Merge branch 'master' into staging-next

1 files changed, 131 insertions, 106 deletions

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 5daedcb21dad..b19eb6db5f64 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -129,8 +129,7 @@ with pkgs;
 
   digitalbitbox = libsForQt5.callPackage ../applications/misc/digitalbitbox { };
 
-  # go 1.9 pin until https://github.com/moby/moby/pull/35739
-  dockerTools = callPackage ../build-support/docker { go = go_1_9; };
+  dockerTools = callPackage ../build-support/docker { };
 
   docker_compose = pythonPackages.docker_compose;
 
@@ -152,6 +151,8 @@ with pkgs;
 
   ebook2cw = callPackage ../applications/misc/ebook2cw { };
 
+  etBook = callPackage ../data/fonts/et-book { };
+
   fetchbower = callPackage ../build-support/fetchbower {
     inherit (nodePackages) bower2nix;
   };
@@ -1462,6 +1463,8 @@ with pkgs;
 
   noteshrink = callPackage ../tools/misc/noteshrink { };
 
+  noti = callPackage ../tools/misc/noti { };
+
   nrsc5 = callPackage ../applications/misc/nrsc5 { };
 
   nwipe = callPackage ../tools/security/nwipe { };
@@ -2342,7 +2345,9 @@ with pkgs;
 
   enblend-enfuse = callPackage ../tools/graphics/enblend-enfuse { };
 
-  cryfs = callPackage ../tools/filesystems/cryfs { };
+  cryfs = callPackage ../tools/filesystems/cryfs {
+    spdlog = spdlog_0;
+  };
 
   encfs = callPackage ../tools/filesystems/encfs {
     tinyxml2 = tinyxml-2;
@@ -2382,7 +2387,7 @@ with pkgs;
 
   exempi = callPackage ../development/libraries/exempi { };
 
-  execline = callPackage ../tools/misc/execline { };
+  execline = skawarePackages.execline;
 
   exif = callPackage ../tools/graphics/exif { };
 
@@ -2906,7 +2911,10 @@ with pkgs;
   }) (x: { configureFlags = x.configureFlags ++ ["--with-cgraph=no"];});
 
   grin = callPackage ../tools/text/grin { };
-  ripgrep = callPackage ../tools/text/ripgrep { };
+
+  ripgrep = callPackage ../tools/text/ripgrep {
+    inherit (darwin.apple_sdk.frameworks) Security;
+  };
 
   grive2 = callPackage ../tools/filesystems/grive2 { };
 
@@ -3191,6 +3199,8 @@ with pkgs;
 
   hwinfo = callPackage ../tools/system/hwinfo { };
 
+  hylafaxplus = callPackage ../servers/hylafaxplus { };
+
   i2c-tools = callPackage ../os-specific/linux/i2c-tools { };
 
   i2p = callPackage ../tools/networking/i2p {};
@@ -3353,7 +3363,7 @@ with pkgs;
   jaaa = callPackage ../applications/audio/jaaa { };
 
   jackett = callPackage ../servers/jackett {
-    mono = mono50;
+    mono = mono5;
   };
 
   jade = callPackage ../tools/text/sgml/jade { };
@@ -3677,11 +3687,11 @@ with pkgs;
   nodejs-slim-8_x = callPackage ../development/web/nodejs/v8.nix { enableNpm = false; };
 
   nodejs-10_x = callPackage ../development/web/nodejs/v10.nix {
-    openssl = openssl_1_1_0;
+    openssl = openssl_1_1;
   };
   nodejs-slim-10_x = callPackage ../development/web/nodejs/v10.nix {
     enableNpm = false;
-    openssl = openssl_1_1_0;
+    openssl = openssl_1_1;
   };
 
   nodePackages_10_x = callPackage ../development/node-packages/default-v10.nix {
@@ -3717,7 +3727,7 @@ with pkgs;
   ldapvi = callPackage ../tools/misc/ldapvi { };
 
   ldns = callPackage ../development/libraries/ldns {
-    openssl = openssl_1_1_0;
+    openssl = openssl_1_1;
   };
 
   leafpad = callPackage ../applications/editors/leafpad { };
@@ -4583,6 +4593,8 @@ with pkgs;
 
   pdfcrack = callPackage ../tools/security/pdfcrack { };
 
