp<Promotion, Promotion>::is_supported) {
+       // The fast op may be available with the promoted type.
+diff --git a/base/numerics/clamped_math_impl.h b/base/numerics/clamped_math_impl.h
+index 7b5e4346f2..303a7e945a 100644
+--- a/base/numerics/clamped_math_impl.h
++++ b/base/numerics/clamped_math_impl.h
+@@ -87,7 +87,7 @@ struct ClampedAddOp<T,
+                   "The saturation result cannot be determined from the "
+                   "provided types.");
+     const V saturated = CommonMaxOrMin<V>(IsValueNegative(y));
+-    V result;
++    V result = {};
+     return BASE_NUMERICS_LIKELY((CheckedAddOp<T, U>::Do(x, y, &result)))
+                ? result
+                : saturated;
+@@ -114,7 +114,7 @@ struct ClampedSubOp<T,
+                   "The saturation result cannot be determined from the "
+                   "provided types.");
+     const V saturated = CommonMaxOrMin<V>(!IsValueNegative(y));
+-    V result;
++    V result = {};
+     return BASE_NUMERICS_LIKELY((CheckedSubOp<T, U>::Do(x, y, &result)))
+                ? result
+                : saturated;
+@@ -136,7 +136,7 @@ struct ClampedMulOp<T,
+     if (ClampedMulFastOp<T, U>::is_supported)
+       return ClampedMulFastOp<T, U>::template Do<V>(x, y);
+ 
+-    V result;
++    V result = {};
+     const V saturated =
+         CommonMaxOrMin<V>(IsValueNegative(x) ^ IsValueNegative(y));
+     return BASE_NUMERICS_LIKELY((CheckedMulOp<T, U>::Do(x, y, &result)))
+@@ -156,7 +156,7 @@ struct ClampedDivOp<T,
+   using result_type = typename MaxExponentPromotion<T, U>::type;
+   template <typename V = result_type>
+   static constexpr V Do(T x, U y) {
+-    V result;
++    V result = {};
+     if (BASE_NUMERICS_LIKELY((CheckedDivOp<T, U>::Do(x, y, &result))))
+       return result;
+     // Saturation goes to max, min, or NaN (if x is zero).
+@@ -176,7 +176,7 @@ struct ClampedModOp<T,
+   using result_type = typename MaxExponentPromotion<T, U>::type;
+   template <typename V = result_type>
+   static constexpr V Do(T x, U y) {
+-    V result;
++    V result = {};
+     return BASE_NUMERICS_LIKELY((CheckedModOp<T, U>::Do(x, y, &result)))
+                ? result
+                : x;
+-- 
+2.14.2
+

pkgs/applications/networking/browsers/chromium/upstream-info.nix

@@ -1,18 +1,18 @@
 # This file is autogenerated from update.sh in the same directory.
 {
   beta = {
-    sha256 = "0c8qn2i7iygl3kgrdwwd8h3l5j8hg66dw99qgr618cgca1b4im68";
+    sha256 = "0qn3pjq5n3ri3qh25wg5gd2as5a8wlkncqvi975xsab771833pz8";
-    sha256bin64 = "04mfg18zpx19ha0mrlwx2aabn0vhl08n9c60hazivmw99pzlg8dn";
+    sha256bin64 = "10d1v9sa0wnnhjz6ria315aml20v1jl2bnkhcqi125rqk5fw9wrq";
-    version = "62.0.3202.29";
+    version = "62.0.3202.62";
   };
   dev = {
-    sha256 = "1zd7rid626fglbyrp7c6517jldhgfk3vjn357vhlhy6pgj1ydrrn";
+    sha256 = "0dx9n9j1apngs4gc1n0kyccczm58045l342jr06azaw5yamsk8xb";
-    sha256bin64 = "0hqb5prf0ags4bnla6skyi5vmkrazhd8n3ri4ijhbqjbb536bfpb";
+    sha256bin64 = "1syqi1fx3kkn7865m6ldicg9cxcg1pfy9l1fr2k5mcqxsdblcyyv";
-    version = "63.0.3218.0";
+    version = "63.0.3239.9";
   };
   stable = {
-    sha256 = "06r89jim9cq87668ya8wwk69hh17rl04cj94nb9c28v6mj69cda1";
+    sha256 = "0qn3pjq5n3ri3qh25wg5gd2as5a8wlkncqvi975xsab771833pz8";
-    sha256bin64 = "1cm9snw29nkzq4bafqgi6fd0gqcc3jp60y6vfsrf9k4dvdard2sv";
+    sha256bin64 = "1ijpv76wbxgwcvgr3nd9ciyyf26z56gxw4caga4x6600pa2lm8wq";
-    version = "61.0.3163.100";
+    version = "62.0.3202.62";
   };
 }

pkgs/applications/networking/firehol/default.nix

@@ -8,13 +8,13 @@
 
 stdenv.mkDerivation rec {
   name = "firehol-${version}";
-  version = "3.1.4";
+  version = "3.1.5";
 
   src = fetchFromGitHub {
     owner = "firehol";
     repo = "firehol";
     rev = "v${version}";
-    sha256 = "121kjq5149r11k58lr9mkqns2k8jbdbjg2k93v8v7axhng6js7s9";
+    sha256 = "15cy1zxfpprma2zkmhj61zzhmw1pfnyhln7pca5lzvr1ifn2d0y0";
   };
 
   patches = [

pkgs/applications/networking/firehol/iprange.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "iprange-${version}";
-  version = "1.0.3";
+  version = "1.0.4";
 
   src = fetchurl {
     url = "https://github.com/firehol/iprange/releases/download/v${version}/iprange-${version}.tar.xz";
-    sha256 = "0lwgl5ybrhsv43llq3kgdjpvgyfl43f3nxm0g8a8cd7zmn754bg2";
+    sha256 = "0rymw4ydn09dng34q4g5111706fyppzs2gd5br76frgvfj4x2f71";
   };
 
