Merge branch 'julia-0.4'

pkgs/development/compilers/julia/0.2.nix

@@ -1,143 +0,0 @@
-{ stdenv, fetchgit, gfortran, perl, m4, llvm, gmp, pcre, zlib
- , readline, fftwSinglePrec, fftw, libunwind, suitesparse, glpk, fetchurl
- , ncurses, libunistring, lighttpd, patchelf, openblas
- , tcl, tk, xproto, libX11, git, mpfr
- } :
-let
-  realGcc = stdenv.cc.cc;
-in
-stdenv.mkDerivation rec {
-  pname = "julia";
-  version = "0.2.1";
-  name = "${pname}-${version}";
-
-  grisu_ver = "1.1.1";
-  dsfmt_ver = "2.2";
-  openblas_ver = "v0.2.2";
-  lapack_ver = "3.4.1";
-  arpack_ver = "3.1.3";
-  clp_ver = "1.14.5";
-  lighttpd_ver = "1.4.29";
-  patchelf_ver = "0.6";
-  pcre_ver = "8.31";
-
-  grisu_src = fetchurl {
-    url = "http://double-conversion.googlecode.com/files/double-conversion-${grisu_ver}.tar.gz";
-    sha256 = "e1cabb73fd69e74f145aea91100cde483aef8b79dc730fcda0a34466730d4d1d";
-  };
-  dsfmt_src = fetchurl {
-    url = "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-${dsfmt_ver}.tar.gz";
-    name = "dsfmt-${dsfmt_ver}.tar.gz";
-    sha256 = "bc3947a9b2253a869fcbab8ff395416cb12958be9dba10793db2cd7e37b26899";
-  };
-  openblas_src = fetchurl {
-    url = "https://github.com/xianyi/OpenBLAS/tarball/${openblas_ver}";
-    name = "openblas-${openblas_ver}.tar.gz";
-    sha256 = "19ffec70f9678f5c159feadc036ca47720681b782910fbaa95aa3867e7e86d8e";
-  };
-  arpack_src = fetchurl {
-    url = "http://forge.scilab.org/index.php/p/arpack-ng/downloads/607/get/";
-    name = "arpack-ng-${arpack_ver}.tar.gz";
-    sha256 = "039w7j3dr1xy35a3hp92zg2g92gmjq6xsv0g4awlb4cffy09nr2d";
-  };
-  lapack_src = fetchurl {
-    url = "http://www.netlib.org/lapack/lapack-${lapack_ver}.tgz";
-    name = "lapack-${lapack_ver}.tgz";
-    sha256 = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f";
-  };
-  clp_src = fetchurl {
-    url = "http://www.coin-or.org/download/source/Clp/Clp-${clp_ver}.tgz";
-    name = "clp-${clp_ver}.tar.gz";
-    sha256 = "e6cabe8b4319c17a9bbe6fe172194ab6cd1fe6e376f5e9969d3040636ea3a817";
-  };
-  lighttpd_src = fetchurl {
-    url = "http://download.lighttpd.net/lighttpd/releases-1.4.x/lighttpd-${lighttpd_ver}.tar.gz";
-    sha256 = "ff9f4de3901d03bb285634c5b149191223d17f1c269a16c863bac44238119c85";
-  };
-  patchelf_src = fetchurl {
-    url = "http://hydra.nixos.org/build/1524660/download/2/patchelf-${patchelf_ver}.tar.bz2";
-    sha256 = "00bw29vdsscsili65wcb5ay0gvg1w0ljd00sb5xc6br8bylpyzpw";
-  };
-  pcre_src = fetchurl {
-    url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-${pcre_ver}.tar.bz2";
-    sha256 = "0g4c0z4h30v8g8qg02zcbv7n67j5kz0ri9cfhgkpwg276ljs0y2p";
