NixOS
diff --git a/doc/builders/images/dockertools.xml b/doc/builders/images/dockertools.xml
@@ -8,12 +8,6 @@
   <varname>pkgs.dockerTools</varname> is a set of functions for creating and manipulating Docker images according to the <link xlink:href="https://github.com/moby/moby/blob/master/image/spec/v1.2.md#docker-image-specification-v120"> Docker Image Specification v1.2.0 </link>. Docker itself is not used to perform any of the operations done by these functions.
  </para>
 
- <warning>
-  <para>
-   The <varname>dockerTools</varname> API is unstable and may be subject to backwards-incompatible changes in the future.
-  </para>
- </warning>
-
  <section xml:id="ssec-pkgs-dockerTools-buildImage">
   <title>buildImage</title>
 

diff --git a/nixos/modules/module-list.nix b/nixos/modules/module-list.nix
@@ -443,6 +443,7 @@
   ./services/misc/logkeys.nix
   ./services/misc/leaps.nix
   ./services/misc/lidarr.nix
+  ./services/misc/mame.nix
   ./services/misc/mathics.nix
   ./services/misc/matrix-synapse.nix
   ./services/misc/mbpfan.nix

diff --git a/nixos/modules/services/admin/oxidized.nix b/nixos/modules/services/admin/oxidized.nix
@@ -111,6 +111,7 @@ in
         Restart  = "always";
         WorkingDirectory = cfg.dataDir;
         KillSignal = "SIGKILL";
+        PIDFile = "${cfg.dataDir}.config/oxidized/pid";
       };
     };
   };

diff --git a/nixos/modules/services/misc/mame.nix b/nixos/modules/services/misc/mame.nix
@@ -0,0 +1,67 @@
+{ config, lib, pkgs, ... }:
+
+with lib;
+
+let
+  cfg = config.services.mame;
+  mame = "mame${lib.optionalString pkgs.stdenv.is64bit "64"}";
+in
+{
+  options = {
+    services.mame = {
+      enable = mkOption {
+        type = types.bool;
+        default = false;
+        description = ''
+          Whether to setup TUN/TAP Ethernet interface for MAME emulator.
+        '';
+      };
+      user = mkOption {
+        type = types.str;
+        description = ''
+          User from which you run MAME binary.
+        '';
+      };
+      hostAddr = mkOption {
+        type = types.str;
+        description = ''
+          IP address of the host system. Usually an address of the main network
+          adapter or the adapter through which you get an internet connection.
+        '';
+        example = "192.168.31.156";
+      };
+      emuAddr = mkOption {
+        type = types.str;
+        description = ''
+          IP address of the guest system. The same you set inside guest OS under
+          MAME. Should be on the same subnet as <option>services.mame.hostAddr</option>.
+        '';
+        example = "192.168.31.155";
+      };
+    };
+  };
+
+  config = mkIf cfg.enable {
+    environment.systemPackages = [ pkgs.mame ];
+
+    security.wrappers."${mame}" = {
+      source = "${pkgs.mame}/bin/${mame}";
+      capabilities = "cap_net_admin,cap_net_raw+eip";
+    };
+
+    systemd.services.mame = {
+      description = "MAME TUN/TAP Ethernet interface";
+      after = [ "network.target" ];
+      wantedBy = [ "multi-user.target" ];
+      path = [ pkgs.iproute ];
+      serviceConfig = {
+        Type = "oneshot";
+        RemainAfterExit = true;
+        ExecStart = "${pkgs.mame}/bin/taputil.sh -c ${cfg.user} ${cfg.emuAddr} ${cfg.hostAddr} -";
+        ExecStop = "${pkgs.mame}/bin/taputil.sh -d ${cfg.user}";
+      };
+    };
+  };
+
+  meta.maintainers = with lib.maintainers; [ gnidorah ];
+}
diff --git a/pkgs/applications/audio/gpodder/default.nix b/pkgs/applications/audio/gpodder/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchFromGitHub, python3, python3Packages, intltool
 , glibcLocales, gnome3, gtk3, wrapGAppsHook
-, ipodSupport ? false, libgpod, gobject-introspection
+, gobject-introspection
 }:
 
