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-rw-r--r--pkgs/top-level/all-packages.nix310
1 files changed, 223 insertions, 87 deletions
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 15ca1f810f98..88cd6e977525 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -157,6 +157,8 @@ in
 
   deadcode = callPackage ../development/tools/deadcode { };
 
+  demoit = callPackage ../servers/demoit { };
+
   diffPlugins = (callPackage ../build-support/plugins.nix {}).diffPlugins;
 
   dieHook = makeSetupHook {} ../build-support/setup-hooks/die.sh;
@@ -328,10 +330,7 @@ in
 
   makeAutostartItem = callPackage ../build-support/make-startupitem { };
 
-  makeInitrd = { contents, compressor ? "gzip -9n", prepend ? [ ] }:
-    callPackage ../build-support/kernel/make-initrd.nix {
-      inherit contents compressor prepend;
-    };
+  makeInitrd = callPackage ../build-support/kernel/make-initrd.nix; # Args intentionally left out
 
   makeWrapper = makeSetupHook { deps = [ dieHook ]; substitutions = { shell = pkgs.runtimeShell; }; }
                               ../build-support/setup-hooks/make-wrapper.sh;
@@ -703,6 +702,8 @@ in
 
   cozy = callPackage ../applications/audio/cozy-audiobooks { };
 
+  crumbs = callPackage ../applications/misc/crumbs { };
+
   deskew = callPackage ../applications/graphics/deskew { };
 
   detect-secrets = python3Packages.callPackage ../development/tools/detect-secrets { };
@@ -865,6 +866,7 @@ in
 
   aria2 = callPackage ../tools/networking/aria2 {
     inherit (darwin.apple_sdk.frameworks) Security;
+    inherit (pythonPackages) sphinx;
   };
   aria = aria2;
 
@@ -920,6 +922,8 @@ in
 
   bar = callPackage ../tools/system/bar {};
 
+  base16-shell-preview = callPackage ../misc/base16-shell-preview { };
+
   base16-builder = callPackage ../misc/base16-builder { };
 
   basex = callPackage ../tools/text/xml/basex { };
@@ -950,24 +954,43 @@ in
 
   bchunk = callPackage ../tools/cd-dvd/bchunk { };
 
-  inherit (callPackages ../misc/logging/beats/6.x.nix { })
+  inherit (callPackages ../misc/logging/beats/5.x.nix {
+    # XXX: this is failing with Go 1.12. Error is related to cgo, an
+    # update to this package might fix it.
+    buildGoPackage = buildGo111Package;
+  })
+    filebeat5
+    heartbeat5
+    metricbeat5
+    packetbeat5;
+
+  inherit (callPackages ../misc/logging/beats/6.x.nix {
+    # XXX: this is failing with Go 1.12. Error is related to cgo, an
+    # update to this package might fix it.
+    buildGoPackage = buildGo111Package;
+  })
     filebeat6
     heartbeat6
     metricbeat6
     packetbeat6
     journalbeat6;
 
+  inherit (callPackages ../misc/logging/beats/7.x.nix {
+    # XXX: this is failing with Go 1.12. Error is related to cgo, an
+    # update to this package might fix it.
+    buildGoPackage = buildGo111Package;
+  })
+    filebeat7
+    heartbeat7
+    metricbeat7
+    packetbeat7
+    journalbeat7;
+
   filebeat = filebeat6;
   heartbeat = heartbeat6;
   metricbeat = metricbeat6;
   packetbeat = packetbeat6;
 
-  inherit (callPackages ../misc/logging/beats/5.x.nix { })
-    filebeat5
-    heartbeat5
-    metricbeat5
-    packetbeat5;
-
   bfr = callPackage ../tools/misc/bfr { };
 
   bibtool = callPackage ../tools/misc/bibtool { };
@@ -976,6 +999,8 @@ in
 
   bibtex2html = callPackage ../tools/misc/bibtex2html { };
 
+  bicon = callPackage ../applications/misc/bicon { };
+
   bindfs = callPackage ../tools/filesystems/bindfs { };
 
   bitbucket-cli = python2Packages.bitbucket-cli;
@@ -1036,6 +1061,8 @@ in
 
   borgbackup = callPackage ../tools/backup/borg { };
 
+  boringtun = callPackage ../tools/networking/boringtun { };
+
   boomerang = libsForQt5.callPackage ../development/tools/boomerang { };
 
   boost-build = callPackage ../development/tools/boost-build { };
@@ -1058,6 +1085,8 @@ in
 
   bro = callPackage ../applications/networking/ids/bro { };
 
+  brook = callPackage ../tools/networking/brook { };
+
   broot = callPackage ../tools/misc/broot { };
 
   bruteforce-luks = callPackage ../tools/security/bruteforce-luks { };
@@ -1304,6 +1333,8 @@ in
 
   deja-dup = callPackage ../applications/backup/deja-dup { };
 
