diff --git a/doc/languages-frameworks/gnome.xml b/doc/languages-frameworks/gnome.xml
index 3d69d77a1c84..9c3afe127a48 100644
--- a/doc/languages-frameworks/gnome.xml
+++ b/doc/languages-frameworks/gnome.xml
@@ -74,7 +74,7 @@
 preFixup = ''
   for f in $(find $out/bin/ $out/libexec/ -type f -executable); do
     wrapProgram "$f" \
-      --prefix GIO_EXTRA_MODULES : "${getLib gnome3.dconf}/lib/gio/modules" \
+      --prefix GIO_EXTRA_MODULES : "${getLib dconf}/lib/gio/modules" \
       --prefix XDG_DATA_DIRS : "$out/share" \
       --prefix XDG_DATA_DIRS : "$out/share/gsettings-schemas/${name}" \
       --prefix XDG_DATA_DIRS : "${gsettings-desktop-schemas}/share/gsettings-schemas/${gsettings-desktop-schemas.name}" \
@@ -102,7 +102,7 @@ preFixup = ''
     </listitem>
     <listitem xml:id="ssec-gnome-hooks-dconf">
      <para>
-      <package>gnome3.dconf.lib</package> is a dependency of <package>wrapGAppsHook</package>, which then also adds it to the <envar>GIO_EXTRA_MODULES</envar> variable.
+      <package>dconf.lib</package> is a dependency of <package>wrapGAppsHook</package>, which then also adds it to the <envar>GIO_EXTRA_MODULES</envar> variable.
      </para>
     </listitem>
     <listitem xml:id="ssec-gnome-hooks-hicolor-icon-theme">
diff --git a/nixos/modules/config/no-x-libs.nix b/nixos/modules/config/no-x-libs.nix
index 873b8073fed9..d0f62d05870a 100644
--- a/nixos/modules/config/no-x-libs.nix
+++ b/nixos/modules/config/no-x-libs.nix
@@ -35,6 +35,7 @@ with lib;
       networkmanager-vpnc = super.networkmanager-vpnc.override { withGnome = false; };
       networkmanager-iodine = super.networkmanager-iodine.override { withGnome = false; };
       gobject-introspection = super.gobject-introspection.override { x11Support = false; };
+      polkit = super.polkit.override { withGnome = false; };
     }));
   };
 }
diff --git a/nixos/modules/i18n/input-method/ibus.nix b/nixos/modules/i18n/input-method/ibus.nix
index 8109ef76c402..956c521dde05 100644
--- a/nixos/modules/i18n/input-method/ibus.nix
+++ b/nixos/modules/i18n/input-method/ibus.nix
@@ -55,7 +55,7 @@ in
 
     # Without dconf enabled it is impossible to use IBus
     environment.systemPackages = with pkgs; [
-      gnome3.dconf ibusAutostart
+      dconf ibusAutostart
     ];
 
     environment.variables = {
diff --git a/nixos/modules/programs/dconf.nix b/nixos/modules/programs/dconf.nix
index eeebc3558bdf..e0e2ffd80cff 100644
--- a/nixos/modules/programs/dconf.nix
+++ b/nixos/modules/programs/dconf.nix
@@ -32,13 +32,13 @@ in
     environment.etc = optionals (cfg.profiles != {})
       (mapAttrsToList mkDconfProfile cfg.profiles);
 
-    services.dbus.packages = [ pkgs.gnome3.dconf ];
+    services.dbus.packages = [ pkgs.dconf ];
 
     # For dconf executable
-    environment.systemPackages = [ pkgs.gnome3.dconf ];
+    environment.systemPackages = [ pkgs.dconf ];
 
     # Needed for unwrapped applications
-    environment.variables.GIO_EXTRA_MODULES = mkIf cfg.enable [ "${pkgs.gnome3.dconf.lib}/lib/gio/modules" ];
+    environment.variables.GIO_EXTRA_MODULES = mkIf cfg.enable [ "${pkgs.dconf.lib}/lib/gio/modules" ];
   };
 
 }
diff --git a/nixos/modules/services/x11/display-managers/gdm.nix b/nixos/modules/services/x11/display-managers/gdm.nix
index 912ec5bd38ed..29a80aac6e68 100644
--- a/nixos/modules/services/x11/display-managers/gdm.nix
+++ b/nixos/modules/services/x11/display-managers/gdm.nix
@@ -281,7 +281,7 @@ in
       customDconfDb = pkgs.stdenv.mkDerivation {
         name = "gdm-dconf-db";
         buildCommand = ''
-          ${pkgs.gnome3.dconf}/bin/dconf compile $out ${customDconf}/dconf
+          ${pkgs.dconf}/bin/dconf compile $out ${customDconf}/dconf
         '';
       };
     in pkgs.stdenv.mkDerivation {
diff --git a/pkgs/applications/audio/spotify-tui/default.nix b/pkgs/applications/audio/spotify-tui/default.nix
index 606abc86ae28..bd4aaf5a2d63 100644
--- a/pkgs/applications/audio/spotify-tui/default.nix
+++ b/pkgs/applications/audio/spotify-tui/default.nix
@@ -1,21 +1,22 @@
-{ stdenv, fetchFromGitHub, rustPlatform, pkgconfig, openssl, Security }:
+{ stdenv, fetchFromGitHub, rustPlatform, pkgconfig, openssl, python3, libxcb, AppKit, Security }:
 
 rustPlatform.buildRustPackage rec {
   pname = "spotify-tui";
-  version = "0.9.0";
+  version = "0.10.0";
 
   src = fetchFromGitHub {
     owner = "Rigellute";
     repo = "spotify-tui";
     rev = "v${version}";
-    sha256 = "1bbh9df4gfgb5pqavgvmy8fqnr2j5rbqbanv0y31j4i0kv2wrh6a";
+    sha256 = "10wrlfi50lsf6qjsi9qklw2mk2fbf0jib7f841v842l9k9zw0hrg";
   };
 
-  cargoSha256 = "1rb4dl9zn3xx2yrapx5cfsli93ggmdq8w9fqi8cy8giyja1mnqfl";
+  cargoSha256 = "140m3pryvbc96xvl5ymz68msrx93rmvvy0y8skvc40yxwl401inc";
 
-  nativeBuildInputs = [ pkgconfig ];
+  nativeBuildInputs = [ pkgconfig python3 ];
   buildInputs = [ openssl ]
-    ++ stdenv.lib.optional stdenv.isDarwin Security;
+  	++ stdenv.lib.optional stdenv.isLinux libxcb
+    ++ stdenv.lib.optionals stdenv.isDarwin [ AppKit Security ];
 
   meta = with stdenv.lib; {
     description = "Spotify for the terminal written in Rust";
diff --git a/pkgs/applications/editors/jucipp/default.nix b/pkgs/applications/editors/jucipp/default.nix
index cb9f10281c70..70b2d3c148db 100644
--- a/pkgs/applications/editors/jucipp/default.nix
+++ b/pkgs/applications/editors/jucipp/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchgit, gnome3, gtksourceview3, at-spi2-core, gtksourceviewmm,
+{ stdenv, fetchgit, dconf, gtksourceview3, at-spi2-core, gtksourceviewmm,
   boost, epoxy, cmake, aspell, llvmPackages, libgit2, pkgconfig, pcre,
   libXdmcp, libxkbcommon, libpthreadstubs, wrapGAppsHook, aspellDicts, gtkmm3,
   coreutils, glibc, dbus, openssl, libxml2, gnumake, ctags }:
@@ -44,7 +44,7 @@ stdenv.mkDerivation rec {
     gtksourceviewmm
     llvmPackages.clang.cc
     llvmPackages.lldb
-    gnome3.dconf
+    dconf
   ];
 
 
diff --git a/pkgs/applications/graphics/gthumb/default.nix b/pkgs/applications/graphics/gthumb/default.nix
index d7c0f0e0a0cf..f0057f3a1a88 100644
--- a/pkgs/applications/graphics/gthumb/default.nix
+++ b/pkgs/applications/graphics/gthumb/default.nix
@@ -33,11 +33,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gthumb";
-  version = "3.8.1";
+  version = "3.8.2";
 