+  pdftag = callPackage ../tools/graphics/pdftag { };
+
   pdf2svg = callPackage ../tools/graphics/pdf2svg { };
 
   fmodex = callPackage ../games/zandronum/fmod.nix { };
@@ -4735,6 +4747,8 @@ with pkgs;
 
   pptpd = callPackage ../tools/networking/pptpd {};
 
+  prettyping = callPackage ../tools/networking/prettyping { };
+
   prey-bash-client = callPackage ../tools/security/prey { };
 
   profile-cleaner = callPackage ../tools/misc/profile-cleaner { };
@@ -5061,13 +5075,13 @@ with pkgs;
 
   s3gof3r = callPackage ../tools/networking/s3gof3r { };
 
-  s6-dns = callPackage ../tools/networking/s6-dns { };
+  s6-dns = skawarePackages.s6-dns;
 
-  s6-linux-utils = callPackage ../os-specific/linux/s6-linux-utils { };
+  s6-linux-utils = skawarePackages.s6-linux-utils;
 
-  s6-networking = callPackage ../tools/networking/s6-networking { };
+  s6-networking = skawarePackages.s6-networking;
 
-  s6-portable-utils = callPackage ../tools/misc/s6-portable-utils { };
+  s6-portable-utils = skawarePackages.s6-portable-utils;
 
   sablotron = callPackage ../tools/text/xml/sablotron { };
 
@@ -5559,7 +5573,7 @@ with pkgs;
   tokei = callPackage ../development/tools/misc/tokei { };
 
   tor = callPackage ../tools/security/tor {
-    openssl = openssl_1_1_0;
+    openssl = openssl_1_1;
     # remove this, when libevent's openssl is upgraded to 1_1_0 or newer.
     libevent = libevent.override {
       sslSupport = false;
@@ -6035,9 +6049,7 @@ with pkgs;
 
   wireguard-go = callPackage ../tools/networking/wireguard-go { };
 
-  wkhtmltopdf = callPackage ../tools/graphics/wkhtmltopdf {
-    overrideDerivation = lib.overrideDerivation;
-  };
+  wkhtmltopdf = callPackage ../tools/graphics/wkhtmltopdf { };
 
   wml = callPackage ../development/web/wml { };
 
@@ -6198,6 +6210,8 @@ with pkgs;
 
   zsh-git-prompt = callPackage ../shells/zsh/zsh-git-prompt { };
 
+  zsh-history-substring-search = callPackage ../shells/zsh/zsh-history-substring-search { };
+
   zsh-navigation-tools = callPackage ../tools/misc/zsh-navigation-tools { };
 
   zsh-syntax-highlighting = callPackage ../shells/zsh/zsh-syntax-highlighting { };
@@ -6219,7 +6233,7 @@ with pkgs;
 
   ### SHELLS
 
-  runtimeShell = "${runtimeShellPackage}/bin/bash";
+  runtimeShell = "${runtimeShellPackage}${runtimeShellPackage.shellPath}";
   runtimeShellPackage = bash;
 
   bash = lowPrio (callPackage ../shells/bash/4.4.nix { });
@@ -6303,10 +6317,6 @@ with pkgs;
 
   binaryen = callPackage ../development/compilers/binaryen { };
 
-  boo = callPackage ../development/compilers/boo {
-    inherit (gnome2) gtksourceview;
-  };
-
   colm = callPackage ../development/compilers/colm { };
 
   fetchegg = callPackage ../build-support/fetchegg { };
@@ -6903,7 +6913,7 @@ with pkgs;
 
   jikes = callPackage ../development/compilers/jikes { };
 
-  julia = callPackage ../development/compilers/julia {
+  julia_06 = callPackage ../development/compilers/julia {
     gmp = gmp6;
     openblas = openblasCompat;
     inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
@@ -6922,6 +6932,8 @@ with pkgs;
     inherit (darwin.apple_sdk.frameworks) CoreServices ApplicationServices;
   };
 