+  dejsonlz4 = callPackage ../tools/compression/dejsonlz4 { };
+
   desync = callPackage ../applications/networking/sync/desync { };
 
   devmem2 = callPackage ../os-specific/linux/devmem2 { };
@@ -1587,6 +1618,8 @@ in
 
   long-shebang = callPackage ../misc/long-shebang {};
 
+  numatop = callPackage ../os-specific/linux/numatop { };
+
   iio-sensor-proxy = callPackage ../os-specific/linux/iio-sensor-proxy { };
 
   ipvsadm = callPackage ../os-specific/linux/ipvsadm { };
@@ -1633,6 +1666,8 @@ in
 
   nfdump = callPackage ../tools/networking/nfdump { };
 
+  nixpkgs-pytools = with python3.pkgs; toPythonApplication nixpkgs-pytools;
+
   noteshrink = callPackage ../tools/misc/noteshrink { };
 
   noti = callPackage ../tools/misc/noti {
@@ -1660,6 +1695,8 @@ in
 
   pbzx = callPackage ../tools/compression/pbzx { };
 
+  persepolis = python3Packages.callPackage ../tools/networking/persepolis { };
+
   pev = callPackage ../development/tools/analysis/pev { };
 
   photon = callPackage ../tools/networking/photon { };
@@ -1757,7 +1794,11 @@ in
 
   mongodb-compass = callPackage ../tools/misc/mongodb-compass { };
 
-  mongodb-tools = callPackage ../tools/misc/mongodb-tools { };
+  mongodb-tools = callPackage ../tools/misc/mongodb-tools {
+    # XXX: this is failing with Go 1.12. Error is related to cgo, an
+    # update to this package might fix it.
+    buildGoPackage = buildGo111Package;
+  };
 
   moosefs = callPackage ../tools/filesystems/moosefs { };
 
@@ -1840,7 +1881,11 @@ in
 
   bepasty = callPackage ../tools/misc/bepasty { };
 
-  bettercap = callPackage ../tools/security/bettercap { };
+  bettercap = callPackage ../tools/security/bettercap {
+    # XXX: this is failing with Go 1.12. Error is related to cgo, an
+    # update to this package might fix it.
+    buildGoPackage = buildGo111Package;
+  };
 
   bfg-repo-cleaner = gitAndTools.bfg-repo-cleaner;
 
@@ -2076,7 +2121,6 @@ in
   libkkc = callPackage ../tools/inputmethods/libkkc { };
 
   ibus = callPackage ../tools/inputmethods/ibus {
-    gconf = gnome2.GConf;
     inherit (gnome3) dconf;
   };
 
@@ -2096,7 +2140,7 @@ in
     mozc = callPackage ../tools/inputmethods/ibus-engines/ibus-mozc rec {
       python = python2;
       inherit (python2Packages) gyp;
-      protobuf = pkgs.protobuf.overrideDerivation (oldAttrs: { stdenv = clangStdenv; });
+      protobuf = pkgs.protobuf3_6.overrideDerivation (oldAttrs: { stdenv = clangStdenv; });
     };
 
     table = callPackage ../tools/inputmethods/ibus-engines/ibus-table {
@@ -2169,6 +2213,8 @@ in
 
   cocoapods = callPackage ../development/mobile/cocoapods { };
 
+  cocoapods-beta = lowPrio (callPackage ../development/mobile/cocoapods { beta = true; });
+
   compass = callPackage ../development/tools/compass { };
 
   conda = callPackage ../tools/package-management/conda { };
@@ -2266,7 +2312,9 @@ in
 
   davfs2 = callPackage ../tools/filesystems/davfs2 { };
 
-  dbeaver = callPackage ../applications/misc/dbeaver { };
+  dbeaver = callPackage ../applications/misc/dbeaver {
+    jdk = jdk11;
+  };
 
   dbench = callPackage ../development/tools/misc/dbench { };
 
@@ -2520,6 +2568,8 @@ in
     inherit (pythonPackages) sphinx;
   };
 
+  wallutils = callPackage ../tools/graphics/wallutils { };
+
   wl-clipboard = callPackage ../tools/misc/wl-clipboard { };
 
   zabbix-cli = callPackage ../tools/misc/zabbix-cli { };
@@ -2534,7 +2584,7 @@ in
 
   cholmod-extra = callPackage ../development/libraries/science/math/cholmod-extra { };
 
-  emscriptenVersion = "1.37.36";
+  emscriptenVersion = "1.38.28";
 
   emscripten = callPackage ../development/compilers/emscripten { };
 
