Merge branch 'master' into staging-next

Hydra: ?compare=1474536

4 files changed, 248 insertions, 13 deletions

diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index ece6c03e168a..634a3e4c17e4 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -173,6 +173,7 @@ mapAliases ({
   module_init_tools = kmod; # added 2016-04-22
   mpich2 = mpich;  # added 2018-08-06
   msf = metasploit; # added 2018-04-25
+  libmsgpack = msgpack; # added 2018-08-17
   mssys = ms-sys; # added 2015-12-13
   multipath_tools = multipath-tools;  # added 2016-01-21
   mupen64plus1_5 = mupen64plus; # added 2016-02-12
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 60aa4d9e89c7..91e91bdd3a7d 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -1488,6 +1488,10 @@ with pkgs;
 
   syslogng_incubator = callPackage ../tools/system/syslog-ng-incubator { };
 
+  inherit (callPackages ../servers/rainloop { })
+    rainloop-community
+    rainloop-standard;
+
   ring-daemon = callPackage ../applications/networking/instant-messengers/ring-daemon { };
 
   riot-web = callPackage ../applications/networking/instant-messengers/riot/riot-web.nix {
@@ -7020,6 +7024,11 @@ with pkgs;
     inherit (darwin.apple_sdk.frameworks) Foundation;
   };
 
+  mono514 = callPackage ../development/compilers/mono/5.14.nix {
+    inherit (darwin) libobjc;
+    inherit (darwin.apple_sdk.frameworks) Foundation;
+  };
+
   monoDLLFixer = callPackage ../build-support/mono-dll-fixer { };
 
   mosml = callPackage ../development/compilers/mosml { };
@@ -7160,6 +7169,13 @@ with pkgs;
 
   sqldeveloper = callPackage ../development/tools/database/sqldeveloper { };
 
+  # sqldeveloper_18 needs JavaFX, which currently only is available inside the
+  # (non-free and net yet packaged for Darwin) OracleJDK
+  # we might be able to get rid of it, as soon as we have an OpenJDK with OpenJFX included
+  sqldeveloper_18 = callPackage ../development/tools/database/sqldeveloper/18.2.nix {
+    jdk = oraclejdk;
+  };
+
   squeak = callPackage ../development/compilers/squeak { };
 
   squirrel-sql = callPackage ../development/tools/database/squirrel-sql {
@@ -8095,6 +8111,8 @@ with pkgs;
 
   ddd = callPackage ../development/tools/misc/ddd { };
 
+  lattice-diamond = callPackage ../development/tools/lattice-diamond { };
+
   distcc = callPackage ../development/tools/misc/distcc { };
 
   # distccWrapper: wrapper that works as gcc or g++
@@ -8492,6 +8510,8 @@ with pkgs;
 
   pup = callPackage ../development/tools/pup { };
 
+  puppet-lint = callPackage ../development/tools/puppet/puppet-lint { };
+
   pyrseas = callPackage ../development/tools/database/pyrseas { };
 
   qtcreator = libsForQt5.callPackage ../development/tools/qtcreator { };
@@ -9182,9 +9202,19 @@ with pkgs;
 
   ffcast = callPackage ../tools/X11/ffcast { };
 
-  fflas-ffpack = callPackage ../development/libraries/fflas-ffpack {};
+  fflas-ffpack = callPackage ../development/libraries/fflas-ffpack {
+    # We need to use blas instead of openblas on darwin,
+    # see https://github.com/NixOS/nixpkgs/pull/45013.
+    blas = if stdenv.isDarwin then blas else openblas;
+  };
+
   fflas-ffpack_1 = callPackage ../development/libraries/fflas-ffpack/1.nix {};
-  linbox = callPackage ../development/libraries/linbox {};
+  linbox = callPackage ../development/libraries/linbox {
+    # We need to use blas instead of openblas on darwin, see
+    # https://github.com/NixOS/nixpkgs/pull/45013 and
+    # https://github.com/NixOS/nixpkgs/pull/45015.
+    blas = if stdenv.isDarwin then blas else openblas;
+  };
 
   ffmpeg_0_10 = callPackage ../development/libraries/ffmpeg/0.10.nix {
     inherit (darwin.apple_sdk.frameworks) Cocoa;
@@ -9662,7 +9692,6 @@ with pkgs;
 
   gtk2 = callPackage ../development/libraries/gtk+/2.x.nix {
     cupsSupport = config.gtk2.cups or stdenv.isLinux;
-    gdktarget = if stdenv.isDarwin then "quartz" else "x11";
     inherit (darwin.apple_sdk.frameworks) AppKit Cocoa;
   };
 
@@ -9670,7 +9699,9 @@ with pkgs;
     gdktarget = "x11";
   };
 
