Merge master into staging-next

maintainers/maintainer-list.nix

@@ -393,6 +393,11 @@
     github = "aneeshusa";
     name = "Aneesh Agrawal";
   };
+  angristan = {
+    email = "angristan@pm.me";
+    github = "angristan";
+    name = "Stanislas Lange";
+  };
   ankhers = {
     email = "justin.k.wood@gmail.com";
     github = "ankhers";

nixos/doc/manual/release-notes/rl-1909.xml

@@ -214,6 +214,11 @@
       have a look at the <link xlink:href="https://github.com/nginxinc/nginx-prometheus-exporter">official repo</link>.
     </para>
    </listitem>
+   <listitem>
+     <para>
+       Nodejs 8 is scheduled EOL under the lifetime of 19.09 and has been dropped.
+     </para>
+   </listitem>
   </itemizedlist>
  </section>
 

nixos/modules/config/xdg/portal.nix

@@ -51,7 +51,7 @@ with lib;
       systemd.packages = packages;
 
       environment.variables = {
-        GTK_USE_PORTAL = optional cfg.gtkUsePortal "1";
+        GTK_USE_PORTAL = mkIf cfg.gtkUsePortal "1";
         XDG_DESKTOP_PORTAL_PATH = map (p: "${p}/share/xdg-desktop-portal/portals") cfg.extraPortals;
       };
     };

nixos/modules/programs/ssh.nix

@@ -235,6 +235,7 @@ in
     systemd.user.services.ssh-agent = mkIf cfg.startAgent
       { description = "SSH Agent";
         wantedBy = [ "default.target" ];
+        unitConfig.ConditionUser = "!@system";
         serviceConfig =
           { ExecStartPre = "${pkgs.coreutils}/bin/rm -f %t/ssh-agent";
             ExecStart =

nixos/modules/services/misc/gitlab.nix

@@ -502,6 +502,7 @@ in {
       "d ${cfg.statePath} 0750 ${cfg.user} ${cfg.group} -"
       "d ${cfg.statePath}/builds 0750 ${cfg.user} ${cfg.group} -"
       "d ${cfg.statePath}/config 0750 ${cfg.user} ${cfg.group} -"
+      "d ${cfg.statePath}/config/initializers 0750 ${cfg.user} ${cfg.group} -"
       "d ${cfg.statePath}/db 0750 ${cfg.user} ${cfg.group} -"
       "d ${cfg.statePath}/log 0750 ${cfg.user} ${cfg.group} -"
       "d ${cfg.statePath}/repositories 2770 ${cfg.user} ${cfg.group} -"

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

@@ -28,6 +28,7 @@ let
     "dovecot"
     "fritzbox"
     "json"
+    "mail"
     "minio"
     "nginx"
     "node"
@@ -162,13 +163,19 @@ in
   };
 
   config = mkMerge ([{
-    assertions = [{
+    assertions = [ {
       assertion = (cfg.snmp.configurationPath == null) != (cfg.snmp.configuration == null);
       message = ''
         Please ensure you have either `services.prometheus.exporters.snmp.configuration'
           or `services.prometheus.exporters.snmp.configurationPath' set!
       '';
-    }];
+    } {
+      assertion = (cfg.mail.configFile == null) != (cfg.mail.configuration == {});
+      message = ''
+        Please specify either 'services.prometheus.exporters.mail.configuration'
+          or 'services.prometheus.exporters.mail.configFile'.
+      '';
+    } ];
   }] ++ [(mkIf config.services.minio.enable {
     services.prometheus.exporters.minio.minioAddress  = mkDefault "http://localhost:9000";
     services.prometheus.exporters.minio.minioAccessKey = mkDefault config.services.minio.accessKey;

nixos/modules/services/monitoring/prometheus/exporters/mail.nix

@@ -0,0 +1,156 @@
+{ config, lib, pkgs, options }:
+
+with lib;
+
+let
+  cfg = config.services.prometheus.exporters.mail;
+
+  configurationFile = pkgs.writeText "prometheus-mail-exporter.conf" (builtins.toJSON (
+    # removes the _module attribute, null values and converts attrNames to lowercase
+    mapAttrs' (name: value:
+      if name == "servers"
+      then nameValuePair (toLower name)
+        ((map (srv: (mapAttrs' (n: v: nameValuePair (toLower n) v)
+          (filterAttrs (n: v: !(n == "_module" || v == null)) srv)
+        ))) value)
+      else nameValuePair (toLower name) value
+    ) (filterAttrs (n: _: !(n == "_module")) cfg.configuration)
+  ));
+
+  serverOptions.options = {
+    name = mkOption {
+      type = types.str;
+      description = ''
+        Value for label 'configname' which will be added to all metrics.
+      '';
+    };
+    server = mkOption {
+      type = types.str;
+      description = ''
+        Hostname of the server that should be probed.
+      '';
+    };
+    port = mkOption {
+      type = types.int;
+      example = 587;
+      description = ''
+        Port to use for SMTP.
+      '';
+    };
+    from = mkOption {
+      type = types.str;
+      example = "exporteruser@domain.tld";
+      description = ''
+        Content of 'From' Header for probing mails.
+      '';
+    };
+    to = mkOption {
+      type = types.str;
+      example = "exporteruser@domain.tld";
+      description = ''
+        Content of 'To' Header for probing mails.
+      '';
+    };
+    detectionDir = mkOption {
+      type = types.path;
+      example = "/var/spool/mail/exporteruser/new";
+      description = ''
+        Directory in which new mails for the exporter user are placed.
+        Note that this needs to exist when the exporter starts.
+      '';
+    };
+    login = mkOption {
+      type = types.nullOr types.str;
+      default = null;
+      example = "exporteruser@domain.tld";
+      description = ''
+        Username to use for SMTP authentication.
+      '';
+    };
+    passphrase = mkOption {
+      type = types.nullOr types.str;
+      default = null;
+      description = ''
+        Password to use for SMTP authentication.
+      '';
+    };
+  };
+
+  exporterOptions.options = {
+    monitoringInterval = mkOption {
+      type = types.str;
+      example = "10s";
+      description = ''
+        Time interval between two probe attempts.
+      '';
+    };
+    mailCheckTimeout = mkOption {
+      type = types.str;
+      description = ''
+        Timeout until mails are considered "didn't make it".
+      '';
+    };
+    disableFileDelition = mkOption {
+      type = types.bool;
+      default = false;
+      description = ''
+        Disables the exporter's function to delete probing mails.
+      '';
+    };
+    servers = mkOption {
+      type = types.listOf (types.submodule serverOptions);
+      default = [];
+      example = literalExample ''
+        [ {
+          name = "testserver";
+          server = "smtp.domain.tld";
+          port = 587;
+          from = "exporteruser@domain.tld";
+          to = "exporteruser@domain.tld";
+          detectionDir = "/path/to/Maildir/new";
+        } ]
+      '';
+      description = ''
+        List of servers that should be probed.
+      '';
+    };
+  };
+in
+{
+  port = 9225;
+  extraOpts = {
+    configFile = mkOption {
+      type = types.nullOr types.path;
+      default = null;
+      description = ''
+        Specify the mailexporter configuration file to use.
+      '';
+    };
+    configuration = mkOption {
+      type = types.submodule exporterOptions;
+      default = {};
+      description = ''
+        Specify the mailexporter configuration file to use.
+      '';
+    };
+    telemetryPath = mkOption {
+      type = types.str;
+      default = "/metrics";
+      description = ''
+        Path under which to expose metrics.
+      '';
+    };
+  };
+  serviceOpts = {
+    serviceConfig = {
+      ExecStart = ''
+        ${pkgs.prometheus-mail-exporter}/bin/mailexporter \
+          --web.listen-address ${cfg.listenAddress}:${toString cfg.port} \
+          --config.file ${
+            if cfg.configuration != {} then configurationFile else cfg.configFile
+          } \
+          ${concatStringsSep " \\\n  " cfg.extraFlags}
+      '';
+    };
+  };
+}

nixos/modules/services/network-filesystems/kbfs.nix

@@ -48,6 +48,7 @@ in {
       requires = [ "keybase.service" ];
       after = [ "keybase.service" ];
       path = [ "/run/wrappers" ];
+      unitConfig.ConditionUser = "!@system";
       serviceConfig = {
         ExecStartPre = "${pkgs.coreutils}/bin/mkdir -p ${cfg.mountPoint}";
         ExecStart = "${pkgs.kbfs}/bin/kbfsfuse ${toString cfg.extraFlags} ${cfg.mountPoint}";

nixos/modules/services/networking/keybase.nix

@@ -26,6 +26,7 @@ in {
 
     systemd.user.services.keybase = {
       description = "Keybase service";
+      unitConfig.ConditionUser = "!@system";
       serviceConfig = {
         ExecStart = ''
           ${pkgs.keybase}/bin/keybase service --auto-forked

nixos/modules/services/networking/syncthing.nix

@@ -372,16 +372,18 @@ in {
 
     systemd.packages = [ pkgs.syncthing ];
 
-    users = mkIf (cfg.systemService && cfg.user == defaultUser) {
+    users.users = mkIf (cfg.systemService && cfg.user == defaultUser) {
-      users."${defaultUser}" =
+      "${defaultUser}" =
         { group = cfg.group;
           home  = cfg.dataDir;
           createHome = true;
           uid = config.ids.uids.syncthing;
           description = "Syncthing daemon user";
         };
+    };
 
-      groups."${defaultUser}".gid =
+    users.groups = mkIf (cfg.systemService && cfg.group == defaultUser) {
+      "${defaultUser}".gid =
         config.ids.gids.syncthing;
     };
 

nixos/tests/prometheus-exporters.nix

@@ -188,6 +188,48 @@ let
       '';
     };
 
+    mail = {
+      exporterConfig = {
+        enable = true;
+        user = "mailexporter";
+        configuration = {
+          monitoringInterval = "2s";
+          mailCheckTimeout = "10s";
+          servers = [ {
+            name = "testserver";
+            server = "localhost";
+            port = 25;
+            from = "mailexporter@localhost";
+            to = "mailexporter@localhost";
+            detectionDir = "/var/spool/mail/mailexporter/new";
+          } ];
+        };
+      };
+      metricProvider = {
+        services.postfix.enable = true;
+        systemd.services.prometheus-mail-exporter = {
+          after = [ "postfix.service" ];
+          requires = [ "postfix.service" ];
+          preStart = ''
+            mkdir -p 0600 mailexporter/new
+          '';
+          serviceConfig = {
+            ProtectHome = true;
+            ReadOnlyPaths = "/";
+            ReadWritePaths = "/var/spool/mail";
+            WorkingDirectory = "/var/spool/mail";
+          };
+        };
+        users.users.mailexporter.isSystemUser = true;
+      };
+      exporterTest = ''
+        waitForUnit("postfix.service")
+        waitForUnit("prometheus-mail-exporter.service")
+        waitForOpenPort(9225)
+        waitUntilSucceeds("curl -sSf http://localhost:9225/metrics | grep -q 'mail_deliver_success{configname=\"testserver\"} 1'")
+      '';
+    };
+
     nginx = {
       exporterConfig = {
         enable = true;

pkgs/applications/audio/spotify/default.nix

@@ -1,7 +1,7 @@
 { fetchurl, stdenv, squashfsTools, xorg, alsaLib, makeWrapper, openssl, freetype
 , glib, pango, cairo, atk, gdk-pixbuf, gtk2, cups, nspr, nss, libpng, libnotify
 , libgcrypt, systemd, fontconfig, dbus, expat, ffmpeg_3, curl, zlib, gnome3
-, at-spi2-atk
+, at-spi2-atk, at-spi2-core, apulse
 }:
 
 let
@@ -10,20 +10,22 @@ let
   # If an update breaks things, one of those might have valuable info:
   # https://aur.archlinux.org/packages/spotify/
   # https://community.spotify.com/t5/Desktop-Linux
-  version = "1.0.96.181.gf6bc1b6b-12";
+  version = "1.1.10.546.ge08ef575-19";
   # To get the latest stable revision:
   # curl -H 'X-Ubuntu-Series: 16' 'https://api.snapcraft.io/api/v1/snaps/details/spotify?channel=stable' | jq '.download_url,.version,.last_updated'
   # To get general information:
   # curl -H 'Snap-Device-Series: 16' 'https://api.snapcraft.io/v2/snaps/info/spotify' | jq '.'
   # More examples of api usage:
   # https://github.com/canonical-websites/snapcraft.io/blob/master/webapp/publisher/snaps/views.py
-  rev = "30";
+  rev = "36";
 
 
   deps = [
     alsaLib
+    apulse
     atk
     at-spi2-atk
+    at-spi2-core
     cairo
     cups
     curl
@@ -72,7 +74,7 @@ stdenv.mkDerivation {
   # https://community.spotify.com/t5/Desktop-Linux/Redistribute-Spotify-on-Linux-Distributions/td-p/1695334
   src = fetchurl {
     url = "https://api.snapcraft.io/api/v1/snaps/download/pOBIoZ2LrCB3rDohMxoYGnbN14EHOgD7_${rev}.snap";
-    sha512 = "859730fbc80067f0828f7e13eee9a21b13b749f897a50e17c2da4ee672785cfd79e1af6336e609529d105e040dc40f61b6189524783ac93d49f991c4ea8b3c56";
+    sha512 = "c49f1a86a9b737e64a475bbe62754a36f607669e908eb725a2395f0a0a6b95968e0c8ce27ab2c8b6c92fe8cbacb1ef58de11c79b92dc0f58c2c6d3a140706a1f";
   };
 
   buildInputs = [ squashfsTools makeWrapper ];
@@ -134,6 +136,8 @@ stdenv.mkDerivation {
       librarypath="${stdenv.lib.makeLibraryPath deps}:$libdir"
       wrapProgram $out/share/spotify/spotify \
         --prefix LD_LIBRARY_PATH : "$librarypath" \
+        --prefix LD_LIBRARY_PATH : "${apulse}/lib/apulse" \
+        --set APULSE_PLAYBACK_DEVICE plug:dmix \
         --prefix PATH : "${gnome3.zenity}/bin"
 
