Julia language: update to a fresh version

Update julia and some of its dependencies

Split PCRE because a lot of packages depend on it and I am not sure we
want to test them in a hurry (and Julia specifies exact version).

6 files changed, 99 insertions, 140 deletions

diff --git a/pkgs/development/libraries/fftw/default.nix b/pkgs/development/libraries/fftw/default.nix
index 845ec772010..6b4fbe7df6c 100644
--- a/pkgs/development/libraries/fftw/default.nix
+++ b/pkgs/development/libraries/fftw/default.nix
@@ -1,15 +1,19 @@
-{fetchurl, stdenv, builderDefs, stringsWithDeps, singlePrecision ? false}:
-let localDefs = builderDefs.passthru.function { 
+{fetchurl, stdenv, builderDefs, stringsWithDeps, singlePrecision ? false, pthreads ? false}:
+let
+  version = "3.3.2";
+  localDefs = builderDefs.passthru.function { 
   src = 
     fetchurl {
-      url = ftp://ftp.fftw.org/pub/fftw/fftw-3.2.2.tar.gz;
-      sha256 = "13vnglardq413q2518zi4a8pam3znydrz28m9w09kss9xrjsx9va";
+      url = "ftp://ftp.fftw.org/pub/fftw/fftw-${version}.tar.gz";
+      sha256 = "b1236a780ca6e66fc5f8eda6ef0665d680e8253d9f01d7bf211b714a50032d01";
     };
   buildInputs = [];
-  configureFlags = ["--enable-shared" "--enable-openmp"]
+  configureFlags = ["--enable-shared"]
                         # some distros seem to be shipping both versions within the same package?
                         # why does --enable-float still result in ..3f.so instead of ..3.so?
                    ++ (if singlePrecision then [ "--enable-single" ] else [ ])
+		   ++ (stdenv.lib.optional (!pthreads) "--enable-openmp")
+		   ++ (stdenv.lib.optional pthreads "--enable-threads")
                         # I think all i686 has sse
                    ++ (if (stdenv.isi686 || stdenv.isx86_64) && singlePrecision then [ "--enable-sse" ] else [ ])
                         # I think all x86_64 has sse2
@@ -18,8 +22,8 @@ let localDefs = builderDefs.passthru.function {
   };
 in with localDefs;
 stdenv.mkDerivation {
-  name = "fftw-3.2.2" + ( if singlePrecision then "-single" else "-double" );
-  builder = writeScript "fftw-3.2.1-builder"
+  name = "fftw-3.3.2" + ( if singlePrecision then "-single" else "-double" );
+  builder = writeScript "fftw-3.3.2-builder"
     (textClosure localDefs [doConfigure doMakeInstall doForceShare]);
   meta = {
     description = "Fastest Fourier Transform in the West library";
diff --git a/pkgs/development/libraries/pcre/8.30.nix b/pkgs/development/libraries/pcre/8.30.nix
new file mode 100644
index 00000000000..2f636492eb6
--- /dev/null
+++ b/pkgs/development/libraries/pcre/8.30.nix
@@ -0,0 +1,38 @@
+{ stdenv, fetchurl, unicodeSupport ? true, cplusplusSupport ? true }:
+
+stdenv.mkDerivation rec {
+  name = "pcre-8.30";
+
+  src = fetchurl {
+    url = "ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/${name}.tar.bz2";
+    sha256 = "c1113fd7db934e97ad8b3917d432e5b642e9eb9afd127eb797804937c965f4ac";
+  };
+
+  # The compiler on Darwin crashes with an internal error while building the
+  # C++ interface. Disabling optimizations on that platform remedies the
+  # problem. In case we ever update the Darwin GCC version, the exception for
+  # that platform ought to be removed.
+  configureFlags = ''
+    ${if unicodeSupport then "--enable-unicode-properties" else ""}
+    ${if !cplusplusSupport then "--disable-cpp" else ""}
+  '' + stdenv.lib.optionalString stdenv.isDarwin "CXXFLAGS=-O0";
+
+  doCheck = !stdenv.isCygwin;                   # XXX: test failure on Cygwin
+
+  meta = {
+    homepage = "http://www.pcre.org/";
+    description = "A library for Perl Compatible Regular Expressions";
+    license = "BSD-3";
+
+    longDescription = ''
+      The PCRE library is a set of functions that implement regular
+      expression pattern matching using the same syntax and semantics as
+      Perl 5. PCRE has its own native API, as well as a set of wrapper
+      functions that correspond to the POSIX regular expression API. The
+      PCRE library is free, even for building proprietary software.
+    '';
+
+    platforms = stdenv.lib.platforms.all;
+    maintainers = [ stdenv.lib.maintainers.simons ];
+  };
+}
diff --git a/pkgs/development/libraries/science/math/liblapack/default.nix b/pkgs/development/libraries/science/math/liblapack/default.nix
index e2b43b6b053..9f25011b76f 100644
--- a/pkgs/development/libraries/science/math/liblapack/default.nix
+++ b/pkgs/development/libraries/science/math/liblapack/default.nix
@@ -4,10 +4,10 @@ let
   usedLibExtension = if shared then ".so" else ".a";
 in
 stdenv.mkDerivation {
-  name = "liblapack-3.4.0";
+  name = "liblapack-3.4.1";
   src = fetchurl {
-    url = "http://www.netlib.org/lapack/lapack-3.4.0.tgz";
-    sha256 = "1sf30v1ps5icg67dvw5sbx5yhypx13am470gqg2f7l04f3wrw4x7";
+    url = "http://www.netlib.org/lapack/lapack-3.4.1.tgz";
+    sha256 = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f";
   };
 