+  julia = julia_06;
+
   jwasm =  callPackage ../development/compilers/jwasm { };
 
   kotlin = callPackage ../development/compilers/kotlin { };
@@ -7130,7 +7142,8 @@ with pkgs;
 
   opaline = callPackage ../development/tools/ocaml/opaline { };
 
-  opam = callPackage ../development/tools/ocaml/opam {
+  opam = callPackage ../development/tools/ocaml/opam { };
+  opam_1_2 = callPackage ../development/tools/ocaml/opam/1.2.2.nix {
     inherit (ocaml-ng.ocamlPackages_4_05) ocaml;
   };
 
@@ -7184,6 +7197,7 @@ with pkgs;
       };
     });
 
+  cargo-download = callPackage ../tools/package-management/cargo-download { };
   cargo-edit = callPackage ../tools/package-management/cargo-edit { };
   cargo-release = callPackage ../tools/package-management/cargo-release { };
   cargo-tree = callPackage ../tools/package-management/cargo-tree { };
@@ -7948,6 +7962,11 @@ with pkgs;
     inherit (darwin) cctools;
     inherit (darwin.apple_sdk.frameworks) CoreFoundation CoreServices Foundation;
   };
+  bazel_jdk10 = callPackage ../development/tools/build-managers/bazel {
+    inherit (darwin) cctools;
+    inherit (darwin.apple_sdk.frameworks) CoreFoundation CoreServices Foundation;
+    runJdk = jdk10;
+  };
 
   bazel-buildtools = callPackage ../development/tools/build-managers/bazel/buildtools { };
   buildifier = bazel-buildtools;
@@ -8485,14 +8504,12 @@ with pkgs;
 
   nailgun = callPackage ../development/tools/nailgun { };
 
-  nant = callPackage ../development/tools/build-managers/nant { };
-
   ninja = callPackage ../development/tools/build-managers/ninja { };
 
   gn = callPackage ../development/tools/build-managers/gn { };
 
   nixbang = callPackage ../development/tools/misc/nixbang {
-      pythonPackages = python3Packages;
+    pythonPackages = python3Packages;
   };
 
   nexus = callPackage ../development/tools/repository-managers/nexus { };
@@ -8737,13 +8754,9 @@ with pkgs;
   texinfo5 = callPackage ../development/tools/misc/texinfo/5.2.nix { };
   texinfo6 = callPackage ../development/tools/misc/texinfo/6.5.nix { };
   texinfo = texinfo6;
-  texinfoInteractive = appendToName "interactive" (texinfo.override {
-    interactive = true;
-    # doCheck = true -> some xlocale.h problem with perl 5.28.0
-    # (it's mistakenly trying to include the non-existent header)
-    perl = perl526;
-    buildPackages = buildPackages // { perl = buildPackages.perl526; };
-  });
+  texinfoInteractive = appendToName "interactive" (
+    texinfo.override { interactive = true; }
+  );
 
   texi2html = callPackage ../development/tools/misc/texi2html { };
 
@@ -9835,7 +9848,7 @@ with pkgs;
   heimdal = callPackage ../development/libraries/kerberos/heimdal.nix {
     inherit (darwin.apple_sdk.frameworks) CoreFoundation Security SystemConfiguration;
   };
-  libheimdal = heimdal.override { type = "lib"; };
+  libheimdal = heimdal;
 
   harfbuzz = callPackage ../development/libraries/harfbuzz {
     inherit (darwin.apple_sdk.frameworks) ApplicationServices CoreText;
@@ -10379,6 +10392,8 @@ with pkgs;
 
   libgrss = callPackage ../development/libraries/libgrss { };
 
+  libiio = callPackage ../development/libraries/libiio { };
+
   libseccomp = callPackage ../development/libraries/libseccomp { };
 
   libsecret = callPackage ../development/libraries/libsecret { };
@@ -11236,6 +11251,8 @@ with pkgs;
 
   mtpfs = callPackage ../tools/filesystems/mtpfs { };
 
