diff --git a/nixos/doc/manual/release-notes/rl-1412.xml b/nixos/doc/manual/release-notes/rl-1412.xml
index 4d93aa644c1d..139f61c2a550 100644
--- a/nixos/doc/manual/release-notes/rl-1412.xml
+++ b/nixos/doc/manual/release-notes/rl-1412.xml
@@ -17,7 +17,7 @@
    </listitem>
    <listitem>
     <para>
-     <link xlink:href="http://thread.gmane.org/gmane.linux.distributions.nixos/15165">
+     <link xlink:href="https://www.mail-archive.com/nix-dev@lists.science.uu.nl/msg13957.html">
      Nix has been updated to 1.8.</link>
     </para>
    </listitem>
diff --git a/nixos/modules/services/desktops/geoclue2.nix b/nixos/modules/services/desktops/geoclue2.nix
index dafb0af20756..840aa5294ed0 100644
--- a/nixos/modules/services/desktops/geoclue2.nix
+++ b/nixos/modules/services/desktops/geoclue2.nix
@@ -61,6 +61,8 @@ in
         wantedBy = [ "default.target" ];
       };
     };
+
+    environment.etc."geoclue/geoclue.conf".source = "${package}/etc/geoclue/geoclue.conf";
   };
 
 }
diff --git a/pkgs/applications/editors/eclipse/plugins.nix b/pkgs/applications/editors/eclipse/plugins.nix
index 9595bfe4d8ba..30f381644ac1 100644
--- a/pkgs/applications/editors/eclipse/plugins.nix
+++ b/pkgs/applications/editors/eclipse/plugins.nix
@@ -555,12 +555,12 @@ rec {
 
   spotbugs = buildEclipseUpdateSite rec {
     name = "spotbugs-${version}";
-    version = "3.1.9";
+    version = "3.1.10";
 
     src = fetchzip {
       stripRoot = false;
       url = "https://github.com/spotbugs/spotbugs/releases/download/${version}/eclipsePlugin.zip";
-      sha256 = "0m68jbyaiz0rm4qq3nnwnvgndzv2c6ay6i29kh0p0vdbanggq3xz";
+      sha256 = "0xrflgw0h05z3za784ach2fx6dh04lgmfr426m1q235vv2ibds5y";
     };
 
     meta = with stdenv.lib; {
diff --git a/pkgs/applications/misc/girara/default.nix b/pkgs/applications/misc/girara/default.nix
index 0dfeac3cf8b2..919f20f13983 100644
--- a/pkgs/applications/misc/girara/default.nix
+++ b/pkgs/applications/misc/girara/default.nix
@@ -3,11 +3,11 @@
 
 stdenv.mkDerivation rec {
   name = "girara-${version}";
-  version = "0.3.1";
+  version = "0.3.2";
 
   src = fetchurl {
     url = "https://pwmt.org/projects/girara/download/${name}.tar.xz";
-    sha256 = "1ddwap5q5cnfdr1q1b110wy7mw1z3khn86k01jl8lqmn02n9nh1w";
+    sha256 = "1kc6n1mxjxa7wvwnqy94qfg8l9jvx9qrvrr2kc7m4g0z20x3a00p";
   };
 
   nativeBuildInputs = [ meson ninja pkgconfig gettext ];
diff --git a/pkgs/applications/misc/masterpdfeditor/default.nix b/pkgs/applications/misc/masterpdfeditor/default.nix
index 1cb472ff0194..2928d271efcf 100644
--- a/pkgs/applications/misc/masterpdfeditor/default.nix
+++ b/pkgs/applications/misc/masterpdfeditor/default.nix
@@ -1,14 +1,14 @@
 { stdenv, fetchurl, sane-backends, qtbase, qtsvg, nss, autoPatchelfHook, lib, makeWrapper }:
 
 let
-  version = "5.1.60";
+  version = "5.2.20";
 
 in stdenv.mkDerivation {
   name = "masterpdfeditor-${version}";
 
   src = fetchurl {
     url = "https://code-industry.net/public/master-pdf-editor-${version}_qt5.amd64.tar.gz";
-    sha256 = "0br5f04klzpbd25igbjjj1dqasmrcrw2zsan5bv0ydnr2lmpb2fz";
+    sha256 = "1399zv3m7a2rxvmy213f5yii3krsqyahpwdzsw8j535xrb9f3z1m";
   };
 
   nativeBuildInputs = [ autoPatchelfHook makeWrapper ];
diff --git a/pkgs/applications/misc/pcmanfm/default.nix b/pkgs/applications/misc/pcmanfm/default.nix
index a77b2d17ecb4..2649c7cbd6a9 100644
--- a/pkgs/applications/misc/pcmanfm/default.nix
+++ b/pkgs/applications/misc/pcmanfm/default.nix
@@ -7,10 +7,10 @@ let
   inherit (stdenv.lib) optional;
 in
 stdenv.mkDerivation rec {
-  name = "pcmanfm-1.3.0";
+  name = "pcmanfm-1.3.1";
   src = fetchurl {
     url = "mirror://sourceforge/pcmanfm/${name}.tar.xz";
-    sha256 = "1ywgfyklms5hqkapsbjps4kyx20ac0d1qk16ww74yagkyfdkwsas";
+    sha256 = "0mb8hg76x1z0szdyl0w7jpz0bdblc6a29is1vvnh79z37qxh8138";
   };
 
   buildInputs = [ glib gtk libfm' libX11 pango gnome3.defaultIconTheme ];
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
   configureFlags = optional withGtk3 "--with-gtk=3";
 
   meta = with stdenv.lib; {
-    homepage = http://blog.lxde.org/?cat=28/;
+    homepage = https://blog.lxde.org/category/pcmanfm/;
     license = licenses.gpl2Plus;
     description = "File manager with GTK+ interface";
     maintainers = [ maintainers.ttuegel ];
diff --git a/pkgs/applications/networking/instant-messengers/psi-plus/default.nix b/pkgs/applications/networking/instant-messengers/psi-plus/default.nix
index d01019a56197..e1a2fb40c5ae 100644
--- a/pkgs/applications/networking/instant-messengers/psi-plus/default.nix
+++ b/pkgs/applications/networking/instant-messengers/psi-plus/default.nix
@@ -5,13 +5,13 @@
 
 stdenv.mkDerivation rec {
   name = "psi-plus-${version}";
-  version = "1.4.404";
+  version = "1.4.504";
 
   src = fetchFromGitHub {
     owner = "psi-plus";
     repo = "psi-plus-snapshots";
     rev = "${version}";
-    sha256 = "05dcr1i7ic6nff70w4zfpdcmwf19kkhgxm7mcznmlr484d5i1v2m";
+    sha256 = "1nv1ynad2gcn7r8mm2w3kixmahaql7xax1lccsqyxqmj1r0klk8q";
   };
 
   resources = fetchFromGitHub {
diff --git a/pkgs/applications/office/skrooge/default.nix b/pkgs/applications/office/skrooge/default.nix
index 070ef4845d83..5168b2fef533 100644
--- a/pkgs/applications/office/skrooge/default.nix
+++ b/pkgs/applications/office/skrooge/default.nix
@@ -7,11 +7,11 @@
 
 mkDerivation rec {
   name = "skrooge-${version}";
-  version = "2.16.2";
+  version = "2.17.0";
 