 python3Packages.buildPythonApplication rec {
@@ -50,7 +50,7 @@ python3Packages.buildPythonApplication rec {
     podcastparser
     html5lib
     gtk3
-  ] ++ stdenv.lib.optional ipodSupport libgpod;
+  ];
 
   makeFlags = [
     "PREFIX=$(out)"

diff --git a/pkgs/applications/audio/sonata/default.nix b/pkgs/applications/audio/sonata/default.nix
@@ -2,7 +2,7 @@
 , python3Packages, gnome3, gtk3, gsettings-desktop-schemas, gobject-introspection }:
 
 let
-  inherit (python3Packages) buildPythonApplication isPy3k dbus-python pygobject3 mpd2;
+  inherit (python3Packages) buildPythonApplication isPy3k dbus-python pygobject3 mpd2 setuptools;
 in buildPythonApplication rec {
   pname = "sonata";
   version = "1.7b1";
@@ -29,7 +29,7 @@ in buildPythonApplication rec {
   '';
 
   propagatedBuildInputs = [
-    gobject-introspection gtk3 pygobject3
+    gobject-introspection gtk3 pygobject3 setuptools
   ];
 
   # The optional tagpy dependency (for editing metadata) is not yet

diff --git a/pkgs/applications/audio/whipper/default.nix b/pkgs/applications/audio/whipper/default.nix
@@ -3,19 +3,24 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "whipper";
-  version = "0.9.0";
+  version = "0.9.1.dev7+g${stdenv.lib.substring 0 7 src.rev}";
 
   src = fetchFromGitHub {
     owner = "whipper-team";
     repo = "whipper";
-    rev = "v${version}";
-    sha256 = "0x1qsp021i0l5sdcm2kcv9zfwp696k4izhw898v6marf8phll7xc";
+    rev = "9e95f0604fa30ab06445fe46e3bc93bba6092a05";
+    sha256 = "1c2qldw9vxpvdfh5wl6mfcd7zzz3v8r86ffqll311lcp2zin33dg";
   };
 
   pythonPath = with python3.pkgs; [
-    pygobject3 musicbrainzngs urllib3 chardet
-    pycdio setuptools setuptools_scm mutagen
+    musicbrainzngs
+    mutagen
+    pycdio
+    pygobject3
     requests
+    ruamel_yaml
+    setuptools
+    setuptools_scm
   ];
 
   buildInputs = [ libsndfile ];
@@ -36,7 +41,7 @@ python3.pkgs.buildPythonApplication rec {
   ];
 
   preBuild = ''
-    export SETUPTOOLS_SCM_PRETEND_VERSION="v${version}"
+    export SETUPTOOLS_SCM_PRETEND_VERSION="${version}"
   '';
 
   # some tests require internet access

diff --git a/pkgs/applications/graphics/gscan2pdf/default.nix b/pkgs/applications/graphics/gscan2pdf/default.nix
@@ -10,11 +10,11 @@ with stdenv.lib;
 
 perlPackages.buildPerlPackage rec {
   pname = "gscan2pdf";
-  version = "2.5.6";
+  version = "2.6.2";
 
   src = fetchurl {
     url = "mirror://sourceforge/gscan2pdf/${version}/${pname}-${version}.tar.xz";
-    sha256 = "0wp81nsi5jfypabwmjqiamxr739jq5ij79n5fzn5pbw1hg5gcmfz";
+    sha256 = "0z35lglf4anfczizynjp8sd1jpix5mkmm1nh39n1v94l7ahjxsww";
   };
 
   nativeBuildInputs = [ wrapGAppsHook ];