+  mtxclient = callPackage ../development/libraries/mtxclient { };
+
   mu = callPackage ../tools/networking/mu {
     texinfo = texinfo4;
   };
@@ -11309,6 +11326,8 @@ with pkgs;
 
   nss_wrapper = callPackage ../development/libraries/nss_wrapper { };
 
+  nsss = skawarePackages.nsss;
+
   ntbtls = callPackage ../development/libraries/ntbtls { };
 
   ntk = callPackage ../development/libraries/audio/ntk { };
@@ -11432,7 +11451,7 @@ with pkgs;
       };
     })
     openssl_1_0_2
-    openssl_1_1_0;
+    openssl_1_1;
 
   openssl-chacha = callPackage ../development/libraries/openssl/chacha.nix {
     cryptodevHeaders = linuxPackages.cryptodev.override {
@@ -11999,7 +12018,24 @@ with pkgs;
 
   shibboleth-sp = callPackage ../development/libraries/shibboleth-sp { };
 
-  skalibs = callPackage ../development/libraries/skalibs { };
+  skalibs = skawarePackages.skalibs;
+
+  skawarePackages = recurseIntoAttrs {
+    buildPackage = callPackage ../build-support/skaware/build-skaware-package.nix { };
+
+    skalibs = callPackage ../development/libraries/skalibs { };
+    execline = callPackage ../tools/misc/execline { };
+
+    s6 = callPackage ../tools/system/s6 { };
+    s6-dns = callPackage ../tools/networking/s6-dns { };
+    s6-linux-utils = callPackage ../os-specific/linux/s6-linux-utils { };
+    s6-networking = callPackage ../tools/networking/s6-networking { };
+    s6-portable-utils = callPackage ../tools/misc/s6-portable-utils { };
+    s6-rc = callPackage ../tools/system/s6-rc { };
+
+    nsss = callPackage ../development/libraries/nsss { };
+
+  };
 
   skydive = callPackage ../tools/networking/skydive { };
 
@@ -12821,8 +12857,8 @@ with pkgs;
 
   rdf4store = callPackage ../servers/http/4store { };
 
-  apacheHttpd = pkgs.apacheHttpd_2_4;
   apacheHttpd_2_4 = callPackage ../servers/http/apache-httpd/2.4.nix { };
+  apacheHttpd = pkgs.apacheHttpd_2_4;
 
   apacheHttpdPackagesFor = apacheHttpd: self: let callPackage = newScope self; in {
     inherit apacheHttpd;
@@ -12846,8 +12882,8 @@ with pkgs;
     subversion = pkgs.subversion.override { httpServer = true; inherit apacheHttpd; };
   };
 
-  apacheHttpdPackages = apacheHttpdPackagesFor pkgs.apacheHttpd pkgs.apacheHttpdPackages;
   apacheHttpdPackages_2_4 = apacheHttpdPackagesFor pkgs.apacheHttpd_2_4 pkgs.apacheHttpdPackages_2_4;
+  apacheHttpdPackages = apacheHttpdPackages_2_4;
 
   appdaemon = callPackage ../servers/home-assistant/appdaemon.nix { };
 
@@ -13095,6 +13131,8 @@ with pkgs;
 
   nas = callPackage ../servers/nas { };
 
+  nats-streaming-server = callPackage ../servers/nats-streaming-server { };
+
   neard = callPackage ../servers/neard { };
 
   nginx = nginxStable;
@@ -13279,6 +13317,8 @@ with pkgs;
 
   newrelic-sysmond = callPackage ../servers/monitoring/newrelic-sysmond { };
 
+  nullidentdmod = callPackage ../servers/identd/nullidentdmod {};
+
   riemann = callPackage ../servers/monitoring/riemann { };
   riemann-dash = callPackage ../servers/monitoring/riemann-dash { };
 
@@ -13409,9 +13449,9 @@ with pkgs;
     boost = boost159;
   };
 
-  s6 = callPackage ../tools/system/s6 { };
+  s6 = skawarePackages.s6;
 
