Merged develop into branch

46 files changed, 1494 insertions, 329 deletions

diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py
index 001dde5329..07bb6b6b03 100644
--- a/var/spack/repos/builtin/packages/R/package.py
+++ b/var/spack/repos/builtin/packages/R/package.py
@@ -40,6 +40,7 @@ class R(Package):
 
     extendable = True
 
+    version('3.3.1', 'f50a659738b73036e2f5635adbd229c5')
     version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
     version('3.2.3', '1ba3dac113efab69e706902810cc2970')
     version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
@@ -87,6 +88,29 @@ class R(Package):
         make()
         make('install')
 
+        self.filter_compilers(spec, prefix)
+
+    def filter_compilers(self, spec, prefix):
+        """Run after install to tell the configuration files and Makefiles
+        to use the compilers that Spack built the package with.
+
+        If this isn't done, they'll have CC and CXX set to Spack's generic
+        cc and c++. We want them to be bound to whatever compiler
+        they were built with."""
+
+        etcdir = join_path(prefix, 'rlib', 'R', 'etc')
+
+        kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
+
+        filter_file(env['CC'],  self.compiler.cc,
+                    join_path(etcdir, 'Makeconf'), **kwargs)
+        filter_file(env['CXX'], self.compiler.cxx,
+                    join_path(etcdir, 'Makeconf'), **kwargs)
+        filter_file(env['F77'], self.compiler.f77,
+                    join_path(etcdir, 'Makeconf'), **kwargs)
+        filter_file(env['FC'], self.compiler.fc,
+                    join_path(etcdir, 'Makeconf'), **kwargs)
+
     # ========================================================================
     # Set up environment to make install easy for R extensions.
     # ========================================================================
diff --git a/var/spack/repos/builtin/packages/arpack-ng/make_install.patch b/var/spack/repos/builtin/packages/arpack-ng/make_install.patch
new file mode 100644
index 0000000000..ad5cffcc19
--- /dev/null
+++ b/var/spack/repos/builtin/packages/arpack-ng/make_install.patch
@@ -0,0 +1,24 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 607d221..50426c3 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -389,3 +389,19 @@ target_link_libraries(bug_1323 arpack ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES})
+ add_test(bug_1323 Tests/bug_1323)
+
+ add_dependencies(check dnsimp_test bug_1315_single bug_1315_double bug_1323)
++
++############################
++# install
++############################
++# 'make install' to the correct location
++install(TARGETS arpack
++    ARCHIVE  DESTINATION lib
++    LIBRARY  DESTINATION lib
++    RUNTIME  DESTINATION bin)
++
++if (MPI)
++  install(TARGETS parpack
++      ARCHIVE  DESTINATION lib
++      LIBRARY  DESTINATION lib
++      RUNTIME  DESTINATION bin)
++endif ()
diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index fcd5171a7d..d9021f8043 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -27,7 +27,8 @@ from spack import *
 
 class ArpackNg(Package):
     """
-    ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
+    ARPACK-NG is a collection of Fortran77 subroutines designed to solve large
+    scale eigenvalue problems.
 
     Important Features:
 
@@ -38,43 +39,76 @@ class ArpackNg(Package):
       Generalized Problems.
     * Routines for Banded Matrices - Standard or Generalized Problems.
     * Routines for The Singular Value Decomposition.
-    * Example driver routines that may be used as templates to implement numerous
-      Shift-Invert strategies for all problem types, data types and precision.
+    * Example driver routines that may be used as templates to implement
+      numerous Shift-Invert strategies for all problem types, data types and
+      precision.
 
-    This project is a joint project between Debian, Octave and Scilab in order to
-    provide a common and maintained version of arpack.
+    This project is a joint project between Debian, Octave and Scilab in order
+    to provide a common and maintained version of arpack.
 
-    Indeed, no single release has been published by Rice university for the last
-    few years and since many software (Octave, Scilab, R, Matlab...) forked it and
-    implemented their own modifications, arpack-ng aims to tackle this by providing
-    a common repository and maintained versions.
+    Indeed, no single release has been published by Rice university for the
+    last few years and since many software (Octave, Scilab, R, Matlab...)
+    forked it and implemented their own modifications, arpack-ng aims to tackle
+    this by providing a common repository and maintained versions.
 
     arpack-ng is replacing arpack almost everywhere.
     """
     homepage = 'https://github.com/opencollab/arpack-ng'
     url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz'
 
+    version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4')
     version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5')
 
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('mpi', default=False, description='Activates MPI support')
 
-    # The function pdlamch10 does not set the return variable. This is fixed upstream
+    # The function pdlamch10 does not set the return variable.
+    # This is fixed upstream
     # see https://github.com/opencollab/arpack-ng/issues/34
-    patch('pdlamch10.patch', when='@3.3:')
+    patch('pdlamch10.patch', when='@3.3.0')
+
+    patch('make_install.patch', when='@3.4.0')
+    patch('parpack_cmake.patch', when='@3.4.0')
 
     depends_on('blas')
     depends_on('lapack')
-    depends_on('automake')
-    depends_on('autoconf')
-    depends_on('libtool@2.4.2:')
+    depends_on('automake', when='@3.3.0')
+    depends_on('autoconf', when='@3.3.0')
+    depends_on('libtool@2.4.2:', when='@3.3.0')
+    depends_on('cmake@2.8.6:', when='@3.4.0:')
 
     depends_on('mpi', when='+mpi')
 
+    @when('@3.4.0:')
+    def install(self, spec, prefix):
+
+        options = ['-DEXAMPLES=ON']
+        options.extend(std_cmake_args)
+        options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
+
+        # TODO:
+        # Arpack calls directly find_package(BLAS REQUIRED) and
+        # find_package(LAPACK REQUIRED). Make sure correct Blas/Lapack are
+        # picked up.
+
+        if '+mpi' in spec:
+            options.append('-DMPI=ON')
+
+        # TODO: -DINTERFACE64=ON
+
+        if '+shared' in spec:
+            options.append('-DBUILD_SHARED_LIBS=ON')
+
+        cmake('.', *options)
+        make()
+        # TODO: make test does not work
+        # make('test')
+
+        make('install')
+
+    @when('@3.3.0')
     def install(self, spec, prefix):
         # Apparently autotools are not bootstrapped
-        # TODO: switch to use the CMake build in the next version
-        # rather than bootstrapping.
         which('libtoolize')()
         bootstrap = Executable('./bootstrap')
 
@@ -83,7 +117,7 @@ class ArpackNg(Package):
         if '+mpi' in spec:
             options.extend([
                 '--enable-mpi',
-                'F77=mpif77' #FIXME: avoid hardcoding MPI wrapper names
+                'F77=%s' % spec['mpi'].mpif77
             ])
 
         if '~shared' in spec:
diff --git a/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch
new file mode 100644
index 0000000000..9b11bea6ac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/arpack-ng/parpack_cmake.patch
@@ -0,0 +1,18 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 607d221..345b7fc 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -113,11 +113,12 @@ set_target_properties(arpack PROPERTIES OUTPUT_NAME arpack${LIBSUFFIX})
+ 
+ if (MPI)
+ #    add_library(parpack SHARED
+-    add_library(parpack 
++    add_library(parpack
+                         ${parpacksrc_STAT_SRCS}
+                         ${parpackutil_STAT_SRCS})
+ 
+     target_link_libraries(parpack ${MPI_Fortran_LIBRARIES})
++    target_link_libraries(parpack arpack)
+     set_target_properties(parpack PROPERTIES OUTPUT_NAME parpack${LIBSUFFIX})
+ endif ()
+ 
diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py
index c53c667efb..80198fa224 100644
--- a/var/spack/repos/builtin/packages/cereal/package.py
+++ b/var/spack/repos/builtin/packages/cereal/package.py
@@ -31,6 +31,7 @@ class Cereal(Package):
     homepage = "http://uscilab.github.io/cereal/"
     url      = "https://github.com/USCiLab/cereal/archive/v1.1.2.tar.gz"
 
+    version('1.2.0', 'e372c9814696481dbdb7d500e1410d2b')
     version('1.1.2', '34d4ad174acbff005c36d4d10e48cbb9')
     version('1.1.1', '0ceff308c38f37d5b5f6df3927451c27')
     version('1.1.0', '9f2d5f72e935c54f4c6d23e954ce699f')
diff --git a/var/spack/repos/builtin/packages/docbook-xml/package.py b/var/spack/repos/builtin/packages/docbook-xml/package.py
index 9c22174610..87137168f3 100644
--- a/var/spack/repos/builtin/packages/docbook-xml/package.py
+++ b/var/spack/repos/builtin/packages/docbook-xml/package.py
@@ -23,7 +23,6 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 import os
-import glob
 from spack import *
 