   src = fetchurl {
     url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
-    sha256 = "184zn79w4s9y1zy42ar31p3jsg8rmkxy8k6iry51nz8aizbcs7jb";
+    sha256 = "15wqks35ks5dm7zj046dfd45vvrilan2ayfy2sxiprv7q74cip2q";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/misc/onboard/default.nix b/pkgs/applications/misc/onboard/default.nix
index 79e3317e64da..1e578cde512a 100644
--- a/pkgs/applications/misc/onboard/default.nix
+++ b/pkgs/applications/misc/onboard/default.nix
@@ -7,7 +7,7 @@
 , bash
 , glib
 , glibcLocales
-, gnome3
+, dconf
 , gobject-introspection
 , gsettings-desktop-schemas
 , gtk3
@@ -66,7 +66,7 @@ python3.pkgs.buildPythonApplication rec {
   buildInputs = [
     bash
     glib
-    gnome3.dconf
+    dconf
     gsettings-desktop-schemas
     gtk3
     hunspell
@@ -89,7 +89,7 @@ python3.pkgs.buildPythonApplication rec {
   ];
 
   propagatedUserEnvPkgs = [
-    gnome3.dconf
+    dconf
   ];
 
   checkInputs = [
diff --git a/pkgs/applications/misc/plank/default.nix b/pkgs/applications/misc/plank/default.nix
index dfc92e38f63c..0ae9e7379e7c 100644
--- a/pkgs/applications/misc/plank/default.nix
+++ b/pkgs/applications/misc/plank/default.nix
@@ -3,6 +3,7 @@
 , vala
 , atk
 , cairo
+, dconf
 , glib
 , gnome3
 , gtk3
@@ -51,7 +52,7 @@ stdenv.mkDerivation rec {
     gdk-pixbuf
     glib
     gnome-menus
-    gnome3.dconf
+    dconf
     gtk3
     libX11
     libXfixes
diff --git a/pkgs/applications/misc/tilix/default.nix b/pkgs/applications/misc/tilix/default.nix
index 922b3fd20286..2fa193fc8e7a 100644
--- a/pkgs/applications/misc/tilix/default.nix
+++ b/pkgs/applications/misc/tilix/default.nix
@@ -6,7 +6,7 @@
 , python3
 , pkgconfig
 , dmd
-, gnome3
+, dconf
 , dbus
 , gsettings-desktop-schemas
 , desktop-file-utils
@@ -47,7 +47,7 @@ stdenv.mkDerivation {
   buildInputs = [
     dbus
     gettext
-    gnome3.dconf
+    dconf
     gsettings-desktop-schemas
     gtkd
     libsecret
diff --git a/pkgs/applications/networking/cawbird/default.nix b/pkgs/applications/networking/cawbird/default.nix
index 5179cc9090d6..6462dd499493 100644
--- a/pkgs/applications/networking/cawbird/default.nix
+++ b/pkgs/applications/networking/cawbird/default.nix
@@ -11,7 +11,7 @@
 , meson
 , ninja
 , pkgconfig
-, gnome3
+, dconf
 , gst_all_1
 , wrapGAppsHook
 , gobject-introspection
@@ -47,7 +47,7 @@ stdenv.mkDerivation rec {
     sqlite
     libsoup
     gettext
-    gnome3.dconf
+    dconf
     gspell
     glib-networking
   ] ++ (with gst_all_1; [
diff --git a/pkgs/applications/networking/instant-messengers/telepathy/idle/default.nix b/pkgs/applications/networking/instant-messengers/telepathy/idle/default.nix
index 3368ec1124eb..f3d1e6cfd750 100644
--- a/pkgs/applications/networking/instant-messengers/telepathy/idle/default.nix
+++ b/pkgs/applications/networking/instant-messengers/telepathy/idle/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, glib, gnome3, pkgconfig, dbus-glib, telepathy-glib, libxslt, makeWrapper }:
+{ stdenv, fetchurl, glib, dconf, pkgconfig, dbus-glib, telepathy-glib, libxslt, makeWrapper }:
 
 stdenv.mkDerivation rec {
   pname = "telepathy-idle";
@@ -10,11 +10,11 @@ stdenv.mkDerivation rec {
   };
 
   nativeBuildInputs = [ pkgconfig ];
-  buildInputs = [ glib telepathy-glib dbus-glib libxslt telepathy-glib.python (stdenv.lib.getLib gnome3.dconf) makeWrapper ];
+  buildInputs = [ glib telepathy-glib dbus-glib libxslt telepathy-glib.python (stdenv.lib.getLib dconf) makeWrapper ];
 
   preFixup = ''
     wrapProgram "$out/libexec/telepathy-idle" \
-      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib gnome3.dconf}/lib/gio/modules"
+      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib dconf}/lib/gio/modules"
   '';
 
   meta = {
diff --git a/pkgs/applications/networking/instant-messengers/telepathy/logger/default.nix b/pkgs/applications/networking/instant-messengers/telepathy/logger/default.nix
index 8c777cd3f7d6..af0ca1589e5a 100644
--- a/pkgs/applications/networking/instant-messengers/telepathy/logger/default.nix
+++ b/pkgs/applications/networking/instant-messengers/telepathy/logger/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchurl, dbus-glib, libxml2, sqlite, telepathy-glib, pkgconfig
-, gnome3, makeWrapper, intltool, libxslt, gobject-introspection, dbus }:
+, dconf, makeWrapper, intltool, libxslt, gobject-introspection, dbus }:
 
 stdenv.mkDerivation rec {
   project = "telepathy-logger";
@@ -22,7 +22,7 @@ stdenv.mkDerivation rec {
 
   preFixup = ''
     wrapProgram "$out/libexec/telepathy-logger" \
-      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib gnome3.dconf}/lib/gio/modules" \
+      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib dconf}/lib/gio/modules" \
       --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH"
   '';
 
diff --git a/pkgs/applications/networking/instant-messengers/telepathy/mission-control/default.nix b/pkgs/applications/networking/instant-messengers/telepathy/mission-control/default.nix
index 6bbe82c4a28e..ef842275a5de 100644
--- a/pkgs/applications/networking/instant-messengers/telepathy/mission-control/default.nix
+++ b/pkgs/applications/networking/instant-messengers/telepathy/mission-control/default.nix
@@ -1,7 +1,7 @@
 { stdenv
 , fetchurl
 , pkgconfig
-, gnome3
+, dconf
 , telepathy-glib
 , python3
 , libxslt
@@ -39,7 +39,7 @@ stdenv.mkDerivation rec {
 
   preFixup = ''
     wrapProgram "$lib/libexec/mission-control-5" \
-      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib gnome3.dconf}/lib/gio/modules" \
+      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib dconf}/lib/gio/modules" \
       --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH"
   '';
 
diff --git a/pkgs/applications/networking/p2p/transmission-remote-gtk/default.nix b/pkgs/applications/networking/p2p/transmission-remote-gtk/default.nix
index 55bdced74b52..68babaddd1bc 100644
--- a/pkgs/applications/networking/p2p/transmission-remote-gtk/default.nix
+++ b/pkgs/applications/networking/p2p/transmission-remote-gtk/default.nix
@@ -1,5 +1,5 @@
 { stdenv, autoconf, automake, libtool, wrapGAppsHook, fetchFromGitHub, pkgconfig
-, intltool, gtk3, json-glib, curl, glib, autoconf-archive, appstream-glib }:
+, intltool, gtk3, json-glib, curl, glib, autoconf-archive, appstream-glib, fetchpatch }:
 
 
 stdenv.mkDerivation rec {
@@ -13,6 +13,13 @@ stdenv.mkDerivation rec {
     sha256 = "1pipc1f94jdppv597mqmcj2kw2rdvaqcbl512v7z8vir76p1a7gk";
   };
 