-  };
-
-  src = fetchgit {
-    url = "git://github.com/JuliaLang/julia.git";
-    rev = "refs/tags/v${version}";
-    sha256 = "7ee0f267bc1ae286764ced3c0c695c335a6f8d67bd7b3ca7e4de259333c9426a";
-  };
-
-  buildInputs = [ gfortran perl m4 gmp pcre llvm readline zlib
-    fftw fftwSinglePrec libunwind suitesparse glpk ncurses libunistring patchelf
-    openblas tcl tk xproto libX11 git mpfr
-    ];
-
-  configurePhase = ''
-    for i in GMP LLVM PCRE LAPACK OPENBLAS BLAS READLINE FFTW LIBUNWIND SUITESPARSE GLPK LIGHTTPD ZLIB MPFR;
-    do
-      makeFlags="$makeFlags USE_SYSTEM_$i=1 "
-    done
-	makeFlags="$makeFlags JULIA_CPU_TARGET=core2";
-
-    copy_kill_hash(){
-      cp "$1" "$2/$(basename "$1" | sed -e 's/^[a-z0-9]*-//')"
-    }
-
-    for i in "${grisu_src}" "${dsfmt_src}" "${arpack_src}" "${clp_src}" "${patchelf_src}" "${pcre_src}" ; do
-      copy_kill_hash "$i" deps
-    done
-    copy_kill_hash "${dsfmt_src}" deps/random
-
-    ${if realGcc ==null then "" else 
-    ''export NIX_LDFLAGS="$NIX_LDFLAGS -L${realGcc}/lib -L${realGcc}/lib64 -lpcre -lopenblas -lm -lfftw3f -lfftw3 -lglpk -lunistring -lz -lgmp -lmpfr"''}
-    export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE -fPIC "
-
-    export LDFLAGS="-L${suitesparse}/lib -L$out/lib/julia -Wl,-rpath,$out/lib/julia"
-
-    export GLPK_PREFIX="${glpk}/include"
-
-    sed -e "s@/usr/local/lib@$out/lib@g" -i deps/Makefile
-    sed -e "s@/usr/lib@$out/lib@g" -i deps/Makefile
-
-    export makeFlags="$makeFlags PREFIX=$out SHELL=${stdenv.shell}"
-
-    export dontPatchELF=1
-
-    export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$PWD/usr/lib:$PWD/usr/lib/julia"
-  '';
-
-  preBuild = ''
-    mkdir -p usr/lib
-
-    mkdir -p "$out/lib"
-    ln -s "${openblas}/lib/libopenblas.so" "$out/lib/libblas.so"
-    ln -s "${openblas}/lib/libopenblas.so" "$out/lib/liblapack.so"
-
-    echo "$out"
-    (
-    cd "$(mktemp -d)"
-    for i in "${suitesparse}"/lib/lib*.a; do
-      ar -x $i
-    done
-    gcc *.o --shared -o "$out/lib/libsuitesparse.so"
-    )
-    cp "$out/lib/libsuitesparse.so" usr/lib
-    for i in umfpack cholmod amd camd colamd spqr; do
-      ln -s libsuitesparse.so "$out"/lib/lib$i.so;
-      ln -s libsuitesparse.so "usr"/lib/lib$i.so;
-    done
-  '';
-
-  preInstall = ''
-  '';
-
-  meta = {
-    description = "High-level performance-oriented dynamical language for technical computing";
-    homepage = "http://julialang.org/";
-    license = stdenv.lib.licenses.mit;
-    maintainers = [ stdenv.lib.maintainers.raskin ];
-    platforms = with stdenv.lib.platforms; linux;
-  };
-}