   propagatedBuildInputs = [ atlasMaybeShared ];
diff --git a/pkgs/development/libraries/science/math/openblas/default.nix b/pkgs/development/libraries/science/math/openblas/default.nix
new file mode 100644
index 00000000000..4d30671c488
--- /dev/null
+++ b/pkgs/development/libraries/science/math/openblas/default.nix
@@ -0,0 +1,36 @@
+{ stdenv, fetchurl, gfortran, perl }:
+
+stdenv.mkDerivation rec {
+  version = "0.2.2";
+  lapack_version = "3.4.1";
+  lapack_src = fetchurl {
+    url = "http://www.netlib.org/lapack/lapack-${lapack_version}.tgz";
+    sha256 = "93b910f94f6091a2e71b59809c4db4a14655db527cfc5821ade2e8c8ab75380f";
+  };
+
+  name = "openblas-${version}";
+  src = fetchurl {
+    url = "https://github.com/xianyi/OpenBLAS/tarball/v${version}";
+    sha256 = "13kdx3knff5ajnmgn419g0dnh83plin07p7akwamr3v7z5qfrzqr";
+    name = "openblas-${version}.tar.gz";
+  };
+
+  preBuild = "cp ${lapack_src} lapack-${lapack_version}.tgz";
+
+  buildInputs = [gfortran perl];
+
+  cpu = builtins.head (stdenv.lib.splitString "-" stdenv.system);
+
+  target = if cpu == "i686" then "P6" else 
+    if cpu == "x86_64" then "CORE2" else
+     # allow autodetect
+      "";
+
+  makeFlags = "${if target != "" then "TARGET=" else ""}${target} FC=gfortran CC=cc PREFIX=\"\$(out)\"";
+
+  meta = {
+    description = "Basic Linear Algebra Subprograms";
+    license = stdenv.lib.licenses.bsd3;
+    homepage = "https://github.com/xianyi/OpenBLAS";
+  };
+}
diff --git a/pkgs/development/libraries/suitesparse/default.nix b/pkgs/development/libraries/suitesparse/default.nix
index b3fe6db059a..e3a7fbb5a08 100644
--- a/pkgs/development/libraries/suitesparse/default.nix
+++ b/pkgs/development/libraries/suitesparse/default.nix
@@ -1,9 +1,10 @@
 { stdenv, fetchurl, blas, liblapack, gfortran } :
-stdenv.mkDerivation {
-  name = "suitesparse";
+stdenv.mkDerivation rec {
+  version = "4.0.0";
+  name = "suitesparse-${version}";
   src = fetchurl {
-    url = http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-3.5.0.tar.gz ;
-    sha256 = "0npn7c1j5qag5m2r0cmh3bwc42c1jk8k2yg2cfyxlcrp0h7wn4rc";  			
+    url = "http://www.cise.ufl.edu/research/sparse/SuiteSparse/SuiteSparse-${version}.tar.gz" ;
+    sha256 = "1nvbdw10wa6654k8sa2vhr607q6fflcywyji5xd767cqpwag4v5j";  			
   };
   buildInputs = [blas liblapack gfortran] ;
   patches = [./disable-metis.patch];
@@ -14,6 +15,8 @@ stdenv.mkDerivation {
     mkdir -p $out/include
   '';
 
