Merge branch 'develop' into features/hwloc

* develop: (85 commits)
  Make libxcb compile with gcc 4.9.
  disable parallel install for glib (found races)
  disable cairo-trace, which is incompatible with older libiberty.h.
  Fix LaunchMon on newer gcc versions.
  Simplify output redirection in spack.util.executable
  Allow completely empty config files.
  Update cmake package to use http in all URLs.
  Fix create, diy, edit, and repo commands to use multiple repos.
  Add namespace option to find command.
  Temporary fix: Clang is the default compiler on Mac OS X.
  Netcdf requires cmake >=2.8.12
  Mbedtls depends on cmake
  Update libtool to 2.4.6
  Update Julia to 0.4.3
  Make binutils build on OS X
  Add verbs and psm variants
  py-matplotlib: depend on freetype
  py-numpy: make blas/lapack optional dependencies
  qhull: apply patch to work with libc++'s standard library
  New package GNU tar
  ...

var/spack/mock_configs/site_spackconfig/compilers.yaml

@@ -1,12 +0,0 @@
-compilers:
-  all:
-    clang@3.3:
-      cc: /path/to/clang
-      cxx: /path/to/clang++
-      f77: None
-      fc: None
-    gcc@4.5.0:
-      cc: /path/to/gcc
-      cxx: /path/to/g++
-      f77: /path/to/gfortran
-      fc: /path/to/gfortran

var/spack/packages/R/package.py

@@ -1,33 +0,0 @@
-from spack import *
-
-class R(Package):
-    """R is 'GNU S', a freely available language and environment for
-       statistical computing and graphics which provides a wide va
-       riety of statistical and graphical techniques: linear and
-       nonlinear modelling, statistical tests, time series analysis,
-       classification, clustering, etc. Please consult the R project
-       homepage for further information."""
-    homepage = "http://www.example.com"
-    url      = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
-
-    version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
-
-    depends_on("readline")
-    depends_on("ncurses")
-    depends_on("icu")
-    depends_on("glib")
-    depends_on("zlib")
-    depends_on("libtiff")
-    depends_on("jpeg")
-    depends_on("cairo")
-    depends_on("pango")
-    depends_on("freetype")
-    depends_on("tcl")
-    depends_on("tk")
-
-    def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
-                  "--enable-R-shlib",
-                  "--enable-BLAS-shlib")
-        make()
-        make("install")

