Merge master into staging

54 files changed, 257 insertions, 176 deletions

diff --git a/pkgs/applications/altcoins/go-ethereum.nix b/pkgs/applications/altcoins/go-ethereum.nix
index 74d38b59fc23..79c8e0dfde8a 100644
--- a/pkgs/applications/altcoins/go-ethereum.nix
+++ b/pkgs/applications/altcoins/go-ethereum.nix
@@ -12,17 +12,6 @@ buildGoPackage rec {
   # Fixes Cgo related build failures (see https://github.com/NixOS/nixpkgs/issues/25959 )
   hardeningDisable = [ "fortify" ];
 
-  # Only install binaries in $out, source is not interesting and takes ~50M
-  outputs = [ "out" ];
-  preFixup = ''
-    export bin="''${out}"
-  '';
-  installPhase = ''
-    mkdir -p $out/bin $out
-    dir="$NIX_BUILD_TOP/go/bin"
-    [ -e "$dir" ] && cp -r $dir $out
-  '';
-
   src = fetchFromGitHub {
     owner = "ethereum";
     repo = "go-ethereum";
diff --git a/pkgs/applications/altcoins/parity-ui/default.nix b/pkgs/applications/altcoins/parity-ui/default.nix
index 33e72125c6bd..b22302d0d39a 100644
--- a/pkgs/applications/altcoins/parity-ui/default.nix
+++ b/pkgs/applications/altcoins/parity-ui/default.nix
@@ -6,11 +6,11 @@ uiEnv = pkgs.callPackage ./env.nix { };
 
 in stdenv.mkDerivation rec {
   name = "parity-ui-${version}";
-  version = "0.2.5";
+  version = "0.2.8";
 
   src = fetchurl {
     url = "https://github.com/parity-js/shell/releases/download/v${version}/parity-ui_${version}_amd64.deb";
-    sha256 = "1jk7ac6qqxs47hf16vhr94ix4wf51qzpm55q8h6wsx1lrgy1y3g6";
+    sha256 = "1nyarq73jdknhax68cq2i868sznghzj70kvk4ixypxnjb1q6a53a";
     name = "${name}.deb";
   };
 
diff --git a/pkgs/applications/altcoins/parity/default.nix b/pkgs/applications/altcoins/parity/default.nix
index 4ee13665d1be..a41488c48b50 100644
--- a/pkgs/applications/altcoins/parity/default.nix
+++ b/pkgs/applications/altcoins/parity/default.nix
@@ -1,6 +1,6 @@
 let
-  version     = "1.10.8";
-  sha256      = "0q6blsbxn48afqf3cmxvmdlyzvf0cpqcymsjbsk8nyx0zxzf1dpk";
+  version     = "1.10.9";
+  sha256      = "1irfksx887vvvdf97q26qacn22kmyj8fgb3ghh9wv5qnzrn3564g";
   cargoSha256 = "0rzhabyhprmcg0cdmibbb8zgqf6z4izsdq8m060mppkkv675x0lf";
   patches     = [ ./patches/vendored-sources-1.10.patch ];
 in
diff --git a/pkgs/applications/audio/elisa/default.nix b/pkgs/applications/audio/elisa/default.nix
index 4f2ec36152ae..90ea4c58ea4a 100644
--- a/pkgs/applications/audio/elisa/default.nix
+++ b/pkgs/applications/audio/elisa/default.nix
@@ -7,13 +7,13 @@
 
 mkDerivation rec {
   name = "elisa-${version}";
-  version = "0.2.0";
+  version = "0.2.1";
 
   src = fetchFromGitHub {
     owner  = "KDE";
     repo   = "elisa";
     rev    = "v${version}";
-    sha256 = "0lpzn55b8gf3byzwv9909x40p98aqlh35vidkrwnnbwgygsa85bw";
+    sha256 = "0b3rx3gh6adlrbmgj75dicqv6qzzn4fyfxbf1nwh3zd2hi0ca89w";
   };
 
   nativeBuildInputs = [ extra-cmake-modules kdoctools wrapGAppsHook ];
diff --git a/pkgs/applications/audio/mopidy/soundcloud.nix b/pkgs/applications/audio/mopidy/soundcloud.nix
index 0fda09fd5220..8002feb0f901 100644
--- a/pkgs/applications/audio/mopidy/soundcloud.nix
+++ b/pkgs/applications/audio/mopidy/soundcloud.nix
@@ -2,13 +2,13 @@
 
 pythonPackages.buildPythonApplication rec {
   pname = "mopidy-soundcloud";
-  version = "2.0.2";
+  version = "2.1.0";
 
   src = fetchFromGitHub {
     owner = "mopidy";
     repo = "mopidy-soundcloud";
     rev = "v${version}";
-    sha256 = "13n44975n1wwcf7qg1c7drc2bavhjnr9hnq1v0n5hdgyx8ji67gi";
+    sha256 = "131qdm9i0j3ayff0js11qcmbjv50ws5s6iiqr6x5b66ymjl4scfv";
   };
 
   propagatedBuildInputs = [ mopidy ];
diff --git a/pkgs/applications/audio/musescore/default.nix b/pkgs/applications/audio/musescore/default.nix
index 14610faff0af..a5c38a477415 100644
--- a/pkgs/applications/audio/musescore/default.nix
+++ b/pkgs/applications/audio/musescore/default.nix
@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   name = "musescore-${version}";
-  version = "2.3";
+  version = "2.3.1";
 
   src = fetchFromGitHub {
     owner  = "musescore";
     repo   = "MuseScore";
     rev    = "v${version}";
-    sha256 = "1rmnqblh4irrwdszh0glpnf3q6f8xk8gxfmmjk8swxr59bmqk3gz";
+    sha256 = "00inrw9g8g34g74bhg5gp0rr5nydhjraiyn7vpl7kaqi5yzmhawd";
   };
 
   cmakeFlags = [
diff --git a/pkgs/applications/editors/android-studio/default.nix b/pkgs/applications/editors/android-studio/default.nix
index ed18d34e4a9c..60566a0fcf89 100644
--- a/pkgs/applications/editors/android-studio/default.nix
+++ b/pkgs/applications/editors/android-studio/default.nix
@@ -13,9 +13,9 @@ let
     sha256Hash = "196yaswbxh2nd83gimjxr8ggr5xkdxq7n3xlh6ax73v59pj4hryq";
   };
   latestVersion = {
-    version = "3.3.0.1"; # "Android Studio 3.3 Canary 2"
-    build = "181.4869471";
-    sha256Hash = "1v2v09gd5vxh4nzbnrjfh0blpzz71i3i7lq5bkjsfl0g82r8j512";
+    version = "3.3.0.2"; # "Android Studio 3.3 Canary 3"
+    build = "181.4884283";
+    sha256Hash = "0r93yzw87cgzz60p60gknij5vaqmv1a1kyd4cr9gx8cbxw46lhwh";
   };
 in rec {
   # Old alias
@@ -43,9 +43,9 @@ in rec {
   beta = mkStudio (latestVersion // {
     pname = "android-studio-preview";
     #pname = "android-studio-beta"; # TODO: Rename and provide symlink
-    version = "3.2.0.19"; # "Android Studio 3.2 Beta 2"
-    build = "181.4860949";
-    sha256Hash = "1v1h42xp2fxj8366q9l9b0shk0y1vz9kny0rf7y48kyr5h9glnwr";
+    version = "3.2.0.20"; # "Android Studio 3.2 Beta 3"
+    build = "181.4868252";
+    sha256Hash = "17r7gvy317vh2r56yvhnn7dym0q6gs8r04fdr7hx53s9rb79sd1j";
 
