Fix deleting by r-rmpfr

var/spack/repos/builtin/packages/magics/no_hardcoded_python.patch

@@ -1,5 +0,0 @@
---- a/tools/xml2mv.py	2016-06-27 17:49:27.000000000 +0200
-+++ a/tools/xml2mv.py	2016-09-13 16:25:17.246960456 +0200
-@@ -1 +1 @@
--#!/usr/bin/python
-+#!/usr/bin/env python

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

@@ -41,10 +41,6 @@ class Magics(Package):
     version('2.29.4', '91c561f413316fb665b3bb563f3878d1')
     version('2.29.0', 'db20a4d3c51a2da5657c31ae3de59709', preferred=True)
 
-    # The patch changes the hardcoded path to python in shebang to enable the
-    # usage of the first python installation that appears in $PATH
-    patch('no_hardcoded_python.patch', when='@:2.29.6')
-
     # The patch reorders includes and adds namespaces where necessary to
     # resolve ambiguity of invocations of isnan and isinf functions. The
     # patch is not needed since the version 2.29.1
@@ -55,6 +51,7 @@ class Magics(Package):
     variant('cairo', default=True, description='Enable cairo support[png/jpeg]')
     variant('metview', default=False, description='Enable metview support')
     variant('qt', default=False, description='Enable metview support with qt')
+    variant('eccodes', default=False, description='Use eccodes instead of grib-api')
 
     depends_on('cmake', type='build')
     depends_on('pkg-config', type='build')
@@ -64,8 +61,8 @@ class Magics(Package):
     depends_on('python', type='build')
     depends_on('perl', type='build')
     depends_on('perl-xml-parser', type='build')
-    depends_on('eccodes', when='@2.30.0:')
+    depends_on('eccodes', when='+eccodes')
-    depends_on('grib-api', when='@:2.29.6')
+    depends_on('grib-api', when='~eccodes')
     depends_on('proj')
     depends_on('boost')
     depends_on('expat')
@@ -74,9 +71,14 @@ class Magics(Package):
     depends_on('libemos', when='+bufr')
     depends_on('qt', when='+metview+qt')
 
+    conflicts('+eccodes', when='@:2.29.0')
+
+    # Replace system python and perl by spack versions:
     def patch(self):
         for plfile in glob.glob('*/*.pl'):
             filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', plfile)
+        for pyfile in glob.glob('*/*.py'):
+            filter_file('#!/usr/bin/python', '#!/usr/bin/env python', pyfile)
 
     def install(self, spec, prefix):
         options = []
@@ -87,11 +89,6 @@ def install(self, spec, prefix):
         options.append('-DPROJ4_PATH=%s' % spec['proj'].prefix)
         options.append('-DENABLE_TESTS=OFF')
 
-        if self.version >= Version('2.30.0'):
-            options.append('-DECCODES_PATH=%s' % spec['eccodes'].prefix)
-        else:
-            options.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
-
         if '+bufr' in spec:
             options.append('-DENABLE_BUFR=ON')
             options.append('-DLIBEMOS_PATH=%s' % spec['libemos'].prefix)
@@ -119,6 +116,13 @@ def install(self, spec, prefix):
         else:
             options.append('-DENABLE_METVIEW=OFF')
 
+        if '+eccodes' in spec:
+            options.append('-DENABLE_ECCODES=ON')
+            options.append('-DECCODES_PATH=%s' % spec['eccodes'].prefix)
+        else:
+            options.append('-DENABLE_ECCODES=OFF')
+            options.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
+
         if (self.compiler.f77 is None) or (self.compiler.fc is None):
             options.append('-DENABLE_FORTRAN=OFF')
 

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

@@ -113,6 +113,8 @@ class Plumed(AutotoolsPackage):
 
     force_autoreconf = True
 
+    parallel = False
+
     def apply_patch(self, other):
         plumed = subprocess.Popen(
             [join_path(self.spec.prefix.bin, 'plumed'), 'patch', '-p'],
@@ -126,7 +128,7 @@ def apply_patch(self, other):
 
     def setup_dependent_package(self, module, dependent_spec):
         # Make plumed visible from dependent packages
-        module.plumed = self.spec['plumed'].command
+        module.plumed = dependent_spec['plumed'].command
 
     @run_before('autoreconf')
     def filter_gslcblas(self):
@@ -162,6 +164,14 @@ def configure_args(self):
                     'STATIC_LIBS=-mt_mpi'
                 ])
 
+        # Set flags to help find gsl
+        if '+gsl' in self.spec:
+            gsl_libs = self.spec['gsl'].libs
+            blas_libs = self.spec['blas'].libs
+            configure_opts.append('LDFLAGS={0}'.format(
+                (gsl_libs + blas_libs).ld_flags
+            ))
+
         # Additional arguments
         configure_opts.extend([
             '--enable-shared={0}'.format('yes' if '+shared' in spec else 'no'),

var/spack/repos/builtin/packages/r-rmpi/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 RRmpi(RPackage):
+    """An interface (wrapper) to MPI APIs. It also provides interactive R
+       manager and worker environment."""
+
+    homepage = "http://www.stats.uwo.ca/faculty/yu/Rmpi"
+    url      = "https://cran.r-project.org/src/contrib/Rmpi_0.6-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/Rmpi"
+
+    version('0.6-6', '59ae8ce62ff0ff99342d53942c745779')
+
+    depends_on('mpi')
+    depends_on('r@2.15.1:')
+
+    def install(self, spec, prefix):
+        if 'mpich' in spec:
+            Rmpi_type = 'MPICH'
+        elif 'mvapich' in spec:
+            Rmpi_type = 'MVAPICH'
+        else:
+            Rmpi_type = 'OPENMPI'
+
+        my_mpi = spec['mpi']
+
+        R('CMD', 'INSTALL',
+          '--configure-args=--with-Rmpi-type=%s' % Rmpi_type +
+          ' --with-mpi=%s' % my_mpi.prefix,
+          '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-snow/package.py

@@ -0,0 +1,38 @@
+##############################################################################
+# 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 RSnow(RPackage):
+    """Support for simple parallel computing in R."""
+
+    homepage = "https://cran.r-project.org/web/packages/snow/index.html"
+    url      = "https://cran.r-project.org/src/contrib/snow_0.4-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/snow"
+
+    version('0.4-2', 'afc7b0dfd4518aedb6fc81712fd2ac70')
+
+    depends_on('r-rmpi', type='run')
+    depends_on('r@2.13.1:', type=('build', 'run'))