@@ -2554,11 +2604,16 @@ in
 
   # The latest version used by elasticsearch, logstash, kibana and the the beats from elastic.
   elk5Version = "5.6.9";
-  elk6Version = "6.5.1";
+  elk6Version = "6.7.1";
+  elk7Version = "7.0.0";
 
   elasticsearch5 = callPackage ../servers/search/elasticsearch/5.x.nix { };
-  elasticsearch6 = callPackage ../servers/search/elasticsearch { };
-  elasticsearch6-oss = callPackage ../servers/search/elasticsearch {
+  elasticsearch6 = callPackage ../servers/search/elasticsearch/6.x.nix { };
+  elasticsearch6-oss = callPackage ../servers/search/elasticsearch/6.x.nix {
+    enableUnfree = false;
+  };
+  elasticsearch7 = callPackage ../servers/search/elasticsearch/7.x.nix { };
+  elasticsearch7-oss = callPackage ../servers/search/elasticsearch/7.x.nix {
     enableUnfree = false;
   };
   elasticsearch = elasticsearch6;
@@ -2694,7 +2749,7 @@ in
     mozc = callPackage ../tools/inputmethods/fcitx-engines/fcitx-mozc rec {
       python = python2;
       inherit (python2Packages) gyp;
-      protobuf = pkgs.protobuf.overrideDerivation (oldAttrs: { stdenv = clangStdenv; });
+      protobuf = pkgs.protobuf3_6.overrideDerivation (oldAttrs: { stdenv = clangStdenv; });
     };
 
     table-extra = callPackage ../tools/inputmethods/fcitx-engines/fcitx-table-extra { };
@@ -3672,10 +3727,14 @@ in
 
   junkie = callPackage ../tools/networking/junkie { };
 
+  just = callPackage ../development/tools/just { };
+
   go-jira = callPackage ../applications/misc/go-jira { };
 
   john = callPackage ../tools/security/john { };
 
+  joplin = nodePackages.joplin;
+
   joplin-desktop = callPackage ../applications/misc/joplin-desktop { };
 
   journalbeat = callPackage ../tools/system/journalbeat { };
@@ -3761,8 +3820,12 @@ in
   keyfuzz = callPackage ../tools/inputmethods/keyfuzz { };
 
   kibana5 = callPackage ../development/tools/misc/kibana/5.x.nix { };
-  kibana6 = callPackage ../development/tools/misc/kibana/default.nix { };
-  kibana6-oss = callPackage ../development/tools/misc/kibana/default.nix {
+  kibana6 = callPackage ../development/tools/misc/kibana/6.x.nix { };
+  kibana6-oss = callPackage ../development/tools/misc/kibana/6.x.nix {
+    enableUnfree = false;
+  };
+  kibana7 = callPackage ../development/tools/misc/kibana/7.x.nix { };
+  kibana7-oss = callPackage ../development/tools/misc/kibana/7.x.nix {
     enableUnfree = false;
   };
   kibana = kibana6;
@@ -3851,8 +3914,12 @@ in
   lockfileProgs = callPackage ../tools/misc/lockfile-progs { };
 
   logstash5 = callPackage ../tools/misc/logstash/5.x.nix { };
-  logstash6 = callPackage ../tools/misc/logstash { };
-  logstash6-oss = callPackage ../tools/misc/logstash {
+  logstash6 = callPackage ../tools/misc/logstash/6.x.nix { };
+  logstash6-oss = callPackage ../tools/misc/logstash/6.x.nix {
+    enableUnfree = false;
+  };
+  logstash7 = callPackage ../tools/misc/logstash/7.x.nix { };
+  logstash7-oss = callPackage ../tools/misc/logstash/7.x.nix {
     enableUnfree = false;
   };
   logstash = logstash6;
@@ -4349,7 +4416,11 @@ in
 
   miredo = callPackage ../tools/networking/miredo { };
 
-  mirrorbits = callPackage ../servers/mirrorbits { };
+  mirrorbits = callPackage ../servers/mirrorbits {
+    # XXX: this is failing with Go 1.12. Error is related to cgo, an
+    # update to this package might fix it.
+    buildGoPackage = buildGo111Package;
+  };
 
   mitmproxy = callPackage ../tools/networking/mitmproxy { };
 
@@ -4968,6 +5039,7 @@ in
 
   pinentry = callPackage ../tools/security/pinentry {
     libcap = if stdenv.isDarwin then null else libcap;
+    gcr = null;
   };
 
   pinentry_ncurses = res.pinentry.override {
@@ -5647,7 +5719,9 @@ in
     inherit (darwin.apple_sdk.frameworks) Security;
   };
 
-  solr = callPackage ../servers/search/solr { };
+  solr = solr_8;
+  solr_7 = callPackage ../servers/search/solr { };
+  solr_8 = callPackage ../servers/search/solr/8.x.nix { };
 
   solvespace = callPackage ../applications/graphics/solvespace { };
 
@@ -5973,6 +6047,8 @@ in
 
   torsocks = callPackage ../tools/security/tor/torsocks.nix { };
 