 
@@ -35,9 +34,10 @@ class DocbookXml(Package):
     version('4.5', '03083e288e87a7e829e437358da7ef9e')
 
     def install(self, spec, prefix):
-        cp = which('cp')
-
-        install_args = ['-a', '-t', prefix]
-        install_args.extend(glob.glob('*'))
-
-        cp(*install_args)
+        for item in os.listdir('.'):
+            src = os.path.abspath(item)
+            dst = os.path.join(prefix, item)
+            if os.path.isdir(item):
+                install_tree(src, dst, symlinks=True)
+            else:
+                install(src, dst)
diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py
new file mode 100644
index 0000000000..8e6cf429a7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ibmisc/package.py
@@ -0,0 +1,46 @@
+from spack import *
+
+class Ibmisc(CMakePackage):
+    """Misc. reusable utilities used by IceBin."""
+
+    homepage = "https://github.com/citibeth/ibmisc"
+    url      = "https://github.com/citibeth/ibmisc/tarball/123"
+
+    version('0.1.0', '12f2a32432a11db48e00217df18e59fa')
+
+    variant('everytrace', default=False, description='Report errors through Everytrace')
+    variant('proj', default=True, description='Compile utilities for PROJ.4 library')
+    variant('blitz', default=True, description='Compile utilities for Blitz library')
+    variant('netcdf', default=True, description='Compile utilities for NetCDF library')
+    variant('boost', default=True, description='Compile utilities for Boost library')
+    variant('udunits2', default=True, description='Compile utilities for UDUNITS2 library')
+    variant('googletest', default=True, description='Compile utilities for Google Test library')
+    variant('python', default=True, description='Compile utilities for use with Python/Cython')
+
+    extends('python')
+
+    depends_on('eigen')
+    depends_on('everytrace', when='+everytrace')
+    depends_on('proj', when='+proj')
+    depends_on('blitz', when='+blitz')
+    depends_on('netcdf-cxx4', when='+netcdf')
+    depends_on('udunits2', when='+udunits2')
+    depends_on('googletest', when='+googletest')
+    depends_on('py-cython', when='+python')
+    depends_on('py-numpy', when='+python')
+    depends_on('boost', when='+boost')
+
+    # Build dependencies
+    depends_on('cmake')
+    depends_on('doxygen')
+
+    def configure_args(self):
+        spec = self.spec
+        return [
+            '-DUSE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO'),
+            '-DUSE_PROJ4=%s' % ('YES' if '+proj' in spec else 'NO'),
+            '-DUSE_BLITZ=%s' % ('YES' if '+blitz' in spec else 'NO'),
+            '-DUSE_NETCDF=%s' % ('YES' if '+netcdf' in spec else 'NO'),
+            '-DUSE_BOOST=%s' % ('YES' if '+boost' in spec else 'NO'),
+            '-DUSE_UDUNITS2=%s' % ('YES' if '+udunits2' in spec else 'NO'),
+            '-DUSE_GTEST=%s' % ('YES' if '+googletest' in spec else 'NO')]
diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py
index ec3192380a..56d9fabddf 100644
--- a/var/spack/repos/builtin/packages/intel/package.py
+++ b/var/spack/repos/builtin/packages/intel/package.py
@@ -73,7 +73,7 @@ CONTINUE_WITH_OPTIONAL_ERROR=yes
 COMPONENTS=%s
 """ % (self.intel_prefix, self.global_license_file, self.intel_components))
 
-        install_script = which("install.sh")
+        install_script = Executable("./install.sh")
         install_script('--silent', silent_config_filename)
 
 
diff --git a/var/spack/repos/builtin/packages/libjson-c/package.py b/var/spack/repos/builtin/packages/libjson-c/package.py
index 75f3e130ad..662ed3cb5a 100644
--- a/var/spack/repos/builtin/packages/libjson-c/package.py
+++ b/var/spack/repos/builtin/packages/libjson-c/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 from spack import *
 
+
 class LibjsonC(Package):
     """ A JSON implementation in C """
     homepage = "https://github.com/json-c/json-c/wiki"
@@ -34,5 +35,5 @@ class LibjsonC(Package):
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
 
-        make()
+        make(parallel=False)
         make("install")
diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py
index 761932361b..48c1c6a919 100644
--- a/var/spack/repos/builtin/packages/lua/package.py
+++ b/var/spack/repos/builtin/packages/lua/package.py
@@ -140,11 +140,11 @@ class Lua(Package):
 
     @property
     def lua_lib_dir(self):
-        return os.path.join('lib', 'lua', '%d.%d' % self.version[:2])
+        return os.path.join('lib', 'lua', self.version.up_to(2))
 
     @property
     def lua_share_dir(self):
-        return os.path.join('share', 'lua', '%d.%d' % self.version[:2])
+        return os.path.join('share', 'lua', self.version.up_to(2))
 
     def setup_dependent_package(self, module, ext_spec):
         """
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
index 504efb5e35..1b4456380b 100644
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -31,11 +31,13 @@ class Mfem(Package):
     homepage = 'http://www.mfem.org'
     url      = 'https://github.com/mfem/mfem'
 
-#    version('3.1', git='https://github.com/mfem/mfem.git',
-#            commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574')
+    version('3.2', '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340',
+            url='http://goo.gl/Y9T75B', expand=False, preferred=True)
 
     version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
             url='http://goo.gl/xrScXn', expand=False)
+#    version('3.1', git='https://github.com/mfem/mfem.git',
+#            commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574')
 