-  gtk3 = callPackage ../development/libraries/gtk+/3.x.nix { };
+  gtk3 = callPackage ../development/libraries/gtk+/3.x.nix {
+    inherit (darwin.apple_sdk.frameworks) AppKit Cocoa;
+  };
 
   gtkmm2 = callPackage ../development/libraries/gtkmm/2.x.nix { };
   gtkmm3 = callPackage ../development/libraries/gtkmm/3.x.nix { };
@@ -9954,6 +9985,8 @@ with pkgs;
 
   lmdb = callPackage ../development/libraries/lmdb { };
 
+  lmdbxx = callPackage ../development/libraries/lmdbxx { };
+
   levmar = callPackage ../development/libraries/levmar { };
 
   leptonica = callPackage ../development/libraries/leptonica { };
@@ -10427,8 +10460,6 @@ with pkgs;
 
   libmtp = callPackage ../development/libraries/libmtp { };
 
-  libmsgpack = callPackage ../development/libraries/libmsgpack { };
-
   libmypaint = callPackage ../development/libraries/libmypaint { };
 
   libmysofa = callPackage ../development/libraries/audio/libmysofa { };
@@ -11108,6 +11139,8 @@ with pkgs;
 
   mqtt-bench = callPackage ../applications/misc/mqtt-bench {};
 
+  msgpack = callPackage ../development/libraries/msgpack { };
+
   msilbc = callPackage ../development/libraries/msilbc { };
 
   mp4v2 = callPackage ../development/libraries/mp4v2 { };
@@ -13724,9 +13757,7 @@ with pkgs;
 
   iproute = callPackage ../os-specific/linux/iproute { };
 
-  iputils = callPackage ../os-specific/linux/iputils {
-    inherit (buildPackages.buildPackages.perlPackages) SGMLSpm;
-  };
+  iputils = callPackage ../os-specific/linux/iputils { };
 
   iptables = callPackage ../os-specific/linux/iptables { };
 
@@ -15133,6 +15164,8 @@ with pkgs;
 
   vdrsymbols = callPackage ../data/fonts/vdrsymbols { };
 
+  vegur = callPackage ../data/fonts/vegur { };
+
   vistafonts = callPackage ../data/fonts/vista-fonts { };
 
   vistafonts-chs = callPackage ../data/fonts/vista-fonts-chs { };
@@ -16132,6 +16165,8 @@ with pkgs;
 
   fetchmail = callPackage ../applications/misc/fetchmail { };
 
+  fig2dev = callPackage ../applications/graphics/fig2dev { };
+
   flacon = callPackage ../applications/audio/flacon { };
 
   flexget = callPackage ../applications/networking/flexget { };
@@ -16975,7 +17010,7 @@ with pkgs;
       recurseIntoAttrs (makeOverridable mkApplications attrs);
 
   inherit (kdeApplications)
-    akonadi akregator ark dolphin ffmpegthumbs filelight gwenview k3b
+    akonadi akregator ark dolphin dragon ffmpegthumbs filelight gwenview k3b
     kaddressbook kate kcachegrind kcalc kcolorchooser kcontacts kdenlive kdf kdialog keditbookmarks
     kget kgpg khelpcenter kig kleopatra kmail kmix kolourpaint kompare konsole
     kontact korganizer krdc krfb ksystemlog kwalletmanager marble minuet okular spectacle;
@@ -17314,7 +17349,7 @@ with pkgs;
 
   minitube = libsForQt5.callPackage ../applications/video/minitube { };
 
-  mimic = callPackage ../applications/audio/mimic { 
+  mimic = callPackage ../applications/audio/mimic {
     pulseaudioSupport = config.pulseaudio or false;
   };
 
@@ -18044,6 +18079,8 @@ with pkgs;
     qt = qt4;
   };
 
+  qsstv = qt5.callPackage ../applications/misc/qsstv { };
+
   qsyncthingtray = libsForQt5.callPackage ../applications/misc/qsyncthingtray { };
 
   qstopmotion = libsForQt5.callPackage ../applications/video/qstopmotion { };
@@ -20513,6 +20550,8 @@ with pkgs;
 
   star = callPackage ../applications/science/biology/star { };
 
+  strelka = callPackage ../applications/science/biology/strelka { };
+
   varscan = callPackage ../applications/science/biology/varscan { };
 
   hmmer = callPackage ../applications/science/biology/hmmer { };
@@ -20551,6 +20590,8 @@ with pkgs;
 
   cliquer = callPackage ../development/libraries/science/math/cliquer { };
 
+  ecos = callPackage ../development/libraries/science/math/ecos { };
+
   flintqs = callPackage ../development/libraries/science/math/flintqs { };
 
   gurobi = callPackage ../applications/science/math/gurobi { };
diff --git a/pkgs/top-level/lua-packages.nix b/pkgs/top-level/lua-packages.nix
index c7d4c18810f0..7933ca46b98a 100644
--- a/pkgs/top-level/lua-packages.nix
+++ b/pkgs/top-level/lua-packages.nix
@@ -7,7 +7,7 @@
 