+  tox-node = callPackage ../tools/networking/tox-node { };
+
   toxvpn = callPackage ../tools/networking/toxvpn { };
 
   toybox = callPackage ../tools/misc/toybox { };
@@ -6226,7 +6302,7 @@ in
   wal_e = callPackage ../tools/backup/wal-e { };
 
   watchexec = callPackage ../tools/misc/watchexec {
-    inherit (darwin.apple_sdk.frameworks) CoreServices CoreFoundation;
+    inherit (darwin.apple_sdk.frameworks) CoreServices;
   };
 
   watchman = callPackage ../development/tools/watchman {
@@ -6434,7 +6510,11 @@ in
   waf = callPackage ../development/tools/build-managers/waf { python = python3; };
   wafHook = makeSetupHook {
     deps = [ python ];
-    substitutions = { inherit waf; };
+    substitutions = {
+      inherit waf;
+      crossFlags = lib.optionalString (stdenv.hostPlatform != stdenv.targetPlatform)
+        ''--cross-compile "--cross-execute=${stdenv.targetPlatform.emulator pkgs}"'';
+    };
   } ../development/tools/build-managers/waf/setup-hook.sh;
 
   wakelan = callPackage ../tools/networking/wakelan { };
@@ -6588,9 +6668,6 @@ in
 
   yarn = callPackage ../development/tools/yarn  { };
 
-  yarn2nix = throw "Use upstream https://github.com/moretea/yarn2nix";
-  mkYarnPackage = yarn2nix;
-
   yasr = callPackage ../applications/audio/yasr { };
 
   yank = callPackage ../tools/misc/yank { };
@@ -6966,7 +7043,7 @@ in
 
   crossLibcStdenv = overrideCC stdenv
     (if stdenv.targetPlatform.useLLVM or false
-     then buildPackages.llvmPackages_7.lldClangNoLibc
+     then buildPackages.llvmPackages_8.lldClangNoLibc
      else buildPackages.gccCrossStageStatic);
 
   # The GCC used to build libc for the target platform. Normal gccs will be
@@ -7660,14 +7737,12 @@ in
     inherit (darwin) apple_sdk;
   };
 
-  # For beta and nightly releases use the nixpkgs-mozilla overlay
-  rust = callPackage ../development/compilers/rust ({
+  rust = callPackage ../development/compilers/rust {
     inherit (darwin.apple_sdk.frameworks) CoreFoundation Security;
-    llvm = llvm_7;
-  } // stdenv.lib.optionalAttrs (stdenv.cc.isGNU && stdenv.hostPlatform.isi686) {
-    stdenv = overrideCC stdenv gcc6; # with gcc-7: undefined reference to `__divmoddi4'
-  });
-  inherit (rust) cargo rustc;
+  };
+  rustPackages = rust.packages.stable;
+  inherit (rustPackages) cargo rustc rustPlatform;
+  inherit (rust) makeRustPlatform;
 
   buildRustCrate = callPackage ../build-support/rust/build-rust-crate { };
   buildRustCrateHelpers = callPackage ../build-support/rust/build-rust-crate/helpers.nix { };
@@ -7683,9 +7758,6 @@ in
 
   defaultCrateOverrides = callPackage ../build-support/rust/default-crate-overrides.nix { };
 
-  makeRustPlatform = callPackage ../build-support/rust/make-rust-platform.nix {};
-  rustPlatform = recurseIntoAttrs (makeRustPlatform rust);
-
   cargo-download = callPackage ../tools/package-management/cargo-download { };
   cargo-edit = callPackage ../tools/package-management/cargo-edit { };
   cargo-release = callPackage ../tools/package-management/cargo-release {
@@ -7697,7 +7769,10 @@ in
   cargo-asm = callPackage ../development/tools/rust/cargo-asm {
     inherit (darwin.apple_sdk.frameworks) Security;
   };
+  cargo-bloat = callPackage ../development/tools/rust/cargo-bloat { };
+  cargo-expand = callPackage ../development/tools/rust/cargo-expand { };
   cargo-fuzz = callPackage ../development/tools/rust/cargo-fuzz { };
+  cargo-xbuild = callPackage ../development/tools/rust/cargo-xbuild { };
 
   pyo3-pack = callPackage ../development/tools/rust/pyo3-pack { };
   rainicorn = callPackage ../development/tools/rust/rainicorn { };
@@ -7800,6 +7875,7 @@ in
     vala_0_38
     vala_0_40
     vala_0_42
+    vala_0_44
     vala;
 
   valadoc = callPackage ../development/tools/valadoc { };
@@ -8086,8 +8162,6 @@ in
 
   ocropus = callPackage ../applications/misc/ocropus { };
 
-  inherit (callPackages ../development/interpreters/perl {}) perl528 perldevel;
-
   pachyderm = callPackage ../applications/networking/cluster/pachyderm { };
 
   php = php72;
@@ -8176,6 +8250,7 @@ in
 
   polyml = callPackage ../development/compilers/polyml { };
   polyml56 = callPackage ../development/compilers/polyml/5.6.nix { };
+  polyml57 = callPackage ../development/compilers/polyml/5.7.nix { };
 
   pure = callPackage ../development/interpreters/pure {
     llvm = llvm_35;
@@ -8521,6 +8596,8 @@ in
 
   automake111x = callPackage ../development/tools/misc/automake/automake-1.11.x.nix { };
 