     variant('metis', default=False, description='Activate support for metis')
     variant('hypre', default=False, description='Activate support for hypre')
diff --git a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch b/var/spack/repos/builtin/packages/mumps/mumps-shared.patch
deleted file mode 100644
index 592f48037c..0000000000
--- a/var/spack/repos/builtin/packages/mumps/mumps-shared.patch
+++ /dev/null
@@ -1,119 +0,0 @@
-diff -Naur MUMPS_5.0.1/libseq/Makefile MUMPS_5.0.1.new/libseq/Makefile
---- MUMPS_5.0.1/libseq/Makefile	2015-07-23 19:08:32.000000000 +0200
-+++ MUMPS_5.0.1.new/libseq/Makefile	2016-06-07 10:41:16.585179151 +0200
-@@ -8,11 +8,15 @@
- 
- include ../Makefile.inc
- 
--libmpiseq: libmpiseq$(PLAT)$(LIBEXT)
-+libmpiseq: libmpiseq$(PLAT)$(LIBEXT) libmpiseq$(PLAT)$(SHLIBEXT)
- 
- libmpiseq$(PLAT)$(LIBEXT): mpi.o mpic.o elapse.o
- 	$(AR)$@ mpi.o mpic.o elapse.o
- 	$(RANLIB) $@
-+
-+libmpiseq$(PLAT)$(SHLIBEXT): mpi.o mpic.o elapse.o
-+	$(FC) $(LDFLAGS) $^ -o libmpiseq$(PLAT)$(SHLIBEXT)
-+
- .f.o:
- 	$(FC) $(OPTF)              -c $*.f $(OUTF)$*.o
- .c.o:
-diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1.new/Makefile
---- MUMPS_5.0.1/Makefile	2015-07-23 19:08:29.000000000 +0200
-+++ MUMPS_5.0.1.new/Makefile	2016-06-07 10:50:21.863281217 +0200
-@@ -51,7 +51,7 @@
- dexamples:	d
- 	(cd examples ; $(MAKE) d)
- 
--requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT)
-+requiredobj: Makefile.inc $(LIBSEQNEEDED) $(libdir)/libpord$(PLAT)$(LIBEXT) $(libdir)/libpord$(PLAT)$(SHLIBEXT)
- 
- # dummy MPI library (sequential version)
- 
-@@ -62,16 +62,25 @@
- $(libdir)/libpord$(PLAT)$(LIBEXT):
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cd $(LPORDDIR); \
--	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
-+	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT); \
- 	fi;
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cp $(LPORDDIR)/libpord$(LIBEXT) $@; \
- 	fi;
- 
-+$(libdir)/libpord$(PLAT)$(SHLIBEXT):
-+	if [ "$(LPORDDIR)" != "" ] ; then \
-+	  cd $(LPORDDIR); \
-+	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" LDFLAGS="$(LDFLAGS)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT) PLAT=$(PLAT) SHLIBEXT=$(SHLIBEXT) libpord$(PLAT)$(SHLIBEXT); \
-+	fi;
-+	if [ "$(LPORDDIR)" != "" ] ; then \
-+	  cp $(LPORDDIR)/libpord$(PLAT)$(SHLIBEXT) $@; \
-+	fi;
-+
- clean:
- 	(cd src; $(MAKE) clean)
- 	(cd examples; $(MAKE) clean)
--	(cd $(libdir); $(RM) *$(PLAT)$(LIBEXT))
-+	(cd $(libdir); $(RM) *$(PLAT)$(LIBEXT) *$(PLAT)$(SHLIBEXT))
- 	(cd libseq; $(MAKE) clean)
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cd $(LPORDDIR); $(MAKE) realclean; \
-diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1.new/PORD/lib/Makefile
---- MUMPS_5.0.1/PORD/lib/Makefile	2015-07-23 19:08:29.000000000 +0200
-+++ MUMPS_5.0.1.new/PORD/lib/Makefile	2016-06-07 10:49:48.889000958 +0200
-@@ -13,7 +13,7 @@
- 
- OBJS = graph.o gbipart.o gbisect.o ddcreate.o ddbisect.o nestdiss.o \
-        multisector.o gelim.o bucket.o tree.o \
--       symbfac.o interface.o sort.o minpriority.o 
-+       symbfac.o interface.o sort.o minpriority.o
- 
- # Note: numfac.c read.c mapping.c triangular.c matrix.c kernel.c
- # were not direcly used by MUMPS and have been removed from the
-@@ -24,12 +24,15 @@
- .c.o:
- 	$(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o
- 
--libpord$(LIBEXT):$(OBJS)
-+libpord$(PLAT)$(LIBEXT):$(OBJS)
- 	$(AR)$@ $(OBJS)
- 	$(RANLIB) $@
- 
-+libpord$(PLAT)$(SHLIBEXT): $(OBJS)
-+	$(CC) $(LDFLAGS) $(OBJS) -o libpord$(PLAT)$(SHLIBEXT)
-+
- clean:
- 	rm -f *.o
- 
- realclean:
--	rm -f *.o libpord.a
-+	rm -f *.o libpord$(PLAT)$(SHLIBEXT) libpord$(PLAT)$(LIBEXT)
-diff -Naur MUMPS_5.0.1/src/Makefile MUMPS_5.0.1.new/src/Makefile
---- MUMPS_5.0.1/src/Makefile	2015-07-23 19:08:29.000000000 +0200
-+++ MUMPS_5.0.1.new/src/Makefile	2016-06-07 10:40:52.534703722 +0200
-@@ -24,7 +24,10 @@
- include $(topdir)/Makefile.inc
- 
- mumps_lib:    $(libdir)/libmumps_common$(PLAT)$(LIBEXT) \
--              $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT)
-+              $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT) \
-+              $(libdir)/lib$(ARITH)mumps$(PLAT)$(LIBEXT) \
-+              $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT)
-+
- 
- OBJS_COMMON_MOD = \
-         ana_omp_m.o\
-@@ -162,6 +165,13 @@
- 	$(AR)$@ $?
- 	$(RANLIB) $@
- 
-+$(libdir)/libmumps_common$(PLAT)$(SHLIBEXT):	$(OBJS_COMMON_MOD) $(OBJS_COMMON_OTHER)
-+	$(FC) $(LDFLAGS) $^ -L$(libdir) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/libmumps_common$(PLAT)$(SHLIBEXT)
-+
-+
-+$(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT):    $(OBJS_MOD) $(OBJS_OTHER)
-+	$(FC) $(LDFLAGS) $^ -L$(libdir) -lmumps_common$(PLAT) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS) -o $(libdir)/lib$(ARITH)mumps$(PLAT)$(SHLIBEXT)
-+
- # Dependencies between modules:
- $(ARITH)mumps_load.o:		$(ARITH)mumps_comm_buffer.o \
- 				$(ARITH)mumps_struc_def.o \
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index 8a90ef72d0..92c45c9b95 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -23,10 +23,7 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os
-import sys
-import subprocess
-
+import os, sys, glob
 
 class Mumps(Package):
     """MUMPS: a MUltifrontal Massively Parallel sparse direct Solver"""
@@ -47,6 +44,7 @@ class Mumps(Package):
     variant('idx64', default=False, description='Use int64_t/integer*8 as default index type')
     variant('shared', default=True, description='Build shared libraries')
 
+
     depends_on('scotch + esmumps', when='~ptscotch+scotch')
     depends_on('scotch + esmumps + mpi', when='+ptscotch')
     depends_on('metis@5:', when='+metis')
@@ -56,64 +54,49 @@ class Mumps(Package):
     depends_on('scalapack', when='+mpi')
     depends_on('mpi', when='+mpi')
 
-    patch('mumps-shared.patch', when='+shared')
-
     # this function is not a patch function because in case scalapack
     # is needed it uses self.spec['scalapack'].fc_link set by the
     # setup_dependent_environment in scalapck. This happen after patch
     # end before install
     # def patch(self):
     def write_makefile_inc(self):
-        if (('+parmetis' in self.spec or
-             '+ptscotch' in self.spec)) and '+mpi' not in self.spec:
-            raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')  # NOQA: E501
+        if ('+parmetis' in self.spec or '+ptscotch' in self.spec) and '+mpi' not in self.spec:
+            raise RuntimeError('You cannot use the variants parmetis or ptscotch without mpi')
 
-        makefile_conf = [
-            "LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib
-        ]
+        makefile_conf = ["LIBBLAS = -L%s -lblas" % self.spec['blas'].prefix.lib]
 
         orderings = ['-Dpord']
 
         if '+ptscotch' in self.spec or '+scotch' in self.spec:
             join_lib = ' -l%s' % ('pt' if '+ptscotch' in self.spec else '')
-            makefile_conf.extend([
-                "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
-                "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
-                                         join_lib,
-                                         join_lib.join(['esmumps',
-                                                        'scotch',
-                                                        'scotcherr']))
-            ])
+            makefile_conf.extend(
+                ["ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
+                 "LSCOTCH = -L%s %s%s" % (self.spec['scotch'].prefix.lib,
+                                          join_lib,
+                                          join_lib.join(['esmumps', 'scotch', 'scotcherr']))])
             orderings.append('-Dscotch')
             if '+ptscotch' in self.spec:
                 orderings.append('-Dptscotch')
 
         if '+parmetis' in self.spec and '+metis' in self.spec:
-            makefile_conf.extend([
-                "IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
-                "LMETIS = -L%s -l%s -L%s -l%s" % (
-                    self.spec['parmetis'].prefix.lib, 'parmetis',
-                    self.spec['metis'].prefix.lib, 'metis')
-            ])
+            libname = 'parmetis' if '+parmetis' in self.spec else 'metis'
+            makefile_conf.extend(
+                ["IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
+                 "LMETIS = -L%s -l%s -L%s -l%s" % (self.spec['parmetis'].prefix.lib, 'parmetis',self.spec['metis'].prefix.lib, 'metis')])
 
             orderings.append('-Dparmetis')
         elif '+metis' in self.spec:
-            makefile_conf.extend([
-                "IMETIS = -I%s" % self.spec['metis'].prefix.include,
-                "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib,
-                                        'metis')
-            ])
+            makefile_conf.extend(
+                ["IMETIS = -I%s" % self.spec['metis'].prefix.include,
+                 "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')])
 
             orderings.append('-Dmetis')
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
-        # when building shared libs need -fPIC, otherwise /usr/bin/ld:
-        # graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can
-        # not be used when making a shared object; recompile with
-        # -fPIC
+        # when building shared libs need -fPIC, otherwise
+        # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared object; recompile with -fPIC
         fpic = '-fPIC' if '+shared' in self.spec else ''
-
         # TODO: test this part, it needs a full blas, scalapack and
         # partitionning environment with 64bit integers
         if '+idx64' in self.spec:
@@ -121,7 +104,7 @@ class Mumps(Package):
                 # the fortran compilation flags most probably are
                 # working only for intel and gnu compilers this is
                 # perhaps something the compiler should provide
-                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),  # NOQA: E501
+                ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic,'-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O -DINTSIZE64' % fpic])
         else:
@@ -130,47 +113,49 @@ class Mumps(Package):
                  'OPTL    = %s -O ' % fpic,
                  'OPTC    = %s -O ' % fpic])
 