   meta = with stdenv.lib; {

pkgs/applications/networking/gns3/default.nix

@@ -2,7 +2,7 @@
 
 let
   stableVersion = "2.0.3";
-  previewVersion = "2.1.0rc2";
+  previewVersion = "2.1.0rc3";
   addVersion = args:
     let version = if args.stable then stableVersion else previewVersion;
         branch = if args.stable then "stable" else "preview";
@@ -16,7 +16,7 @@ in {
   };
   guiPreview = mkGui {
     stable = false;
-    sha256Hash = "1frfhys5s5lnqzk216y3wj2pli5g3b5imfzcmddxdcibksx13i17";
+    sha256Hash = "0yc5lr01xb7lk4dsrwx79mimbr91vldpvqbrx37j3kym6p5m84cn";
   };
 
   serverStable = mkServer {
@@ -25,6 +25,6 @@ in {
   };
   serverPreview = mkServer {
     stable = false;
-    sha256Hash = "0vm4hir8yqj7xhykgg3x5rv1nj1qq6sg19sjj7r5w60brrlsw7v9";
+    sha256Hash = "1lac88d9cmlhrwmlvxv1sk86600rwznw3lpsm440bax6qbdfcis3";
   };
 }

pkgs/applications/networking/ids/bro/default.nix

@@ -2,11 +2,11 @@
 , geoip, gperftools, python, swig }:
 
 stdenv.mkDerivation rec {
-  name = "bro-2.5.1";
+  name = "bro-2.5.2";
 
   src = fetchurl {
     url = "http://www.bro.org/downloads/${name}.tar.gz";
-    sha256 = "04cmm0vs8q31mgaq3pxybjk834py3ji16qp4qcir7vjbhq1fav1c";
+    sha256 = "0w5rynw278nl6pdl5s7gsmxjwkl6z1g5pcm6byg930k26yyb35db";
   };
 
   nativeBuildInputs = [ cmake flex bison file ];

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

@@ -1,12 +1,16 @@
-{ stdenv, fetchurl, ncurses, gtk2, pkgconfig, autoconf, automake, perl, halibut, libtool }:
+{ stdenv, fetchurl, autoconf, automake, pkgconfig, libtool
+, gtk2, halibut, ncurses, perl }:
 
 stdenv.mkDerivation rec {
-  version = "0.67";
+  version = "0.70";
   name = "putty-${version}";
 
   src = fetchurl {
-    url = "http://the.earth.li/~sgtatham/putty/latest/${name}.tar.gz";
+    urls = [
-    sha256 = "0isak6dy5vmfzf9ckcq6jvhgrn3xfmfcmziaa7g2jqm4x1c286c0";
+      "https://the.earth.li/~sgtatham/putty/${version}/${name}.tar.gz"
+      "ftp://ftp.wayne.edu/putty/putty-website-mirror/${version}/${name}.tar.gz"
+    ];
+    sha256 = "1gmhwwj1y7b5hgkrkxpf4jddjpk9l5832zq5ibhsiicndsfs92mv";
   };
 
   preConfigure = ''
@@ -19,8 +23,9 @@ stdenv.mkDerivation rec {
     cd unix
   '';
 
-  nativeBuildInputs = [ pkgconfig ];
+  nativeBuildInputs = [ autoconf automake halibut libtool perl pkgconfig ];
-  buildInputs = [ gtk2 ncurses autoconf automake perl halibut libtool ];
+  buildInputs = [ gtk2 ncurses ];
+  enableParallelBuilding = true;
 
   meta = with stdenv.lib; {
     description = "A Free Telnet/SSH Client";

pkgs/applications/office/homebank/default.nix

@@ -2,10 +2,10 @@
 , hicolor_icon_theme, libsoup, gnome3 }:
 
 stdenv.mkDerivation rec {
-  name = "homebank-5.1.5";
+  name = "homebank-5.1.6";
   src = fetchurl {
     url = "http://homebank.free.fr/public/${name}.tar.gz";
-    sha256 = "03rkl4bvi1cmb8rqyvmhxhg63bdmb3nzqa3firfimsbphm3x6gsw";
+    sha256 = "1q4h890g6a6pm6kfiavbq9sbpsnap0f854sja2y5q3x0j0ay2q98";
   };
 
   nativeBuildInputs = [ pkgconfig wrapGAppsHook ];

pkgs/applications/office/zim/default.nix

@@ -9,11 +9,11 @@
 
 python2Packages.buildPythonApplication rec {
   name = "zim-${version}";
-  version = "0.67-rc2";
+  version = "0.67";
 
   src = fetchurl {
     url = "http://zim-wiki.org/downloads/${name}.tar.gz";
-    sha256 = "0l4q2dfnvyn0jr1lggf8g7515q4z7qr1lnmy0lsyhjf477ldszqf";
+    sha256 = "1gdbzy9qyzj3rn9fsl0ss7lbk9kyka99656bphx2dah694yyyz5k";
   };
 
   propagatedBuildInputs = with python2Packages; [ pyGtkGlade pyxdg pygobject2 ];

pkgs/applications/science/biology/bowtie2/default.nix

@@ -0,0 +1,26 @@
+{ stdenv, fetchFromGitHub, zlib, tbb }:
+
+stdenv.mkDerivation rec {
+  pname = "bowtie2";
+  version = "2.3.3.1";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "BenLangmead";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1pcyks76bnnkq6h0gqjw4fkdddjjnw7k5ibim7ajkbvfw58a99y0";
+  };
+
+  buildInputs = [ zlib tbb ];
+
+  installFlags = [ "prefix=$(out)" ];
+
+  meta = with stdenv.lib; {
+    description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences";
+    license = licenses.gpl3;
+    homepage = http://bowtie-bio.sf.net/bowtie2;
+    maintainers = with maintainers; [ rybern ];
+    platforms = platforms.all;
+  };
+}

pkgs/desktops/gnome-3/core/gnome-themes-standard/src.nix

@@ -1,10 +1,10 @@
 # Autogenerated by maintainers/scripts/gnome.sh update
 
 fetchurl: {
-  name = "gnome-themes-standard-3.22.1";
+  name = "gnome-themes-standard-3.22.3";
 
   src = fetchurl {
-    url = mirror://gnome/sources/gnome-themes-standard/3.22/gnome-themes-standard-3.22.1.tar.xz;
+    url = mirror://gnome/sources/gnome-themes-standard/3.22/gnome-themes-standard-3.22.3.tar.xz;
-    sha256 = "90f6f4e79eaa42e424fa35144cdbcb5db93db56e73200ac045742ba320febb54";
+    sha256 = "61dc87c52261cfd5b94d65e8ffd923ddeb5d3944562f84942eeeb197ab8ab56a";
   };
 }