   src = fetchurl {
     url = "http://download.kde.org/stable/skrooge/${name}.tar.xz";
-    sha256 = "0idvqbra8a71jb5kq9y5v377l7k3shf4z7w71apc3rjvb4l0jkhj";
+    sha256 = "0v83bcabchsz5fs0iv5i75ps01sga48hq4cx29dajcq3kf9xgwhr";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/version-management/gitlab/data.json b/pkgs/applications/version-management/gitlab/data.json
index 1f8f627f5ed6..1e0d5de0847e 100644
--- a/pkgs/applications/version-management/gitlab/data.json
+++ b/pkgs/applications/version-management/gitlab/data.json
@@ -1,12 +1,12 @@
 {
   "ce": {
-    "version": "11.5.4",
-    "repo_hash": "1mk7zj79cz9g8y6b5p4cznv90h94mwgy14w9vdvmqbgbnx9bayc8",
-    "deb_hash": "18i3w1k8l5hj3732w3adw3cma78l9hx77wlrgvssg9gz609kqvx6",
-    "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ce/packages/debian/stretch/gitlab-ce_11.5.4-ce.0_amd64.deb/download.deb",
+    "version": "11.5.5",
+    "repo_hash": "1dxky06im18s4kxbb33qwm22pkkhgvyjggx31164iy71zcxxj1jr",
+    "deb_hash": "0wnyfl1bb5wb8kdyarjk9y4ydla84f3alnk3m3zwmdqfg9jsqgb8",
+    "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ce/packages/debian/stretch/gitlab-ce_11.5.5-ce.0_amd64.deb/download.deb",
     "owner": "gitlab-org",
     "repo": "gitlab-ce",
-    "rev": "v11.5.4",
+    "rev": "v11.5.5",
     "passthru": {
       "GITALY_SERVER_VERSION": "0.129.0",
       "GITLAB_PAGES_VERSION": "1.3.1",
@@ -15,13 +15,13 @@
     }
   },
   "ee": {
-    "version": "11.5.4",
-    "repo_hash": "1rpj34wblhk6yirix16grrlhg4dfna3mjvhn8bz82m94dkhx06lc",
-    "deb_hash": "05lizhf45xv4j0y0yafrpcrqmav1xmncxxgsm97s2mlhdwn5rfnd",
-    "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ee/packages/debian/stretch/gitlab-ee_11.5.4-ee.0_amd64.deb/download.deb",
+    "version": "11.5.5",
+    "repo_hash": "1j5g0x7rxrdb39b12psjirsa3s0lhqgnxh0q3r22cgzgxv0332b8",
+    "deb_hash": "193s1f7w9lcamqnmrc7c3klmybqqra7yr16x6ay0cznwcdgirisp",
+    "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ee/packages/debian/stretch/gitlab-ee_11.5.5-ee.0_amd64.deb/download.deb",
     "owner": "gitlab-org",
     "repo": "gitlab-ee",
-    "rev": "v11.5.4-ee",
+    "rev": "v11.5.5-ee",
     "passthru": {
       "GITALY_SERVER_VERSION": "0.129.0",
       "GITLAB_PAGES_VERSION": "1.3.1",
diff --git a/pkgs/build-support/fetchgit/nix-prefetch-git b/pkgs/build-support/fetchgit/nix-prefetch-git
index 34dfe67df4bd..fa4e504c908f 100755
--- a/pkgs/build-support/fetchgit/nix-prefetch-git
+++ b/pkgs/build-support/fetchgit/nix-prefetch-git
@@ -152,7 +152,7 @@ checkout_ref(){
     if "$deepClone"; then
         # The caller explicitly asked for a deep clone.  Deep clones
         # allow "git describe" and similar tools to work.  See
-        # http://thread.gmane.org/gmane.linux.distributions.nixos/3569
+        # https://marc.info/?l=nix-dev&m=139641582514772
         # for a discussion.
         return 1
     fi
diff --git a/pkgs/development/compilers/jsonnet/default.nix b/pkgs/development/compilers/jsonnet/default.nix
index 15eec4134acf..6104ffc7aaa3 100644
--- a/pkgs/development/compilers/jsonnet/default.nix
+++ b/pkgs/development/compilers/jsonnet/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "jsonnet-${version}";
-  version = "0.11.2";
+  version = "0.12.1";
 
   src = fetchFromGitHub {
     rev = "v${version}";
     owner = "google";
     repo = "jsonnet";
-    sha256 = "05rl5i4g36k2ikxv4sw726mha1qf5bb66wiqpi0s09wj9azm7vym";
+    sha256 = "13a0sf1k8ivxhc28w0d0axzr0sj3jccl9sjq6l0dkyzrnmbxzmkb";
   };
 
   enableParallelBuilding = true;
diff --git a/pkgs/development/libraries/adns/default.nix b/pkgs/development/libraries/adns/default.nix
index 0f0e30ef0f3b..76e49768d53d 100644
--- a/pkgs/development/libraries/adns/default.nix
+++ b/pkgs/development/libraries/adns/default.nix
@@ -18,7 +18,7 @@ stdenv.mkDerivation {
   preConfigure =
     stdenv.lib.optionalString stdenv.isDarwin "sed -i -e 's|-Wl,-soname=$(SHLIBSONAME)||' configure";
 
-  # http://thread.gmane.org/gmane.linux.distributions.nixos/1328 for details.
+  # https://www.mail-archive.com/nix-dev@cs.uu.nl/msg01347.html for details.
   doCheck = false;
 
   postInstall = stdenv.lib.optionalString stdenv.isDarwin ''
diff --git a/pkgs/development/libraries/geoclue/add-option-for-installation-sysconfdir.patch b/pkgs/development/libraries/geoclue/add-option-for-installation-sysconfdir.patch
new file mode 100644
index 000000000000..629ea102971b
--- /dev/null
+++ b/pkgs/development/libraries/geoclue/add-option-for-installation-sysconfdir.patch
@@ -0,0 +1,55 @@
+--- a/data/meson.build
++++ b/data/meson.build
+@@ -7,7 +7,7 @@
+         conf.set('demo_agent', '')
+     endif
+ 
+-    conf_dir = join_paths(get_option('sysconfdir'), 'geoclue')
++    conf_dir = join_paths(sysconfdir_install, 'geoclue')
+     configure_file(output: 'geoclue.conf',
+                    input: 'geoclue.conf.in',
+                    configuration: conf,
+@@ -26,7 +26,7 @@
+     # DBus Service policy file
+     dbus_service_dir = get_option('dbus-sys-dir')
+     if dbus_service_dir  == ''
+-        dbus_service_dir = join_paths(get_option('sysconfdir'), 'dbus-1', 'system.d')
++        dbus_service_dir = join_paths(sysconfdir_install, 'dbus-1', 'system.d')
+     endif
+     configure_file(output: 'org.freedesktop.GeoClue2.conf',
+                    input: 'org.freedesktop.GeoClue2.conf.in',
+--- a/demo/meson.build
++++ b/demo/meson.build
+@@ -56,8 +56,7 @@
+                                    install_dir: desktop_dir)
+ 
+     # Also install in the autostart directory.
+-    autostart_dir = join_paths(get_option('prefix'),
+-                               get_option('sysconfdir'),
++    autostart_dir = join_paths(sysconfdir_install,
+                                'xdg', 'autostart')
+     meson.add_install_script('install-file.py',
+                              desktop_file.full_path(),
+--- a/meson.build
++++ b/meson.build
+@@ -22,6 +22,11 @@
+ datadir = join_paths(get_option('prefix'), get_option('datadir'))
+ conf.set_quoted('LOCALEDIR', datadir + '/locale')
+ conf.set_quoted('SYSCONFDIR', get_option('sysconfdir'))
++if get_option('sysconfdir_install') != ''
++  sysconfdir_install = join_paths(get_option('prefix'), get_option('sysconfdir_install'))
++else
++  sysconfdir_install = get_option('sysconfdir')
++endif
+ 
+ configure_file(output: 'config.h', configuration : conf)
+ configinc = include_directories('.')
+--- a/meson_options.txt
++++ b/meson_options.txt
+@@ -34,3 +34,6 @@
+ option('dbus-srv-user',
+        type: 'string', value: 'root',
+        description: 'The user (existing) as which the service will run')
++option('sysconfdir_install',
++       type: 'string', value: '',
++       description: 'sysconfdir to use during installation')
diff --git a/pkgs/development/libraries/geoclue/default.nix b/pkgs/development/libraries/geoclue/default.nix
index f2eeb9ae40b8..5e83ba71c1bc 100644
--- a/pkgs/development/libraries/geoclue/default.nix
+++ b/pkgs/development/libraries/geoclue/default.nix
@@ -17,6 +17,10 @@ stdenv.mkDerivation rec {
     sha256 = "0vww6irijw5ss7vawkdi5z5wdpcgw4iqljn5vs3vbd4y3d0lzrbs";
   };
 
+  patches = [
+    ./add-option-for-installation-sysconfdir.patch
+  ];
+
   outputs = [ "out" "dev" "devdoc" ];
 
   nativeBuildInputs = [
@@ -36,6 +40,8 @@ stdenv.mkDerivation rec {
   mesonFlags = [
     "-Dsystemd-system-unit-dir=${placeholder "out"}/etc/systemd/system"
     "-Ddemo-agent=${if withDemoAgent then "true" else "false"}"
+    "--sysconfdir=/etc"
+    "-Dsysconfdir_install=${placeholder "out"}/etc"
   ] ++ optionals stdenv.isDarwin [
     "-D3g-source=false"
     "-Dcdma-source=false"
diff --git a/pkgs/development/libraries/gnome-sharp/Makefile.in.patch b/pkgs/development/libraries/gnome-sharp/Makefile.in.patch
deleted file mode 100644
index 46b644f2471a..000000000000
--- a/pkgs/development/libraries/gnome-sharp/Makefile.in.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/sample/gnomevfs/Makefile.in	2009-03-03 16:09:52.000000000 +0000
-+++ b/sample/gnomevfs/Makefile.in	2014-10-14 13:35:51.020427244 +0100
-@@ -218,7 +218,7 @@
- 
- @ENABLE_GNOMEVFS_FALSE@EXTRA_TARGETS = 
- @ENABLE_GNOMEVFS_TRUE@@ENABLE_MONOGETOPTIONS_FALSE@EXTRA_TARGETS = 
--@ENABLE_GNOMEVFS_TRUE@@ENABLE_MONOGETOPTIONS_TRUE@EXTRA_TARGETS = TestXfer.exe
-+@ENABLE_GNOMEVFS_TRUE@@ENABLE_MONOGETOPTIONS_TRUE@EXTRA_TARGETS =
- assemblies = ../../gnomevfs/gnome-vfs-sharp.dll
- references = $(GTKSHARP_LIBS) $(addprefix /r:, $(assemblies))
- noinst_SCRIPTS = $(TARGETS) $(EXTRA_TARGETS)
diff --git a/pkgs/development/libraries/gnome-sharp/default.nix b/pkgs/development/libraries/gnome-sharp/default.nix
index d80144b3d719..db93bdf27af3 100644
--- a/pkgs/development/libraries/gnome-sharp/default.nix
+++ b/pkgs/development/libraries/gnome-sharp/default.nix
@@ -1,17 +1,35 @@
-{stdenv, fetchurl, pkgconfig, gtk2, mono, gtk-sharp-2_0, gnome2}:
+{ stdenv
+, lib
+, fetchFromGitHub
+, pkgconfig
+, gtk2
+, mono
+, gtk-sharp-2_0
+, gnome2
+, autoconf
+, automake
+, libtool
+, which
+}:
 