+
         if '+mpi' in self.spec:
             makefile_conf.extend(
-                ["CC = %s" % self.spec['mpi'].mpicc,
-                 "FC = %s" % self.spec['mpi'].mpifc,
+                ["CC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpicc'),
+                 "FC = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
+                 "FL = %s" % join_path(self.spec['mpi'].prefix.bin, 'mpif90'),
                  "SCALAP = %s" % self.spec['scalapack'].fc_link,
                  "MUMPS_TYPE = par"])
         else:
             makefile_conf.extend(
                 ["CC = cc",
                  "FC = fc",
+                 "FL = fc",
                  "MUMPS_TYPE = seq"])
 
         # TODO: change the value to the correct one according to the
         # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
-        makefile_conf.extend([
-            'CDEFS   = -DAdd_',
-            'FL = $(FC)',
-        ])
+        makefile_conf.append("CDEFS   = -DAdd_")
 
         if '+shared' in self.spec:
-            makefile_conf.append('SHLIBEXT = .%s' % dso_suffix)
             if sys.platform == 'darwin':
-                makefile_conf.append(
-                    'LDFLAGS = -dynamiclib -Wl,-install_name -Wl,{0}/$(notdir $@) {1}{0} -undefined dynamic_lookup'.format(prefix.lib, self.compiler.fc_rpath_arg)  # NOQA: E501
-                )
+                # Building dylibs with mpif90 causes segfaults on 10.8 and 10.10. Use gfortran. (Homebrew)
+                makefile_conf.extend([
+                    'LIBEXT=.dylib',
+                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'],prefix.lib),
+                    'RANLIB=echo'
+                ])
             else:
-                makefile_conf.append(
-                    'LDFLAGS = -shared {0}{1}'.format(
-                        self.compiler.fc_rpath_arg,
-                        prefix.lib)
-                )
-
-        makefile_conf.extend([
-            'LIBEXT  = .a',
-            'AR = ar vr ',
-            'RANLIB = ranlib'
-        ])
-
-        makefile_inc_template = \
-            join_path(os.path.dirname(self.module.__file__),
-                      'Makefile.inc')
+                makefile_conf.extend([
+                    'LIBEXT=.so',
+                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,
+                    'RANLIB=echo'
+                ])
+        else:
+            makefile_conf.extend([
+                'LIBEXT  = .a',
+                'AR = ar vr',
+                'RANLIB = ranlib'
+            ])
+
+
+        makefile_inc_template = join_path(os.path.dirname(self.module.__file__),
+                                          'Makefile.inc')
         with open(makefile_inc_template, "r") as fh:
             makefile_conf.extend(fh.read().split('\n'))
 
@@ -179,53 +164,46 @@ class Mumps(Package):
                 makefile_inc = '\n'.join(makefile_conf)
                 fh.write(makefile_inc)
 
+
+
     def install(self, spec, prefix):
         make_libs = []
 
         # the choice to compile ?examples is to have kind of a sanity
         # check on the libraries generated.
         if '+float' in spec:
-            make_libs.append('s')
+            make_libs.append('sexamples')
             if '+complex' in spec:
-                make_libs.append('c')
+                make_libs.append('cexamples')
 
         if '+double' in spec:
-            make_libs.append('d')
+            make_libs.append('dexamples')
             if '+complex' in spec:
-                make_libs.append('z')
+                make_libs.append('zexamples')
 
         self.write_makefile_inc()
 
-        make('mumps_lib', parallel=False)
-        make(*make_libs)
+        # Build fails in parallel
+        make(*make_libs, parallel=False)
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
 
-        if '~mpi' in spec:
-            install('libseq/libmpiseq.a', prefix.lib)
-            if '+shared' in spec:
-                install('libseq/libmpiseq.{0}'.format(dso_suffix), prefix.lib)
-            install('libseq/mpi.h', prefix.include)
-            install('libseq/mpif.h', prefix.include)
-
-        # FIXME: extend the tests to mpirun -np 2 (or alike) when
-        # build with MPI
-        # FIXME: use something like numdiff to compare blessed output
-        # with the current
-        # TODO: test the installed mumps and not the one in stage
-        if '~mpi' in spec:
-            for t in make_libs:
-                make('{0}examples'.format(t))
-
-            with working_dir('examples'):
-                for t in make_libs:
-                    input_file = 'input_simpletest_{0}'.format(
-                        'real' if t in ['s', 'd'] else 'cmplx')
-                    with open(input_file) as input:
-                        test = './{0}simpletest'.format(t)
-                        ret = subprocess.call(test,
-                                              stdin=input)
-                        if ret is not 0:
-                            raise RuntimeError(
-                                'The test {0} did not pass'.format(test))
+        if '~mpi' in spec:            
+            lib_dsuffix = '.dylib' if sys.platform == 'darwin' else '.so'
+            lib_suffix = lib_dsuffix if '+shared' in spec else '.a'
+            install('libseq/libmpiseq%s' % lib_suffix, prefix.lib)
+            for f in glob.glob(join_path('libseq','*.h')):
+                install(f, prefix.include)
+
+        # FIXME: extend the tests to mpirun -np 2 (or alike) when build with MPI
+        # FIXME: use something like numdiff to compare blessed output with the current
+        with working_dir('examples'):
+            if '+float' in spec:
+                os.system('./ssimpletest < input_simpletest_real')
+                if '+complex' in spec:
+                    os.system('./csimpletest < input_simpletest_real')
+            if '+double' in spec:
+                os.system('./dsimpletest < input_simpletest_real')
+                if '+complex' in spec:
+                    os.system('./zsimpletest < input_simpletest_cmplx')
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index 0f0fcfb733..06b6b7cbb0 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -23,20 +23,22 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import platform, sys
+import platform
+
 
 class Oce(Package):
-    """
-    Open CASCADE Community Edition:
-    patches/improvements/experiments contributed by users over the official Open CASCADE library.
+    """Open CASCADE Community Edition:
+    patches/improvements/experiments contributed by users over the official
+    Open CASCADE library.
     """
     homepage = "https://github.com/tpaviot/oce"
     url      = "https://github.com/tpaviot/oce/archive/OCE-0.17.tar.gz"
 
+    version('0.17.2', 'bf2226be4cd192606af677cf178088e5')
     version('0.17.1', '36c67b87093c675698b483454258af91')
-    version('0.17'  , 'f1a89395c4b0d199bea3db62b85f818d')
+    version('0.17',   'f1a89395c4b0d199bea3db62b85f818d')
     version('0.16.1', '4d591b240c9293e879f50d86a0cb2bb3')
-    version('0.16'  , '7a4b4df5a104d75a537e25e7dd387eca')
+    version('0.16',   '7a4b4df5a104d75a537e25e7dd387eca')
 
     variant('tbb', default=True, description='Build with Intel Threading Building Blocks')
 
@@ -49,8 +51,7 @@ class Oce(Package):
     # http://tracker.dev.opencascade.org/view.php?id=26042
     # https://github.com/tpaviot/oce/issues/605
     # https://github.com/tpaviot/oce/commit/61cb965b9ffeca419005bc15e635e67589c421dd.patch
-    patch('null.patch',when='@0.16:0.17.1')
-
+    patch('null.patch', when='@0.16:0.17.1')
 
     def install(self, spec, prefix):
         options = []
@@ -63,7 +64,8 @@ class Oce(Package):
             '-DOCE_DISABLE_X11:BOOL=ON',
             '-DOCE_DRAW:BOOL=OFF',
             '-DOCE_MODEL:BOOL=ON',
-            '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % ('TBB' if '+tbb' in spec else 'NONE'),
+            '-DOCE_MULTITHREAD_LIBRARY:STRING=%s' % (
+                'TBB' if '+tbb' in spec else 'NONE'),
             '-DOCE_OCAF:BOOL=ON',
             '-DOCE_USE_TCL_TEST_FRAMEWORK:BOOL=OFF',
             '-DOCE_VISUALISATION:BOOL=OFF',
@@ -77,15 +79,8 @@ class Oce(Package):
                 '-DOCE_OSX_USE_COCOA:BOOL=ON',
             ])
 