var/spack/packages/clang/package.py

@@ -1,95 +0,0 @@
-##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-
-
-from spack import *
-
-import os
-import os.path
-
-class Clang(Package):
-    """The goal of the Clang project is to create a new C, C++,
-       Objective C and Objective C++ front-end for the LLVM compiler.
-    """
-    homepage = 'http://clang.llvm.org'
-    url = 'http://llvm.org/releases/3.7.0/cfe-3.7.0.src.tar.xz'
-
-    depends_on('llvm@3.7.0', when='@3.7.0')
-    depends_on('llvm@3.6.2', when='@3.6.2')
-    depends_on('llvm@3.5.1', when='@3.5.1')
-
-    version('3.7.0', '8f9d27335e7331cf0a4711e952f21f01', url='http://llvm.org/releases/3.7.0/cfe-3.7.0.src.tar.xz')
-    version('3.6.2', 'ff862793682f714bb7862325b9c06e20', url='http://llvm.org/releases/3.6.2/cfe-3.6.2.src.tar.xz')
-    version('3.5.1', '93f9532f8f7e6f1d8e5c1116907051cb', url='http://llvm.org/releases/3.5.1/cfe-3.5.1.src.tar.xz')
-
-    ##########
-    # @3.7.0
-    resource(name='clang-tools-extra',
-             url='http://llvm.org/releases/3.7.0/clang-tools-extra-3.7.0.src.tar.xz',
-             md5='d5a87dacb65d981a427a536f6964642e', destination='tools', when='@3.7.0')
-    ##########
-
-    def install(self, spec, prefix):
-        env['CXXFLAGS'] = self.compiler.cxx11_flag
-
-        with working_dir('spack-build', create=True):
-
-            options = []
-            if '@3.7.0:' in spec:
-                options.append('-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp')
-            options.extend(std_cmake_args)
-
-            cmake('..',
-                  '-DCLANG_PATH_TO_LLVM_BUILD:PATH=%s' % spec['llvm'].prefix,
-                  '-DLLVM_MAIN_SRC_DIR:PATH=%s' % spec['llvm'].prefix,
-                  *options)
-            make()
-            make("install")
-            # CLang doesn't look in llvm folders for system headers...
-            self.link_llvm_directories(spec)
-
-    def link_llvm_directories(self, spec):
-
-        def clang_include_dir_at(root):
-            return join_path(root, 'include')
-
-        def clang_lib_dir_at(root):
-            return join_path(root, 'lib/clang/', str(self.version), 'include')
-
-        def do_link(source_dir, destination_dir):
-            if os.path.exists(source_dir):
-                for name in os.listdir(source_dir):
-                    source = join_path(source_dir, name)
-                    link = join_path(destination_dir, name)
-                    os.symlink(source, link)
-
-        # Link folder and files in include
-        llvm_dir = clang_include_dir_at(spec['llvm'].prefix)
-        clang_dir = clang_include_dir_at(self.prefix)
-        do_link(llvm_dir, clang_dir)
-        # Link folder and files in lib
-        llvm_dir = clang_lib_dir_at(spec['llvm'].prefix)
-        clang_dir = clang_lib_dir_at(self.prefix)
-        do_link(llvm_dir, clang_dir)

var/spack/packages/llvm/package.py

@@ -1,72 +0,0 @@
-##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
-#
-# This file is part of Spack.
-# Written by David Beckingsale, david@llnl.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/llnl/spack
-# Please also see the LICENSE file for our notice and the LGPL.
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License (as published by
-# the Free Software Foundation) version 2.1 dated February 1999.
-#
-# This program is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
-# conditions of the GNU General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public License
-# along with this program; if not, write to the Free Software Foundation,
-# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-##############################################################################
-from spack import *
-
-
-class Llvm(Package):
-    """The LLVM Project is a collection of modular and reusable compiler and
-       toolchain technologies. Despite its name, LLVM has little to do with
-       traditional virtual machines, though it does provide helpful libraries
-       that can be used to build them. The name "LLVM" itself is not an acronym;
-       it is the full name of the project.
-    """
-    homepage = 'http://llvm.org/'
-    url = 'http://llvm.org/releases/3.7.0/llvm-3.7.0.src.tar.xz'
-
-    version('3.7.0', 'b98b9495e5655a672d6cb83e1a180f8e', url='http://llvm.org/releases/3.7.0/llvm-3.7.0.src.tar.xz')
-    version('3.6.2', '0c1ee3597d75280dee603bae9cbf5cc2', url='http://llvm.org/releases/3.6.2/llvm-3.6.2.src.tar.xz')
-    version('3.5.1', '2d3d8004f38852aa679e5945b8ce0b14', url='http://llvm.org/releases/3.5.1/llvm-3.5.1.src.tar.xz')
-    version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # currently required by mesa package
-
-    depends_on('python@2.7:')
-
-    variant('libcxx', default=False, description="Builds the LLVM Standard C++ library targeting C++11")
-
-    ##########
-    # @3.7.0
-    resource(name='compiler-rt',
-             url='http://llvm.org/releases/3.7.0/compiler-rt-3.7.0.src.tar.xz', md5='383c10affd513026f08936b5525523f5',
-             destination='projects', when='@3.7.0')
-    resource(name='openmp',
-             url='http://llvm.org/releases/3.7.0/openmp-3.7.0.src.tar.xz', md5='f482c86fdead50ba246a1a2b0bbf206f',
-             destination='projects', when='@3.7.0')
-    resource(name='libcxx',
-             url='http://llvm.org/releases/3.7.0/libcxx-3.7.0.src.tar.xz', md5='46aa5175cbe1ad42d6e9c995968e56dd',
-             destination='projects', placement='libcxx', when='+libcxx@3.7.0')
-    resource(name='libcxxabi',
-             url='http://llvm.org/releases/3.7.0/libcxxabi-3.7.0.src.tar.xz', md5='5aa769e2fca79fa5335cfae8f6258772',
-             destination='projects', placement='libcxxabi', when='+libcxx@3.7.0')
-    ##########
-
-    def install(self, spec, prefix):
-        env['CXXFLAGS'] = self.compiler.cxx11_flag
-
-        with working_dir('spack-build', create=True):
-            cmake('..',
-                  '-DLLVM_REQUIRES_RTTI:BOOL=ON',
-                  '-DPYTHON_EXECUTABLE:PATH=%s/bin/python' % spec['python'].prefix,
-                  *std_cmake_args)
-            make()
-            make("install")