     meta = stable.meta // {
       description = "The Official IDE for Android (beta channel)";
diff --git a/pkgs/applications/gis/whitebox-tools/default.nix b/pkgs/applications/gis/whitebox-tools/default.nix
new file mode 100644
index 000000000000..f6adf7857ede
--- /dev/null
+++ b/pkgs/applications/gis/whitebox-tools/default.nix
@@ -0,0 +1,24 @@
+{ stdenv, rustPlatform , fetchFromGitHub, Security }:
+rustPlatform.buildRustPackage rec {
+  name = "whitebox_tools-${version}";
+  version = "0.9.0";
+
+  src = fetchFromGitHub {
+    owner = "jblindsay";
+    repo = "whitebox-tools";
+    rev = "6221cdf327be70f0ee4f2053b76bfa01c3f37caa";
+    sha256 = "1423ga964mz7qkl88vkcm8qfprsksx04aq4sz9v5ghnmdzzvl89x";
+  };
+
+  buildInputs = stdenv.lib.optional stdenv.isDarwin Security;
+
+  cargoSha256 = "1gbgirng21ak0kl3fiyr6lxwzrjd5v79gcrbzf941nb8y8rlvz7k";
+
+  meta = with stdenv.lib; {
+    description = "An advanced geospatial data analysis platform";
+    homepage = http://www.uoguelph.ca/~hydrogeo/WhiteboxTools/index.html;
+    license = licenses.mit;
+    maintainers = [ maintainers.mpickering ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/applications/graphics/ImageMagick/7.0.nix b/pkgs/applications/graphics/ImageMagick/7.0.nix
index d8c11f33439a..63cf950f02a4 100644
--- a/pkgs/applications/graphics/ImageMagick/7.0.nix
+++ b/pkgs/applications/graphics/ImageMagick/7.0.nix
@@ -14,8 +14,8 @@ let
     else throw "ImageMagick is not supported on this platform.";
 
   cfg = {
-    version = "7.0.8-2";
-    sha256 = "06cpvvv8xikw5jm1pa2xxxlnsy743ham67yshpndn2x3fyf48267";
+    version = "7.0.8-6";
+    sha256 = "1v7m1g9a7fqc8nravvv3dy54nzd3ip75hcnkdrpb5wbiz9pqgzi3";
     patches = [];
   };
 in
diff --git a/pkgs/applications/graphics/exrdisplay/default.nix b/pkgs/applications/graphics/exrdisplay/default.nix
index e698fb8f2341..34e7b1f23088 100644
--- a/pkgs/applications/graphics/exrdisplay/default.nix
+++ b/pkgs/applications/graphics/exrdisplay/default.nix
@@ -1,7 +1,5 @@
 { stdenv, fetchurl, pkgconfig, fltk, openexr, libGLU_combined, openexr_ctl }:
 
-assert fltk.glSupport;
-
 stdenv.mkDerivation {
   name ="openexr_viewers-2.2.1";
 
@@ -14,14 +12,14 @@ stdenv.mkDerivation {
     ./configure --prefix=$out --with-fltk-config=${fltk}/bin/fltk-config
   '';
 
-  buildPahse = ''
+  buildPhase = ''
     make LDFLAGS="`fltk-config --ldflags` -lGL -lfltk_gl"
   '';
 
   nativeBuildInputs = [ pkgconfig ];
   buildInputs = [ openexr fltk libGLU_combined openexr_ctl ];
 
-  meta = { 
+  meta = {
     description = "Application for viewing OpenEXR images on a display at various exposure settings";
     homepage = http://openexr.com;
     platforms = stdenv.lib.platforms.linux;
diff --git a/pkgs/applications/graphics/freecad/default.nix b/pkgs/applications/graphics/freecad/default.nix
index 8001080a170a..6362d6c06fe9 100644
--- a/pkgs/applications/graphics/freecad/default.nix
+++ b/pkgs/applications/graphics/freecad/default.nix
@@ -1,5 +1,5 @@
 { stdenv, fetchurl, cmake, coin3d, xercesc, ode, eigen, qt4, opencascade, gts
-, hdf5, vtk, medfile, boost, zlib, python27Packages, swig, gfortran, fetchpatch
+, hdf5, vtk, medfile, zlib, python27Packages, swig, gfortran, fetchpatch
 , soqt, libf2c, makeWrapper, makeDesktopItem
 , mpi ? null }:
 
@@ -16,7 +16,7 @@ in stdenv.mkDerivation rec {
     sha256 = "1yv6abdzlpn4wxy315943xwrnbywxqfgkjib37qwfvbb8y9p60df";
   };
 
-  buildInputs = with pythonPackages; [ cmake coin3d xercesc ode eigen qt4 opencascade gts
+  buildInputs = [ cmake coin3d xercesc ode eigen qt4 opencascade gts
     zlib  swig gfortran soqt libf2c makeWrapper  mpi vtk hdf5 medfile
   ] ++ (with pythonPackages; [
     matplotlib pycollada pyside pysideShiboken pysideTools pivy python boost
diff --git a/pkgs/applications/misc/cherrytree/default.nix b/pkgs/applications/misc/cherrytree/default.nix
index 0b2bee9122e0..03709c30373d 100644
--- a/pkgs/applications/misc/cherrytree/default.nix
+++ b/pkgs/applications/misc/cherrytree/default.nix
@@ -4,11 +4,11 @@ with stdenv.lib;
 stdenv.mkDerivation rec {
 
   name = "cherrytree-${version}";
-  version = "0.38.4";
+  version = "0.38.5";
 
   src = fetchurl {
     url = "https://www.giuspen.com/software/${name}.tar.xz";
-    sha256 = "1zazyxkrli77wahn4c1z24qyz5bwlayl335f2kdxb44dicrx58g2";
+    sha256 = "1ja3b14vm3yd26pf82p2qlld0flqkqvgdg2g33r5dav6wfq3pz6y";
   };
 
   buildInputs = with pythonPackages;
diff --git a/pkgs/applications/misc/chirp/default.nix b/pkgs/applications/misc/chirp/default.nix
index 148031273bed..6e0152c71ed0 100644
--- a/pkgs/applications/misc/chirp/default.nix
+++ b/pkgs/applications/misc/chirp/default.nix
@@ -3,11 +3,11 @@
 
 stdenv.mkDerivation rec {
   name = "chirp-daily-${version}";
-  version = "20180623";
+  version = "20180707";
 
   src = fetchurl {
     url = "https://trac.chirp.danplanet.com/chirp_daily/daily-${version}/${name}.tar.gz";
-    sha256 = "0s7b5w98rblqfcpvaxkkri0sfqxmqjwgdf8syzva50vm7swrg946";
+    sha256 = "09siq74k0ss65ssck7i7h515dxp7fhdz5klc3y0yp9wajn706ic3";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/applications/misc/ephemeralpg/default.nix b/pkgs/applications/misc/ephemeralpg/default.nix
index 65df422599ca..0ade32d99899 100644
--- a/pkgs/applications/misc/ephemeralpg/default.nix
+++ b/pkgs/applications/misc/ephemeralpg/default.nix
@@ -1,10 +1,10 @@
 { stdenv, fetchurl, postgresql, makeWrapper }:
 stdenv.mkDerivation rec {
   name = "ephemeralpg-${version}";
-  version = "2.2";
+  version = "2.5";
   src = fetchurl {
     url = "http://ephemeralpg.org/code/${name}.tar.gz";
-    sha256 = "1v48bcmc23zzqbha80p3spxd5l347qnjzs4z44wl80i2s8fdzlyz";
+    sha256 = "004fcll7248h73adkqawn9bhkqj9wsxyi3w99x64f7s37r2518wk";
   };
   buildInputs = [ makeWrapper ];
   installPhase = ''
diff --git a/pkgs/applications/misc/ipmiview/default.nix b/pkgs/applications/misc/ipmiview/default.nix
index 638765840cb9..58fcd59a2b2f 100644
--- a/pkgs/applications/misc/ipmiview/default.nix
+++ b/pkgs/applications/misc/ipmiview/default.nix
@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
    name = "IPMIView-${version}";
-   version = "2.13.0";
-   buildVersion = "170504";
+   version = "2.14.0";
+   buildVersion = "180213";
 