pkgs/development/compilers/julia/0.3.nix

@@ -1,154 +0,0 @@
-{ stdenv, fetchgit, fetchurl
-# build tools
-, gfortran, git, m4, patchelf, perl, which, python2
-# libjulia dependencies
-, libunwind, llvm, readline, utf8proc, zlib
-# standard library dependencies
-, double_conversion, fftwSinglePrec, fftw, glpk, gmp, mpfr, pcre
-# linear algebra
-, openblas, arpack, suitesparse
-}:
-
-with stdenv.lib;
-
-# All dependencies should use the same OpenBLAS.
-let
-  arpack_ = arpack;
-  suitesparse_ = suitesparse;
-in
-let
-  arpack = arpack_.override { inherit openblas; };
-  suitesparse = suitesparse_.override { inherit openblas; };
-in
-
-stdenv.mkDerivation rec {
-  pname = "julia";
-  version = "0.3.11";
-  name = "${pname}-${version}";
-
-  src = fetchgit {
-    url = "git://github.com/JuliaLang/julia.git";
-    rev = "refs/tags/v${version}";
-    sha256 = "06xmv2l8hskdh1s5y2dh28vpb5pc0gzmfl5a03yp0qjjsl5cb284";
-    name = "julia-git-v${version}";
-  };
-
-  patches = [ ./0001-work-around-buggy-wcwidth.patch ];
-
-  extraSrcs =
-    let
-      dsfmt_ver = "2.2";
-
-      dsfmt_src = fetchurl {
-        url = "http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/SFMT/dSFMT-src-${dsfmt_ver}.tar.gz";
-        name = "dsfmt-${dsfmt_ver}.tar.gz";
-        md5 = "cb61be3be7254eae39684612c524740d";
-      };
-
-    in [ dsfmt_src ];
-
-  prePatch = ''
-    copy_kill_hash(){
-      cp "$1" "$2/$(basename "$1" | sed -e 's/^[a-z0-9]*-//')"
-    }
-
-    for i in $extraSrcs; do
-      copy_kill_hash "$i" deps
-    done
-  '';
-
-  postPatch = ''
-    sed -i deps/Makefile \
-        -e "s@/usr/local/lib@$out/lib@g" \
-        -e "s@/usr/lib@$out/lib@g" \
-        -e "s@/usr/include/double-conversion@${double_conversion}/include/double-conversion@g"
-
-    patchShebangs . contrib
-
-    # ldconfig doesn't seem to ever work on NixOS; system-wide ldconfig cache
-    # is probably not what we want anyway on non-NixOS
-    sed -e "s@/sbin/ldconfig@true@" -i src/ccall.*
-  '';
-
-  buildInputs = [
-    arpack double_conversion fftw fftwSinglePrec glpk gmp libunwind
-    llvm mpfr pcre openblas readline suitesparse utf8proc zlib
-  ];
-
-  nativeBuildInputs = [ gfortran git m4 patchelf perl python2 which ];
-
-  makeFlags =
-    let
-      arch = head (splitString "-" stdenv.system);
-      march = { "x86_64" = "x86-64"; "i686" = "i686"; }."${arch}"
-              or (throw "unsupported architecture: ${arch}");
-    in [
-      "ARCH=${arch}"
-      "MARCH=${march}"
-      "JULIA_CPU_TARGET=${march}"
-      "PREFIX=$(out)"
-      "prefix=$(out)"
-      "SHELL=${stdenv.shell}"
-
-      "USE_SYSTEM_BLAS=1"
-      "LIBBLAS=-lopenblas"
-      "LIBBLASNAME=libopenblas"
-
-      "USE_SYSTEM_LAPACK=1"
-      "LIBLAPACK=-lopenblas"
-      "LIBLAPACKNAME=libopenblas"
-
-      "USE_SYSTEM_ARPACK=1"
-      "USE_SYSTEM_FFTW=1"
-      "USE_SYSTEM_GLPK=1"
-      "USE_SYSTEM_GMP=1"
-      "USE_SYSTEM_GRISU=1"
-      "USE_SYSTEM_LIBUNWIND=1"
-      "USE_SYSTEM_LLVM=1"
-      "USE_SYSTEM_MPFR=1"
-      "USE_SYSTEM_PATCHELF=1"
-      "USE_SYSTEM_PCRE=1"
-      "USE_SYSTEM_READLINE=1"
-      "USE_SYSTEM_SUITESPARSE=1"
-      "USE_SYSTEM_UTF8PROC=1"
-      "USE_SYSTEM_ZLIB=1"
-    ];
-
-  GLPK_PREFIX = "${glpk}/include";
-
-  NIX_CFLAGS_COMPILE = [ "-fPIC" ];
-
-  # Julia tries to load these libraries dynamically at runtime, but they can't be found.
-  # Easier by far to link against them as usual.
-  # These go in LDFLAGS, where they affect only Julia itself, and not NIX_LDFLAGS,
-  # where they would also be used for all the private libraries Julia builds.
-  LDFLAGS = [
-    "-larpack"
-    "-lfftw3_threads"
-    "-lfftw3f_threads"
-    "-lglpk"
-    "-lgmp"
-    "-lmpfr"
-    "-lopenblas"
-    "-lpcre"
-    "-lsuitesparse"
-    "-lz"
-  ];
-
-  dontStrip = true;
-  dontPatchELF = true;
-
-  enableParallelBuilding = true;
-
-  # Test fail on i686 (julia version 0.3.10)
-  doCheck = !stdenv.isi686;
-  checkTarget = "testall";
-
-  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/julia/0001-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/0002-use-system-suitesparse.patch