-  s6-rc = callPackage ../tools/system/s6-rc { };
+  s6-rc = skawarePackages.s6-rc;
 
   supervise = callPackage ../tools/system/supervise { };
 
@@ -13665,6 +13705,8 @@ with pkgs;
 
   bluez5 = callPackage ../os-specific/linux/bluez { };
 
+  pulseaudio-modules-bt = callPackage ../applications/audio/pulseaudio-modules-bt { };
+
   bluez = bluez5;
 
   inherit (python3Packages) bedup;
@@ -13993,16 +14035,6 @@ with pkgs;
       ];
   };
 
-  linux_4_17 = callPackage ../os-specific/linux/kernel/linux-4.17.nix {
-    kernelPatches =
-      [ kernelPatches.bridge_stp_helper
-        # See pkgs/os-specific/linux/kernel/cpu-cgroup-v2-patches/README.md
-        # when adding a new linux version
-        # kernelPatches.cpu-cgroup-v2."4.11"
-        kernelPatches.modinst_arg_list_too_long
-      ];
-  };
-
   linux_4_18 = callPackage ../os-specific/linux/kernel/linux-4.18.nix {
     kernelPatches =
       [ kernelPatches.bridge_stp_helper
@@ -14010,6 +14042,18 @@ with pkgs;
         # when adding a new linux version
         # kernelPatches.cpu-cgroup-v2."4.11"
         kernelPatches.modinst_arg_list_too_long
+
+        # https://github.com/NixOS/nixpkgs/issues/45165
+        # TODO: remove this patch once it is merged upstream and released.
+        (rec {
+          name = "hid-core-fix-grouping-by-application";
+          patch = fetchpatch {
+            name = name + ".patch";
+            # https://patchwork.kernel.org/patch/10587369/
+            url = https://git.kernel.org/pub/scm/linux/kernel/git/jikos/hid.git/patch/?id=0d6c3011409135ea84e2a231b013a22017ff999a;
+            sha256 = "0bdrv0aqjh0rdjlaaaqpdgrnd9452fa4ggaa1nq2kmik3q00cq4m";
+          };
+        })
       ];
   };
 
@@ -14213,7 +14257,6 @@ with pkgs;
   linuxPackages_4_4 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_4_4);
   linuxPackages_4_9 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_4_9);
   linuxPackages_4_14 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_4_14);
-  linuxPackages_4_17 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_4_17);
   linuxPackages_4_18 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_4_18);
   # Don't forget to update linuxPackages_latest!
 
@@ -14426,6 +14469,8 @@ with pkgs;
 
   govers = callPackage ../development/tools/govers { };
 
+  govendor = callPackage ../development/tools/govendor { };
+
   gotools = callPackage ../development/tools/gotools { };
 
   gotop = callPackage ../tools/system/gotop { };
@@ -14509,6 +14554,8 @@ with pkgs;
 
   policycoreutils = callPackage ../os-specific/linux/policycoreutils { };
 
+  semodule-utils = callPackage ../os-specific/linux/semodule-utils { };
+
   powerdns = callPackage ../servers/dns/powerdns { };
 
   dnsdist = callPackage ../servers/dns/dnsdist { };
@@ -15112,6 +15159,7 @@ with pkgs;
 
   powerline-rs = callPackage ../tools/misc/powerline-rs {
     inherit (darwin.apple_sdk.frameworks) Security;
+    openssl = openssl_1_1;
   };
 
   profont = callPackage ../data/fonts/profont { };
@@ -15502,11 +15550,6 @@ with pkgs;
 
   barrier = callPackage ../applications/misc/barrier {};
 
-  banshee = callPackage ../applications/audio/banshee {
-    gconf = pkgs.gnome2.GConf;
-    libgpod = pkgs.libgpod.override { monoSupport = true; };
-  };
-
   bashSnippets = callPackage ../applications/misc/bashSnippets { };
 
   batik = callPackage ../applications/graphics/batik { };
@@ -16016,7 +16059,7 @@ with pkgs;
       ImageCaptureCore GSS ImageIO;
   };
 