    src = fetchurl {
     url = "ftp://ftp.supermicro.com/utility/IPMIView/Linux/IPMIView_${version}_build.${buildVersion}_bundleJRE_Linux_x64.tar.gz";
-    sha256 = "1hfw5g6lxg3vqg0nc3g2sv2h6bn8za35bxxms0ri0sgb9v3xg1y6";
+    sha256 = "1wp22wm7smlsb25x0cck4p660cycfczxj381930crd1qrf68mw4h";
   };
 
    buildInputs = [ patchelf makeWrapper ];
diff --git a/pkgs/applications/misc/jgmenu/default.nix b/pkgs/applications/misc/jgmenu/default.nix
index 0bccc8bcc7ef..b868808ec3dc 100644
--- a/pkgs/applications/misc/jgmenu/default.nix
+++ b/pkgs/applications/misc/jgmenu/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "jgmenu-${version}";
-  version = "1.0";
+  version = "1.1";
 
   src = fetchFromGitHub {
     owner = "johanmalm";
     repo = "jgmenu";
     rev = "v${version}";
-    sha256 = "068mm0b2npz6qh9j8m9xd8sbznjp5g195vfav8a6016wgm6fhrx7";
+    sha256 = "0hnxzy5mm5z6r9gaimfsf7kbpr23khck2fhh3j8bk2lkp53420fz";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/applications/misc/wikicurses/default.nix b/pkgs/applications/misc/wikicurses/default.nix
index 84f7d4fd2913..d8628b794d71 100644
--- a/pkgs/applications/misc/wikicurses/default.nix
+++ b/pkgs/applications/misc/wikicurses/default.nix
@@ -1,24 +1,16 @@
-{ stdenv, fetchurl, pythonPackages }:
+{ stdenv, fetchFromGitHub, pythonPackages }:
 
 pythonPackages.buildPythonApplication rec {
-  version = "1.3";
+  version = "1.4";
   name = "wikicurses-${version}";
 
-  src = fetchurl {
-    url = "http://github.com/ids1024/wikicurses/archive/v${version}.tar.gz";
-    sha256 = "1yxgafk1sczg1xi2p6nhrvr3hchp7ydw98n48lp3qzwnryn1kxv8";
+  src = fetchFromGitHub {
+    owner = "ids1024";
+    repo = "wikicurses";
+    rev = "v${version}";
+    sha256 = "0f14s4qx3q5pr5vn460c34b5mbz2xs62d8ljs3kic8gmdn8x2knm";
   };
 
-  patches = [
-    # This is necessary to build without a config file.
-    # It can be safely removed after updating to wikicurses to 1.4
-    # or when commit 4b944ac339312b642c6dc5d6b5a2f7be7503218f is included
-    (fetchurl {
-      url = "https://github.com/ids1024/wikicurses/commit/4b944ac339312b642c6dc5d6b5a2f7be7503218f.patch";
-      sha256 = "0ii4b0c4hb1zdhcpp4ij908mfy5b8khpm1l7xr7lp314lfhsg9as";
-    })
-  ];
-
   propagatedBuildInputs = with pythonPackages; [ urwid beautifulsoup4 lxml ];
 
   meta = {
@@ -26,6 +18,7 @@ pythonPackages.buildPythonApplication rec {
     homepage = https://github.com/ids1024/wikicurses/;
     license = stdenv.lib.licenses.mit;
     platforms = stdenv.lib.platforms.unix;
+    maintainers = with stdenv.lib.maintainers; [ pSub ];
   };
 
 }
diff --git a/pkgs/applications/misc/wsjtx/default.nix b/pkgs/applications/misc/wsjtx/default.nix
index 311983e8f527..23be3a5dc4fa 100644
--- a/pkgs/applications/misc/wsjtx/default.nix
+++ b/pkgs/applications/misc/wsjtx/default.nix
@@ -4,12 +4,12 @@
 
 stdenv.mkDerivation rec {
   name = "wsjtx-${version}";
-  version = "1.9.0";
+  version = "1.9.1";
 
   # This is a composite source tarball containing both wsjtx and a hamlib fork
   src = fetchurl {
     url = "http://physics.princeton.edu/pulsar/K1JT/wsjtx-${version}.tgz";
-    sha256 = "1qxwiylnykh37kw780hh9xfphzbj8ndpfqz4xazld16v3qx2g0jc";
+    sha256 = "143r17fri08mwz28g17wcfxy60h3xgfk46mln5lmdr9k6355aqqc";
   };
 
   # Hamlib builds with autotools, wsjtx builds with cmake
diff --git a/pkgs/applications/misc/xmrig/default.nix b/pkgs/applications/misc/xmrig/default.nix
index 340d84fd2aaf..f61cbf397597 100644
--- a/pkgs/applications/misc/xmrig/default.nix
+++ b/pkgs/applications/misc/xmrig/default.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   name = "xmrig-${version}";
-  version = "2.6.3";
+  version = "2.6.4";
 
   src = fetchFromGitHub {
     owner = "xmrig";
     repo = "xmrig";
     rev = "v${version}";
-    sha256 = "1ssiq2yv8b3xg4kfp2cfzl41m5apjw2r2k74lh3fz0g0ix3cq55b";
+    sha256 = "1c68qg7433chri6q1yhyggy4mbq2vnn3p2fxs8gqmgij9vpqn3m2";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/applications/misc/xmrig/proxy.nix b/pkgs/applications/misc/xmrig/proxy.nix
index aacf71e17b6c..c013a9cc44ec 100644
--- a/pkgs/applications/misc/xmrig/proxy.nix
+++ b/pkgs/applications/misc/xmrig/proxy.nix
@@ -4,13 +4,13 @@
 
 stdenv.mkDerivation rec {
   name = "xmrig-proxy-${version}";
-  version = "2.6.3";
+  version = "2.6.4";
 
   src = fetchFromGitHub {
     owner = "xmrig";
     repo = "xmrig-proxy";
     rev = "v${version}";
-    sha256 = "1f573shf0qv1kh0sb9sljagpb2q1rn8h7qc1hxlb5nlchs9qcnnn";
+    sha256 = "0h6ihrrkgwi8k642iqq13qx3zlxl9r8q7wm417hb7j35rnmwn8lq";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/applications/misc/xscope/default.nix b/pkgs/applications/misc/xscope/default.nix
new file mode 100644
index 000000000000..28ce4a0d500d
--- /dev/null
+++ b/pkgs/applications/misc/xscope/default.nix
@@ -0,0 +1,24 @@
+{ stdenv, fetchurl, pkgconfig, libXt }:
+
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "xscope";
+  version = "1.4.1";
+
+  src = fetchurl {
+    url = "mirror://xorg/individual/app/${name}.tar.bz2";
+    sha256 = "08zl3zghvbcqy0r5dn54dim84lp52s0ygrr87jr3a942a6ypz01k";
+  };
+
+  nativeBuildInputs = [ pkgconfig ];
+  buildInputs = [ libXt ];
+
+  meta = with stdenv.lib; {
+    description = "program to monitor X11/Client conversations";
+    homepage = https://cgit.freedesktop.org/xorg/app/xscope/;
+    license = with licenses; [ mit ];
+    maintainers = with maintainers; [ ];
+    platforms = with platforms; unix;
+  };
+}
+
diff --git a/pkgs/applications/networking/browsers/chromium/plugins.nix b/pkgs/applications/networking/browsers/chromium/plugins.nix
index 70d457028292..775ae960eb7d 100644
--- a/pkgs/applications/networking/browsers/chromium/plugins.nix
+++ b/pkgs/applications/networking/browsers/chromium/plugins.nix
@@ -98,12 +98,11 @@ let
 