+  patches = [
+    (fetchpatch {
+      url = "https://github.com/transmission-remote-gtk/transmission-remote-gtk/commit/0f5cc8a9942e220ea0f7d0b17db4a78d094e3b65.patch";
+      sha256 = "195rsjpbc0gzmr9bycvq4mra7abp3hd9by3a5vvcmxsh5ipikycf";
+    })
+  ];
+
   preConfigure = "./autogen.sh";
 
   nativeBuildInputs= [
diff --git a/pkgs/applications/networking/remote/citrix-workspace/default.nix b/pkgs/applications/networking/remote/citrix-workspace/default.nix
index 26e8cf59a9e9..dc6f85f2130e 100644
--- a/pkgs/applications/networking/remote/citrix-workspace/default.nix
+++ b/pkgs/applications/networking/remote/citrix-workspace/default.nix
@@ -9,6 +9,7 @@
 , makeDesktopItem
 , tzdata
 , cacert
+, dconf
 , glib
 , gtk2
 , atk
@@ -137,7 +138,7 @@ let
         gdk-pixbuf
         cairo
         pango
-        gnome3.dconf
+        dconf
         xorg.libX11
         xorg.libXext
         xorg.libXrender
diff --git a/pkgs/applications/office/zotero/default.nix b/pkgs/applications/office/zotero/default.nix
index 8ebf0e666ffe..a84d9c1b169d 100644
--- a/pkgs/applications/office/zotero/default.nix
+++ b/pkgs/applications/office/zotero/default.nix
@@ -5,6 +5,7 @@
 , cups
 , dbus-glib
 , dbus
+, dconf
 , fontconfig
 , freetype
 , gdk-pixbuf
@@ -41,7 +42,7 @@ stdenv.mkDerivation rec {
     sha256 = "1dgxzprpb8f5wpmvlvkxix0xxckfgjsi3wfcy9mb221a17cv0029";
   };
 
-  buildInputs= [ wrapGAppsHook gsettings-desktop-schemas gtk3 gnome3.adwaita-icon-theme gnome3.dconf ];
+  buildInputs= [ wrapGAppsHook gsettings-desktop-schemas gtk3 gnome3.adwaita-icon-theme dconf ];
 
   phases = [ "unpackPhase" "patchPhase" "installPhase" "fixupPhase" ];
 
diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix
index de93ae5d7829..1a6555e0d634 100644
--- a/pkgs/applications/science/biology/kallisto/default.nix
+++ b/pkgs/applications/science/biology/kallisto/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "kallisto";
-  version = "0.46.0";
+  version = "0.46.1";
 
   src = fetchFromGitHub {
     repo = "kallisto";
     owner = "pachterlab";
     rev = "v${version}";
-    sha256 = "09vgdqwpigl4x3sdw5vjfyknsllkli339mh8xapbf7ldm0jldfn9";
+    sha256 = "09ldgy70wziw51ma4a3b7vyrphzf2v1cnq1j5r1wwgfmx8fgbh2z";
   };
 
   nativeBuildInputs = [ autoconf cmake ];
diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix
index 64c1c3daba82..9b52e8c50519 100644
--- a/pkgs/applications/science/electronics/gtkwave/default.nix
+++ b/pkgs/applications/science/electronics/gtkwave/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "gtkwave";
-  version = "3.3.102";
+  version = "3.3.103";
 
   src = fetchurl {
     url    = "mirror://sourceforge/gtkwave/${pname}-${version}.tar.gz";
-    sha256 = "1izyfx6b1n9nr08c7q0gkgcf0q04bb4qz92ckwh74n5l5nwprfw0";
+    sha256 = "1xzaxqbabj4sb4n10yki5acglx3736pwl3kwlq4k7i96rzvsn9f3";
   };
 
   nativeBuildInputs = [ pkgconfig ];
diff --git a/pkgs/applications/science/electronics/verilator/default.nix b/pkgs/applications/science/electronics/verilator/default.nix
index b59f628dfe9f..98deda0ae6b2 100644
--- a/pkgs/applications/science/electronics/verilator/default.nix
+++ b/pkgs/applications/science/electronics/verilator/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "verilator";
-  version = "4.020";
+  version = "4.022";
 
   src = fetchurl {
     url    = "https://www.veripool.org/ftp/${pname}-${version}.tgz";
-    sha256 = "06n3vds762vza4byrav0j3kp3aivvadndkgw7nirvasclp19zmxb";
+    sha256 = "1sj0qzl387pl2ygii3ssx35c3m601nb07j16lqj5zcxzhcg62i9p";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/applications/science/math/pspp/default.nix b/pkgs/applications/science/math/pspp/default.nix
index c53e87caa9ad..3c263916a0eb 100644
--- a/pkgs/applications/science/math/pspp/default.nix
+++ b/pkgs/applications/science/math/pspp/default.nix
@@ -1,7 +1,6 @@
 { stdenv, fetchurl, libxml2, readline, zlib, perl, cairo, gtk3, gsl
-, pkgconfig, gtksourceview, pango, gettext
+, pkgconfig, gtksourceview, pango, gettext, dconf
 , makeWrapper, gsettings-desktop-schemas, hicolor-icon-theme
-, gnome3
 }:
 
 stdenv.mkDerivation rec {
@@ -26,7 +25,7 @@ stdenv.mkDerivation rec {
      --prefix XDG_DATA_DIRS : "$out/share" \
      --prefix XDG_DATA_DIRS : "$XDG_ICON_DIRS" \
      --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH" \
-     --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib gnome3.dconf}/lib/gio/modules"
+     --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib dconf}/lib/gio/modules"
   '';
 
   meta = {
diff --git a/pkgs/applications/search/catfish/default.nix b/pkgs/applications/search/catfish/default.nix
index bce5795a9c7e..3190c5e5d10f 100644
--- a/pkgs/applications/search/catfish/default.nix
+++ b/pkgs/applications/search/catfish/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchurl, file, which, intltool, gobject-introspection,
-  findutils, xdg_utils, gnome3, gtk3, pythonPackages,
+  findutils, xdg_utils, dconf, gtk3, pythonPackages,
   wrapGAppsHook
 }:
 
@@ -25,7 +25,7 @@ pythonPackages.buildPythonApplication rec {
 
   buildInputs = [
     gtk3
-    gnome3.dconf
+    dconf
     pythonPackages.pyxdg
     pythonPackages.ptyprocess
     pythonPackages.pycairo
diff --git a/pkgs/desktops/deepin/deepin-desktop-schemas/default.nix b/pkgs/desktops/deepin/deepin-desktop-schemas/default.nix
index fe2062a3d965..745b2992c5fb 100644
--- a/pkgs/desktops/deepin/deepin-desktop-schemas/default.nix
+++ b/pkgs/desktops/deepin/deepin-desktop-schemas/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, python3, gnome3, glib, deepin-gtk-theme,
+{ stdenv, fetchFromGitHub, python3, dconf, glib, deepin-gtk-theme,
   deepin-icon-theme, deepin-sound-theme, deepin-wallpapers, deepin }:
 
 stdenv.mkDerivation rec {
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
-    gnome3.dconf
+    dconf
     deepin-gtk-theme
     deepin-icon-theme
     deepin-sound-theme
diff --git a/pkgs/desktops/gnome-3/core/dconf-editor/default.nix b/pkgs/desktops/gnome-3/core/dconf-editor/default.nix
index c7a126034f2b..5934f56274cb 100644
--- a/pkgs/desktops/gnome-3/core/dconf-editor/default.nix
+++ b/pkgs/desktops/gnome-3/core/dconf-editor/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, meson, ninja, vala, libxslt, pkgconfig, glib, gtk3, gnome3, python3
+{ stdenv, fetchurl, meson, ninja, vala, libxslt, pkgconfig, glib, gtk3, gnome3, python3, dconf
 , libxml2, gettext, docbook_xsl, wrapGAppsHook, gobject-introspection }:
 
 let
@@ -17,7 +17,7 @@ in stdenv.mkDerivation rec {
     gettext docbook_xsl libxml2 gobject-introspection python3
   ];
 