pkgs/development/compilers/ghcjs/default.nix

@@ -2,5 +2,4 @@
 
 bootPkgs.callPackage ./base.nix {
   inherit bootPkgs;
-  broken = true;  # https://hydra.nixos.org/build/62184741
 }

pkgs/development/compilers/zig/default.nix

@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, cmake, llvmPackages_5, llvm_5 }:
+
+stdenv.mkDerivation rec {
+  version = "0.1.1";
+  name = "zig-${version}";
+
+  src = fetchFromGitHub {
+    owner = "zig-lang";
+    repo = "zig";
+    rev = "${version}";
+    sha256 = "01yqjyi25f99bfmxxwyh45k7j84z0zg7n9jl8gg0draf96mzdh06";
+  };
+
+  buildInputs = [ cmake llvmPackages_5.clang-unwrapped llvm_5 ];
+
+  cmakeFlags = [
+    "-DZIG_LIBC_INCLUDE_DIR=${stdenv.cc.libc_dev}/include"
+    "-DZIG_LIBC_LIB_DIR=${stdenv.cc.libc}/lib"
+    "-DCMAKE_BUILD_TYPE=Release"
+    "-DZIG_EACH_LIB_RPATH=On"
+  ];
+
+  preConfigure = ''
+    cmakeFlags="$cmakeFlags -DZIG_LIBC_STATIC_LIB_DIR=$(dirname $(cc -print-file-name=crtbegin.o)) -DZIG_DYNAMIC_LINKER=$(cc -print-file-name=ld-linux-x86-64.so.2)"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Programming languaged designed for robustness, optimality, and clarity";
+    homepage = http://ziglang.org/;
+    license = licenses.mit;
+    platforms = platforms.unix;
+    maintainers = [ maintainers.andrewrk ];
+  };
+}

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

@@ -969,4 +969,8 @@ self: super: {
   # Depends on broken fluid.
   fluid-idl-http-client = markBroken super.fluid-idl-http-client;
 
+  # depends on amqp >= 0.17
+  amqp-utils = super.amqp-utils.override {
+    amqp = dontCheck super.amqp_0_18_1;
+  };
 }

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

@@ -2850,7 +2850,6 @@ dont-distribute-packages:
   AMI:                                          [ i686-linux, x86_64-linux, x86_64-darwin ]
   ampersand:                                    [ i686-linux, x86_64-linux, x86_64-darwin ]
   amqp-conduit:                                 [ i686-linux, x86_64-linux, x86_64-darwin ]
-  amqp-utils:                                   [ i686-linux, x86_64-linux, x86_64-darwin ]
   analyze-client:                               [ i686-linux, x86_64-linux, x86_64-darwin ]
   anansi-pandoc:                                [ i686-linux, x86_64-linux, x86_64-darwin ]
   anatomy:                                      [ i686-linux, x86_64-linux, x86_64-darwin ]

pkgs/development/libraries/v8/3.14.nix

@@ -0,0 +1,86 @@
+# This old version of V8 is still needed for the R V8 module
+{ stdenv, callPackage, fetchFromGitHub, gyp, readline, python, which, icu, ... }:
+
+assert readline != null;
+
+with stdenv.lib;
+let
+  version = "3.14.5.10";
+  sha256 = "08vhl84166x13b3cbx8y0g99yqx772zd33gawsa1nxqkyrykql6k";
+
+  arch = if stdenv.is64bit then "x64" else "ia32";
+
+in
+stdenv.mkDerivation rec {
+  name = "v8-${version}";
+  inherit version;
+
+  src = fetchFromGitHub {
+    owner = "v8";
+    repo = "v8";
+    rev = "${version}";
+    inherit sha256;
+  };
+  patchPhase = ''
+    sed -i 's,#!/usr/bin/env python,#!${python}/bin/python,' build/gyp_v8
+    sed -i 's,#!/usr/bin/python,#!${python}/bin/python,' build/gyp_v8
+  '';
+
+  configurePhase = ''
+    PYTHONPATH="tools/generate_shim_headers:$PYTHONPATH" \
+    PYTHONPATH="$(toPythonPath ${gyp}):$PYTHONPATH" \
+      build/gyp_v8 \
+        -f make \
+        --generator-output="out" \
+        -Dflock_index=0 \
+        -Dv8_enable_i18n_support=1 \
+        -Duse_system_icu=1 \
+        -Dconsole=readline \
+        -Dcomponent=shared_library \
+        -Dv8_target_arch=${arch}
+  '';
+
+  nativeBuildInputs = [ which ];
+  buildInputs = [ readline python icu ];
+
+  # http://code.google.com/p/v8/issues/detail?id=2149
+  NIX_CFLAGS_COMPILE = concatStringsSep " " [
+    "-Wno-error=strict-overflow"
+    "-Wno-unused-local-typedefs"
+    "-Wno-aggressive-loop-optimizations"
+  ];
+
+  buildFlags = [
+    "LINK=g++"
+    "-C out"
+    "builddir=$(CURDIR)/Release"
+    "BUILDTYPE=Release"
+  ];
+
+  postPatch = stdenv.lib.optionalString (!stdenv.cc.isClang) ''
+    sed -i build/standalone.gyp -e 's,-Wno-format-pedantic,,g'
+  '';
+
+  enableParallelBuilding = true;
+
+  installPhase = ''
+    install -vD out/Release/d8 "$out/bin/d8"
+    ${if stdenv.system == "x86_64-darwin" then ''
+    install -vD out/Release/lib.target/libv8.dylib "$out/lib/libv8.dylib"
+    '' else ''
+    install -vD out/Release/lib.target/libv8.so "$out/lib/libv8.so"
+    ''}
+    cp -vr include "$out/"
+  '';
+
+  postFixup = if stdenv.isDarwin then ''
+    install_name_tool -change /usr/local/lib/libv8.dylib $out/lib/libv8.dylib -change /usr/lib/libgcc_s.1.dylib ${stdenv.cc.cc.lib}/lib/libgcc_s.1.dylib $out/bin/d8
+    install_name_tool -id $out/lib/libv8.dylib -change /usr/lib/libgcc_s.1.dylib ${stdenv.cc.cc.lib}/lib/libgcc_s.1.dylib $out/lib/libv8.dylib
+  '' else null;
+
+  meta = with stdenv.lib; {
+    description = "Google's open source JavaScript engine";
+    platforms = platforms.linux;
+    license = licenses.bsd3;
+  };
+}

