Merge branch 'master' into staging

pkgs/development/compilers/colm/default.nix

@@ -2,17 +2,16 @@
 
 stdenv.mkDerivation rec {
   name = "colm-${version}";
-  version = "0.12.0";
+  version = "0.13.0.3";
 
   src = fetchurl {
     url = "http://www.colm.net/files/colm/${name}.tar.gz";
-    sha256 = "0kbfipxv3nvggd1a2nahk3jg22iifp2l7lkm55i5r7qkpms5sm3v";
+    sha256 = "0dadfsnkbxcrf5kihvncbprb6w64jz2myylfmj952gdmcsim4zj2";
   };
 
   buildInputs = [ makeWrapper ];
 
   doCheck = true;
-  checkPhase = ''sh ./test/runtests.sh'';
 
   postInstall = ''
     wrapProgram $out/bin/colm \

pkgs/development/compilers/ghc/8.0.1.nix

@@ -3,12 +3,12 @@
 }:
 
 stdenv.mkDerivation rec {
-  version = "8.0.0.20160111";
+  version = "8.0.0.20160204";
   name = "ghc-${version}";
 
   src = fetchurl {
-    url = "https://downloads.haskell.org/~ghc/8.0.1-rc1/${name}-src.tar.xz";
-    sha256 = "0y4nha46mw01ysw90kh8szcbsfdc37rqjm7r5fyk6flqwr8b6pvr";
+    url = "https://downloads.haskell.org/~ghc/8.0.1-rc2/${name}-src.tar.xz";
+    sha256 = "0v8pciva93i4a6h0l76vq6bbvrg76b1y4awwbxcg3m9gnqkvmy2k";
   };
 
   patches = [

pkgs/development/compilers/icedtea-web/default.nix

@@ -3,11 +3,11 @@
 stdenv.mkDerivation rec {
   name = "icedtea-web-${version}";
 
-  version = "1.6.1";
+  version = "1.6.2";
 
   src = fetchurl {
     url = "http://icedtea.wildebeest.org/download/source/${name}.tar.gz";
-    sha256 = "0869j9jn0z5b5pfspp4v5cj2ksmbqmmmjhqicn4kqc6wr6v6md59";
+    sha256 = "004kwrngyxxlrlzby4vzxjr0xcyngcdc9dfgnvi61ffnjr006ryf";
   };
 
   nativeBuildInputs = [ pkgconfig bc perl ];

pkgs/development/compilers/julia/0001.1-use-system-utf8proc.patch

@@ -0,0 +1,29 @@
+From 54a66b5728ec98f44a1768f064509be4fd3f2ef6 Mon Sep 17 00:00:00 2001
+From: Thomas Tuegel <ttuegel@gmail.com>
+Date: Sat, 10 Oct 2015 13:09:48 -0500
+Subject: [PATCH 1/3] use system utf8proc
+
+---
+ src/flisp/Makefile | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/src/flisp/Makefile b/src/flisp/Makefile
+index bec8624..5437b5c 100644
+--- a/src/flisp/Makefile
++++ b/src/flisp/Makefile
+@@ -24,9 +24,9 @@ DOBJS = $(SRCS:%.c=$(BUILDDIR)/%.dbg.obj)
+ LLTDIR := ../support
+ LLT_release := $(BUILDDIR)/$(LLTDIR)/libsupport.a
+ LLT_debug := $(BUILDDIR)/$(LLTDIR)/libsupport-debug.a
+-LIBFILES_release := $(LLT_release) $(LIBUV) $(LIBUTF8PROC)
+-LIBFILES_debug := $(LLT_debug) $(LIBUV) $(LIBUTF8PROC)
+-LIBS :=
++LIBFILES_release := $(LLT_release) $(LIBUV)
++LIBFILES_debug := $(LLT_debug) $(LIBUV)
++LIBS := $(LIBUTF8PROC)
+ ifneq ($(OS),WINNT)
+ LIBS += -lpthread
+ endif
+-- 
+2.5.2
+