-stdenv.mkDerivation {
-  name = "gnome-sharp-2.24.1";
-  src = fetchurl {
-    url = http://ftp.gnome.org/pub/gnome/sources/gnome-sharp/2.24/gnome-sharp-2.24.1.tar.gz;
-    sha256 = "0cfvs7hw67fp0wimskqd0gdfx323gv6hi0c5pf59krnmhdrl6z8p";
+stdenv.mkDerivation rec {
+  name = "gnome-sharp-${version}";
+  version = "2.24.4";
+
+  src = fetchFromGitHub {
+    owner = "mono";
+    repo = "gnome-sharp";
+    rev = "${version}";
+    sha256 = "15jsm6n0sih0nf3w8vmvik97q7l3imz4vkdzmp9k7bssiz4glj1z";
   };
 
-  nativeBuildInputs = [ pkgconfig ];
+  nativeBuildInputs = [ pkgconfig autoconf automake libtool which ];
   buildInputs = [ gtk2 mono gtk-sharp-2_0 ]
-  ++ (with gnome2; [ libart_lgpl gnome_vfs libgnome libgnomecanvas libgnomeui]);
+  ++ (with gnome2; [ libart_lgpl gnome_vfs libgnome libgnomecanvas libgnomeui ]);
 
-  patches = [ ./Makefile.in.patch ];
+  preConfigure = ''
+    ./bootstrap-${lib.versions.majorMinor version}
+  '';
 
   dontStrip = true;
 
diff --git a/pkgs/development/libraries/gtest/default.nix b/pkgs/development/libraries/gtest/default.nix
index cf4069871d1d..06fffc4f5240 100644
--- a/pkgs/development/libraries/gtest/default.nix
+++ b/pkgs/development/libraries/gtest/default.nix
@@ -3,6 +3,8 @@ stdenv.mkDerivation rec {
   name = "gtest-${version}";
   version = "1.8.1";
 
+  outputs = [ "out" "dev" ];
+
   src = fetchFromGitHub {
     owner = "google";
     repo = "googletest";
@@ -12,6 +14,10 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ cmake ninja ];
 
+  cmakeFlags = [
+    "-DBUILD_SHARED_LIBS=ON"
+  ];
+
   meta = with stdenv.lib; {
     description = "Google's framework for writing C++ tests";
     homepage = https://github.com/google/googletest;
diff --git a/pkgs/development/libraries/gtk-sharp/2.0.nix b/pkgs/development/libraries/gtk-sharp/2.0.nix
index c037db97c044..659dc14800e1 100644
--- a/pkgs/development/libraries/gtk-sharp/2.0.nix
+++ b/pkgs/development/libraries/gtk-sharp/2.0.nix
@@ -1,4 +1,8 @@
-{ stdenv, fetchurl, pkgconfig, mono
+{ stdenv
+, lib
+, fetchFromGitHub
+, pkgconfig
+, mono
 , glib
 , pango
 , gtk2
@@ -12,32 +16,44 @@
 , libgnomeprintui ? null
 , libxml2
 , monoDLLFixer
+, autoconf
+, automake
+, libtool
+, which
 }:
 
-stdenv.mkDerivation {
-  name = "gtk-sharp-2.12.10";
+stdenv.mkDerivation rec {
+  name = "gtk-sharp-${version}";
+  version = "2.12.45";
 
   builder = ./builder.sh;
-  src = fetchurl {
-    url = mirror://gnome/sources/gtk-sharp/2.12/gtk-sharp-2.12.10.tar.gz;
-    sha256 = "1y55vc2cp4lggmbil2lb28d0gn71iq6wfyja1l9mya5xll8svzwc";
+  src = fetchFromGitHub {
+    owner = "mono";
+    repo = "gtk-sharp";
+    rev = version;
+    sha256 = "1vy6yfwkfv6bb45bzf4g6dayiqkvqqvlr02rsnhd10793hlpqlgg";
   };
 
-  # patches = [ ./dllmap-glue.patch ];
-
-  # patch bad usage of glib, which wasn't tolerated anymore
-  prePatch = ''
-    for f in glib/glue/{thread,list,slist}.c; do
-      sed -i 's,#include <glib/.*\.h>,#include <glib.h>,g' "$f"
+  postInstall = ''
+    pushd $out/bin
+    for f in gapi2-*
+    do
+      substituteInPlace $f --replace mono ${mono}/bin/mono
     done
+    popd
   '';
 
-  nativeBuildInputs = [ pkgconfig ];
+  nativeBuildInputs = [ pkgconfig autoconf automake libtool which ];
+
   buildInputs = [
     mono glib pango gtk2 GConf libglade libgnomecanvas
     libgtkhtml libgnomeui libgnomeprint libgnomeprintui gtkhtml libxml2
   ];
 
+  preConfigure = ''
+    ./bootstrap-${lib.versions.majorMinor version}
+  '';
+
   dontStrip = true;
 
   inherit monoDLLFixer;
diff --git a/pkgs/development/libraries/libdeflate/default.nix b/pkgs/development/libraries/libdeflate/default.nix
new file mode 100644
index 000000000000..0328a2215b48
--- /dev/null
+++ b/pkgs/development/libraries/libdeflate/default.nix
@@ -0,0 +1,31 @@
+{ stdenv, lib, fetchFromGitHub }:
+
+stdenv.mkDerivation rec {
+  name = "libdeflate-${version}";
+  version = "1.1";
+
+  src = fetchFromGitHub {
+    owner = "ebiggers";
+    repo = "libdeflate";
+    rev = "v${version}";
+    sha256 = "1wqxwza6rwmhrsy9sw86pdcd0w742gbzsy9qxnq6kk59m6h1dbsb";
+  };
+
+  postPatch = ''
+    substituteInPlace Makefile --replace /usr $out
+  '';
+
+  configurePhase = ''
+    make programs/config.h
+  '';
+
+  enableParallelBuilding = true;
+
+  meta = with lib; {
+    description = "Fast DEFLATE/zlib/gzip compressor and decompressor";
+    license = licenses.mit;
+    homepage = https://github.com/ebiggers/libdeflate;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ orivej ];
+  };
+}
diff --git a/pkgs/development/libraries/libfm/default.nix b/pkgs/development/libraries/libfm/default.nix
index 796c03dab5ee..a0323481be9a 100644
--- a/pkgs/development/libraries/libfm/default.nix
+++ b/pkgs/development/libraries/libfm/default.nix
@@ -9,23 +9,29 @@ stdenv.mkDerivation rec {
   name = if extraOnly
     then "libfm-extra-${version}"
     else "libfm-${version}";
-  version = "1.3.0.2";
+  version = "1.3.1";
 
   src = fetchurl {
     url = "mirror://sourceforge/pcmanfm/libfm-${version}.tar.xz";
-    sha256 = "0wkwbi1nyvqza3r1dhrq846axiiq0fy0dqgngnagh76fjrwnzl0q";
+    sha256 = "1r6gl49xrykldwz8y4h2s7gjarxigg3bbkrj0gphxjj1vr5j9ccn";
   };
 
   nativeBuildInputs = [ vala pkgconfig intltool ];
   buildInputs = [ glib gtk pango ] ++ optional (!extraOnly) menu-cache;
 
-  configureFlags = optional extraOnly "--with-extra-only"
+  configureFlags = [
+    "--sysconfdir=/etc"
+  ] ++ optional extraOnly "--with-extra-only"
     ++ optional withGtk3 "--with-gtk=3";
 
+  installFlags = [
+    "sysconfdir=${placeholder "out"}/etc"
+  ];
+
   enableParallelBuilding = true;
 
   meta = with stdenv.lib; {
-    homepage = http://blog.lxde.org/?cat=28/;
+    homepage = https://blog.lxde.org/category/pcmanfm/;
     license = licenses.lgpl21Plus;
     description = "A glib-based library for file management";
     maintainers = [ maintainers.ttuegel ];
diff --git a/pkgs/development/libraries/libhandy/default.nix b/pkgs/development/libraries/libhandy/default.nix
index 7e80ec817d19..1d07fe6ca268 100644
--- a/pkgs/development/libraries/libhandy/default.nix
+++ b/pkgs/development/libraries/libhandy/default.nix
@@ -6,7 +6,7 @@
 
 let
   pname = "libhandy";
-  version = "0.0.5";
+  version = "0.0.6";
 in stdenv.mkDerivation rec {
   name = "${pname}-${version}";
 