var/spack/repos/builtin.mock/repo.yaml

@@ -0,0 +1,2 @@
+repo:
+  namespace: builtin.mock

var/spack/repos/builtin/packages/R/package.py

@@ -0,0 +1,49 @@
+from spack import *
+
+
+class R(Package):
+    """
+    R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a
+    wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series
+    analysis, classification, clustering, etc. Please consult the R project homepage for further information.
+    """
+    homepage = "https://www.r-project.org"
+    url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
+
+    version('3.2.3', '1ba3dac113efab69e706902810cc2970')
+    version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
+    version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
+    version('3.2.0', '66fa17ad457d7e618191aa0f52fc402e')
+    version('3.1.3', '53a85b884925aa6b5811dfc361d73fc4')
+    version('3.1.2', '3af29ec06704cbd08d4ba8d69250ae74')
+
+    variant('external-lapack', default=False, description='Links to externally installed BLAS/LAPACK')
+
+    # Virtual dependencies
+    depends_on('blas', when='+external-lapack')
+    depends_on('lapack', when='+external-lapack')
+
+    # Concrete dependencies
+    depends_on('readline')
+    depends_on('ncurses')
+    depends_on('icu')
+    depends_on('glib')
+    depends_on('zlib')
+    depends_on('libtiff')
+    depends_on('jpeg')
+    depends_on('cairo')
+    depends_on('pango')
+    depends_on('freetype')
+    depends_on('tcl')
+    depends_on('tk')
+
+    def install(self, spec, prefix):
+        options = ['--prefix=%s' % prefix,
+                   '--enable-R-shlib',
+                   '--enable-BLAS-shlib']
+        if '+external-lapack' in spec:
+            options.extend(['--with-blas', '--with-lapack'])
+
+        configure(*options)
+        make()
+        make('install')

var/spack/repos/builtin/packages/binutils/cr16.patch

@@ -0,0 +1,26 @@
+--- old/opcodes/cr16-dis.c	2014-10-14 03:32:04.000000000 -0400
++++ new/opcodes/cr16-dis.c	2016-01-14 21:54:26.000000000 -0500
+@@ -78,7 +78,7 @@
+ REG_ARG_TYPE;
+ 
+ /* Current opcode table entry we're disassembling.  */
+-const inst *instruction;
++extern const inst *instruction;
+ /* Current instruction we're disassembling.  */
+ ins cr16_currInsn;
+ /* The current instruction is read into 3 consecutive words.  */
+@@ -86,12 +86,12 @@
+ /* Contains all words in appropriate order.  */
+ ULONGLONG cr16_allWords;
+ /* Holds the current processed argument number.  */
+-int processing_argument_number;
++extern int processing_argument_number;
+ /* Nonzero means a IMM4 instruction.  */
+ int imm4flag;
+ /* Nonzero means the instruction's original size is
+    incremented (escape sequence is used).  */
+-int size_changed;
++extern int size_changed;
+ 
+ 
+ /* Print the constant expression length.  */

var/spack/repos/builtin/packages/binutils/package.py

@@ -11,8 +11,11 @@ class Binutils(Package):
 
     # Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell
     variant('krellpatch', default=False, description="build with openspeedshop based patch.")
+    variant('gold', default=True, description="build the gold linker")
     patch('binutilskrell-2.24.patch', when='@2.24+krellpatch')
 
+    patch('cr16.patch')
+
     variant('libiberty', default=False, description='Also install libiberty.')
 
     def install(self, spec, prefix):
@@ -26,6 +29,9 @@ def install(self, spec, prefix):
             '--enable-targets=all',
             '--with-sysroot=/']
 
+        if '+gold' in spec:
+            configure_args.append('--enable-gold')
+
         if '+libiberty' in spec:
             configure_args.append('--enable-install-libiberty')
 

var/spack/repos/builtin/packages/cairo/package.py

@@ -14,6 +14,7 @@ class Cairo(Package):
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix,
+                  "--disable-trace", # can cause problems with libiberty
                   "--enable-tee")
         make()
         make("install")

var/spack/repos/builtin/packages/cereal/Werror.patch

@@ -0,0 +1,33 @@
+--- old/sandbox/CMakeLists.txt
++++ new/sandbox/CMakeLists.txt
+@@ -4,9 +4,11 @@
+ add_executable(sandbox_json sandbox_json.cpp)
+ add_executable(sandbox_rtti sandbox_rtti.cpp)
+
++if(Boost_FOUND)
+ add_executable(sandbox_vs sandbox_vs.cpp)
+ target_link_libraries(sandbox_vs sandbox_vs_dll)
+ include_directories(sandbox_shared_lib)
++endif(Boost_FOUND)
+
+ if(Boost_FOUND)
+   add_executable(performance performance.cpp)
+--- old/include/cereal/types/common.hpp
++++ new/include/cereal/types/common.hpp
+@@ -106,14 +106,16 @@
+     t = reinterpret_cast<typename common_detail::is_enum<T>::type const &>( value );
+   }
+
++#ifndef CEREAL_ENABLE_RAW_POINTER_SERIALIZATION
+   //! Serialization for raw pointers
+   /*! This exists only to throw a static_assert to let users know we don't support raw pointers. */
+   template <class Archive, class T> inline
+   void CEREAL_SERIALIZE_FUNCTION_NAME( Archive &, T * & )
+   {
+     static_assert(cereal::traits::detail::delay_static_assert<T>::value,
+       "Cereal does not support serializing raw pointers - please use a smart pointer");
+   }
++#endif
+
+   //! Serialization for C style arrays
+   template <class Archive, class T> inline

var/spack/repos/builtin/packages/cereal/package.py

@@ -0,0 +1,34 @@
+from spack import *
+import shutil
+
+class Cereal(Package):
+    """cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone."""
+    homepage = "http://uscilab.github.io/cereal/"
+    url      = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz"
+
+    version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9')
+    version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27')
+    version('1.1.0', '9f2d5f72e935c54f4c6d23e954ce699f')
+    version('1.0.0', 'd1bacca70a95cec0ddbff68b0871296b')
+    version('0.9.1', '8872d4444ff274ce6cd1ed364d0fc0ad')
+
+    patch("Werror.patch")
+
+    depends_on("cmake @2.6.2:")
+
+    def install(self, spec, prefix):
+        # Don't use -Werror
+        filter_file(r'-Werror', '', 'CMakeLists.txt')
+
+        # configure
+        # Boost is only used for self-tests, which we are not running (yet?)
+        cmake('.', '-DCMAKE_DISABLE_FIND_PACKAGE_Boost=TRUE', *std_cmake_args)
+
+        # Build
+        make()
+
+        # Install
+        shutil.rmtree(join_path(prefix, 'doc'), ignore_errors=True)
+        shutil.rmtree(join_path(prefix, 'include'), ignore_errors=True)
+        shutil.copytree('doc', join_path(prefix, 'doc'), symlinks=True)
+        shutil.copytree('include', join_path(prefix, 'include'), symlinks=True)