pkgs/development/ocaml-modules/omd/default.nix

@@ -1,10 +1,10 @@
 { stdenv, fetchurl, ocaml, findlib, ocamlbuild }:
 
 stdenv.mkDerivation {
-  name = "ocaml${ocaml.version}-omd-1.3.0";
+  name = "ocaml${ocaml.version}-omd-1.3.1";
   src = fetchurl {
-    url = http://pw374.github.io/distrib/omd/omd-1.3.0.tar.gz;
+    url = "https://github.com/Chris00/omd/releases/download/1.3.1/omd-1.3.1.tar.gz";
-    sha256 = "0d0r6c4s3hq11d0qjc0bc1s84hz7k8nfg5q6g239as8myam4a80w";
+    sha256 = "1sgdgzpx96br7npj8mh91cli5mqmzsjpngwm7x4212n3k1d0ivwa";
   };
 
   buildInputs = [ ocaml findlib ocamlbuild ];

pkgs/development/ocaml-modules/zed/default.nix

@@ -1,19 +1,34 @@
-{ stdenv, fetchzip, ocaml, findlib, ocamlbuild, camomile, react }:
+{ stdenv, fetchzip, ocaml, findlib, ocamlbuild, camomile, react, jbuilder }:
 
-stdenv.mkDerivation rec {
+let param =
-  version = "1.4";
+  if stdenv.lib.versionAtLeast ocaml.version "4.02" then
+  {
+    version = "1.5";
+    sha256 = "1nq884cxl1k4daa549bk7bxarwivbpp51k4blbiwyxwfhs29xgfr";
+    buildInputs = [ jbuilder ];
+    extra = {
+     buildPhase = "jbuilder build -p zed";
+     inherit (jbuilder) installPhase; };
+  } else {
+    version = "1.4";
+    sha256 = "0d8qfy0qiydrrqi8qc9rcwgjigql6vx9gl4zp62jfz1lmjgb2a3w";
+    buildInputs = [];
+    extra = { createFindlibDestdir = true; };
+  }
+; in
+
+stdenv.mkDerivation (rec {
+  inherit (param) version;
   name = "ocaml-zed-${version}";
 
   src = fetchzip {
     url = "https://github.com/diml/zed/archive/${version}.tar.gz";
-    sha256 = "0d8qfy0qiydrrqi8qc9rcwgjigql6vx9gl4zp62jfz1lmjgb2a3w";
+    inherit (param) sha256;
   };
 
-  buildInputs = [ ocaml findlib ocamlbuild react ];
+  buildInputs = [ ocaml findlib ocamlbuild ] ++ param.buildInputs;
 
-  propagatedBuildInputs = [ camomile ];
+  propagatedBuildInputs = [ react camomile ];
-
-  createFindlibDestdir = true;
 
   meta = {
     description = "Abstract engine for text edition in OCaml";
@@ -31,4 +46,4 @@ stdenv.mkDerivation rec {
       stdenv.lib.maintainers.gal_bolle
     ];
   };
-}
+} // param.extra)