@@ -18,7 +18,7 @@ in stdenv.mkDerivation rec {
     owner = "Librem5";
     repo = pname;
     rev = "v${version}";
-    sha256 = "0h25ckdfx3slc2mn4vi06bhw42nrqpzn75i9d7wby9iq0cl13l08";
+    sha256 = "0gmqsxkpi288qjfdczfrbvjqyy9sbn3gligqwgqj27ask95zl1q5";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/libraries/libqmatrixclient/default.nix b/pkgs/development/libraries/libqmatrixclient/default.nix
index 2f20150ad164..db9c29469353 100644
--- a/pkgs/development/libraries/libqmatrixclient/default.nix
+++ b/pkgs/development/libraries/libqmatrixclient/default.nix
@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   name = "libqmatrixclient-${version}";
-  version = "0.4.0";
+  version = "0.4.1";
 
   src = fetchFromGitHub {
     owner  = "QMatrixClient";
     repo   = "libqmatrixclient";
     rev    = "v${version}";
-    sha256 = "1llzqjagvp91kcg26q5c4qw9aaz7wna3rh6k06rc3baivrjqf3cn";
+    sha256 = "16hi2xqlb4afspqw31c5w63qp0j4gkd6sl7j637b8cac2yigbbns";
   };
 
   buildInputs = [ qtbase ];
diff --git a/pkgs/development/libraries/libsigcxx/default.nix b/pkgs/development/libraries/libsigcxx/default.nix
index 8eba5377bc34..434dbfb9f725 100644
--- a/pkgs/development/libraries/libsigcxx/default.nix
+++ b/pkgs/development/libraries/libsigcxx/default.nix
@@ -1,20 +1,25 @@
-{ stdenv, fetchurl, pkgconfig, gnum4 }:
-let
-  ver_maj = "2.10"; # odd major numbers are unstable
-  ver_min = "0";
-in
+{ stdenv, fetchurl, pkgconfig, gnum4, gnome3 }:
+
 stdenv.mkDerivation rec {
-  name = "libsigc++-${ver_maj}.${ver_min}";
+  pname = "libsigc++";
+  version = "2.10.1";
 
   src = fetchurl {
-    url = "mirror://gnome/sources/libsigc++/${ver_maj}/${name}.tar.xz";
-    sha256 = "f843d6346260bfcb4426259e314512b99e296e8ca241d771d21ac64f28298d81";
+    url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz";
+    sha256 = "00v08km4wwzbh6vjxb21388wb9dm6g2xh14rgwabnv4c2wk5z8n9";
   };
 
   nativeBuildInputs = [ pkgconfig gnum4 ];
 
   doCheck = true;
 
+  passthru = {
+    updateScript = gnome3.updateScript {
+      packageName = pname;
+      attrPath = "libsigcxx";
+    };
+  };
+
   meta = with stdenv.lib; {
     homepage = https://libsigcplusplus.github.io/libsigcplusplus/;
     description = "A typesafe callback system for standard C++";
diff --git a/pkgs/development/libraries/libuchardet/default.nix b/pkgs/development/libraries/libuchardet/default.nix
index 52bc0ac5cfd4..5aa26a749e4f 100644
--- a/pkgs/development/libraries/libuchardet/default.nix
+++ b/pkgs/development/libraries/libuchardet/default.nix
@@ -1,25 +1,31 @@
-{ stdenv, fetchFromGitHub, cmake }:
+{ stdenv, fetchurl, cmake }:
 
 stdenv.mkDerivation rec {
-  name = "libuchardet-${version}";
+  pname = "uchardet";
+  version = "0.0.6";
 
-  version = "0.0.5";
+  outputs = [ "bin" "out" "man" "dev" ];
 
-  src = fetchFromGitHub {
-    owner  = "BYVoid";
-    repo   = "uchardet";
-    rev    = "v${version}";
-    sha256 = "0rkym5bhq3hn7623fy0fggw0qaghha71k8bi41ywqd2lchpahrrm";
+  src = fetchurl {
+    url = "https://www.freedesktop.org/software/${pname}/releases/${pname}-${version}.tar.xz";
+    sha256 = "0q9c02b6nmw41yfsiqsnphgc3f0yg3fj31wkccp47cmwvy634lc3";
   };
 
   buildInputs = [ cmake ];
 
-  doCheck = false; # fails all the tests (ctest)
+  cmakeFlags = [
+    "-DCMAKE_SKIP_BUILD_RPATH=OFF" # for tests
+    # TODO: move the following to CMake setup hook
+    "-DCMAKE_INSTALL_BINDIR=${placeholder "bin"}/bin"
+    "-DCMAKE_INSTALL_MANDIR=${placeholder "man"}/share/man"
+  ];
+
+  doCheck = true;
 
   meta = with stdenv.lib; {
     description = "Mozilla's Universal Charset Detector C/C++ API";
-    homepage    = https://www.byvoid.com/zht/project/uchardet;
-    license     = licenses.mpl11;
+    homepage = https://www.freedesktop.org/wiki/Software/uchardet/;
+    license = licenses.mpl11;
     maintainers = with maintainers; [ cstrahan ];
     platforms = with platforms; unix;
   };
diff --git a/pkgs/development/libraries/menu-cache/default.nix b/pkgs/development/libraries/menu-cache/default.nix
index c92b6a4e7287..d64b7f123127 100644
--- a/pkgs/development/libraries/menu-cache/default.nix
+++ b/pkgs/development/libraries/menu-cache/default.nix
@@ -14,9 +14,9 @@ stdenv.mkDerivation {
   buildInputs = [ glib libfm-extra ];
 
   meta = with stdenv.lib; {
-    homepage = http://blog.lxde.org/?tag=menu-cache;
-    license = licenses.gpl2Plus;
     description = "Library to read freedesktop.org menu files";
+    homepage = https://blog.lxde.org/tag/menu-cache/;
+    license = licenses.gpl2Plus;
     maintainers = [ maintainers.ttuegel ];
     platforms = platforms.linux ++ platforms.darwin;
   };
diff --git a/pkgs/development/ocaml-modules/ppx_deriving_yojson/default.nix b/pkgs/development/ocaml-modules/ppx_deriving_yojson/default.nix
index 26fa24d8dc0f..53e8265c3a74 100644
--- a/pkgs/development/ocaml-modules/ppx_deriving_yojson/default.nix
+++ b/pkgs/development/ocaml-modules/ppx_deriving_yojson/default.nix
@@ -1,29 +1,30 @@
-{ stdenv, fetchFromGitHub, ocaml, findlib, ocamlbuild, topkg, cppo
-, ppx_deriving, yojson, ounit
+{ lib, buildDunePackage, fetchFromGitHub, ppxfind, ounit
+, ppx_deriving, yojson
 }:
 
-stdenv.mkDerivation rec {
-  name = "ocaml${ocaml.version}-ppx_deriving_yojson-${version}";
-  version = "3.1";
+buildDunePackage rec {
+  pname = "ppx_deriving_yojson";
+  version = "3.3";
+
+  minimumOCamlVersion = "4.04";
 
   src = fetchFromGitHub {
     owner = "ocaml-ppx";
     repo = "ppx_deriving_yojson";
     rev = "v${version}";
-    sha256 = "1pwfnq7z60nchba4gnf58918ll11w3gj5i88qhz1p2jm45hxqgnw";
+    sha256 = "1gbfziw03r9azqlsmyn6izrgrf1xc30s88jgdany1kblpgq41rsz";
   };
 
-  buildInputs = [ ocaml findlib ocamlbuild cppo ounit ];
+  buildInputs = [ ppxfind ounit ];
 
   propagatedBuildInputs = [ ppx_deriving yojson ];
 