+  automake115x = callPackage ../development/tools/misc/automake/automake-1.15.x.nix { };
+
   automake116x = callPackage ../development/tools/misc/automake/automake-1.16.x.nix { };
 
   automoc4 = callPackage ../development/tools/misc/automoc4 { };
@@ -8607,6 +8684,8 @@ in
 
   cadre = callPackage ../development/tools/cadre { };
 
+  cask = callPackage ../development/tools/cask { };
+
   casperjs = callPackage ../development/tools/casperjs {
     inherit (texFunctions) fontsConf;
   };
@@ -8869,6 +8948,7 @@ in
   };
 
   foreman = callPackage ../tools/system/foreman { };
+  goreman = callPackage ../tools/system/goreman { };
 
   framac = callPackage ../development/tools/analysis/frama-c { };
 
@@ -8944,6 +9024,8 @@ in
 
   grail = callPackage ../development/libraries/grail { };
 
+  graphene-hardened-malloc = callPackage ../development/libraries/graphene-hardened-malloc { };
+
   gtk-doc = callPackage ../development/tools/documentation/gtk-doc { };
 
   gtkdialog = callPackage ../development/tools/misc/gtkdialog { };
@@ -9098,6 +9180,8 @@ in
 
   mk = callPackage ../development/tools/build-managers/mk { };
 
+  mkcert = callPackage ../development/tools/misc/mkcert { };
+
   mkdocs = callPackage ../development/tools/documentation/mkdocs { };
 
   moby = callPackage ../development/tools/misc/moby { };
@@ -9266,8 +9350,6 @@ in
     withPEPatterns = true;
   };
 
-  rhc = callPackage ../development/tools/rhc { };
-
   rman = callPackage ../development/tools/misc/rman { };
 
   rolespec = callPackage ../development/tools/misc/rolespec { };
@@ -9495,6 +9577,8 @@ in
 
   aalib = callPackage ../development/libraries/aalib { };
 
+  abseil-cpp = callPackage ../development/libraries/abseil-cpp { };
+
   accountsservice = callPackage ../development/libraries/accountsservice { };
 
   acl = callPackage ../development/libraries/acl { };
@@ -9790,6 +9874,8 @@ in
 
   curlcpp = callPackage ../development/libraries/curlcpp { };
 
+  curlpp = callPackage ../development/libraries/curlpp { };
+
   cutee = callPackage ../development/libraries/cutee { };
 
   cutelyst = libsForQt5.callPackage ../development/libraries/cutelyst { };
@@ -9953,7 +10039,7 @@ in
     inherit (darwin.apple_sdk.frameworks) Cocoa CoreMedia;
   };
   ffmpeg_4 = callPackage ../development/libraries/ffmpeg/4.nix {
-    inherit (darwin.apple_sdk.frameworks) Cocoa CoreMedia;
+    inherit (darwin.apple_sdk.frameworks) Cocoa CoreMedia VideoToolbox;
   };
 
   # Aliases
@@ -10394,6 +10480,8 @@ in
 
   glib-networking = callPackage ../development/libraries/glib-networking {};
 
+  gom = callPackage ../development/libraries/gom { };
+
   ace = callPackage ../development/libraries/ace { };
 
   atk = callPackage ../development/libraries/atk { };
@@ -10531,6 +10619,8 @@ in
 
   hiredis = callPackage ../development/libraries/hiredis { };
 
+  hiredis-vip = callPackage ../development/libraries/hiredis-vip { };
+
   hivex = callPackage ../development/libraries/hivex { };
 
   hound = callPackage ../development/tools/misc/hound { };
@@ -10730,6 +10820,8 @@ in
 
   lcms2 = callPackage ../development/libraries/lcms2 { };
 
+  ldacbt = callPackage ../development/libraries/ldacbt { };
+
   ldb = callPackage ../development/libraries/ldb {
     python = python2;
   };
@@ -11479,6 +11571,8 @@ in
 
   libotr = callPackage ../development/libraries/libotr { };
 
+  libow = callPackage ../development/libraries/libow { };
+
   libp11 = callPackage ../development/libraries/libp11 { };
 
   libpar2 = callPackage ../development/libraries/libpar2 { };
@@ -12263,8 +12357,9 @@ in
     buildPythonApplication click future six;
   };
 
-  protobuf = protobuf3_6;
+  protobuf = protobuf3_7;
 
+  protobuf3_7 = callPackage ../development/libraries/protobuf/3.7.nix { };
   protobuf3_6 = callPackage ../development/libraries/protobuf/3.6.nix { };
   protobuf3_5 = callPackage ../development/libraries/protobuf/3.5.nix { };
   protobuf3_4 = callPackage ../development/libraries/protobuf/3.4.nix { };
@@ -12763,7 +12858,11 @@ in
     sdnotify-wrapper = callPackage ../os-specific/linux/sdnotify-wrapper { };
   };
 
-  skydive = callPackage ../tools/networking/skydive { };
+  skydive = callPackage ../tools/networking/skydive {
+    # XXX: this is failing with Go 1.12. Error is related to cgo, an
+    # update to this package might fix it.
+    buildGoPackage = buildGo111Package;
+  };
 
   slang = callPackage ../development/libraries/slang { };
 