 { fetchurl, stdenv, lua, callPackage, unzip, zziplib, pkgconfig
 , pcre, oniguruma, gnulib, tre, glibc, sqlite, openssl, expat
-, glib, gobjectIntrospection, libevent, zlib, autoreconfHook
+, glib, gobjectIntrospection, libevent, zlib, autoreconfHook, gnum4
 , mysql, postgresql, cyrus_sasl
 , fetchFromGitHub, libmpack, which, fetchpatch, writeText
 }:
@@ -43,6 +43,32 @@ let
     inherit lua;
   };
 
+  basexx = buildLuaPackage rec {
+    version = "0.4.0";
+    name = "basexx-${version}";
+
+    src = fetchFromGitHub {
+      owner = "aiq";
+      repo = "basexx";
+      rev = "v${version}";
+      sha256 = "12y0ng9bp5b98iax35pnp0kc0mb42spv1cbywvfq6amik6l0ya7g";
+    };
+
+    buildPhase = ":";
+    installPhase = ''
+      install -Dt "$out/lib/lua/${lua.luaversion}/" \
+        lib/basexx.lua
+    '';
+
+    meta = with stdenv.lib; {
+      description = "Lua library for base2, base16, base32, base64, base85";
+      homepage = "https://github.com/aiq/basexx";
+      license = licenses.mit;
+      maintainers = with maintainers; [ vcunat ];
+      platforms = platforms.all;
+    };
+  };
+
   bit32 = buildLuaPackage rec {
     version = "5.3.0";
     name = "bit32-${version}";
@@ -72,6 +98,93 @@ let
     };
   };
 
+  compat53 = buildLuaPackage rec {
+    version = "0.7";
+    name = "compat53-${version}";
+
+    src = fetchFromGitHub {
+      owner = "keplerproject";
+      repo = "lua-compat-5.3";
+      rev = "v${version}";
+      sha256 = "02a14nvn7aggg1yikj9h3dcf8aqjbxlws1bfvqbpfxv9d5phnrpz";
+    };
+
+    nativeBuildInputs = [ pkgconfig ];
+
+    postConfigure = ''
+      CFLAGS+=" -shared $(pkg-config --libs ${if isLuaJIT then "luajit" else "lua"})"
+    '';
+
+    buildPhase = ''
+      cc lstrlib.c $CFLAGS -o string.so
+      cc ltablib.c $CFLAGS -o table.so
+      cc lutf8lib.c $CFLAGS -o utf8.so
+    '';
+
+    # There's no need to separate *.lua and *.so, I guess?  TODO: conventions?
+    installPhase = ''
+      install -Dt "$out/lib/lua/${lua.luaversion}/compat53" \
+        compat53/*.lua *.so
+    '';
+
+    meta = with stdenv.lib; {
+      description = "Compatibility module providing Lua-5.3-style APIs for Lua 5.2 and 5.1";
+      homepage = "https://github.com/keplerproject/lua-compat-5.3";
+      license = licenses.mit;
+      maintainers = with maintainers; [ vcunat ];
+      platforms = platforms.all;
+    };
+  };
+
+  cqueues = buildLuaPackage rec {
+    name = "cqueues-${version}";
+    version = "20171014";
+
+    src = fetchurl {
+      url = "https://www.25thandclement.com/~william/projects/releases/${name}.tgz";
+      sha256 = "1dabhpn6r0hlln8vx9hxm34pfcm46qzgpb2apmziwg5z51fi4ksb";
+    };
+
+    preConfigure = ''export prefix=$out'';
+
+    nativeBuildInputs = [ gnum4 ];
+    buildInputs = [ openssl ];
+
+    meta = with stdenv.lib; {
+      description = "A type of event loop for Lua";
+      homepage = "https://www.25thandclement.com/~william/projects/cqueues.html";
+      license = licenses.mit;
+      maintainers = with maintainers; [ vcunat ];
+      platforms = platforms.unix;
+    };
+  };
+
+  fifo = buildLuaPackage rec {
+    version = "0.2";
+    name = "fifo-${version}";
+
+    src = fetchFromGitHub {
+      owner = "daurnimator";
+      repo = "fifo.lua";
+      rev = version;
+      sha256 = "1800k7h5hxsvm05bjdr65djjml678lwb0661cll78z1ys2037nzn";
+    };
+
+    buildPhase = ":";
+    installPhase = ''
+      mkdir -p "$out/lib/lua/${lua.luaversion}"
+      mv fifo.lua "$out/lib/lua/${lua.luaversion}/"
+    '';
+
+    meta = with stdenv.lib; {
+      description = "A lua library/'class' that implements a FIFO";
+      homepage = "https://github.com/daurnimator/fifo.lua";
+      license = licenses.mit;
+      maintainers = with maintainers; [ vcunat ];
+      platforms = platforms.all;
+    };
+  };
+
   luabitop = buildLuaPackage rec {
     version = "1.0.2";
     name = "bitop-${version}";
@@ -109,6 +222,38 @@ let
     };
   };
 