-  buildInputs = [ glib gtk3 gnome3.dconf ];
+  buildInputs = [ glib gtk3 dconf ];
 
   postPatch = ''
     chmod +x meson_post_install.py
diff --git a/pkgs/desktops/gnome-3/core/gdm/default.nix b/pkgs/desktops/gnome-3/core/gdm/default.nix
index 9d1602dfccd3..ba660a64418c 100644
--- a/pkgs/desktops/gnome-3/core/gdm/default.nix
+++ b/pkgs/desktops/gnome-3/core/gdm/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchurl, substituteAll, pkgconfig, glib, itstool, libxml2, xorg
-, accountsservice, libX11, gnome3, systemd, autoreconfHook
+, accountsservice, libX11, gnome3, systemd, autoreconfHook, dconf
 , gtk3, libcanberra-gtk3, pam, libtool, gobject-introspection, plymouth
 , librsvg, coreutils, xwayland, nixos-icons, fetchpatch }:
 
@@ -43,7 +43,7 @@ stdenv.mkDerivation rec {
     "--with-udevdir=$(out)/lib/udev"
   ];
 
-  nativeBuildInputs = [ pkgconfig libxml2 itstool autoreconfHook libtool gnome3.dconf ];
+  nativeBuildInputs = [ pkgconfig libxml2 itstool autoreconfHook libtool dconf ];
   buildInputs = [
     glib accountsservice systemd
     gobject-introspection libX11 gtk3
diff --git a/pkgs/desktops/gnome-3/default.nix b/pkgs/desktops/gnome-3/default.nix
index a4e594331c3a..605ef95656c3 100644
--- a/pkgs/desktops/gnome-3/default.nix
+++ b/pkgs/desktops/gnome-3/default.nix
@@ -35,7 +35,6 @@ lib.makeScope pkgs.newScope (self: with self; {
 
   caribou = callPackage ./core/caribou { };
 
-  dconf = callPackage ./core/dconf { };
   dconf-editor = callPackage ./core/dconf-editor { };
 
   empathy = callPackage ./core/empathy { };
@@ -359,4 +358,6 @@ lib.makeScope pkgs.newScope (self: with self; {
   inherit (pkgs) gjs; # added 2019-01-05
 
   inherit (pkgs) yelp-tools; # added 2019-11-20
+
+  inherit (pkgs) dconf; # added 2019-11-30
 })
diff --git a/pkgs/desktops/gnome-3/extensions/caffeine/default.nix b/pkgs/desktops/gnome-3/extensions/caffeine/default.nix
index 8cf9fb9f0e63..1761887f8fb1 100644
--- a/pkgs/desktops/gnome-3/extensions/caffeine/default.nix
+++ b/pkgs/desktops/gnome-3/extensions/caffeine/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "gnome-shell-extension-caffeine";
-  version = "unstable-2019-04-02";
+  version = "33";
 
   src = fetchFromGitHub {
     owner = "eonpatapon";
     repo = "gnome-shell-extension-caffeine";
-    rev = "a6b37dee108cddf50a0f0a19f0101854a75bf173";
-    sha256 = "1j3q12j36v97551sjb0c8qc8zr7a7gmxibygczryfdfmwjzp6icl";
+    rev = "v${version}";
+    sha256 = "1v74xfk7csgc4kw1fg75brmhk2aby3d453ksnmj4k8ivyxkzxmfg";
   };
 
   uuid = "caffeine@patapon.info";
@@ -32,6 +32,5 @@ stdenv.mkDerivation rec {
     license = licenses.gpl2;
     maintainers = with maintainers; [ eperuffo ];
     homepage = https://github.com/eonpatapon/gnome-shell-extension-caffeine;
-    broken = versionAtLeast gnome3.gnome-shell.version "3.32"; # Doesn't support 3.34
   };
 }
diff --git a/pkgs/desktops/mate/mate-control-center/default.nix b/pkgs/desktops/mate/mate-control-center/default.nix
index e16effed670c..836588e7e2b2 100644
--- a/pkgs/desktops/mate/mate-control-center/default.nix
+++ b/pkgs/desktops/mate/mate-control-center/default.nix
@@ -1,6 +1,6 @@
 { stdenv, fetchurl, pkgconfig, intltool, itstool, libxml2, dbus-glib,
   libxklavier, libcanberra-gtk3, librsvg, libappindicator-gtk3,
-  desktop-file-utils, gnome3, gtk3, mate, hicolor-icon-theme, wrapGAppsHook
+  desktop-file-utils, dconf, gtk3, mate, hicolor-icon-theme, wrapGAppsHook
 }:
 
 stdenv.mkDerivation rec {
@@ -28,7 +28,7 @@ stdenv.mkDerivation rec {
     librsvg
     libappindicator-gtk3
     gtk3
-    gnome3.dconf
+    dconf
     hicolor-icon-theme
     mate.mate-desktop
     mate.libmatekbd
diff --git a/pkgs/desktops/mate/mate-desktop/default.nix b/pkgs/desktops/mate/mate-desktop/default.nix
index 8d157a201bed..35cacee5a4dc 100644
--- a/pkgs/desktops/mate/mate-desktop/default.nix
+++ b/pkgs/desktops/mate/mate-desktop/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, pkgconfig, intltool, isocodes, gnome3, gtk3, wrapGAppsHook }:
+{ stdenv, fetchurl, pkgconfig, intltool, isocodes, gnome3, gtk3, dconf, wrapGAppsHook }:
 
 stdenv.mkDerivation rec {
   pname = "mate-desktop";
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
-    gnome3.dconf
+    dconf
     gtk3
     isocodes
   ];
diff --git a/pkgs/desktops/mate/mate-panel/default.nix b/pkgs/desktops/mate/mate-panel/default.nix
index db45dc9c4725..09744ecfdaa8 100644
--- a/pkgs/desktops/mate/mate-panel/default.nix
+++ b/pkgs/desktops/mate/mate-panel/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, pkgconfig, intltool, itstool, glib, libwnck3, librsvg, libxml2, gnome3, gtk3, mate, hicolor-icon-theme, gobject-introspection, wrapGAppsHook }:
+{ stdenv, fetchurl, pkgconfig, intltool, itstool, glib, libwnck3, librsvg, libxml2, dconf, gtk3, mate, hicolor-icon-theme, gobject-introspection, wrapGAppsHook }:
 
 stdenv.mkDerivation rec {
   pname = "mate-panel";
@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
     librsvg
     libxml2
     gtk3
-    gnome3.dconf
+    dconf
     mate.libmateweather
     mate.mate-desktop
     mate.mate-menus
diff --git a/pkgs/desktops/mate/mate-settings-daemon/default.nix b/pkgs/desktops/mate/mate-settings-daemon/default.nix
index 73dd7011d49d..b7385839242a 100644
--- a/pkgs/desktops/mate/mate-settings-daemon/default.nix
+++ b/pkgs/desktops/mate/mate-settings-daemon/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchurl, pkgconfig, intltool, glib, dbus-glib, libxklavier,
-  libcanberra-gtk3, libnotify, nss, polkit, gnome3, gtk3, mate,
+  libcanberra-gtk3, libnotify, nss, polkit, dconf, gtk3, mate,
   pulseaudioSupport ? stdenv.config.pulseaudio or true, libpulseaudio,
   wrapGAppsHook, fetchpatch, autoreconfHook }:
 
@@ -35,7 +35,7 @@ stdenv.mkDerivation rec {
     nss
     polkit
     gtk3
-    gnome3.dconf
+    dconf
     mate.mate-desktop
     mate.libmatekbd
     mate.libmatemixer
diff --git a/pkgs/desktops/mate/mate-terminal/default.nix b/pkgs/desktops/mate/mate-terminal/default.nix
index 7ec9944aa0e1..704db60ff15c 100644
--- a/pkgs/desktops/mate/mate-terminal/default.nix
+++ b/pkgs/desktops/mate/mate-terminal/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, pkgconfig, intltool, glib, itstool, libxml2, mate, gnome3, gtk3, vte, wrapGAppsHook }:
+{ stdenv, fetchurl, pkgconfig, intltool, glib, itstool, libxml2, mate, dconf, gtk3, vte, wrapGAppsHook }:
 
 stdenv.mkDerivation rec {
   pname = "mate-terminal";
@@ -18,7 +18,7 @@ stdenv.mkDerivation rec {
 
      vte
      gtk3
-     gnome3.dconf
+     dconf
   ];
 
   nativeBuildInputs = [
diff --git a/pkgs/desktops/xfce/default.nix b/pkgs/desktops/xfce/default.nix
index 07773523b3e0..fa666bb556d0 100644
--- a/pkgs/desktops/xfce/default.nix
+++ b/pkgs/desktops/xfce/default.nix
@@ -3,8 +3,6 @@
 lib.makeScope pkgs.newScope (self: with self; {
   #### NixOS support
 