       # fix Icon line in the desktop file (#48062)
@@ -158,7 +162,7 @@ stdenv.mkDerivation {
     homepage = https://www.spotify.com/;
     description = "Play music from the Spotify music service";
     license = licenses.unfree;
-    maintainers = with maintainers; [ eelco ftrvxmtrx sheenobu mudri timokau ];
+    maintainers = with maintainers; [ eelco ftrvxmtrx sheenobu mudri timokau angristan ];
     platforms = [ "x86_64-linux" ];
   };
 }

pkgs/applications/editors/emacs-modes/melpa-packages.nix

@@ -233,6 +233,12 @@ self:
       # upstream issue: missing file header
       textmate = markBroken super.textmate;
 
+      treemacs-magit = super.treemacs-magit.overrideAttrs (attrs: {
+        # searches for Git at build time
+        nativeBuildInputs =
+          (attrs.nativeBuildInputs or []) ++ [ external.git ];
+      });
+
       # missing OCaml
       utop = markBroken super.utop;
 

pkgs/applications/editors/ghostwriter/default.nix

@@ -1,9 +1,8 @@
-{ stdenv, fetchFromGitHub, qmake, pkgconfig, qttools, qtwebengine, hunspell }:
+{ stdenv, mkDerivation, fetchFromGitHub, qmake, pkgconfig, qttools, qtwebengine, hunspell }:
 
-stdenv.mkDerivation rec {
+mkDerivation rec {
   pname = "ghostwriter";
   version = "1.8.0";
-  name = "${pname}-${version}";
 
   src = fetchFromGitHub {
     owner = "wereturtle";

pkgs/applications/graphics/goxel/default.nix

@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   name = "goxel-${version}";
-  version = "0.9.0";
+  version = "0.10.0";
 
   src = fetchFromGitHub {
     owner = "guillaumechereau";
     repo = "goxel";
     rev = "v${version}";
-    sha256 = "1vd1vw5pplm4ig9f5gwnbvndnag1h7j0jj0cnj78gpiv96qak2vw";
+    sha256 = "1mdw4bs7hvfn0yngd9ial5wzlfkcbhr3wzldb1w7s3s48agixkdr";
   };
 
   patches = [ ./disable-imgui_ini.patch ];

pkgs/applications/misc/clipmenu/default.nix

@@ -1,6 +1,6 @@
-{ clipnotify, makeWrapper, xsel, dmenu2, utillinux, gawk, stdenv, fetchFromGitHub, lib }:
+{ clipnotify, makeWrapper, xsel, dmenu, utillinux, gawk, stdenv, fetchFromGitHub, lib }:
 let
-  runtimePath = lib.makeBinPath [ clipnotify xsel dmenu2 utillinux gawk ];
+  runtimePath = lib.makeBinPath [ clipnotify xsel dmenu utillinux gawk ];
 in
 stdenv.mkDerivation rec {
   name = "clipmenu-${version}";

pkgs/applications/misc/dmenu2/default.nix

@@ -1,29 +0,0 @@
-{stdenv, fetchhg, libX11, libXinerama, libXft, zlib}:
-
-with stdenv.lib;
-
-stdenv.mkDerivation rec {
-  name = "dmenu2-0.3pre-2014-07-08";
-
-  src = fetchhg {
-    url = "https://bitbucket.org/melek/dmenu2";
-    rev = "36cb94a16edf928bdaaa636123392517ed469be0";
-    sha256 = "1b17z5ypg6ij7zz3ncp3irc87raccna10y4w490c872a99lp23lv";
-  };
-
-  buildInputs = [ libX11 libXinerama zlib libXft ];
-
-  postPatch = ''
-    sed -ri -e 's!\<(dmenu|stest)\>!'"$out/bin"'/&!g' dmenu_run
-  '';
-
-  preConfigure = [ ''sed -i "s@PREFIX = /usr/local@PREFIX = $out@g" config.mk'' ];
-
-  meta = {
-      description = "A patched fork of the original dmenu - an efficient dynamic menu for X";
-      homepage = https://bitbucket.org/melek/dmenu2;
-      license = licenses.mit;
-      maintainers = [ maintainers.cstrahan ];
-      platforms = platforms.all;
-  };
-}

pkgs/applications/misc/zathura/core/default.nix

@@ -3,11 +3,9 @@
 , gtk, girara, gettext, libxml2, check
 , sqlite, glib, texlive, libintl, libseccomp
 , file, librsvg
-, gtk-mac-integration, synctexSupport ? true
+, gtk-mac-integration
 }:
 
-assert synctexSupport -> texlive != null;
-
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
@@ -29,7 +27,8 @@ stdenv.mkDerivation rec {
     # "-Dseccomp=enabled"
     "-Dmanpages=enabled"
     "-Dconvert-icon=enabled"
-  ] ++ optional synctexSupport "-Dsynctex=enabled";
+    "-Dsynctex=enabled"
+  ];
 
   nativeBuildInputs = [
     meson ninja pkgconfig desktop-file-utils python3.pkgs.sphinx
@@ -38,8 +37,8 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     gtk girara libintl sqlite glib file librsvg
-  ] ++ optional synctexSupport texlive.bin.core
+    texlive.bin.core
-    ++ optional stdenv.isLinux libseccomp
+  ] ++ optional stdenv.isLinux libseccomp
     ++ optional stdenv.isDarwin gtk-mac-integration;
 
   doCheck = true;

pkgs/applications/misc/zathura/default.nix

@@ -1,7 +1,6 @@
 { config, pkgs
 # zathura_pdf_mupdf fails to load _opj_create_decompress at runtime on Darwin (https://github.com/NixOS/nixpkgs/pull/61295#issue-277982980)
-, useMupdf ? config.zathura.useMupdf or (!pkgs.stdenv.isDarwin)
+, useMupdf ? config.zathura.useMupdf or (!pkgs.stdenv.isDarwin) }:
-, synctexSupport ? true }:
 
 let
   callPackage = pkgs.newScope self;
@@ -9,9 +8,7 @@ let
   self = rec {
     gtk = pkgs.gtk3;
 
-    zathura_core = callPackage ./core {
+    zathura_core = callPackage ./core { };
-      inherit synctexSupport;
-    };
 
     zathura_pdf_poppler = callPackage ./pdf-poppler { };
 

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

@@ -67,7 +67,8 @@ let
     in attrs: concatStringsSep " " (attrValues (mapAttrs toFlag attrs));
 
   gnSystemLibraries = [
-    "flac" "libwebp" "libxslt" "yasm" "opus" "snappy" "libpng" "zlib"
+    "flac" "libwebp" "libxslt" "yasm" "opus" "snappy" "libpng"
+    # "zlib" # version 77 reports unresolved dependency on //third_party/zlib:zlib_config
     # "libjpeg" # fails with multiple undefined references to chromium_jpeg_*
     # "re2" # fails with linker errors
     # "ffmpeg" # https://crbug.com/731766

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 = "0pq7q7plbmfg2f6m74wl2l19k15ik2mvw56bfzk4c9cdns8w6b8a";
+    sha256 = "1521vh38mfgy7aj1lw1vpbdm8m6wyh52d5p7bz4x6kvvxsnacp11";
-    sha256bin64 = "09zf3kldvi8zh7arvl94vjmbvgsghwa51b5j0ic8ncdn880dlq0j";
+    sha256bin64 = "0rbc0ld655szg42mqjdby8749d2jg34nlpp4cpq66qb4zi6vvb04";
-    version = "76.0.3809.25";
+    version = "76.0.3809.87";
   };
   dev = {
-    sha256 = "19v1i4ks5rpwdcwmfj8qqni4afyhnddb5hbbisabnjif3b8xrvjw";
+    sha256 = "15v25nwcdxqgw6n0ym7fz5qaq0a74p0wiwcq155xy6zvr3q8q1nw";
-    sha256bin64 = "0vsbxvqidrvw797h0and67pdb4maijsiv6jkpj3kqaxakiwnadxj";
+    sha256bin64 = "1qawl0hsl6qpc10avli8raw4nzwcpmp6dyada5pga7i4k5jpsr95";
-    version = "76.0.3809.21";
+    version = "77.0.3860.5";
   };
   stable = {
-    sha256 = "0f9qjhxvk8sajj7qa061crfmln65q7sniylrgp0qijwyw6xrmddi";
+    sha256 = "1521vh38mfgy7aj1lw1vpbdm8m6wyh52d5p7bz4x6kvvxsnacp11";
-    sha256bin64 = "1xvqfrq119iwgvd2d4z2v2ladi2kl52kji55yxdmyi377dpk5rfa";
+    sha256bin64 = "0hnfn2zxdrp96a4p98r08w4krzwkpb1kp4rjk03754akjyg1b3xx";
-    version = "75.0.3770.90";
+    version = "76.0.3809.87";
   };
 }

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

@@ -97,8 +97,8 @@ in rec {
   terraform_0_11-full = terraform_0_11.full;
 
   terraform_0_12 = pluggable (generic {
-    version = "0.12.5";
+    version = "0.12.6";
-    sha256 = "0p064rhaanwx4szs8hv6mdqad8d2bgfd94h2la11j58xbsxc7hap";
+    sha256 = "0vxvciv4amblxx50wivlm60fyj1ardfgdpj3l8cj9fhi79b3khxl";
     patches = [ ./provider-path.patch ];
     passthru = { inherit plugins; };
   });

pkgs/applications/networking/dsvpn/default.nix

@@ -0,0 +1,29 @@
+{ stdenv, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  pname = "dsvpn";
+  version = "0.1.0";
+
+  src = fetchFromGitHub {
+    owner = "jedisct1";
+    repo = pname;
+    rev = version;
+    sha256 = "1g747197zpg83ba9l9vxg8m3jv13wcprhnyr8asdxq745kzmynsr";
+  };
+
+  installPhase = ''
+    runHook preInstall
+
+    install -Dm755 -t $out/bin dsvpn
+
+    runHook postInstall
+  '';
+
+  meta = with stdenv.lib; {
+    description = "A Dead Simple VPN";
+    homepage = "https://github.com/jedisct1/dsvpn";
+    license = licenses.mit;
+    maintainers = [ maintainers.marsam ];
+    platforms = platforms.unix;
+  };
+}

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

@@ -1,36 +1,83 @@
-{ stdenv, fetchFromGitLab, meson, ninja, gettext, cargo, rustc, python3, rustPlatform, pkgconfig, gtksourceview
+{ stdenv
-, hicolor-icon-theme, glib, libhandy, gtk3, libsecret, dbus, openssl, sqlite, gst_all_1, wrapGAppsHook, fetchpatch }:
+, fetchFromGitLab
+, fetchpatch
+, meson
+, ninja
+, gettext
+, cargo
+, rustc
+, python3
+, rustPlatform
+, pkgconfig
+, gtksourceview
+, hicolor-icon-theme
+, glib
+, libhandy
+, gtk3
+, dbus
+, openssl
+, sqlite
+, gst_all_1
+, cairo
+, gdk_pixbuf
+, gspell
+, wrapGAppsHook
+}:
 
 rustPlatform.buildRustPackage rec {
-  version = "4.0.0";
+  pname = "fractal";
-  name = "fractal-${version}";
+  version = "4.2.0";
 
   src = fetchFromGitLab {
     domain = "gitlab.gnome.org";
     owner = "GNOME";
     repo = "fractal";
     rev = version;
-    sha256 = "05q47jdgbi5jz01280msb8gxnbsrgf2jvglfm6k40f1xw4wxkrzy";
+    sha256 = "0clwsmd6h759bzlazfq5ig56dbx7npx3h43yspk87j1rm2dp1177";
   };
 
+  cargoSha256 = "1hwjajkphl5439dymglgj3h92hxgbf7xpipzrga7ga8m10nx1dhl";
+
   nativeBuildInputs = [
-    meson ninja pkgconfig gettext cargo rustc python3 wrapGAppsHook
+    cargo
-  ];
+    gettext
-  buildInputs = [
+    meson
-    glib gtk3 libhandy dbus openssl sqlite gst_all_1.gstreamer gst_all_1.gst-plugins-base gst_all_1.gst-plugins-bad
+    ninja
-    gtksourceview hicolor-icon-theme libsecret
+    pkgconfig
+    python3
+    rustc
+    wrapGAppsHook
   ];
 
-  patches = [
+  buildInputs = [
-    # Fixes build with >= gstreamer 1.15.1
+    cairo
+    dbus
+    gdk_pixbuf
+    glib
+    gspell
+    gst_all_1.gst-editing-services
+    gst_all_1.gst-plugins-bad
+    gst_all_1.gst-plugins-base
+    gst_all_1.gstreamer
+    gtk3
+    gtksourceview
+    hicolor-icon-theme
+    libhandy
+    openssl
+    sqlite
+  ];
+
+  cargoPatches = [
+    # https://gitlab.gnome.org/GNOME/fractal/merge_requests/446
     (fetchpatch {
-      url = "https://gitlab.gnome.org/GNOME/fractal/commit/e78f36c25c095ea09c9c421187593706ad7c4065.patch";
+      url = "https://gitlab.gnome.org/GNOME/fractal/commit/2778acdc6c50bc6f034513029b66b0b092bc4c38.patch";
-      sha256 = "1qv7ayhkhgrrldag2lzs9ql17nbc1d72j375ljhhf6cms89r19ir";
+      sha256 = "08v17xmbwrjw688ps4hsnd60d5fm26xj72an3zf6yszha2b97j6y";
     })
   ];
 
   postPatch = ''
-    patchShebangs scripts/meson_post_install.py
+    chmod +x scripts/test.sh
+    patchShebangs scripts/meson_post_install.py scripts/test.sh
   '';
 
   # Don't use buildRustPackage phases, only use it for rust deps setup
@@ -39,13 +86,11 @@ rustPlatform.buildRustPackage rec {
   checkPhase = null;
   installPhase = null;
 