@@ -13220,6 +13319,8 @@ in
 
   wayland-protocols = callPackage ../development/libraries/wayland/protocols.nix { };
 
+  waylandpp = callPackage ../development/libraries/waylandpp { };
+
   wcslib = callPackage ../development/libraries/wcslib { };
 
   webkitgtk = callPackage ../development/libraries/webkitgtk {
@@ -13396,7 +13497,7 @@ in
   zmqpp = callPackage ../development/libraries/zmqpp { };
 
   zig = callPackage ../development/compilers/zig {
-    llvmPackages = llvmPackages_7;
+    llvmPackages = llvmPackages_8;
   };
 
   zimlib = callPackage ../development/libraries/zimlib { };
@@ -13527,8 +13628,11 @@ in
   buildGo111Package = callPackage ../development/go-packages/generic {
     go = buildPackages.go_1_11;
   };
+  buildGo112Package = callPackage ../development/go-packages/generic {
+    go = buildPackages.go_1_12;
+  };
 
-  buildGoPackage = buildGo111Package;
+  buildGoPackage = buildGo112Package;
 
   buildGo111Module = callPackage ../development/go-modules/generic {
     go = buildPackages.go_1_11;
@@ -13589,19 +13693,14 @@ in
 
   ### DEVELOPMENT / PERL MODULES
 
-  # the latest Maint version
-  perl528Packages = recurseIntoAttrs (callPackage ./perl-packages.nix {
-    perl = perl528;
-    overrides = (config.perlPackageOverrides or (p: {})) pkgs;
-  });
-  # the latest Devel version
-  perldevelPackages = recurseIntoAttrs (callPackage ./perl-packages.nix {
-    perl = perldevel;
-    overrides = (config.perlPackageOverrides or (p: {})) pkgs;
-  });
+  perlInterpreters = callPackages ../development/interpreters/perl {};
+  inherit (perlInterpreters) perl528 perldevel;
+
+  perl528Packages = recurseIntoAttrs perl528.pkgs;
+  perldevelPackages = perldevel.pkgs;
 
+  perl = perl528;
   perlPackages = perl528Packages;
-  inherit (perlPackages) perl;
 
   ack = perlPackages.ack;
 
@@ -14293,7 +14392,7 @@ in
   samba3 = callPackage ../servers/samba/3.x.nix { };
 
   samba4 = callPackage ../servers/samba/4.x.nix {
-    python = python2;
+    python = python3;
   };
 
   sambaMaster = callPackage ../servers/samba/master.nix { };
@@ -14581,7 +14680,11 @@ in
 
   cifs-utils = callPackage ../os-specific/linux/cifs-utils { };
 
-  cockroachdb = callPackage ../servers/sql/cockroachdb { };
+  cockroachdb = callPackage ../servers/sql/cockroachdb {
+    # XXX: this is failing with Go 1.12. Error is related to cgo, an
+    # update to this package might fix it.
+    buildGoPackage = buildGo111Package;
+  };
 
   conky = callPackage ../os-specific/linux/conky ({
     lua = lua5_3_compat;
@@ -14661,9 +14764,7 @@ in
 
   fatrace = callPackage ../os-specific/linux/fatrace { };
 
-  ffado = callPackage ../os-specific/linux/ffado {
-    inherit (python2Packages) python pyqt4 dbus-python;
-  };
+  ffado = callPackage ../os-specific/linux/ffado { };
   libffado = ffado;
 
   fbterm = callPackage ../os-specific/linux/fbterm { };
@@ -14792,6 +14893,8 @@ in
 
   openisns = callPackage ../os-specific/linux/open-isns { };
 
+  osxfuse = callPackage ../os-specific/darwin/osxfuse { };
+
   powerstat = callPackage ../os-specific/linux/powerstat { };
 
   smemstat = callPackage ../os-specific/linux/smemstat { };
@@ -15318,9 +15421,7 @@ in
 
   gomodifytags = callPackage ../development/tools/gomodifytags { };
 
-  go-langserver = callPackage ../development/tools/go-langserver {
-    buildGoPackage = buildGo110Package;
-  };
+  go-langserver = callPackage ../development/tools/go-langserver { };
 
   gotests = callPackage ../development/tools/gotests { };
 
@@ -16067,7 +16168,7 @@ in
 
   papirus-icon-theme = callPackage ../data/icons/papirus-icon-theme { };
 
-  papis = callPackage ../tools/misc/papis { };
+  papis = with python3Packages; toPythonApplication papis;
 
   paps = callPackage ../tools/misc/paps { };
 
@@ -16372,7 +16473,6 @@ in
   androidStudioPackages = recurseIntoAttrs
     (callPackage ../applications/editors/android-studio { });
   android-studio = androidStudioPackages.stable;
-  android-studio-preview = androidStudioPackages.preview;
 
   animbar = callPackage ../applications/graphics/animbar { };
 