-  inherit (topkg) installPhase;
+  doCheck = true;
 
   meta = {
-    description = "A Yojson codec generator for OCaml >= 4.02.";
+    description = "A Yojson codec generator for OCaml >= 4.04";
     inherit (src.meta) homepage;
-    license = stdenv.lib.licenses.mit;
-    maintainers = [ stdenv.lib.maintainers.vbgl ];
-    inherit (ocaml.meta) platforms;
+    license = lib.licenses.mit;
+    maintainers = [ lib.maintainers.vbgl ];
   };
 }
diff --git a/pkgs/development/ocaml-modules/ppxfind/default.nix b/pkgs/development/ocaml-modules/ppxfind/default.nix
new file mode 100644
index 000000000000..ebb592dddd29
--- /dev/null
+++ b/pkgs/development/ocaml-modules/ppxfind/default.nix
@@ -0,0 +1,21 @@
+{ lib, buildDunePackage, fetchurl, ocaml-migrate-parsetree }:
+
+buildDunePackage rec {
+	pname = "ppxfind";
+	version = "1.2";
+	src = fetchurl {
+		url = "https://github.com/diml/ppxfind/releases/download/${version}/ppxfind-${version}.tbz";
+		sha256 = "1687jbgii5w5dvvid3ri2cx006ysv0rrspn8dz8x7ma8615whz2h";
+	};
+
+	minimumOCamlVersion = "4.03";
+
+	buildInputs = [ ocaml-migrate-parsetree ];
+
+	meta = {
+		homepage = "https://github.com/diml/ppxfind";
+		description = "ocamlfind ppx tool";
+		license = lib.licenses.bsd3;
+		maintainers = [ lib.maintainers.vbgl ];
+	};
+}
diff --git a/pkgs/development/python-modules/affine/default.nix b/pkgs/development/python-modules/affine/default.nix
index 5bd957ae731e..e2fd802cf80e 100644
--- a/pkgs/development/python-modules/affine/default.nix
+++ b/pkgs/development/python-modules/affine/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "affine";
-  version = "2.2.1";
+  version = "2.2.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0j3mvcnmgjvvm0znqyf7xylq7i89zjf4dq0g8280xs6bwbl5cvih";
+    sha256 = "146slzpj2b220dmbmrxib030wymvplawxzn7gcgnbahgm500y3gz";
   };
 
   checkInputs = [ pytest ];
diff --git a/pkgs/development/python-modules/biopython/default.nix b/pkgs/development/python-modules/biopython/default.nix
index 39be67e6e51f..beb03c894bed 100644
--- a/pkgs/development/python-modules/biopython/default.nix
+++ b/pkgs/development/python-modules/biopython/default.nix
@@ -6,11 +6,11 @@
 
 buildPythonPackage rec {
   pname = "biopython";
-  version = "1.72";
+  version = "1.73";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "ab6b492443adb90c66267b3d24d602ae69a93c68f4b9f135ba01cb06d36ce5a2";
+    sha256 = "1q55jhf76z3k6is3psis0ckbki7df26x7dikpcc3vhk1vhkwribh";
   };
 
   propagatedBuildInputs = [ numpy ];
diff --git a/pkgs/development/python-modules/buildbot/default.nix b/pkgs/development/python-modules/buildbot/default.nix
index c8bc14d3dc11..011cd879b1f3 100644
--- a/pkgs/development/python-modules/buildbot/default.nix
+++ b/pkgs/development/python-modules/buildbot/default.nix
@@ -1,7 +1,7 @@
 { stdenv, lib, buildPythonPackage, fetchPypi, makeWrapper, isPy3k,
   python, twisted, jinja2, zope_interface, future, sqlalchemy,
   sqlalchemy_migrate, dateutil, txaio, autobahn, pyjwt, treq, txrequests,
-  txgithub, pyjade, boto3, moto, mock, lz4, setuptoolsTrial, isort, pylint,
+  txgithub, pyjade, boto3, moto, mock, python-lz4, setuptoolsTrial, isort, pylint,
   flake8, buildbot-worker, buildbot-pkg, glibcLocales }:
 
 let
@@ -55,7 +55,7 @@ let
       boto3
       moto
       mock
-      lz4
+      python-lz4
       setuptoolsTrial
       isort
       pylint
diff --git a/pkgs/development/python-modules/dpkt/default.nix b/pkgs/development/python-modules/dpkt/default.nix
index e45d651f3245..c8c7f255afa8 100644
--- a/pkgs/development/python-modules/dpkt/default.nix
+++ b/pkgs/development/python-modules/dpkt/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "dpkt";
-  version = "1.9.1";
+  version = "1.9.2";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0rr9ygczhxkfb61778jx0cxs0sq46zwlcj5l3wn6xmd3iy3yx9y6";
+    sha256 = "0m0ym219zsqfjl6jwivw5as3igjbmhpcn4dvabc5nkd0bk6jxaaj";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/easyprocess/default.nix b/pkgs/development/python-modules/easyprocess/default.nix
index dc5784aafb7e..46948f2485c1 100644
--- a/pkgs/development/python-modules/easyprocess/default.nix
+++ b/pkgs/development/python-modules/easyprocess/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "EasyProcess";
-  version = "0.2.3";
+  version = "0.2.5";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "07z6485bjxkmx26mp1p1ww19d10qavw0s006bidzailsvk543qll";
+    sha256 = "0gdl6y37g8rns2i26d2zlx7x4kbpql9h5qd8k23ka69q6frcpb8k";
   };
 
   # No tests
diff --git a/pkgs/development/python-modules/goobook/default.nix b/pkgs/development/python-modules/goobook/default.nix
index 599132f0f2c2..4a3c3dc3bcb7 100644
--- a/pkgs/development/python-modules/goobook/default.nix
+++ b/pkgs/development/python-modules/goobook/default.nix
@@ -4,6 +4,7 @@
 , isPy3k
 , oauth2client
 , gdata
+, google_api_python_client
 , simplejson
 , httplib2
 , keyring
@@ -21,7 +22,7 @@ buildPythonPackage rec {
     sha256 = "139a98d646d5c5963670944d5cfcc1a107677ee11fa98329221bd600457fda6d";
   };
 
-  propagatedBuildInputs = [ oauth2client gdata simplejson httplib2 keyring six rsa ];
+  propagatedBuildInputs = [ oauth2client gdata google_api_python_client simplejson httplib2 keyring six rsa ];
 
   preConfigure = ''
     sed -i '/distribute/d' setup.py
diff --git a/pkgs/development/python-modules/jsonrpclib-pelix/default.nix b/pkgs/development/python-modules/jsonrpclib-pelix/default.nix
index 2e3ef0545984..5e6d6ceab9b0 100644
--- a/pkgs/development/python-modules/jsonrpclib-pelix/default.nix
+++ b/pkgs/development/python-modules/jsonrpclib-pelix/default.nix
@@ -12,6 +12,8 @@ buildPythonPackage rec {
     sha256 = "14d288d1b3d3273cf96a729dd21a2470851c4962be8509f3dd62f0137ff90339";
   };
 
+  doCheck = false; # test_suite="tests" in setup.py but no tests in pypi.
+
   meta = with lib; {
     description = "JSON RPC client library - Pelix compatible fork";
     homepage = https://pypi.python.org/pypi/jsonrpclib-pelix/;
diff --git a/pkgs/development/python-modules/lz4/default.nix b/pkgs/development/python-modules/lz4/default.nix
deleted file mode 100644
index a9a7783fe777..000000000000
--- a/pkgs/development/python-modules/lz4/default.nix
+++ /dev/null
@@ -1,29 +0,0 @@
-{ stdenv
-, buildPythonPackage
-, fetchPypi
-, pytestrunner
-, pytest
-, psutil
-, pkgconfig
-, setuptools_scm
-}:
-
-buildPythonPackage rec {
-  pname = "lz4";
-  version = "2.1.2";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "ec265f7c3fc3df706e9579bde632ceeef9278858d7ae87c376a2954d11e9ea39";
-  };
-
-  buildInputs = [ setuptools_scm pytestrunner pkgconfig ];
-  checkInputs = [ pytest psutil ];
-
-  meta = with stdenv.lib; {
-    description = "Compression library";
-    homepage = https://github.com/python-lz4/python-lz4;
-    license = licenses.bsd3;
-  };
-
-}
diff --git a/pkgs/development/python-modules/ofxparse/default.nix b/pkgs/development/python-modules/ofxparse/default.nix
index fbbd3899420b..377138877c9c 100644
--- a/pkgs/development/python-modules/ofxparse/default.nix
+++ b/pkgs/development/python-modules/ofxparse/default.nix
@@ -3,6 +3,7 @@
 , fetchPypi
 , six
 , beautifulsoup4
+, lxml
 }:
 
 buildPythonPackage rec {
@@ -14,7 +15,7 @@ buildPythonPackage rec {
     sha256 = "d8c81fd5089332106da1a2e8919c412c7c677f08af04d557ca767701a04e0918";
   };
 
-  propagatedBuildInputs = [ six beautifulsoup4 ];
+  propagatedBuildInputs = [ six beautifulsoup4 lxml ];
 
   meta = with stdenv.lib; {
     homepage = "http://sites.google.com/site/ofxparse";
diff --git a/pkgs/development/python-modules/parsel/default.nix b/pkgs/development/python-modules/parsel/default.nix
index 0135b98cbda7..9ebd5e9b9ea2 100644
--- a/pkgs/development/python-modules/parsel/default.nix
+++ b/pkgs/development/python-modules/parsel/default.nix
@@ -1,8 +1,9 @@
-{ stdenv
+{ lib
 , buildPythonPackage
 , fetchPypi
 , pytest
 , pytestrunner
+, functools32
 , six
 , w3lib
 , lxml
@@ -19,13 +20,13 @@ buildPythonPackage rec {
   };
 
   buildInputs = [ pytest pytestrunner ];
-  propagatedBuildInputs = [ six w3lib lxml cssselect ];
+  propagatedBuildInputs = [ functools32 six w3lib lxml cssselect ];
 
   checkPhase = ''
     py.test
   '';
 