-  inherit (pkgs.gnome3) dconf;
-
   mkXfceDerivation = callPackage ./mkXfceDerivation.nix { };
 
   automakeAddFlags = pkgs.makeSetupHook { } ./automakeAddFlags.sh;
@@ -217,4 +215,7 @@ lib.makeScope pkgs.newScope (self: with self; {
   thunar-bare = thunar.override {
     thunarPlugins = [];
   };
+
+  # added 2019-11-30
+  inherit (pkgs) dconf;
 })
diff --git a/pkgs/development/compilers/intel-graphics-compiler/default.nix b/pkgs/development/compilers/intel-graphics-compiler/default.nix
index 183e1f2a0850..a365761b014f 100644
--- a/pkgs/development/compilers/intel-graphics-compiler/default.nix
+++ b/pkgs/development/compilers/intel-graphics-compiler/default.nix
@@ -24,13 +24,13 @@ in
 
 stdenv.mkDerivation rec {
   pname = "intel-graphics-compiler";
-  version = "1.0.2714.1";
+  version = "1.0.2878";
 
   src = fetchFromGitHub {
     owner = "intel";
     repo = "intel-graphics-compiler";
     rev = "igc-${version}";
-    sha256 = "0ys03sv08fg8q06lb6k5088xirnwms4nzazxp3kbdjm973n7imxc";
+    sha256 = "0rgij1013fy2x2szfchy3z6390mjfqw3nz4zprcb5v2v6mpvcj4l";
   };
 
   nativeBuildInputs = [ clang cmake bison flex llvm python ];
diff --git a/pkgs/development/interpreters/jimtcl/default.nix b/pkgs/development/interpreters/jimtcl/default.nix
index 91b4c0b9a9e6..09d7fa622fc1 100644
--- a/pkgs/development/interpreters/jimtcl/default.nix
+++ b/pkgs/development/interpreters/jimtcl/default.nix
@@ -5,35 +5,53 @@ let
 
 in stdenv.mkDerivation rec {
   pname = "jimtcl";
-  version = "0.78";
+  version = "0.79";
 
   src = fetchFromGitHub {
     owner = "msteveb";
     repo = "jimtcl";
     rev = version;
-    sha256 = "1nrjxjfh69i35ig8sxdlal4ydd3cl0x68c05s6svnf1y2i1bl23j";
+    sha256 = "1k88hz0v3bi19xdvlp0i9nsx38imzwpjh632w7326zwbv2wldf0h";
   };
 
-  buildInputs = [
-    sqlite readline asciidoc SDL SDL_gfx
+  nativeBuildInputs = [
+    asciidoc
   ];
 
-  NIX_CFLAGS_COMPILE = makeSDLFlags [ SDL SDL_gfx ];
+  buildInputs = [
+    sqlite readline SDL SDL_gfx
+  ];
 
   configureFlags = [
+    "--shared"
     "--with-ext=oo"
     "--with-ext=tree"
     "--with-ext=binary"
     "--with-ext=sqlite3"
     "--with-ext=readline"
     "--with-ext=sdl"
+    "--with-ext=json"
     "--enable-utf8"
     "--ipv6"
   ];
 
+  NIX_CFLAGS_COMPILE = makeSDLFlags [ SDL SDL_gfx ];
+
+  enableParallelBuilding = true;
+
+  doCheck = true;
+  preCheck = ''
+    # test exec2-3.2 fails depending on platform or sandboxing (?)
+    rm tests/exec2.test
+  '';
+
+  postInstall = ''
+    ln -sr $out/lib/libjim.so.${version} $out/lib/libjim.so
+  '';
+
   meta = {
     description = "An open source small-footprint implementation of the Tcl programming language";
-    homepage = http://jim.tcl.tk/;
+    homepage = "http://jim.tcl.tk/";
     license = stdenv.lib.licenses.bsd2;
     platforms = stdenv.lib.platforms.all;
     maintainers = with stdenv.lib.maintainers; [ dbohdan vrthra ];
diff --git a/pkgs/development/libraries/at-spi2-core/default.nix b/pkgs/development/libraries/at-spi2-core/default.nix
index bda809b1a5a9..84a8a6b90265 100644
--- a/pkgs/development/libraries/at-spi2-core/default.nix
+++ b/pkgs/development/libraries/at-spi2-core/default.nix
@@ -10,6 +10,7 @@
 
 , dbus
 , glib
+, dconf
 , libX11
 , libXtst # at-spi2-core can be build without X support, but due it is a client-side library, GUI-less usage is a very rare case
 , libXi
@@ -48,7 +49,7 @@ stdenv.mkDerivation rec {
   postFixup = ''
     # Cannot use wrapGAppsHook'due to a dependency cycle
     wrapProgram $out/libexec/at-spi-bus-launcher \
-      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib gnome3.dconf}/lib/gio/modules" \
+      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib dconf}/lib/gio/modules" \
       --prefix XDG_DATA_DIRS : ${gsettings-desktop-schemas}/share/gsettings-schemas/${gsettings-desktop-schemas.name}
   '';
 
diff --git a/pkgs/desktops/gnome-3/core/dconf/default.nix b/pkgs/development/libraries/dconf/default.nix
similarity index 100%
rename from pkgs/desktops/gnome-3/core/dconf/default.nix
rename to pkgs/development/libraries/dconf/default.nix
diff --git a/pkgs/development/libraries/flatpak/default.nix b/pkgs/development/libraries/flatpak/default.nix
index c0cbb763d36f..945f1d4931fb 100644
--- a/pkgs/development/libraries/flatpak/default.nix
+++ b/pkgs/development/libraries/flatpak/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchurl, autoreconfHook, docbook_xml_dtd_412, docbook_xml_dtd_42, docbook_xml_dtd_43, docbook_xsl, which, libxml2
 , gobject-introspection, gtk-doc, intltool, libxslt, pkgconfig, xmlto, appstream-glib, substituteAll, glibcLocales, yacc, xdg-dbus-proxy, p11-kit
 , bubblewrap, bzip2, dbus, glib, gpgme, json-glib, libarchive, libcap, libseccomp, coreutils, gettext, hicolor-icon-theme, fuse, nixosTests
-, libsoup, lzma, ostree, polkit, python3, systemd, xorg, valgrind, glib-networking, wrapGAppsHook, gnome3, gsettings-desktop-schemas, librsvg }:
+, libsoup, lzma, ostree, polkit, python3, systemd, xorg, valgrind, glib-networking, wrapGAppsHook, dconf, gsettings-desktop-schemas, librsvg }:
 
 stdenv.mkDerivation rec {
   pname = "flatpak";
@@ -42,7 +42,7 @@ stdenv.mkDerivation rec {
   ];
 