-        cmake('.', *options)
+        options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
+        cmake('.', *options)
         make("install/strip")
-
-        # OCE tests build is brocken at least on Darwin.
-        # Unit tests are linked against libTKernel.10.dylib isntead of /full/path/libTKernel.10.dylib
-        # see https://github.com/tpaviot/oce/issues/612
-        # make("test")
-
-        # The shared libraries are not installed correctly on Darwin; correct this
-        if (sys.platform == 'darwin'):
-            fix_darwin_install_name(prefix.lib)
+        make("test")
diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
index f97bfc7d12..6535f528ee 100644
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -61,7 +61,7 @@ class Octave(Package):
     variant('qrupdate',   default=False)
     variant('qscintilla', default=False)
     variant('qt',         default=False)
-    variant('suiteparse', default=False)
+    variant('suitesparse', default=False)
     variant('zlib',       default=False)
 
     # Required dependencies
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 377bffe723..e7c105d5f5 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -35,7 +35,7 @@ class Openssl(Package):
        Transport Layer Security (TLS v1) protocols as well as a
        full-strength general purpose cryptography library."""
     homepage = "http://www.openssl.org"
-    url      = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz"
+    url = "https://www.openssl.org/source/openssl-1.0.1h.tar.gz"
 
     version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
     version('1.0.1r', '1abd905e079542ccae948af37e393d28')
@@ -50,21 +50,25 @@ class Openssl(Package):
     parallel = False
 
     def url_for_version(self, version):
-        # This URL is computed pinging the place where the latest version is stored. To avoid slowdown
-        # due to repeated pinging, we store the URL in a private class attribute to do the job only once per version
+        # This URL is computed pinging the place where the latest version is
+        # stored. To avoid slowdown due to repeated pinging, we store the URL
+        # in a private class attribute to do the job only once per version
         openssl_urls = getattr(Openssl, '_openssl_url', {})
         openssl_url = openssl_urls.get(version, None)
         # Same idea, but just to avoid issuing the same message multiple times
         warnings_given_to_user = getattr(Openssl, '_warnings_given', {})
         if openssl_url is None:
-            if self.spec.satisfies('@external'):
-                # The version @external is reserved to system openssl. In that case return a fake url and exit
-                openssl_url = '@external (reserved version for system openssl)'
+            if self.spec.satisfies('@system'):
+                # The version @system is reserved to system openssl. In that
+                # case return a fake url and exit
+                openssl_url = '@system (reserved version for system openssl)'
                 if not warnings_given_to_user.get(version, False):
-                    tty.msg('Using openssl@external : the version @external is reserved for system openssl')
+                    tty.msg('Using openssl@system: '
+                            'the version @system is reserved for system openssl')
                     warnings_given_to_user[version] = True
             else:
-                openssl_url = self.check_for_outdated_release(version, warnings_given_to_user)  # Store the computed URL
+                openssl_url = self.check_for_outdated_release(
+                    version, warnings_given_to_user)  # Store the computed URL
             openssl_urls[version] = openssl_url
             # Store the updated dictionary of URLS
             Openssl._openssl_url = openssl_urls
@@ -75,45 +79,55 @@ class Openssl(Package):
 
     def check_for_outdated_release(self, version, warnings_given_to_user):
         latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz'
-        older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz'
-        # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then
-        # return the url for older format
+        older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz'  # NOQA: ignore=E501
+        # Try to use the url where the latest tarballs are stored.
+        # If the url does not exist (404), then return the url for
+        # older format
         version_number = '.'.join([str(x) for x in version[:-1]])
         try:
             openssl_url = latest.format(version=version)
             urllib.urlopen(openssl_url)
         except IOError:
-            openssl_url = older.format(version_number=version_number, version_full=version)
-            # Checks if we already warned the user for this particular version of OpenSSL.
-            # If not we display a warning message and mark this version
+            openssl_url = older.format(
+                version_number=version_number, version_full=version)
+            # Checks if we already warned the user for this particular
+            # version of OpenSSL. If not we display a warning message
+            # and mark this version
             if not warnings_given_to_user.get(version, False):
                 tty.warn(
-                    'This installation depends on an old version of OpenSSL, which may have known security issues. ')
-                tty.warn('Consider updating to the latest version of this package.')
-                tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage))
+                    'This installation depends on an old version of OpenSSL, '
+                    'which may have known security issues. ')
+                tty.warn(
+                    'Consider updating to the latest version of this package.')
+                tty.warn('More details at {homepage}'.format(
+                    homepage=Openssl.homepage))
                 warnings_given_to_user[version] = True
 
         return openssl_url
 
+
     def install(self, spec, prefix):
         # OpenSSL uses a variable APPS in its Makefile. If it happens to be set
         # in the environment, then this will override what is set in the
         # Makefile, leading to build errors.
         env.pop('APPS', None)
-        if spec.satisfies("target=x86_64") or spec.satisfies("target=ppc64"):
+
+        if spec.satisfies('target=x86_64') or spec.satisfies('target=ppc64'):
             # This needs to be done for all 64-bit architectures (except Linux,
             # where it happens automatically?)
             env['KERNEL_BITS'] = '64'
-        config = Executable("./config")
-        config("--prefix=%s" % prefix,
-               "--openssldir=%s" % join_path(prefix, 'etc', 'openssl'),
-               "zlib",
-               "no-krb5",
-               "shared")
+
+        options = ['zlib', 'no-krb5', 'shared']
+
+        config = Executable('./config')
+        config('--prefix=%s' % prefix,
+               '--openssldir=%s' % join_path(prefix, 'etc', 'openssl'),
+               *options)
+
         # Remove non-standard compiler options if present. These options are
         # present e.g. on Darwin. They are non-standard, i.e. most compilers
         # (e.g. gcc) will not accept them.
         filter_file(r'-arch x86_64', '', 'Makefile')
 
         make()
-        make("install")
+        make('install')
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 6a7bee9788..11f5c36c22 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -149,20 +149,22 @@ class Petsc(Package):
         make("install")
 
         # solve Poisson equation in 2D to make sure nothing is broken:
-        with working_dir('src/ksp/ksp/examples/tutorials'):
-            cc = os.environ['CC'] if '~mpi' in self.spec else self.spec['mpi'].mpicc  # NOQA: ignore=E501
-            os.system('%s ex50.c -I%s -L%s -lpetsc -o ex50' % (
-                cc, prefix.include, prefix.lib))
-            ex50 = Executable('./ex50')
-            ex50('-da_grid_x', '4', '-da_grid_y', '4')
-            if 'superlu-dist' in spec:
-                ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist')  # NOQA: ignore=E501
-
-            if 'mumps' in spec:
-                ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps')  # NOQA: ignore=E501
-
-            if 'hypre' in spec:
-                ex50('-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg')  # NOQA: ignore=E501
+        if ('mpi' in spec) and self.run_tests:
+            with working_dir('src/ksp/ksp/examples/tutorials'):
+                env['PETSC_DIR'] = self.prefix
+                cc = Executable(spec['mpi'].mpicc)
+                cc('ex50.c', '-I%s' % prefix.include, '-L%s' % prefix.lib,
+                   '-lpetsc', '-lm', '-o', 'ex50')
+                run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun'))
+                run('ex50', '-da_grid_x', '4', '-da_grid_y', '4')
+                if 'superlu-dist' in spec:
+                    run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'superlu_dist')  # NOQA: ignore=E501
+
+                if 'mumps' in spec:
+                    run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'lu', '-pc_factor_mat_solver_package', 'mumps')  # NOQA: ignore=E501
+
+                if 'hypre' in spec:
+                    run('ex50', '-da_grid_x', '4', '-da_grid_y', '4', '-pc_type', 'hypre', '-pc_hypre_type', 'boomeramg')  # NOQA: ignore=E501
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # set up PETSC_DIR for everyone using PETSc package
diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py
index 0180b658f5..67461babe7 100644
--- a/var/spack/repos/builtin/packages/py-h5py/package.py
+++ b/var/spack/repos/builtin/packages/py-h5py/package.py
@@ -43,8 +43,8 @@ class PyH5py(Package):
     # Build dependencies
     depends_on('py-cython@0.19:')
     depends_on('pkg-config')
-    depends_on('hdf5@1.8.4:+mpi', when='+mpi')
-    depends_on('hdf5@1.8.4:~mpi', when='~mpi')
+    depends_on('hdf5@1.8.4:')
+    depends_on('hdf5+mpi', when='+mpi')
     depends_on('mpi', when='+mpi')
 