-  meta = with stdenv.lib; {
+  meta = with lib; {
     homepage = "https://github.com/scrapy/parsel";
     description = "Parsel is a library to extract data from HTML and XML using XPath and CSS selectors";
     license = licenses.bsd3;
diff --git a/pkgs/development/python-modules/pytesseract/default.nix b/pkgs/development/python-modules/pytesseract/default.nix
index 7d96f4d39bd0..8fae56e9a23c 100644
--- a/pkgs/development/python-modules/pytesseract/default.nix
+++ b/pkgs/development/python-modules/pytesseract/default.nix
@@ -2,11 +2,11 @@
 
 buildPythonPackage rec {
   pname = "pytesseract";
-  version = "0.2.5";
+  version = "0.2.6";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0wlz1vbg1k8cdrpzvrahjnbsfs4ki6xqhbkv17ycfchh7h6kfkfm";
+    sha256 = "0w4phjw0gn52hqlm3ixs2cmj25x7y7nk6ijr9f82wvjvb4hh7hhi";
   };
 
   patches = [
diff --git a/pkgs/development/python-modules/python-lz4/default.nix b/pkgs/development/python-modules/python-lz4/default.nix
index a0fe6666d849..544d8f6254d6 100644
--- a/pkgs/development/python-modules/python-lz4/default.nix
+++ b/pkgs/development/python-modules/python-lz4/default.nix
@@ -12,14 +12,14 @@
 
 buildPythonPackage rec {
   pname = "python-lz4";
-  version = "2.1.0";
+  version = "2.1.2";
 
   # get full repository inorder to run tests
   src = fetchFromGitHub {
     owner = pname;
     repo = pname;
     rev = "v${version}";
-    sha256 = "1vjfplj37jcw1mf8l810dv76dx0raia3ylgyfy7sfsb3g17brjq6";
+    sha256 = "1kzzdfkrq9nnlh0wssa6ccncvv0sk4wmhivhgyndjxz6d6przl5d";
   };
 
   buildInputs = [ setuptools_scm pkgconfig pytestrunner ];
@@ -34,7 +34,7 @@ buildPythonPackage rec {
   meta = {
      description = "LZ4 Bindings for Python";
      homepage = https://github.com/python-lz4/python-lz4;
-     license = lib.licenses.bsd0;
+     license = lib.licenses.bsd3;
      maintainers = with lib.maintainers; [ costrouc ];
   };
 }
diff --git a/pkgs/development/python-modules/pytorch/default.nix b/pkgs/development/python-modules/pytorch/default.nix
index b0ae9ef0cf55..8b9ba07ce953 100644
--- a/pkgs/development/python-modules/pytorch/default.nix
+++ b/pkgs/development/python-modules/pytorch/default.nix
@@ -1,6 +1,6 @@
-{ buildPythonPackage, pythonOlder,
+{ stdenv, fetchurl, buildPythonPackage, pythonOlder,
   cudaSupport ? false, cudatoolkit ? null, cudnn ? null,
-  fetchFromGitHub, lib, numpy, pyyaml, cffi, typing, cmake,
+  fetchFromGitHub, lib, numpy, pyyaml, cffi, typing, cmake, hypothesis, numactl,
   linkFarm, symlinkJoin,
   utillinux, which }:
 
@@ -25,7 +25,7 @@ let
     "LD_LIBRARY_PATH=${cudaStub}\${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH} ";
 
 in buildPythonPackage rec {
-  version = "0.4.1";
+  version = "1.0.0";
   pname = "pytorch";
 
   src = fetchFromGitHub {
@@ -33,9 +33,17 @@ in buildPythonPackage rec {
     repo   = "pytorch";
     rev    = "v${version}";
     fetchSubmodules = true;
-    sha256 = "1cr8h47jxgfar5bamyvlayvqymnb2qvp7rr0ka2d2d4rdldf9lrp";
+    sha256 = "076cpbig4sywn9vv674c0xdg832sdrd5pk1d0725pjkm436kpvlm";
   };
 
+  patches =
+    [ # Skips two tests that are only meant to run on multi GPUs
+      (fetchurl {
+        url = "https://github.com/pytorch/pytorch/commit/bfa666eb0deebac21b03486e26642fd70d66e478.patch";
+        sha256 = "1fgblcj02gjc0y62svwc5gnml879q3x2z7m69c9gax79dpr37s9i";
+      })
+    ];
+
   preConfigure = lib.optionalString cudaSupport ''
     export CC=${cudatoolkit.cc}/bin/gcc CXX=${cudatoolkit.cc}/bin/g++
   '' + lib.optionalString (cudaSupport && cudnn != null) ''
@@ -58,12 +66,24 @@ in buildPythonPackage rec {
     done
   '';
 
+  # Override the (weirdly) wrong version set by default. See
+  # https://github.com/NixOS/nixpkgs/pull/52437#issuecomment-449718038
+  # https://github.com/pytorch/pytorch/blob/v1.0.0/setup.py#L267
+  PYTORCH_BUILD_VERSION = version;
+  PYTORCH_BUILD_NUMBER = 0;
+
+  # Suppress a weird warning in mkl-dnn, part of ideep in pytorch
+  # (upstream seems to have fixed this in the wrong place?)
+  # https://github.com/intel/mkl-dnn/commit/8134d346cdb7fe1695a2aa55771071d455fae0bc
+  NIX_CFLAGS_COMPILE = lib.optionals (numpy.blasImplementation == "mkl") [ "-Wno-error=array-bounds" ];
+
   buildInputs = [
      cmake
      numpy.blas
      utillinux
      which
-  ] ++ lib.optionals cudaSupport [cudatoolkit_joined cudnn];
+  ] ++ lib.optionals cudaSupport [ cudatoolkit_joined cudnn ]
+    ++ lib.optionals stdenv.isLinux [ numactl ];
 
   propagatedBuildInputs = [
     cffi
@@ -71,15 +91,16 @@ in buildPythonPackage rec {
     pyyaml
   ] ++ lib.optional (pythonOlder "3.5") typing;
 
+  checkInputs = [ hypothesis ];
   checkPhase = ''
-    ${cudaStubEnv}python test/run_test.py --exclude dataloader sparse torch utils distributed
+    ${cudaStubEnv}python test/run_test.py --exclude dataloader sparse torch utils thd_distributed distributed cpp_extensions
   '';
 
   meta = {
-    description = "Tensors and Dynamic neural networks in Python with strong GPU acceleration.";
-    homepage = https://pytorch.org/;
-    license = lib.licenses.bsd3;
-    platforms = lib.platforms.linux;
-    maintainers = with lib.maintainers; [ teh ];
+    description = "Open source, prototype-to-production deep learning platform";
+    homepage    = https://pytorch.org/;
+    license     = lib.licenses.bsd3;
+    platforms   = lib.platforms.linux;
+    maintainers = with lib.maintainers; [ teh thoughtpolice ];
   };
 }
diff --git a/pkgs/development/python-modules/qrcode/default.nix b/pkgs/development/python-modules/qrcode/default.nix
index ca751e4ce783..fedff05d8133 100644
--- a/pkgs/development/python-modules/qrcode/default.nix
+++ b/pkgs/development/python-modules/qrcode/default.nix
@@ -1,5 +1,6 @@
 { stdenv
 , buildPythonPackage
+, isPy27
 , fetchPypi
 , six
 , pillow
@@ -18,6 +19,7 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [ six pillow pymaging_png ];
   checkInputs = [ mock ];
+  doCheck = isPy27; # https://github.com/lincolnloop/python-qrcode/issues/163
 
   meta = with stdenv.lib; {
     description = "Quick Response code generation for Python";
diff --git a/pkgs/development/python-modules/secretstorage/2.nix b/pkgs/development/python-modules/secretstorage/2.nix
new file mode 100644
index 000000000000..8fa044e638a4
--- /dev/null
+++ b/pkgs/development/python-modules/secretstorage/2.nix
@@ -0,0 +1,24 @@
+{ lib, fetchPypi, buildPythonPackage, cryptography, dbus-python }:
+
+buildPythonPackage rec {
+  pname = "secretstorage";
+  version = "2.3.1";
+
+  src = fetchPypi {
+    pname = "SecretStorage";
+    inherit version;
+    sha256 = "1di9gx4m27brs6ar774m64s017iz742mnmw39kvfc8skfs3mrxis";
+  };
+
+  propagatedBuildInputs = [ cryptography dbus-python ];
+
+  # Needs a D-Bus Sesison
+  doCheck = false;
+
+  meta = with lib; {
+    homepage = https://github.com/mitya57/secretstorage;
+    description = "Python bindings to FreeDesktop.org Secret Service API";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ orivej ];
+  };
+}
diff --git a/pkgs/development/python-modules/secretstorage/default.nix b/pkgs/development/python-modules/secretstorage/default.nix
index c0df4d4a878e..bff45c7f2c3c 100644
--- a/pkgs/development/python-modules/secretstorage/default.nix
+++ b/pkgs/development/python-modules/secretstorage/default.nix
@@ -24,7 +24,7 @@ buildPythonPackage rec {
   meta = with lib; {
     homepage = https://github.com/mitya57/secretstorage;
     description = "Python bindings to FreeDesktop.org Secret Service API";
-    license = licenses.bsdOriginal;
+    license = licenses.bsd3;
     maintainers = with maintainers; [ teto ];
   };
 }
diff --git a/pkgs/development/python-modules/shellingham/default.nix b/pkgs/development/python-modules/shellingham/default.nix
index 6fa265517dfa..b2c63ea97e3b 100644
--- a/pkgs/development/python-modules/shellingham/default.nix
+++ b/pkgs/development/python-modules/shellingham/default.nix
@@ -3,11 +3,11 @@
 