-  emacsPackagesGen = emacs: self: let callPackage = newScope self; in rec {
+  emacsPackagesFor = emacs: self: let callPackage = newScope self; in rec {
     inherit emacs;
 
     autoComplete = callPackage ../applications/editors/emacs-modes/auto-complete { };
@@ -16159,10 +16202,10 @@ with pkgs;
     cask = callPackage ../applications/editors/emacs-modes/cask { };
   };
 
-  emacs25Packages = emacsPackagesGen emacs25 pkgs.emacs25Packages;
-  emacs26Packages = emacsPackagesGen emacs26 pkgs.emacs26Packages;
+  emacs25Packages = emacsPackagesFor emacs25 pkgs.emacs25Packages;
+  emacs26Packages = emacsPackagesFor emacs26 pkgs.emacs26Packages;
 
-  emacsPackagesNgGen = emacs: import ./emacs-packages.nix {
+  emacsPackagesNgFor = emacs: import ./emacs-packages.nix {
     inherit lib newScope stdenv;
     inherit fetchFromGitHub fetchgit fetchhg fetchurl fetchpatch;
     inherit emacs texinfo makeWrapper runCommand writeText;
@@ -16184,9 +16227,9 @@ with pkgs;
     };
   };
 
-  emacs25PackagesNg = emacsPackagesNgGen emacs25;
+  emacs25PackagesNg = emacsPackagesNgFor emacs25;
   emacs25WithPackages = emacs25PackagesNg.emacsWithPackages;
-  emacs26PackagesNg = emacsPackagesNgGen emacs26;
+  emacs26PackagesNg = emacsPackagesNgFor emacs26;
   emacs26WithPackages = emacs26PackagesNg.emacsWithPackages;
   emacsWithPackages = emacsPackagesNg.emacsWithPackages;
 
@@ -17274,15 +17317,12 @@ with pkgs;
     harfbuzz = harfbuzz.override {
       withIcu = true; withGraphite2 = true;
     };
-    # checking whether g++ supports C++14 or C++11... configure: error: no
-    # Still relevant: 2018-04-13
-    stdenv = overrideCC stdenv gcc5;
   };
 
-  libreoffice-unwrapped =callPackage ../applications/office/libreoffice
+  libreoffice-unwrapped = callPackage ../applications/office/libreoffice
   (libreoffice-args // {
   });
-  libreoffice-still-unwrapped =callPackage ../applications/office/libreoffice/still.nix
+  libreoffice-still-unwrapped = callPackage ../applications/office/libreoffice/still.nix
   (libreoffice-args // {
       poppler = poppler_0_61;
   });
@@ -17815,6 +17855,8 @@ with pkgs;
 
   nanoblogger = callPackage ../applications/misc/nanoblogger { };
 
+  nanorc = callPackage ../applications/editors/nano/nanorc { };
+
   navipowm = callPackage ../applications/misc/navipowm { };
 
   navit = libsForQt5.callPackage ../applications/misc/navit { };
@@ -18749,7 +18791,7 @@ with pkgs;
   teamspeak_client = libsForQt5.callPackage ../applications/networking/instant-messengers/teamspeak/client.nix { };
   teamspeak_server = callPackage ../applications/networking/instant-messengers/teamspeak/server.nix { };
 
-  uaskjuggler = callPackage ../applications/misc/taskjuggler { };
+  taskjuggler = callPackage ../applications/misc/taskjuggler { };
 
   tasknc = callPackage ../applications/misc/tasknc { };
 
@@ -18805,6 +18847,8 @@ with pkgs;
 
   nylas-mail-bin = callPackage ../applications/networking/mailreaders/nylas-mail-bin { };
 
+  thonny = callPackage ../applications/editors/thonny { };
+
   thunderbird = callPackage ../applications/networking/mailreaders/thunderbird {
     inherit (gnome2) libIDL;
     libpng = libpng_apng;
@@ -19171,13 +19215,7 @@ with pkgs;
     guile = guile_2_0;
   };
 