pkgs/development/r-modules/default.nix

@@ -253,6 +253,7 @@ let
     fftwtools = [ pkgs.fftw.dev ];
     Formula = [ pkgs.gmp ];
     geoCount = [ pkgs.gsl_1 ];
+    gdtools = [ pkgs.cairo.dev pkgs.fontconfig.lib pkgs.freetype.dev ];
     git2r = [ pkgs.zlib.dev pkgs.openssl.dev ];
     GLAD = [ pkgs.gsl_1 ];
     glpkAPI = [ pkgs.gmp pkgs.glpk ];
@@ -260,32 +261,37 @@ let
     graphscan = [ pkgs.gsl_1 ];
     gsl = [ pkgs.gsl_1 ];
     h5 = [ pkgs.hdf5-cpp pkgs.which ];
+    haven = [ pkgs.libiconv ];
     h5vc = [ pkgs.zlib.dev ];
     HiCseg = [ pkgs.gsl_1 ];
     imager = [ pkgs.x11 ];
     iBMQ = [ pkgs.gsl_1 ];
-    igraph = [ pkgs.gmp ];
+    igraph = [ pkgs.gmp pkgs.libxml2.dev ];
     JavaGD = [ pkgs.jdk ];
     jpeg = [ pkgs.libjpeg.dev ];
     KFKSDS = [ pkgs.gsl_1 ];
     kza = [ pkgs.fftw.dev ];
     libamtrack = [ pkgs.gsl_1 ];
+    magick = [ pkgs.imagemagick.dev ];
     mixcat = [ pkgs.gsl_1 ];
     mvabund = [ pkgs.gsl_1 ];
     mwaved = [ pkgs.fftw.dev ];
     ncdf4 = [ pkgs.netcdf ];
     nloptr = [ pkgs.nlopt ];
-    openssl = [ pkgs.openssl.dev ];
+    odbc = [ pkgs.unixODBC ];
+    openssl = [ pkgs.openssl pkgs.openssl.dev ];
     outbreaker = [ pkgs.gsl_1 ];
     pander = [ pkgs.pandoc pkgs.which ];
     pbdMPI = [ pkgs.openmpi ];
     pbdNCDF4 = [ pkgs.netcdf ];
     pbdPROF = [ pkgs.openmpi ];
     pbdZMQ = [ pkgs.which ];
+    pdftools = [ pkgs.poppler.dev ];
     PKI = [ pkgs.openssl.dev ];
     png = [ pkgs.libpng.dev ];
     PopGenome = [ pkgs.zlib.dev ];
     proj4 = [ pkgs.proj ];
+    protolite = [ pkgs.protobuf ];
     qtbase = [ pkgs.qt4 ];
     qtpaint = [ pkgs.qt4 ];
     R2GUESS = [ pkgs.gsl_1 ];
@@ -293,6 +299,7 @@ let
     RAppArmor = [ pkgs.libapparmor ];
     rapportools = [ pkgs.which ];
     rapport = [ pkgs.which ];
+    readxl = [ pkgs.libiconv ];
     rbamtools = [ pkgs.zlib.dev ];
     rcdd = [ pkgs.gmp.dev ];
     RcppCNPy = [ pkgs.zlib.dev ];
@@ -315,14 +322,15 @@ let
     rmatio = [ pkgs.zlib.dev ];
     Rmpfr = [ pkgs.gmp pkgs.mpfr.dev ];
     Rmpi = [ pkgs.openmpi ];
-    RMySQL = [ pkgs.zlib pkgs.mysql.lib ];
+    RMySQL = [ pkgs.zlib pkgs.mysql.lib pkgs.mariadb pkgs.openssl.dev ];
     RNetCDF = [ pkgs.netcdf pkgs.udunits ];
     RODBCext = [ pkgs.libiodbc ];
     RODBC = [ pkgs.libiodbc ];
+    rpanel = [ pkgs.bwidget ];
     rpg = [ pkgs.postgresql ];
     rphast = [ pkgs.pcre.dev pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
     Rpoppler = [ pkgs.poppler ];
-    RPostgreSQL = [ pkgs.postgresql ];
+    RPostgreSQL = [ pkgs.postgresql pkgs.postgresql ];
     RProtoBuf = [ pkgs.protobuf ];
     rPython = [ pkgs.python ];
     RSclient = [ pkgs.openssl.dev ];
@@ -331,6 +339,7 @@ let
     rtfbs = [ pkgs.zlib pkgs.pcre.dev pkgs.bzip2 pkgs.gzip pkgs.readline ];
     rtiff = [ pkgs.libtiff.dev ];
     runjags = [ pkgs.jags ];
+    RSymphony = [ pkgs.symphony ];
     RVowpalWabbit = [ pkgs.zlib.dev pkgs.boost ];
     rzmq = [ pkgs.zeromq3 ];
     SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
@@ -338,6 +347,7 @@ let
     seewave = [ pkgs.fftw.dev pkgs.libsndfile.dev ];
     seqinr = [ pkgs.zlib.dev ];
     seqminer = [ pkgs.zlib.dev pkgs.bzip2 ];
+    sf = [ pkgs.gdal pkgs.proj pkgs.geos ];
     showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype.dev ];
     simplexreg = [ pkgs.gsl_1 ];
     SOD = [ pkgs.opencl-headers ];
@@ -349,12 +359,13 @@ let
     survSNP = [ pkgs.gsl_1 ];
     sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype.dev ];
     TAQMNGR = [ pkgs.zlib.dev ];
+    tesseract = [ pkgs.tesseract pkgs.leptonica ];
     tiff = [ pkgs.libtiff.dev ];
     TKF = [ pkgs.gsl_1 ];
     tkrplot = [ pkgs.xorg.libX11 pkgs.tk.dev ];
     topicmodels = [ pkgs.gsl_1 ];
     udunits2 = [ pkgs.udunits pkgs.expat ];
-    V8 = [ pkgs.v8 ];
+    V8 = [ pkgs.v8_3_14 ];
     VBLPCM = [ pkgs.gsl_1 ];
     VBmix = [ pkgs.gsl_1 pkgs.fftw pkgs.qt4 ];
     WhopGenome = [ pkgs.zlib.dev ];
@@ -401,12 +412,20 @@ let
     chebpol = [ pkgs.pkgconfig ];
     fftw = [ pkgs.pkgconfig ];
     geoCount = [ pkgs.pkgconfig ];
+    gdtools = [ pkgs.pkgconfig ];
     kza = [ pkgs.pkgconfig ];
+    magick = [ pkgs.pkgconfig ];
     mwaved = [ pkgs.pkgconfig ];
+    odbc = [ pkgs.pkgconfig ];
+    openssl = [ pkgs.pkgconfig ];
+    pdftools = [ pkgs.pkgconfig ];
+    sf = [ pkgs.pkgconfig ];
     showtext = [ pkgs.pkgconfig ];
     spate = [ pkgs.pkgconfig ];
     stringi = [ pkgs.pkgconfig ];
+    sys = [ pkgs.libapparmor ];
     sysfonts = [ pkgs.pkgconfig ];
+    tesseract = [ pkgs.pkgconfig ];
     Cairo = [ pkgs.pkgconfig ];
     Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
     qtutils = [ pkgs.qt4 ];
@@ -782,8 +801,10 @@ let
     });
 
     RMySQL = old.RMySQL.overrideDerivation (attrs: {
-      patches = [ ./patches/RMySQL.patch ];
       MYSQL_DIR="${pkgs.mysql.lib}";
+      preConfigure = ''
+        patchShebangs configure
+        '';
     });
 
     devEMF = old.devEMF.overrideDerivation (attrs: {
@@ -818,6 +839,9 @@ let
 
     openssl = old.openssl.overrideDerivation (attrs: {
       OPENSSL_INCLUDES = "${pkgs.openssl.dev}/include";
+      preConfigure = ''
+        sed -i.bak 's|^\( *PKG_LIBS_VERSIONED=\).*$|\1$PKG_LIBS|' configure
+        '';
     });
 
     Rserve = old.Rserve.overrideDerivation (attrs: {
@@ -835,7 +859,71 @@ let
     });
 
     V8 = old.V8.overrideDerivation (attrs: {
-      preConfigure = "export V8_INCLUDES=${pkgs.v8}/include";
+      preConfigure = ''
+        export INCLUDE_DIR=${pkgs.v8_3_14}/include
+        export LIB_DIR=${pkgs.v8_3_14}/lib
+        patchShebangs configure
+        '';
+    });
+
+    acs = old.acs.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    gdtools = old.gdtools.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+      NIX_LDFLAGS = "-lfontconfig -lfreetype";
+    });
+
+    magick = old.magick.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    protolite = old.protolite.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    rpanel = old.rpanel.overrideDerivation (attrs: {
+      preConfigure = ''
+        export TCLLIBPATH="${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}"
+      '';
+      TCLLIBPATH = "${pkgs.bwidget}/lib/bwidget${pkgs.bwidget.version}";
+    });
+
+    OpenMx = old.OpenMx.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    odbc = old.odbc.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    x13binary = old.x13binary.overrideDerivation (attrs: {
+      preConfigure = ''
+        patchShebangs configure
+        '';
+    });
+
+    geojsonio = old.geojsonio.overrideDerivation (attrs: {
+      preConfigure = ''
+        export SSL_CERT_FILE=${pkgs.cacert}/etc/ssl/certs/ca-bundle.crt
+        '';
+    });
+
+    rstan = old.rstan.overrideDerivation (attrs: {
+      NIX_CFLAGS_COMPILE = "${attrs.NIX_CFLAGS_COMPILE} -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION";
     });
 
