Merge master into stdenv-updates

Conflicts:
	pkgs/applications/version-management/gource/default.nix
	pkgs/top-level/all-packages.nix

3 files changed, 107 insertions, 51 deletions

diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index d831463406c5..897fae64af57 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -1192,6 +1192,7 @@ let
   ised = callPackage ../tools/misc/ised {};
 
   isl = callPackage ../development/libraries/isl { };
+  isl_0_12 = callPackage ../development/libraries/isl/0.12.2.nix { };
 
   isync = callPackage ../tools/networking/isync { };
 
@@ -1277,7 +1278,7 @@ let
 
   logrotate = callPackage ../tools/system/logrotate { };
 
-  logstalgica = callPackage ../tools/graphics/logstalgica {};
+  logstalgia = callPackage ../tools/graphics/logstalgia {};
 
   lout = callPackage ../tools/typesetting/lout { };
 
@@ -1832,6 +1833,8 @@ let
 
   silc_server = callPackage ../servers/silc-server { };
 
+  silver-searcher = callPackage ../tools/text/silver-searcher { };
+
   sleuthkit = callPackage ../tools/system/sleuthkit {};
 
   slimrat = callPackage ../tools/networking/slimrat {
@@ -2295,19 +2298,11 @@ let
 
   ccl = builderDefsPackage ../development/compilers/ccl {};
 
-  clangUnwrapped = callPackage ../development/compilers/llvm/clang.nix {
-    stdenv = if stdenv.isDarwin
-      then stdenvAdapters.overrideGCC stdenv gccApple
-      else stdenv;
-  };
+  clang = wrapClang llvmFull;
 
-  clang = wrapClang clangUnwrapped;
+  llvmFullSelf = clangWrapSelf (llvmFull.override {
 
-  libcxxLLVM = callPackage ../development/compilers/llvm { stdenv = libcxxStdenv; version="3.3"; };
-
-  clangSelf = clangWrapSelf (callPackage ../development/compilers/llvm/clang.nix {
      stdenv = libcxxStdenv;
-     llvm = libcxxLLVM;
   });
 
   clangWrapSelf = build: (import ../build-support/clang-wrapper) {
@@ -2323,8 +2318,7 @@ let
 
   #Use this instead of stdenv to build with clang
   clangStdenv = lowPrio (stdenvAdapters.overrideGCC stdenv clang);
-
-  libcxxStdenv = stdenvAdapters.overrideGCC stdenv (clangWrapSelf clangUnwrapped);
+  libcxxStdenv = stdenvAdapters.overrideGCC stdenv (clangWrapSelf llvmFull);
 
   clean = callPackage ../development/compilers/clean { };
 
@@ -2713,11 +2707,14 @@ let
     else
       let
         openjdkBootstrap = callPackage ../development/compilers/openjdk/bootstrap.nix { };
-      in callPackage ../development/compilers/openjdk {
+      in (callPackage ../development/compilers/openjdk {
         jdk = openjdkBootstrap;
-      };
+      }) // { outputs = [ "out" ]; };
 
-  openjre = pkgs.openjdk.jre;
+  # FIXME: Need a way to set per-output meta attributes.
+  openjre = (lib.setName "openjre-${lib.getVersion pkgs.openjdk.jre}" (lib.addMetaAttrs
+    { description = "The open-source Java Runtime Environment"; }
+    pkgs.openjdk.jre)) // { outputs = [ "jre" ]; };
 
   jdk = if stdenv.isDarwin || stdenv.system == "i686-linux" || stdenv.system == "x86_64-linux"
     then pkgs.openjdk
@@ -2764,7 +2761,7 @@ let
 
   lessc = callPackage ../development/compilers/lessc { };
 
-  llvm = llvm_33; # deprecated, depend on llvm_* directly
+  llvm = llvm_33;
   llvm_34 = callPackage ../development/compilers/llvm {
     version = "3.4";
     stdenv = if stdenv.isDarwin
@@ -2772,6 +2769,9 @@ let
       else stdenv;
   };
   llvm_33 = llvm_34.override { version = "3.3"; };
+  llvmFull = callPackage ../development/compilers/llvm/full.nix {
+    isl = isl_0_12;
+  };
 
   mentorToolchains = recurseIntoAttrs (
     callPackage_i686 ../development/compilers/mentor {}
@@ -2951,8 +2951,7 @@ let
 
   roadsend = callPackage ../development/compilers/roadsend { };
 