var/spack/repos/builtin/packages/cmake/package.py

@@ -31,12 +31,12 @@ class Cmake(Package):
 
     version('2.8.10.2', '097278785da7182ec0aea8769d06860c',
             url = 'http://www.cmake.org/files/v2.8/cmake-2.8.10.2.tar.gz')
- 
+
     version('3.0.2', 'db4c687a31444a929d2fdc36c4dfb95f',
             url = 'http://www.cmake.org/files/v3.0/cmake-3.0.2.tar.gz')
- 
+
     version('3.4.0', 'cd3034e0a44256a0917e254167217fc8',
-            url = 'https://cmake.org/files/v3.4/cmake-3.4.0.tar.gz')
+            url = 'http://cmake.org/files/v3.4/cmake-3.4.0.tar.gz')
 
     variant('ncurses', default=True, description='Enables the build of the ncurses gui')
 

var/spack/repos/builtin/packages/fltk/font.patch

@@ -0,0 +1,44 @@
+Index: FL/x.H
+===================================================================
+--- a/FL/x.H	(revision 10476)
++++ b/FL/x.H	(working copy)
+@@ -132,6 +132,7 @@
+   XFontStruct *ptr;
+ };
+ extern FL_EXPORT Fl_XFont_On_Demand fl_xfont;
++extern FL_EXPORT XFontStruct* fl_core_font();
+
+ // this object contains all X-specific stuff about a window:
+ // Warning: this object is highly subject to change!
+Index: src/fl_font.cxx
+===================================================================
+--- a/src/fl_font.cxx	(revision 10476)
++++ b/src/fl_font.cxx	(working copy)
+@@ -55,6 +55,14 @@
+ #  include "fl_font_x.cxx"
+ #endif // WIN32
+
++#ifdef WIN32
++#elif defined(__APPLE__)
++#else
++XFontStruct *fl_core_font()
++{
++  return fl_xfont.value();
++}
++#endif
+
+ double fl_width(const char* c) {
+   if (c) return fl_width(c, (int) strlen(c));
+Index: src/gl_draw.cxx
+===================================================================
+--- a/src/gl_draw.cxx	(revision 10476)
++++ b/src/gl_draw.cxx	(working copy)
+@@ -84,7 +84,7 @@
+  * then sorting through them at draw time (for normal X rendering) to find which one can
+  * render the current glyph... But for now, just use the first font in the list for GL...
+  */
+-    XFontStruct *font = fl_xfont;
++    XFontStruct *font = fl_core_font();
+     int base = font->min_char_or_byte2;
+     int count = font->max_char_or_byte2-base+1;
+     fl_fontsize->listbase = glGenLists(256);

var/spack/repos/builtin/packages/fltk/package.py

@@ -0,0 +1,58 @@
+##############################################################################
+# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Fltk(Package):
+    """
+    FLTK (pronounced "fulltick") is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and
+    MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its
+    built-in GLUT emulation.
+
+    FLTK is designed to be small and modular enough to be statically linked, but works fine as a shared library. FLTK
+    also includes an excellent UI builder called FLUID that can be used to create applications in minutes.
+    """
+    homepage = 'http://www.fltk.org/'
+    url = 'http://fltk.org/pub/fltk/1.3.3/fltk-1.3.3-source.tar.gz'
+
+    version('1.3.3', '9ccdb0d19dc104b87179bd9fd10822e3')
+
+    patch('font.patch', when='@1.3.3')
+
+    variant('shared', default=True, description='Enables the build of shared libraries')
+
+    def install(self, spec, prefix):
+        options = ['--prefix=%s' % prefix,
+                   '--enable-localjpeg',
+                   '--enable-localpng',
+                   '--enable-localzlib']
+
+        if '+shared' in spec:
+            options.append('--enable-shared')
+
+        # FLTK needs to be built in-source
+        configure(*options)
+        make()
+        make('install')