+  makeFlags = ''PREFIX=\"$(out)\" INSTALL_LIB=$(out)/lib INSTALL_INCLUDE=$(out)/include'';
+
   NIX_CFLAGS = "-fPIC";
 
 }
diff --git a/pkgs/development/libraries/suitesparse/disable-metis.patch b/pkgs/development/libraries/suitesparse/disable-metis.patch
index 68fd22bc643..5b735eb7d3c 100644
--- a/pkgs/development/libraries/suitesparse/disable-metis.patch
+++ b/pkgs/development/libraries/suitesparse/disable-metis.patch
@@ -1,140 +1,18 @@
-diff -Nrc SuiteSparse/UFconfig/Makefile SuiteSparse-new/UFconfig/Makefile
-*** SuiteSparse/UFconfig/Makefile	2009-11-11 20:59:08.000000000 +0100
---- SuiteSparse-new/UFconfig/Makefile	2010-08-02 13:14:04.000000000 +0200
-***************
-*** 25,31 ****
-  
-  # install UFconfig
-  install:
-! 	$(CP) Lib/libufconfig.a $(INSTALL_LIB)/libufconfig.$(VERSION).a
-  	( cd $(INSTALL_LIB) ; ln -s libufconfig.$(VERSION).a libufconfig.a )
-  	$(CP) UFconfig.h $(INSTALL_INCLUDE)
-  
---- 25,31 ----
-  
-  # install UFconfig
-  install:
-! 	$(CP) libufconfig.a $(INSTALL_LIB)/libufconfig.$(VERSION).a
-  	( cd $(INSTALL_LIB) ; ln -s libufconfig.$(VERSION).a libufconfig.a )
-  	$(CP) UFconfig.h $(INSTALL_INCLUDE)
-  
-diff -Nrc SuiteSparse/UFconfig/UFconfig.mk SuiteSparse-new/UFconfig/UFconfig.mk
-*** SuiteSparse/UFconfig/UFconfig.mk	2010-06-02 17:40:42.000000000 +0200
---- SuiteSparse-new/UFconfig/UFconfig.mk	2010-08-02 14:55:27.000000000 +0200
-***************
-*** 34,40 ****
-  # performance.  You should select the optimization parameters that are best
-  # for your system.  On Linux, use "CFLAGS = -O3 -fexceptions" for example.
-  CC = cc
-! CFLAGS = -O3 -fexceptions
-  
-  # C++ compiler (also uses CFLAGS)
-  CPLUSPLUS = g++
---- 34,40 ----
-  # performance.  You should select the optimization parameters that are best
-  # for your system.  On Linux, use "CFLAGS = -O3 -fexceptions" for example.
-  CC = cc
-! CFLAGS = -O3 -fexceptions -fPIC
-  
-  # C++ compiler (also uses CFLAGS)
-  CPLUSPLUS = g++
-***************
-*** 71,78 ****
-  # MAKE = gmake
-  
-  # For "make install"
-! INSTALL_LIB = /usr/local/lib
-! INSTALL_INCLUDE = /usr/local/include
-  
-  #------------------------------------------------------------------------------
-  # BLAS and LAPACK configuration:
---- 71,78 ----
-  # MAKE = gmake
-  
-  # For "make install"
-! INSTALL_LIB = $(out)/lib
-! INSTALL_INCLUDE = $(out)/include
-  
-  #------------------------------------------------------------------------------
-  # BLAS and LAPACK configuration:
-***************
-*** 127,134 ****
-  # The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
-  # You may wish to use an absolute path.  METIS is optional.  Compile
-  # CHOLMOD with -DNPARTITION if you do not wish to use METIS.