     # Build and runtime dependencies
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 8033c52b91..d019133585 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -47,6 +47,8 @@ class Python(Package):
 
     extendable = True
 
+    variant('ucs4', default=False, description='Enable UCS4 unicode strings')
+
     depends_on("openssl")
     depends_on("bzip2")
     depends_on("readline")
@@ -82,6 +84,9 @@ class Python(Package):
             "LDFLAGS=-L{0}".format(ldflags)
         ]
 
+        if '+ucs4' in spec:
+            config_args.append('--enable-unicode=ucs4')
+
         if spec.satisfies('@3:'):
             config_args.append('--without-ensurepip')
 
diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py
new file mode 100644
index 0000000000..a0f30b779f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bh/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RBh(Package):
+    """Boost provides free peer-reviewed portable C++ source libraries. A large
+    part of Boost is provided as C++ template code which is resolved entirely
+    at compile-time without linking. This package aims to provide the most
+    useful subset of Boost libraries for template use among CRAN package. By
+    placing these libraries in this package, we offer a more efficient
+    distribution system for CRAN as replication of this code in the sources of
+    other packages is avoided. As of release 1.60.0-2, the following Boost
+    libraries are included: 'algorithm' 'any' 'bimap' 'bind' 'circular_buffer'
+    'concept' 'config' 'container' 'date'_'time' 'detail' 'dynamic_bitset'
+    'exception' 'filesystem' 'flyweight' 'foreach' 'functional' 'fusion'
+    'geometry' 'graph' 'heap' 'icl' 'integer' 'interprocess' 'intrusive' 'io'
+    'iostreams' 'iterator' 'math' 'move' 'mpl' 'multiprcecision' 'numeric'
+    'pending' 'phoenix' 'preprocessor' 'random' 'range' 'smart_ptr' 'spirit'
+    'tuple' 'type_trains' 'typeof' 'unordered' 'utility' 'uuid'."""
+
+    homepage = "https://cran.r-project.org/web/packages/BH/index.html"
+    url      = "https://cran.r-project.org/src/contrib/BH_1.60.0-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/BH"
+
+    version('1.60.0-2', 'b50fdc85285da05add4e9da664a2d551')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py
new file mode 100644
index 0000000000..a7622cad95
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-colorspace/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RColorspace(Package):
+    """Carries out mapping between assorted color spaces including RGB, HSV,
+    HLS, CIEXYZ, CIELUV, HCL (polar CIELUV), CIELAB and polar CIELAB.
+    Qualitative, sequential, and diverging color palettes based on HCL colors
+    are provided."""
+
+    homepage = "https://cran.r-project.org/web/packages/colorspace/index.html"
+    url      = "https://cran.r-project.org/src/contrib/colorspace_1.2-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/colorspace"
+
+    version('1.2-6', 'a30191e9caf66f77ff4e99c062e9dce1')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py
new file mode 100644
index 0000000000..663e5295af
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dichromat/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RDichromat(Package):
+    """Collapse red-green or green-blue distinctions to simulate the effects of
+    different types of color-blindness."""
+
+    homepage = "https://cran.r-project.org/web/packages/dichromat/index.html"
+    url      = "https://cran.r-project.org/src/contrib/dichromat_2.0-0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/dichromat"
+
+    version('2.0-0', '84e194ac95a69763d740947a7ee346a6')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py
new file mode 100644
index 0000000000..2d1f53af26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py
@@ -0,0 +1,54 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RGgplot2(Package):
+    """An implementation of the grammar of graphics in R. It combines the
+    advantages of both base and lattice graphics: conditioning and shared axes
+    are handled automatically, and you can still build up a plot step by step
+    from multiple data sources. It also implements a sophisticated
+    multidimensional conditioning system and a consistent interface to map data
+    to aesthetic attributes. See http://ggplot2.org for more information,
+    documentation and examples."""
+
+    homepage = "http://ggplot2.org/"
+    url      = "https://cran.r-project.org/src/contrib/ggplot2_2.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ggplot2"
+
+    version('2.1.0', '771928cfb97c649c720423deb3ec7fd3')
+
+    extends('R')
+
+    depends_on('r-digest')
+    depends_on('r-gtable')
+    depends_on('r-mass')
+    depends_on('r-plyr')
+    depends_on('r-reshape2')
+    depends_on('r-scales')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py
new file mode 100644
index 0000000000..d215d10678
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gridextra/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RGridextra(Package):
+    """Provides a number of user-level functions to work with "grid" graphics,
+    notably to arrange multiple grid-based plots on a page, and draw tables."""
+
+    homepage = "https://github.com/baptiste/gridextra"
+    url      = "https://cran.r-project.org/src/contrib/gridExtra_2.2.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gridExtra"
+
+    version('2.2.1', '7076c2122d387c7ef3add69a1c4fc1b2')
+
+    extends('R')
+
+    depends_on('r-gtable')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py
new file mode 100644
index 0000000000..74dee0b3d5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gtable/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RGtable(Package):
+    """Tools to make it easier to work with "tables" of 'grobs'."""
+
+    homepage = "https://cran.r-project.org/web/packages/gtable/index.html"
+    url      = "https://cran.r-project.org/src/contrib/gtable_0.2.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gtable"
+
+    version('0.2.0', '124090ae40b2dd3170ae11180e0d4cab')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py
new file mode 100644
index 0000000000..35eb8ca76f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-inline/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RInline(Package):
+    """Functionality to dynamically define R functions and S4 methods with
+    inlined C, C++ or Fortran code supporting .C and .Call calling
+    conventions."""
+
+    homepage = "https://cran.r-project.org/web/packages/inline/index.html"
+    url      = "https://cran.r-project.org/src/contrib/inline_0.3.14.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/inline"
+
+    version('0.3.14', '9fe304a6ebf0e3889c4c6a7ad1c50bca')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py
new file mode 100644
index 0000000000..02e5da9d85
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-labeling/package.py
@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RLabeling(Package):
+    """Provides a range of axis labeling algorithms."""
+
+    homepage = "https://cran.r-project.org/web/packages/labeling/index.html"
+    url      = "https://cran.r-project.org/src/contrib/labeling_0.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/labeling"
+
+    version('0.3', 'ccd7082ec0b211aba8a89d85176bb534')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py
new file mode 100644
index 0000000000..ba29feefc4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lattice/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RLattice(Package):
+    """A powerful and elegant high-level data visualization system inspired by
+    Trellis graphics, with an emphasis on multivariate data. Lattice is
+    sufficient for typical graphics needs, and is also flexible enough to
+    handle most nonstandard requirements. See ?Lattice for an introduction."""
+
+    homepage = "http://lattice.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/lattice_0.20-33.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lattice"
+
+    version('0.20-33', 'd487c94db1bfe00a27270f4c71baf53e')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py
new file mode 100644
index 0000000000..11476c3d1e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-magrittr/package.py
@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RMagrittr(Package):
+    """Provides a mechanism for chaining commands with a new forward-pipe
+    operator, %>%. This operator will forward a value, or the result of an
+    expression, into the next function call/expression. There is flexible
+    support for the type of right-hand side expressions. For more information,
+    see package vignette."""
+
+    homepage = "https://cran.r-project.org/web/packages/magrittr/index.html"
+    url      = "https://cran.r-project.org/src/contrib/magrittr_1.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/magrittr"
+
+    version('1.5', 'e74ab7329f2b9833f0c3c1216f86d65a')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py
new file mode 100644
index 0000000000..1ab01d2256
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mass/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RMass(Package):
+    """Functions and datasets to support Venables and Ripley, "Modern Applied
+    Statistics with S" (4th edition, 2002)."""
+
+    homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
+    url      = "https://cran.r-project.org/src/contrib/MASS_7.3-45.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/MASS"
+
+    version('7.3-45', 'aba3d12fab30f1793bee168a1efea88b')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py
new file mode 100644
index 0000000000..fbd8a7b4df
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-matrix/package.py
@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RMatrix(Package):
+    """Classes and methods for dense and sparse matrices and operations on them
+    using 'LAPACK' and 'SuiteSparse'."""
+
+    homepage = "http://matrix.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/Matrix_1.2-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix"
+
+    version('1.2-6', 'f545307fb1284861e9266c4e9712c55e')
+
+    extends('R')
+
+    depends_on('r-lattice')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py
new file mode 100644
index 0000000000..3216c95e00
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-munsell/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RMunsell(Package):
+    """Provides easy access to, and manipulation of, the Munsell colours.
+    Provides a mapping between Munsell's original notation (e.g. "5R 5/10") and
+    hexadecimal strings suitable for use directly in R graphics. Also provides
+    utilities to explore slices through the Munsell colour tree, to transform
+    Munsell colours and display colour palettes."""
+
+    homepage = "https://cran.r-project.org/web/packages/munsell/index.html"
+    url      = "https://cran.r-project.org/src/contrib/munsell_0.4.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/munsell"
+
+    version('0.4.3', 'ebd205323dc37c948f499ee08be9c476')
+
+    extends('R')
+