   };

pkgs/development/tools/build-managers/bazel/0.4.nix

@@ -38,6 +38,15 @@ stdenv.mkDerivation rec {
     for f in $(grep -l -r '/usr/bin/env'); do
       substituteInPlace "$f" --replace '/usr/bin/env' '${coreutils}/bin/env'
     done
+  '' + lib.optionalString stdenv.isDarwin ''
+    sed -i 's,/usr/bin/xcrun clang,clang,g' \
+      scripts/bootstrap/compile.sh \
+      src/tools/xcode/realpath/BUILD \
+      src/tools/xcode/stdredirect/BUILD \
+      src/tools/xcode/xcrunwrapper/xcrunwrapper.sh
+    sed -i 's,/usr/bin/xcrun "''${TOOLNAME}","''${TOOLNAME}",g' \
+      src/tools/xcode/xcrunwrapper/xcrunwrapper.sh
+    sed -i 's/"xcrun", "clang"/"clang"/g' tools/osx/xcode_configure.bzl
   '';
 
   buildInputs = [

pkgs/development/tools/continuous-integration/buildkite-agent/default.nix

@@ -1,32 +1,38 @@
-{ stdenv, fetchurl, makeWrapper, coreutils, git, openssh, bash, gnused, gnugrep }:
+{ stdenv, buildGoPackage, fetchFromGitHub, makeWrapper, coreutils, git, openssh, bash, gnused, gnugrep }:
-
+let
-stdenv.mkDerivation rec {
+  version = "2.6.6";
-  version = "2.1.13";
+  goPackagePath = "github.com/buildkite/agent";
+in
+buildGoPackage {
   name = "buildkite-agent-${version}";
-  dontBuild = true;
 
-  src = fetchurl {
+  inherit goPackagePath;
-    url = "https://github.com/buildkite/agent/releases/download/v${version}/buildkite-agent-linux-386-${version}.tar.gz";
+
-    sha256 = "bd40c2ba37b3b54b875241a32b62190a4cf4c15e2513c573f1626a3ca35c8657";
+  src = fetchFromGitHub {
+    owner = "buildkite";
+    repo = "agent";
+    rev = "v${version}";
+    sha256 = "0rpi63mfzlm39517l4xjcka3m4dnfjzwvpi0i1rpf1z2288cnkyx";
   };
 
   nativeBuildInputs = [ makeWrapper ];
-  sourceRoot = ".";
-  installPhase = ''
-    install -Dt "$out/bin/" buildkite-agent
 
-    mkdir -p $out/share
+  postInstall = ''
-    mv hooks bootstrap.sh $out/share/
+    # Install bootstrap.sh
+    mkdir -p $bin/libexec/buildkite-agent
+    cp $NIX_BUILD_TOP/go/src/${goPackagePath}/templates/bootstrap.sh $bin/libexec/buildkite-agent
+    sed -e "s|#!/bin/bash|#!${bash}/bin/bash|g" -i $bin/libexec/buildkite-agent/bootstrap.sh
+
+    # Fix binary name
+    mv $bin/bin/{agent,buildkite-agent}
+
+    # These are runtime dependencies
+    wrapProgram $bin/bin/buildkite-agent \
+      --prefix PATH : '${stdenv.lib.makeBinPath [ openssh git coreutils gnused gnugrep ]}' \
+      --set BUILDKITE_BOOTSTRAP_SCRIPT_PATH $bin/libexec/buildkite-agent/bootstrap.sh
   '';
 
-  postFixup = ''
+  meta = with stdenv.lib; {
-    substituteInPlace $out/share/bootstrap.sh \
-      --replace "#!/bin/bash" "#!$(type -P bash)"
-    wrapProgram $out/bin/buildkite-agent \
-      --set PATH '"${stdenv.lib.makeBinPath [ openssh git coreutils gnused gnugrep ]}:$PATH"'
-  '';
-
-  meta = {
     description = "Build runner for buildkite.com";
     longDescription = ''
       The buildkite-agent is a small, reliable, and cross-platform build runner
@@ -36,8 +42,8 @@ stdenv.mkDerivation rec {
       and uploading the job's artifacts.
     '';
     homepage = https://buildkite.com/docs/agent;
-    license = stdenv.lib.licenses.mit;
+    license = licenses.mit;
-    maintainers = [ stdenv.lib.maintainers.pawelpacana ];
+    maintainers = with maintainers; [ pawelpacana zimbatm ];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = platforms.linux;
   };
 }

pkgs/misc/vim-plugins/default.nix

@@ -2550,4 +2550,14 @@ rec {
 
   };
 
+  zig-vim = buildVimPluginFrom2Nix { # created by nix#NixDerivation
+    name = "zig-vim-2017-10-17";
+    src = fetchgit {
+      url = "https://github.com/zig-lang/zig.vim";
+      rev = "6059db59f61b517f5d65303b61f03324e01fdc2f";
+      sha256 = "0w3pa63s0r6h6w1iqmc444qrsc99xcccwapd6nyh3gb72z228d7z";
+    };
+    dependencies = [];
+
+  };
 }

pkgs/misc/vim-plugins/vim-plugin-names

@@ -161,6 +161,7 @@
 "github:zah/nim.vim"
 "github:zchee/deoplete-go"
 "github:zchee/deoplete-jedi"
+"github:zig-lang/zig.vim"
 "goyo"
 "gruvbox"
 "matchit.zip"

pkgs/os-specific/linux/nvme-cli/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "nvme-cli-${version}";
-  version = "0.9";
+  version = "1.4";
 
   src = fetchFromGitHub {
     owner = "linux-nvme";
     repo = "nvme-cli";
     rev = "v${version}";
-    sha256 = "16n0gg1zx4fgadcq94kx6bgysqw60jvybjwynk7mj3fzdbvzrqyh";
+    sha256 = "00jrr1mya9wkapiapph3nch3kpqas6vlc8kl8dbrjjfb5hg35gqf";
   };
 
   makeFlags = [ "DESTDIR=$(out)" "PREFIX=" ];
@@ -16,8 +16,8 @@ stdenv.mkDerivation rec {
   meta = with lib; {
     inherit (src.meta) homepage;
     description = "NVM-Express user space tooling for Linux";
-    license = licenses.gpl2;
+    license = licenses.gpl2Plus;
     platforms = platforms.linux;
-    maintainers = with maintainers; [ tavyc ];
+    maintainers = with maintainers; [ primeos tavyc ];
   };
 }