@@ -16680,8 +16780,6 @@ in
     amdappsdk = amdappsdk28;
   };
 
-  chatzilla = callPackage ../applications/networking/irc/chatzilla { };
-
   chirp = callPackage ../applications/radio/chirp {
     inherit (pythonPackages) pyserial pygtk;
   };
@@ -16847,7 +16945,6 @@ in
     headerbar-gtk3 = callPackage ../applications/audio/deadbeef/plugins/headerbar-gtk3.nix { };
     infobar = callPackage ../applications/audio/deadbeef/plugins/infobar.nix { };
     mpris2 = callPackage ../applications/audio/deadbeef/plugins/mpris2.nix { };
-    opus = callPackage ../applications/audio/deadbeef/plugins/opus.nix { };
   };
 
   deadbeef-with-plugins = callPackage ../applications/audio/deadbeef/wrapper.nix {
@@ -16924,6 +17021,10 @@ in
   dragonfly-reverb = callPackage ../applications/audio/dragonfly-reverb { };
 
   drawpile = libsForQt5.callPackage ../applications/graphics/drawpile { };
+  drawpile-server-headless = libsForQt5.callPackage ../applications/graphics/drawpile {
+    buildClient = false;
+    buildServerGui = false;
+  };
 
   droopy = callPackage ../applications/networking/droopy {
     inherit (python3Packages) wrapPython;
@@ -17477,14 +17578,13 @@ in
   welle-io = libsForQt5.callPackage ../applications/radio/welle-io { };
 
   wireshark = callPackage ../applications/networking/sniffers/wireshark {
-    qt5 = qt59;
     inherit (darwin.apple_sdk.frameworks) ApplicationServices SystemConfiguration;
   };
   wireshark-qt = wireshark;
 
   # The GTK UI is deprecated by upstream. You probably want the QT version.
-  wireshark-gtk = wireshark.override { withGtk = true; withQt = false; };
-  wireshark-cli = wireshark.override { withGtk = false; withQt = false; };
+  wireshark-gtk = throw "Not supported anymore. Use wireshark-qt or wireshark-cli instead.";
+  wireshark-cli = wireshark.override { withQt = false; };
 
   fbida = callPackage ../applications/graphics/fbida { };
 
@@ -17875,6 +17975,8 @@ in
 
   howl = callPackage ../applications/editors/howl { };
 
+  hpl = callPackage ../tools/misc/hpl { mpi = openmpi; };
+
   ht = callPackage ../applications/editors/ht { };
 
   hubstaff = callPackage ../applications/misc/hubstaff { };
@@ -17918,10 +18020,7 @@ in
 
   slack-term = callPackage ../applications/networking/instant-messengers/slack-term { };
 
-  singularity = callPackage ../applications/virtualization/singularity {
-    # XXX: the build is finding references to Go when compiled with go v1.12
-    go = go_1_11;
-  };
+  singularity = callPackage ../applications/virtualization/singularity { };
 
   spectmorph = callPackage ../applications/audio/spectmorph { };
 
@@ -18450,6 +18549,8 @@ in
 
   mac = callPackage ../development/libraries/mac { };
 
+  macdylibbundler = callPackage ../development/tools/misc/macdylibbundler { };
+
   magic-wormhole = with python3Packages; toPythonApplication magic-wormhole;
 
   mail-notification = callPackage ../desktops/gnome-2/desktop/mail-notification {};
@@ -18553,7 +18654,7 @@ in
 
   mirage = callPackage ../applications/graphics/mirage { };
 
-  mixxx = callPackage ../applications/audio/mixxx {
+  mixxx = libsForQt5.callPackage ../applications/audio/mixxx {
     inherit (vamp) vampSDK;
   };
 
@@ -18809,6 +18910,8 @@ in
 
   shogun = callPackage ../applications/science/machine-learning/shogun { };
 
+  sky = callPackage ../applications/networking/instant-messengers/sky {};
+
   smplayer = libsForQt5.callPackage ../applications/video/smplayer { };
 
   smtube = libsForQt5.callPackage ../applications/video/smtube {};
@@ -19686,6 +19789,8 @@ in
 
   peru = callPackage ../applications/version-management/peru {};
 
+  petrinizer = haskellPackages.callPackage ../applications/science/logic/petrinizer {};
+
   pmidi = callPackage ../applications/audio/pmidi { };
 
   printrun = callPackage ../applications/misc/printrun { };
@@ -19766,6 +19871,10 @@ in
     bison = bison2;
   };
 
+  stretchly = callPackage ../applications/misc/stretchly {
+    inherit (gnome2) GConf;
+  };
+
   stumpish = callPackage ../applications/window-managers/stumpish {};
 
   stumpwm = callPackage ../applications/window-managers/stumpwm {
@@ -20486,12 +20595,18 @@ in
 
   kodiPlain = callPackage ../applications/video/kodi { };
 