+    depends_on('r-colorspace')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py
new file mode 100644
index 0000000000..192e7e8b18
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-plyr/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RPlyr(Package):
+    """A set of tools that solves a common set of problems: you need to break a
+    big problem down into manageable pieces, operate on each piece and then put
+    all the pieces back together. For example, you might want to fit a model to
+    each spatial location or time point in your study, summarise data by panels
+    or collapse high-dimensional arrays to simpler summary statistics. The
+    development of 'plyr' has been generously supported by 'Becton
+    Dickinson'."""
+
+    homepage = "http://had.co.nz/plyr"
+    url      = "https://cran.r-project.org/src/contrib/plyr_1.8.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/plyr"
+
+    version('1.8.4', 'ef455cf7fc06e34837692156b7b2587b')
+
+    extends('R')
+
+    depends_on('r-rcpp')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
new file mode 100644
index 0000000000..b81ec2561c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RRcolorbrewer(Package):
+    """Provides color schemes for maps (and other graphics) designed by Cynthia
+    Brewer as described at http://colorbrewer2.org"""
+
+    homepage = "http://colorbrewer2.org"
+    url      = "https://cran.r-project.org/src/contrib/RColorBrewer_1.1-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RColorBrewer"
+
+    version('1.1-2', '66054d83eade4dff8a43ad4732691182')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py
new file mode 100644
index 0000000000..2428f4af3b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcpp/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RRcpp(Package):
+    """The 'Rcpp' package provides R functions as well as C++ classes which
+    offer a seamless integration of R and C++. Many R data types and objects
+    can be mapped back and forth to C++ equivalents which facilitates both
+    writing of new code as well as easier integration of third-party libraries.
+    Documentation about 'Rcpp' is provided by several vignettes included in
+    this package, via the 'Rcpp Gallery' site at <http://gallery.rcpp.org>, the
+    paper by Eddelbuettel and Francois (2011, JSS), and the book by
+    Eddelbuettel (2013, Springer); see 'citation("Rcpp")' for details on these
+    last two."""
+
+    homepage = "http://dirk.eddelbuettel.com/code/rcpp.html"
+    url      = "https://cran.r-project.org/src/contrib/Rcpp_0.12.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp"
+
+    version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
new file mode 100644
index 0000000000..3175628a73
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
@@ -0,0 +1,56 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RRcppeigen(Package):
+    """R and 'Eigen' integration using 'Rcpp'. 'Eigen' is a C++ template
+    library for linear algebra: matrices, vectors, numerical solvers and
+    related algorithms. It supports dense and sparse matrices on integer,
+    floating point and complex numbers, decompositions of such matrices, and
+    solutions of linear systems. Its performance on many algorithms is
+    comparable with some of the best implementations based on 'Lapack' and
+    level-3 'BLAS'. The 'RcppEigen' package includes the header files from the
+    'Eigen' C++ template library (currently version 3.2.8). Thus users do not
+    need to install 'Eigen' itself in order to use 'RcppEigen'. Since version
+    3.1.1, 'Eigen' is licensed under the Mozilla Public License (version 2);
+    earlier version were licensed under the GNU LGPL version 3 or later.
+    'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under the
+    GNU GPL version 2 or later, as is the rest of 'Rcpp'."""
+
+    homepage = "http://eigen.tuxfamily.org/"
+    url      = "https://cran.r-project.org/src/contrib/RcppEigen_0.3.2.8.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RcppEigen"
+
+    version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f')
+
+    extends('R')
+
+    depends_on('r-matrix')
+    depends_on('r-rcpp')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py
new file mode 100644
index 0000000000..a96a314008
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-reshape2/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RReshape2(Package):
+    """Flexibly restructure and aggregate data using just two functions: melt
+    and dcast (or acast)."""
+
+    homepage = "https://github.com/hadley/reshape"
+    url      = "https://cran.r-project.org/src/contrib/reshape2_1.4.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/reshape2"
+
+    version('1.4.1', '41e9dffdf5c6fa830321ac9c8ebffe00')
+
+    extends('R')
+
+    depends_on('r-plyr')
+    depends_on('r-stringr')
+    depends_on('r-rcpp')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py
new file mode 100644
index 0000000000..00fd5116d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rstan/package.py
@@ -0,0 +1,57 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RRstan(Package):
+    """User-facing R functions are provided to parse, compile, test, estimate,
+    and analyze Stan models by accessing the header-only Stan library provided
+    by the 'StanHeaders' package. The Stan project develops a probabilistic
+    programming language that implements full Bayesian statistical inference
+    via Markov Chain Monte Carlo, rough Bayesian inference via variational
+    approximation, and (optionally penalized) maximum likelihood estimation via
+    optimization. In all three cases, automatic differentiation is used to
+    quickly and accurately evaluate gradients without burdening the user with
+    the need to derive the partial derivatives."""
+
+    homepage = "http://mc-stan.org/"
+    url      = "https://cran.r-project.org/src/contrib/rstan_2.10.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rstan"
+
+    version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a')
+
+    extends('R')
+
+    depends_on('r-ggplot2')
+    depends_on('r-stanheaders')
+    depends_on('r-inline')
+    depends_on('r-gridextra')
+    depends_on('r-rcpp')
+    depends_on('r-rcppeigen')
+    depends_on('r-bh')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py
new file mode 100644
index 0000000000..046a05d48e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-scales/package.py
@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RScales(Package):
+    """Graphical scales map data to aesthetics, and provide methods for
+    automatically determining breaks and labels for axes and legends."""
+
+    homepage = "https://github.com/hadley/scales"
+    url      = "https://cran.r-project.org/src/contrib/scales_0.4.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/scales"
+
+    version('0.4.0', '7b5602d9c55595901192248bca25c099')
+
+    extends('R')
+
+    depends_on('r-rcolorbrewer')
+    depends_on('r-dichromat')
+    depends_on('r-plyr')
+    depends_on('r-munsell')
+    depends_on('r-labeling')
+    depends_on('r-rcpp')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py
new file mode 100644
index 0000000000..c77b5aa8b6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RStanheaders(Package):
+    """The C++ header files of the Stan project are provided by this package,
+    but it contains no R code, vignettes, or function documentation. There is a
+    shared object containing part of the CVODES library, but it is not
+    accessible from R. StanHeaders is only useful for developers who want to
+    utilize the LinkingTo directive of their package's DESCRIPTION file to
+    build on the Stan library without incurring unnecessary dependencies. The
+    Stan project develops a probabilistic programming language that implements
+    full or approximate Bayesian statistical inference via Markov Chain Monte
+    Carlo or variational methods and implements (optionally penalized) maximum
+    likelihood estimation via optimization. The Stan library includes an
+    advanced automatic differentiation scheme, templated statistical and linear
+    algebra functions that can handle the automatically differentiable scalar
+    types (and doubles, ints, etc.), and a parser for the Stan language. The
+    'rstan' package provides user-facing R functions to parse, compile, test,
+    estimate, and analyze Stan models."""
+
+    homepage = "http://mc-stan.org/"
+    url      = "https://cran.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/StanHeaders"
+
+    version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py
new file mode 100644
index 0000000000..22774dedec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-stringi/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RStringi(Package):
+    """Allows for fast, correct, consistent, portable, as well as convenient
+    character string/text processing in every locale and any native encoding.
+    Owing to the use of the ICU library, the package provides R users with
+    platform-independent functions known to Java, Perl, Python, PHP, and Ruby
+    programmers. Among available features there are: pattern searching (e.g.,
+    with ICU Java-like regular expressions or the Unicode Collation Algorithm),
+    random string generation, case mapping, string transliteration,
+    concatenation, Unicode normalization, date-time formatting and parsing,
+    etc."""
+
+    homepage = "http://www.gagolewski.com/software/stringi/"
+    url      = "https://cran.r-project.org/src/contrib/stringi_1.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/stringi"
+
+    version('1.1.1', '32b919ee3fa8474530c4942962a6d8d9')
+
+    extends('R')
+
+    depends_on('icu')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py
new file mode 100644
index 0000000000..01fd969522
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-stringr/package.py
@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created 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 Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, 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 Lesser 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 RStringr(Package):
+    """A consistent, simple and easy to use set of wrappers around the
+    fantastic 'stringi' package. All function and argument names (and
+    positions) are consistent, all functions deal with "NA"'s and zero length
+    vectors in the same way, and the output from one function is easy to feed
+    into the input of another."""
+
+    homepage = "https://cran.r-project.org/web/packages/stringr/index.html"
+    url      = "https://cran.r-project.org/src/contrib/stringr_1.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/stringr"
+
+    version('1.0.0', '5ca977c90351f78b1b888b379114a7b4')
+
+    extends('R')
+
+    depends_on('r-stringi')
+    depends_on('r-magrittr')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index dd71913fc9..8dc314c171 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -35,9 +35,20 @@ class Ruby(Package):
     extendable = True
 