   buildInputs = [
-    bubblewrap bzip2 dbus gnome3.dconf glib gpgme json-glib libarchive libcap libseccomp
+    bubblewrap bzip2 dbus dconf glib gpgme json-glib libarchive libcap libseccomp
     libsoup lzma ostree polkit python3 systemd xorg.libXau fuse
     gsettings-desktop-schemas glib-networking
     librsvg # for flatpak-validate-icon
diff --git a/pkgs/development/python-modules/rpy2/2.nix b/pkgs/development/python-modules/rpy2/2.nix
new file mode 100644
index 000000000000..aef184d4afc2
--- /dev/null
+++ b/pkgs/development/python-modules/rpy2/2.nix
@@ -0,0 +1,108 @@
+{ lib
+, python
+, buildPythonPackage
+, fetchPypi
+, isPyPy
+, isPy27
+, readline
+, R
+, rWrapper
+, rPackages
+, pcre
+, lzma
+, bzip2
+, zlib
+, icu
+, singledispatch
+, six
+, jinja2
+, pytz
+, numpy
+, pytest
+, mock
+, extraRPackages ? []
+}:
+
+buildPythonPackage rec {
+    version = "2.8.6"; # python2 support dropped in 2.9.x
+    pname = "rpy2";
+    disabled = isPyPy;
+    src = fetchPypi {
+      inherit version pname;
+      sha256 = "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80";
+    };
+    buildInputs = [
+      readline
+      R
+      pcre
+      lzma
+      bzip2
+      zlib
+      icu
+    ] ++ (with rPackages; [
+      # packages expected by the test framework
+      ggplot2
+      dplyr
+      RSQLite
+      broom
+      DBI
+      dbplyr
+      hexbin
+      lme4
+      tidyr
+
+      # is in upstream's `requires` although it shouldn't be -- this is easier than patching it away
+      pytest
+    ]) ++ extraRPackages ++ rWrapper.recommendedPackages;
+
+    nativeBuildInputs = [
+      R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
+    ];
+
+    patches = [
+      # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
+      # This patch sets R_LIBS_SITE when rpy2 is imported.
+      ./r-libs-site.patch
+    ];
+    postPatch = ''
+      substituteInPlace ${ if isPy27 then "rpy/rinterface/__init__.py" else "rpy2/rinterface_lib/embedded.py" } --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
+    '';
+
+    doPatchelf = false; # fails because of "missing filename"
+    patchelfPhase = "";
+
+    propagatedBuildInputs = [
+      singledispatch
+      six
+      jinja2
+      pytz
+      numpy
+    ];
+
+    checkInputs = [
+      pytest
+      mock
+    ];
+    # One remaining test failure caused by different unicode encoding.
+    # https://bitbucket.org/rpy2/rpy2/issues/488
+    doCheck = false;
+    checkPhase = ''
+      ${python.interpreter} -m 'rpy2'
+    '';
+
+    # For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries:
+    # libreadline.so.6 => not found
+    # libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000)
+    # There must be a better way to fix this, but I don't know it.
+    postFixup = ''
+      patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so
+    '';
+
+    meta = {
+      homepage = http://rpy.sourceforge.net/rpy2;
+      description = "Python interface to R";
+      license = lib.licenses.gpl2Plus;
+      platforms = lib.platforms.unix;
+      maintainers = with lib.maintainers; [ joelmo ];
+    };
+  }
diff --git a/pkgs/development/python-modules/rpy2/default.nix b/pkgs/development/python-modules/rpy2/default.nix
index 1b4ab4d40db9..bc4bc0bcb5b8 100644
--- a/pkgs/development/python-modules/rpy2/default.nix
+++ b/pkgs/development/python-modules/rpy2/default.nix
@@ -3,8 +3,6 @@
 , buildPythonPackage
 , fetchPypi
 , isPyPy
-, isPy27
-, readline
 , R
 , rWrapper
 , rPackages
@@ -13,38 +11,38 @@
 , bzip2
 , zlib
 , icu
-, singledispatch
-, six
+, ipython
 , jinja2
 , pytz
+, pandas
 , numpy
+, cffi
+, tzlocal
+, simplegeneric
 , pytest
-, mock
 , extraRPackages ? []
 }:
 
 buildPythonPackage rec {
-    version = if isPy27 then
-      "2.8.6" # python2 support dropped in 2.9.x
-    else
-      "2.9.5";
+    version = "3.2.2";
     pname = "rpy2";
+
     disabled = isPyPy;
     src = fetchPypi {
       inherit version pname;
-      sha256 = if isPy27 then
-        "162zki5c1apgv6qbafi7n66y4hgpgp43xag7q75qb6kv99ri6k80" # 2.8.x
-      else
-        "1nrj8pgyxrwrfdrxzb4j3z1adjwjx1mr8d1n5cmrz4nhlzy8w7xr"; # 2.9.x
+      sha256 = "0b3jpn9x7m2pccriyzgfsdb68qp6nq4ffhvjy1q2ar8wdxvmf5xp";
     };
+
     buildInputs = [
-      readline
       R
       pcre
       lzma
       bzip2
       zlib
       icu
+
+      # is in the upstream `requires` although it shouldn't be -- this is easier than patching it away
+      pytest
     ] ++ (with rPackages; [
       # packages expected by the test framework
       ggplot2
@@ -58,6 +56,10 @@ buildPythonPackage rec {
       tidyr
     ]) ++ extraRPackages ++ rWrapper.recommendedPackages;
 
+    checkPhase = ''
+      pytest
+    '';
+
     nativeBuildInputs = [
       R # needed at setup time to detect R_HOME (alternatively set R_HOME explicitly)
     ];
@@ -65,38 +67,26 @@ buildPythonPackage rec {
     patches = [
       # R_LIBS_SITE is used by the nix r package to point to the installed R libraries.
       # This patch sets R_LIBS_SITE when rpy2 is imported.
-      ./r-libs-site.patch
+      ./rpy2-3.x-r-libs-site.patch
     ];
     postPatch = ''
-      substituteInPlace rpy/rinterface/__init__.py --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
+      substituteInPlace 'rpy2/rinterface_lib/embedded.py' --replace '@NIX_R_LIBS_SITE@' "$R_LIBS_SITE"
     '';
 
     propagatedBuildInputs = [
-      singledispatch
-      six
+      ipython
       jinja2
       pytz
+      pandas
       numpy
+      cffi
+      tzlocal
+      simplegeneric
     ];
 
     checkInputs = [
       pytest
-      mock
     ];
-    # One remaining test failure caused by different unicode encoding.
-    # https://bitbucket.org/rpy2/rpy2/issues/488
-    doCheck = false;
-    checkPhase = ''
-      ${python.interpreter} -m 'rpy2.tests'
-    '';
-
-    # For some reason libreadline.so is not found. Curiously `ldd _rinterface.so | grep readline` shows two readline entries:
-    # libreadline.so.6 => not found
-    # libreadline.so.6 => /nix/store/z2zhmrg6jcrn5iq2779mav0nnq4vm2q6-readline-6.3p08/lib/libreadline.so.6 (0x00007f333ac43000)
-    # There must be a better way to fix this, but I don't know it.
-    postFixup = ''
-      patchelf --add-needed ${readline}/lib/libreadline.so "$out/${python.sitePackages}/rpy2/rinterface/"_rinterface*.so
-    '';
 
     meta = {
       homepage = http://rpy.sourceforge.net/rpy2;
diff --git a/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch b/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch
new file mode 100644
index 000000000000..177e4f9a83d1
--- /dev/null
+++ b/pkgs/development/python-modules/rpy2/rpy2-3.x-r-libs-site.patch
@@ -0,0 +1,21 @@
+diff --git a/rpy2/rinterface_lib/embedded.py b/rpy2/rinterface_lib/embedded.py
+index cc32b6d..3969ad0 100644
+--- a/rpy2/rinterface_lib/embedded.py
++++ b/rpy2/rinterface_lib/embedded.py
+@@ -113,6 +113,16 @@ def _initr(interactive: bool = True,
+         if isinitialized():
+             return None
+         os.environ['R_HOME'] = openrlib.R_HOME
++
++        # path to libraries
++        existing = os.environ.get('R_LIBS_SITE')
++        if existing is not None:
++            prefix = existing + ':'
++        else:
++            prefix = ''
++        additional = '@NIX_R_LIBS_SITE@'
++        os.environ['R_LIBS_SITE'] = prefix + additional
++
+         options_c = [ffi.new('char[]', o.encode('ASCII')) for o in _options]
+         n_options = len(options_c)
+         n_options_c = ffi.cast('int', n_options)
diff --git a/pkgs/development/tools/analysis/rr/default.nix b/pkgs/development/tools/analysis/rr/default.nix
index 844fd38d9be6..a8d95eb05deb 100644
--- a/pkgs/development/tools/analysis/rr/default.nix
+++ b/pkgs/development/tools/analysis/rr/default.nix
@@ -25,6 +25,7 @@ stdenv.mkDerivation rec {
   buildInputs = [
     cmake libpfm zlib python2Packages.python python2Packages.pexpect which procps gdb capnproto
   ];
+  propagatedBuildInputs = [ gdb ]; # needs GDB to replay programs at runtime
   cmakeFlags = [
     "-DCMAKE_C_FLAGS_RELEASE:STRING="
     "-DCMAKE_CXX_FLAGS_RELEASE:STRING="
diff --git a/pkgs/servers/http/jetty/default.nix b/pkgs/servers/http/jetty/default.nix
index 845fd41c12c4..8d2340647cb4 100644
--- a/pkgs/servers/http/jetty/default.nix
+++ b/pkgs/servers/http/jetty/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "jetty";
-  version = "9.4.22.v20191022";
+  version = "9.4.24.v20191120";
   src = fetchurl {
     url = "https://repo1.maven.org/maven2/org/eclipse/jetty/jetty-distribution/${version}/jetty-distribution-${version}.tar.gz";
     name = "jetty-distribution-${version}.tar.gz";
-    sha256 = "1a5av6ygsmjwbnlax7f7l58d7hlw3xm0cpk5ml7mb54vrlrcb7hv";
+    sha256 = "072vr8gfly2xdwxx1c771yymf145l8nv0j31liwqrih8zqvvhsd4";
   };
 