+  http = buildLuaPackage rec {
+    version = "0.2";
+    name = "http-${version}";
+
+    src = fetchFromGitHub {
+      owner = "daurnimator";
+      repo = "lua-http";
+      rev = "v${version}";
+      sha256 = "0a8vsj49alaf1fkhv51n5mgpjq8izfff3shcjs8xk7p2bc46vd7i";
+    };
+
+    /* TODO: separate docs derivation? (pandoc is heavy)
+    nativeBuildInputs = [ pandoc ];
+    makeFlags = [ "-C doc" "lua-http.html" "lua-http.3" ];
+    */
+
+    buildPhase = ":";
+    installPhase = ''
+      install -Dt "$out/lib/lua/${lua.luaversion}/http" \
+        http/*.lua
+      install -Dt "$out/lib/lua/${lua.luaversion}/http/compat" \
+        http/compat/*.lua
+    '';
+
+    meta = with stdenv.lib; {
+      description = "HTTP library for lua";
+      homepage = "https://daurnimator.github.io/lua-http/${version}/";
+      license = licenses.mit;
+      maintainers = with maintainers; [ vcunat ];
+    };
+  };
+
   luacheck = buildLuaPackage rec {
     pname = "luacheck";
     version = "0.20.0";
@@ -298,6 +443,28 @@ let
     };
   };
 
+  luaossl = buildLuaPackage rec {
+    name = "luaossl-${version}";
+    version = "20170903";
+
+    src = fetchurl {
+      url = "https://www.25thandclement.com/~william/projects/releases/${name}.tgz";
+      sha256 = "10392bvd0lzyibipblgiss09zlqh3a5zgqg1b9lgbybpqb9cv2k3";
+    };
+
+    preConfigure = ''export prefix=$out'';
+
+    buildInputs = [ openssl ];
+
+    meta = with stdenv.lib; {
+      description = "Comprehensive binding to OpenSSL for Lua 5.1+";
+      homepage = "https://www.25thandclement.com/~william/projects/luaossl.html";
+      license = licenses.mit;
+      maintainers = with maintainers; [ vcunat ];
+      platforms = platforms.unix;
+    };
+  };
+
   luaposix = buildLuaPackage rec {
     name = "posix-${version}";
     version = "34.0.4";
@@ -688,6 +855,32 @@ let
     };
   };
 
+  lpeg_patterns = buildLuaPackage rec {
+    version = "0.5";
+    name = "lpeg_patterns-${version}";
+
+    src = fetchFromGitHub {
+      owner = "daurnimator";
+      repo = "lpeg_patterns";
+      rev = "v${version}";
+      sha256 = "1s3c179a64r45ffkawv9dnxw4mzwkzj00nr9z2gs5haajgpjivw6";
+    };
+
+    buildPhase = ":";
+    installPhase = ''
+      mkdir -p "$out/lib/lua/${lua.luaversion}"
+      mv lpeg_patterns "$out/lib/lua/${lua.luaversion}/"
+    '';
+
+    meta = with stdenv.lib; {
+      description = "A collection of LPEG patterns";
+      homepage = "https://github.com/daurnimator/lpeg_patterns";
+      license = licenses.mit;
+      maintainers = with maintainers; [ vcunat ];
+      inherit (lpeg.meta) platforms;
+    };
+  };
+
   cjson = buildLuaPackage rec {
     name = "cjson-${version}";
     version = "2.1.0";
diff --git a/pkgs/top-level/perl-packages.nix b/pkgs/top-level/perl-packages.nix
index e389315162c0..0a2a9f386a13 100644
--- a/pkgs/top-level/perl-packages.nix
+++ b/pkgs/top-level/perl-packages.nix
@@ -16148,7 +16148,7 @@ let
       install_name_tool -change "$oldPath" "$newPath" "$out/bin/biblex"
       install_name_tool -change "$oldPath" "$newPath" "$out/bin/bibparse"
       install_name_tool -change "$oldPath" "$newPath" "$out/bin/dumpnames"
-      install_name_tool -change "$oldPath" "$newPath" "$out/lib/perl5/site_perl/5.24.4/darwin-2level/auto/Text/BibTeX/BibTeX.bundle"
+      install_name_tool -change "$oldPath" "$newPath" "$out/lib/perl5/site_perl/${perl.version}/darwin-2level/auto/Text/BibTeX/BibTeX.bundle"
     '';
     meta = {
       description = "Interface to read and parse BibTeX files";