-  # TODO: the corresponding nix file is missing
-  # rust = pkgsi686Linux.callPackage ../development/compilers/rust {};
+  rust = callPackage ../development/compilers/rust {};
 
   sbcl = builderDefsPackage (import ../development/compilers/sbcl) {
     inherit makeWrapper;
@@ -3016,9 +3015,9 @@ let
   };
 
   wrapClangWith = clangWrapper: glibc: baseClang: clangWrapper {
-    nativeTools = stdenv ? gcc && stdenv.gcc.nativeTools;
-    nativeLibc = stdenv ? gcc && stdenv.gcc.nativeLibc;
-    nativePrefix = if stdenv ? gcc then stdenv.gcc.nativePrefix else "";
+    nativeTools = stdenv.gcc.nativeTools or false;
+    nativeLibc = stdenv.gcc.nativeLibc or false;
+    nativePrefix = stdenv.gcc.nativePrefix or "";
     clang = baseClang;
     libc = glibc;
     shell = bash;
@@ -3252,6 +3251,7 @@ let
   spidermonkey = callPackage ../development/interpreters/spidermonkey { };
   spidermonkey_1_8_0rc1 = callPackage ../development/interpreters/spidermonkey/1.8.0-rc1.nix { };
   spidermonkey_185 = callPackage ../development/interpreters/spidermonkey/185-1.0.0.nix { };
+  spidermonkey_17 = callPackage ../development/interpreters/spidermonkey/17.0.nix { };
 
   supercollider = callPackage ../development/interpreters/supercollider {
     qt = qt4;
@@ -3461,6 +3461,7 @@ let
   csslint = callPackage ../development/web/csslint { };
 
   libcxx = callPackage ../development/libraries/libc++ { stdenv = pkgs.clangStdenv; };
+  libcxxabi = callPackage ../development/libraries/libc++abi { stdenv = pkgs.clangStdenv; };
 
   dejagnu = callPackage ../development/tools/misc/dejagnu { };
 
@@ -3960,7 +3961,7 @@ let
 
   dssi = callPackage ../development/libraries/dssi {};
 
-  dragonegg = callPackage ../development/compilers/llvm/dragonegg.nix { };
+  dragonegg = callPackage ../development/compilers/llvm/dragonegg.nix { llvm = llvmFull; };
 
   dxflib = callPackage ../development/libraries/dxflib {};
 
@@ -4194,6 +4195,8 @@ let
       '' # */
       ;
 
+  glm = callPackage ../development/libraries/glm { };
+
   glpk = callPackage ../development/libraries/glpk { };
 
   glsurf = callPackage ../applications/science/math/glsurf {
@@ -5045,6 +5048,8 @@ let
     ccrtp = ccrtp_1_8;
   };
 
+  libwacom = callPackage ../development/libraries/libwacom { };
+
   lightning = callPackage ../development/libraries/lightning { };
 
   lirc = callPackage ../development/libraries/lirc { };
@@ -6224,6 +6229,8 @@ let
 
   postgresql92 = callPackage ../servers/sql/postgresql/9.2.x.nix { };
 
+  postgresql93 = callPackage ../servers/sql/postgresql/9.3.x.nix { };
+
   postgresql_jdbc = callPackage ../servers/sql/postgresql/jdbc { };
 
   psqlodbc = callPackage ../servers/sql/postgresql/psqlodbc { };
@@ -6429,6 +6436,8 @@ let
     python = pythonFull;
   };
 
+  libossp_uuid = callPackage ../development/libraries/libossp-uuid { };
+
   libuuid =
     if crossSystem != null && crossSystem.config == "i586-pc-gnu"
     then (utillinux // {
@@ -6663,6 +6672,18 @@ let
       ];
   };
 