   phases = [ "unpackPhase" "installPhase" ];
@@ -18,7 +18,7 @@ stdenv.mkDerivation rec {
 
   meta = {
     description = "A Web server and javax.servlet container";
-    homepage = http://www.eclipse.org/jetty/;
+    homepage = "https://www.eclipse.org/jetty/";
     platforms = stdenv.lib.platforms.all;
     license = [ stdenv.lib.licenses.asl20 stdenv.lib.licenses.epl10 ];
   };
diff --git a/pkgs/servers/pulseaudio/default.nix b/pkgs/servers/pulseaudio/default.nix
index 2ce78a048c45..da201765e55e 100644
--- a/pkgs/servers/pulseaudio/default.nix
+++ b/pkgs/servers/pulseaudio/default.nix
@@ -1,6 +1,6 @@
 { lib, stdenv, fetchurl, pkgconfig, autoreconfHook
 , libsndfile, libtool, makeWrapper, perlPackages
-, xorg, libcap, alsaLib, glib, gnome3
+, xorg, libcap, alsaLib, glib, dconf
 , avahi, libjack2, libasyncns, lirc, dbus
 , sbc, bluez5, udev, openssl, fftwFloat
 , speexdsp, systemd, webrtc-audio-processing
@@ -113,7 +113,7 @@ stdenv.mkDerivation rec {
   preFixup = lib.optionalString stdenv.isLinux ''
     wrapProgram $out/libexec/pulse/gsettings-helper \
      --prefix XDG_DATA_DIRS : "$out/share/gsettings-schemas/${name}" \
-     --prefix GIO_EXTRA_MODULES : "${lib.getLib gnome3.dconf}/lib/gio/modules"
+     --prefix GIO_EXTRA_MODULES : "${lib.getLib dconf}/lib/gio/modules"
   '';
 
   meta = {
diff --git a/pkgs/tools/graphics/luxcorerender/default.nix b/pkgs/tools/graphics/luxcorerender/default.nix
index 4826bd64984b..6a0db954da64 100644
--- a/pkgs/tools/graphics/luxcorerender/default.nix
+++ b/pkgs/tools/graphics/luxcorerender/default.nix
@@ -1,7 +1,7 @@
 { stdenv, fetchFromGitHub, cmake, boost165, pkgconfig, python35
 , tbb, openimageio, libjpeg, libpng, zlib, libtiff, ilmbase
 , freetype, openexr, libXdmcp, libxkbcommon, epoxy, at-spi2-core
-, dbus, doxygen, qt5, c-blosc, libGLU, gnome3, gtk3, pcre
+, dbus, doxygen, qt5, c-blosc, libGLU, gnome3, dconf, gtk3, pcre
 , bison, flex, libpthreadstubs, libX11
 , embree2, makeWrapper, gsettings-desktop-schemas, glib
 , withOpenCL ? true , opencl-headers, ocl-icd, opencl-clhpp
@@ -35,7 +35,7 @@ in stdenv.mkDerivation {
      # needed for XDG_ICON_DIRS
      gnome3.adwaita-icon-theme
      makeWrapper
-     (stdenv.lib.getLib gnome3.dconf)
+     (stdenv.lib.getLib dconf)
    ] ++ stdenv.lib.optionals withOpenCL [opencl-headers ocl-icd opencl-clhpp];
 
   cmakeFlags = [
@@ -66,7 +66,7 @@ in stdenv.mkDerivation {
     wrapProgram "$out/bin/luxcoreui" \
       --prefix XDG_DATA_DIRS : "$GSETTINGS_SCHEMAS_PATH" \
       --suffix XDG_DATA_DIRS : '${gnome3.adwaita-icon-theme}/share' \
-      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib gnome3.dconf}/lib/gio/modules"
+      --prefix GIO_EXTRA_MODULES : "${stdenv.lib.getLib dconf}/lib/gio/modules"
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/tools/misc/hyperfine/default.nix b/pkgs/tools/misc/hyperfine/default.nix
index 8f3d245280c9..9a27c4df7721 100644
--- a/pkgs/tools/misc/hyperfine/default.nix
+++ b/pkgs/tools/misc/hyperfine/default.nix
@@ -4,22 +4,22 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "hyperfine";
-  version = "1.8.0";
+  version = "1.9.0";
 
   src = fetchFromGitHub {
     owner  = "sharkdp";
     repo   = pname;
     rev    = "refs/tags/v${version}";
-    sha256 = "12bj5xifnpj5yni563b6b33lzmkgm7j1wk0c9859zw59b33ifd1l";
+    sha256 = "0jx2lqhayp14c51dfvgmqrmmadyvxf0p4dsn770ndqpzv66rh6zb";
   };
 
-  cargoSha256 = "1ias944wg55njjnap7w02b87bvb502vzkpjvsb704q5i9sr8hjry";
+  cargoSha256 = "0sqmqfig40ragjx3jvwrng6hqz8l1zbmxzq470lk66x0gy4gziag";
 
   buildInputs = stdenv.lib.optional stdenv.isDarwin Security;
 
   meta = with stdenv.lib; {
     description = "Command-line benchmarking tool";
-    homepage    = https://github.com/sharkdp/hyperfine;
+    homepage    = "https://github.com/sharkdp/hyperfine";
     license     = with licenses; [ asl20 /* or */ mit ];
     maintainers = [ maintainers.thoughtpolice ];
     platforms   = platforms.all;
diff --git a/pkgs/tools/misc/topgrade/default.nix b/pkgs/tools/misc/topgrade/default.nix
index 8514b4b9b594..3adf37c22182 100644
--- a/pkgs/tools/misc/topgrade/default.nix
+++ b/pkgs/tools/misc/topgrade/default.nix
@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "topgrade";
-  version = "3.4.0";
+  version = "3.5.0";
 
   src = fetchFromGitHub {
     owner = "r-darwish";
     repo = pname;
     rev = "v${version}";
-    sha256 = "14p7lpdp85ay5p2r9npm2adp9njcssi47mb1fh2iyn8lp51d22bi";
+    sha256 = "15w1qi38dsx573nadqpvarxx63xla53w775fwkdds2iyspaljsg6";
   };
 