   flash = stdenv.mkDerivation rec {
     name = "flashplayer-ppapi-${version}";
-    version = "30.0.0.113";
+    version = "30.0.0.134";
 
     src = fetchzip {
-      url = "https://fpdownload.adobe.com/pub/flashplayer/pdc/"
-          + "${version}/flash_player_ppapi_linux.x86_64.tar.gz";
-      sha256 = "0bcsrsz2dd12xs9vn2977k4s6hag1cknkrsgxz3c9pxk4jz99f3k";
+      url = "https://fpdownload.adobe.com/pub/flashplayer/pdc/${version}/flash_player_ppapi_linux.x86_64.tar.gz";
+      sha256 = "1g6695w1ijqs8jbkbrb403ca1vvrf298ayvxslrvk70x6l7lp2ys";
       stripRoot = false;
     };
 
diff --git a/pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/default.nix b/pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/default.nix
index 507697f0c2c3..78e410cda0fc 100644
--- a/pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/default.nix
+++ b/pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/default.nix
@@ -73,7 +73,7 @@ let
 in
 stdenv.mkDerivation rec {
   name = "flashplayer-${version}";
-  version = "30.0.0.113";
+  version = "30.0.0.134";
 
   src = fetchurl {
     url =
@@ -84,14 +84,14 @@ stdenv.mkDerivation rec {
     sha256 =
       if debug then
         if arch == "x86_64" then
-          "1s4i9lmlydm8b373pi8jw5xf3fhcq75fgqyp7xd7aava8hay7x0j"
+          "1ld9ldsqd5vgghpidskxqmlz8gwdyf3mi3wmfdiaabdjxgzbg8sk"
         else
-          "1jhzvrn6f9zcynx3zq0vxidaps946aymm7l16c42p1f7q9s8msb4"
+          "1n96rx95spj4r34amapqr1i1klhv944fpvhdmn7gqjawr2hf36js"
       else
         if arch == "x86_64" then
-          "05dv4cn9i3zz5fmy16dxs9m1rpvlaih4gzsrf0q1zfjn46jbyw2l"
+          "0331r5af4zrvwc4h7dp5qyy91dfam5z03yjggls3x04i10nz5myw"
         else
-          "0pn159rzx6nb6lmkghccl0ynnc9ihfbr4rvfp14gm4n6jzbl6vg8";
+          "01ibzqzlscpkfqp33bx7qcpz6gfqp4dq9ny3zasvjhi5xqd78j1k";
   };
 
   nativeBuildInputs = [ unzip ];
diff --git a/pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/standalone.nix b/pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/standalone.nix
index 8664b20e82d7..563c8db418d4 100644
--- a/pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/standalone.nix
+++ b/pkgs/applications/networking/browsers/mozilla-plugins/flashplayer/standalone.nix
@@ -55,7 +55,7 @@ let
 in
 stdenv.mkDerivation rec {
   name = "flashplayer-standalone-${version}";
-  version = "30.0.0.113";
+  version = "30.0.0.134";
 
   src = fetchurl {
     url =
@@ -65,9 +65,9 @@ stdenv.mkDerivation rec {
         "https://fpdownload.macromedia.com/pub/flashplayer/updaters/30/flash_player_sa_linux.x86_64.tar.gz";
     sha256 =
       if debug then
-        "0vdzmk9l04jq9mfkdddsqrga7ndikq910indl7wa3vndghrahmn0"
+        "0snkhs9w192azgv3nykxmgb47z395yrx7faxshasmc7abvvnfpx1"
       else
-        "10rm48i3h6x1dygjivv2mvd0jq6n40j5c2ik090s7i0ily5z97m8";
+        "1wgcsbm9w46sp8347agd5m05x3xrki8vi6pf208ifihljw04hbx3";
   };
 
   nativeBuildInputs = [ unzip ];
diff --git a/pkgs/applications/networking/browsers/qutebrowser/default.nix b/pkgs/applications/networking/browsers/qutebrowser/default.nix
index 4e0f362360df..47a273e99f98 100644
--- a/pkgs/applications/networking/browsers/qutebrowser/default.nix
+++ b/pkgs/applications/networking/browsers/qutebrowser/default.nix
@@ -28,12 +28,12 @@ let
 
 in python3Packages.buildPythonApplication rec {
   pname = "qutebrowser";
-  version = "1.4.0";
+  version = "1.4.1";
 
   # the release tarballs are different from the git checkout!
   src = fetchurl {
     url = "https://github.com/qutebrowser/qutebrowser/releases/download/v${version}/${pname}-${version}.tar.gz";
-    sha256 = "169xgwizw9kpdg0xll5jrxkb1k107cl4j1zx3jhmpsfbgykcnxpz";
+    sha256 = "0n2z92vb91gpfchdm9wsm712r9grbvxwdp4npl5c1nbq247dxwm3";
   };
 
   # Needs tox
diff --git a/pkgs/applications/networking/browsers/tor-browser-bundle/default.nix b/pkgs/applications/networking/browsers/tor-browser-bundle/default.nix
index 65ebaa3f80c5..031c520275fe 100644
--- a/pkgs/applications/networking/browsers/tor-browser-bundle/default.nix
+++ b/pkgs/applications/networking/browsers/tor-browser-bundle/default.nix
@@ -340,7 +340,7 @@ stdenv.mkDerivation rec {
   meta = with stdenv.lib; {
     description = "An unofficial version of the tor browser bundle, built from source";
     homepage = https://torproject.org/;
-    license = licenses.unfreeRedistributable; # TODO: check this
+    license = licenses.free;
     platforms = [ "x86_64-linux" ];
     hydraPlatforms = [ ];
     maintainers = with maintainers; [ joachifm ];
diff --git a/pkgs/applications/networking/cluster/flink/default.nix b/pkgs/applications/networking/cluster/flink/default.nix
index aed6987e2738..402a03b77f4a 100644
--- a/pkgs/applications/networking/cluster/flink/default.nix
+++ b/pkgs/applications/networking/cluster/flink/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl, makeWrapper, jre
-, version ? "1.4" }:
+, version ? "1.5" }:
 
 let
   versionMap = {
     "1.3" = {
-      flinkVersion = "1.3.2";
+      flinkVersion = "1.3.3";
       scalaVersion = "2.11";
-      sha256 = "0mf4qz0963bflzidgslvwpdlvj9za9sj20dfybplw9lhd4sf52rp";
+      sha256 = "0gfm48k5adr14gnhqri9cd01i9dprd0nwmnnz3yrpd20nq4ap4qy";
       hadoopBundle = "-hadoop27";
     };
     "1.4" = {
@@ -15,6 +15,12 @@ let
       sha256 = "0x3cikys5brin0kx9zr69xfp8k5w6g8141yrrr26ks7gpss2x636";
       hadoopBundle = "";
     };
+    "1.5" = {
+      flinkVersion = "1.5.0";
+      scalaVersion = "2.11";
+      sha256 = "0n5023dj8ivmbhqxmb3abmfh3ahb9vmcywq5i0ll5p7xxcw2c1cv";
+      hadoopBundle = "";
+    };
   };
 in
 
@@ -24,7 +30,7 @@ stdenv.mkDerivation rec {
   name = "flink-${flinkVersion}";
 
   src = fetchurl {
-    url = "mirror://apache/flink/${name}/${name}-bin-scala_${hadoopBundle}${scalaVersion}.tgz";
+    url = "mirror://apache/flink/${name}/${name}-bin${hadoopBundle}-scala_${scalaVersion}.tgz";
     inherit sha256;
   };
 
diff --git a/pkgs/applications/networking/cluster/heptio-ark/default.nix b/pkgs/applications/networking/cluster/heptio-ark/default.nix
index d24c307fcce5..1860874c436c 100644
--- a/pkgs/applications/networking/cluster/heptio-ark/default.nix
+++ b/pkgs/applications/networking/cluster/heptio-ark/default.nix
@@ -2,7 +2,7 @@
 
 buildGoPackage rec {
   name = "heptio-ark-${version}";
-  version = "0.7.1";
+  version = "0.9.0";
 
   goPackagePath = "github.com/heptio/ark";
 