@@ -0,0 +1,25 @@
+From e2b0ed6664fe4adfd0f9ce8fa14732d47b30ab5c Mon Sep 17 00:00:00 2001
+From: Thomas Tuegel <ttuegel@gmail.com>
+Date: Sat, 10 Oct 2015 16:18:53 -0500
+Subject: [PATCH 2/3] use system suitesparse
+
+---
+ base/sparse/cholmod.jl | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/base/sparse/cholmod.jl b/base/sparse/cholmod.jl
+index ec7e980..f834cc1 100644
+--- a/base/sparse/cholmod.jl
++++ b/base/sparse/cholmod.jl
+@@ -151,7 +151,7 @@ function __init__()
+ 
+         # Register gc tracked allocator if CHOLMOD is new enough
+         if current_version >= v"3.0.0"
+-            cnfg = cglobal((:SuiteSparse_config, :libsuitesparseconfig), Ptr{Void})
++            cnfg = cglobal((:SuiteSparse_config, :libsuitesparse), Ptr{Void})
+             unsafe_store!(cnfg, cglobal(:jl_malloc, Ptr{Void}), 1)
+             unsafe_store!(cnfg, cglobal(:jl_calloc, Ptr{Void}), 2)
+             unsafe_store!(cnfg, cglobal(:jl_realloc, Ptr{Void}), 3)
+-- 
+2.5.2
+

pkgs/development/compilers/julia/0003-no-ldconfig.patch

@@ -0,0 +1,29 @@
+From 8802fe583eda93a928739cb3bc3517e19d1a6fa1 Mon Sep 17 00:00:00 2001
+From: Thomas Tuegel <ttuegel@gmail.com>
+Date: Sun, 11 Oct 2015 07:19:42 -0500
+Subject: [PATCH 3/3] no ldconfig
+
+---
+ src/ccall.cpp | 6 +-----
+ 1 file changed, 1 insertion(+), 5 deletions(-)
+
+diff --git a/src/ccall.cpp b/src/ccall.cpp
+index 22015ff..2821192 100644
+--- a/src/ccall.cpp
++++ b/src/ccall.cpp
+@@ -13,11 +13,7 @@ extern "C" DLLEXPORT void jl_read_sonames(void)
+ {
+     char *line=NULL;
+     size_t sz=0;
+-#if defined(__linux__)
+-    FILE *ldc = popen("/sbin/ldconfig -p", "r");
+-#else
+-    FILE *ldc = popen("/sbin/ldconfig -r", "r");
+-#endif
++    FILE *ldc = popen("true", "r");
+ 
+     while (!feof(ldc)) {
+         ssize_t n = getline(&line, &sz, ldc);
+-- 
+2.5.2
+