pkgs/development/compilers/julia/git.nix

@@ -0,0 +1,170 @@
+{ stdenv, fetchgit, fetchurl
+# build tools
+, gfortran, m4, makeWrapper, patchelf, perl, which, python2
+# libjulia dependencies
+, libunwind, llvm, readline, utf8proc, zlib
+# standard library dependencies
+, curl, fftwSinglePrec, fftw, gmp, libgit2, mpfr, openlibm, openspecfun, pcre2
+# linear algebra
+, openblas, arpack, suitesparse
+}:
+
+with stdenv.lib;
+
+# All dependencies must use the same OpenBLAS.
+let
+  arpack_ = arpack;
+  suitesparse_ = suitesparse;
+in
+let
+  arpack = arpack_.override { inherit openblas; };
+  suitesparse = suitesparse_.override { inherit openblas; };
+in
+
+let
+  dsfmtVersion = "2.2.3";
+  dsfmt = fetchurl {
+    url = "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-${dsfmtVersion}.tar.gz";
+    sha256 = "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42";
+  };
+
+  libuvVersion = "07730c4bd595b4d45a498a8ee0bcd53878ff7c10";
+  libuv = fetchurl {
+    url = "https://api.github.com/repos/JuliaLang/libuv/tarball/${libuvVersion}";
+    sha256 = "19nk8vdvx2mxyrwpndb7888c3b237ja5xvxr3jk5ah77ix3srr3h";
+  };
+
+  rmathVersion = "0.1";
+  rmath-julia = fetchurl {
+    url = "https://api.github.com/repos/JuliaLang/Rmath-julia/tarball/v${rmathVersion}";
+    sha256 = "0ai5dhjc43zcvangz123ryxmlbm51s21rg13bllwyn98w67arhb4";
+  };
+  
+  virtualenvVersion = "1.11.6";
+  virtualenv = fetchurl {
+    url = "https://pypi.python.org/packages/source/v/virtualenv/virtualenv-${virtualenvVersion}.tar.gz";
+    sha256 = "1xq4prmg25n9cz5zcvbqx68lmc3kl39by582vd8pzs9f3qalqyiy";
+  };
+in
+
+stdenv.mkDerivation rec {
+  pname = "julia";
+  version = "0.4.4-pre-2016-02-08";
+  name = "${pname}-${version}";
+
+  src = fetchgit {
+    url = "https://github.com/JuliaLang/${pname}";
+    rev = "cb93e6b70b4b1313b4de8c54e55e85c8eb43daa3";
+    sha256 = "11dmbjqiidlbh8sj5s09zsbfslm3zs0kw7iq40281hl5dfsr7zm6";
+  };
+
+  prePatch = ''
+    mkdir deps/srccache
+    cp "${dsfmt}" "./deps/srccache/dsfmt-${dsfmtVersion}.tar.gz"
+    cp "${rmath-julia}" "./deps/srccache/Rmath-julia-${rmathVersion}.tar.gz"
+    cp "${libuv}" "./deps/srccache/libuv-${libuvVersion}.tar.gz"
+    cp "${virtualenv}" "./deps/srccache/virtualenv-${virtualenvVersion}.tar.gz"
+  '';
+
+  patches = [
+    ./0001.1-use-system-utf8proc.patch
+    ./0002-use-system-suitesparse.patch
+  ];
+
+  postPatch = ''
+    patchShebangs . contrib
+  '';
+
+  buildInputs = [
+    arpack fftw fftwSinglePrec gmp libgit2 libunwind llvm mpfr
+    pcre2 openblas openlibm openspecfun readline suitesparse utf8proc
+    zlib
+  ];
+
+  nativeBuildInputs = [ curl gfortran m4 makeWrapper patchelf perl python2 which ];
+
+  makeFlags =
+    let
+      arch = head (splitString "-" stdenv.system);
+      march = { "x86_64" = "x86-64"; "i686" = "i686"; }."${arch}"
+              or (throw "unsupported architecture: ${arch}");
+      # Julia requires Pentium 4 (SSE2) or better
+      cpuTarget = { "x86_64" = "x86-64"; "i686" = "pentium4"; }."${arch}"
+                  or (throw "unsupported architecture: ${arch}");
+    in [
+      "ARCH=${arch}"
+      "MARCH=${march}"
+      "JULIA_CPU_TARGET=${cpuTarget}"
+      "PREFIX=$(out)"
+      "prefix=$(out)"
+      "SHELL=${stdenv.shell}"
+
+      "USE_SYSTEM_BLAS=1"
+      "USE_BLAS64=${if openblas.blas64 then "1" else "0"}"
+      "LIBBLAS=-lopenblas"
+      "LIBBLASNAME=libopenblas"
+
+      "USE_SYSTEM_LAPACK=1"
+      "LIBLAPACK=-lopenblas"
+      "LIBLAPACKNAME=libopenblas"
+
+      "USE_SYSTEM_SUITESPARSE=1"
+      "SUITESPARSE_LIB=-lsuitesparse"
+      "SUITESPARSE_INC=-I${suitesparse}/include"
+
+      "USE_SYSTEM_ARPACK=1"
+      "USE_SYSTEM_FFTW=1"
+      "USE_SYSTEM_GMP=1"
+      "USE_SYSTEM_LIBGIT2=1"
+      "USE_SYSTEM_LIBUNWIND=1"
+      "USE_SYSTEM_LLVM=1"
+      "USE_SYSTEM_MPFR=1"
+      "USE_SYSTEM_OPENLIBM=1"
+      "USE_SYSTEM_OPENSPECFUN=1"
+      "USE_SYSTEM_PATCHELF=1"
+      "USE_SYSTEM_PCRE=1"
+      "USE_SYSTEM_READLINE=1"
+      "USE_SYSTEM_UTF8PROC=1"
+      "USE_SYSTEM_ZLIB=1"
+    ];
+
+  NIX_CFLAGS_COMPILE = [ "-fPIC" ];
+
+  LD_LIBRARY_PATH = makeSearchPath "lib" [
+    arpack fftw fftwSinglePrec gmp libgit2 mpfr openblas openlibm
+    openspecfun pcre2 suitesparse
+  ];
+
+  dontStrip = true;
+  dontPatchELF = true;
+
+  enableParallelBuilding = true;
+
+  doCheck = true;
+  checkTarget = "testall";
+  # Julia's tests require read/write access to $HOME
+  preCheck = ''
+    export HOME="$NIX_BUILD_TOP"
+  '';
+
+  preBuild = ''
+    sed -e '/^install:/s@[^ ]*/doc/[^ ]*@@' -i Makefile
+    sed -e '/[$](DESTDIR)[$](docdir)/d' -i Makefile
+  '';
+
+  postInstall = ''
+    for prog in "$out/bin/julia" "$out/bin/julia-debug"; do
+        wrapProgram "$prog" \
+            --prefix LD_LIBRARY_PATH : "$LD_LIBRARY_PATH" \
+            --prefix PATH : "${curl}/bin"
+    done
+  '';
+
+  meta = {
+    description = "High-level performance-oriented dynamical language for technical computing";
+    homepage = "http://julialang.org/";
+    license = stdenv.lib.licenses.mit;
+    maintainers = with stdenv.lib.maintainers; [ raskin ttuegel ];
+    platforms = [ "i686-linux" "x86_64-linux" "x86_64-darwin" ];
+  };
+}

