Merge branch 'master' into staging-next

There's been some large rebuild on master.
I don't really have time ATM to find what it was.

10 files changed, 213 insertions, 69 deletions

diff --git a/pkgs/development/libraries/appstream/default.nix b/pkgs/development/libraries/appstream/default.nix
index 61ee182ce627..5e4218852e51 100644
--- a/pkgs/development/libraries/appstream/default.nix
+++ b/pkgs/development/libraries/appstream/default.nix
@@ -1,36 +1,27 @@
 { stdenv, fetchpatch, fetchFromGitHub, meson, ninja, pkgconfig, gettext
 , xmlto, docbook_xsl, docbook_xml_dtd_45, libxslt
 , libstemmer, glib, xapian, libxml2, libyaml, gobjectIntrospection
-, pcre, itstool
+, pcre, itstool, gperf, vala
 }:
 
 stdenv.mkDerivation rec {
   name = "appstream-${version}";
-  version = "0.11.8";
+  version = "0.12.2";
 
   src = fetchFromGitHub {
     owner  = "ximion";
     repo   = "appstream";
     rev    = "APPSTREAM_${stdenv.lib.replaceStrings ["."] ["_"] version}";
-    sha256 = "07vzz57g1p5byj2jfg17y5n3il0g07d9wkiynzwra71mcxar1p08";
+    sha256 = "1g15c4bhyl730rgaiqia3jppraixh05c3yx098lyilidbddxp5xb";
   };
 
-  patches = [
-    # drop this in version 0.11.9 and above
-    (fetchpatch {
-      name   = "define-location-and-soname.patch";
-      url    = "https://github.com/ximion/appstream/commit/3e58f9c9.patch";
-      sha256 = "1ffgbdfg80yq5vahjrvdd4f8xsp32ksm9vyasfmc7hzhx294s78w";
-    })
-  ];
-
   nativeBuildInputs = [
     meson ninja pkgconfig gettext
     libxslt xmlto docbook_xsl docbook_xml_dtd_45
-    gobjectIntrospection itstool
+    gobjectIntrospection itstool vala
   ];
 
-  buildInputs = [ libstemmer pcre glib xapian libxml2 libyaml ];
+  buildInputs = [ libstemmer pcre glib xapian libxml2 libyaml gperf ];
 
   prePatch = ''
     substituteInPlace meson.build \
@@ -43,7 +34,7 @@ stdenv.mkDerivation rec {
   mesonFlags = [
     "-Dapidocs=false"
     "-Ddocs=false"
-    "-Dgir=false"
+    "-Dvapi=true"
   ];
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/appstream/qt.nix b/pkgs/development/libraries/appstream/qt.nix
index beff83f2365b..c5a251cd5f9f 100644
--- a/pkgs/development/libraries/appstream/qt.nix
+++ b/pkgs/development/libraries/appstream/qt.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   name = "appstream-qt-${version}";
-  inherit (appstream) version src patches prePatch;
+  inherit (appstream) version src prePatch;
 
   buildInputs = appstream.buildInputs ++ [ appstream qtbase ];
 
diff --git a/pkgs/development/libraries/cddlib/default.nix b/pkgs/development/libraries/cddlib/default.nix
index ee56b50e1da5..058ee893c37a 100644
--- a/pkgs/development/libraries/cddlib/default.nix
+++ b/pkgs/development/libraries/cddlib/default.nix
@@ -1,55 +1,33 @@
 { stdenv
-, fetchurl
-, fetchpatch
+, fetchFromGitHub
 , gmp
 , autoreconfHook
+, texlive
 }:
 