pkgs/development/compilers/julia/default.nix

@@ -0,0 +1,157 @@
+{ 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-${dsfmtVersion}.tar.gz";
+    sha256 = "03kaqbjbi6viz0n33dk5jlf6ayxqlsq4804n7kwkndiga9s4hd42";
+  };
+
+  libuvVersion = "28f5f06b5ff6f010d666ec26552e0badaca5cdcd";
+  libuv = fetchurl {
+    url = "https://api.github.com/repos/JuliaLang/libuv/tarball/${libuvVersion}";
+    sha256 = "1ksns0aiayxmxffvq2kc96904mxlmbkfc30xxck69xnidr2jvr4a";
+  };
+
+  rmathVersion = "0.1";
+  rmath-julia = fetchurl {
+    url = "https://api.github.com/repos/JuliaLang/Rmath-julia/tarball/v${rmathVersion}";
+    sha256 = "0ai5dhjc43zcvangz123ryxmlbm51s21rg13bllwyn98w67arhb4";
+  };
+in
+
+stdenv.mkDerivation rec {
+  pname = "julia";
+  version = "0.4.0";
+  name = "${pname}-${version}";
+
+  src = fetchurl {
+    url = "https://github.com/JuliaLang/${pname}/releases/download/v${version}/${name}.tar.gz";
+    sha256 = "00k53hzbawpqvmkkyzcvbmf1d0ycshzdqk19nwsifv1rmiwjj7ss";
+  };
+
+  prePatch = ''
+    cp "${dsfmt}" "./deps/dsfmt-${dsfmtVersion}.tar.gz"
+    cp "${rmath-julia}" "./deps/Rmath-julia-${rmathVersion}.tar.gz"
+    cp "${libuv}" "./deps/libuv-${libuvVersion}.tar.gz"
+  '';
+
+  patches = [
+    ./0001-use-system-utf8proc.patch
+    ./0002-use-system-suitesparse.patch
+    ./0003-no-ldconfig.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"
+  '';
+
+  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/llvm/3.3/llvm.nix

@@ -14,9 +14,17 @@ in stdenv.mkDerivation rec {
     ./no-rule-aarch64.patch          # http://llvm.org/bugs/show_bug.cgi?id=16625
     # Patch needed for Julia, backports fixes from LLVM 3.5
     (fetchurl {
-      url = "https://raw.githubusercontent.com/JuliaLang/julia/3bdda3750efc4ebf8ce7eda8a0888ffef3851605/deps/llvm-3.3.patch";
+      url = "https://raw.githubusercontent.com/JuliaLang/julia/release-0.4/deps/llvm-3.3.patch";
       sha256 = "0j6chyx4k8zr1qha5dks8lqlcraqrj4q1hwnk2kj3qi6cajsd8k3";
     })
+    (fetchurl {
+      url = "https://raw.githubusercontent.com/JuliaLang/julia/release-0.4/deps/instcombine-llvm-3.3.patch";
+      sha256 = "161frq3wxrkxah78krb24hp4zkcnphzcgnvkwfq1abq2vjx3f8sn";
+    })
+    (fetchurl {
+      url = "https://raw.githubusercontent.com/JuliaLang/julia/release-0.4/deps/int128-vector.llvm-3.3.patch";
+      sha256 = "0lzkv6hvsdaalwsyf6sq0vdrf8x5nk58qg6nn5dlw7n3hxaxpm4m";
+    })
   ];
 
   buildInputs = [ perl groff cmake python libffi ];

pkgs/development/libraries/pcre2/default.nix

@@ -0,0 +1,23 @@
+{ stdenv, fetchurl }:
+
+stdenv.mkDerivation {
+  name = "pcre2-10.20";
+  src = fetchurl {
+    url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre2-10.20.tar.bz2";
+    sha256 = "0yj8mm9ll9zj3v47rvmmqmr1ybxk72rr2lym3rymdsf905qjhbik";
+  };
+
+  configureFlags = [
+    "--enable-pcre2-16"
+    "--enable-pcre2-32"
+    "--enable-jit"
+  ];
+
+  meta = {
+    description = "Perl Compatible Regular Expressions";
+    homepage = "http://www.pcre.org/";
+    license = stdenv.lib.licenses.bsd3;
+    maintainers = [ stdenv.lib.maintainers.ttuegel ];
+    platforms = stdenv.lib.platforms.all;
+  };
+}

pkgs/development/libraries/science/math/openblas/default.nix

@@ -6,6 +6,8 @@
 
 with stdenv.lib;
 