-  cargoSha256 = "07h8d8fm20dp9xcz9vic63xnx2rbvanf2ivks1jiv32iy0kgz74p";
+  cargoSha256 = "0xhrgs2rpkgjzgsipq5rb3fmqwvxrl2wi0fly1xaa6p304k1710m";
 
   meta = with stdenv.lib; {
     description = "Upgrade all the things";
diff --git a/pkgs/tools/networking/gnirehtet/default.nix b/pkgs/tools/networking/gnirehtet/default.nix
index 37d2eea825f0..06faa0640257 100644
--- a/pkgs/tools/networking/gnirehtet/default.nix
+++ b/pkgs/tools/networking/gnirehtet/default.nix
@@ -1,12 +1,12 @@
 {stdenv, rustPlatform, fetchFromGitHub, fetchzip, androidenv, substituteAll}:
 let
-version = "2.3";
+version = "2.4";
 apk = stdenv.mkDerivation {
   pname = "gnirehtet.apk";
   inherit version;
   src = fetchzip {
     url = "https://github.com/Genymobile/gnirehtet/releases/download/v${version}/gnirehtet-rust-linux64-v${version}.zip";
-    sha256 = "08pgmpbz82cd8ndr2syiv25l5xk1gvh9gzji4pgva5gw269bjmpz";
+    sha256 = "13gsh5982v961j86j5y71pgas94g2d1v1fgnbslbqw4h69fbf48g";
   };
   installPhase = ''
     mkdir $out
@@ -22,10 +22,10 @@ rustPlatform.buildRustPackage {
       owner = "Genymobile";
       repo = "gnirehtet";
       rev = "v${version}";
-      sha256 = "118ig42qzr2xyra7r8zfxq38xidaxfc98ja9836jwnn9fgbigczr";
+      sha256 = "1c99d6zpjxa8xlrg0n1825am20d2pjiicfcjwv8iay9ylfdnvygl";
   };
   sourceRoot = "source/relay-rust";
-  cargoSha256 = "1500lfwbfnc0k2hn7r1n629fq11zfqm3fg13dddmhchq4i3sqkfb";
+  cargoSha256 = "1l1cirhmfkpa466vksynlhwggsfiahws7cpsxydrc414l415l283";
 
   patchFlags = [ "-p2" ];
   patches = [
diff --git a/pkgs/tools/networking/uget/default.nix b/pkgs/tools/networking/uget/default.nix
index 78dcb00eb78a..b2da1384557d 100644
--- a/pkgs/tools/networking/uget/default.nix
+++ b/pkgs/tools/networking/uget/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchurl, pkgconfig, intltool, openssl, curl, libnotify,
-  libappindicator-gtk3, gst_all_1, gtk3, gnome3, wrapGAppsHook, aria2 ? null
+  libappindicator-gtk3, gst_all_1, gtk3, dconf, wrapGAppsHook, aria2 ? null
 }:
 
 stdenv.mkDerivation rec {
@@ -23,7 +23,7 @@ stdenv.mkDerivation rec {
     libnotify
     libappindicator-gtk3
     gtk3
-    (stdenv.lib.getLib gnome3.dconf)
+    (stdenv.lib.getLib dconf)
   ]
   ++ (with gst_all_1; [ gstreamer gst-plugins-base gst-plugins-good ])
   ++ (stdenv.lib.optional (aria2 != null) aria2);
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index cca5aad02002..43e1197f2578 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -456,7 +456,7 @@ in
   findXMLCatalogs = makeSetupHook { } ../build-support/setup-hooks/find-xml-catalogs.sh;
 
   wrapGAppsHook = makeSetupHook {
-    deps = lib.optional (!stdenv.isDarwin) gnome3.dconf.lib ++ [ gtk3 librsvg makeWrapper ];
+    deps = lib.optional (!stdenv.isDarwin) dconf.lib ++ [ gtk3 librsvg makeWrapper ];
   } ../build-support/setup-hooks/wrap-gapps-hook.sh;
 
   separateDebugInfo = makeSetupHook { } ../build-support/setup-hooks/separate-debug-info.sh;
@@ -1512,6 +1512,8 @@ in
 
   datovka = libsForQt5.callPackage ../applications/networking/datovka { };
 
+  dconf = callPackage ../development/libraries/dconf { };
+
   ddar = callPackage ../tools/backup/ddar { };
 
   ddate = callPackage ../tools/misc/ddate { };
@@ -2438,9 +2440,7 @@ in
 
   libkkc = callPackage ../tools/inputmethods/libkkc { };
 
-  ibus = callPackage ../tools/inputmethods/ibus {
-    inherit (gnome3) dconf;
-  };
+  ibus = callPackage ../tools/inputmethods/ibus { };
 
   ibus-qt = callPackage ../tools/inputmethods/ibus/ibus-qt.nix { };
 
@@ -2461,9 +2461,7 @@ in
       protobuf = pkgs.protobuf.overrideDerivation (oldAttrs: { stdenv = clangStdenv; });
     };
 
-    table = callPackage ../tools/inputmethods/ibus-engines/ibus-table {
-      inherit (gnome3) dconf;
-    };
+    table = callPackage ../tools/inputmethods/ibus-engines/ibus-table { };
 
     table-chinese = callPackage ../tools/inputmethods/ibus-engines/ibus-table-chinese {
       ibus-table = ibus-engines.table;
@@ -2482,9 +2480,7 @@ in
     };
   };
 
-  ibus-with-plugins = callPackage ../tools/inputmethods/ibus/wrapper.nix {
-    inherit (gnome3) dconf;
-  };
+  ibus-with-plugins = callPackage ../tools/inputmethods/ibus/wrapper.nix { };
 
   interception-tools = callPackage ../tools/inputmethods/interception-tools { };
   interception-tools-plugins = {
@@ -13586,11 +13582,11 @@ in
       inherit stdenv fetchurl fetchpatch fetchFromGitHub makeSetupHook makeWrapper;
       bison = bison2; # error: too few arguments to function 'int yylex(...
       inherit cups;
+      inherit dconf;
       inherit harfbuzz;
       inherit libGL;
       inherit perl;
       inherit gtk3;
-      inherit (gnome3) dconf;
       inherit (gst_all_1) gstreamer gst-plugins-base;
       inherit llvmPackages_5;
     });
@@ -19025,9 +19021,7 @@ in
 
   gmrun = callPackage ../applications/misc/gmrun {};
 
-  gnucash = callPackage ../applications/office/gnucash {
-    inherit (gnome3) dconf;
-  };
+  gnucash = callPackage ../applications/office/gnucash { };
 
   goffice = callPackage ../development/libraries/goffice { };
 
@@ -19748,9 +19742,7 @@ in
 
   lifelines = callPackage ../applications/misc/lifelines { };
 
-  liferea = callPackage ../applications/networking/newsreaders/liferea {
-    inherit (gnome3) dconf;
-  };
+  liferea = callPackage ../applications/networking/newsreaders/liferea { };
 
   lightworks = callPackage ../applications/video/lightworks {
     portaudio = portaudio2014;
@@ -19888,7 +19880,7 @@ in
   };
 
   matchbox = callPackage ../applications/window-managers/matchbox { };
-  
+
   matrixcli = callPackage ../applications/networking/instant-messengers/matrixcli {
     inherit (python3Packages) buildPythonApplication buildPythonPackage
       pygobject3 pytestrunner requests responses pytest python-olm
@@ -20786,9 +20778,7 @@ in
 
   quantomatic = callPackage ../applications/science/physics/quantomatic { };
 
-  quassel = libsForQt5.callPackage ../applications/networking/irc/quassel {
-    inherit (gnome3) dconf;
-  };
+  quassel = libsForQt5.callPackage ../applications/networking/irc/quassel { };
 
   quasselClient = quassel.override {
     monolithic = false;
@@ -21063,7 +21053,7 @@ in
   split2flac = callPackage ../applications/audio/split2flac { };
 
   spotify-tui = callPackage ../applications/audio/spotify-tui {
-    inherit (darwin.apple_sdk.frameworks) Security;
+    inherit (darwin.apple_sdk.frameworks) AppKit Security;
   };
 
   squishyball = callPackage ../applications/audio/squishyball {
@@ -21660,7 +21650,6 @@ in
   virt-what = callPackage ../applications/virtualization/virt-what { };
 
   virt-manager = callPackage ../applications/virtualization/virt-manager {
-    dconf = gnome3.dconf;
     system-libvirt = libvirt;
   };
 
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index a496fee16a23..129074d6039c 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -5042,7 +5042,9 @@ in {
 
   rpmfluff = callPackage ../development/python-modules/rpmfluff {};
 
-  rpy2 = callPackage ../development/python-modules/rpy2 {};
+  rpy2 = if isPy3k
+    then callPackage ../development/python-modules/rpy2 { }
+    else callPackage ../development/python-modules/rpy2/2.nix { };
 
   rtslib = callPackage ../development/python-modules/rtslib {};