-  cargoSha256 = "1ax5dv200v8mfx0418bx8sbwpbp6zj469xg75hp78kqfiv83pn1g";
-
   meta = with stdenv.lib; {
     description = "Matrix group messaging app";
     homepage = https://gitlab.gnome.org/GNOME/fractal;
     license = licenses.gpl3;
-    maintainers = with maintainers; [ dtzWill ];
+    maintainers = with maintainers; [ dtzWill worldofpeace ];
   };
 }
 

pkgs/applications/networking/instant-messengers/rambox/bare.nix

@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, fetchNodeModules, nodejs-8_x, ruby, sencha
+{ stdenv, fetchFromGitHub, fetchNodeModules, nodejs-10_x, ruby, sencha
 , auth0ClientID, auth0Domain }:
 
 stdenv.mkDerivation rec {
@@ -12,12 +12,12 @@ stdenv.mkDerivation rec {
     sha256 = "1h44srl2gzkhjaazpwz1pwy4dp5x776fc685kahlvjlsfls0fvy9";
   };
 
-  nativeBuildInputs = [ nodejs-8_x ruby sencha ];
+  nativeBuildInputs = [ nodejs-10_x ruby sencha ];
 
   node_modules = fetchNodeModules {
     inherit src;
 
-    nodejs = nodejs-8_x;
+    nodejs = nodejs-10_x;
     sha256 = "0qsgr8cq81yismal5sqr02skakqpynwwzk5s98dr5bg91y361fgy";
   };
 

pkgs/applications/networking/instant-messengers/rambox/pro.nix

@@ -2,26 +2,19 @@
 
 stdenv.mkDerivation rec {
   pname = "rambox-pro";
-  version = "1.1.2";
+  version = "1.1.4";
 
   dontBuild = true;
   dontStrip = true;
 
-  buildInputs = [ nss xorg.libxkbfile ];
+  buildInputs = [ nss xorg.libXext xorg.libxkbfile xorg.libXScrnSaver ];
   nativeBuildInputs = [ autoPatchelfHook makeWrapper nodePackages.asar ];
 
   src = fetchurl {
     url = "https://github.com/ramboxapp/download/releases/download/v${version}/RamboxPro-${version}-linux-x64.tar.gz";
-    sha256 = "0rrfpl371hp278b02b9b6745ax29yrdfmxrmkxv6d158jzlv0dlr";
+    sha256 = "0vwh3km3h46bgynd10s8ijl3aj5sskzncdj14h3k7h4sibd8r71a";
   };
 
-  postPatch = ''
-    substituteInPlace resources/app.asar.unpacked/node_modules/ad-block/vendor/depot_tools/create-chromium-git-src \
-      --replace "/usr/bin/env -S bash -e" "${stdenv.shell}"
-    substituteInPlace resources/app.asar.unpacked/node_modules/ad-block/node_modules/bloom-filter-cpp/vendor/depot_tools/create-chromium-git-src \
-      --replace "/usr/bin/env -S bash -e" "${stdenv.shell}"
-  '';
-
   installPhase = ''
     mkdir -p $out/bin $out/opt/RamboxPro $out/share/applications
     asar e resources/app.asar $out/opt/RamboxPro/resources/app.asar.unpacked   

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

@@ -6,7 +6,7 @@ at-spi2-atk, libuuid, nodePackages
 
 let
 
-  version = "4.0.0";
+  version = "4.0.1";
 
   rpath = stdenv.lib.makeLibraryPath [
     alsaLib
@@ -51,7 +51,7 @@ let
     if stdenv.hostPlatform.system == "x86_64-linux" then
       fetchurl {
         url = "https://downloads.slack-edge.com/linux_releases/slack-desktop-${version}-amd64.deb";
-        sha256 = "911a4c05fb4f85181df13f013e82440b0d171862c9cb137dc19b6381d47bd57e";
+        sha256 = "1g7c8jka750pblsfzjvfyf7sp1m409kybqagml9miif1v71scxv2";
       }
     else
       throw "Slack is not supported on ${stdenv.hostPlatform.system}";
@@ -113,6 +113,7 @@ in stdenv.mkDerivation {
     description = "Desktop client for Slack";
     homepage = https://slack.com;
     license = licenses.unfree;
+    maintainers = [ maintainers.mmahut ];
     platforms = [ "x86_64-linux" ];
   };
 }

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

@@ -1,5 +1,5 @@
-{ stdenv, fetchurl, mkDerivation, makeWrapper, makeDesktopItem, autoPatchelfHook
+{ stdenv, fetchurl, mkDerivation, autoPatchelfHook
-, wrapQtAppsHook
+, fetchFromGitHub
 # Dynamic libraries
 , dbus, glib, libGL, libX11, libXfixes, libuuid, libxcb, qtbase, qtdeclarative
 , qtimageformats, qtlocation, qtquickcontrols, qtquickcontrols2, qtscript, qtsvg
@@ -22,12 +22,20 @@ let
     };
   };
 
+  # Used for icons, appdata, and desktop file.
+  desktopIntegration = fetchFromGitHub {
+    owner = "flathub";
+    repo = "us.zoom.Zoom";
+    rev = "0d294e1fdd2a4ef4e05d414bc680511f24d835d7";
+    sha256 = "0rm188844a10v8d6zgl2pnwsliwknawj09b02iabrvjw5w1lp6wl";
+  };
+
 in mkDerivation {
   name = "zoom-us-${version}";
 
   src = srcs.${stdenv.hostPlatform.system};
 
-  nativeBuildInputs = [ autoPatchelfHook makeWrapper wrapQtAppsHook ];
+  nativeBuildInputs = [ autoPatchelfHook ];
 
   buildInputs = [
     dbus glib libGL libX11 libXfixes libuuid libxcb libjpeg_turbo
@@ -66,15 +74,26 @@ in mkDerivation {
       runHook postInstall
     '';
 
-  postInstall = (makeDesktopItem {
+  postInstall = ''
-    name = "zoom-us";
+    mkdir -p $out/share/{applications,appdata,icons}
-    exec = "$out/bin/zoom-us %U";
+
-    icon = "$out/share/zoom-us/application-x-zoom.png";
+    # Desktop File
-    desktopName = "Zoom";
+    cp ${desktopIntegration}/us.zoom.Zoom.desktop $out/share/applications
-    genericName = "Video Conference";
+    substituteInPlace $out/share/applications/us.zoom.Zoom.desktop \
-    categories = "Network;Application;";
+        --replace "Exec=zoom" "Exec=$out/bin/zoom-us"
-    mimeType = "x-scheme-handler/zoommtg;";
+
-  }).buildCommand + ''
+    # Appdata
+    cp ${desktopIntegration}/us.zoom.Zoom.appdata.xml $out/share/appdata
+
+    # Icons
+    for icon_size in 64 96 128 256; do
+        path=$icon_size'x'$icon_size
+        icon=${desktopIntegration}/us.zoom.Zoom.$icon_size.png
+
+        mkdir -p $out/share/icons/hicolor/$path/apps
+        cp $icon $out/share/icons/hicolor/$path/apps/us.zoom.Zoom.png
+    done
+
     ln -s $out/share/zoom-us/zoom $out/bin/zoom-us
   '';
 

pkgs/applications/networking/mumble/default.nix

@@ -14,7 +14,7 @@ assert iceSupport -> zeroc_ice != null;
 
 with stdenv.lib;
 let
-  generic = overrides: source: stdenv.mkDerivation (source // overrides // {
+  generic = overrides: source: (if source.qtVersion == 5 then qt5.mkDerivation else stdenv.mkDerivation) (source // overrides // {
     name = "${overrides.type}-${source.version}";
 
     patches = (source.patches or []) ++ optional jackSupport ./mumble-jack-support.patch;
@@ -26,7 +26,7 @@ let
     # protobuf is freezed to 3.6 because of this bug: https://github.com/mumble-voip/mumble/issues/3617
     # this could be reverted to the latest version in a future release of mumble as it is already fixed in master
     buildInputs = [ boost protobuf3_6 avahi ]
-      ++ { qt4 = [ qt4 ]; qt5 = [ qt5.qtbase ]; }."qt${toString source.qtVersion}"
+      ++ optional (source.qtVersion == 4) qt4
       ++ (overrides.buildInputs or [ ]);
 
     qmakeFlags = [
@@ -45,20 +45,23 @@ let
       ++ (overrides.configureFlags or [ ]);
 
     preConfigure = ''
-       qmakeFlags="$qmakeFlags DEFINES+=PLUGIN_PATH=$out/lib"
+       qmakeFlags="$qmakeFlags DEFINES+=PLUGIN_PATH=$out/lib/mumble"
        patchShebangs scripts
     '';
 
     makeFlags = [ "release" ];
 
     installPhase = ''
-      mkdir -p $out/{lib,bin}
+      runHook preInstall
-      find release -type f -not -name \*.\* -exec cp {} $out/bin \;
-      find release -type f -name \*.\* -exec cp {} $out/lib \;
 
+      ${overrides.installPhase}
+
+      # doc stuff
       mkdir -p $out/share/man/man1
-      cp man/mum* $out/share/man/man1
+      install -Dm644 man/mum* $out/share/man/man1/
-    '' + (overrides.installPhase or "");
+
+      runHook postInstall
+    '';
 
     enableParallelBuilding = true;
 
@@ -74,7 +77,7 @@ let
   client = source: generic {
     type = "mumble";
 
-    nativeBuildInputs = optionals (source.qtVersion == 5) [ qt5.qttools ];
+    nativeBuildInputs = optional (source.qtVersion == 5) qt5.qttools;
     buildInputs = [ libopus libsndfile speex ]
       ++ optional (source.qtVersion == 5) qt5.qtsvg
       ++ optional stdenv.isLinux alsaLib
@@ -89,12 +92,19 @@ let
     NIX_CFLAGS_COMPILE = optional speechdSupport "-I${speechd}/include/speech-dispatcher";
 
     installPhase = ''
-      mkdir -p $out/share/applications
+      # bin stuff
-      cp scripts/mumble.desktop $out/share/applications
+      install -Dm755 release/mumble $out/bin/mumble
+      install -Dm755 scripts/mumble-overlay $out/bin/mumble-overlay
 
-      mkdir -p $out/share/icons{,/hicolor/scalable/apps}
+      # lib stuff
-      cp icons/mumble.svg $out/share/icons
+      mkdir -p $out/lib/mumble
-      ln -s $out/share/icons/mumble.svg $out/share/icons/hicolor/scalable/apps
+      cp -P release/libmumble.so* $out/lib
+      cp -P release/libcelt* $out/lib/mumble
+      cp -P release/plugins/* $out/lib/mumble
+
+      # icons
+      install -Dm644 scripts/mumble.desktop $out/share/applications/mumble.desktop
+      install -Dm644 icons/mumble.svg $out/share/icons/hicolor/scalable/apps/mumble.svg
     '';
   } source;
 
@@ -110,6 +120,11 @@ let
     ];
 
     buildInputs = [ libcap ] ++ optional iceSupport zeroc_ice;
+
+    installPhase = ''
+      # bin stuff
+      install -Dm755 release/murmurd $out/bin/murmurd
+    '';
   };
 
   stableSource = rec {
@@ -138,26 +153,24 @@ let
     ];
   };
 
-  gitSource = rec {
+  rcSource = rec {
-    version = "2019-07-10";
+    version = "1.3.0-rc2";
     qtVersion = 5;
 
     # Needs submodules
     src = fetchFromGitHub {
       owner = "mumble-voip";
       repo = "mumble";
-      rev = "41b265584654c7ac216fd3ccb9c141734d3f839b";
+      rev = version;
       sha256 = "00irlzz5q4drmsfbwrkyy7p7w8a5fc1ip5vyicq3g3cy58dprpqr";
       fetchSubmodules = true;
     };
   };
 in {
   mumble     = client stableSource;
-  mumble_git = client gitSource;
+  mumble_rc  = client rcSource;
   murmur     = server stableSource;
-  murmur_git = (server gitSource).overrideAttrs (old: {
+  murmur_rc  = (server rcSource).overrideAttrs (old: {
     meta = old.meta // { broken = iceSupport; };
-
-    nativeBuildInputs = old.nativeBuildInputs or [] ++ [ qt5.wrapQtAppsHook ];
   });
 }

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

@@ -2,16 +2,17 @@
 
 stdenv.mkDerivation rec {
   name = "strelka-${version}";
-  version = "2.9.5";
+  version = "2.9.10";
 
   src = fetchFromGitHub {
     owner = "Illumina";
     repo = "strelka";
     rev = "v${version}";
-    sha256 = "0x4a6nkx1jnyag9svghsdjz1fz6q7qx5pn77wphdfnk81f9yspf8";
+    sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
   };
 
-  buildInputs = [ cmake zlib python2 ];
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib python2 ];
 
   preConfigure = ''
     sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py

pkgs/desktops/gnome-3/default.nix

@@ -345,8 +345,6 @@ lib.makeScope pkgs.newScope (self: with self; {
 
   nautilus-python = callPackage ./misc/nautilus-python { };
 