+let blas64_ = blas64; in
+
 let local = config.openblas.preferLocalBuild or false;
     binary =
       { i686-linux = "32";
@@ -18,11 +20,11 @@ let local = config.openblas.preferLocalBuild or false;
       ];
     localFlags = config.openblas.flags or
       optionals (hasAttr "target" config.openblas) [ "TARGET=${config.openblas.target}" ];
-    blas64Orig = blas64;
+    blas64 = if blas64_ != null then blas64_ else hasPrefix "x86_64" stdenv.system;
-in
-stdenv.mkDerivation rec {
-  version = "0.2.14";
 
+    version = "0.2.14";
+in
+stdenv.mkDerivation {
   name = "openblas-${version}";
   src = fetchurl {
     url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}";
@@ -30,6 +32,8 @@ stdenv.mkDerivation rec {
     name = "openblas-${version}.tar.gz";
   };
 
+  inherit blas64;
+
   preBuild = "cp ${liblapack.src} lapack-${liblapack.meta.version}.tgz";
 
   nativeBuildInputs = optionals stdenv.isDarwin [coreutils] ++ [gfortran perl];
@@ -50,7 +54,8 @@ stdenv.mkDerivation rec {
       "INTERFACE64=${if blas64 then "1" else "0"}"
     ];
 
-  blas64 = if blas64Orig != null then blas64Orig else hasPrefix "x86_64" stdenv.system;
+  doCheck = true;
+  checkTarget = "tests";
 
   meta = with stdenv.lib; {
     description = "Basic Linear Algebra Subprograms";

pkgs/development/libraries/science/math/openlibm/default.nix

@@ -0,0 +1,19 @@
+{ stdenv, fetchurl }:
+
+stdenv.mkDerivation {
+  name = "openlibm-0.4.1";
+  src = fetchurl {
+    url = "https://github.com/JuliaLang/openlibm/archive/v0.4.1.tar.gz";
+    sha256 = "0cwqqqlblj3kzp9aq1wnpfs1fl0qd1wp1xzm5shb09w06i4rh9nn";
+  };
+
+  makeFlags = [ "prefix=$(out)" ];
+
+  meta = {
+    description = "High quality system independent, portable, open source libm implementation";
+    homepage = "http://www.openlibm.org/";
+    license = stdenv.lib.licenses.mit;
+    maintainers = [ stdenv.lib.maintainers.ttuegel ];
+    platforms = stdenv.lib.platforms.all;
+  };
+}

pkgs/development/libraries/science/math/openspecfun/default.nix

@@ -0,0 +1,21 @@
+{ stdenv, fetchurl, gfortran }:
+
+stdenv.mkDerivation {
+  name = "openspecfun-0.4";
+  src = fetchurl {
+    url = "https://github.com/JuliaLang/openspecfun/archive/v0.4.tar.gz";
+    sha256 = "0nsa3jjmlhcqkw5ba5ypbn3n0c8b6lc22zzlxnmxkxi9shhdx65z";
+  };
+
+  makeFlags = [ "prefix=$(out)" ];
+
+  nativeBuildInputs = [ gfortran ];
+
+  meta = {
+    description = "A collection of special mathematical functions";
+    homepage = "https://github.com/JuliaLang/openspecfun";
+    license = stdenv.lib.licenses.mit;
+    maintainers = [ stdenv.lib.maintainers.ttuegel ];
+    platforms = stdenv.lib.platforms.all;
+  };
+}