 stdenv.mkDerivation rec {
   name = "cddlib-${version}";
-  version = "0.94i";
-  src = let
-    fileVersion = stdenv.lib.replaceStrings ["."] [""] version;
-  in fetchurl {
-    # Might switch to github in the future, see
-    # https://trac.sagemath.org/ticket/21952#comment:20
-    urls = [
-      "http://archive.ubuntu.com/ubuntu/pool/universe/c/cddlib/cddlib_${fileVersion}.orig.tar.gz"
-      "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-${fileVersion}.tar.gz"
-    ];
-    sha256 = "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq";
+  version = "0.94j";
+  src = fetchFromGitHub {
+    owner = "cddlib";
+    repo = "cddlib";
+    rev = "${version}";
+    sha256 = "1z03ljy3rrr0qq5gq54vynnif6fn0xhn05g90nnv0dpyc3ps8lzp";
   };
   buildInputs = [gmp];
   nativeBuildInputs = [
     autoreconfHook
+    texlive.combined.scheme-small # for building the documentation
   ];
-  # compute reduced H and V representation of polytope
-  # this patch is included by most distributions (Debian, Conda, ArchLinux, SageMath)
-  # proposed upstream (no answer yet): https://github.com/cddlib/cddlib/pull/3
-  both_reps_c = (fetchurl {
-    name = "cdd_both_reps.c";
-    url = "https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-libs/cddlib/files/cdd_both_reps.c?id=56bd759df1d0c750a065b8c845e93d5dfa6b549d";
-    sha256 = "0r9yc5bgiz8i72c6vsn2y2mjk5581iw94gji9v7lg16kzzgrk9x0";
-  });
-  preAutoreconf = ''
-    # Required by sage.geometry.polyhedron
-    cp ${both_reps_c} src/cdd_both_reps.c
-    cp ${both_reps_c} src-gmp/cdd_both_reps.c
-  '';
-  patches = [
-    # add the cdd_both_reps binary
-    (fetchpatch {
-      name = "add-cdd_both_reps-binary.patch";
-      url = "https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-libs/cddlib/files/cddlib-094h-add-cdd_both_reps-binary.patch?id=78e3a61a68c916450aa4e5ceecd20041583af901";
-      sha256 = "162ni2fr7dpbdkz0b5nizxq7qr5k1i1d75g0smiylpzfb0hb761a";
-    })
-  ];
-  meta = {
+  # No actual checks yet (2018-05-05), but maybe one day.
+  # Requested here: https://github.com/cddlib/cddlib/issues/25
+  doCheck = true;
+  meta = with stdenv.lib; {
     inherit version;
     description = ''An implementation of the Double Description Method for generating all vertices of a convex polyhedron'';
-    license = stdenv.lib.licenses.gpl2Plus ;
-    maintainers = [stdenv.lib.maintainers.raskin];
-    platforms = stdenv.lib.platforms.linux;
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [raskin timokau];
+    platforms = platforms.linux;
     homepage = https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html;
   };
 }
diff --git a/pkgs/development/libraries/exiv2/default.nix b/pkgs/development/libraries/exiv2/default.nix
index 7f5f19035179..f573a275aaab 100644
--- a/pkgs/development/libraries/exiv2/default.nix
+++ b/pkgs/development/libraries/exiv2/default.nix
@@ -1,11 +1,15 @@
-{ stdenv, fetchurl, fetchpatch, zlib, expat, gettext }:
+{ stdenv, fetchurl, fetchFromGitHub, fetchpatch, zlib, expat, gettext
+, autoconf }:
 
 stdenv.mkDerivation rec {
-  name = "exiv2-0.26";
+  name = "exiv2-0.26.2018.06.09";
 
-  src = fetchurl {
-    url = "http://www.exiv2.org/builds/${name}-trunk.tar.gz";
-    sha256 = "1yza317qxd8yshvqnay164imm0ks7cvij8y8j86p1gqi1153qpn7";
+    #url = "http://www.exiv2.org/builds/${name}-trunk.tar.gz";
+  src = fetchFromGitHub rec {
+    owner = "exiv2";
+    repo  = "exiv2";
+    rev = "4aa57ad";
+    sha256 = "1kblpxbi4wlb0l57xmr7g23zn9adjmfswhs6kcwmd7skwi2yivcd";
   };
 
   patches = [
@@ -16,25 +20,36 @@ stdenv.mkDerivation rec {
           + "/sha512/${sha512}/${patchname}";
       sha512 = "3f9242dbd4bfa9dcdf8c9820243b13dc14990373a800c4ebb6cf7eac5653cfef"
              + "e6f2c47a94fbee4ed24f0d8c2842729d721f6100a2b215e0f663c89bfefe9e32";
-     })
-     (fetchpatch {
-       # many CVEs - see https://github.com/Exiv2/exiv2/pull/120
-       url = "https://patch-diff.githubusercontent.com/raw/Exiv2/exiv2/pull/120.patch";
-       sha256 = "1szl22xmh12hibzaqf2zi8zl377x841m52x4jm5lziw6j8g81sj8";
-       excludes = [ "test/bugfixes-test.sh" ];
-     })
+    })
+    # Two backports from master, submitted as https://github.com/Exiv2/exiv2/pull/398
+    (fetchpatch {
+      name = "CVE-2018-12264.diff";
+      url = "https://github.com/vcunat/exiv2/commit/fd18e853.diff";
+      sha256 = "0y7ahh45lpaiazjnfllndfaa5pyixh6z4kcn2ywp7qy4ra7qpwdr";
+    })
+    (fetchpatch {
+      name = "CVE-2018-12265.diff";
+      url = "https://github.com/vcunat/exiv2/commit/9ed1671bd4.diff";
+      sha256 = "1cn446pfcgsh1bn9vxikkkcy1cqq7ghz2w291h1094ydqg6w7q6w";
+    })
   ];
 
   postPatch = "patchShebangs ./src/svn_version.sh";
 