+  linux_3_13 = makeOverridable (import ../os-specific/linux/kernel/linux-3.13.nix) {
+    inherit fetchurl stdenv perl linuxManualConfig;
+    kernelPatches =
+      [
+        kernelPatches.sec_perm_2_6_24
+      ] ++ lib.optionals ((platform.kernelArch or null) == "mips")
+      [ kernelPatches.mips_fpureg_emu
+        kernelPatches.mips_fpu_sigill
+        kernelPatches.mips_ext3_n32
+      ];
+  };
+
 
   /* Linux kernel modules are inherently tied to a specific kernel.  So
      rather than provide specific instances of those packages for a
@@ -6752,8 +6773,9 @@ let
   linuxPackages_3_11 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_3_11 linuxPackages_3_11);
   linuxPackages_3_12 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_3_12 linuxPackages_3_12);
   linuxPackages_3_12_grsecurity = linuxPackagesFor pkgs.linux_3_12_grsecurity linuxPackages_3_12_grsecurity;
+  linuxPackages_3_13 = recurseIntoAttrs (linuxPackagesFor pkgs.linux_3_13 linuxPackages_3_13);
   # Update this when adding a new version!
-  linuxPackages_latest = pkgs.linuxPackages_3_12;
+  linuxPackages_latest = pkgs.linuxPackages_3_13;
 
   # The current default kernel / kernel modules.
   linux = linuxPackages.kernel;
@@ -9653,25 +9675,6 @@ let
 
   ### SCIENCE
 
-  celestia = callPackage ../applications/science/astronomy/celestia {
-    lua = lua5_1;
-    inherit (xlibs) libXmu;
-    inherit (pkgs.gnome) gtkglext;
-  };
-
-  xplanet = callPackage ../applications/science/astronomy/xplanet { };
-
-  gravit = callPackage ../applications/science/astronomy/gravit { };
-
-  spyder = callPackage ../applications/science/spyder {
-    inherit (pythonPackages) pyflakes rope sphinx numpy scipy matplotlib; # recommended
-    inherit (pythonPackages) ipython pep8; # optional
-    inherit pylint;
-  };
-
-  stellarium = callPackage ../applications/science/astronomy/stellarium { };
-
-
   ### SCIENCE/GEOMETRY
 
   drgeo = builderDefsPackage (import ../applications/science/geometry/drgeo) {
@@ -9860,6 +9863,8 @@ let
 
   eukleides = callPackage ../applications/science/math/eukleides { };
 
+  fricas = callPackage ../applications/science/math/fricas { };
+
   gap = callPackage ../applications/science/math/gap { };
 
   maxima = callPackage ../applications/science/math/maxima { };
@@ -9905,14 +9910,33 @@ let
 
   boinc = callPackage ../applications/science/misc/boinc { };
 
+  celestia = callPackage ../applications/science/astronomy/celestia {
+    lua = lua5_1;
+    inherit (xlibs) libXmu;
+    inherit (pkgs.gnome) gtkglext;
+  };
+
+  gravit = callPackage ../applications/science/astronomy/gravit { };
+
   golly = callPackage ../applications/science/misc/golly { };
 
+  root = callPackage ../applications/science/misc/root { };
+
   simgrid = callPackage ../applications/science/misc/simgrid { };
 
+  spyder = callPackage ../applications/science/spyder {
+    inherit (pythonPackages) pyflakes rope sphinx numpy scipy matplotlib; # recommended
+    inherit (pythonPackages) ipython pep8; # optional
+    inherit pylint;
+  };
+
+  stellarium = callPackage ../applications/science/astronomy/stellarium { };
+
   tulip = callPackage ../applications/science/misc/tulip { };
 
   vite = callPackage ../applications/science/misc/vite { };
 
+  xplanet = callPackage ../applications/science/astronomy/xplanet { };
 