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

@@ -3,7 +3,8 @@
   python, python3, pam, popt, talloc, tdb, tevent, pkgconfig, ldb, openldap,
   pcre, kerberos, cifs_utils, glib, keyutils, dbus, fakeroot, libxslt, libxml2,
   docbook_xml_xslt, ldap, systemd, nspr, check, cmocka, uid_wrapper,
-  nss_wrapper, docbook_xml_dtd_44, ncurses, Po4a, http-parser, jansson }:
+  nss_wrapper, docbook_xml_dtd_44, ncurses, Po4a, http-parser, jansson
+  , withSudo ? false }:
 
 let
   docbookFiles = "${pkgs.docbook_xml_xslt}/share/xml/docbook-xsl/catalog.xml:${pkgs.docbook_xml_dtd_44}/xml/dtd/docbook/catalog.xml";
@@ -41,6 +42,8 @@ stdenv.mkDerivation rec {
       --with-ldb-lib-dir=$out/modules/ldb
       --with-nscd=${glibc.bin}/sbin/nscd
     )
+  '' + stdenv.lib.optionalString withSudo ''
+    configureFlagsArray+=("--with-sudo")
   '';
 
   enableParallelBuilding = true;

pkgs/servers/web-apps/shaarli/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "shaarli-${version}";
-  version = "0.9.1";
+  version = "0.9.2";
 
   src = fetchurl {
     url = "https://github.com/shaarli/Shaarli/releases/download/v${version}/shaarli-v${version}-full.tar.gz";
-    sha256 = "10arm3sm9dbzi97x1mjh46r5f6zii4f1w8nl0zfw3knbapab8xv5";
+    sha256 = "07wn5pg7pkya8d4k2khp2jyvkdkmm5431fj1k0m1i5k65yyvfqzr";
   };
 
   outputs = [ "out" "doc" ];
@@ -55,7 +55,7 @@ stdenv.mkDerivation rec {
     description = "The personal, minimalist, super-fast, database free, bookmarking service";
     license = licenses.gpl3Plus;
     homepage = https://github.com/shaarli/Shaarli;
-    maintainers = with maintainers; [ ];
+    maintainers = with maintainers; [ schneefux ];
     platforms = platforms.all;
   };
 }

pkgs/servers/web-apps/shaarli/material-theme.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "shaarli-material-${version}";
-  version = "0.8.3";
+  version = "0.9.1";
 
   src = fetchFromGitHub {
     owner = "kalvn";
     repo = "Shaarli-Material";
     rev = "v${version}";
-    sha256 = "0ivq35183r5vyzvf47sgxwdxllmvhd5w9w75xgyp3kbw2na4yrmr";
+    sha256 = "0x8d9425n3jrwzsyxclbxfspvi91v1klq8r3m6wcj81kys7vmzgh";
   };
 
   patchPhase = ''

pkgs/tools/misc/tmuxinator/default.nix

@@ -8,8 +8,8 @@ buildRubyGem rec {
   inherit ruby;
   name = "${gemName}-${version}";
   gemName = "tmuxinator";
-  version = "0.9.0";
+  version = "0.10.0";
-  sha256 = "13p8rvf1naknjin1n97370ifyj475lyyh60cbw2v6gczi9rs84p3";
+  sha256 = "199pq15qknpcafw8ryb9kk1jsrwnncg6k5l9d4n0nmms4knxlqlf";
 
   erubis = buildRubyGem rec {
     inherit ruby;
@@ -27,7 +27,15 @@ buildRubyGem rec {
     sha256 = "08p5gx18yrbnwc6xc0mxvsfaxzgy2y9i78xq7ds0qmdm67q39y4z";
   };
 
-  propagatedBuildInputs = [ erubis thor ];
+  xdg = buildRubyGem rec {
+    inherit ruby;
+    name = "ruby${ruby.version}-${gemName}-${version}";
+    gemName = "xdg";
+    version = "2.2.3";
+    sha256 = "1bn47fdbwxqbdvjcfg86i32hmwm36k0xl876kb85f5da5v84lzmq";
+  };
+
+  propagatedBuildInputs = [ erubis thor xdg ];
 
   meta = with lib; {
     description = "Manage complex tmux sessions easily";

pkgs/tools/misc/youtube-dl/default.nix

@@ -15,11 +15,11 @@ with stdenv.lib;
 buildPythonApplication rec {
 
   name = "youtube-dl-${version}";
-  version = "2017.10.01";
+  version = "2017.10.20";
 
   src = fetchurl {
     url = "https://yt-dl.org/downloads/${version}/${name}.tar.gz";
-    sha256 = "047zinsczn6c96fzkarlb29y7sjwyh84nxlpfpa6mi4rn090wkqb";
+    sha256 = "0npr8b1xg1dylz717kfllw433h1y16251npzch48lchq69bhm4iy";
   };
 
   nativeBuildInputs = [ makeWrapper ];

pkgs/tools/package-management/librepo/default.nix

@@ -1,21 +1,16 @@
 { stdenv, fetchFromGitHub, cmake, python2, pkgconfig, expat, glib, pcre, openssl, curl, check, attr, gpgme }:
 
 stdenv.mkDerivation rec {
-  version = "1.7.20";
+  version = "1.8.1";
   name = "librepo-${version}";
 
   src = fetchFromGitHub {
     owner  = "rpm-software-management";
     repo   = "librepo";
-    rev    = name;
+    rev    = version;
-    sha256 = "17fgj2wifn2qxmh1p285fbwys0xbvwbnmxsdfvqyr5njpyl2s99h";
+    sha256 = "11rypnxjgsc2klyg294ndxy1cyp0nyk00zpjhcvqkhp58vvkkv12";
   };
 