@@ -10,7 +10,7 @@ buildGoPackage rec {
     rev = "v${version}";
     owner = "heptio";
     repo = "ark";
-    sha256 = "0j3x9zxcffxhlw0fxq2cw9ph37bqw90cbmf9xshmnj8yl9rbxp7y";
+    sha256 = "0b3jsgs35l8kk63pjnqn3911pyb397fyvsmd3jd8vzjawisgpdp7";
   };
 
   postInstall = "rm $bin/bin/generate";
diff --git a/pkgs/applications/networking/cluster/hetzner-kube/default.nix b/pkgs/applications/networking/cluster/hetzner-kube/default.nix
new file mode 100644
index 000000000000..fe2420a719d5
--- /dev/null
+++ b/pkgs/applications/networking/cluster/hetzner-kube/default.nix
@@ -0,0 +1,24 @@
+{ lib, buildGoPackage, fetchFromGitHub, ... }:
+
+let version = "0.3.1"; in
+
+buildGoPackage {
+  name = "hetzner-kube-${version}";
+
+  src = fetchFromGitHub {
+    owner = "xetys";
+    repo = "hetzner-kube";
+    rev = "${version}";
+    sha256 = "1xldh1ca8ym8cg3w5cxizmhqxwi5kmiin28f320mxdr28fzljc2w";
+  };
+
+  goPackagePath = "github.com/xetys/hetzner-kube";
+
+  meta = {
+    description = "A CLI tool for provisioning Kubernetes clusters on Hetzner Cloud";
+    homepage = https://github.com/xetys/hetzner-kube;
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ eliasp ];
+    platforms = lib.platforms.unix;
+  };
+}
diff --git a/pkgs/applications/networking/cluster/terraform-landscape/Gemfile.lock b/pkgs/applications/networking/cluster/terraform-landscape/Gemfile.lock
index 047ddaadad07..ccc2294b6a09 100644
--- a/pkgs/applications/networking/cluster/terraform-landscape/Gemfile.lock
+++ b/pkgs/applications/networking/cluster/terraform-landscape/Gemfile.lock
@@ -2,17 +2,17 @@ GEM
   remote: https://rubygems.org/
   specs:
     colorize (0.8.1)
-    commander (4.4.4)
+    commander (4.4.5)
       highline (~> 1.7.2)
-    diffy (3.2.0)
+    diffy (3.2.1)
     highline (1.7.10)
     polyglot (0.3.5)
-    terraform_landscape (0.1.17)
+    terraform_landscape (0.1.18)
       colorize (~> 0.7)
       commander (~> 4.4)
       diffy (~> 3.0)
       treetop (~> 1.6)
-    treetop (1.6.9)
+    treetop (1.6.10)
       polyglot (~> 0.3)
 
 PLATFORMS
diff --git a/pkgs/applications/networking/cluster/terraform-landscape/gemset.nix b/pkgs/applications/networking/cluster/terraform-landscape/gemset.nix
index 38321b9d37aa..8dd57af4c73b 100644
--- a/pkgs/applications/networking/cluster/terraform-landscape/gemset.nix
+++ b/pkgs/applications/networking/cluster/terraform-landscape/gemset.nix
@@ -11,18 +11,18 @@
     dependencies = ["highline"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "165yr8qzan3gnk241mnwxsvdfwp6p1afg13z0mqdily6lh95acl9";
+      sha256 = "0sry6raysvg9qsx5nqqw09n8r8hvcsqzvci7xp2qk7jq3s9mgvnn";
       type = "gem";
     };
-    version = "4.4.4";
+    version = "4.4.5";
   };
   diffy = {
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "015nn9zaciqj43mfpjlw619r5dvnfkrjcka8nsa6j260v6qya941";
+      sha256 = "119imrkn01agwhx5raxhknsi331y5i4yda7r0ws0an6905ximzjg";
       type = "gem";
     };
-    version = "3.2.0";
+    version = "3.2.1";
   };
   highline = {
     source = {
@@ -44,18 +44,18 @@
     dependencies = ["colorize" "commander" "diffy" "treetop"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "1bx8nfqbpxb2hnxnnl1m4sq6jlzf451c85m047jfq04b6w9691fl";
+      sha256 = "0476q2kx88w9srj7rlzl6skrza3pdgyym7zksw78infsb2105lg9";
       type = "gem";
     };
-    version = "0.1.17";
+    version = "0.1.18";
   };
   treetop = {
     dependencies = ["polyglot"];
     source = {
       remotes = ["https://rubygems.org"];
-      sha256 = "0sdkd1v2h8dhj9ncsnpywmqv7w1mdwsyc5jwyxlxwriacv8qz8bd";
+      sha256 = "0g31pijhnv7z960sd09lckmw9h8rs3wmc8g4ihmppszxqm99zpv7";
       type = "gem";
     };
-    version = "1.6.9";
+    version = "1.6.10";
   };
 }
\ No newline at end of file
diff --git a/pkgs/applications/networking/cluster/terraform-provider-ibm/default.nix b/pkgs/applications/networking/cluster/terraform-provider-ibm/default.nix
index 66bf20c2b843..69de076cd1cf 100644
--- a/pkgs/applications/networking/cluster/terraform-provider-ibm/default.nix
+++ b/pkgs/applications/networking/cluster/terraform-provider-ibm/default.nix
@@ -12,7 +12,7 @@
 
 buildGoPackage rec {
   name = "terraform-provider-ibm-${version}";
-  version = "0.10.0";
+  version = "0.11.0";
 
   goPackagePath = "github.com/terraform-providers/terraform-provider-ibm";
   subPackages = [ "./" ];
@@ -20,7 +20,7 @@ buildGoPackage rec {
   src = fetchFromGitHub {
     owner = "IBM-Cloud";
     repo = "terraform-provider-ibm";
-    sha256 = "03drvhhh6pkk8yzzp8iiq478kcky9swxvxadxzxh0v4jzdprg9lr";
+    sha256 = "0zgzzs2l9p06angqw6vjpkd88gcn2mswmmwycc31ihkglzs6yw2p";
     rev = "v${version}";
   };
 
diff --git a/pkgs/applications/networking/instant-messengers/quaternion/default.nix b/pkgs/applications/networking/instant-messengers/quaternion/default.nix
index 6c716cc3e1c0..2e2489870ed1 100644
--- a/pkgs/applications/networking/instant-messengers/quaternion/default.nix
+++ b/pkgs/applications/networking/instant-messengers/quaternion/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "quaternion-${version}";
-  version = "0.0.9";
+  version = "0.0.9.2";
 
   src = fetchFromGitHub {
     owner  = "QMatrixClient";
     repo   = "Quaternion";
     rev    = "v${version}";
-    sha256 = "0zdpll953a7biwnklhgmgg3k2vz7j58lc1nmfkmvsfcj1fmdf408";
+    sha256 = "0zrr4khbbdf5ziq65gi0cb1yb1d0y5rv18wld22w1x96f7fkmrib";
   };
 
   buildInputs = [ qtbase qtquickcontrols libqmatrixclient ];
diff --git a/pkgs/applications/networking/instant-messengers/riot/riot-web.nix b/pkgs/applications/networking/instant-messengers/riot/riot-web.nix
index 279f347ccbbb..dbf17d9cbdb1 100644
--- a/pkgs/applications/networking/instant-messengers/riot/riot-web.nix
+++ b/pkgs/applications/networking/instant-messengers/riot/riot-web.nix
@@ -3,11 +3,11 @@
 let configFile = writeText "riot-config.json" conf; in
 stdenv.mkDerivation rec {
   name= "riot-web-${version}";
-  version = "0.15.6";
+  version = "0.15.7";
 