   ### MISC
 
diff --git a/pkgs/top-level/haskell-packages.nix b/pkgs/top-level/haskell-packages.nix
index c3addca97d1e..798103153ece 100644
--- a/pkgs/top-level/haskell-packages.nix
+++ b/pkgs/top-level/haskell-packages.nix
@@ -143,7 +143,7 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
     inherit (self) cabal ghc;
     async        = self.async_2_0_1_5;
     attoparsec   = self.attoparsec_0_11_1_0;
-    caseInsensitive = self.caseInsensitive_1_1_0_2;
+    caseInsensitive = self.caseInsensitive_1_1_0_3;
     cgi          = self.cgi_3001_1_8_4;
     fgl          = self.fgl_5_4_2_4;
     GLUT         = self.GLUT_2_5_0_2;
@@ -176,7 +176,7 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
     cabalInstall = self.cabalInstall_1_18_0_2;
     alex         = self.alex_3_1_3;
     haddock      = self.haddock_2_13_2_1;
-    happy        = self.happy_1_19_2;
+    happy        = self.happy_1_19_3;
     primitive    = self.primitive_0_5_1_0;      # semi-official, but specified
   };
 
@@ -522,7 +522,9 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
 
   abstractPar = callPackage ../development/libraries/haskell/abstract-par {};
 
-  aeson = callPackage ../development/libraries/haskell/aeson {};
+  aeson_0_6_2_1 = callPackage ../development/libraries/haskell/aeson/0.6.2.1.nix {};
+  aeson_0_7_0_0 = callPackage ../development/libraries/haskell/aeson/0.7.0.0.nix {};
+  aeson = self.aeson_0_6_2_1;
 
   aesonLens = callPackage ../development/libraries/haskell/aeson-lens {};
 
@@ -699,8 +701,8 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
   cassava = callPackage ../development/libraries/haskell/cassava {};
 
   caseInsensitive_1_0_0_1 = callPackage ../development/libraries/haskell/case-insensitive/1.0.0.1.nix {};
-  caseInsensitive_1_1_0_2 = callPackage ../development/libraries/haskell/case-insensitive/1.1.0.2.nix {};
-  caseInsensitive = self.caseInsensitive_1_1_0_2;
+  caseInsensitive_1_1_0_3 = callPackage ../development/libraries/haskell/case-insensitive/1.1.0.3.nix {};
+  caseInsensitive = self.caseInsensitive_1_1_0_3;
 
   cautiousFile = callPackage ../development/libraries/haskell/cautious-file {};
 
@@ -800,6 +802,8 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
 
   cookie = callPackage ../development/libraries/haskell/cookie {};
 
+  coroutineObject = callPackage ../development/libraries/haskell/coroutine-object {};
+
   cprngAes = callPackage ../development/libraries/haskell/cprng-aes {};
 
   criterion = callPackage ../development/libraries/haskell/criterion {};
@@ -1005,7 +1009,7 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
 
   eventList = callPackage ../development/libraries/haskell/event-list {};
 
-  exPool = callPackage ../development/libraries/haskell/ex-pool { hashable = self.hashable_1_2_1_0; };
+  exPool = callPackage ../development/libraries/haskell/ex-pool { };
 
   exceptionMtl = callPackage ../development/libraries/haskell/exception-mtl {};
 
@@ -1325,6 +1329,18 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
 
   hoauth = callPackage ../development/libraries/haskell/hoauth {};
 
+  hoodle = callPackage ../applications/graphics/hoodle {};
+
+  hoodleBuilder = callPackage ../development/libraries/haskell/hoodle-builder {};
+
+  hoodleCore = callPackage ../development/libraries/haskell/hoodle-core {}; 
+
+  hoodleParser = callPackage ../development/libraries/haskell/hoodle-parser {}; 
+
+  hoodleRender = callPackage ../development/libraries/haskell/hoodle-render {}; 
+
+  hoodleTypes = callPackage ../development/libraries/haskell/hoodle-types {}; 
+
   hoogle = callPackage ../development/libraries/haskell/hoogle {};
 
   hopenssl = callPackage ../development/libraries/haskell/hopenssl {};
@@ -2205,6 +2221,8 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
 
   tastyQuickcheck = callPackage ../development/libraries/haskell/tasty-quickcheck {};
 