pkgs/development/compilers/kotlin/default.nix

@@ -1,16 +1,16 @@
-{ stdenv, fetchurl, makeWrapper, jre, unzip }:
+{ stdenv, fetchurl, makeWrapper, jre, unzip, which }:
 
 stdenv.mkDerivation rec {
-  version = "1.0.0-rc-1036";
+  version = "1.0.0";
   name = "kotlin-${version}";
 
   src = fetchurl {
     url = "https://github.com/JetBrains/kotlin/releases/download/build-${version}/kotlin-compiler-${version}.zip";
-    sha256 = "8d72ff925678a2172fbbefcb6f0c5a195a300dccf240e5add16c3e8d86e13d67";
+    sha256 = "0dp5mab35sv3nsgj488ibyn6x6xw2rka76s7kygbhqhjc429kpgy";
   };
 
   propagatedBuildInputs = [ jre ] ;
-  buildInputs = [ makeWrapper unzip ] ;
+  buildInputs = [ makeWrapper unzip which ] ;
 
   installPhase = ''
     mkdir -p $out

pkgs/development/compilers/oraclejdk/jdk8-linux.nix

@@ -1,9 +1,9 @@
 import ./jdk-linux-base.nix {
   productVersion = "8";
-  patchVersion = "71";
+  patchVersion = "73";
   downloadUrl = http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html;
-  sha256_i686 = "11wcizv4gvlffzn2wj34ffwrq21xwh4ikg2vjv63avdfp2hazjqv";
-  sha256_x86_64 = "18jqdrlbv4sdds2hlmp437waq7r9b33f7hdp8kb6l7pkrizr9nwv";
+  sha256_i686 = "1bi3yj2ds9w13p2lzvmxffk5gax8syi3bw52w8pam1jr3fmzgwgl";
+  sha256_x86_64 = "1rp3nbnhkncyr48m0nn3pf5fr4bp3lzm0ki4gca7mn7rzag19a26";
   jceName = "jce_policy-8.zip";
   jceDownloadUrl = http://www.oracle.com/technetwork/java/javase/downloads/jce8-download-2133166.html;
   sha256JCE = "0n8b6b8qmwb14lllk2lk1q1ahd3za9fnjigz5xn65mpg48whl0pk";

pkgs/development/compilers/oraclejdk/jdk8psu-linux.nix

@@ -1,9 +1,9 @@
 import ./jdk-linux-base.nix {
   productVersion = "8";
-  patchVersion = "72";
+  patchVersion = "74";
   downloadUrl = http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html;
-  sha256_i686 = "023rnlm5v7d9w4d7bgcac8j0r1vqkbv6fl20k8354pzpdjg6liaq";
-  sha256_x86_64 = "167ca39a6y0n8l87kdm5nv2hrp0wf6g4mw1rbychjc04f5igkrs6";
+  sha256_i686 = "1vc3g89fbrmznb10bhh5gs143hcjg4wsy4j4hwnr1djfj83y8188";
+  sha256_x86_64 = "1pfx7il1h42w3kigscdvm9vfy616lmsp1d2cqvplim3nyxwmvz8b";
   jceName = "jce_policy-8.zip";
   jceDownloadUrl = http://www.oracle.com/technetwork/java/javase/downloads/jce8-download-2133166.html;
   sha256JCE = "0n8b6b8qmwb14lllk2lk1q1ahd3za9fnjigz5xn65mpg48whl0pk";