   src = fetchurl {
     url = "https://github.com/vector-im/riot-web/releases/download/v${version}/riot-v${version}.tar.gz";
-    sha256 = "032svv30dhj9gl0v37djn9bnwh7f9bfg2czhmcszdygsd0879x08";
+    sha256 = "09sa2qcmns4b9by3hzmyppc6fi3845vppkal2ylrf2vi9yczb2ch";
   };
 
   installPhase = ''
diff --git a/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix b/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix
index 48fcfa19d976..80eba81fb47f 100644
--- a/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix
+++ b/pkgs/applications/networking/instant-messengers/signal-desktop/default.nix
@@ -40,11 +40,11 @@ let
 
 in stdenv.mkDerivation rec {
   name = "signal-desktop-${version}";
-  version = "1.13.0";
+  version = "1.14.0";
 
   src = fetchurl {
     url = "https://updates.signal.org/desktop/apt/pool/main/s/signal-desktop/signal-desktop_${version}_amd64.deb";
-    sha256 = "1iapkkfqssbjcksgic7i8x0cwp6gwcbbrfxlw7vp6k1cfvjwv9pf";
+    sha256 = "1f76dzm9qq12i4s95c51d9s923n69y8cbg8yz79qjpd6k30j8vkq";
   };
 
   phases = [ "unpackPhase" "installPhase" ];
diff --git a/pkgs/applications/networking/instant-messengers/zoom-us/default.nix b/pkgs/applications/networking/instant-messengers/zoom-us/default.nix
index 98beced062a4..dc2bb4ba1e12 100644
--- a/pkgs/applications/networking/instant-messengers/zoom-us/default.nix
+++ b/pkgs/applications/networking/instant-messengers/zoom-us/default.nix
@@ -3,7 +3,7 @@
 , dbus, glib, libGL, libX11, libXfixes, libuuid, libxcb, qtbase, qtdeclarative
 , qtlocation, qtquickcontrols2, qtscript, qtwebchannel, qtwebengine
 # Runtime
-, libjpeg_turbo, pciutils, procps
+, libjpeg_turbo, pciutils, procps, qtimageformats
 , pulseaudioSupport ? true, libpulseaudio ? null
 }:
 
@@ -30,7 +30,7 @@ in stdenv.mkDerivation {
   buildInputs = [
     dbus glib libGL libX11 libXfixes libuuid libxcb qtbase qtdeclarative
     qtlocation qtquickcontrols2 qtscript qtwebchannel qtwebengine
-    libjpeg_turbo pciutils procps
+    libjpeg_turbo
   ];
 
   runtimeDependencies = optional pulseaudioSupport libpulseaudio;
@@ -70,6 +70,8 @@ in stdenv.mkDerivation {
       makeWrapper $packagePath/zoom $out/bin/zoom-us \
         --prefix PATH : "${makeBinPath [ pciutils procps ]}" \
         --set QSG_INFO 1 \
+        --set QT_QPA_PLATFORM_PLUGIN_PATH ${qtbase.bin}/lib/qt-${qtbase.qtCompatVersion}/plugins/platforms \
+        --set QT_PLUGIN_PATH ${qtbase.bin}/${qtbase.qtPluginPrefix}:${qtimageformats}/${qtbase.qtPluginPrefix} \
         --run "cd $packagePath"
 
       runHook postInstall
@@ -92,7 +94,7 @@ in stdenv.mkDerivation {
     description = "zoom.us video conferencing application";
     license = stdenv.lib.licenses.unfree;
     platforms = builtins.attrNames srcs;
-    maintainers = with stdenv.lib.maintainers; [ danbst ];
+    maintainers = with stdenv.lib.maintainers; [ danbst tadfisher ];
   };
 
 }
diff --git a/pkgs/applications/networking/mumble/default.nix b/pkgs/applications/networking/mumble/default.nix
index d8029f02a6f0..13f7bce49218 100644
--- a/pkgs/applications/networking/mumble/default.nix
+++ b/pkgs/applications/networking/mumble/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchurl, fetchgit, fetchpatch, pkgconfig
+{ stdenv, fetchurl, fetchFromGitHub, fetchpatch, pkgconfig
 , qt4, qmake4Hook, qt5, avahi, boost, libopus, libsndfile, protobuf, speex, libcap
 , alsaLib, python
 , jackSupport ? false, libjack2 ? null
@@ -126,14 +126,16 @@ let
   };
 
   gitSource = rec {
-    version = "2018-01-12";
+    version = "2018-07-01";
     qtVersion = 5;
 
     # Needs submodules
-    src = fetchgit {
-      url = "https://github.com/mumble-voip/mumble";
-      rev = "e348e47f4af68eaa8e0f87d1d9fc28c5583e421e";
-      sha256 = "12z41qfaq6w3i4wcw8pvyb8wwwa8gs3ar5zx6aqx6yssc6513lr3";
+    src = fetchFromGitHub {
+      owner = "mumble-voip";
+      repo = "mumble";
+      rev = "c19ac8c0b0f934d2ff206858d7cb66352d6eb418";
+      sha256 = "1mzp1bgn49ycs16d6r8icqq35wq25198fs084vyq6j5f78ni7pvz";
+      fetchSubmodules = true;
     };
   };
 in {
diff --git a/pkgs/applications/networking/p2p/frostwire/frostwire-bin.nix b/pkgs/applications/networking/p2p/frostwire/frostwire-bin.nix
index bf1545ff3983..01672aa71a80 100644
--- a/pkgs/applications/networking/p2p/frostwire/frostwire-bin.nix
+++ b/pkgs/applications/networking/p2p/frostwire/frostwire-bin.nix
@@ -3,12 +3,12 @@
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
-  version = "6.6.7";
+  version = "6.7.0";
   name = "frostwire-${version}";
 
   src = fetchurl {
     url = "https://dl.frostwire.com/frostwire/${version}/frostwire-${version}.noarch.tar.gz";
-    sha256 = "01ah0cwr3ahihfz1xxs0irw4rsa7wjgnlkcqfyg5q9rmzwbnxkyh";
+    sha256 = "1qvk4w2ly2nz3ibsd6qdxaqb3g1a3l9f5a15b5zpzhsziln1fbxf";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/applications/networking/remote/x2goclient/default.nix b/pkgs/applications/networking/remote/x2goclient/default.nix
index 2521a4b0daf9..01aaa2219bf3 100644
--- a/pkgs/applications/networking/remote/x2goclient/default.nix
+++ b/pkgs/applications/networking/remote/x2goclient/default.nix
@@ -3,11 +3,11 @@ makeWrapper, qtbase, qtsvg, qtx11extras, qttools, phonon }:
 
 stdenv.mkDerivation rec {
   name = "x2goclient-${version}";
-  version = "4.1.2.0";
+  version = "4.1.2.1";
 
   src = fetchurl {
     url = "https://code.x2go.org/releases/source/x2goclient/${name}.tar.gz";
-    sha256 = "1x1iiyszz6mbrnsqacxzclyx172djq865bw3y83ya7lc9j8a71zn";
+    sha256 = "1bzjzz2m9bqqndnk1p9p522cfapsqgkb0wllvqj9d4ir18grh60w";
   };
 
   buildInputs = [ cups libssh libXpm nxproxy openldap openssh
diff --git a/pkgs/applications/networking/seafile-client/default.nix b/pkgs/applications/networking/seafile-client/default.nix
index c9d2a111753d..ea0a756e76d1 100644
--- a/pkgs/applications/networking/seafile-client/default.nix
+++ b/pkgs/applications/networking/seafile-client/default.nix
@@ -5,14 +5,14 @@
 with stdenv.lib;
 