     version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852')
+    depends_on('libffi')
+    depends_on('zlib')
+    variant('openssl', default=False, description="Enable OpenSSL support")
+    depends_on('openssl', when='+openssl')
+    variant('readline', default=False, description="Enable Readline support")
+    depends_on('readline', when='+readline')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        options = ["--prefix=%s" % prefix]
+        if '+openssl' in spec:
+            options.append("--with-openssl-dir=%s" % spec['openssl'].prefix)
+        if '+readline' in spec:
+            options.append("--with-readline-dir=%s" % spec['readline'].prefix)
+        configure(*options)
         make()
         make("install")
 
diff --git a/var/spack/repos/builtin/packages/slepc/install_name_371.patch b/var/spack/repos/builtin/packages/slepc/install_name_371.patch
new file mode 100644
index 0000000000..d02ca88657
--- /dev/null
+++ b/var/spack/repos/builtin/packages/slepc/install_name_371.patch
@@ -0,0 +1,32 @@
+From 7489a3f3d569e2fbf5513ac9dcd769017d9f7eb7 Mon Sep 17 00:00:00 2001
+From: Lisandro Dalcin <dalcinl@gmail.com>
+Date: Thu, 2 Jun 2016 21:57:38 +0300
+Subject: [PATCH] OS X: Fix library path in invocation of install_name_tool
+
+---
+ config/install.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/config/install.py b/config/install.py
+index 09acd03..6ce98ae 100755
+--- a/config/install.py
++++ b/config/install.py
+@@ -25,6 +25,7 @@ class Installer:
+ 
+   def setupDirectories(self):
+     self.installDir        = self.destDir
++    self.archDir           = os.path.join(self.rootDir, self.arch)
+     self.rootIncludeDir    = os.path.join(self.rootDir, 'include')
+     self.archIncludeDir    = os.path.join(self.rootDir, self.arch, 'include')
+     self.rootConfDir       = os.path.join(self.rootDir, 'lib','slepc','conf')
+@@ -220,7 +221,7 @@ for dir in dirs:
+     if os.path.splitext(dst)[1] == '.dylib' and os.path.isfile('/usr/bin/install_name_tool'):
+       (result, output) = commands.getstatusoutput('otool -D '+src)
+       oldname = output[output.find("\n")+1:]
+-      installName = oldname.replace(self.destDir, self.installDir)
++      installName = oldname.replace(self.archDir, self.installDir)
+       (result, output) = commands.getstatusoutput('/usr/bin/install_name_tool -id ' + installName + ' ' + dst)
+     # preserve the original timestamps - so that the .a vs .so time order is preserved
+     shutil.copystat(src,dst)
+-- 
+2.7.4.1.g5468f9e
diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
index d3739bf6a6..fd6c42d9fc 100644
--- a/var/spack/repos/builtin/packages/slepc/package.py
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -28,7 +28,7 @@ from spack import *
 
 class Slepc(Package):
     """
-    Scalable Library for Eigenvalue Computations.
+    Scalable Library for Eigenvalue Problem Computations.
     """
 
     homepage = "http://www.grycap.upv.es/slepc"
@@ -45,9 +45,13 @@ class Slepc(Package):
     depends_on('arpack-ng~mpi', when='+arpack^petsc~mpi')
     depends_on('arpack-ng+mpi', when='+arpack^petsc+mpi')
 
+    patch('install_name_371.patch', when='@3.7.1')
+
     def install(self, spec, prefix):
         # set SLEPC_DIR for installation
-        os.environ['SLEPC_DIR'] = self.stage.source_path
+        # Note that one should set the current (temporary) directory instead
+        # its symlink in spack/stage/ !
+        os.environ['SLEPC_DIR'] = os.getcwd()
 
         options = []
 
@@ -67,9 +71,10 @@ class Slepc(Package):
         configure('--prefix=%s' % prefix, *options)
 
         make('MAKE_NP=%s' % make_jobs, parallel=False)
-        # FIXME:
-        # make('test')
-        make('install')
+        if self.run_tests:
+            make('test', parallel=False)
+
+        make('install', parallel=False)
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # set up SLEPC_DIR for everyone using SLEPc package
diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index dd0dfa3e23..2cc89b843f 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -33,6 +33,7 @@ class SuiteSparse(Package):
     url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz'
 
     version('4.5.1', 'f0ea9aad8d2d1ffec66a5b6bfeff5319')
+    version('4.5.3', '8ec57324585df3c6483ad7f556afccbd')
 
     # FIXME: (see below)
     # variant('tbb', default=True, description='Build with Intel TBB')
@@ -40,34 +41,35 @@ class SuiteSparse(Package):
     depends_on('blas')
     depends_on('lapack')
 
-    depends_on('metis@5.1.0', when='@4.5.1')
+    depends_on('metis@5.1.0', when='@4.5.1:')
     # FIXME:
-    # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng flags
-    # does not seem to be used, which leads to linking errors on Linux.
+    # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng
+    # flags does not seem to be used, which leads to linking errors on Linux.
     # Try re-enabling in future versions.
     # depends_on('tbb', when='+tbb')
 
     def install(self, spec, prefix):
-        # The build system of SuiteSparse is quite old-fashioned
-        # It's basically a plain Makefile which include an header (SuiteSparse_config/SuiteSparse_config.mk)
-        # with a lot of convoluted logic in it.
-        # Any kind of customization will need to go through filtering of that file
+        # The build system of SuiteSparse is quite old-fashioned.
+        # It's basically a plain Makefile which include an header
+        # (SuiteSparse_config/SuiteSparse_config.mk)with a lot of convoluted
+        # logic in it. Any kind of customization will need to go through
+        # filtering of that file
 
         make_args = ['INSTALL=%s' % prefix]
 
         # inject Spack compiler wrappers
         make_args.extend([
-             'AUTOCC=no',
-             'CC=cc',
-             'CXX=c++',
-             'F77=f77',
+            'AUTOCC=no',
+            'CC=cc',
+            'CXX=c++',
+            'F77=f77',
         ])
 
         # use Spack's metis in CHOLMOD/Partition module,
         # otherwise internal Metis will be compiled
         make_args.extend([
-             'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib,
-             'MY_METIS_INC=%s' % spec['metis'].prefix.include,
+            'MY_METIS_LIB=-L%s -lmetis' % spec['metis'].prefix.lib,
+            'MY_METIS_INC=%s' % spec['metis'].prefix.include,
         ])
 
         # Intel TBB in SuiteSparseQR
@@ -78,10 +80,13 @@ class SuiteSparse(Package):
             ])
 
         # BLAS arguments require path to libraries
-        # FIXME : (blas / lapack always provide libblas and liblapack as aliases)
-        make_args.extend([
-            'BLAS=-lblas',
-            'LAPACK=-llapack'
-        ])
+        # FIXME: (blas/lapack always provide libblas and liblapack as aliases)
+        if '@4.5.1' in spec:
+            # adding -lstdc++ is clearly an ugly way to do this, but it follows
+            # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk
+            make_args.extend([
+                'BLAS=-lblas -lstdc++',
+                'LAPACK=-llapack'
+            ])
 
         make('install', *make_args)