-  weechat-matrix-bridge = callPackage ../applications/networking/instant-messengers/weechat-matrix-bridge {
-    inherit (luaPackages) cjson;
-  };
-
-  weechat-xmpp = callPackage ../applications/networking/instant-messengers/weechat-xmpp {
-    inherit (pythonPackages) pydns;
-  };
+  weechatScripts = callPackage ../applications/networking/irc/weechat/scripts { };
 
   westonLite = weston.override {
     pango = null;
@@ -19563,6 +19601,8 @@ with pkgs;
 
   yate = callPackage ../applications/misc/yate { };
 
+  ydiff = callPackage ../development/tools/ydiff { };
+
   yed = callPackage ../applications/graphics/yed {};
 
   inherit (gnome3) yelp;
@@ -19706,7 +19746,7 @@ with pkgs;
 
   chessdb = callPackage ../games/chessdb { };
 
-  chessx = libsForQt5.callPackage ../games/chessx { };
+  chessx = libsForQt59.callPackage ../games/chessx { };
 
   chocolateDoom = callPackage ../games/chocolate-doom { };
 
@@ -20158,7 +20198,7 @@ with pkgs;
     lua = lua5_1;
   };
 
-  solarus = callPackage ../games/solarus { };
+  solarus = libsForQt5.callPackage ../games/solarus { };
 
   solarus-quest-editor = libsForQt5.callPackage ../development/tools/solarus-quest-editor { };
 
@@ -20191,6 +20231,8 @@ with pkgs;
     nativeOnly = true;
   }).run;
 
+  steamcmd = steamPackages.steamcmd;
+
   linux-steam-integration = callPackage ../games/linux-steam-integration {
     gtk = pkgs.gtk3;
   };
@@ -20596,6 +20638,8 @@ with pkgs;
 
   ezminc = callPackage ../applications/science/biology/EZminc { };
 
+  hisat2 = callPackage ../applications/science/biology/hisat2 { };
+
   htslib = callPackage ../development/libraries/science/biology/htslib { };
 
   igv = callPackage ../applications/science/biology/igv { };
@@ -21275,29 +21319,7 @@ with pkgs;
 
   fastnlo = callPackage ../development/libraries/physics/fastnlo { };
 
-  geant4 = callPackage ../development/libraries/physics/geant4 {
-    enableMultiThreading = true;
-    enableG3toG4         = false;
-    enableInventor       = false;
-    enableGDML           = false;
-    enableQT             = false;
-    enableXM             = false;
-    enableOpenGLX11      = true;
-    enableRaytracerX11   = false;
-
-    # Optional system packages, otherwise internal GEANT4 packages are used.
-    clhep = null;
-    zlib  = null;
-
-    # For enableGDML.
-    xercesc = null;
-
-    # For enableQT.
-    qt = null; # qt4SDK or qt5SDK
-
-    # For enableXM.
-    motif = null; # motif or lesstif
-  };
+  geant4 = libsForQt5.callPackage ../development/libraries/physics/geant4 { };
 
   cernlib = callPackage ../development/libraries/physics/cernlib { };
 
@@ -22019,9 +22041,7 @@ with pkgs;
 
   valauncher = callPackage ../applications/misc/valauncher { };
 
-  vault = callPackage ../tools/security/vault {
-    go = go_1_10;
-  };
+  vault = callPackage ../tools/security/vault { };
 
   vaultenv = haskellPackages.vaultenv;
 
@@ -22208,9 +22228,14 @@ with pkgs;
     inherit (gnome2) gtksourceview;
   };
 
-  bullet = callPackage ../development/libraries/bullet {};
+  bullet = callPackage ../development/libraries/bullet {
+    inherit (darwin.apple_sdk.frameworks) Cocoa OpenGL;
+  };
+
+  inherit (callPackages ../development/libraries/spdlog { })
+    spdlog_0 spdlog_1;
 
-  spdlog = callPackage ../development/libraries/spdlog { };
+  spdlog = spdlog_1;
 
   dart = callPackage ../development/interpreters/dart { };
   dart_stable = dart.override { version = "1.24.3"; };