pkgs/development/libraries/science/math/suitesparse/default.nix

@@ -42,7 +42,7 @@ stdenv.mkDerivation {
         for i in "$out"/lib/lib*.a; do
           ar -x $i
         done
-        gcc *.o --shared -o "$out/lib/libsuitesparse.so"
+        gcc *.o --shared -o "$out/lib/libsuitesparse.so" -lopenblas
     )
     for i in umfpack cholmod amd camd colamd spqr; do
       ln -s libsuitesparse.so "$out"/lib/lib$i.so;

pkgs/development/libraries/utf8proc/default.nix

@@ -1,14 +1,12 @@
-{ stdenv, fetchFromGitHub }:
+{ stdenv, fetchurl }:
 
 stdenv.mkDerivation rec {
   name = "utf8proc-${version}";
-  version = "v1.2";
+  version = "1.3";
 
-  src = fetchFromGitHub {
+  src = fetchurl {
-    owner = "JuliaLang";
+    url = "https://github.com/JuliaLang/utf8proc/archive/v${version}.tar.gz";
-    repo = "utf8proc";
+    sha256 = "07r7djkmd399wl9cn0s2iqjhmm7l5iifp5h1yf2in9s366mlhkkg";
-    rev = "${version}";
-    sha256 = "1ryjlcnpfm7fpkq6444ybi576hbnh2l0w7kjhbqady5lxwjyg3pf";
   };
 
   makeFlags = [ "prefix=$(out)" ];

pkgs/top-level/all-packages.nix

@@ -4137,16 +4137,12 @@ let
 
   jikes = callPackage ../development/compilers/jikes { };
 
-  julia02 = callPackage ../development/compilers/julia/0.2.nix {
+  julia = callPackage ../development/compilers/julia {
+    gmp = gmp6;
     llvm = llvm_33;
-    suitesparse = suitesparse_4_2;
+    openblas = openblasCompat;
   };
 
-  julia03 = callPackage ../development/compilers/julia/0.3.nix {
-    llvm = llvm_33;
-  };
-  julia = julia03;
-
   lazarus = callPackage ../development/compilers/fpc/lazarus.nix {
     fpc = fpc;
   };
@@ -6356,6 +6352,7 @@ let
 
   gmp4 = callPackage ../development/libraries/gmp/4.3.2.nix { }; # required by older GHC versions
   gmp5 = callPackage ../development/libraries/gmp/5.1.x.nix { };
+  gmp6 = callPackage ../development/libraries/gmp/6.x.nix { };
   gmp = gmp5;
   gmpxx = appendToName "with-cxx" (gmp.override { cxx = true; });
 
@@ -7824,6 +7821,8 @@ let
     unicodeSupport = config.pcre.unicode or true;
   };
 
+  pcre2 = callPackage ../development/libraries/pcre2 { };
+
   pdf2xml = callPackage ../development/libraries/pdf2xml {} ;
 
   phonon = callPackage ../development/libraries/phonon/qt4 {};
@@ -14266,13 +14265,17 @@ let
   # standard BLAS and LAPACK.
   openblasCompat = openblas.override { blas64 = false; };
 
+  openlibm = callPackage ../development/libraries/science/math/openlibm {};
+
+  openspecfun = callPackage ../development/libraries/science/math/openspecfun {};
+
   mathematica = callPackage ../applications/science/math/mathematica { };
   mathematica9 = callPackage ../applications/science/math/mathematica/9.nix { };
 
-  sage = callPackage ../applications/science/math/sage { };
-
   metis = callPackage ../development/libraries/science/math/metis {};
 
+  sage = callPackage ../applications/science/math/sage { };
+
   suitesparse_4_2 = callPackage ../development/libraries/science/math/suitesparse/4.2.nix { };
   suitesparse_4_4 = callPackage ../development/libraries/science/math/suitesparse {};
   suitesparse = suitesparse_4_4;