diff --git a/pkgs/applications/graphics/pick-colour-picker/default.nix b/pkgs/applications/graphics/pick-colour-picker/default.nix
@@ -0,0 +1,66 @@
+{ stdenv
+, fetchFromGitHub
+, buildPythonPackage
+, pygobject3
+, pycairo
+, glib
+, gtk3
+, gobject-introspection
+, wrapGAppsHook
+, python
+}:
+
+buildPythonPackage rec {
+  pname = "pick-colour-picker";
+  version = "unstable-2019-10-11"; # "1.5.0-3ec940"
+
+  src = fetchFromGitHub {
+    owner = "stuartlangridge";
+    repo = "ColourPicker";
+    rev = "3ec9406d787ce373f6db0d520ed38a921edb9473";
+    sha256 = "04l8ch9297nhkgcmyhsbg0il424c8vy0isns1c7aypn0zp0dc4zd";
+  };
+
+  nativeBuildInputs = [
+    gobject-introspection
+    wrapGAppsHook
+  ];
+
+  pythonPath = [
+    pygobject3
+    pycairo
+  ];
+
+  buildInputs = [
+    glib
+    gtk3
+  ];
+
+  # https://github.com/NixOS/nixpkgs/issues/56943
+  # this must be false, otherwise the gobject-introspection hook doesn't run
+  strictDeps = false;
+
+  preDistPhases = [ "fixupIconPath" ];
+
+  fixupIconPath = ''
+    pickLoc="$out/${python.sitePackages}/pick"
+    shareLoc=$(echo "$out/${python.sitePackages}/nix/store/"*)
+    mv "$shareLoc/share" "$out/share"
+
+    sed "s|os.environ.get('SNAP'), \"usr\"|'$out'|g" -i "$pickLoc/__main__.py"
+    '';
+
+  meta = with stdenv.lib; {
+    homepage = "https://kryogenix.org/code/pick/";
+    license = licenses.mit;
+    platforms = platforms.linux;
+    description = "A colour picker that remembers where you picked colours from";
+    maintainers = [ maintainers.mkg20001 ];
+
+    longDescription = ''
+      Pick lets you pick colours from anywhere on your screen. Choose the colour you want and Pick remembers it, names it, and shows you a screenshot so you can remember where you got it from.
+
+      Zoom all the way in to pixels to pick just the right one. Show your colours in your choice of format: rgba() or hex, CSS or Gdk or Qt, whichever you prefer. Copy to the clipboard ready for pasting into code or graphics apps.
+      '';
+  };
+}
diff --git a/pkgs/applications/networking/hydroxide/default.nix b/pkgs/applications/networking/hydroxide/default.nix
@@ -0,0 +1,33 @@
+{ lib, buildGoModule, fetchFromGitHub, fetchpatch }:
+
+buildGoModule rec {
+  pname = "hydroxide";
+  version = "0.2.11";
+
+  src = fetchFromGitHub {
+    owner = "emersion";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0rn35iyli80kgj3yn93lrx0ybgc8fhvmkvx1d18ill7r4cmavand";
+  };
+
+  modSha256 = "0b19rcif8yiyvhrsjd3q5nsvr580lklamlphx4dk47n456ckcqfp";
+
+  # FIXME: remove with next release
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/emersion/hydroxide/commit/80e0fa6f3e0154338fb0af8a82ca32ae6281dd15.patch";
+      sha256 = "1xi0clzgz14a7sxnwr0li7sz9p05sfh3zh5iqg2qz5f415k9jknj";
+    })
+  ];
+
+  subPackages = [ "cmd/hydroxide" ];
+
+  meta = with lib; {
+    description = "A third-party, open-source ProtonMail bridge";
+    homepage = "https://github.com/emersion/hydroxide";
+    license = licenses.mit;
+    maintainers = with maintainers; [ filalex77 ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/pkgs/applications/networking/instant-messengers/riot/riot-desktop-package.json b/pkgs/applications/networking/instant-messengers/riot/riot-desktop-package.json
@@ -2,7 +2,7 @@
   "name": "riot-web",
   "productName": "Riot",
   "main": "src/electron-main.js",
-  "version": "1.5.5",
+  "version": "1.5.6",
   "description": "A feature-rich client for Matrix.org",
   "author": "New Vector Ltd.",
   "dependencies": {

diff --git a/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix b/pkgs/applications/networking/instant-messengers/riot/riot-desktop.nix
@@ -6,12 +6,12 @@
 
 let
   executableName = "riot-desktop";
-  version = "1.5.5";
+  version = "1.5.6";
   riot-web-src = fetchFromGitHub {
     owner = "vector-im";
     repo = "riot-web";
     rev = "v${version}";
-    sha256 = "18xhqniwxp1sv49qcd9ah8nyy2n2yliy3wg613raxjl16qvvzxmc";
+    sha256 = "148rg6wc84xy53bj16v5riw78s999ridid59x6v9jas827l0bdpk";
   };
 