 buildPythonPackage rec {
   pname = "shellingham";
-  version = "1.2.7";
+  version = "1.2.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "06biyiwq9571mryzbr50am3mxpc3blscwqhiq8c66ac4xm3maszm";
+    sha256 = "115k1z2klgsvyzg4q5ip0iqxyb565pkchhf2fsr846k68gqcgrjn";
   };
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/python-modules/taskw/default.nix b/pkgs/development/python-modules/taskw/default.nix
index 328eb158eefb..d2d12ca0b962 100644
--- a/pkgs/development/python-modules/taskw/default.nix
+++ b/pkgs/development/python-modules/taskw/default.nix
@@ -5,6 +5,7 @@
 , tox
 , six
 , dateutil
+, kitchen
 , pytz
 , pkgs
 }:
@@ -28,7 +29,7 @@ buildPythonPackage rec {
   doCheck = false;
 
   buildInputs = [ nose pkgs.taskwarrior tox ];
-  propagatedBuildInputs = [ six dateutil pytz ];
+  propagatedBuildInputs = [ six dateutil kitchen pytz ];
 
   meta = with stdenv.lib; {
     homepage =  https://github.com/ralphbean/taskw;
diff --git a/pkgs/development/python-modules/taskw/use-template-for-taskwarrior-install-path.patch b/pkgs/development/python-modules/taskw/use-template-for-taskwarrior-install-path.patch
index 006d964d4016..8c7685c9d03b 100644
--- a/pkgs/development/python-modules/taskw/use-template-for-taskwarrior-install-path.patch
+++ b/pkgs/development/python-modules/taskw/use-template-for-taskwarrior-install-path.patch
@@ -4,45 +4,11 @@ Date:   Sun Nov 16 15:19:38 2014 +0100
 
     Use a template for taskwarrior install path.
 
-diff --git a/taskw/warrior.py b/taskw/warrior.py
-index 21dde88..e0509f2 100644
 --- a/taskw/warrior.py
 +++ b/taskw/warrior.py
-@@ -451,17 +451,17 @@ class TaskWarriorShellout(TaskWarriorBase):
-     def _execute(self, *args):
-         """ Execute a given taskwarrior command with arguments
- 
-         Returns a 2-tuple of stdout and stderr (respectively).
- 
-         """
-         command = (
-             [
+@@ -449 +449 @@ class TaskWarriorShellout(TaskWarriorBase):
 -                'task',
 +                '@@taskwarrior@@/bin/task',
-                 'rc:%s' % self.config_filename,
-             ]
-             + self.get_configuration_override_args()
-             + [six.text_type(arg) for arg in args]
-         )
- 
-         # subprocess is expecting bytestrings only, so nuke unicode if present
-         for i in range(len(command)):
-@@ -525,17 +525,17 @@ class TaskWarriorShellout(TaskWarriorBase):
-         except OSError:
-             # OSError is raised if subprocess.Popen fails to find
-             # the executable.
-             return False
- 
-     @classmethod
-     def get_version(cls):
-         taskwarrior_version = subprocess.Popen(
--            ['task', '--version'],
-+            ['@@taskwarrior@@/bin/task', '--version'],
-             stdout=subprocess.PIPE
-         ).communicate()[0]
-         return LooseVersion(taskwarrior_version.decode())
- 
-     def sync(self, init=False):
-         if self.get_version() < LooseVersion('2.3'):
-             raise UnsupportedVersionException(
-                 "'sync' requires version 2.3 of taskwarrior or later."
+@@ -553 +553 @@ class TaskWarriorShellout(TaskWarriorBase):
+-                ['task', '--version'],
++                ['@@taskwarrior@@/bin/task', '--version'],
diff --git a/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix b/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix
index 04f0c5cb66fa..93f389e6879a 100644
--- a/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix
+++ b/pkgs/development/tools/continuous-integration/gitlab-runner/default.nix
@@ -1,16 +1,16 @@
 { lib, buildGoPackage, fetchFromGitLab, fetchurl }:
 
 let
-  version = "11.5.0";
+  version = "11.6.0";
   # Gitlab runner embeds some docker images these are prebuilt for arm and x86_64
   docker_x86_64 = fetchurl {
     url = "https://gitlab-runner-downloads.s3.amazonaws.com/v${version}/helper-images/prebuilt-x86_64.tar.xz";
-    sha256 = "1siiws19qzfv2nnyp9fy215yd08iv70x830b61kr1742ywc0jcbn";
+    sha256 = "16xwj962biny18ci8lvfc6r6jq9vcdlc8vs6w7d5yzvd9x55rvwd";
   };
 
   docker_arm = fetchurl {
     url = "https://gitlab-runner-downloads.s3.amazonaws.com/v${version}/helper-images/prebuilt-arm.tar.xz";
-    sha256 = "0d7wnpry4861dcmpspbaar97mkf0jf2bcxvr4nph9xnkw8w7fs2z";
+    sha256 = "05wb7imly0c5zqmxrgdpls8izsq1g409nh31yf6j0sr76m8qkvf9";
   };
 in
 buildGoPackage rec {
@@ -29,7 +29,7 @@ buildGoPackage rec {
     owner = "gitlab-org";
     repo = "gitlab-runner";
     rev = "v${version}";
-    sha256 = "028bl249yfccdnwskbn6sxzf1xsg94chbm107n2h83j7a81cz8kw";
+    sha256 = "1g9wyi9n9xvynvn7c8kjzm5pznyw7w4ziklxjniaa69idzgvbl5g";
   };
 
   patches = [ ./fix-shell-path.patch ];
diff --git a/pkgs/development/tools/misc/dejagnu/default.nix b/pkgs/development/tools/misc/dejagnu/default.nix
index 26eaf707b2bd..c04031bc41db 100644
--- a/pkgs/development/tools/misc/dejagnu/default.nix
+++ b/pkgs/development/tools/misc/dejagnu/default.nix
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
 
   # Note: The test-suite *requires* /dev/pts among the `build-chroot-dirs' of
   # the build daemon when building in a chroot.  See
-  # <http://thread.gmane.org/gmane.linux.distributions.nixos/1036> for
+  # <https://www.mail-archive.com/nix-dev@cs.uu.nl/msg01056.html> for
   # details.
 
   # The test-suite needs to have a non-empty stdin:
diff --git a/pkgs/os-specific/linux/ati-drivers/default.nix b/pkgs/os-specific/linux/ati-drivers/default.nix
index cda7e03cd066..bc35d14321b4 100644
--- a/pkgs/os-specific/linux/ati-drivers/default.nix
+++ b/pkgs/os-specific/linux/ati-drivers/default.nix
@@ -19,7 +19,7 @@ with stdenv.lib;
 # make sure libglx.so of ati is used. xorg.xorgserver does provide it as well
 # which is a problem because it doesn't contain the xorgserver patch supporting
 # the XORG_DRI_DRIVER_PATH env var.
-# See http://thread.gmane.org/gmane.linux.distributions.nixos/4145 for a
+# See https://marc.info/?l=nix-dev&m=139641585515351 for a
 # workaround (TODO)
 
 # The gentoo ebuild contains much more "magic" and is usually a great resource to
diff --git a/pkgs/servers/monitoring/net-snmp/default.nix b/pkgs/servers/monitoring/net-snmp/default.nix
index 0e7a53306eb4..d86eac719a60 100644
--- a/pkgs/servers/monitoring/net-snmp/default.nix
+++ b/pkgs/servers/monitoring/net-snmp/default.nix
@@ -28,7 +28,7 @@ stdenv.mkDerivation rec {
       perlarchname=$(perl -e 'use Config; print $Config{archname};')
       installFlags="INSTALLSITEARCH=$out/lib/perl5/site_perl/$perlversion/$perlarchname INSTALLSITEMAN3DIR=$out/share/man/man3"
 
-      # http://comments.gmane.org/gmane.network.net-snmp.user/32434
+      # http://article.gmane.org/gmane.network.net-snmp.user/32434
       substituteInPlace "man/Makefile.in" --replace 'grep -vE' '@EGREP@ -v'
     '';
 
diff --git a/pkgs/servers/monitoring/uchiwa/bower-packages.nix b/pkgs/servers/monitoring/uchiwa/bower-packages.nix
index a8180c5de3dc..40789fa34f8d 100644
--- a/pkgs/servers/monitoring/uchiwa/bower-packages.nix
+++ b/pkgs/servers/monitoring/uchiwa/bower-packages.nix
@@ -1,7 +1,7 @@
 # Generated by bower2nix v3.2.0 (https://github.com/rvl/bower2nix)
 { fetchbower, buildEnv }:
 buildEnv { name = "bower-env"; ignoreCollisions = true; paths = [
-  (fetchbower "uchiwa-web" "1.3.1" "1.3.1" "0vhfwm4z3d4v4p2vfq1vvk4fifxm43f8lyccwpgmw153z4gj14gk")
+  (fetchbower "uchiwa-web" "1.5.0" "1.5.0" "0z7g4nb7cm5w5l8w1856sbib15sx022mqpap9d49s6ppnn53vcs1")
   (fetchbower "angular" "1.6.10" "~1.6.3" "0ag8xddsgxx5yka4wjq4ala4y6z3x2g1vc3x7a1n291fzz26p7ws")
   (fetchbower "angular-bootstrap" "2.2.0" "~2.2.0" "11r2nlwp6xrim2y6lnrr8v064mx3bmlxchqpg1i803v9zxz3q53d")
   (fetchbower "angular-cookies" "1.6.10" "~1.6.3" "0bjgmz5jnw06dfxhq9sajj62fk0b3v4j9p7nb45x8bl8rzkf25pn")
@@ -19,7 +19,7 @@ buildEnv { name = "bower-env"; ignoreCollisions = true; paths = [
   (fetchbower "highlightjs" "9.1.0" "~9.1.0" "0ld1da3h416a5j8v3v50rrpm4xwvvq8k8y2vwncvaqm9cqddz4s3")
   (fetchbower "moment" "2.16.0" "~2.16.0" "1mji892i60f2aw3vhl6878acrcgh0ycn3r4af0ivnjf8az2b9n71")
   (fetchbower "moment-picker" "0.9.11" "~0.9.7" "0p2g6rp2kcixydrga9lfihg4bxb598rvpi8n8l59mp549diy7vsb")
-  (fetchbower "ua-parser-js" "0.7.18" "~0.7.12" "0qi7y5yrsdh2brpmwx0xs53bzr4pja5x1k2875x6zh259ag3zdkn")
+  (fetchbower "ua-parser-js" "0.7.19" "~0.7.12" "0s1yaspccz234hm772hlybjsi0kndzwpjx5lzy3y1s4wfk248ks4")
   (fetchbower "jsoneditor" "5.5.11" "~5.5.10" "1gfsf8jqnd3hb3r9s9246mg40iqxk2ix8k4bjnrsbfmg6cd3xw6x")
   (fetchbower "jquery" "3.3.1" ">= 1.9.0" "1l891s3vgnpi1g8ksplid9jvrvnnv6lci8vraix4ssy50i264rkx")
 ]; }
diff --git a/pkgs/servers/monitoring/uchiwa/src.nix b/pkgs/servers/monitoring/uchiwa/src.nix
index 51c343d01da8..cf5376318b45 100644
--- a/pkgs/servers/monitoring/uchiwa/src.nix
+++ b/pkgs/servers/monitoring/uchiwa/src.nix
@@ -1,4 +1,4 @@
 {
-    version = "1.3.1-1";
-    sha256  = "1cjb7k19iy79hh9gbjx67yrz44y92s516d0h403bf6w272g23yzi";
+    version = "1.5.0-1";
+    sha256  = "05idwiv47zav46wi1hfly6rylpw8qryr12xlz47ic04ggdlga13b";
 }
diff --git a/pkgs/tools/compression/mozlz4a/default.nix b/pkgs/tools/compression/mozlz4a/default.nix
index abd094836664..ce2aa9520d67 100644
--- a/pkgs/tools/compression/mozlz4a/default.nix
+++ b/pkgs/tools/compression/mozlz4a/default.nix
@@ -1,4 +1,5 @@
-{stdenv, fetchurl, python3, pylz4}:
+{ stdenv, fetchurl, python3 }:
+
 stdenv.mkDerivation rec {
   name = "${pname}-${version}";
   pname = "mozlz4a";
@@ -21,7 +22,7 @@ stdenv.mkDerivation rec {
     chmod a+x "$out/bin/mozlz4a"
   '';
 
-  buildInputs = [ pylz4 python3 ];
+  buildInputs = [ python3 python3.pkgs.python-lz4 ];
 
   meta = {
     inherit version;
diff --git a/pkgs/tools/misc/coreutils/default.nix b/pkgs/tools/misc/coreutils/default.nix
index 0ddfad65a7a1..c252a8748bce 100644
--- a/pkgs/tools/misc/coreutils/default.nix
+++ b/pkgs/tools/misc/coreutils/default.nix
@@ -63,8 +63,8 @@ stdenv.mkDerivation rec {
     ++ optional (stdenv.hostPlatform != stdenv.buildPlatform && stdenv.hostPlatform.libc != "glibc") libiconv;
 
   # The tests are known broken on Cygwin
-  # (http://thread.gmane.org/gmane.comp.gnu.core-utils.bugs/19025),
-  # Darwin (http://thread.gmane.org/gmane.comp.gnu.core-utils.bugs/19351),
+  # (http://article.gmane.org/gmane.comp.gnu.core-utils.bugs/19025),
+  # Darwin (http://article.gmane.org/gmane.comp.gnu.core-utils.bugs/19351),
   # and {Open,Free}BSD.
   # With non-standard storeDir: https://github.com/NixOS/nix/issues/512
   doCheck = stdenv.hostPlatform == stdenv.buildPlatform
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b9765628fffe..dbf1c2e4e39d 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -1693,9 +1693,7 @@ in
 
   mongodb-tools = callPackage ../tools/misc/mongodb-tools { };
 
-  mozlz4a = callPackage ../tools/compression/mozlz4a {
-    pylz4 = python3Packages.lz4;
-  };
+  mozlz4a = callPackage ../tools/compression/mozlz4a { };
 
   msr-tools = callPackage ../os-specific/linux/msr-tools { };
 
@@ -4796,7 +4794,7 @@ in
 
   fmodex = callPackage ../games/zandronum/fmod.nix { };
 
-  pdfmod = callPackage ../applications/misc/pdfmod { mono = mono4; };
+  pdfmod = callPackage ../applications/misc/pdfmod { };
 
   pdf-quench = callPackage ../applications/misc/pdf-quench { };
 
@@ -10313,7 +10311,7 @@ in
 
   hydraAntLogger = callPackage ../development/libraries/java/hydra-ant-logger { };
 
-  hyena = callPackage ../development/libraries/hyena { mono = mono4; };
+  hyena = callPackage ../development/libraries/hyena { };
 
   hyperscan = callPackage ../development/libraries/hyperscan { };
 
@@ -10700,6 +10698,8 @@ in
 
   libde265 = callPackage ../development/libraries/libde265 {};
 
+  libdeflate = callPackage ../development/libraries/libdeflate { };
+
   libdevil = callPackage ../development/libraries/libdevil {
     inherit (darwin.apple_sdk.frameworks) OpenGL;
   };
diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix
index ba583418163a..c670db817728 100644
--- a/pkgs/top-level/ocaml-packages.nix
+++ b/pkgs/top-level/ocaml-packages.nix
@@ -580,6 +580,8 @@ let
     piqi = callPackage ../development/ocaml-modules/piqi { };
     piqi-ocaml = callPackage ../development/ocaml-modules/piqi-ocaml { };
 
+    ppxfind = callPackage ../development/ocaml-modules/ppxfind { };
+
     ppxlib = callPackage ../development/ocaml-modules/ppxlib { };
 
     psmt2-frontend = callPackage ../development/ocaml-modules/psmt2-frontend { };
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index b8fbcaa194c1..d3e384d8ed26 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -648,6 +648,7 @@ in {
   python-hosts = callPackage ../development/python-modules/python-hosts { };
 
   python-lz4 = callPackage ../development/python-modules/python-lz4 { };
+  lz4 = self.python-lz4; # alias 2018-12-05
 
   python-ldap-test = callPackage ../development/python-modules/python-ldap-test { };
 
@@ -3268,8 +3269,6 @@ in {
 
   ldappool = callPackage ../development/python-modules/ldappool { };
 
-  lz4 = callPackage ../development/python-modules/lz4 { };
-
   retrying = callPackage ../development/python-modules/retrying { };
 
   fasteners = callPackage ../development/python-modules/fasteners { };
@@ -4259,7 +4258,9 @@ in {
 
   blessings = callPackage ../development/python-modules/blessings { };
 
-  secretstorage = callPackage ../development/python-modules/secretstorage { };
+  secretstorage = if isPy3k
+    then callPackage ../development/python-modules/secretstorage { }
+    else callPackage ../development/python-modules/secretstorage/2.nix { };
 
   semantic = callPackage ../development/python-modules/semantic { };