-  pidgin-im-gnome-shell-extension = callPackage ./misc/pidgin { };
-
   gtkhtml = callPackage ./misc/gtkhtml { enchant = pkgs.enchant1; };
 
   pomodoro = callPackage ./misc/pomodoro { };
@@ -398,4 +396,6 @@ lib.makeScope pkgs.newScope (self: with self; {
   gtk = gtk3;
   gtkmm = gtkmm3;
   rest = librest;
+
+  pidgin-im-gnome-shell-extension = pkgs.gnomeExtensions.pidgin-im-integration; # added 2019-08-01
 })

pkgs/desktops/gnome-3/extensions/pidgin-im-integration/default.nix

@@ -0,0 +1,31 @@
+{ stdenv, fetchFromGitHub, glib }:
+
+stdenv.mkDerivation rec {
+  pname = "gnome-shell-extension-pidgin-im-integration";
+  version = "32";
+
+  src = fetchFromGitHub {
+    owner = "muffinmad";
+    repo = "pidgin-im-gnome-shell-extension";
+    rev = "v${version}";
+    sha256 = "1jyg8r0s1v83sgg6y0jbsj2v37mglh8rvd8vi27fxnjq9xmg8kpc";
+  };
+
+  dontConfigure = true;
+  dontBuild = true;
+
+  installPhase = ''
+    share_dir="$prefix/share"
+    extensions_dir="$share_dir/gnome-shell/extensions/pidgin@muffinmad"
+    mkdir -p "$extensions_dir"
+    mv *.js metadata.json dbus.xml schemas locale "$extensions_dir"
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/muffinmad/pidgin-im-gnome-shell-extension;
+    description = "Make Pidgin IM conversations appear in the Gnome Shell message tray";
+    license = licenses.gpl2;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ ];
+  };
+}

pkgs/desktops/gnome-3/misc/pidgin/default.nix

@@ -1,42 +0,0 @@
-{ stdenv, fetchFromGitHub, glib }:
-
-stdenv.mkDerivation rec {
-  version = "1.0.1";
-  basename = "pidgin-im-gnome-shell-extension";
-  name = "${basename}-${version}";
-
-  src = fetchFromGitHub {
-    owner = "muffinmad";
-    repo = "${basename}";
-    rev = "v${version}";
-    sha256 = "1567s2sfqig4jw0nrn134f5vkx0yq31q044grv3xk4vpl1f3z2lr";
-  };
-
-  buildInputs = [ glib ];
-
-  configurePhase = "";
-  buildPhase = "";
-  installPhase = ''
-    share_dir="$prefix/share"
-    extensions_dir="$share_dir/gnome-shell/extensions/pidgin@muffinmad"
-    mkdir -p "$extensions_dir"
-    mv *.js metadata.json dbus.xml gnome-shell-extension-pidgin.pot "$extensions_dir"
-
-    schemas_dir="$share_dir/gsettings-schemas/${name}/glib-2.0/schemas"
-    mkdir -p "$schemas_dir"
-    mv schemas/* "$schemas_dir" # fix Emacs syntax highlighting: */
-    glib-compile-schemas "$schemas_dir"
-
-    locale_dir="$share_dir/locale"
-    mkdir -p "$locale_dir"
-    mv locale/* $locale_dir # fix Emacs syntax highlighting: */
-  '';
-
-  meta = with stdenv.lib; {
-    homepage = https://github.com/muffinmad/pidgin-im-gnome-shell-extension;
-    description = "Make Pidgin IM conversations appear in the Gnome Shell message tray";
-    license = licenses.gpl2;
-    platforms = platforms.linux;
-    maintainers = with maintainers; [ ];
-  };
-}

pkgs/development/compilers/reason/default.nix

@@ -1,5 +1,5 @@
 { stdenv, makeWrapper, fetchFromGitHub, ocaml, findlib, dune
-, menhir, merlin_extend, ppx_tools_versioned, utop
+, menhir, merlin-extend, ppx_tools_versioned, utop
 }:
 
 stdenv.mkDerivation rec {
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ makeWrapper ];
 
-  propagatedBuildInputs = [ menhir merlin_extend ppx_tools_versioned ];
+  propagatedBuildInputs = [ menhir merlin-extend ppx_tools_versioned ];
 
   buildInputs = [ ocaml findlib dune utop menhir ];
 

pkgs/development/interpreters/joker/default.nix

@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "joker-${version}";
-  version = "0.12.2";
+  version = "0.12.4";
 
   goPackagePath = "github.com/candid82/joker";
 
@@ -10,11 +10,13 @@ buildGoPackage rec {
     rev = "v${version}";
     owner = "candid82";
     repo = "joker";
-    sha256 = "0cqz8k53fzz3xqx9czk3hgq164dsbvnk51s0j29g1bmkbl51c2vm";
+    sha256 = "1swi991khmyhxn6w6xsdqp1wbyx3qmd9d7yhpwvqasyxp8gg3szm";
   };
 
   preBuild = "go generate ./...";
 
+  postBuild = "rm go/bin/sum256dir";
+
   dontInstallSrc = true;
 
   excludedPackages = "gen"; # Do not install private generators.

pkgs/development/libraries/languagemachines/packages.nix

@@ -1,13 +1,17 @@
-{ callPackage }:
+{ pkgs }:
+let
+  inherit (pkgs) callPackage;
+  icu = pkgs.icu60;
+in
 {
   ticcutils = callPackage ./ticcutils.nix { };
-  libfolia = callPackage ./libfolia.nix { };
+  libfolia = callPackage ./libfolia.nix { inherit icu; };
-  ucto = callPackage ./ucto.nix { };
+  ucto = callPackage ./ucto.nix { inherit icu; };
   uctodata = callPackage ./uctodata.nix { };
   timbl = callPackage ./timbl.nix { };
   timblserver = callPackage ./timblserver.nix { };
   mbt = callPackage ./mbt.nix { };
-  frog = callPackage ./frog.nix { };
+  frog = callPackage ./frog.nix { inherit icu; };
   frogdata = callPackage ./frogdata.nix { };
 
   test = callPackage ./test.nix { };

pkgs/development/libraries/protobuf/3.8.nix

@@ -0,0 +1,6 @@
+{ callPackage, ... }:
+
+callPackage ./generic-v3.nix {
+  version = "3.8.0";
+  sha256 = "0vll02a6k46k720wfh25sl4hdai0130s3ix2l1wh6j1lm9pi7bm8";
+}

pkgs/development/libraries/protobuf/3.9.nix

@@ -0,0 +1,6 @@
+{ callPackage, ... }:
+
+callPackage ./generic-v3.nix {
+  version = "3.9.0";
+  sha256 = "1xq2njqrbmizwg91ggi1lqr0n26cm2jdyk668ljc24ihrpk0z9bw";
+}

pkgs/development/mobile/titaniumenv/default.nix

@@ -12,7 +12,7 @@ rec {
 
   buildApp = import ./build-app.nix {
     inherit (pkgs) stdenv python which file jdk nodejs;
-    inherit (pkgs.nodePackages_8_x) alloy titanium;
+    inherit (pkgs.nodePackages_10_x) alloy titanium;
     inherit (androidenv) composeAndroidPackages;
     inherit (xcodeenv) composeXcodeWrapper;
     inherit titaniumsdk;

pkgs/development/node-packages/composition-v10.nix

@@ -1,4 +1,4 @@
-# This file has been generated by node2nix 1.7.0. Do not edit!
+# This file has been generated by node2nix 1.6.0. Do not edit!
 
 {pkgs ? import <nixpkgs> {
     inherit system;

pkgs/development/node-packages/composition-v12.nix

@@ -1,8 +1,8 @@
-# This file has been generated by node2nix 1.7.0. Do not edit!
+# This file has been generated by node2nix 1.6.0. Do not edit!
 
 {pkgs ? import <nixpkgs> {
     inherit system;
-  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-12_x"}:
+  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-6_x"}:
 
 let
   nodeEnv = import ./node-env.nix {

pkgs/development/node-packages/composition-v8.nix

@@ -1,17 +0,0 @@
-# This file has been generated by node2nix 1.7.0. Do not edit!
-
-{pkgs ? import <nixpkgs> {
-    inherit system;
-  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-8_x"}:
-
-let
-  nodeEnv = import ./node-env.nix {
-    inherit (pkgs) stdenv python2 utillinux runCommand writeTextFile;
-    inherit nodejs;
-    libtool = if pkgs.stdenv.isDarwin then pkgs.darwin.cctools else null;
-  };
-in
-import ./node-packages-v8.nix {
-  inherit (pkgs) fetchurl fetchgit;
-  inherit nodeEnv;
-}

pkgs/development/node-packages/default-v10.nix

@@ -7,15 +7,6 @@ let
   };
 in
 nodePackages // {
-  aws-azure-login = nodePackages.aws-azure-login.override {
-    PUPPETEER_SKIP_CHROMIUM_DOWNLOAD = "true";
-
-    buildInputs = [ pkgs.makeWrapper ];
-    postInstall = ''
-      wrapProgram "$out/bin/aws-azure-login" --set PUPPETEER_EXECUTABLE_PATH "${pkgs.chromium}/bin/chromium"
-    '';
-  };
-
   bower2nix = nodePackages.bower2nix.override {
     buildInputs = [ pkgs.makeWrapper ];
     postInstall = ''

pkgs/development/node-packages/default-v8.nix

@@ -1,27 +0,0 @@
-{ pkgs, nodejs, stdenv }:
-
-let
-  nodePackages = import ./composition-v8.nix {
-    inherit pkgs nodejs;
-    inherit (stdenv.hostPlatform) system;
-  };
-in
-nodePackages // {
-  pnpm = nodePackages.pnpm.override {
-    nativeBuildInputs = [ pkgs.makeWrapper ];
-    postInstall = let
-      pnpmLibPath = stdenv.lib.makeBinPath [
-        nodejs.passthru.python
-        nodejs
-      ];
-    in ''
-      for prog in $out/bin/*; do
-        wrapProgram "$prog" --prefix PATH : ${pnpmLibPath}
-      done
-    '';
-  };
-
-  stf = nodePackages.stf.override {
-    nativeBuildInputs = with pkgs; [ yasm czmq protobufc ];
-  };
-}

pkgs/development/node-packages/generate.sh

@@ -4,6 +4,5 @@
 set -eu -o pipefail
 
 rm -f node-env.nix
-node2nix -8 -i node-packages-v8.json -o node-packages-v8.nix -c composition-v8.nix
 node2nix --nodejs-10 -i node-packages-v10.json -o node-packages-v10.nix -c composition-v10.nix
 node2nix --nodejs-12 -i node-packages-v12.json -o node-packages-v12.nix -c composition-v12.nix

pkgs/development/node-packages/node-env.nix

@@ -11,7 +11,7 @@ let
 
     cat > $out/bin/tar <<EOF
     #! ${stdenv.shell} -e
-    $(type -p tar) "\$@" --warning=no-unknown-keyword --delay-directory-restore
+    $(type -p tar) "\$@" --warning=no-unknown-keyword
     EOF
 
     chmod +x $out/bin/tar
@@ -72,7 +72,7 @@ let
           packageDir="$(find . -maxdepth 1 -type d | tail -1)"
 
           # Restore write permissions to make building work
-          find "$packageDir" -type d -exec chmod u+x {} \;
+          find "$packageDir" -type d -print0 | xargs -0 chmod u+x
           chmod -R u+w "$packageDir"
 
           # Move the extracted tarball into the output folder
@@ -219,16 +219,7 @@ let
                       packageObj["_integrity"] = "sha1-000000000000000000000000000="; // When no _integrity string has been provided (e.g. by Git dependencies), add a dummy one. It does not seem to harm and it bypasses downloads.
                   }
 
-                  if(dependency.resolved) {
+                  packageObj["_resolved"] = dependency.version; // Set the resolved version to the version identifier. This prevents NPM from cloning Git repositories.
-                      packageObj["_resolved"] = dependency.resolved; // Adopt the resolved property if one has been provided
-                  } else {
-                      packageObj["_resolved"] = dependency.version; // Set the resolved version to the version identifier. This prevents NPM from cloning Git repositories.
-                  }
-
-                  if(dependency.from !== undefined) { // Adopt from property if one has been provided
-                      packageObj["_from"] = dependency.from;
-                  }
-
                   fs.writeFileSync(packageJSONPath, JSON.stringify(packageObj, null, 2));
               }
 
@@ -317,11 +308,50 @@ let
     '';
   };
 
-  prepareAndInvokeNPM = {packageName, bypassCache, reconstructLock, npmFlags, production}:
+  # Builds and composes an NPM package including all its dependencies
+  buildNodePackage =
+    { name
+    , packageName
+    , version
+    , dependencies ? []
+    , buildInputs ? []
+    , production ? true
+    , npmFlags ? ""
+    , dontNpmInstall ? false
+    , bypassCache ? false
+    , preRebuild ? ""
+    , dontStrip ? true
+    , unpackPhase ? "true"
+    , buildPhase ? "true"
+    , ... }@args:
+
     let
       forceOfflineFlag = if bypassCache then "--offline" else "--registry http://www.example.com";
+      extraArgs = removeAttrs args [ "name" "dependencies" "buildInputs" "dontStrip" "dontNpmInstall" "preRebuild" "unpackPhase" "buildPhase" ];
     in
-    ''
+    stdenv.mkDerivation ({
+      name = "node-${name}-${version}";
+      buildInputs = [ tarWrapper python nodejs ]
+        ++ stdenv.lib.optional (stdenv.isLinux) utillinux
+        ++ stdenv.lib.optional (stdenv.isDarwin) libtool
+        ++ buildInputs;
+
+      inherit dontStrip; # Stripping may fail a build for some package deployments
+      inherit dontNpmInstall preRebuild unpackPhase buildPhase;
+
+      compositionScript = composePackage args;
+      pinpointDependenciesScript = pinpointDependenciesOfPackage args;
+
+      passAsFile = [ "compositionScript" "pinpointDependenciesScript" ];
+
+      installPhase = ''
+        # Create and enter a root node_modules/ folder
+        mkdir -p $out/lib/node_modules
+        cd $out/lib/node_modules
+
+        # Compose the package and all its dependencies
+        source $compositionScriptPath
+
         # Pinpoint the versions of all dependencies to the ones that are actually being used
         echo "pinpointing versions of dependencies..."
         source $pinpointDependenciesScriptPath
@@ -345,18 +375,11 @@ let
         runHook preRebuild
 