 stdenv.mkDerivation rec {
-  version = "6.2.1";
+  version = "6.2.2";
   name = "seafile-client-${version}";
 
   src = fetchFromGitHub {
     owner = "haiwen";
     repo = "seafile-client";
     rev = "v${version}";
-    sha256 = "02nzihs720pmgr5139s7fz88f7gm19dn1x2kqdpi81k7gdwqq0bp";
+    sha256 = "19204fqi4x4q7hsc500y6gj0qdfzf4kjgfsr808w13qnh1lxhvr4";
   };
 
   nativeBuildInputs = [ pkgconfig cmake makeWrapper ];
diff --git a/pkgs/applications/office/mytetra/default.nix b/pkgs/applications/office/mytetra/default.nix
index b752f552ba97..c94d79a0ced7 100644
--- a/pkgs/applications/office/mytetra/default.nix
+++ b/pkgs/applications/office/mytetra/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl, qmake, qtsvg }:
 
 let
-  version = "1.42.2";
+  version = "1.43.27";
 in stdenv.mkDerivation rec {
   name = "mytetra-${version}";
   src = fetchurl {
     url = "https://github.com/xintrea/mytetra_dev/archive/v.${version}.tar.gz";
-    sha256 = "1ah44nf4ksxkh01a2zmgvvby4pwczhyq5vcp270rf6visp8v9804";
+    sha256 = "1gzr11jy1bvnp28w2ar3wmh76g55jn9nra5la5qasnal6b5pg28h";
   };
 
   nativeBuildInputs = [ qmake ];
diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix
index 0c9a6bda2c23..2df8b188f785 100644
--- a/pkgs/applications/science/biology/igv/default.nix
+++ b/pkgs/applications/science/biology/igv/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "igv-${version}";
-  version = "2.4.11";
+  version = "2.4.13";
 
   src = fetchurl {
     url = "https://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_${version}.zip";
-    sha256 = "11zbbasqpvf7inbgrk6jzd9pqdfn4v4g4nl149bivg475mmqpnwl";
+    sha256 = "0cl6fs1v9rqkzjq4syx0m1pr71hbhvidwa3ym57pvz8ardfs3qa1";
   };
 
   buildInputs = [ unzip jre ];
diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix
index 4c4278c30faa..d5dae364cc3d 100644
--- a/pkgs/applications/science/chemistry/jmol/default.nix
+++ b/pkgs/applications/science/chemistry/jmol/default.nix
@@ -1,4 +1,5 @@
 { stdenv
+, lib
 , fetchurl
 , unzip
 , makeDesktopItem
@@ -16,15 +17,15 @@ let
   };
 in
 stdenv.mkDerivation rec {
-  version = "${baseVersion}.${patchVersion}";
-  baseVersion = "14.29";
-  patchVersion = "12";
+  version = "14.29.17";
   pname = "jmol";
   name = "${pname}-${version}";
 
-  src = fetchurl {
+  src = let 
+    baseVersion = "${lib.versions.major version}.${lib.versions.minor version}";
+  in fetchurl {
     url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz";
-    sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv";
+    sha256 = "1dnxbvi8ha9z2ldymkjpxydd216afv6k7fdp3j70sql10zgy0isk";
   };
 
   patchPhase = ''
diff --git a/pkgs/applications/science/logic/abc/default.nix b/pkgs/applications/science/logic/abc/default.nix
index bab9b302d7d1..6e7a3cfc88ac 100644
--- a/pkgs/applications/science/logic/abc/default.nix
+++ b/pkgs/applications/science/logic/abc/default.nix
@@ -1,20 +1,21 @@
-{ fetchhg, stdenv, readline }:
+{ fetchFromGitHub, stdenv, readline, cmake }:
 
 stdenv.mkDerivation rec {
   name = "abc-verifier-${version}";
-  version = "20160818";
+  version = "2018-07-08";
 
-  src = fetchhg {
-    url    = "https://bitbucket.org/alanmi/abc";
-    rev    = "a2e5bc66a68a72ccd267949e5c9973dd18f8932a";
-    sha256 = "09yvhj53af91nc54gmy7cbp7yljfcyj68a87494r5xvdfnsj11gy";
+  src = fetchFromGitHub {
+    owner = "berkeley-abc";
+    repo = "abc";
+    rev    = "24407e13db4b8ca16c3996049b2d33ec3722de39";
+    sha256 = "1rckji7nk81n6v1yajz7daqwipxacv7zlafknvmbiwji30j47sq5";
   };
 
+  nativeBuildInputs = [ cmake ];
   buildInputs = [ readline ];
-  preBuild = ''
-    export buildFlags="CC=$CC CXX=$CXX LD=$CXX"
-  '';
+
   enableParallelBuilding = true;
+
   installPhase = ''
     mkdir -p $out/bin
     mv abc $out/bin
@@ -22,7 +23,7 @@ stdenv.mkDerivation rec {
 
   meta = {
     description = "A tool for squential logic synthesis and formal verification";
-    homepage    = "https://people.eecs.berkeley.edu/~alanmi/abc/abc.htm";
+    homepage    = https://people.eecs.berkeley.edu/~alanmi/abc;
     license     = stdenv.lib.licenses.mit;
     platforms   = stdenv.lib.platforms.unix;
     maintainers = [ stdenv.lib.maintainers.thoughtpolice ];
diff --git a/pkgs/applications/science/logic/poly/default.nix b/pkgs/applications/science/logic/poly/default.nix
index 1b401c927b6e..2f765572f9ad 100644
--- a/pkgs/applications/science/logic/poly/default.nix
+++ b/pkgs/applications/science/logic/poly/default.nix
@@ -1,17 +1,20 @@
-{stdenv, fetchurl, gmp, cmake, python}:
+{stdenv, fetchFromGitHub, gmp, cmake, python}:
 
-let version = "0.1.4";
-in
+stdenv.mkDerivation rec {
+  name = "${pname}-${version}";
+  pname = "libpoly";
+  version = "0.1.7";
 
-stdenv.mkDerivation {
-  name = "libpoly-${version}";
-
-  src = fetchurl {
-    url = "https://github.com/SRI-CSL/libpoly/archive/v${version}.tar.gz";
-    sha256 = "16x1pk2a3pcb5a0dzyw28ccjwkhmbsck4hy80ss7kx0dd7qgpi7j";
+  src = fetchFromGitHub {
+    owner = "SRI-CSL";
+    repo = "libpoly";
+    rev = "v${version}";
+    sha256 = "0i5ar4lhs88glk0rvkmag656ii434i6i1q5dspx6d0kyg78fii64";
   };
 
-  buildInputs = [ cmake gmp python ];
+  nativeBuildInputs = [ cmake ];
+
+  buildInputs = [ gmp python ];
 
   meta = with stdenv.lib; {
     homepage = https://github.com/SRI-CSL/libpoly;
diff --git a/pkgs/applications/science/logic/yices/default.nix b/pkgs/applications/science/logic/yices/default.nix
index a607f1066395..3121a83e5b98 100644
--- a/pkgs/applications/science/logic/yices/default.nix
+++ b/pkgs/applications/science/logic/yices/default.nix
@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   name    = "yices-${version}";
-  version = "2.5.4";
+  version = "2.6.0";
 
   src = fetchurl {
     url = "https://github.com/SRI-CSL/yices2/archive/Yices-${version}.tar.gz";
     name = "${name}-src.tar.gz";
-    sha256 = "1k8wmlddi3zv5kgg6xbch3a0s0xqsmsfc7y6z8zrgcyhswl36h7p";
+    sha256 = "10ikq7ib8jhx7hlxfm6mp5qg6r8dflqs8242q5zaicn80qixpm12";
   };
 
   nativeBuildInputs = [ autoreconfHook ];
@@ -26,9 +26,11 @@ stdenv.mkDerivation rec {
 