-! METIS_PATH = ../../metis-4.0
-! METIS = ../../metis-4.0/libmetis.a
-  
-  # If you use CHOLMOD_CONFIG = -DNPARTITION then you must use the following
-  # options:
---- 127,134 ----
-  # The path is relative to where it is used, in CHOLMOD/Lib, CHOLMOD/MATLAB, etc.
-  # You may wish to use an absolute path.  METIS is optional.  Compile
-  # CHOLMOD with -DNPARTITION if you do not wish to use METIS.
-! #METIS_PATH = ../../metis-4.0
-! #METIS = 
-  
-  # If you use CHOLMOD_CONFIG = -DNPARTITION then you must use the following
-  # options:
-***************
-*** 189,195 ****
-  # -DNSUNPERF	    for Solaris only.  If defined, do not use the Sun
-  #			Performance Library
-  
-! CHOLMOD_CONFIG =
-  
-  #------------------------------------------------------------------------------
-  # SuiteSparseQR configuration:
---- 189,195 ----
-  # -DNSUNPERF	    for Solaris only.  If defined, do not use the Sun
-  #			Performance Library
-  
-! CHOLMOD_CONFIG = -DNPARTITION
-  
-  #------------------------------------------------------------------------------
-  # SuiteSparseQR configuration:
-***************
-*** 203,209 ****
-  # -DHAVE_TBB        enable the use of Intel's Threading Building Blocks (TBB)
-  
-  # default, without timing, without TBB:
-! SPQR_CONFIG =
-  # with timing and TBB:
-  # SPQR_CONFIG = -DTIMING -DHAVE_TBB
-  # with timing
---- 203,209 ----
-  # -DHAVE_TBB        enable the use of Intel's Threading Building Blocks (TBB)
-  
-  # default, without timing, without TBB:
-! SPQR_CONFIG = -DNPARTITION
-  # with timing and TBB:
-  # SPQR_CONFIG = -DTIMING -DHAVE_TBB
-  # with timing
 diff -Nrc SuiteSparse/UMFPACK/Demo/Makefile SuiteSparse-new/UMFPACK/Demo/Makefile
 *** SuiteSparse/UMFPACK/Demo/Makefile	2009-11-11 21:09:45.000000000 +0100
 --- SuiteSparse-new/UMFPACK/Demo/Makefile	2010-08-02 12:53:16.000000000 +0200
 ***************
-*** 40,51 ****
+*** 40,46 ****
   ../../CAMD/Lib/libcamd.a:
   	( cd ../../CAMD ; $(MAKE) library )
   
-- ../../metis-4.0/libmetis.a:
-- 	( cd ../../metis-4.0/Lib ; $(MAKE) )
+- $(METIS):
+- 	( cd $(METIS_PATH) && $(MAKE) )
   
   UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \
-      ../../CHOLMOD/Lib/libcholmod.a ../../COLAMD/Lib/libcolamd.a \
-!     ../../CAMD/Lib/libcamd.a ../../metis-4.0/libmetis.a \
-      ../../CCOLAMD/Lib/libccolamd.a
-  
-  libs: $(UMFPACK)
---- 40,49 ----
+--- 40,44 ----
   ../../CAMD/Lib/libcamd.a:
   	( cd ../../CAMD ; $(MAKE) library )
   
   
   UMFPACK = ../Lib/libumfpack.a ../../AMD/Lib/libamd.a \
-      ../../CHOLMOD/Lib/libcholmod.a ../../COLAMD/Lib/libcolamd.a \
-!     ../../CAMD/Lib/libcamd.a \
-      ../../CCOLAMD/Lib/libccolamd.a
-  
-  libs: $(UMFPACK)