         ${stdenv.lib.optionalString bypassCache ''
-          ${stdenv.lib.optionalString reconstructLock ''
+          if [ ! -f package-lock.json ]
-            if [ -f package-lock.json ]
+          then
-            then
+              echo "No package-lock.json file found, reconstructing..."
-                echo "WARNING: Reconstruct lock option enabled, but a lock file already exists!"
+              node ${reconstructPackageLock}
-                echo "This will most likely result in version mismatches! We will remove the lock file and regenerate it!"
+          fi
-                rm package-lock.json
-            else
-                echo "No package-lock.json file found, reconstructing..."
-            fi
-
-            node ${reconstructPackageLock}
-          ''}
 
           node ${addIntegrityFieldsScript}
         ''}
@@ -370,53 +393,6 @@ let
 
             npm ${forceOfflineFlag} --nodedir=${nodeSources} ${npmFlags} ${stdenv.lib.optionalString production "--production"} install
         fi
-    '';
-
-  # Builds and composes an NPM package including all its dependencies
-  buildNodePackage =
-    { name
-    , packageName
-    , version
-    , dependencies ? []
-    , buildInputs ? []
-    , production ? true
-    , npmFlags ? ""
-    , dontNpmInstall ? false
-    , bypassCache ? false
-    , reconstructLock ? false
-    , preRebuild ? ""
-    , dontStrip ? true
-    , unpackPhase ? "true"
-    , buildPhase ? "true"
-    , ... }@args:
-
-    let
-      extraArgs = removeAttrs args [ "name" "dependencies" "buildInputs" "dontStrip" "dontNpmInstall" "preRebuild" "unpackPhase" "buildPhase" ];
-    in
-    stdenv.mkDerivation ({
-      name = "node_${name}-${version}";
-      buildInputs = [ tarWrapper python nodejs ]
-        ++ stdenv.lib.optional (stdenv.isLinux) utillinux
-        ++ stdenv.lib.optional (stdenv.isDarwin) libtool
-        ++ buildInputs;
-
-      inherit dontStrip; # Stripping may fail a build for some package deployments
-      inherit dontNpmInstall preRebuild unpackPhase buildPhase;
-
-      compositionScript = composePackage args;
-      pinpointDependenciesScript = pinpointDependenciesOfPackage args;
-
-      passAsFile = [ "compositionScript" "pinpointDependenciesScript" ];
-
-      installPhase = ''
-        # Create and enter a root node_modules/ folder
-        mkdir -p $out/lib/node_modules
-        cd $out/lib/node_modules
-
-        # Compose the package and all its dependencies
-        source $compositionScriptPath
-
-        ${prepareAndInvokeNPM { inherit packageName bypassCache reconstructLock npmFlags production; }}
 
         # Create symlink to the deployed executable folder, if applicable
         if [ -d "$out/lib/node_modules/.bin" ]
@@ -455,13 +431,14 @@ let
     , npmFlags ? ""
     , dontNpmInstall ? false
     , bypassCache ? false
-    , reconstructLock ? false
     , dontStrip ? true
     , unpackPhase ? "true"
     , buildPhase ? "true"
     , ... }@args:
 
     let
+      forceOfflineFlag = if bypassCache then "--offline" else "--registry http://www.example.com";
+
       extraArgs = removeAttrs args [ "name" "dependencies" "buildInputs" ];
 
       nodeDependencies = stdenv.mkDerivation ({
@@ -496,13 +473,39 @@ let
             fi
           ''}
 
-          # Go to the parent folder to make sure that all packages are pinpointed
+          # Pinpoint the versions of all dependencies to the ones that are actually being used
+          echo "pinpointing versions of dependencies..."
           cd ..
           ${stdenv.lib.optionalString (builtins.substring 0 1 packageName == "@") "cd .."}
 
-          ${prepareAndInvokeNPM { inherit packageName bypassCache reconstructLock npmFlags production; }}
+          source $pinpointDependenciesScriptPath
+          cd ${packageName}
+
+          # Patch the shebangs of the bundled modules to prevent them from
+          # calling executables outside the Nix store as much as possible
+          patchShebangs .
+
+          export HOME=$PWD
+
+          ${stdenv.lib.optionalString bypassCache ''
+            if [ ! -f package-lock.json ]
+            then
+                echo "No package-lock.json file found, reconstructing..."
+                node ${reconstructPackageLock}
+            fi
+
+            node ${addIntegrityFieldsScript}
+          ''}
+
+          npm ${forceOfflineFlag} --nodedir=${nodeSources} ${npmFlags} ${stdenv.lib.optionalString production "--production"} rebuild
+
+          ${stdenv.lib.optionalString (!dontNpmInstall) ''
+            # NPM tries to download packages even when they already exist if npm-shrinkwrap is used.
+            rm -f npm-shrinkwrap.json
+
+            npm ${forceOfflineFlag} --nodedir=${nodeSources} ${npmFlags} ${stdenv.lib.optionalString production "--production"} install
+          ''}
 
-          # Expose the executables that were installed
           cd ..
           ${stdenv.lib.optionalString (builtins.substring 0 1 packageName == "@") "cd .."}
 
@@ -529,7 +532,6 @@ let
       inherit nodeDependencies;
       shellHook = stdenv.lib.optionalString (dependencies != []) ''
         export NODE_PATH=$nodeDependencies/lib/node_modules
-        export PATH="$nodeDependencies/bin:$PATH"
       '';
     };
 in

pkgs/development/node-packages/node-packages-v10.json

@@ -2,8 +2,15 @@
   "@angular/cli"
 , "@antora/cli"
 , "@antora/site-generator-default" 
+, "@vue/cli"
+, "@webassemblyjs/cli"
+, "@webassemblyjs/repl"
+, "@webassemblyjs/wasm-strip"
+, "@webassemblyjs/wasm-text-gen"
+, "@webassemblyjs/wast-refmt"
+, "alloy"
 , "asar"
-, "aws-azure-login"
+, "azure-cli"
 , "azure-functions-core-tools"
 , "bash-language-server"
 , "bower"
@@ -27,10 +34,10 @@
 , "elm-live"
 , "elm-oracle"
 , "emoj"
+, "emojione"
 , "eslint"
 , "eslint_d"
-, "emojione"
+, {"fast-cli": "1.x"}
-, { "fast-cli": "1.x" }
 , "fkill-cli"
 , "forever"
 , "git-run"
@@ -40,26 +47,26 @@
 , "grunt-cli"
 , "gulp"
 , "gulp-cli"
-, "htmlhint"
 , "html-minifier"
+, "htmlhint"
 , "http-server"
 , "hueadm"
-, "ionic"
-, "ios-deploy"
 , "imapnotify"
 , "indium"
+, "ionic"
+, "ios-deploy"
 , "jake"
 , "javascript-typescript-langserver"
 , "joplin"
+, "js-beautify"
+, "js-yaml"
 , "jsdoc"
 , "jshint"
 , "json"
-, "js-beautify"
-, "jsonlint"
 , "json-diff"
 , "json-refs"
 , "json-server"
-, "js-yaml"
+, "jsonlint"
 , "karma"
 , "lcov-result-merger"
 , "leetcode-cli"
@@ -68,7 +75,7 @@
 , "less-plugin-clean-css"
 , "live-server"
 , "livedown"
-, { "lumo-build-deps": "../interpreters/clojurescript/lumo" }
+, {"lumo-build-deps": "../interpreters/clojurescript/lumo" }
 , "madoko"
 , "markdown-link-check"
 , "mathjax"
@@ -78,24 +85,25 @@
 , "multi-file-swagger"
 , "neovim"
 , "nijs"
-, "node2nix"
 , "node-gyp"
 , "node-gyp-build"
 , "node-inspector"
 , "node-pre-gyp"
-, "nodemon"
 , "node-red"
+, "node2nix"
+, "nodemon"
 , "npm"
 , "npm-check-updates"
+, {"npm2nix": "git://github.com/NixOS/npm2nix.git#5.12.0"}
 , "ocaml-language-server"
+, "parcel-bundler"
 , "peerflix"
 , "peerflix-server"
 , "pnpm"
-, "parcel-bundler"
 , "prettier"
 , "pulp"
-, "react-tools"
 , "react-native-cli"
+, "react-tools"
 , "reveal.js"
 , "s3http"
 , "semver"
@@ -108,9 +116,10 @@
 , "speed-test"
 , "ssb-server"
 , "stackdriver-statsd-backend"
+, "stf"
 , "svgo"
 , "swagger"
-, { "tedicross": "git+https://github.com/TediCross/TediCross.git#v0.8.7" }
+, {"tedicross": "git+https://github.com/TediCross/TediCross.git#v0.8.7"}
 , "tern"
 , "textlint"
 , "textlint-plugin-latex"
@@ -129,6 +138,7 @@
 , "thelounge"
 , "three"
 , "tiddlywiki"
+, "titanium"
 , "triton"
 , "tsun"
 , "ttf2eot"
@@ -139,17 +149,11 @@
 , "vscode-css-languageserver-bin"
 , "vscode-html-languageserver-bin"
 , "vue-cli"
-, "@vue/cli"
 , "vue-language-server"
-, "@webassemblyjs/cli"
+, "web-ext"
-, "@webassemblyjs/repl"
-, "@webassemblyjs/wasm-strip"
-, "@webassemblyjs/wasm-text-gen"
-, "@webassemblyjs/wast-refmt"
 , "webpack"
 , "webpack-cli"
 , "webtorrent-cli"
-, "web-ext"
 , "wring"
 , "write-good"
 , "yarn"

pkgs/development/node-packages/node-packages-v12.nix

@@ -1,4 +1,4 @@
-# This file has been generated by node2nix 1.7.0. Do not edit!
+# This file has been generated by node2nix 1.6.0. Do not edit!
 
 {nodeEnv, fetchurl, fetchgit, globalBuildInputs ? []}:
 
@@ -1624,13 +1624,13 @@ let
         sha1 = "212d5bfe1318306a420f6402b8e26ff39647a849";
       };
     };
-    "psl-1.2.0" = {
+    "psl-1.3.0" = {
       name = "psl";
       packageName = "psl";
-      version = "1.2.0";
+      version = "1.3.0";
       src = fetchurl {
-        url = "https://registry.npmjs.org/psl/-/psl-1.2.0.tgz";
+        url = "https://registry.npmjs.org/psl/-/psl-1.3.0.tgz";
-        sha512 = "GEn74ZffufCmkDDLNcl3uuyF/aSD6exEyh1v/ZSdAomB82t6G9hzJVRx0jBmLDW+VfZqks3aScmMw9DszwUalA==";
+        sha512 = "avHdspHO+9rQTLbv1RO+MPYeP/SzsCoxofjVnHanETfQhTJrmB0HlDoW+EiN/R+C0BZ+gERab9NY0lPN2TxNag==";
       };
     };
     "punycode-1.4.1" = {
@@ -1714,13 +1714,13 @@ let
         sha512 = "NAqBSrijGLZdM0WZNsInLJpkJokL72XYjUpnB0iwsRgxh7dB6COrHnTBNwN0E+lHDAJzu7kLAkDeY08z2/A0hg==";
       };
     };
-    "resolve-1.11.1" = {
+    "resolve-1.12.0" = {
       name = "resolve";
       packageName = "resolve";
-      version = "1.11.1";
+      version = "1.12.0";
       src = fetchurl {
-        url = "https://registry.npmjs.org/resolve/-/resolve-1.11.1.tgz";
+        url = "https://registry.npmjs.org/resolve/-/resolve-1.12.0.tgz";
-        sha512 = "vIpgF6wfuJOZI7KKKSP+HmiKggadPQAdsp5HiC1mvqnfp0gF1vdwgBWZIdrVft9pgqoMFQN+R7BSWZiBxx+BBw==";
+        sha512 = "B/dOmuoAik5bKcD6s6nXDCjzUKnaDvdkRyAk6rsmsKLipWj4797iothd7jmmUhWTfinVMU+wc56rYKsit2Qy4w==";
       };
     };
     "resolve-dir-1.0.1" = {
@@ -2303,8 +2303,7 @@ in
       license = "MIT";
     };
     production = true;
-    bypassCache = true;
+    bypassCache = false;
-    reconstructLock = true;
   };
   coffee-script = nodeEnv.buildNodePackage {
     name = "coffee-script";
@@ -2321,8 +2320,7 @@ in
       license = "MIT";
     };
     production = true;
-    bypassCache = true;
+    bypassCache = false;
-    reconstructLock = true;
   };
   grunt-cli = nodeEnv.buildNodePackage {
     name = "grunt-cli";
@@ -2497,7 +2495,7 @@ in
       sources."regex-not-1.0.2"
       sources."repeat-element-1.1.3"
       sources."repeat-string-1.6.1"
-      sources."resolve-1.11.1"
+      sources."resolve-1.12.0"
       sources."resolve-dir-1.0.1"
       sources."resolve-url-0.2.1"
       sources."ret-0.1.15"
@@ -2587,8 +2585,7 @@ in
       license = "MIT";
     };
     production = true;
-    bypassCache = true;
+    bypassCache = false;
-    reconstructLock = true;
   };
   node2nix = nodeEnv.buildNodePackage {
     name = "node2nix";
@@ -2716,7 +2713,7 @@ in
       sources."performance-now-2.1.0"
       sources."process-nextick-args-2.0.1"
       sources."proto-list-1.2.4"
-      sources."psl-1.2.0"
+      sources."psl-1.3.0"
       sources."punycode-2.1.1"
       sources."qs-6.5.2"
       (sources."readable-stream-2.3.6" // {
@@ -2725,7 +2722,7 @@ in
         ];
       })
       sources."request-2.88.0"
-      sources."resolve-1.11.1"
+      sources."resolve-1.12.0"
       sources."retry-0.10.1"
       sources."rimraf-2.6.3"
       sources."safe-buffer-5.2.0"
@@ -2777,7 +2774,6 @@ in
       license = "MIT";
     };
     production = true;
-    bypassCache = true;
+    bypassCache = false;
-    reconstructLock = true;
   };
 }

pkgs/development/node-packages/node-packages-v8.json

@@ -1,13 +0,0 @@
-[
-  "alloy"
-, "azure-cli"
-, "bower"
-, "coffee-script"
-, "grunt-cli"
-, "node-gyp"
-, "node-gyp-build"
-, "node-pre-gyp"
-, "pnpm"
-, "stf"
-, "titanium"
-]

pkgs/development/ocaml-modules/merlin-extend/default.nix

@@ -0,0 +1,22 @@
+{ lib, buildDunePackage, fetchFromGitHub, cppo }:
+
+buildDunePackage rec {
+  pname = "merlin-extend";
+  version = "0.4";
+
+  src = fetchFromGitHub {
+    owner = "let-def";
+    repo = pname;
+    sha256 = "1dxiqmm7ry24gvw6p9n4mrz37mnq4s6m8blrccsv3rb8yq82acx9";
+    rev = "v${version}";
+  };
+
+  buildInputs = [ cppo ];
+
+  meta = with lib; {
+    inherit (src.meta) homepage;
+    description = "SDK to extend Merlin";
+    license = licenses.mit;
+    maintainers = [ maintainers.volth ];
+  };
+}