+  preConfigure = "make config"; # needed because not using tarball
+
   outputs = [ "out" "dev" ];
 
-  nativeBuildInputs = [ gettext ];
+  nativeBuildInputs = [
+    gettext
+    autoconf # needed because not using tarball
+  ];
   propagatedBuildInputs = [ zlib expat ];
 
-  meta = {
+  meta = with stdenv.lib; {
     homepage = http://www.exiv2.org/;
     description = "A library and command-line utility to manage image metadata";
-    platforms = stdenv.lib.platforms.all;
+    platforms = platforms.all;
+    license = licenses.gpl2;
   };
 }
diff --git a/pkgs/development/libraries/libunity/default.nix b/pkgs/development/libraries/libunity/default.nix
new file mode 100644
index 000000000000..3d3764e9258b
--- /dev/null
+++ b/pkgs/development/libraries/libunity/default.nix
@@ -0,0 +1,53 @@
+{ stdenv, fetchurl, pkgconfig, automake, autoconf, libtool
+, glib, vala, dee, gobjectIntrospection, libdbusmenu-glib
+, gtk3, intltool, gnome-common, python3, icu }:
+
+stdenv.mkDerivation rec {
+  pname = "libunity";
+  version = "7.1.4";
+
+  name = "${pname}-${version}";
+
+  outputs = [ "out" "dev" ];
+
+  src = fetchurl {
+    url = "https://launchpad.net/ubuntu/+archive/primary/+files/${pname}_${version}+15.10.20151002.orig.tar.gz";
+    sha256 = "1sf98qcjkxfibxk03firnc12dm6il8jzaq5763qam8ydg4li4gij";
+  };
+
+  nativeBuildInputs = [
+    autoconf
+    automake
+    gnome-common
+    gobjectIntrospection
+    intltool
+    libtool
+    pkgconfig
+    python3
+    vala
+  ];
+
+  buildInputs = [
+    glib
+    gtk3
+  ];
+
+  propagatedBuildInputs = [ dee libdbusmenu-glib ];
+
+  preConfigure = "NOCONFIGURE=1 ./autogen.sh";
+
+  configureFlags = [
+    "--disable-static"
+    "--with-pygi-overrides-dir=$(out)/${python3.sitePackages}/gi/overrides"
+  ];
+
+  NIX_LDFLAGS = "-L${icu}/lib";
+
+  meta = with stdenv.lib; {
+    description = "A library for instrumenting and integrating with all aspects of the Unity shell";
+    homepage = https://launchpad.net/libunity;
+    license = licenses.lgpl3;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ worldofpeace ];
+  };
+}
diff --git a/pkgs/development/libraries/oracle-instantclient/default.nix b/pkgs/development/libraries/oracle-instantclient/default.nix
index 56f0cc084d14..a4196e0dc9f0 100644
--- a/pkgs/development/libraries/oracle-instantclient/default.nix
+++ b/pkgs/development/libraries/oracle-instantclient/default.nix
@@ -52,6 +52,9 @@ in stdenv.mkDerivation rec {
     install -Dm644 *.jar $out/share/java
     install -Dm644 sdk/include/* $out/include
     install -Dm644 sdk/demo/* $out/share/${name}/demo
+
+    # PECL::oci8 will not build without this
+    ln -s $out/lib/libclntsh.so.12.1 $out/lib/libclntsh.so
   '';
 