-  patchPhase = ''
-    substituteInPlace librepo/python/python2/CMakeLists.txt \
-      --replace ' ''${PYTHON_INSTALL_DIR}' " $out/lib/python2.7/site-packages"
-  '';
-
   nativeBuildInputs = [ cmake pkgconfig ];
 
   buildInputs = [ python2 expat glib pcre openssl curl check attr gpgme ];
@@ -25,9 +20,9 @@ stdenv.mkDerivation rec {
 
   meta = with stdenv.lib; {
     description = "Library providing C and Python (libcURL like) API for downloading linux repository metadata and packages";
+    homepage    = https://rpm-software-management.github.io/librepo/;
     license     = licenses.lgpl2Plus;
     platforms   = platforms.linux;
     maintainers = with maintainers; [ copumpkin ];
   };
 }
-

pkgs/tools/security/sudo/default.nix

@@ -1,6 +1,7 @@
-{ stdenv, fetchurl, coreutils, pam, groff
+{ stdenv, fetchurl, coreutils, pam, groff, sssd
 , sendmailPath ? "/run/wrappers/bin/sendmail"
 , withInsults ? false
+, withSssd ? false
 }:
 
 stdenv.mkDerivation rec {
@@ -30,6 +31,9 @@ stdenv.mkDerivation rec {
   ] ++ stdenv.lib.optional withInsults [
     "--with-insults"
     "--with-all-insults"
+  ] ++ stdenv.lib.optional withSssd [
+    "--with-sssd"
+    "--with-sssd-lib=${sssd}/lib"
   ];
 
   configureFlagsArray = [

pkgs/tools/security/vault/default.nix

@@ -9,13 +9,13 @@ let
   };
 in stdenv.mkDerivation rec {
   name = "vault-${version}";
-  version = "0.8.1";
+  version = "0.8.3";
 
   src = fetchFromGitHub {
     owner = "hashicorp";
     repo = "vault";
     rev = "v${version}";
-    sha256 = "19y688nvi0vr7cdnaa5sy2m65xicjwi5qgkgzyjvb7r3zb0dnli1";
+    sha256 = "1dcmqbcdkj42614am2invb6wf8v29z4sp4d354a4d83rwhyb0qly";
   };
 
   nativeBuildInputs = [ go gox removeReferencesTo ];
@@ -27,6 +27,8 @@ in stdenv.mkDerivation rec {
     mkdir -p src/github.com/hashicorp
     ln -s $(pwd) src/github.com/hashicorp/vault
 
+    mkdir -p .git/hooks
+
     GOPATH=$(pwd) make
   '';
 

pkgs/tools/typesetting/asciidoctor/Gemfile.lock

@@ -5,7 +5,7 @@ GEM
     addressable (2.5.0)
       public_suffix (~> 2.0, >= 2.0.2)
     afm (0.2.2)
-    asciidoctor (1.5.5)
+    asciidoctor (1.5.6.1)
     asciidoctor-bespoke (1.0.0.alpha.1)
       asciidoctor (>= 1.5.0)
       slim (~> 3.0.6)
@@ -16,7 +16,7 @@ GEM
       asciidoctor (~> 1.5, >= 1.5.2)
       htmlentities (~> 4.3)
       opal (~> 0.6.3)
-    asciidoctor-pdf (1.5.0.alpha.13)
+    asciidoctor-pdf (1.5.0.alpha.16)
       asciidoctor (>= 1.5.0)
       prawn (>= 1.3.0, < 3.0.0)
       prawn-icon (= 1.2.0)

pkgs/tools/typesetting/asciidoctor/gemset.nix

@@ -26,10 +26,10 @@
   asciidoctor = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0kj2lls8f83nlhfkdkmbf7k5q9c9kk1cc15b1a4dy6arx4yzmvw7";
+      sha256 = "c4371c419306d69152809eb896c291ca09969dc26ca34be36f4eab82914fceca";
       type = "gem";
     };
-    version = "1.5.5";
+    version = "1.5.6.1";
   };
   asciidoctor-bespoke = {
     source = {
@@ -58,10 +58,10 @@
   asciidoctor-pdf = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0lp1q1yxy4y9k3znxxgj6pl0cbymz0yk5hsif73sg2bnpk62id9i";
+      sha256 = "0f6b2a1533577dfba218de5dd886771447e4d1cb670b81d2c3bf3a180e6029a1";
       type = "gem";
     };
-    version = "1.5.0.alpha.13";
+    version = "1.5.0.alpha.16";
   };
   concurrent-ruby = {
     source = {
@@ -287,4 +287,4 @@
     };
     version = "1.4.0";
   };
-}
+}

pkgs/top-level/all-packages.nix

@@ -762,6 +762,8 @@ with pkgs;
 
   bootchart = callPackage ../tools/system/bootchart { };
 
+  bowtie2 = callPackage ../applications/science/biology/bowtie2 { };
+
   boxfs = callPackage ../tools/filesystems/boxfs { };
 
   brasero-original = lowPrio (callPackage ../tools/cd-dvd/brasero { });
@@ -7709,7 +7711,6 @@ with pkgs;
     inherit (python3Packages) fetchPypi buildPythonApplication lxml typed-ast;
   };
 
-
   ### DEVELOPMENT / LIBRARIES
 
   a52dec = callPackage ../development/libraries/a52dec { };
@@ -10858,6 +10859,13 @@ with pkgs;
     gnutls = gnutls;
   });
 
+  # 3.14 is needed for R V8 module in ../development/r-modules/default.nix
+  v8_3_14 = callPackage ../development/libraries/v8/3.14.nix {
+    inherit (python2Packages) python gyp;
+    cctools = darwin.cctools;
+    stdenv = overrideCC stdenv gcc5;
+  };
+
   v8_3_16_14 = callPackage ../development/libraries/v8/3.16.14.nix {
     inherit (python2Packages) python gyp;
     cctools = darwin.cctools;
@@ -11113,6 +11121,8 @@ with pkgs;
     czmq = czmq3;
   };
 
+  zig = callPackage ../development/compilers/zig {};
+
   zimlib = callPackage ../development/libraries/zimlib { };
 
   zita-convolver = callPackage ../development/libraries/audio/zita-convolver { };