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

@@ -1,26 +0,0 @@
-{ stdenv, buildOcaml, fetchFromGitHub, cppo }:
-
-buildOcaml rec {
-  name = "merlin_extend";
-  version = "0.3";
-
-  minimumSupportedOcamlVersion = "4.02";
-
-  src = fetchFromGitHub {
-    owner = "let-def";
-    repo = "merlin-extend";
-    sha256 = "1z6hybcb7ry0bkzjd0r2dlcgjnhhxdsr06x3h03sj7h5fihsc7vd";
-    rev = "v${version}";
-  };
-
-  buildInputs = [ cppo ];
-
-  createFindlibDestdir = true;
-
-  meta = with stdenv.lib; {
-    homepage = https://github.com/let-def/merlin-extend;
-    description = "SDK to extend Merlin";
-    license = licenses.mit;
-    maintainers = [ maintainers.volth ];
-  };
-}

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

@@ -1,11 +1,16 @@
-{ lib
+{ blessed
 , buildPythonPackage
 , fetchPypi
-, pythonOlder
+, lib
+, libcxx
+, libcxxabi
 , llvm
-, typesentry
+, openmp
-, blessed
 , pytest
+, pythonOlder
+, stdenv
+, substituteAll
+, typesentry
 }:
 
 buildPythonPackage rec {
@@ -17,10 +22,25 @@ buildPythonPackage rec {
     sha256 = "1s8z81zffrckvdwrrl0pkjc7gsdvjxw59xgg6ck81dl7gkh5grjk";
   };
 
+  patches = [
+    # Disable the compiler monkey patching, and remove the task that's copying
+    # the native dependencies to the build directory.
+    ./remove-compiler-monkeypatch_disable-native-relocation.patch
+  ] ++ lib.optionals stdenv.isDarwin [
+    # Replace the library auto-detection with hardcoded paths.
+    (substituteAll {
+      src = ./hardcode-library-paths.patch;
+
+      libomp_dylib = "${lib.getLib openmp}/lib/libomp.dylib";
+      libcxx_dylib = "${lib.getLib libcxx}/lib/libc++.1.dylib";
+      libcxxabi_dylib = "${lib.getLib libcxxabi}/lib/libc++abi.dylib";
+    })
+  ];
+
   disabled = pythonOlder "3.5";
 
   propagatedBuildInputs = [ typesentry blessed ];
-  buildInputs = [ llvm ];
+  buildInputs = [ llvm ] ++ lib.optionals stdenv.isDarwin [ openmp ];
   checkInputs = [ pytest ];
 
   LLVM = llvm;

pkgs/development/python-modules/datatable/hardcode-library-paths.patch

@@ -0,0 +1,43 @@
+diff --git a/ci/setup_utils.py b/ci/setup_utils.py
+index 66b385a..6255af0 100644
+--- a/ci/setup_utils.py
++++ b/ci/setup_utils.py
+@@ -600,37 +600,7 @@ def find_linked_dynamic_libraries():
+     them as a list of absolute paths.
+     """
+     with TaskContext("Find the required dynamic libraries") as log:
+-        llvm = get_llvm()
+-        libs = required_link_libraries()
+-        resolved = []
+-        for libname in libs:
+-            if llvm:
+-                fullpath = os.path.join(llvm, "lib", libname)
+-                if os.path.isfile(fullpath):
+-                    resolved.append(fullpath)
+-                    log.info("Library `%s` found at %s" % (libname, fullpath))
+-                    continue
+-                else:
+-                    log.info("%s does not exist" % fullpath)
+-            # Rely on the shell `locate` command to find the dynamic libraries.
+-            proc = subprocess.Popen(["locate", libname], stdout=subprocess.PIPE,
+-                                    stderr=subprocess.PIPE)
+-            stdout, stderr = proc.communicate()
+-            if proc.returncode == 0:
+-                results = stdout.decode().strip().split("\n")
+-                results = [r for r in results if r]
+-                if results:
+-                    results.sort(key=len)
+-                    fullpath = results[0]
+-                    assert os.path.isfile(fullpath), "Invalid path: %r" % (fullpath,)
+-                    resolved.append(fullpath)
+-                    log.info("Library `%s` found at %s" % (libname, fullpath))
+-                    continue
+-                else:
+-                    log.fatal("Cannot locate dynamic library `%s`" % libname)
+-            else:
+-                log.fatal("`locate` command returned the following error:\n%s"
+-                          % stderr.decode())
++        resolved = ["@libomp_dylib@", "@libcxx_dylib@", "@libcxxabi_dylib@"]
+         return resolved
+ 
+ 

pkgs/development/python-modules/datatable/remove-compiler-monkeypatch_disable-native-relocation.patch

@@ -0,0 +1,28 @@
+diff --git a/setup.py b/setup.py
+index 58fc875..8032561 100644
+--- a/setup.py
++++ b/setup.py
+@@ -141,23 +141,6 @@ if cmd in ("build", "bdist_wheel", "build_ext", "install"):
+     extra_link_args = get_extra_link_args()
+     cpp_files = get_c_sources("c")
+ 
+-    with TaskContext("Copy dynamic libraries") as log:
+-        # Copy system libraries into the datatable/lib folder, so that they can
+-        # be packaged with the wheel
+-        libs = find_linked_dynamic_libraries()
+-        for libpath in libs:
+-            trgfile = os.path.join("datatable", "lib",
+-                                   os.path.basename(libpath))
+-            if os.path.exists(trgfile):
+-                log.info("File %s already exists, skipped" % trgfile)
+-            else:
+-                log.info("Copying %s to %s" % (libpath, trgfile))
+-                shutil.copy(libpath, trgfile)
+-
+-    if ismacos():
+-        monkey_patch_compiler()
+-
+-
+ # Create the git version file
+ if cmd in ("build", "sdist", "bdist_wheel", "install"):
+     make_git_version_file(True)

pkgs/development/python-modules/mysql-connector/default.nix

@@ -4,13 +4,13 @@
 
 buildPythonPackage rec {
   pname = "mysql-connector";
-  version = "8.0.16";
+  version = "8.0.17";
 
   src = fetchFromGitHub {
     owner = "mysql";
     repo = "mysql-connector-python";
     rev = version;
-    sha256 = "0yl3fkyws24lc2qrbvn42bqy72aqy8q5v8f0j5zy3mkh9a7wlxdp";
+    sha256 = "1by0g7hrbmb1wj2wh3q9y92mjimck2izh1i4fm1xfbp278p2acbd";
   };
 
   propagatedBuildInputs = [ protobuf ];

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

@@ -0,0 +1,33 @@
+{ lib
+, buildPythonPackage
+, botocore
+, fetchPypi
+, mock
+, mypy
+, python-dateutil
+, pytest
+, requests
+}:
+
+buildPythonPackage rec {
+  pname = "pynamodb";
+  version = "3.4.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1cwgqvpqn59y3zq4wv35m1v4jrh3ih6zbyv30g5nxbw13vddxr92";
+  };
+
+  propagatedBuildInputs = [ python-dateutil botocore ];
+  checkInputs = [ requests mock pytest mypy ];
+
+  meta = with lib; {
+    description = "A Pythonic interface for Amazon’s DynamoDB that supports Python 2 and 3.";
+    longDescription = ''
+      DynamoDB is a great NoSQL service provided by Amazon, but the API is
+      verbose. PynamoDB presents you with a simple, elegant API.
+    '';
+    homepage = "http://jlafon.io/pynamodb.html";
+    license = licenses.mit;
+  };
+}

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

@@ -1,4 +1,4 @@
-{ lib, buildPythonPackage, fetchPypi, python, pkgs, pythonOlder, substituteAll
+{ lib, buildPythonPackage, fetchFromGitHub, python, pkgs, pythonOlder, substituteAll
 , aenum
 , cython
 , pytest
@@ -8,11 +8,13 @@
 
 buildPythonPackage rec {
   pname = "pyproj";
-  version = "2.2.1";
+  version = "2.2.2";
 
-  src = fetchPypi {
+  src = fetchFromGitHub {
-    inherit pname version;
+    owner = "pyproj4";
-    sha256 = "0yigcxwmx5cczipf2mpmy2gq1dnl0635yjvjq86ay47j1j5fd2gc";
+    repo = "pyproj";
+    rev = "v${version}rel";
+    sha256 = "0mb0jczgqh3sma69k7237i38h09gxgmvmddls9hpw4f3131f5ax7";
   };
 
   # force pyproj to use ${pkgs.proj}

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

@@ -1,18 +1,20 @@
-{ fetchPypi, buildPythonPackage }:
+{ lib, fetchPypi, buildPythonPackage }:
+
 buildPythonPackage rec {
   pname = "redis";
-  version = "3.1.0";
+  version = "3.3.4";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "7ba8612bbfd966dea8c62322543fed0095da2834dbd5a7c124afbc617a156aa7";
+    sha256 = "18n6k113izfqsm8yysrw1a5ba6kv0vsgfz6ab5n0k6k65yvr690z";
   };
 
   # tests require a running redis
   doCheck = false;
 
-  meta = {
+  meta = with lib; {
     description = "Python client for Redis key-value store";
     homepage = "https://pypi.python.org/pypi/redis/";
+    license = with licenses; [ mit ];
   };
 }

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

@@ -25,18 +25,16 @@
 
 buildPythonPackage rec {
   pname = "spacy";
-  version = "2.1.6";
+  version = "2.1.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1s0a0vir9lg5q8n832kkadbajb4i4zl20zmdg3g20qlp4mcbn25p";
+    sha256 = "0k4kh9jnpdawaqjxwcdi2h01s85s5r338ajgv9kkq59iha4hichh";
   };
 
   prePatch = ''
     substituteInPlace setup.py \
-      --replace "plac<1.0.0,>=0.9.6" "plac>=0.9.6" \
+      --replace "plac<1.0.0,>=0.9.6" "plac>=0.9.6"
-      --replace "regex==" "regex>=" \
-      --replace "wheel>=0.32.0,<0.33.0" "wheel>=0.32.0"
   '';
 
   propagatedBuildInputs = [

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

@@ -30,8 +30,6 @@ buildPythonPackage rec {
     sha256 = "50402545ac92b1a931c2365e341cb35c4ebe5575525f1dcc5265901ff3895a5f";
   };
 
-  disabled = isPy27; # 2.7 requires backports.csv
-
   propagatedBuildInputs = [
     cachetools
     cld2-cffi
@@ -64,5 +62,8 @@ buildPythonPackage rec {
     homepage = "http://textacy.readthedocs.io/";
     license = licenses.asl20;
     maintainers = with maintainers; [ rvl ];
+    # ftfy and jellyfish no longer support python2
+    # latest scikitlearn not supported for this: https://github.com/chartbeat-labs/textacy/issues/260
+    broken = true;
   };
 }

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

@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "zstd";
-  version = "1.4.0.0";
+  version = "1.4.1.0";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "01prq9rwz1gh42idnj2162w79dzs8gf3ac8pn12lz347w280kjbk";
+    sha256 = "0laxg0pag1bzmqmg4x81jb32412pn98p9zg2b0li035m779nka95";
   };
 
   postPatch = ''

pkgs/development/ruby-modules/bundler-app/default.nix

@@ -41,6 +41,7 @@ let
 
     buildInputs = buildInputs ++ lib.optional (scripts != []) makeWrapper;
 
+    meta = { platforms = ruby.meta.platforms; } // meta;
     passthru = basicEnv.passthru // {
       inherit basicEnv;
       inherit (basicEnv) env;

pkgs/development/ruby-modules/solargraph/Gemfile.lock

@@ -15,7 +15,7 @@ GEM
     rainbow (3.0.0)
     reverse_markdown (1.1.0)
       nokogiri
-    rubocop (0.72.0)
+    rubocop (0.74.0)
       jaro_winkler (~> 1.5.1)
       parallel (~> 1.10)
       parser (>= 2.6)
@@ -23,7 +23,7 @@ GEM
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 1.4.0, < 1.7)
     ruby-progressbar (1.10.1)
-    solargraph (0.34.2)
+    solargraph (0.35.1)
       backport (~> 1.1)
       bundler (>= 1.17.2)
       htmlentities (~> 4.3, >= 4.3.4)

pkgs/development/ruby-modules/solargraph/default.nix

@@ -11,7 +11,7 @@ bundlerApp rec {
     description = "IDE tools for the Ruby language";
     homepage = http://www.github.com/castwide/solargraph;
     license = licenses.mit;
-    maintainers = with maintainers; [ worldofpeace nicknovitski ];
+    maintainers = with maintainers; [ worldofpeace nicknovitski angristan ];
     platforms = platforms.unix;
   };
 }

pkgs/development/ruby-modules/solargraph/gemset.nix

@@ -118,10 +118,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "192vmm9ah6b4wyabawaszpr8n3z93y3ymykp3m4pncrbwngmn3m2";
+      sha256 = "0wpyass9qb2wvq8zsc7wdzix5xy2ldiv66wnx8mwwprz2dcvzayk";
       type = "gem";
     };
-    version = "0.72.0";
+    version = "0.74.0";
   };
   ruby-progressbar = {
     groups = ["default"];
@@ -139,10 +139,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1r217wvspg7mmjvkng3ksas3pbcy90iiw46r4b8xzd08y8p66ssy";
+      sha256 = "00pq74a3zvb7x333mwcz7m73p7g4sjwzxmci94jwasl0h35fapzg";
       type = "gem";
     };
-    version = "0.34.2";
+    version = "0.35.1";
   };
   thor = {
     groups = ["default"];

pkgs/development/tools/analysis/oclgrind/default.nix

@@ -0,0 +1,28 @@
+{ stdenv, fetchFromGitHub, cmake, llvmPackages, readline, python }:
+
+stdenv.mkDerivation rec {
+  pname = "oclgrind";
+  version = "18.3"; # see comment in all-packages.nix
+
+  src = fetchFromGitHub {
+    owner = "jrprice";
+    repo = "oclgrind";
+    rev = "v${version}";
+    sha256 = "0s42z3dg684a0gk8qyx2h08cbh95zkrdaaj9y71rrc5bjsg8197x";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ llvmPackages.llvm llvmPackages.clang-unwrapped readline python ];
+
+  cmakeFlags = [
+    "-DCLANG_ROOT=${llvmPackages.clang-unwrapped}"
+  ];
+
+  meta = with stdenv.lib; {
+    description = "An OpenCL device simulator and debugger";
+    homepage = https://github.com/jrprice/oclgrind;
+    license = licenses.bsd3;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ athas ];
+  };
+}

pkgs/development/tools/documentation/mdsh/default.nix

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   name = "mdsh-${version}";
-  version = "0.1.3";
+  version = "0.1.4";
 
   src = fetchFromGitHub {
     owner = "zimbatm";
     repo = "mdsh";
     rev = "v${version}";
-    sha256 = "17pd090wpnx7i8q9pp9rhps35ahm1xn4h6pm1cfsafm072qd7rff";
+    sha256 = "0m3f5mrdmnmkfsy7mc6x3jf4ainmq0z42mv935ikcdbjwwjbd5gq";
   };
 