+  kodiPlainWayland = callPackage ../applications/video/kodi { useWayland = true; };
+
   kodiPlugins = recurseIntoAttrs (callPackage ../applications/video/kodi/plugins.nix {});
 
   kodi = wrapKodi {
     kodi = kodiPlain;
   };
 
+  kodi-wayland = wrapKodi {
+    kodi = kodiPlainWayland;
+  };
+
   kodi-cli = callPackage ../tools/misc/kodi-cli { };
 
   kodi-retroarch-advanced-launchers =
@@ -20945,6 +21060,8 @@ in
 
   exult = callPackage ../games/exult { };
 
+  fltrator = callPackage ../games/fltrator { };
+
   factorio = callPackage ../games/factorio { releaseType = "alpha"; };
 
   factorio-experimental = factorio.override { releaseType = "alpha"; experimental = true; };
@@ -21265,6 +21382,8 @@ in
     };
   };
 
+  riko4 = callPackage ../games/riko4 { };
+
   rili = callPackage ../games/rili { };
 
   rimshot = callPackage ../games/rimshot { love = love_0_7; };
@@ -21544,6 +21663,8 @@ in
 
   xsokoban = callPackage ../games/xsokoban { };
 
+  xtris = callPackage ../games/xtris { };
+
   inherit (callPackage ../games/quake2/yquake2 { })
     yquake2
     yquake2-ctf
@@ -21580,7 +21701,7 @@ in
   clearlooks-phenix = callPackage ../misc/themes/clearlooks-phenix { };
 
   deepin = recurseIntoAttrs (import ../desktops/deepin {
-    inherit pkgs libsForQt5 go_1_11;
+    inherit pkgs libsForQt5;
     inherit (lib) makeScope;
   });
 
@@ -21786,10 +21907,14 @@ in
 
   ecopcr = callPackage ../applications/science/biology/ecopcr { };
 
+  eggnog-mapper = callPackage ../applications/science/biology/eggnog-mapper { };
+
   emboss = callPackage ../applications/science/biology/emboss { };
 
   ezminc = callPackage ../applications/science/biology/EZminc { };
 
+  exonerate = callPackage ../applications/science/biology/exonerate { };
+
   hisat2 = callPackage ../applications/science/biology/hisat2 { };
 
   htslib = callPackage ../development/libraries/science/biology/htslib { };
@@ -21856,6 +21981,8 @@ in
 
   plink-ng = callPackage ../applications/science/biology/plink-ng { };
 
+  prodigal = callPackage ../applications/science/biology/prodigal { };
+
   raxml = callPackage ../applications/science/biology/raxml { };
 
   raxml-mpi = appendToName "mpi" (raxml.override {
@@ -21974,7 +22101,9 @@ in
 
   nauty = callPackage ../applications/science/math/nauty {};
 
-  or-tools = callPackage ../development/libraries/science/math/or-tools {};
+  or-tools = callPackage ../development/libraries/science/math/or-tools {
+    pythonProtobuf = pythonPackages.protobuf;
+  };
 
   rubiks = callPackage ../development/libraries/science/math/rubiks { };
 
@@ -22066,6 +22195,8 @@ in
 
   dafny = dotnetPackages.Dafny;
 
+  groove = callPackage ../applications/science/programming/groove { };
+
   plm = callPackage ../applications/science/programming/plm { };
 
   scyther = callPackage ../applications/science/programming/scyther { };
@@ -22145,7 +22276,7 @@ in
   ifstat-legacy = callPackage ../tools/networking/ifstat-legacy { };
 
   isabelle = callPackage ../applications/science/logic/isabelle {
-    polyml = stdenv.lib.overrideDerivation polyml (attrs: {
+    polyml = stdenv.lib.overrideDerivation polyml57 (attrs: {
       configureFlags = [ "--enable-intinf-as-int" "--with-gmp" "--disable-shared" ];
     });
 
@@ -22583,6 +22714,7 @@ in
   epson-alc1100 = callPackage ../misc/drivers/epson-alc1100 { };
 
   epson-escpr = callPackage ../misc/drivers/epson-escpr { };
+  epson-escpr2 = callPackage ../misc/drivers/epson-escpr2 { };
 
   epson_201207w = callPackage ../misc/drivers/epson_201207w { };
 
@@ -22821,6 +22953,8 @@ in
 
   nixops = callPackage ../tools/package-management/nixops { };
 
+  nixops_1_6_1 = callPackage ../tools/package-management/nixops/nixops-v1_6_1.nix {};
+
   nixopsUnstable = lowPrio (callPackage ../tools/package-management/nixops/unstable.nix { });
 
   nixops-dns = callPackage ../tools/package-management/nixops/nixops-dns.nix { };
@@ -23240,6 +23374,8 @@ in
 
   terragrunt = callPackage ../applications/networking/cluster/terragrunt {};
 
+  tilt = callPackage ../applications/networking/cluster/tilt {};
+
   tetex = callPackage ../tools/typesetting/tex/tetex { libpng = libpng12; };
 
   tetra-gtk-theme = callPackage ../misc/themes/tetra { };