 in mkYarnPackage rec {

diff --git a/pkgs/applications/networking/instant-messengers/riot/riot-web.nix b/pkgs/applications/networking/instant-messengers/riot/riot-web.nix
@@ -5,11 +5,11 @@
 
 stdenv.mkDerivation rec {
   pname = "riot-web";
-  version = "1.5.5";
+  version = "1.5.6";
 
   src = fetchurl {
     url = "https://github.com/vector-im/riot-web/releases/download/v${version}/riot-v${version}.tar.gz";
-    sha256 = "0isln25sl5jvvlqvh822w73a4i82x75g1ywf3p9n5m1a5sr9f537";
+    sha256 = "063ynbil038y201skyldj2ysr0hwgwq981w1iw104xd17x31zmn0";
   };
 
   installPhase = let

diff --git a/pkgs/applications/networking/instant-messengers/zoom-us/default.nix b/pkgs/applications/networking/instant-messengers/zoom-us/default.nix
@@ -14,11 +14,11 @@ assert pulseaudioSupport -> libpulseaudio != null;
 let
   inherit (stdenv.lib) concatStringsSep makeBinPath optional;
 
-  version = "3.5.330166.1202";
+  version = "3.5.336627.1216";
   srcs = {
     x86_64-linux = fetchurl {
       url = "https://zoom.us/client/${version}/zoom_x86_64.tar.xz";
-      sha256 = "1fjirl4hmxvy4kp3b0n97mn8sz355ik10297qx6hcr0fhn2v0nig";
+      sha256 = "04r45z2rjjn9gr7bxhfwg49xkyhmpcn5y6pdbkdnrfwzaqzisavz";
     };
   };
 

diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix
@@ -14,6 +14,8 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake ];
   buildInputs = [ zlib python2 ];
 
+  NIX_CFLAGS_COMPILE = [ "-Wno-error=maybe-uninitialized" ];
+
   preConfigure = ''
     sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py
     patchShebangs .
@@ -33,7 +35,6 @@ stdenv.mkDerivation rec {
     homepage = https://github.com/Illumina/strelka;
     maintainers = with maintainers; [ jbedo ];
     platforms = [ "x86_64-linux" ];
-    broken = true;
   };
 
 }
diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix
@@ -11,11 +11,11 @@
 }:
 
 stdenv.mkDerivation rec {
-  name = "R-3.6.1";
+  name = "R-3.6.2";
 
   src = fetchurl {
     url = "https://cran.r-project.org/src/base/R-3/${name}.tar.gz";
-    sha256 = "128kifbq0w25y8aq77w289ddax5i5w2djcfsqgffrb3i7syrxajv";
+    sha256 = "0m69pfi0nxyriyb2yz74xfzaxwfkinnf9kpvf1rz727vvmfa8rdx";
   };
 
   dontUseImakeConfigure = true;

diff --git a/pkgs/build-support/docker/default.nix b/pkgs/build-support/docker/default.nix
@@ -528,11 +528,9 @@ rec {
     created ? "1970-01-01T00:00:01Z",
     # Optional bash script to run on the files prior to fixturizing the layer.
     extraCommands ? "", uid ? 0, gid ? 0,
-    # Docker's lowest maximum layer limit is 42-layers for an old
-    # version of the AUFS graph driver. We pick 24 to ensure there is
-    # plenty of room for extension. I believe the actual maximum is
-    # 128.
-    maxLayers ? 24
+    # We pick 100 to ensure there is plenty of room for extension. I
+    # believe the actual maximum is 128.
+    maxLayers ? 100
   }:
     let
       baseName = baseNameOf name;

diff --git a/pkgs/build-support/docker/examples.nix b/pkgs/build-support/docker/examples.nix
@@ -236,7 +236,6 @@ rec {
     name = "another-layered-image";
     tag = "latest";
     config.Cmd = [ "${pkgs.hello}/bin/hello" ];
-    contents = [ pkgs.hello ];
   };
 
 }