-  cargoSha256 = "0a2d2qnb0wkxcs2l839p7jsr99ng2frahsfi2viy9fjynsjpvzlm";
+  cargoSha256 = "11kzl0ns84xhdacn0k7nilgzgpwazmaaqdjf2kcarxf2h01b0rjv";
 
   meta = with stdenv.lib; {
     description = "Markdown shell pre-processor";

pkgs/development/tools/rubocop/Gemfile.lock

@@ -7,7 +7,7 @@ GEM
     parser (2.6.3.0)
       ast (~> 2.4.0)
     rainbow (3.0.0)
-    rubocop (0.73.0)
+    rubocop (0.74.0)
       jaro_winkler (~> 1.5.1)
       parallel (~> 1.10)
       parser (>= 2.6)

pkgs/development/tools/rubocop/gemset.nix

@@ -56,10 +56,10 @@
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1b5zc8xaqb5krchjrjqj7sc205awmnpksc4ng0rbckd6xcbr7n0f";
+      sha256 = "0wpyass9qb2wvq8zsc7wdzix5xy2ldiv66wnx8mwwprz2dcvzayk";
       type = "gem";
     };
-    version = "0.73.0";
+    version = "0.74.0";
   };
   ruby-progressbar = {
     groups = ["default"];

pkgs/development/web/nodejs/v8.nix

@@ -1,10 +0,0 @@
-{ callPackage, enableNpm ? true }:
-
-let
-  buildNodejs = callPackage ./nodejs.nix {};
-in
-  buildNodejs {
-    inherit enableNpm;
-    version = "8.16.0";
-    sha256 = "0h3k5y51fyysqnqb8n5v5zxga937pipag49xzx6xr9b82phfh59m";
-  }

pkgs/development/web/remarkjs/nodepkgs.nix

@@ -2,7 +2,7 @@
 
 {pkgs ? import <nixpkgs> {
     inherit system;
-  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-8_x"}:
+  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-10_x"}:
 
 let
   nodeEnv = import ../../node-packages/node-env.nix {

pkgs/misc/base16-builder/node-packages.nix

@@ -2,7 +2,7 @@
 
 {pkgs ? import <nixpkgs> {
     inherit system;
-  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-8_x"}:
+  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-10_x"}:
 
 let
   nodeEnv = import ../../development/node-packages/node-env.nix {

pkgs/misc/emulators/wine/sources.nix

@@ -56,8 +56,8 @@ in rec {
 
   winetricks = fetchFromGitHub rec {
     # https://github.com/Winetricks/winetricks/releases
-    version = "20190310";
+    version = "20190615";
-    sha256 = "0mqzl7k9q7lfkmk8fk9dfzi2dm45h31mrid9265qh2d56nk28ali";
+    sha256 = "1bdvj363yjn7agqq1fxdfz31j1rrs2wc02v874jjx5sw1bfq5qsa";
     owner = "Winetricks";
     repo = "winetricks";
     rev = version;

pkgs/servers/metabase/default.nix

@@ -1,12 +1,12 @@
 { stdenv, fetchurl, makeWrapper, jre }:
 
 stdenv.mkDerivation rec {
-  name = "metabase-${version}";
+  pname = "metabase";
-  version = "0.32.9";
+  version = "0.32.10";
 
   src = fetchurl {
     url = "http://downloads.metabase.com/v${version}/metabase.jar";
-    sha256 = "08iybb1m2pmimn0fs95kd948yf6c1xmg5kkzm9ykx4cpb9pn1yw0";
+    sha256 = "0dzwwwvsi9pr40xbqws02yzjgx89ygjiybjd0n73hj69v6j9f2rn";
   };
 
   nativeBuildInputs = [ makeWrapper ];
@@ -18,8 +18,8 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with stdenv.lib; {
-    description = "The easy, open source way for everyone in your company to ask questions and learn from data.";
+    description = "The easy, open source way for everyone in your company to ask questions and learn from data";
-    homepage    = https://metabase.com;
+    homepage    = "https://metabase.com";
     license     = licenses.agpl3;
     platforms   = platforms.all;
     maintainers = with maintainers; [ schneefux thoughtpolice ];

pkgs/servers/monitoring/prometheus/mail-exporter.nix

@@ -0,0 +1,30 @@
+{ stdenv, buildGoPackage, fetchFromGitHub }:
+
+buildGoPackage rec {
+  name = "mailexporter-${version}";
+  version = "2019-07-14";
+
+  goPackagePath = "github.com/cherti/mailexporter";
+
+  src = fetchFromGitHub {
+    rev = "c60d1970abbedb15e70d6fc858f7fd76fa061ffe";
+    owner = "cherti";
+    repo = "mailexporter";
+    sha256 = "0wlw7jvmhgvg1r2bsifxm2d0vj0iqhplnx6n446625sslvddx3vn";
+  };
+
+  goDeps = ./mail-exporter_deps.nix;
+
+  postInstall = ''
+    install -D -m 0444 -t $bin/share/man/man1 $src/man/mailexporter.1
+    install -D -m 0444 -t $bin/share/man/man5 $src/man/mailexporter.conf.5
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Export Prometheus-style metrics about mail server functionality";
+    homepage = "https://github.com/cherti/mailexporter";
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ willibutz ];
+    platforms = platforms.linux;
+  };
+}

pkgs/servers/monitoring/prometheus/mail-exporter_deps.nix

@@ -0,0 +1,92 @@
+[
+  {
+    goPackagePath = "github.com/beorn7/perks";
+    fetch = {
+      type = "git";
+      url = "https://github.com/beorn7/perks";
+      rev = "4b2b341e8d7715fae06375aa633dbb6e91b3fb46";
+      sha256 = "1i1nz1f6g55xi2y3aiaz5kqfgvknarbfl4f0sx4nyyb4s7xb1z9x";
+    };
+  }
+  {
+    goPackagePath = "github.com/golang/protobuf";
+    fetch = {
+      type = "git";
+      url = "https://github.com/golang/protobuf";
+      rev = "6c65a5562fc06764971b7c5d05c76c75e84bdbf7";
+      sha256 = "1k1wb4zr0qbwgpvz9q5ws9zhlal8hq7dmq62pwxxriksayl6hzym";
+    };
+  }
+  {
+    goPackagePath = "github.com/matttproud/golang_protobuf_extensions";
+    fetch = {
+      type = "git";
+      url = "https://github.com/matttproud/golang_protobuf_extensions";
+      rev = "c182affec369e30f25d3eb8cd8a478dee585ae7d";
+      sha256 = "1xqsf9vpcrd4hp95rl6kgmjvkv1df4aicfw4l5vfcxcwxknfx2xs";
+    };
+  }
+  {
+    goPackagePath = "github.com/prometheus/client_golang";
+    fetch = {
+      type = "git";
+      url = "https://github.com/prometheus/client_golang";
+      rev = "a6c69798cccecfd43070693e4416838767f73e18";
+      sha256 = "0s6xprvkdyfvmx4540454972fn3gvrzy7fyv0yq42h32nw3l7p75";
+    };
+  }
+  {
+    goPackagePath = "github.com/prometheus/client_model";
+    fetch = {
+      type = "git";
+      url = "https://github.com/prometheus/client_model";
+      rev = "fd36f4220a901265f90734c3183c5f0c91daa0b8";
+      sha256 = "1bs5d72k361llflgl94c22n0w53j30rsfh84smgk8mbjbcmjsaa5";
+    };
+  }
+  {
+    goPackagePath = "github.com/prometheus/common";
+    fetch = {
+      type = "git";
+      url = "https://github.com/prometheus/common";
+      rev = "31bed53e4047fd6c510e43a941f90cb31be0972a";
+      sha256 = "1q16br348117ffycxdwsldb0i39p34miclfa8z93k6vjwnrqbh2l";
+    };
+  }
+  {
+    goPackagePath = "github.com/prometheus/procfs";
+    fetch = {
+      type = "git";
+      url = "https://github.com/prometheus/procfs";
+      rev = "8f55e607908ea781ad9d08521730d73e047d9ac4";
+      sha256 = "023581b68mz89yhgnk4w08ch05ix60v0hv9jlqz65w43s4j7g4vb";
+    };
+  }
+  {
+    goPackagePath = "golang.org/x/sys";
+    fetch = {
+      type = "git";
+      url = "https://go.googlesource.com/sys";
+      rev = "04f50cda93cbb67f2afa353c52f342100e80e625";
+      sha256 = "0hmfsz9y1ingwsn482hlzzmzs7kr3cklm0ana0mbdk70isw2bxnw";
+    };
+  }
+  {
+    goPackagePath = "gopkg.in/fsnotify.v1";
+    fetch = {
+      type = "git";
+      url = "https://gopkg.in/fsnotify.v1";
+      rev = "c2828203cd70a50dcccfb2761f8b1f8ceef9a8e9";
+      sha256 = "07va9crci0ijlivbb7q57d2rz9h27zgn2fsm60spjsqpdbvyrx4g";
+    };
+  }
+  {
+    goPackagePath = "gopkg.in/yaml.v2";
+    fetch = {
+      type = "git";
+      url = "https://gopkg.in/yaml.v2";
+      rev = "51d6538a90f86fe93ac480b35f37b2be17fef232";
+      sha256 = "01wj12jzsdqlnidpyjssmj0r4yavlqy7dwrg7adqd8dicjc4ncsa";
+    };
+  }
+]

pkgs/servers/monitoring/prometheus/pushgateway.nix

@@ -43,7 +43,7 @@ buildGoPackage rec {
     description = "Allows ephemeral and batch jobs to expose metrics to Prometheus";
     homepage = https://github.com/prometheus/pushgateway;
     license = licenses.asl20;
-    maintainers = with maintainers; [ benley fpletz ivan ];
+    maintainers = with maintainers; [ benley fpletz ];
     platforms = platforms.unix;
   };
 }

pkgs/servers/sql/mariadb/default.nix

@@ -1,8 +1,9 @@
-{ stdenv, fetchurl, fetchFromGitHub, cmake, pkgconfig, ncurses, zlib, xz, lzo, lz4, bzip2, snappy
+{ stdenv, fetchurl, fetchFromGitHub, cmake, pkgconfig, makeWrapper, ncurses, zlib, xz, lzo, lz4, bzip2, snappy
 , libiconv, openssl, pcre, boost, judy, bison, libxml2, libkrb5
 , libaio, libevent, jemalloc, cracklib, systemd, numactl, perl
 , fixDarwinDylibNames, cctools, CoreServices
 , asio, buildEnv, check, scons
+, less
 }:
 
 with stdenv.lib;
@@ -11,6 +12,8 @@ let # in mariadb # spans the whole file
 
 libExt = stdenv.hostPlatform.extensions.sharedLibrary;
 
+mytopEnv = perl.withPackages (p: with p; [ DataDumper DBDmysql DBI TermReadKey ]);
+
 mariadb = everything // {
   inherit client; # libmysqlclient.so in .out, necessary headers in .dev and utils in .bin
   server = everything; # a full single-output build, including everything in `client` again
@@ -133,12 +136,13 @@ everything = stdenv.mkDerivation (common // {
 
   outputs = [ "out" "dev" "man" ];
 
-  nativeBuildInputs = common.nativeBuildInputs ++ [ bison ];
+  nativeBuildInputs = common.nativeBuildInputs ++ [ bison ] ++ optional (!stdenv.isDarwin) makeWrapper;
 
   buildInputs = common.buildInputs ++ [
     xz lzo lz4 bzip2 snappy
     libxml2 boost judy libevent cracklib
-  ] ++ optional (stdenv.isLinux && !stdenv.isAarch32) numactl;
+  ] ++ optional (stdenv.isLinux && !stdenv.isAarch32) numactl
+    ++ optional (!stdenv.isDarwin) mytopEnv;
 
   cmakeFlags = common.cmakeFlags ++ [
     "-DMYSQL_DATADIR=/var/lib/mysql"
@@ -161,6 +165,8 @@ everything = stdenv.mkDerivation (common // {
     cmakeFlags="$cmakeFlags \
       -DINSTALL_SHAREDIR=$dev/share/mysql
       -DINSTALL_SUPPORTFILESDIR=$dev/share/mysql"
+  '' + optionalString (!stdenv.isDarwin) ''
+    patchShebangs scripts/mytop.sh
   '';
 
   postInstall = ''
@@ -181,6 +187,11 @@ everything = stdenv.mkDerivation (common // {
     sed -i 's/-mariadb/-mysql/' "$out"/bin/galera_new_cluster
   '';
 