+  tastyRerun = callPackage ../development/libraries/haskell/tasty-rerun {};
+
   tastySmallcheck = callPackage ../development/libraries/haskell/tasty-smallcheck {};
 
   tastyTh = callPackage ../development/libraries/haskell/tasty-th {};
@@ -2265,12 +2283,18 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
 
   thyme = callPackage ../development/libraries/haskell/thyme {};
 
+  threepennyGui = callPackage ../development/libraries/haskell/threepenny-gui {};
+
   time_1_1_2_4 = callPackage ../development/libraries/haskell/time/1.1.2.4.nix {};
   time_1_4_1 = callPackage ../development/libraries/haskell/time/1.4.1.nix {};
   # time is in the core package set. It should only be necessary to
   # pass it explicitly in rare circumstances.
   time = null;
 
+  timezoneOlson = callPackage ../development/libraries/haskell/timezone-olson {};
+
+  timezoneSeries = callPackage ../development/libraries/haskell/timezone-series {};
+
   timeCompat = callPackage ../development/libraries/haskell/time-compat {};
 
   tls = callPackage ../development/libraries/haskell/tls {};
@@ -2286,6 +2310,8 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
 
   transformersCompat = callPackage ../development/libraries/haskell/transformers-compat {};
 
+  transformersFree = callPackage ../development/libraries/haskell/transformers-free {};
+
   traverseWithClass = callPackage ../development/libraries/haskell/traverse-with-class {};
 
   trifecta_1_1 = callPackage ../development/libraries/haskell/trifecta/1.1.nix {
@@ -2296,6 +2322,8 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
 
   tuple = callPackage ../development/libraries/haskell/tuple {};
 
+  TypeCompose = callPackage ../development/libraries/haskell/TypeCompose {};
+
   typeEq = callPackage ../development/libraries/haskell/type-eq {};
 
   typeEquality = callPackage ../development/libraries/haskell/type-equality {};
@@ -2475,6 +2503,10 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
 
   xmlTypes = callPackage ../development/libraries/haskell/xml-types {};
 
+  xournalParser = callPackage ../development/libraries/haskell/xournal-parser {};
+
+  xournalTypes = callPackage ../development/libraries/haskell/xournal-types {};
+
   xtest = callPackage ../development/libraries/haskell/xtest {};
 
   xssSanitize = callPackage ../development/libraries/haskell/xss-sanitize {};
@@ -2602,7 +2634,8 @@ let result = let callPackage = x : y : modifyPrio (newScope result.finalReturn x
   happy_1_18_10 = callPackage ../development/tools/parsing/happy/1.18.10.nix {};
   happy_1_18_11 = callPackage ../development/tools/parsing/happy/1.18.11.nix {};
   happy_1_19_2 = callPackage ../development/tools/parsing/happy/1.19.2.nix {};
-  happy = self.happy_1_19_2;
+  happy_1_19_3 = callPackage ../development/tools/parsing/happy/1.19.3.nix {};
+  happy = self.happy_1_19_3;
 
   happyMeta = callPackage ../development/tools/haskell/happy-meta {};
 
diff --git a/pkgs/top-level/release-python.nix b/pkgs/top-level/release-python.nix
index 82af1f439ff1..8eb08d259834 100644
--- a/pkgs/top-level/release-python.nix
+++ b/pkgs/top-level/release-python.nix
@@ -153,7 +153,6 @@ let
   cinepaint = { type = "job"; systems = ["x86_64-linux"]; schedulingPriority = 4; };
   ciopfs = { type = "job"; systems = ["x86_64-linux"]; schedulingPriority = 4; };
   clang = { type = "job"; systems = ["x86_64-linux"]; schedulingPriority = 4; };
-  clangUnwrapped = { type = "job"; systems = ["x86_64-linux"]; schedulingPriority = 4; };
   clanlib = { type = "job"; systems = ["x86_64-linux"]; schedulingPriority = 4; };
   classpath = { type = "job"; systems = ["x86_64-linux"]; schedulingPriority = 4; };
   clearsilver = { type = "job"; systems = ["x86_64-linux"]; schedulingPriority = 4; };