   # Includes a fix for the embedded soname being libyices.so.2.5, but
   # only installing the libyices.so.2.5.x file.
-  installPhase = ''
+  installPhase = let
+    ver_XdotY = builtins.concatStringsSep "." (stdenv.lib.take 2 (stdenv.lib.splitString "." version));
+  in ''
       make install LDCONFIG=true
-      (cd $out/lib && ln -s -f libyices.so.${version} libyices.so.2.5)
+      ln -sfr $out/lib/libyices.so.{${version},${ver_XdotY}}
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix
index 54c9799a01b8..10a526192764 100644
--- a/pkgs/applications/science/logic/z3/default.nix
+++ b/pkgs/applications/science/logic/z3/default.nix
@@ -20,6 +20,20 @@ stdenv.mkDerivation rec {
     cd build
   '';
 
+  postInstall = ''
+    mkdir -p $dev $lib $python/lib
+
+    mv $out/lib/python*  $python/lib/
+    mv $out/lib          $lib/lib
+    mv $out/include      $dev/include
+
+    # clean up a copy of libz3.so and symlink it instead
+    rm $python/${python.sitePackages}/z3/lib/libz3.so
+    ln -s $lib/lib/libz3.so $python/${python.sitePackages}/z3/lib/libz3.so
+  '';
+
+  outputs = [ "out" "lib" "dev" "python" ];
+
   meta = {
     description = "A high-performance theorem prover and SMT solver";
     homepage    = "https://github.com/Z3Prover/z3";
diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix
index 28bd31506874..7990088ffbe9 100644
--- a/pkgs/applications/science/math/qalculate-gtk/default.nix
+++ b/pkgs/applications/science/math/qalculate-gtk/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "qalculate-gtk-${version}";
-  version = "2.6.0";
+  version = "2.6.1";
 
   src = fetchFromGitHub {
     owner = "qalculate";
     repo = "qalculate-gtk";
     rev = "v${version}";
-    sha256 = "0b2g9ziypcplczsm14b4i2k7vpiw9ll28qskv1fdhyqb0fij3qcx";
+    sha256 = "19jw1w29x0r1qq5r8gmqrqr00ml2pfi2w433723vjzxpfg2pp70r";
   };
 
   patchPhase = ''
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
index 9ad112213ffd..afb230cf4287 100644
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@@ -14,16 +14,6 @@ let
 
       cvxopt = super.cvxopt.override { inherit glpk; };
 
-      # https://github.com/sagemath/sagenb/issues/437
-      flask-babel = super.flask-babel.overridePythonAttrs (attrs: rec {
-        version = "0.9";
-        src = attrs.src.override {
-          inherit version;
-          sha256 = "0k7vk4k54y55ma0nx2k5s0phfqbriwslhy5shh3b0d046q7ibzaa";
-        };
-        doCheck = false;
-      });
-
       # python packages that appear unmaintained and were not accepted into the nixpkgs
       # tree because of that. These packages are only dependencies of the more-or-less
       # deprecated sagenb. However sagenb is still a default dependency and the doctests
diff --git a/pkgs/applications/science/math/sage/sagenb.nix b/pkgs/applications/science/math/sage/sagenb.nix
index 5ab387ebc5e1..cc883cc24b42 100644
--- a/pkgs/applications/science/math/sage/sagenb.nix
+++ b/pkgs/applications/science/math/sage/sagenb.nix
@@ -36,6 +36,14 @@ buildPythonPackage rec {
   # tests depend on sage
   doCheck = false;
 
+  patches = [
+    # work with latest flask-babel
+    (fetchpatch {
+      url = "https://github.com/sagemath/sagenb/commit/ba065eca63dd34a383e4c7ba7561430a90fcd087.patch";
+      sha256 = "1lamzsrgymdd618imrasjp6ivhw2aynh83gkybsd7pm1rzjcq4x8";
+    })
+  ];
+
   meta = with stdenv.lib; {
     description = "Sage Notebook";
     license = licenses.gpl3Plus;
diff --git a/pkgs/applications/science/misc/golly/default.nix b/pkgs/applications/science/misc/golly/default.nix
index 8ecbf656a821..0f0b44ccfa5e 100644
--- a/pkgs/applications/science/misc/golly/default.nix
+++ b/pkgs/applications/science/misc/golly/default.nix
@@ -1,11 +1,11 @@
 {stdenv, fetchurl, wxGTK, perl, python2, zlib, libGLU_combined, libX11}:
 stdenv.mkDerivation rec {
   baseName="golly";
-  version = "3.1";
+  version = "3.2";
   name="${baseName}-${version}";
 
   src = fetchurl {
-    sha256 = "0dn74k3rylhx023n047lz4z6qrqijfcxi0b6jryqklhmm2n532f7";
+    sha256 = "0cg9mbwmf4q6qxhqlnzrxh9y047banxdb8pd3hgj3smmja2zf0jd";
     url="mirror://sourceforge/project/golly/golly/golly-${version}/golly-${version}-src.tar.gz";
   };
 
diff --git a/pkgs/applications/version-management/git-and-tools/tig/default.nix b/pkgs/applications/version-management/git-and-tools/tig/default.nix
index 597429c0cc7a..001ee2ddb681 100644
--- a/pkgs/applications/version-management/git-and-tools/tig/default.nix
+++ b/pkgs/applications/version-management/git-and-tools/tig/default.nix
@@ -31,8 +31,9 @@ stdenv.mkDerivation rec {
   installPhase = ''
     make install
     make install-doc
-    mkdir -p $out/etc/bash_completion.d/
-    cp contrib/tig-completion.bash $out/etc/bash_completion.d/
+    install -D contrib/tig-completion.bash $out/etc/bash_completion.d/tig-completion.bash
+    install -D contrib/tig-completion.zsh $out/share/zsh/site-functions/_tig
+    cp contrib/vim.tigrc $out/etc/
 
     wrapProgram $out/bin/tig \
       --prefix PATH ':' "${git}/bin"
diff --git a/pkgs/applications/virtualization/containerd/default.nix b/pkgs/applications/virtualization/containerd/default.nix
index 3854c577188f..46d03ad3d622 100644
--- a/pkgs/applications/virtualization/containerd/default.nix
+++ b/pkgs/applications/virtualization/containerd/default.nix
@@ -5,13 +5,13 @@ with lib;
 
 stdenv.mkDerivation rec {
   name = "containerd-${version}";
-  version = "1.1.0";
+  version = "1.1.1";
 
   src = fetchFromGitHub {
     owner = "containerd";
     repo = "containerd";
     rev = "v${version}";
-    sha256 = "0nknqprmi04jfiivrk158jyddc95q4jggfsm7cg7rpvjamkzn6c8";
+    sha256 = "0pk1kii8bmlvziblrqwb88w5cd486pmb7vw8p7kcyn9lqsw32ria";
   };
 
   hardeningDisable = [ "fortify" ];
diff --git a/pkgs/applications/virtualization/singularity/default.nix b/pkgs/applications/virtualization/singularity/default.nix
index b6f4a5976e44..ff05cb757066 100644
--- a/pkgs/applications/virtualization/singularity/default.nix
+++ b/pkgs/applications/virtualization/singularity/default.nix
@@ -19,7 +19,7 @@
 
 stdenv.mkDerivation rec {
   name = "singularity-${version}";
-  version = "2.5.1";
+  version = "2.5.2";
 
   enableParallelBuilding = true;
 
@@ -47,7 +47,7 @@ stdenv.mkDerivation rec {
     owner = "singularityware";
     repo = "singularity";
     rev = version;
-    sha256 = "1i029qs6dfpyirhbdz0nrx2sh5fddysk4wqkjqj5m60kxs4x8a3d";
+    sha256 = "09wv8xagr5fjfhra5vyig0f1frfp97g99baqkh4avbzpg296q933";
   };
 
   nativeBuildInputs = [ autoreconfHook makeWrapper ];