+  # perlPackages.DBDmysql is broken on darwin
+  postFixup = optionalString (!stdenv.isDarwin) ''
+    wrapProgram $out/bin/mytop --set PATH ${less}/bin/less
+  '';
+
   CXXFLAGS = optionalString stdenv.isi686 "-fpermissive";
 });
 

pkgs/servers/sql/postgresql/ext/timescaledb.nix

@@ -8,7 +8,7 @@
 
 stdenv.mkDerivation rec {
   name = "timescaledb-${version}";
-  version = "1.4.0";
+  version = "1.4.1";
 
   nativeBuildInputs = [ cmake ];
   buildInputs = [ postgresql openssl ];
@@ -17,7 +17,7 @@ stdenv.mkDerivation rec {
     owner  = "timescale";
     repo   = "timescaledb";
     rev    = "refs/tags/${version}";
-    sha256 = "0xjl3pdm36pksbkhl44kixqkfv8qpdm4frfwxv0p4vvjmlhslz48";
+    sha256 = "1gbca0fyaxjkwijdp2ah4iykwq5xabz9kkf8ak76sif4lz64y54b";
   };
 
   cmakeFlags = [ "-DSEND_TELEMETRY_DEFAULT=OFF" ];
@@ -39,7 +39,7 @@ stdenv.mkDerivation rec {
   meta = with stdenv.lib; {
     description = "Scales PostgreSQL for time-series data via automatic partitioning across time and space";
     homepage    = https://www.timescale.com/;
-    maintainers = with maintainers; [ volth ];
+    maintainers = with maintainers; [ volth marsam ];
     platforms   = postgresql.meta.platforms;
     license     = licenses.asl20;
   };

pkgs/servers/unifi/default.nix

@@ -49,8 +49,8 @@ in rec {
   };
 
   unifiStable = generic {
-    version = "5.10.23";
+    version = "5.10.25";
-    sha256  = "0ak8crx3anxsx4r3b9k0rihgafkgsxj7f64z48nrk1l8m7f0wwxg";
+    sha256  = "1v03r7qd09s6lz37wwlsrqiy1jcwxnvj1q87jwpmhdipjprcjfdx";
   };
 
   unifiTesting = generic {

pkgs/servers/web-apps/cryptpad/node-packages.nix

@@ -2,7 +2,7 @@
 
 {pkgs ? import <nixpkgs> {
     inherit system;
-  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-6_x"}:
+  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-10_x"}:
 
 let
   nodeEnv = import ../../../development/node-packages/node-env.nix {

pkgs/shells/xonsh/default.nix

@@ -2,14 +2,14 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "xonsh";
-  version = "0.9.8";
+  version = "0.9.9";
 
   # fetch from github because the pypi package ships incomplete tests
   src = fetchFromGitHub {
     owner  = "xonsh";
     repo   = "xonsh";
     rev    = "refs/tags/${version}";
-    sha256 = "0lnvx1kdk1nwv988wrxyvbzb25xawz517amvi4pwzs22bymcdhws";
+    sha256 = "0c6ywzn72clcclawgf1khwaaj3snn49fmajz8qfhc5mpbnvdp7q0";
   };
 
   LC_ALL = "en_US.UTF-8";

pkgs/tools/misc/jdupes/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "jdupes-${version}";
-  version = "1.13.1";
+  version = "1.13.2";
 
   src = fetchFromGitHub {
     owner = "jbruchon";
     repo  = "jdupes";
     rev   = "v${version}";
-    sha256 = "1f001l56dx7aixlpl7438shzh8b2vanx8k1sywm9ix6cak1k8rzr";
+    sha256 = "1dzw1h9x9addkxf7r8lb8y09wmdkx8i61f5m96589r88jjk965xy";
     # Unicode file names lead to different checksums on HFS+ vs. other
     # filesystems because of unicode normalisation. The testdir
     # directories have such files and will be removed.

pkgs/tools/misc/riemann-tools/Gemfile

@@ -1,3 +1,3 @@
 source 'https://rubygems.org'
 
-gem "riemann-tools", "0.2.13"
+gem "riemann-tools"

pkgs/tools/misc/riemann-tools/Gemfile.lock

@@ -4,21 +4,22 @@ GEM
     beefcake (1.0.0)
     json (1.8.6)
     mtrc (0.0.4)
+    optimist (3.0.0)
     riemann-client (0.2.6)
       beefcake (>= 0.3.5, <= 1.0.0)
       mtrc (>= 0.0.4)
       trollop (>= 1.16.2)
-    riemann-tools (0.2.13)
+    riemann-tools (0.2.14)
       json (~> 1.8)
-      riemann-client (>= 0.2.6)
+      optimist (~> 3.0, >= 3.0.0)
-      trollop (>= 1.16.2)
+      riemann-client (~> 0.2, >= 0.2.6)
     trollop (2.9.9)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  riemann-tools (= 0.2.13)
+  riemann-tools
 
 BUNDLED WITH
    1.17.2

pkgs/tools/misc/riemann-tools/gemset.nix

@@ -29,6 +29,16 @@
     };
     version = "0.0.4";
   };
+  optimist = {
+    groups = ["default"];
+    platforms = [];
+    source = {
+      remotes = ["https://rubygems.org"];
+      sha256 = "05jxrp3nbn5iilc1k7ir90mfnwc5abc9h78s5rpm3qafwqxvcj4j";
+      type = "gem";
+    };
+    version = "3.0.0";
+  };
   riemann-client = {
     dependencies = ["beefcake" "mtrc" "trollop"];
     groups = ["default"];
@@ -41,15 +51,15 @@
     version = "0.2.6";
   };
   riemann-tools = {
-    dependencies = ["json" "riemann-client" "trollop"];
+    dependencies = ["json" "optimist" "riemann-client"];
     groups = ["default"];
     platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0brf44cq4xz0nqhs189zlg76527bfv3jr453yc00410qdzz8fpxa";
+      sha256 = "07w9x3iw32zwpzsm9l63vn0nv1778qls1blqysr45m7l7x6n5wjx";
       type = "gem";
     };
-    version = "0.2.13";
+    version = "0.2.14";
   };
   trollop = {
     groups = ["default"];

pkgs/tools/misc/stow/default.nix

@@ -1,26 +1,18 @@
-{ stdenv, fetchurl, perl, perlPackages, makeWrapper }:
+{ stdenv, fetchurl, perl, perlPackages }:
 
 let
   pname = "stow";
-  version = "2.3.0";
+  version = "2.3.1";
 in
 stdenv.mkDerivation {
   name = "${pname}-${version}";
 
   src = fetchurl {
     url = "mirror://gnu/stow/stow-${version}.tar.bz2";
-    sha256 = "1fnn83wwx3yaxpqkq8xyya3aiibz19fwrfj30nsiikm7igmwgiv5";
+    sha256 = "0bs2b90wjkk1camcasy8kn403kazq6c7fj5m5msfl3navbgwz9i6";
   };
 
-  nativeBuildInputs = [ makeWrapper ];
+  buildInputs = with perlPackages; [ perl IOStringy TestOutput ];
-  buildInputs = with perlPackages; [ perl IOStringy TestOutput HashMerge Clone CloneChoose ];
-
-  postFixup = ''
-    wrapProgram "$out"/bin/stow \
-    --set PERL5LIB "$out/lib/perl5/site_perl:${with perlPackages; makePerlPath [
-      HashMerge Clone CloneChoose
-    ]}"
-  '';
 
   doCheck = true;
 

pkgs/tools/misc/z-lua/default.nix

@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "z-lua";
-  version = "1.7.1";
+  version = "1.7.2";
 
   src = fetchFromGitHub {
     owner = "skywind3000";
     repo = "z.lua";
     rev = "v${version}";
-    sha256 = "01n4x84rpmyjyfga90s2s63gdk17z944hz35fk95qnshc5fapfq8";
+    sha256 = "17klcw2iv7d636mp7fb80kjvqd3xqkzqhwz41ri1l029dxji4zzh";
   };
 
   dontBuild = true;

pkgs/tools/networking/airfield/node.nix

@@ -2,7 +2,7 @@
 
 {pkgs ? import <nixpkgs> {
     inherit system;
-  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-8_x"}:
+  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-10_x"}:
 
 let
   nodeEnv = import ../../../development/node-packages/node-env.nix {

pkgs/tools/package-management/nixui/nixui.nix

@@ -2,7 +2,7 @@
 
 {pkgs ? import <nixpkgs> {
     inherit system;
-  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-8_x"}:
+  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-10_x"}:
 
 let
   nodeEnv = import ../../../development/node-packages/node-env.nix {

pkgs/tools/security/bitwarden-cli/node-packages.nix

@@ -2,7 +2,7 @@
 
 {pkgs ? import <nixpkgs> {
     inherit system;
-  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-8_x"}:
+  }, system ? builtins.currentSystem, nodejs ? pkgs."nodejs-10_x"}:
 
 let
   nodeEnv = import ../../../development/node-packages/node-env.nix {

pkgs/tools/security/ghidra/default.nix

@@ -6,11 +6,11 @@
 
 in stdenv.mkDerivation {
 
-  name = "ghidra-9.0.2";
+  name = "ghidra-9.0.4";
 
   src = fetchurl {
-    url = https://ghidra-sre.org/ghidra_9.0.2_PUBLIC_20190403.zip;
+    url = https://ghidra-sre.org/ghidra_9.0.4_PUBLIC_20190516.zip;
-    sha256 = "10ffd65c266e9f5b631c8ed96786c41ef30e2de939c3c42770573bb3548f8e9f";
+    sha256 = "1gqqxk57hswwgr97qisqivcfgjdxjipfdshyh4r76dyrfpa0q3d5";
   };
 
   nativeBuildInputs = [

pkgs/tools/security/gnupg/1.nix

@@ -27,6 +27,6 @@ stdenv.mkDerivation rec {
       other applications.  A wealth of frontend applications and libraries are
       available.
     '';
-    platforms = platforms.gnu ++ platforms.linux; # arbitrary choice
+    platforms = platforms.all;
   };
 }

pkgs/tools/system/hiera-eyaml/Gemfile

@@ -1,3 +1,3 @@
 source 'https://rubygems.org'
 
-gem 'hiera-eyaml', '2.1.0'
+gem 'hiera-eyaml'

pkgs/tools/system/hiera-eyaml/Gemfile.lock

@@ -1,17 +1,17 @@
 GEM
   remote: https://rubygems.org/
   specs:
-    hiera-eyaml (2.1.0)
+    hiera-eyaml (3.0.0)
       highline (~> 1.6.19)
-      trollop (~> 2.0)
+      optimist
     highline (1.6.21)
-    trollop (2.1.2)
+    optimist (3.0.0)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  hiera-eyaml (= 2.1.0)
+  hiera-eyaml
 
 BUNDLED WITH
-   1.11.2
+   1.17.2

pkgs/tools/system/hiera-eyaml/gemset.nix

@@ -1,11 +1,14 @@
 {
   hiera-eyaml = {
+    dependencies = ["highline" "optimist"];
+    groups = ["default"];
+    platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1h25pfv89macjf3sjdrx7slhlq1af4zybai42ci3gj02b6hli4a6";
+      sha256 = "049rxnwyivqgyjl0sjg7cb2q44ic0wsml288caspd1ps8v31gl18";
       type = "gem";
     };
-    version = "2.1.0";
+    version = "3.0.0";
   };
   highline = {
     source = {
@@ -15,12 +18,14 @@
     };
     version = "1.6.21";
   };
-  trollop = {
+  optimist = {
+    groups = ["default"];
+    platforms = [];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0415y63df86sqj43c0l82and65ia5h64if7n0znkbrmi6y0jwhl8";
+      sha256 = "05jxrp3nbn5iilc1k7ir90mfnwc5abc9h78s5rpm3qafwqxvcj4j";
       type = "gem";
     };
-    version = "2.1.2";
+    version = "3.0.0";
   };
 }

pkgs/tools/text/gnupatch/default.nix

@@ -14,11 +14,11 @@ stdenv.mkDerivation rec {
     # https://git.savannah.gnu.org/cgit/patch.git/patch/?id=f290f48a621867084884bfff87f8093c15195e6a
     ./CVE-2018-6951.patch
     (fetchurl {
-      url = https://sources.debian.org/data/main/p/patch/2.7.6-2/debian/patches/Allow_input_files_to_be_missing_for_ed-style_patches.patch;
+      url = https://git.savannah.gnu.org/cgit/patch.git/patch/?id=b5a91a01e5d0897facdd0f49d64b76b0f02b43e1;
       sha256 = "0iw0lk0yhnhvfjzal48ij6zdr92mgb84jq7fwryy1hdhi47hhq64";
     })
     (fetchurl { # CVE-2018-1000156
-      url = https://sources.debian.org/data/main/p/patch/2.7.6-2/debian/patches/Fix_arbitrary_command_execution_in_ed-style_patches.patch;
+      url = https://git.savannah.gnu.org/cgit/patch.git/patch/?id=123eaff0d5d1aebe128295959435b9ca5909c26d;
       sha256 = "1bpy16n3hm5nv9xkrn6c4wglzsdzj3ss1biq16w9kfv48p4hx2vg";
     })
     # https://git.savannah.gnu.org/cgit/patch.git/commit/?id=9c986353e420ead6e706262bf204d6e03322c300

pkgs/tools/text/ripgrep/default.nix

@@ -5,16 +5,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "ripgrep";
-  version = "11.0.1";
+  version = "11.0.2";
 
   src = fetchFromGitHub {
     owner = "BurntSushi";
     repo = pname;
     rev = version;
-    sha256 = "0vak82d4vyw0w8agswbyxa6g3zs2h9mxm2xjw0xs9qccvmi7whbb";
+    sha256 = "1iga3320mgi7m853la55xip514a3chqsdi1a1rwv25lr9b1p7vd3";
   };
 
-  cargoSha256 = "1k1wg27p7w8b3cgygnkr6yhsc4hpnvrpa227s612vy2zfcmgb1kx";
+  cargoSha256 = "11477l4l1y55klw5dp2kbsnv989vdz1547ml346hcfbkzv7m450v";
 
   cargoBuildFlags = stdenv.lib.optional withPCRE2 "--features pcre2";