   meta = with stdenv.lib; {
diff --git a/pkgs/development/libraries/prototypejs/default.nix b/pkgs/development/libraries/prototypejs/default.nix
new file mode 100644
index 000000000000..a56b14384e5b
--- /dev/null
+++ b/pkgs/development/libraries/prototypejs/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, fetchurl, ... }:
+let
+  version = "1.7.3.0";
+in fetchurl {
+  name = "prototype-${version}.js";
+  url = "https://ajax.googleapis.com/ajax/libs/prototype/${version}/prototype.js";
+  sha256 = "0q43vvrsb22h4jvavs1gk3v4ps61yx9k85b5n6q9mxivhmxprg26";
+
+  meta = with stdenv.lib; {
+    description = "A foundation for ambitious web user interfaces";
+    longDescription = ''
+      Prototype takes the complexity out of client-side web
+      programming. Built to solve real-world problems, it adds
+      useful extensions to the browser scripting environment
+      and provides elegant APIs around the clumsy interfaces
+      of Ajax and the Document Object Model.
+    '';
+    homepage = http://prototypejs.org/;
+    downloadPage = http://prototypejs.org/download/;
+    license = licenses.mit;
+    maintainers = with maintainers; [ das_j ];
+  };
+}
diff --git a/pkgs/development/libraries/science/math/lcalc/default.nix b/pkgs/development/libraries/science/math/lcalc/default.nix
index 6bbd43b0c848..e55244b2a59f 100644
--- a/pkgs/development/libraries/science/math/lcalc/default.nix
+++ b/pkgs/development/libraries/science/math/lcalc/default.nix
@@ -57,6 +57,18 @@ stdenv.mkDerivation rec {
 
     # based on gentoos makefile patch -- fix paths, adhere to flags
     ./makefile.patch
+
+    # (fetchpatch {
+    #   name = "default-double.patch";
+    #   url = "https://github.com/dimpase/lcalc/pull/1/commits/0500c67b6aa1f492715591669f6647c8f7a3ea59.patch";
+    #   sha256 = "0dqwmxpm9wb53qbypsyfkgsvk2f8nf67sydphd4dkc2vw4yz6vla";
+    # })
+
+    (fetchpatch {
+      name = "c++11.patch";
+      url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/lcalc-c++11.patch?h=packages/lcalc&id=3607b97df5a8c231191115b0cb5c62426b339e71";
+      sha256 = "1ccrl61lv2vvx8ggldq54m5d0n1iy6mym7qz0i8nj6yj0dshnpk3";
+    })
   ];
 
   installFlags = [
diff --git a/pkgs/development/libraries/science/math/libbraiding/default.nix b/pkgs/development/libraries/science/math/libbraiding/default.nix
new file mode 100644
index 000000000000..be650f3c3ce8
--- /dev/null
+++ b/pkgs/development/libraries/science/math/libbraiding/default.nix
@@ -0,0 +1,34 @@
+{ stdenv
+, fetchFromGitHub
+, autoreconfHook
+}:
+
+stdenv.mkDerivation rec {
+  version = "1.0";
+  name = "libbraiding-${version}";
+
+  src = fetchFromGitHub {
+    owner = "miguelmarco";
+    repo = "libbraiding";
+    rev = version;
+    sha256 = "0l68rikfr7k2l547gb3pp3g8cj5zzxwipm79xrb5r8ffj466ydxg";
+  };
+
+  nativeBuildInputs = [
+    autoreconfHook
+  ];
+
+  # no tests included for now (2018-08-05), but can't hurt to activate
+  doCheck = true;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/miguelmarco/libbraiding/;
+    description = "C++ library for computations on braid groups";
+    longDescription = ''
+      A library to compute several properties of braids, including centralizer and conjugacy check.
+    '';
+    license = licenses.gpl3;
+    maintainers = with maintainers; [ timokau ];
+    platforms = platforms.all;
+  };
+}
diff --git a/pkgs/development/libraries/science/math/libhomfly/default.nix b/pkgs/development/libraries/science/math/libhomfly/default.nix
new file mode 100644
index 000000000000..e96ee475d7d2
--- /dev/null
+++ b/pkgs/development/libraries/science/math/libhomfly/default.nix
@@ -0,0 +1,35 @@
+{ stdenv
+, fetchFromGitHub
+, autoreconfHook
+, boehmgc
+}:
+
+stdenv.mkDerivation rec {
+  version = "1.02r5";
+  name = "llibhomfly-${version}";
+
+  src = fetchFromGitHub {
+    owner = "miguelmarco";
+    repo = "libhomfly";
+    rev = version;
+    sha256 = "1szv8iwlhvmy3saigi15xz8vgch92p2lbsm6440v5s8vxj455bvd";
+  };
+
+  buildInputs = [
+    boehmgc
+  ];
+
+  nativeBuildInputs = [
+    autoreconfHook
+  ];
+
+  doCheck = true;
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/miguelmarco/libhomfly/;
+    description = "Library to compute the homfly polynomial of knots and links";
+    license = licenses.unlicense;
+    maintainers = with maintainers; [ timokau ];
+    platforms = platforms.all;
+  };
+}