Merge branch 'master' into staging-next

7 files changed, 24 insertions, 16 deletions

diff --git a/pkgs/applications/science/chemistry/avogadro/default.nix b/pkgs/applications/science/chemistry/avogadro/default.nix
index 78cda9d115c..a569b82ff59 100644
--- a/pkgs/applications/science/chemistry/avogadro/default.nix
+++ b/pkgs/applications/science/chemistry/avogadro/default.nix
@@ -14,6 +14,13 @@ stdenv.mkDerivation rec {
 
   NIX_CFLAGS_COMPILE = "-include ${libGLU_combined}/include/GL/glu.h";
 
+  patches = [
+    (fetchurl {
+      url = https://data.gpo.zugaina.org/fusion809/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch;
+      sha256 = "1p113v19z3zwr9gxj2k599f8p97a8rwm93pa4amqvd0snn31mw0k";
+    })
+  ];
+
   meta = {
     description = "Molecule editor and visualizer";
     maintainers = [ ];
diff --git a/pkgs/applications/science/logic/abella/default.nix b/pkgs/applications/science/logic/abella/default.nix
index 7d71a56fa23..bc23454edfc 100644
--- a/pkgs/applications/science/logic/abella/default.nix
+++ b/pkgs/applications/science/logic/abella/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "abella-${version}";
-  version = "2.0.5";
+  version = "2.0.6";
 
   src = fetchurl {
     url = "http://abella-prover.org/distributions/${name}.tar.gz";
-    sha256 = "0bry4pj6p9y7sg79ygdksynml4rdsjhqi959vnnwwsbaysa3bci0";
+    sha256 = "164q9gngckg6q69k13lwx2pq3cnc9ckw1qi8dnpxqfjgwfqr7xyi";
   };
 
   buildInputs = [ rsync ] ++ (with ocamlPackages; [ ocaml ocamlbuild findlib ]);
diff --git a/pkgs/applications/science/logic/symbiyosys/default.nix b/pkgs/applications/science/logic/symbiyosys/default.nix
index e21c274370c..2047bb3fc9f 100644
--- a/pkgs/applications/science/logic/symbiyosys/default.nix
+++ b/pkgs/applications/science/logic/symbiyosys/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "symbiyosys-${version}";
-  version = "2018.09.12";
+  version = "2018.12.09";
 
   src = fetchFromGitHub {
     owner  = "yosyshq";
     repo   = "symbiyosys";
-    rev    = "e90bcb588e97118af0cdba23fae562fb0efbf294";
-    sha256 = "16nlimpdc3g6lghwqpyirgrr1d9mgk4wg3c06fvglzaicvjixnfr";
+    rev    = "0772456a15b5a474c3c90a06b48e46a67d8a6614";
+    sha256 = "00p2l1g9z8nnmkc57l1cfn9ignjjmxwnyaxj2xjd1fim4kzd5475";
   };
 
   buildInputs = [ python3 yosys ];
diff --git a/pkgs/applications/science/logic/yices/default.nix b/pkgs/applications/science/logic/yices/default.nix
index 0ab08db6746..40a4c391e1d 100644
--- a/pkgs/applications/science/logic/yices/default.nix
+++ b/pkgs/applications/science/logic/yices/default.nix
@@ -1,13 +1,14 @@
-{ stdenv, fetchurl, gmp-static, gperf, autoreconfHook, libpoly }:
+{ stdenv, fetchFromGitHub, gmp-static, gperf, autoreconfHook, libpoly }:
 
 stdenv.mkDerivation rec {
   name    = "yices-${version}";
   version = "2.6.1";
 
-  src = fetchurl {
-    url = "https://github.com/SRI-CSL/yices2/archive/Yices-${version}.tar.gz";
-    name = "${name}-src.tar.gz";
-    sha256 = "14xvflv14qn8ssm8rklvckp6l1q94vn49qz2snz73j40nwzshaww";
+  src = fetchFromGitHub {
+    owner  = "SRI-CSL";
+    repo   = "yices2";
+    rev    = "Yices-${version}";
+    sha256 = "04vf468spsh00jh7gj94cjnq8kjyfwy9l6r4z7l2pm0zgwkqgyhm";
   };
 
   nativeBuildInputs = [ autoreconfHook ];
@@ -38,6 +39,6 @@ stdenv.mkDerivation rec {
     homepage    = "http://yices.csl.sri.com";
     license     = licenses.gpl3;
     platforms   = with platforms; linux ++ darwin;
-    maintainers = [ maintainers.thoughtpolice ];
+    maintainers = with maintainers; [ thoughtpolice ];
   };
 }
diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix
index 28a7e783ff3..a4a55e3e851 100644
--- a/pkgs/applications/science/logic/z3/default.nix
+++ b/pkgs/applications/science/logic/z3/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "z3-${version}";
-  version = "4.8.3";
+  version = "4.8.4";
 
   src = fetchFromGitHub {
     owner  = "Z3Prover";
     repo   = "z3";
     rev    = name;
-    sha256 = "0p5gdmhd32x6zwmx7j5cgwh4jyfxa9yapym95nlmyfaqzak92qar";
+    sha256 = "014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn";
   };
 
   buildInputs = [ python fixDarwinDylibNames ];
diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix
index 9bbb695a331..032b2ef0964 100644
--- a/pkgs/applications/science/math/pynac/default.nix
+++ b/pkgs/applications/science/math/pynac/default.nix
@@ -9,14 +9,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "0.7.22";
+  version = "0.7.23";
   name = "pynac-${version}";
 
   src = fetchFromGitHub {
     owner = "pynac";
     repo = "pynac";
     rev = "pynac-${version}";
-    sha256 = "1ribm5vpbgsja4hbca1ckw4ln9kjkv608aaqsvxxvbs4z76ys6yi";
+    sha256 = "02yhl8v9l6aj3wl6dk9iacz4hdv08i1d750rxpygjp43nlgvvb2h";
   };
 
   buildInputs = [
diff --git a/pkgs/applications/science/misc/golly/beta.nix b/pkgs/applications/science/misc/golly/beta.nix
index 6f11caf4d9a..99159fba5b4 100644
--- a/pkgs/applications/science/misc/golly/beta.nix
+++ b/pkgs/applications/science/misc/golly/beta.nix
@@ -30,7 +30,7 @@ stdenv.mkDerivation rec {
   makeFlags=[
     "AM_LDFLAGS="
   ];
-  NIX_LDFLAGS="-l${python2.libPrefix} -lperl";
+  NIX_LDFLAGS="-l${python2.libPrefix} -lperl -ldl -lGL";
   preConfigure=''
     export NIX_LDFLAGS="$NIX_LDFLAGS -L$(dirname "$(find ${perl} -name libperl.so)")"
     export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE