From ee68a76a193890231d6df7fa7934d42e3708540b Mon Sep 17 00:00:00 2001
From: Matthew LeGendre <legendre1@llnl.gov>
Date: Fri, 29 May 2015 14:57:24 -0700
Subject: Bug fixes from testing spack preferred packages

---
 var/spack/mock_packages/mpich/package.py | 1 +
 1 file changed, 1 insertion(+)

(limited to 'var')

diff --git a/var/spack/mock_packages/mpich/package.py b/var/spack/mock_packages/mpich/package.py
index f77d3efc5d..e4110ad530 100644
--- a/var/spack/mock_packages/mpich/package.py
+++ b/var/spack/mock_packages/mpich/package.py
@@ -38,6 +38,7 @@ class Mpich(Package):
     version('3.0.2', 'foobarbaz')
     version('3.0.1', 'foobarbaz')
     version('3.0', 'foobarbaz')
+    version('1.0', 'foobarbas')
 
     provides('mpi@:3', when='@3:')
     provides('mpi@:1', when='@:1')
-- 
cgit v1.2.3-70-g09d2


From 650c9d4e36c6a58cf6bca0e6abd580ee54d8e175 Mon Sep 17 00:00:00 2001
From: Matthew LeGendre <legendre1@llnl.gov>
Date: Wed, 16 Sep 2015 10:56:11 -0700
Subject: Allow spack to build against external non-spack-installed packages.

---
 lib/spack/spack/__init__.py            |   6 ++
 lib/spack/spack/abi.py                 | 128 ++++++++++++++++++++++++++++++
 lib/spack/spack/concretize.py          | 140 ++++++++++++++++++++++++++++++---
 lib/spack/spack/config.py              |  59 +++++++++++++-
 lib/spack/spack/directory_layout.py    |   8 ++
 lib/spack/spack/package.py             |   3 +
 lib/spack/spack/preferred_packages.py  |  10 ++-
 lib/spack/spack/spec.py                |  58 ++++++++------
 var/spack/packages/mpich/package.py    |   1 +
 var/spack/packages/mvapich2/package.py |  17 +++-
 10 files changed, 387 insertions(+), 43 deletions(-)
 create mode 100644 lib/spack/spack/abi.py

(limited to 'var')

diff --git a/lib/spack/spack/__init__.py b/lib/spack/spack/__init__.py
index bd8478fb98..5783005b5b 100644
--- a/lib/spack/spack/__init__.py
+++ b/lib/spack/spack/__init__.py
@@ -77,6 +77,12 @@ install_layout = YamlDirectoryLayout(install_path)
 from spack.preferred_packages import PreferredPackages
 pkgsort = PreferredPackages()
 
+#
+# This tests ABI compatibility between packages
+#
+from spack.abi import ABI
+abi = ABI()
+
 #
 # This controls how things are concretized in spack.
 # Replace it with a subclass if you want different
diff --git a/lib/spack/spack/abi.py b/lib/spack/spack/abi.py
new file mode 100644
index 0000000000..f0a997703c
--- /dev/null
+++ b/lib/spack/spack/abi.py
@@ -0,0 +1,128 @@
+##############################################################################
+# Copyright (c) 2015, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+
+import os
+import spack
+import spack.spec
+from spack.spec import CompilerSpec
+from spack.util.executable import Executable, ProcessError
+from llnl.util.lang import memoized
+
+class ABI(object):
+    """This class provides methods to test ABI compatibility between specs.
+       The current implementation is rather rough and could be improved."""
+
+    def architecture_compatible(self, parent, child):
+        """Returns true iff the parent and child specs have ABI compatible architectures."""
+        return not parent.architecture or not child.architecture or parent.architecture == child.architecture
+
+
+    @memoized
+    def _gcc_get_libstdcxx_version(self, version):
+        """Returns gcc ABI compatibility info by getting the library version of
+           a compiler's libstdc++.so or libgcc_s.so"""
+        spec = CompilerSpec("gcc", version)
+        compilers = spack.compilers.compilers_for_spec(spec)
+        if not compilers:
+            return None
+        compiler = compilers[0]
+        rungcc = None
+        libname = None
+        output = None
+        if compiler.cxx:
+            rungcc = Executable(compiler.cxx)
+            libname = "libstdc++.so"
+        elif compiler.cc:
+            rungcc = Executable(compiler.cc)
+            libname = "libgcc_s.so"
+        else:
+            return None
+        try:
+            output = rungcc("--print-file-name=%s" % libname, return_output=True)
+        except ProcessError, e:
+            return None
+        if not output:
+            return None
+        libpath = os.readlink(output.strip())
+        if not libpath:
+            return None
+        return os.path.basename(libpath)
+        
+        
+    @memoized
+    def _gcc_compiler_compare(self, pversion, cversion):
+        """Returns true iff the gcc version pversion and cversion 
+          are ABI compatible."""
+        plib = self._gcc_get_libstdcxx_version(pversion)
+        clib = self._gcc_get_libstdcxx_version(cversion)
+        if not plib or not clib:
+            return False
+        return plib == clib
+
+
+    def _intel_compiler_compare(self, pversion, cversion):
+        """Returns true iff the intel version pversion and cversion
+           are ABI compatible"""
+
+        #Test major and minor versions.  Ignore build version.
+        if (len(pversion.version) < 2 or len(cversion.version) < 2):
+            return False
+        return (pversion.version[0] == cversion.version[0]) and \
+            (pversion.version[1] == cversion.version[1])
+        
+    
+    def compiler_compatible(self, parent, child, **kwargs):
+        """Returns true iff the compilers for parent and child specs are ABI compatible"""
+        if not parent.compiler or not child.compiler:
+            return True
+        
+        if parent.compiler.name != child.compiler.name:
+            #Different compiler families are assumed ABI incompatible
+            return False
+        
+        if kwargs.get('loose', False):
+            return True
+
+        for pversion in parent.compiler.versions:
+            for cversion in child.compiler.versions:
+                #For a few compilers use specialized comparisons.  Otherwise
+                # match on version match.
+                if pversion.satisfies(cversion):
+                    return True
+                elif parent.compiler.name == "gcc" and \
+                     self._gcc_compiler_compare(pversion, cversion):
+                    return True
+                elif parent.compiler.name == "intel" and \
+                     self._intel_compiler_compare(pversion, cversion):
+                    return True
+        return False
+
+    
+    def compatible(self, parent, child, **kwargs):
+        """Returns true iff a parent and child spec are ABI compatible"""
+        loosematch = kwargs.get('loose', False)
+        return self.architecture_compatible(parent, child) and \
+               self.compiler_compatible(parent, child, loose=loosematch)
+    
diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 0f258c9096..01ff163493 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -33,13 +33,16 @@ or user preferences.
 TODO: make this customizable and allow users to configure
       concretization  policies.
 """
+import spack
 import spack.spec
 import spack.compilers
 import spack.architecture
 import spack.error
 from spack.version import *
 from functools import partial
-
+from spec import DependencyMap
+from itertools import chain
+from spack.config import *
 
 
 class DefaultConcretizer(object):
@@ -48,6 +51,107 @@ class DefaultConcretizer(object):
        default concretization strategies, or you can override all of them.
     """
 
+    def _find_other_spec(self, spec, condition):
+        """Searches the dag from spec in an intelligent order and looks
+           for a spec that matches a condition"""
+        dagiter = chain(spec.traverse(direction='parents'), spec.traverse(direction='children'))
+        found = next((x for x in dagiter if x is not spec and condition(x)), None)
+        if found:
+            return found
+        dagiter = chain(spec.traverse(direction='parents'), spec.traverse(direction='children'))
+        searched = list(dagiter)
+        found = next((x for x in spec.root.traverse() if x not in searched and x is not spec and condition(x)), None)
+        if found:
+            return found
+        if condition(spec):
+            return spec
+        return None
+                                   
+
+    def _valid_virtuals_and_externals(self, spec):
+        """Returns a list of spec/external-path pairs for both virtuals and externals
+           that can concretize this spec.""" 
+
+        # Get a list of candidate packages that could satisfy this spec
+        packages = []
+        if spec.virtual:
+            providers = spack.db.providers_for(spec)
+            if not providers:
+                raise UnsatisfiableProviderSpecError(providers[0], spec)
+            spec_w_preferred_providers = self._find_other_spec(spec, \
+                    lambda(x): spack.pkgsort.spec_has_preferred_provider(x.name, spec.name))
+            if not spec_w_preferred_providers:
+                spec_w_preferred_providers = spec
+            provider_cmp = partial(spack.pkgsort.provider_compare, spec_w_preferred_providers.name, spec.name)
+            packages = sorted(providers, cmp=provider_cmp)
+        else:
+            if not spec_externals(spec) or spec.external:
+                return None
+            packages = [spec]
+
+        # For each candidate package, if it has externals add those to the candidates
+        # if it's a nobuild, then only add the externals.
+        result = []
+        all_compilers = spack.compilers.all_compilers()
+        for pkg in packages:
+            externals = spec_externals(pkg)
+            buildable = not is_spec_nobuild(pkg)
+            if buildable:
+                result.append((pkg, None))
+            if externals:
+                sorted_externals = sorted(externals, cmp=lambda a,b: a[0].__cmp__(b[0]))
+                for external in sorted_externals:
+                    if external[0].satisfies(spec):
+                        result.append(external)
+        if not result:
+            raise NoBuildError(spec)
+        return result
+
+
+    def concretize_virtual_and_external(self, spec):
+        """From a list of candidate virtual and external packages, concretize to one that
+           is ABI compatible with the rest of the DAG."""
+        candidates = self._valid_virtuals_and_externals(spec)
+        if not candidates:
+            return False
+
+        #Find the another spec in the dag that has a compiler.  We'll use that
+        # spec to test compiler compatibility.
+        other_spec = self._find_other_spec(spec, lambda(x): x.compiler)
+        if not other_spec:
+            other_spec = spec.root
+
+        #Choose an ABI-compatible candidate, or the first match otherwise.
+        candidate = None
+        if other_spec:
+            candidate = next((c for c in candidates if spack.abi.compatible(c[0], other_spec)), None)
+            if not candidate:
+                #Try a looser ABI matching
+                candidate = next((c for c in candidates if spack.abi.compatible(c[0], other_spec, loose=True)), None)
+        if not candidate:
+            #Pick the first choice
+            candidate = candidates[0]
+        external = candidate[1]
+        candidate_spec = candidate[0]
+        
+        #Refine this spec to the candidate.
+        changed = False
+        if spec.virtual:
+            spec._replace_with(candidate_spec)
+            changed = True
+        if spec._dup(candidate_spec, deps=False, cleardeps=False):
+            changed = True
+        if not spec.external and external:
+            spec.external = external
+            changed = True
+        #If we're external then trim the dependencies
+        if external and spec.dependencies:
+            changed = True
+            spec.depencencies = DependencyMap()
+        
+        return changed
+        
+        
     def concretize_version(self, spec):
         """If the spec is already concrete, return.  Otherwise take
            the preferred version from spackconfig, and default to the package's
@@ -150,31 +254,32 @@ class DefaultConcretizer(object):
            link to this one, to maximize compatibility.
         """
         all_compilers = spack.compilers.all_compilers()
-
+        
         if (spec.compiler and
             spec.compiler.concrete and
             spec.compiler in all_compilers):
             return False
 
-        # Find the parent spec that has a compiler, or the root if none do
-        parent_spec = next(p for p in spec.traverse(direction='parents')
-                           if p.compiler is not None or not p.dependents)
-        parent_compiler = parent_spec.compiler
-        assert(parent_spec)
+        #Find the another spec that has a compiler, or the root if none do
+        other_spec = self._find_other_spec(spec, lambda(x) : x.compiler)
+        if not other_spec:
+            other_spec = spec.root
+        other_compiler = other_spec.compiler
+        assert(other_spec)
         
         # Check if the compiler is already fully specified
-        if parent_compiler in all_compilers:
-            spec.compiler = parent_compiler.copy()
+        if other_compiler in all_compilers:
+            spec.compiler = other_compiler.copy()
             return True
             
         # Filter the compilers into a sorted list based on the compiler_order from spackconfig
-        compiler_list = all_compilers if not parent_compiler else spack.compilers.find(parent_compiler)
-        cmp_compilers = partial(spack.pkgsort.compiler_compare, parent_spec.name)
+        compiler_list = all_compilers if not other_compiler else spack.compilers.find(other_compiler)
+        cmp_compilers = partial(spack.pkgsort.compiler_compare, other_spec.name)
         matches = sorted(compiler_list, cmp=cmp_compilers)
         if not matches:
-            raise UnavailableCompilerVersionError(parent_compiler)
+            raise UnavailableCompilerVersionError(other_compiler)
             
-        # copy concrete version into parent_compiler
+        # copy concrete version into other_compiler
         spec.compiler = matches[0].copy()
         assert(spec.compiler.concrete)
         return True  # things changed.
@@ -210,3 +315,12 @@ class NoValidVersionError(spack.error.SpackError):
     def __init__(self, spec):
         super(NoValidVersionError, self).__init__(
             "There are no valid versions for %s that match '%s'" % (spec.name, spec.versions))
+
+
+class NoBuildError(spack.error.SpackError):
+    """Raised when a package is configured with the nobuild option, but
+       no satisfactory external versions can be found"""
+    def __init__(self, spec):
+        super(NoBuildError, self).__init__(
+            "The spec '%s' is configured as nobuild, and no matching external installs were found" % spec.name)
+       
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index f3526b19fa..60577c45b3 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -90,9 +90,12 @@ import os
 import exceptions
 import sys
 import copy
-
-from llnl.util.lang import memoized
+import inspect
+import glob
+import imp
+import spack.spec
 import spack.error
+from llnl.util.lang import memoized
 
 from external import yaml
 from external.yaml.error import MarkedYAMLError
@@ -116,6 +119,9 @@ class _ConfigCategory:
 _ConfigCategory('compilers', 'compilers.yaml', True)
 _ConfigCategory('mirrors', 'mirrors.yaml', True)
 _ConfigCategory('preferred', 'preferred.yaml', True)
+_ConfigCategory('view', 'views.yaml', True)
+_ConfigCategory('preferred', 'preferred.yaml', True)
+_ConfigCategory('packages', 'packages.yaml', True)
 
 """Names of scopes and their corresponding configuration files."""
 config_scopes = [('site', os.path.join(spack.etc_path, 'spack')),
@@ -233,6 +239,55 @@ def get_preferred_config():
     return get_config('preferred')
 
 
+@memoized
+def get_packages_config():
+    """Get the externals configuration from config files"""
+    package_config = get_config('packages')
+    if not package_config:
+        return {}
+    indexed_packages = {}
+    for p in package_config:
+        package_name = spack.spec.Spec(p.keys()[0]).name
+        if package_name not in indexed_packages:
+            indexed_packages[package_name] = []
+        indexed_packages[package_name].append({ spack.spec.Spec(key) : val for key, val in p.iteritems() })
+    return indexed_packages
+
+
+def is_spec_nobuild(spec):
+    """Return true if the spec pkgspec is configured as nobuild"""
+    allpkgs = get_packages_config()
+    name = spec.name
+    if not name in allpkgs:
+        return False
+    for itm in allpkgs[name]:
+        for pkg,conf in itm.iteritems():
+            if pkg.satisfies(spec):
+                if conf.get('nobuild', False):
+                    return True
+    return False
+
+
+def spec_externals(spec):
+    """Return a list of spec, directory pairs for each external location for spec"""
+    allpkgs = get_packages_config()
+    name = spec.name
+    spec_locations = []
+    
+    if not name in allpkgs:
+        return []
+    for itm in allpkgs[name]:
+        for pkg,conf in itm.iteritems():
+            if not pkg.satisfies(spec):
+                continue
+            path = conf.get('path', None)
+            if not path:
+                continue
+            spec_locations.append( (pkg, path) )
+    return spec_locations
+        
+    
+
 def get_config_scope_dirname(scope):
     """For a scope return the config directory"""
     global config_scopes
diff --git a/lib/spack/spack/directory_layout.py b/lib/spack/spack/directory_layout.py
index 85ecc1ce2b..83e6eb566a 100644
--- a/lib/spack/spack/directory_layout.py
+++ b/lib/spack/spack/directory_layout.py
@@ -187,6 +187,14 @@ class YamlDirectoryLayout(DirectoryLayout):
 
     def relative_path_for_spec(self, spec):
         _check_concrete(spec)
+        
+        if spec.external:
+            return spec.external
+
+        enabled_variants = (
+            '-' + v.name for v in spec.variants.values()
+            if v.enabled)
+
         dir_name = "%s-%s-%s" % (
             spec.name,
             spec.version,
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index 61606d0590..1e2f0378c8 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -752,6 +752,9 @@ class Package(object):
         if not self.spec.concrete:
             raise ValueError("Can only install concrete packages.")
 
+        if self.spec.external:
+            return
+
         if os.path.exists(self.prefix):
             tty.msg("%s is already installed in %s." % (self.name, self.prefix))
             return
diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index bc5271f693..bc2a4ac234 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -35,9 +35,10 @@ class PreferredPackages(object):
 
     #Given a package name, sort component (e.g, version, compiler, ...), and
     # a second_key (used by providers), return the list 
-    def _order_for_package(self, pkgname, component, second_key):
+    def _order_for_package(self, pkgname, component, second_key, test_all=True):
         pkglist = [pkgname]
-        pkglist.append('all')
+        if test_all:
+            pkglist.append('all')
         for pkg in pkglist:
             if not pkg in self.preferred:
                 continue
@@ -143,6 +144,11 @@ class PreferredPackages(object):
         return self._spec_compare(pkgname, 'providers', a, b, False, provider_str)
 
 
+    def spec_has_preferred_provider(self, pkgname, provider_str):
+        """Return True iff the named package has a list of preferred provider"""
+        return bool(self._order_for_package(pkgname, 'providers', provider_str, False))
+
+
     def version_compare(self, pkgname, a, b):
         """Return less-than-0, 0, or greater than 0 if version a of pkgname is 
            respecively less-than, equal-to, or greater-than version b of pkgname. 
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 41496b0e9d..6984b4a174 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -419,6 +419,7 @@ class Spec(object):
         # package.py files for.
         self._normal = kwargs.get('normal', False)
         self._concrete = kwargs.get('concrete', False)
+        self.external = None
 
         # This allows users to construct a spec DAG with literals.
         # Note that given two specs a and b, Spec(a) copies a, but
@@ -426,7 +427,7 @@ class Spec(object):
         for dep in dep_like:
             spec = dep if isinstance(dep, Spec) else Spec(dep)
             self._add_dependency(spec)
-
+        
 
     #
     # Private routines here are called by the parser when building a spec.
@@ -751,12 +752,11 @@ class Spec(object):
             # Concretize virtual dependencies last.  Because they're added
             # to presets below, their constraints will all be merged, but we'll
             # still need to select a concrete package later.
-            if not self.virtual:
-                changed |= any(
-                    (spack.concretizer.concretize_architecture(self),
-                     spack.concretizer.concretize_compiler(self),
-                     spack.concretizer.concretize_version(self),
-                     spack.concretizer.concretize_variants(self)))
+            changed |= any(
+                (spack.concretizer.concretize_architecture(self),
+                 spack.concretizer.concretize_compiler(self),
+                 spack.concretizer.concretize_version(self),
+                 spack.concretizer.concretize_variants(self)))
             presets[self.name] = self
 
         visited.add(self.name)
@@ -789,21 +789,18 @@ class Spec(object):
               a problem.
         """
         changed = False
-        while True:
-            virtuals =[v for v in self.traverse() if v.virtual]
-            if not virtuals:
-                return changed
-
-            for spec in virtuals:
-                providers = spack.db.providers_for(spec)
-                concrete = spack.concretizer.choose_provider(self, spec, providers)
-                concrete = concrete.copy()
-                spec._replace_with(concrete)
-                changed = True
+        done = False
+        while not done:
+            done = True
+            for spec in list(self.traverse()):
+                if spack.concretizer.concretize_virtual_and_external(spec):
+                    done = False
+                    changed = True
 
-            # If there are duplicate providers or duplicate provider deps, this
-            # consolidates them and merge constraints.
-            changed |= self.normalize(force=True)
+        # If there are duplicate providers or duplicate provider deps, this
+        # consolidates them and merge constraints.
+        changed |= self.normalize(force=True)
+        return changed
 
 
     def concretize(self):
@@ -830,7 +827,6 @@ class Spec(object):
                        self._concretize_helper())
             changed = any(changes)
             force=True
-
         self._concrete = True
 
 
@@ -1346,15 +1342,26 @@ class Spec(object):
                Whether deps should be copied too.  Set to false to copy a
                spec but not its dependencies.
         """
+
+        # We don't count dependencies as changes here
+        changed = True
+        if hasattr(self, 'name'):
+            changed = (self.name != other.name and self.versions != other.versions and \
+                       self.architecture != other.architecture and self.compiler != other.compiler and \
+                       self.variants != other.variants and self._normal != other._normal and \
+                       self.concrete != other.concrete and self.external != other.external)
+                                       
         # Local node attributes get copied first.
         self.name = other.name
         self.versions = other.versions.copy()
         self.architecture = other.architecture
         self.compiler = other.compiler.copy() if other.compiler else None
-        self.dependents = DependencyMap()
-        self.dependencies = DependencyMap()
+        if kwargs.get('cleardeps', True):
+            self.dependents = DependencyMap()
+            self.dependencies = DependencyMap()
         self.variants = other.variants.copy()
         self.variants.spec = self
+        self.external = other.external
 
         # If we copy dependencies, preserve DAG structure in the new spec
         if kwargs.get('deps', True):
@@ -1372,6 +1379,8 @@ class Spec(object):
         # Since we preserved structure, we can copy _normal safely.
         self._normal = other._normal
         self._concrete = other._concrete
+        self.external = other.external
+        return changed
 
 
     def copy(self, **kwargs):
@@ -1796,6 +1805,7 @@ class SpecParser(spack.parse.Parser):
         spec.variants = VariantMap(spec)
         spec.architecture = None
         spec.compiler = None
+        spec.external = None
         spec.dependents   = DependencyMap()
         spec.dependencies = DependencyMap()
 
diff --git a/var/spack/packages/mpich/package.py b/var/spack/packages/mpich/package.py
index b6b2dfde21..dfff22152d 100644
--- a/var/spack/packages/mpich/package.py
+++ b/var/spack/packages/mpich/package.py
@@ -45,6 +45,7 @@ class Mpich(Package):
         os.environ['MPICH_F77'] = 'f77'
         os.environ['MPICH_F90'] = 'f90'
 
+        module.mpicc = join_path(self.prefix.bin, 'mpicc')
 
     def install(self, spec, prefix):
         config_args = ["--prefix=" + prefix,
diff --git a/var/spack/packages/mvapich2/package.py b/var/spack/packages/mvapich2/package.py
index ca0b1287c1..93bce011b7 100644
--- a/var/spack/packages/mvapich2/package.py
+++ b/var/spack/packages/mvapich2/package.py
@@ -11,10 +11,17 @@ class Mvapich2(Package):
 
     version('2.0', '9fbb68a4111a8b6338e476dc657388b4',
             url='http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.0.tar.gz')
+    
+    version('2.1', '0095ceecb19bbb7fb262131cb9c2cdd6', 
+            url='http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.1.tar.gz')
 
     provides('mpi@:2.2', when='@1.9')    # MVAPICH2-1.9 supports MPI 2.2
     provides('mpi@:3.0', when='@2.0')    # MVAPICH2-2.0 supports MPI 3.0
 
+    variant('psm', default=False, description="build with psm")
+
+    variant('pmi', default=False, description="build with pmi")
+    depends_on('pmgr_collective', when='+pmi')
 
     def install(self, spec, prefix):
         # we'll set different configure flags depending on our environment
@@ -80,7 +87,13 @@ class Mvapich2(Package):
             configure_args.append("--with-device=ch3:psm")
         else:
             # throw this flag on IB systems
-            configure_args.append("--with-device=ch3:mrail", "--with-rdma=gen2")
+            configure_args.append("--with-device=ch3:mrail")
+            configure_args.append("--with-rdma=gen2")
+
+        if "+pmi" in spec:
+            configure_args.append("--with-pmi=pmgr_collective" % spec['pmgr_collective'].prefix)
+        else:
+            configure_args.append("--with-pmi=slurm")
 
         # TODO: shared-memory build
 
@@ -93,7 +106,7 @@ class Mvapich2(Package):
             "--enable-f77", "--enable-fc", "--enable-cxx",
             "--enable-shared", "--enable-sharedlibs=gcc",
             "--enable-debuginfo",
-            "--with-pm=no", "--with-pmi=slurm",
+            "--with-pm=no",
             "--enable-romio", "--with-file-system=lustre+nfs+ufs",
             "--disable-mpe", "--without-mpe",
             "--disable-silent-rules",
-- 
cgit v1.2.3-70-g09d2


From 18f0b24a7f21ec7b46510f45867386b7600bbc55 Mon Sep 17 00:00:00 2001
From: Matthew LeGendre <legendre1@llnl.gov>
Date: Mon, 5 Oct 2015 11:30:48 -0700
Subject: Add tests for spack external dependencies, plus fixes for issues
 found by those tests.

---
 lib/spack/spack/concretize.py                      |  9 +++---
 lib/spack/spack/spec.py                            |  2 +-
 lib/spack/spack/test/concretize.py                 | 28 ++++++++++++++++
 .../mock_configs/site_spackconfig/packages.yaml    | 13 ++++++++
 var/spack/mock_packages/externalprereq/package.py  | 34 ++++++++++++++++++++
 var/spack/mock_packages/externaltest/package.py    | 37 ++++++++++++++++++++++
 var/spack/mock_packages/externaltool/package.py    | 36 +++++++++++++++++++++
 var/spack/mock_packages/externalvirtual/package.py | 37 ++++++++++++++++++++++
 8 files changed, 191 insertions(+), 5 deletions(-)
 create mode 100644 var/spack/mock_configs/site_spackconfig/packages.yaml
 create mode 100644 var/spack/mock_packages/externalprereq/package.py
 create mode 100644 var/spack/mock_packages/externaltest/package.py
 create mode 100644 var/spack/mock_packages/externaltool/package.py
 create mode 100644 var/spack/mock_packages/externalvirtual/package.py

(limited to 'var')

diff --git a/lib/spack/spack/concretize.py b/lib/spack/spack/concretize.py
index 01ff163493..c27a023136 100644
--- a/lib/spack/spack/concretize.py
+++ b/lib/spack/spack/concretize.py
@@ -85,8 +85,8 @@ class DefaultConcretizer(object):
             provider_cmp = partial(spack.pkgsort.provider_compare, spec_w_preferred_providers.name, spec.name)
             packages = sorted(providers, cmp=provider_cmp)
         else:
-            if not spec_externals(spec) or spec.external:
-                return None
+            if spec.external:
+                return False
             packages = [spec]
 
         # For each candidate package, if it has externals add those to the candidates
@@ -129,7 +129,7 @@ class DefaultConcretizer(object):
                 #Try a looser ABI matching
                 candidate = next((c for c in candidates if spack.abi.compatible(c[0], other_spec, loose=True)), None)
         if not candidate:
-            #Pick the first choice
+            #No ABI matches. Pick the top choice based on the orignal preferences.
             candidate = candidates[0]
         external = candidate[1]
         candidate_spec = candidate[0]
@@ -144,10 +144,11 @@ class DefaultConcretizer(object):
         if not spec.external and external:
             spec.external = external
             changed = True
+
         #If we're external then trim the dependencies
         if external and spec.dependencies:
             changed = True
-            spec.depencencies = DependencyMap()
+            spec.dependencies = DependencyMap()
         
         return changed
         
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 6984b4a174..49b67cd361 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -1022,7 +1022,7 @@ class Spec(object):
 
         # if we descend into a virtual spec, there's nothing more
         # to normalize.  Concretize will finish resolving it later.
-        if self.virtual:
+        if self.virtual or self.external:
             return False
 
         # Combine constraints from package deps with constraints from
diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index b3a77d076a..f81a2f5af8 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -192,3 +192,31 @@ class ConcretizeTest(MockPackagesTest):
         # TODO: not exactly the syntax I would like.
         self.assertTrue(spec['libdwarf'].compiler.satisfies('clang'))
         self.assertTrue(spec['libelf'].compiler.satisfies('clang'))
+
+
+    def test_external_package(self):
+        spec = Spec('externaltool')
+        spec.concretize()
+
+        self.assertEqual(spec['externaltool'].external, '/path/to/external_tool')
+        self.assertFalse('externalprereq' in spec)
+        self.assertTrue(spec['externaltool'].compiler.satisfies('gcc'))
+
+
+    def test_nobuild_package(self):
+        got_error = False
+        spec = Spec('externaltool%clang')
+        try:
+            spec.concretize()
+        except spack.concretize.NoBuildError:
+            got_error = True
+        self.assertTrue(got_error)
+
+
+    def test_external_and_virtual(self):
+        spec = Spec('externaltest')
+        spec.concretize()
+        self.assertTrue(spec['externaltool'].external, '/path/to/external_tool')
+        self.assertTrue(spec['stuff'].external, '/path/to/external_virtual_gcc')
+        self.assertTrue(spec['externaltool'].compiler.satisfies('gcc'))
+        self.assertTrue(spec['stuff'].compiler.satisfies('gcc'))
diff --git a/var/spack/mock_configs/site_spackconfig/packages.yaml b/var/spack/mock_configs/site_spackconfig/packages.yaml
new file mode 100644
index 0000000000..eb52c6cf11
--- /dev/null
+++ b/var/spack/mock_configs/site_spackconfig/packages.yaml
@@ -0,0 +1,13 @@
+packages:
+  - externaltool:
+      nobuild: True
+  - externaltool@1.0%gcc@4.5.0:
+      path: /path/to/external_tool
+  - externalvirtual@2.0%clang@3.3:
+      path: /path/to/external_virtual_clang
+      nobuild: True
+  - externalvirtual@1.0%gcc@4.5.0:
+      path: /path/to/external_virtual_gcc
+      nobuild: True
+
+
diff --git a/var/spack/mock_packages/externalprereq/package.py b/var/spack/mock_packages/externalprereq/package.py
new file mode 100644
index 0000000000..7d63925693
--- /dev/null
+++ b/var/spack/mock_packages/externalprereq/package.py
@@ -0,0 +1,34 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Externalprereq(Package):
+    homepage = "http://somewhere.com"
+    url      = "http://somewhere.com/prereq-1.0.tar.gz"
+
+    version('1.4', 'f1234567890abcdef1234567890abcde')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/mock_packages/externaltest/package.py b/var/spack/mock_packages/externaltest/package.py
new file mode 100644
index 0000000000..c546922f87
--- /dev/null
+++ b/var/spack/mock_packages/externaltest/package.py
@@ -0,0 +1,37 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Externaltest(Package):
+    homepage = "http://somewhere.com"
+    url      = "http://somewhere.com/test-1.0.tar.gz"
+
+    version('1.0', '1234567890abcdef1234567890abcdef')
+
+    depends_on('stuff')
+    depends_on('externaltool')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/mock_packages/externaltool/package.py b/var/spack/mock_packages/externaltool/package.py
new file mode 100644
index 0000000000..af902bd70e
--- /dev/null
+++ b/var/spack/mock_packages/externaltool/package.py
@@ -0,0 +1,36 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Externaltool(Package):
+    homepage = "http://somewhere.com"
+    url      = "http://somewhere.com/tool-1.0.tar.gz"
+
+    version('1.0', '1234567890abcdef1234567890abcdef')
+
+    depends_on('externalprereq')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/mock_packages/externalvirtual/package.py b/var/spack/mock_packages/externalvirtual/package.py
new file mode 100644
index 0000000000..722c1e1c53
--- /dev/null
+++ b/var/spack/mock_packages/externalvirtual/package.py
@@ -0,0 +1,37 @@
+##############################################################################
+# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://scalability-llnl.github.io/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Externalvirtual(Package):
+    homepage = "http://somewhere.com"
+    url      = "http://somewhere.com/stuff-1.0.tar.gz"
+
+    version('1.0', '1234567890abcdef1234567890abcdef')
+    version('2.0', '234567890abcdef1234567890abcdef1')
+
+    provides('stuff')
+
+    def install(self, spec, prefix):
+        pass
-- 
cgit v1.2.3-70-g09d2


From 5520ce3c4a46476f5eec7a340471dd044932ac06 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 12 Jan 2016 12:19:03 -0600
Subject: Removed unnecessary URLs

---
 var/spack/packages/xz/package.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

(limited to 'var')

diff --git a/var/spack/packages/xz/package.py b/var/spack/packages/xz/package.py
index ba6c9733a7..fdcac95345 100644
--- a/var/spack/packages/xz/package.py
+++ b/var/spack/packages/xz/package.py
@@ -8,11 +8,9 @@ class Xz(Package):
     homepage = "http://tukaani.org/xz/"
     url      = "http://tukaani.org/xz/xz-5.2.0.tar.bz2"
 
-    version('5.2.0', '867cc8611760240ebf3440bd6e170bb9',
-            url = 'http://tukaani.org/xz/xz-5.2.0.tar.bz2')
-    version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af',
-            url = 'http://tukaani.org/xz/xz-5.2.2.tar.bz2')
-   
+    version('5.2.0', '867cc8611760240ebf3440bd6e170bb9')
+    version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
-- 
cgit v1.2.3-70-g09d2


From 180c673c782d10864dce6cd7df43465dd05579a1 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 12 Jan 2016 13:21:53 -0600
Subject: Add different URL for older source code

---
 var/spack/packages/mpc/package.py | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

(limited to 'var')

diff --git a/var/spack/packages/mpc/package.py b/var/spack/packages/mpc/package.py
index 50477a0ccb..65c0ba7ea1 100644
--- a/var/spack/packages/mpc/package.py
+++ b/var/spack/packages/mpc/package.py
@@ -34,8 +34,14 @@ class Mpc(Package):
     version('1.0.3', 'd6a1d5f8ddea3abd2cc3e98f58352d26')
     version('1.0.2', '68fadff3358fb3e7976c7a398a0af4c3')
 
-    depends_on("gmp")
-    depends_on("mpfr")
+    depends_on("gmp@4.3.2:")
+    depends_on("mpfr@2.4.2:")
+
+    def url_for_version(self, version):
+        if version < Version("1.0.1"):
+            return "http://www.multiprecision.org/mpc/download/mpc-%s.tar.gz" % version
+        else:
+            return "ftp://ftp.gnu.org/gnu/mpc/mpc-%s.tar.gz" % version
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
-- 
cgit v1.2.3-70-g09d2


From 7d0256c9fb5c3b8824cdeb0455d2a3e3b3f1eeb4 Mon Sep 17 00:00:00 2001
From: Nicola Varini <nicola.varini@gmail.com>
Date: Fri, 15 Jan 2016 10:27:38 +0100
Subject: Quantum-ESPRESSO package

---
 var/spack/packages/espresso/package.py | 61 ++++++++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 var/spack/packages/espresso/package.py

(limited to 'var')

diff --git a/var/spack/packages/espresso/package.py b/var/spack/packages/espresso/package.py
new file mode 100644
index 0000000000..f9df74c0c0
--- /dev/null
+++ b/var/spack/packages/espresso/package.py
@@ -0,0 +1,61 @@
+# FIXME:
+# This is a template package file for Spack.  We've conveniently
+# put "FIXME" labels next to all the things you'll want to change.
+#
+# Once you've edited all the FIXME's, delete this whole message,
+# save this file, and test out your package like this:
+#
+#     spack install espresso
+#
+# You can always get back here to change things with:
+#
+#     spack edit espresso
+#
+# See the spack documentation for more information on building
+# packages.
+#
+from spack import *
+
+class Espresso(Package):
+    """FIXME: put a proper description of your package here."""
+    # FIXME: add a proper url for your package's homepage here.
+    homepage = "http://quantum-espresso.org"
+    url      = "http://www.qe-forge.org/gf/download/frsrelease/199/855/espresso-5.2.1.tar.gz"
+
+    version('5.2.1', 'da3ec5302e4343804e65de60f6004c2d')
+    variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support')
+    variant('openmp', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
+    variant('scalapack', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
+
+
+    # FIXME: Add dependencies if this package requires them.
+    # depends_on("foo")
+    depends_on('mpi', when='+mpi')
+
+
+#    def install(self, spec, prefix):
+        # FIXME: Modify the configure line to suit your build system here.
+#        configure('--prefix=%s' % prefix)
+
+        # FIXME: Add logic to build and install here
+#        make()
+#        make("install")
+
+    def install(self, spec, prefix):
+        # TAU isn't happy with directories that have '@' in the path.  Sigh.
+
+        # TAU configure, despite the name , seems to be a manually written script (nothing related to autotools).
+        # As such it has a few #peculiarities# that make this build quite hackish.
+        options = ["-prefix=%s" % prefix,
+                   "--enable-parallel"]
+
+        if '+openmp' in spec:
+            options.append('--enable-openmp')
+
+        if '+scalapack' in spec:
+            options.append('--with-scalapack=yes')
+
+        configure(*options)
+        make("all")
+        make("install")
+
-- 
cgit v1.2.3-70-g09d2


From 7fc308ed26d7abfcb71af8165523b421a1f315c0 Mon Sep 17 00:00:00 2001
From: Nicola Varini <nicola.varini@gmail.com>
Date: Fri, 15 Jan 2016 17:04:25 +0100
Subject: Update to version 5.3

---
 var/spack/packages/espresso/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'var')

diff --git a/var/spack/packages/espresso/package.py b/var/spack/packages/espresso/package.py
index f9df74c0c0..ce5dcc2acc 100644
--- a/var/spack/packages/espresso/package.py
+++ b/var/spack/packages/espresso/package.py
@@ -20,9 +20,9 @@ class Espresso(Package):
     """FIXME: put a proper description of your package here."""
     # FIXME: add a proper url for your package's homepage here.
     homepage = "http://quantum-espresso.org"
-    url      = "http://www.qe-forge.org/gf/download/frsrelease/199/855/espresso-5.2.1.tar.gz"
+    url      = "http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz"
 
-    version('5.2.1', 'da3ec5302e4343804e65de60f6004c2d')
+    version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
     variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support')
     variant('openmp', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
     variant('scalapack', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
-- 
cgit v1.2.3-70-g09d2


From ea9d0c0263126c370119e5fc435652c7214e658a Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Thu, 21 Jan 2016 09:58:47 -0600
Subject: Remove constraints on dependency versions

---
 var/spack/repos/builtin/packages/mpc/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/mpc/package.py b/var/spack/repos/builtin/packages/mpc/package.py
index 65c0ba7ea1..108fec678f 100644
--- a/var/spack/repos/builtin/packages/mpc/package.py
+++ b/var/spack/repos/builtin/packages/mpc/package.py
@@ -34,8 +34,8 @@ class Mpc(Package):
     version('1.0.3', 'd6a1d5f8ddea3abd2cc3e98f58352d26')
     version('1.0.2', '68fadff3358fb3e7976c7a398a0af4c3')
 
-    depends_on("gmp@4.3.2:")
-    depends_on("mpfr@2.4.2:")
+    depends_on("gmp")
+    depends_on("mpfr")
 
     def url_for_version(self, version):
         if version < Version("1.0.1"):
-- 
cgit v1.2.3-70-g09d2


From 07bb6fef01bfe48aa22c39e53b75e4c779ac0c2e Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 28 Jan 2016 10:58:56 +0100
Subject: resource directive : now works with all the fetch strategies
 available

---
 lib/spack/spack/directives.py                    |  2 +-
 lib/spack/spack/fetch_strategy.py                | 19 ++++++++++++++++---
 lib/spack/spack/package.py                       |  1 -
 var/spack/repos/builtin/packages/llvm/package.py | 19 +++++++++++++++++++
 4 files changed, 36 insertions(+), 5 deletions(-)

(limited to 'var')

diff --git a/lib/spack/spack/directives.py b/lib/spack/spack/directives.py
index 0b98211cb9..5745adce63 100644
--- a/lib/spack/spack/directives.py
+++ b/lib/spack/spack/directives.py
@@ -296,8 +296,8 @@ def resource(pkg, **kwargs):
         raise RuntimeError(message)
     when_spec = parse_anonymous_spec(when, pkg.name)
     resources = pkg.resources.setdefault(when_spec, [])
-    fetcher = from_kwargs(**kwargs)
     name = kwargs.get('name')
+    fetcher = from_kwargs(**kwargs)
     resources.append(Resource(name, fetcher, destination, placement))
 
 
diff --git a/lib/spack/spack/fetch_strategy.py b/lib/spack/spack/fetch_strategy.py
index b2ff587a60..83a2dbb59c 100644
--- a/lib/spack/spack/fetch_strategy.py
+++ b/lib/spack/spack/fetch_strategy.py
@@ -44,6 +44,7 @@ import os
 import sys
 import re
 import shutil
+import copy
 from functools import wraps
 import llnl.util.tty as tty
 from llnl.util.filesystem import *
@@ -370,8 +371,12 @@ class GitFetchStrategy(VCSFetchStrategy):
     required_attributes = ('git',)
 
     def __init__(self, **kwargs):
+        # Discards the keywords in kwargs that may conflict with the next call to __init__
+        forwarded_args = copy.copy(kwargs)
+        forwarded_args.pop('name', None)
+
         super(GitFetchStrategy, self).__init__(
-                'git', 'tag', 'branch', 'commit', **kwargs)
+                'git', 'tag', 'branch', 'commit', **forwarded_args)
         self._git = None
 
     @property
@@ -479,8 +484,12 @@ class SvnFetchStrategy(VCSFetchStrategy):
     required_attributes = ['svn']
 
     def __init__(self, **kwargs):
+        # Discards the keywords in kwargs that may conflict with the next call to __init__
+        forwarded_args = copy.copy(kwargs)
+        forwarded_args.pop('name', None)
+
         super(SvnFetchStrategy, self).__init__(
-                'svn', 'revision', **kwargs)
+                'svn', 'revision', **forwarded_args)
         self._svn = None
         if self.revision is not None:
             self.revision = str(self.revision)
@@ -556,8 +565,12 @@ class HgFetchStrategy(VCSFetchStrategy):
     required_attributes = ['hg']
 
     def __init__(self, **kwargs):
+        # Discards the keywords in kwargs that may conflict with the next call to __init__
+        forwarded_args = copy.copy(kwargs)
+        forwarded_args.pop('name', None)
+
         super(HgFetchStrategy, self).__init__(
-                'hg', 'revision', **kwargs)
+                'hg', 'revision', **forwarded_args)
         self._hg = None
 
     @property
diff --git a/lib/spack/spack/package.py b/lib/spack/spack/package.py
index a1b8d12ec2..8019b29cba 100644
--- a/lib/spack/spack/package.py
+++ b/lib/spack/spack/package.py
@@ -435,7 +435,6 @@ class Package(object):
 
     def _make_resource_stage(self, root_stage, fetcher, resource):
         resource_stage_folder = self._resource_stage(resource)
-        # FIXME : works only for URLFetchStrategy
         resource_mirror = join_path(self.name, os.path.basename(fetcher.url))
         stage = ResourceStage(resource.fetcher, root=root_stage, resource=resource,
                               name=resource_stage_folder, mirror_path=resource_mirror)
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index a2b2c6eccc..1805d3ded8 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -171,6 +171,25 @@ class Llvm(Package):
                      when='@%(version)s' % release,
                      placement=resources[name].get('placement', None))
 
+    # SVN - current develop
+    version('develop', svn='http://llvm.org/svn/llvm-project/llvm/trunk')
+    resource(name='clang', svn='http://llvm.org/svn/llvm-project/cfe/trunk',
+             destination='tools', when='@develop', placement='clang')
+    resource(name='compiler-rt', svn='http://llvm.org/svn/llvm-project/compiler-rt/trunk',
+             destination='projects', when='@develop', placement='compiler-rt')
+    resource(name='openmp', svn='http://llvm.org/svn/llvm-project/openmp/trunk',
+             destination='projects', when='@develop', placement='openmp')
+    resource(name='libcxx', svn='http://llvm.org/svn/llvm-project/libcxx/trunk',
+             destination='projects', when='@develop', placement='libcxx')
+    resource(name='libcxxabi', svn='http://llvm.org/svn/llvm-project/libcxxabi/trunk',
+             destination='projects', when='@develop', placement='libcxxabi')
+    resource(name='polly', svn='http://llvm.org/svn/llvm-project/polly/trunk',
+             destination='tools', when='@develop', placement='polly')
+    resource(name='lldb', svn='http://llvm.org/svn/llvm-project/lldb/trunk',
+             destination='tools', when='@develop', placement='lldb')
+
+
+
     def install(self, spec, prefix):
         env['CXXFLAGS'] = self.compiler.cxx11_flag
         cmake_args = [ arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg ]
-- 
cgit v1.2.3-70-g09d2


From 587d356d6ec8820cf04043b3650ac66b82a651b2 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 3 Feb 2016 08:58:34 +0100
Subject: openssl : added logic to version computation. The package now warns
 user if he depends on an old version of the library

---
 .../repos/builtin/packages/openssl/package.py      | 40 ++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 05de35fca0..c73102f05d 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -1,3 +1,6 @@
+import urllib
+import llnl.util.tty as tty
+
 from spack import *
 
 class Openssl(Package):
@@ -10,6 +13,7 @@ class Openssl(Package):
     url      = "http://www.openssl.org/source/openssl-1.0.1h.tar.gz"
 
     version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
+    version('1.0.1r', '1abd905e079542ccae948af37e393d28')
     version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
     version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
     version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
@@ -17,6 +21,42 @@ class Openssl(Package):
     depends_on("zlib")
     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
+        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:
+            latest = 'http://www.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
+            version_number = '.'.join([str(x) for x in version[:-1]])
+            older_url = older.format(version_number=version_number, version_full=version)
+            latest_url = latest.format(version=version)
+            response = urllib.urlopen(latest.format(version=version))
+            if response.getcode() == 404:
+                openssl_url = older_url
+                # 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))
+                    warnings_given_to_user[version] = True
+            else:
+                openssl_url = latest_url
+            # Store the computed URL
+            openssl_urls[version] = openssl_url
+            # Store the updated dictionary of URLS
+            Openssl._openssl_url = openssl_urls
+            # Store the updated dictionary of warnings
+            Openssl._warnings_given = warnings_given_to_user
+
+        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
-- 
cgit v1.2.3-70-g09d2


From 157ec210a74c2897abc093c14824975c49944f16 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 11 Feb 2016 13:05:31 +0100
Subject: espresso : synchronized with current develop

---
 var/spack/packages/espresso/package.py             | 61 ----------------------
 .../repos/builtin/packages/espresso/package.py     | 61 ++++++++++++++++++++++
 2 files changed, 61 insertions(+), 61 deletions(-)
 delete mode 100644 var/spack/packages/espresso/package.py
 create mode 100644 var/spack/repos/builtin/packages/espresso/package.py

(limited to 'var')

diff --git a/var/spack/packages/espresso/package.py b/var/spack/packages/espresso/package.py
deleted file mode 100644
index ce5dcc2acc..0000000000
--- a/var/spack/packages/espresso/package.py
+++ /dev/null
@@ -1,61 +0,0 @@
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-#     spack install espresso
-#
-# You can always get back here to change things with:
-#
-#     spack edit espresso
-#
-# See the spack documentation for more information on building
-# packages.
-#
-from spack import *
-
-class Espresso(Package):
-    """FIXME: put a proper description of your package here."""
-    # FIXME: add a proper url for your package's homepage here.
-    homepage = "http://quantum-espresso.org"
-    url      = "http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz"
-
-    version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
-    variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support')
-    variant('openmp', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
-    variant('scalapack', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
-
-
-    # FIXME: Add dependencies if this package requires them.
-    # depends_on("foo")
-    depends_on('mpi', when='+mpi')
-
-
-#    def install(self, spec, prefix):
-        # FIXME: Modify the configure line to suit your build system here.
-#        configure('--prefix=%s' % prefix)
-
-        # FIXME: Add logic to build and install here
-#        make()
-#        make("install")
-
-    def install(self, spec, prefix):
-        # TAU isn't happy with directories that have '@' in the path.  Sigh.
-
-        # TAU configure, despite the name , seems to be a manually written script (nothing related to autotools).
-        # As such it has a few #peculiarities# that make this build quite hackish.
-        options = ["-prefix=%s" % prefix,
-                   "--enable-parallel"]
-
-        if '+openmp' in spec:
-            options.append('--enable-openmp')
-
-        if '+scalapack' in spec:
-            options.append('--with-scalapack=yes')
-
-        configure(*options)
-        make("all")
-        make("install")
-
diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
new file mode 100644
index 0000000000..ce5dcc2acc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -0,0 +1,61 @@
+# FIXME:
+# This is a template package file for Spack.  We've conveniently
+# put "FIXME" labels next to all the things you'll want to change.
+#
+# Once you've edited all the FIXME's, delete this whole message,
+# save this file, and test out your package like this:
+#
+#     spack install espresso
+#
+# You can always get back here to change things with:
+#
+#     spack edit espresso
+#
+# See the spack documentation for more information on building
+# packages.
+#
+from spack import *
+
+class Espresso(Package):
+    """FIXME: put a proper description of your package here."""
+    # FIXME: add a proper url for your package's homepage here.
+    homepage = "http://quantum-espresso.org"
+    url      = "http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz"
+
+    version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
+    variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support')
+    variant('openmp', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
+    variant('scalapack', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
+
+
+    # FIXME: Add dependencies if this package requires them.
+    # depends_on("foo")
+    depends_on('mpi', when='+mpi')
+
+
+#    def install(self, spec, prefix):
+        # FIXME: Modify the configure line to suit your build system here.
+#        configure('--prefix=%s' % prefix)
+
+        # FIXME: Add logic to build and install here
+#        make()
+#        make("install")
+
+    def install(self, spec, prefix):
+        # TAU isn't happy with directories that have '@' in the path.  Sigh.
+
+        # TAU configure, despite the name , seems to be a manually written script (nothing related to autotools).
+        # As such it has a few #peculiarities# that make this build quite hackish.
+        options = ["-prefix=%s" % prefix,
+                   "--enable-parallel"]
+
+        if '+openmp' in spec:
+            options.append('--enable-openmp')
+
+        if '+scalapack' in spec:
+            options.append('--with-scalapack=yes')
+
+        configure(*options)
+        make("all")
+        make("install")
+
-- 
cgit v1.2.3-70-g09d2


From ca3cdb445825126776c5269481540d3afac02c9f Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 11 Feb 2016 17:45:09 +0100
Subject: espresso : current working tree

---
 .../repos/builtin/packages/espresso/package.py     | 73 ++++++++++------------
 1 file changed, 33 insertions(+), 40 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index ce5dcc2acc..56b8c056b8 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -1,53 +1,44 @@
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-#     spack install espresso
-#
-# You can always get back here to change things with:
-#
-#     spack edit espresso
-#
-# See the spack documentation for more information on building
-# packages.
-#
+import llnl.util.tty as tty
+
 from spack import *
 
+
 class Espresso(Package):
-    """FIXME: put a proper description of your package here."""
-    # FIXME: add a proper url for your package's homepage here.
-    homepage = "http://quantum-espresso.org"
-    url      = "http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz"
+    """
+    QE is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials
+    modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
+    """
+    homepage = 'http://quantum-espresso.org'
+    url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz'
 
     version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
+
     variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support')
-    variant('openmp', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
-    variant('scalapack', default=False, description='Build Quantum-ESPRESSO with mpi openmp')
+    variant('openmp', default=False, description='Enables openMP support')
+    variant('scalapack', default=False, description='Enables scalapack support')
+    variant('elpa', default=True, description='Use elpa as an eigenvalue solver')
 
+    depends_on('blas')
+    depends_on('lapack')
 
-    # FIXME: Add dependencies if this package requires them.
-    # depends_on("foo")
     depends_on('mpi', when='+mpi')
+    depends_on('elpa', when='+elpa')
+    depends_on('scalapack', when='+scalapack')
 
-
-#    def install(self, spec, prefix):
-        # FIXME: Modify the configure line to suit your build system here.
-#        configure('--prefix=%s' % prefix)
-
-        # FIXME: Add logic to build and install here
-#        make()
-#        make("install")
+    def check_variants(self, spec):
+        error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
+        if '+scalapack' in spec and '~mpi' in spec:
+            raise RuntimeError(error.format(variant='scalapack'))
+        if '+elpa' in spec and '~mpi' in spec:
+            raise RuntimeError(error.format(variant='elpa'))
 
     def install(self, spec, prefix):
-        # TAU isn't happy with directories that have '@' in the path.  Sigh.
+        self.check_variants(spec)
+
+        options = ['-prefix=%s' % prefix]
 
-        # TAU configure, despite the name , seems to be a manually written script (nothing related to autotools).
-        # As such it has a few #peculiarities# that make this build quite hackish.
-        options = ["-prefix=%s" % prefix,
-                   "--enable-parallel"]
+        if '+mpi' in spec:
+            options.append('--enable-parallel')
 
         if '+openmp' in spec:
             options.append('--enable-openmp')
@@ -55,7 +46,9 @@ class Espresso(Package):
         if '+scalapack' in spec:
             options.append('--with-scalapack=yes')
 
-        configure(*options)
-        make("all")
-        make("install")
+        if '+elpa' in spec:
+            options.append('--with-elpa=%s' % spec['elpa'].prefix)
 
+        configure(*options)
+        make('all')
+        make('install')
-- 
cgit v1.2.3-70-g09d2


From b272a8881becf205c09ac11228dd035b99fa0fcd Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 11 Feb 2016 18:18:05 +0100
Subject: espresso : fixed dependency handling

---
 var/spack/repos/builtin/packages/espresso/package.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index 56b8c056b8..df37bb0d71 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -1,5 +1,3 @@
-import llnl.util.tty as tty
-
 from spack import *
 
 
@@ -15,21 +13,21 @@ class Espresso(Package):
 
     variant('mpi', default=True, description='Build Quantum-ESPRESSO with mpi support')
     variant('openmp', default=False, description='Enables openMP support')
-    variant('scalapack', default=False, description='Enables scalapack support')
+    variant('scalapack', default=True, description='Enables scalapack support')
     variant('elpa', default=True, description='Use elpa as an eigenvalue solver')
 
     depends_on('blas')
     depends_on('lapack')
 
     depends_on('mpi', when='+mpi')
-    depends_on('elpa', when='+elpa')
-    depends_on('scalapack', when='+scalapack')
+    depends_on('elpa', when='+elpa+scalapack+mpi')  # TODO : + mpi needed to avoid false dependencies installation
+    depends_on('scalapack', when='+scalapack+mpi')  # TODO : + mpi needed to avoid false dependencies installation
 
     def check_variants(self, spec):
         error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
         if '+scalapack' in spec and '~mpi' in spec:
             raise RuntimeError(error.format(variant='scalapack'))
-        if '+elpa' in spec and '~mpi' in spec:
+        if '+elpa' in spec and ('~mpi' in spec or '~scalapack' in spec):
             raise RuntimeError(error.format(variant='elpa'))
 
     def install(self, spec, prefix):
-- 
cgit v1.2.3-70-g09d2


From e8704433debe35d7893c0c20672d06973226c4e8 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Thu, 11 Feb 2016 18:57:40 +0100
Subject: espresso : added directories to search path

---
 var/spack/repos/builtin/packages/espresso/package.py | 8 ++++++++
 1 file changed, 8 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index df37bb0d71..f85257b3cc 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -47,6 +47,14 @@ class Espresso(Package):
         if '+elpa' in spec:
             options.append('--with-elpa=%s' % spec['elpa'].prefix)
 
+        # Add a list of directories to search
+        search_list = []
+        for name, dependency_spec in spec.dependencies.iteritems():
+            print name
+            search_list.extend([dependency_spec.prefix.lib,
+                                dependency_spec.prefix.lib64])
+        search_list = " ".join(search_list)
+        options.append('LIBDIRS=%s' % search_list)
         configure(*options)
         make('all')
         make('install')
-- 
cgit v1.2.3-70-g09d2


From d7f674ce9678ddb3b964ad457b29ed058e2cb3c7 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Thu, 14 Jan 2016 17:41:44 -0500
Subject: libedit depends on ncurses

---
 var/spack/repos/builtin/packages/libedit/package.py | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py
index bcd5212b9e..faed8bad37 100644
--- a/var/spack/repos/builtin/packages/libedit/package.py
+++ b/var/spack/repos/builtin/packages/libedit/package.py
@@ -7,6 +7,8 @@ class Libedit(Package):
 
     version('3.1', '43cdb5df3061d78b5e9d59109871b4f6', url="http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz")
 
+    depends_on('ncurses')
+
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
 
-- 
cgit v1.2.3-70-g09d2


From 70985170e5f248d0d6a1b6245bd5581185ecaa64 Mon Sep 17 00:00:00 2001
From: Massimiliano Culpo <massimiliano.culpo@googlemail.com>
Date: Fri, 12 Feb 2016 12:08:31 +0100
Subject: qe : compiled on rhle6

---
 var/spack/repos/builtin/packages/espresso/package.py | 15 ++++++++++-----
 var/spack/repos/builtin/packages/mpich/package.py    |  8 ++++----
 var/spack/repos/builtin/packages/openblas/package.py |  2 ++
 3 files changed, 16 insertions(+), 9 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/espresso/package.py
index f85257b3cc..a2bf58f585 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/espresso/package.py
@@ -1,5 +1,6 @@
 from spack import *
 
+import os
 
 class Espresso(Package):
     """
@@ -20,9 +21,10 @@ class Espresso(Package):
     depends_on('lapack')
 
     depends_on('mpi', when='+mpi')
-    depends_on('elpa', when='+elpa+scalapack+mpi')  # TODO : + mpi needed to avoid false dependencies installation
+    depends_on('fftw~mpi', when='~mpi')
+    depends_on('fftw+mpi', when='+mpi')
     depends_on('scalapack', when='+scalapack+mpi')  # TODO : + mpi needed to avoid false dependencies installation
-
+    
     def check_variants(self, spec):
         error = 'you cannot ask for \'+{variant}\' when \'+mpi\' is not active'
         if '+scalapack' in spec and '~mpi' in spec:
@@ -45,16 +47,19 @@ class Espresso(Package):
             options.append('--with-scalapack=yes')
 
         if '+elpa' in spec:
-            options.append('--with-elpa=%s' % spec['elpa'].prefix)
+            options.append('--with-elpa=yes')
 
         # Add a list of directories to search
         search_list = []
         for name, dependency_spec in spec.dependencies.iteritems():
-            print name
             search_list.extend([dependency_spec.prefix.lib,
                                 dependency_spec.prefix.lib64])
+
         search_list = " ".join(search_list)
         options.append('LIBDIRS=%s' % search_list)
+        options.append('F90=%s' % os.environ['FC'])
+
         configure(*options)
         make('all')
-        make('install')
+        make('install')        
+
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index c856cfe277..26d3bc0c94 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -48,10 +48,10 @@ class Mpich(Package):
 
     def setup_dependent_environment(self, module, spec, dep_spec):
         """For dependencies, make mpicc's use spack wrapper."""
-        os.environ['MPICH_CC']  = 'cc'
-        os.environ['MPICH_CXX'] = 'c++'
-        os.environ['MPICH_F77'] = 'f77'
-        os.environ['MPICH_F90'] = 'f90'
+        os.environ['MPICH_CC']  = os.environ['CC']
+        os.environ['MPICH_CXX'] = os.environ['CXX']
+        os.environ['MPICH_F77'] = os.environ['F77']
+        os.environ['MPICH_FC'] = os.environ['FC']
 
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index 9c8fa1c694..3c909360a4 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -19,7 +19,9 @@ class Openblas(Package):
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'blas.a')
             symlink('libopenblas.a', 'libblas.a')
+            symlink('libopenblas.so', 'libblas.so')
 
         # Lapack virtual package should provide liblapack.a
         with working_dir(prefix.lib):
             symlink('libopenblas.a', 'liblapack.a')
+            symlink('libopenblas.so', 'liblapack.so')
-- 
cgit v1.2.3-70-g09d2


From 247a4bc75108aa2106c1b191345a0c3387a8afac Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 12 Feb 2016 12:15:09 +0100
Subject: mpich : added back MPI_F90

---
 var/spack/repos/builtin/packages/mpich/package.py | 1 +
 1 file changed, 1 insertion(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 26d3bc0c94..c517defa83 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -51,6 +51,7 @@ class Mpich(Package):
         os.environ['MPICH_CC']  = os.environ['CC']
         os.environ['MPICH_CXX'] = os.environ['CXX']
         os.environ['MPICH_F77'] = os.environ['F77']
+        os.environ['MPICH_F90'] = os.environ['FC']
         os.environ['MPICH_FC'] = os.environ['FC']
 
 
-- 
cgit v1.2.3-70-g09d2


From d8c0edcc818b8f0fb2220993d469381ae072ebe4 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sun, 14 Feb 2016 14:40:25 -0800
Subject: Minor code cleanup for gcc.

---
 var/spack/repos/builtin/packages/gcc/package.py | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index 3e5895cfb8..f8958ee290 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -36,8 +36,6 @@ class Gcc(Package):
     list_url = 'http://open-source-box.org/gcc/'
     list_depth = 2
 
-    DEPENDS_ON_ISL_PREDICATE = '@5.0:'
-
     version('5.3.0', 'c9616fd448f980259c31de613e575719')
     version('5.2.0', 'a51bcfeb3da7dd4c623e27207ed43467')
     version('4.9.3', '6f831b4d251872736e8e9cc09746f327')
@@ -53,12 +51,11 @@ class Gcc(Package):
 
     depends_on("mpfr")
     depends_on("gmp")
-    depends_on("mpc")     # when @4.5:
+    depends_on("mpc", when='@4.5:')
+    depends_on("isl", when='@5.0:')
     depends_on("binutils~libiberty", when='~gold')
     depends_on("binutils~libiberty+gold", when='+gold')
 
-    # Save these until we can do optional deps.
-    depends_on("isl", when=DEPENDS_ON_ISL_PREDICATE)
     #depends_on("ppl")
     #depends_on("cloog")
 
@@ -91,7 +88,7 @@ class Gcc(Package):
                             "--with-as=%s/bin/as" % spec['binutils'].prefix]
         options.extend(binutils_options)
         # Isl
-        if spec.satisfies(Gcc.DEPENDS_ON_ISL_PREDICATE):
+        if 'isl' in spec:
             isl_options = ["--with-isl=%s" % spec['isl'].prefix]
             options.extend(isl_options)
 
-- 
cgit v1.2.3-70-g09d2


From bf162e60f17f8aebcd62184d72a194eb91e4ef4f Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 15 Feb 2016 10:53:50 -0600
Subject: Add latest version

---
 var/spack/repos/builtin/packages/py-mpi4py/package.py | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py
index 8001689a18..f599205644 100644
--- a/var/spack/repos/builtin/packages/py-mpi4py/package.py
+++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py
@@ -5,7 +5,9 @@ class PyMpi4py(Package):
     homepage = "https://pypi.python.org/pypi/mpi4py"
     url      = "https://pypi.python.org/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz"
 
+    version('2.0.0', '4f7d8126d7367c239fd67615680990e3')
     version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c')
+
     extends('python')
     depends_on('py-setuptools')
     depends_on('mpi')
-- 
cgit v1.2.3-70-g09d2


From db50f52bbc47ef6dbe2e26c54ce828c0e6076e96 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 16 Feb 2016 11:40:00 -0800
Subject: Adding the "Crypto++" package installation files.

---
 .../repos/builtin/packages/cryptopp/package.py     | 31 ++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/cryptopp/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
new file mode 100644
index 0000000000..1693c4b160
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -0,0 +1,31 @@
+import glob
+from spack import *
+
+class Cryptopp(Package):
+    """Crypto++ is an open-source C++ library of cryptographic schemes. The
+       library supports a number of different cryptography algorithms, including
+       authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2),
+       public-key encryption (RSA, DSA), and a few obsolete/historical encryption
+       algorithms (MD5, Panama)."""
+
+    homepage = "http://www.cryptopp.com/"
+    url      = "http://www.cryptopp.com/cryptopp563.zip"
+
+    version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
+    version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
+
+    def install(self, spec, prefix):
+        make()
+
+        mkdirp(prefix.include)
+        for hfile in glob.glob('*.h*'):
+            install(hfile, prefix.include)
+
+        mkdirp(prefix.lib)
+        install('libcryptopp.a', prefix.lib)
+
+    def url_for_version(self, version):
+        version_tuple = tuple(v for v in iter(version))
+        version_string = reduce(lambda vs, nv: vs + str(nv), version_tuple, "")
+
+        return "%scryptopp%s.zip" % (Cryptopp.homepage, version_string)
-- 
cgit v1.2.3-70-g09d2


From 9a6221ea40e8cda3bdfa495b7c4a93284e8f4895 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 16 Feb 2016 12:47:14 -0800
Subject: Added the installation files for the "ndiff" package.

---
 var/spack/repos/builtin/packages/ndiff/package.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/ndiff/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/ndiff/package.py b/var/spack/repos/builtin/packages/ndiff/package.py
new file mode 100644
index 0000000000..10e445c81e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ndiff/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+class Ndiff(Package):
+    """The ndiff tool is a binary utility that compares putatively similar files
+       while ignoring small numeric differernces. This utility is most often used
+       to compare files containing a lot of floating-point numeric data that
+       may be slightly different due to numeric error."""
+
+    homepage = "http://ftp.math.utah.edu/pub/ndiff/"
+    url      = "http://ftp.math.utah.edu/pub/ndiff/ndiff-2.00.tar.gz"
+
+    version('2.00', '885548b4dc26e72c5455bebb5ba6c16d')
+    version('1.00', 'f41ffe5d12f36cd36b6311acf46eccdc')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        mkdirp(prefix.bin)
+        mkdirp('%s/lib' % prefix.share)
+
+        make('install-exe', 'install-shrlib')
-- 
cgit v1.2.3-70-g09d2


From 3c8bbeafc78c00cd93fa4526a0e55bf16d36b454 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 16 Feb 2016 13:01:18 -0800
Subject: Added the installation files for the "Triangle" package.

---
 var/spack/repos/builtin/packages/Triangle/package.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/Triangle/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/Triangle/package.py b/var/spack/repos/builtin/packages/Triangle/package.py
new file mode 100644
index 0000000000..f65d93776d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/Triangle/package.py
@@ -0,0 +1,20 @@
+from spack import *
+
+class Triangle(Package):
+    """Triangle is a two-dimensional mesh generator and Delaunay
+       triangulator. Triangle generates exact Delaunay triangulations,
+       constrained Delaunay triangulations, conforming Delaunay
+       triangulations, Voronoi diagrams, and high-quality triangular
+       meshes."""
+
+    homepage = "http://www.cs.cmu.edu/~quake/triangle.html"
+    url      = "http://www.netlib.org/voronoi/triangle.zip"
+
+    version('1.6', '10aff8d7950f5e0e2fb6dd2e340be2c9')
+
+    def install(self, spec, prefix):
+        make()
+        mkdirp(prefix.bin)
+
+        install('triangle', prefix.bin)
+        install('showme', prefix.bin)
-- 
cgit v1.2.3-70-g09d2


From 09254014b182ccf4cbc4ce291141b7ab39b9171d Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 16 Feb 2016 13:24:01 -0800
Subject: Added the installation files for the "TetGen" package.

---
 var/spack/repos/builtin/packages/tetgen/package.py | 28 ++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/tetgen/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py
new file mode 100644
index 0000000000..30c2b76655
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tetgen/package.py
@@ -0,0 +1,28 @@
+from spack import *
+
+class Tetgen(Package):
+    """TetGen is a program and library that can be used to generate tetrahedral
+       meshes for given 3D polyhedral domains. TetGen generates exact constrained
+       Delaunay tetrahedralizations, boundary conforming Delaunay meshes, and
+       Voronoi paritions."""
+
+    homepage = "http://www.tetgen.org"
+    url      = "http://www.tetgen.org/files/tetgen1.4.3.tar.gz"
+
+    version('1.4.3', 'd6a4bcdde2ac804f7ec66c29dcb63c18')
+
+    # TODO: Make this a build dependency once build dependencies are supported
+    # (see: https://github.com/LLNL/spack/pull/378).
+    depends_on('cmake@2.8.7:', when='@1.5.0:')
+
+    def install(self, spec, prefix):
+        make('tetgen', 'tetlib')
+
+        mkdirp(prefix.bin)
+        install('tetgen', prefix.bin)
+
+        mkdirp(prefix.include)
+        install('tetgen.h', prefix.include)
+
+        mkdirp(prefix.lib)
+        install('libtet.a', prefix.lib)
-- 
cgit v1.2.3-70-g09d2


From 8cab10214e63344b77ffc34df3609dbc9f1690a5 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 16 Feb 2016 16:43:24 -0800
Subject: Added the installation files for the "ExodusII" package. Added the
 "+static" variant to "hdf5" to enable "ExodusII" support.

---
 .../builtin/packages/exodusii/exodus-cmake.patch   | 12 ++++++
 .../repos/builtin/packages/exodusii/package.py     | 49 ++++++++++++++++++++++
 var/spack/repos/builtin/packages/hdf5/package.py   |  4 ++
 3 files changed, 65 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch
 create mode 100644 var/spack/repos/builtin/packages/exodusii/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch b/var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch
new file mode 100644
index 0000000000..25355269ca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch
@@ -0,0 +1,12 @@
+diff --git a/cmake-exodus b/cmake-exodus
+index 787fd9d..ed073a2 100755
+--- a/cmake-exodus
++++ b/cmake-exodus
+@@ -1,4 +1,6 @@
+-EXTRA_ARGS=$@
++#!/bin/bash
++
++EXTRA_ARGS=-DSEACASProj_ENABLE_CXX11=OFF
+ 
+ ### Change this to point to the compilers you want to use
+ CC=gcc
diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py
new file mode 100644
index 0000000000..89c04bf79c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/exodusii/package.py
@@ -0,0 +1,49 @@
+from spack import *
+
+# TODO: Add support for a C++11 enabled installation that filters out the
+# TODO: "C++11-Disabled" flag (but only if the spec compiler supports C++11).
+
+# TODO: Add support for parallel installation that uses MPI.
+
+# TODO: Create installation options for NetCDF that support larger page size
+# TODO: suggested by Exodus (see the repository "README" file).
+
+class Exodusii(Package):
+    """Exodus II is a C++/Fortran library developed to store and retrieve data for
+       finite element analyses. It's used for preprocessing (problem definition),
+       postprocessing (results visualization), and data transfer between codes.
+       An Exodus II data file is a random access, machine independent, binary
+       file that is written and read via C, C++, or Fortran API routines."""
+
+    homepage = "https://github.com/gsjaardema/seacas"
+    url      = "https://github.com/gsjaardema/seacas/archive/master.zip"
+
+    version('2016-02-08', git='https://github.com/gsjaardema/seacas.git', commit='dcf3529')
+
+    # TODO: Make this a build dependency once build dependencies are supported
+    # (see: https://github.com/LLNL/spack/pull/378).
+    depends_on('cmake@2.8.7:')
+    depends_on('hdf5+static~mpi')
+    depends_on('netcdf~mpi')
+
+    patch('exodus-cmake.patch')
+
+    def patch(self):
+        ff = FileFilter('cmake-exodus')
+
+        ff.filter('CMAKE_INSTALL_PREFIX:PATH=${ACCESS}',
+            'CMAKE_INSTALL_PREFIX:PATH=%s' % self.spec.prefix, string=True)
+        ff.filter('NetCDF_DIR:PATH=${TPL}',
+            'NetCDF_DIR:PATH=%s' % self.spec['netcdf'].prefix, string=True)
+        ff.filter('HDF5_ROOT:PATH=${TPL}',
+            'HDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix, string=True)
+
+    def install(self, spec, prefix):
+        mkdirp('build')
+        cd('build')
+
+        cmake_exodus = Executable('../cmake-exodus')
+        cmake_exodus()
+
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 80f79539c0..7db4aff631 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -42,6 +42,7 @@ class Hdf5(Package):
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
 
     variant('debug', default=False, description='Builds a debug version of the library')
+    variant('static', default=False, description='Builds a static executable version of the library')
 
     variant('cxx', default=True, description='Enable C++ support')
     variant('fortran', default=True, description='Enable Fortran support')
@@ -78,6 +79,9 @@ class Hdf5(Package):
         else:
             extra_args.append('--enable-production')
 
+        if '+static' in spec:
+            extra_args.append('--enable-static-exec')
+
         if '+unsupported' in spec:
             extra_args.append("--enable-unsupported")
 
-- 
cgit v1.2.3-70-g09d2


From fca7ef2f7b3d8091e935073ec24570ebb163fe6d Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 16 Feb 2016 17:23:37 -0800
Subject: Moved "Triangle" to "triangle" to be more in line with Spack package
 naming conventions.

---
 var/spack/repos/builtin/packages/Triangle/package.py | 20 --------------------
 var/spack/repos/builtin/packages/triangle/package.py | 20 ++++++++++++++++++++
 2 files changed, 20 insertions(+), 20 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/Triangle/package.py
 create mode 100644 var/spack/repos/builtin/packages/triangle/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/Triangle/package.py b/var/spack/repos/builtin/packages/Triangle/package.py
deleted file mode 100644
index f65d93776d..0000000000
--- a/var/spack/repos/builtin/packages/Triangle/package.py
+++ /dev/null
@@ -1,20 +0,0 @@
-from spack import *
-
-class Triangle(Package):
-    """Triangle is a two-dimensional mesh generator and Delaunay
-       triangulator. Triangle generates exact Delaunay triangulations,
-       constrained Delaunay triangulations, conforming Delaunay
-       triangulations, Voronoi diagrams, and high-quality triangular
-       meshes."""
-
-    homepage = "http://www.cs.cmu.edu/~quake/triangle.html"
-    url      = "http://www.netlib.org/voronoi/triangle.zip"
-
-    version('1.6', '10aff8d7950f5e0e2fb6dd2e340be2c9')
-
-    def install(self, spec, prefix):
-        make()
-        mkdirp(prefix.bin)
-
-        install('triangle', prefix.bin)
-        install('showme', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py
new file mode 100644
index 0000000000..f65d93776d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/triangle/package.py
@@ -0,0 +1,20 @@
+from spack import *
+
+class Triangle(Package):
+    """Triangle is a two-dimensional mesh generator and Delaunay
+       triangulator. Triangle generates exact Delaunay triangulations,
+       constrained Delaunay triangulations, conforming Delaunay
+       triangulations, Voronoi diagrams, and high-quality triangular
+       meshes."""
+
+    homepage = "http://www.cs.cmu.edu/~quake/triangle.html"
+    url      = "http://www.netlib.org/voronoi/triangle.zip"
+
+    version('1.6', '10aff8d7950f5e0e2fb6dd2e340be2c9')
+
+    def install(self, spec, prefix):
+        make()
+        mkdirp(prefix.bin)
+
+        install('triangle', prefix.bin)
+        install('showme', prefix.bin)
-- 
cgit v1.2.3-70-g09d2


From 0388093f7aed92bd1d3282fe4f53c27e66030fd4 Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Tue, 16 Feb 2016 17:33:19 -0800
Subject: Changed the hdf5 "+static" variant to become the "+shared" variant.

---
 var/spack/repos/builtin/packages/exodusii/package.py | 2 +-
 var/spack/repos/builtin/packages/hdf5/package.py     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py
index 89c04bf79c..d68baaa6d9 100644
--- a/var/spack/repos/builtin/packages/exodusii/package.py
+++ b/var/spack/repos/builtin/packages/exodusii/package.py
@@ -23,7 +23,7 @@ class Exodusii(Package):
     # TODO: Make this a build dependency once build dependencies are supported
     # (see: https://github.com/LLNL/spack/pull/378).
     depends_on('cmake@2.8.7:')
-    depends_on('hdf5+static~mpi')
+    depends_on('hdf5+shared~mpi')
     depends_on('netcdf~mpi')
 
     patch('exodus-cmake.patch')
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 7db4aff631..f4de92aa83 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -42,7 +42,7 @@ class Hdf5(Package):
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
 
     variant('debug', default=False, description='Builds a debug version of the library')
-    variant('static', default=False, description='Builds a static executable version of the library')
+    variant('shared', default=False, description='Builds a static executable version of the library')
 
     variant('cxx', default=True, description='Enable C++ support')
     variant('fortran', default=True, description='Enable Fortran support')
-- 
cgit v1.2.3-70-g09d2


From 6cd76d69c3fa4b9eb2d30660de28206697af722d Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Wed, 17 Feb 2016 11:51:24 -0800
Subject: Fixed the "+shared" variant in the "hdf5" package.

---
 var/spack/repos/builtin/packages/exodusii/package.py | 2 +-
 var/spack/repos/builtin/packages/hdf5/package.py     | 7 ++++---
 2 files changed, 5 insertions(+), 4 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py
index d68baaa6d9..af258b7e6e 100644
--- a/var/spack/repos/builtin/packages/exodusii/package.py
+++ b/var/spack/repos/builtin/packages/exodusii/package.py
@@ -23,7 +23,7 @@ class Exodusii(Package):
     # TODO: Make this a build dependency once build dependencies are supported
     # (see: https://github.com/LLNL/spack/pull/378).
     depends_on('cmake@2.8.7:')
-    depends_on('hdf5+shared~mpi')
+    depends_on('hdf5~shared~mpi')
     depends_on('netcdf~mpi')
 
     patch('exodus-cmake.patch')
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index f4de92aa83..ed4e7c35c9 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -42,7 +42,7 @@ class Hdf5(Package):
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
 
     variant('debug', default=False, description='Builds a debug version of the library')
-    variant('shared', default=False, description='Builds a static executable version of the library')
+    variant('shared', default=True, description='Builds a shared version of the library')
 
     variant('cxx', default=True, description='Enable C++ support')
     variant('fortran', default=True, description='Enable Fortran support')
@@ -79,7 +79,9 @@ class Hdf5(Package):
         else:
             extra_args.append('--enable-production')
 
-        if '+static' in spec:
+        if '+shared' in spec:
+            extra_args.append('--enable-shared')
+        else:
             extra_args.append('--enable-static-exec')
 
         if '+unsupported' in spec:
@@ -123,7 +125,6 @@ class Hdf5(Package):
         configure(
             "--prefix=%s" % prefix,
             "--with-zlib=%s" % spec['zlib'].prefix,
-            "--enable-shared",  # TODO : this should be enabled by default, remove it?
             *extra_args)
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 19d10291bfeae45315fcef852baddec63b69247a Mon Sep 17 00:00:00 2001
From: "Gregory L. Lee" <lee218@surface86.llnl.gov>
Date: Thu, 18 Feb 2016 15:45:29 -0800
Subject: modify compiler commands in python config files, fix for #431

---
 var/spack/repos/builtin/packages/python/package.py | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index a1ce06feb0..58d401244e 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -55,6 +55,20 @@ class Python(Package):
         make()
         make("install")
 
+        # Modify compiler paths in configuration files. This is necessary for
+        # building site packages outside of spack
+        filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
+                    (r'\4\5'),
+                    join_path(prefix.lib, 'python%d.%d' % self.version[:2], '_sysconfigdata.py'))
+
+        python3_version = ''
+        if spec.satisfies('@3:'):
+            python3_version = '-%d.%dm' % self.version[:2]
+        makefile_filepath = join_path(prefix.lib, 'python%d.%d' % self.version[:2], 'config%s' % python3_version, 'Makefile')
+        filter_file(r'([/s]=?)([\S=]*)/lib/spack/env(/[^\s/]*)?/(\S*)(\s)',
+                    (r'\4\5'),
+                    makefile_filepath)
+
 
     # ========================================================================
     # Set up environment to make install easy for python extensions.
-- 
cgit v1.2.3-70-g09d2


From 30c304748213bee3669c75d4384bad146f68dbd7 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Fri, 19 Feb 2016 12:39:38 +0100
Subject: gromacs : added package

---
 var/spack/repos/builtin/packages/fftw/package.py   |  2 +
 .../repos/builtin/packages/gromacs/package.py      | 56 ++++++++++++++++++++++
 2 files changed, 58 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/gromacs/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py
index 4d2b964242..bc129aaf1a 100644
--- a/var/spack/repos/builtin/packages/fftw/package.py
+++ b/var/spack/repos/builtin/packages/fftw/package.py
@@ -47,6 +47,8 @@ class Fftw(Package):
 
     depends_on('mpi', when='+mpi')
 
+    # TODO : add support for architecture specific optimizations as soon as targets are supported
+
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix,
                    '--enable-shared',
diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py
new file mode 100644
index 0000000000..5fe8399308
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gromacs/package.py
@@ -0,0 +1,56 @@
+from spack import *
+
+
+class Gromacs(Package):
+    """
+    GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for
+    simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry
+    department of University of Groningen, and is now maintained by contributors in universities and research centers
+    across the world.
+
+    GROMACS is one of the fastest and most popular software packages available and can run on CPUs as well as GPUs.
+    It is free, open source released under the GNU General Public License. Starting from version 4.6, GROMACS is
+    released under the GNU Lesser General Public License.
+    """
+
+    homepage = 'http://www.gromacs.org'
+    url = 'ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.1.2.tar.gz'
+
+    version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98')
+
+    variant('mpi', default=True, description='Activate MPI support')
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('debug', default=False, description='Enables debug mode')
+    variant('double', default=False, description='Produces a double precision version of the executables')
+
+    depends_on('mpi', when='+mpi')
+
+    depends_on('fftw')
+
+    # TODO : add GPU support
+
+    def install(self, spec, prefix):
+
+        options = []
+
+        if '+mpi' in spec:
+            options.append('-DGMX_MPI:BOOL=ON')
+
+        if '+double' in spec:
+            options.append('-DGMX_DOUBLE:BOOL=ON')
+
+        if '~shared' in spec:
+            options.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
+
+        if '+debug' in spec:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Debug')
+        else:
+            options.append('-DCMAKE_BUILD_TYPE:STRING=Release')
+
+        options.extend(std_cmake_args)
+
+        with working_dir('spack-build', create=True):
+
+            cmake('..', *options)
+            make()
+            make('install')
-- 
cgit v1.2.3-70-g09d2


From 5c8dd6c3c86400ac82b061ce45f58b543526bfff Mon Sep 17 00:00:00 2001
From: Tom Scogland <scogland1@llnl.gov>
Date: Sat, 20 Feb 2016 17:18:49 -0800
Subject: llvm trunk version

Adding a trunk version to the llvm package.  This has all the features
and requirements of the others, with the additional caveat that the llvm
project makes no guarantee that trunk on all repositories together will
necessarily make a working compiler.  It has been tested, and worked
with a version today, but not yesterday, so if you test keep that in
mind.
---
 var/spack/repos/builtin/packages/llvm/package.py | 43 +++++++++++++++++++-----
 1 file changed, 34 insertions(+), 9 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 1805d3ded8..a8f19f9071 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -117,6 +117,21 @@ class Llvm(Package):
                     },
                 }
     releases = [
+                  {
+                    'version' : 'trunk',
+                    'repo' : 'http://llvm.org/svn/llvm-project/llvm/trunk',
+                    'resources' : {
+                        'compiler-rt' : 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
+                        'openmp' : 'http://llvm.org/svn/llvm-project/openmp/trunk',
+                        'polly' : 'http://llvm.org/svn/llvm-project/polly/trunk',
+                        'libcxx' : 'http://llvm.org/svn/llvm-project/libcxx/trunk',
+                        'libcxxabi' : 'http://llvm.org/svn/llvm-project/libcxxabi/trunk',
+                        'clang' : 'http://llvm.org/svn/llvm-project/cfe/trunk',
+                        'clang-tools-extra' : 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
+                        'lldb' : 'http://llvm.org/svn/llvm-project/lldb/trunk',
+                        'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
+                        }
+                  },
                   {
                     'version' : '3.7.0',
                     'md5':'b98b9495e5655a672d6cb83e1a180f8e',
@@ -161,15 +176,25 @@ class Llvm(Package):
                ]
 
     for release in releases:
-        version(release['version'], release['md5'], url=llvm_url % release)
-
-        for name, md5 in release['resources'].items():
-            resource(name=name,
-                     url=resources[name]['url'] % release,
-                     md5=md5,
-                     destination=resources[name]['destination'],
-                     when='@%(version)s' % release,
-                     placement=resources[name].get('placement', None))
+        if release['version'] == 'trunk' :
+            version(release['version'], svn=release['repo'])
+
+            for name, repo in release['resources'].items():
+                resource(name=name,
+                         svn=repo,
+                         destination=resources[name]['destination'],
+                         when='@%(version)s' % release,
+                         placement=resources[name].get('placement', None))
+        else:
+            version(release['version'], release['md5'], url=llvm_url % release)
+
+            for name, md5 in release['resources'].items():
+                resource(name=name,
+                         url=resources[name]['url'] % release,
+                         md5=md5,
+                         destination=resources[name]['destination'],
+                         when='@%(version)s' % release,
+                         placement=resources[name].get('placement', None))
 
     # SVN - current develop
     version('develop', svn='http://llvm.org/svn/llvm-project/llvm/trunk')
-- 
cgit v1.2.3-70-g09d2


From 976ae91dccd36d1feb6d0d20cd1ef5b3470c4c39 Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 24 Feb 2016 14:11:57 +0100
Subject: llvm : removed duplicate version

---
 var/spack/repos/builtin/packages/llvm/package.py | 19 -------------------
 1 file changed, 19 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index a8f19f9071..934d994bd3 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -196,25 +196,6 @@ class Llvm(Package):
                          when='@%(version)s' % release,
                          placement=resources[name].get('placement', None))
 
-    # SVN - current develop
-    version('develop', svn='http://llvm.org/svn/llvm-project/llvm/trunk')
-    resource(name='clang', svn='http://llvm.org/svn/llvm-project/cfe/trunk',
-             destination='tools', when='@develop', placement='clang')
-    resource(name='compiler-rt', svn='http://llvm.org/svn/llvm-project/compiler-rt/trunk',
-             destination='projects', when='@develop', placement='compiler-rt')
-    resource(name='openmp', svn='http://llvm.org/svn/llvm-project/openmp/trunk',
-             destination='projects', when='@develop', placement='openmp')
-    resource(name='libcxx', svn='http://llvm.org/svn/llvm-project/libcxx/trunk',
-             destination='projects', when='@develop', placement='libcxx')
-    resource(name='libcxxabi', svn='http://llvm.org/svn/llvm-project/libcxxabi/trunk',
-             destination='projects', when='@develop', placement='libcxxabi')
-    resource(name='polly', svn='http://llvm.org/svn/llvm-project/polly/trunk',
-             destination='tools', when='@develop', placement='polly')
-    resource(name='lldb', svn='http://llvm.org/svn/llvm-project/lldb/trunk',
-             destination='tools', when='@develop', placement='lldb')
-
-
-
     def install(self, spec, prefix):
         env['CXXFLAGS'] = self.compiler.cxx11_flag
         cmake_args = [ arg for arg in std_cmake_args if 'BUILD_TYPE' not in arg ]
-- 
cgit v1.2.3-70-g09d2


From 20845a739f15190cf9610da4375d3e3c9fc61b6b Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Wed, 24 Feb 2016 22:18:51 -0500
Subject: Libevent depends on OpenSSL

---
 var/spack/repos/builtin/packages/libevent/package.py | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py
index 11b1083d67..2a44c49325 100644
--- a/var/spack/repos/builtin/packages/libevent/package.py
+++ b/var/spack/repos/builtin/packages/libevent/package.py
@@ -23,6 +23,9 @@ class Libevent(Package):
     version('2.0.12', '42986228baf95e325778ed328a93e070')
 
 
+    depends_on('openssl')
+
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
 
-- 
cgit v1.2.3-70-g09d2


From 30d9ca2bde033da28b6f6105f93ee05f4fd0acfa Mon Sep 17 00:00:00 2001
From: Joseph Ciurej <ciurej1@llnl.gov>
Date: Fri, 26 Feb 2016 16:06:17 -0800
Subject: Updated the silo package and added the '+fortran' variant.

---
 var/spack/repos/builtin/packages/silo/package.py | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index 9eda11df15..d1aed78e0e 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -1,19 +1,28 @@
 from spack import *
 
 class Silo(Package):
-    """Silo is a library for reading and writing a wide variety of scientific data to binary, disk files."""
+    """Silo is a library for reading and writing a wide variety of scientific
+       data to binary, disk files."""
 
     homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
     url      = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.8/silo-4.8.tar.gz"
 
-    #version('4.9', 'a83eda4f06761a86726e918fc55e782a')
     version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
 
-    depends_on("hdf5@:1.8.12")
+    variant('fortran', default=True, description='Enable Fortran support')
+
+    depends_on("hdf5")
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
-                  "--with-hdf5=%s" %spec['hdf5'].prefix)
+        config_args = [
+            '--enable-fortran' if '+fortran' in spec else '--disable-fortran',
+        ]
+
+        configure(
+            "--prefix=%s" % prefix,
+            "--with-hdf5=%s,%s" % (spec['hdf5'].prefix.include, spec['hdf5'].prefix.lib),
+            "--with-zlib=%s,%s" % (spec['zlib'].prefix.include, spec['zlib'].prefix.lib),
+            *config_args)
 
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 8f3ac9ac8b7b1d16672e7a52f691966de1f8483f Mon Sep 17 00:00:00 2001
From: Luigi Calori <luigi.calori@gmail.com>
Date: Sat, 27 Feb 2016 01:40:32 +0100
Subject: adding new version to praview, compiled with spack -d install -j 8
 --keep-stage paraview@5.0.0+qt+python+tcl+opengl2%gcc@4.8.2 ^netcdf -mpi

---
 var/spack/repos/builtin/packages/paraview/package.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index e43bdd4493..ccf2d14c06 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -2,9 +2,11 @@ from spack import *
 
 class Paraview(Package):
     homepage = 'http://www.paraview.org'
-    url      = 'http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz'
+    url      = 'http://www.paraview.org/files/v5.0/ParaView-v'
+    _url_str = 'http://www.paraview.org/files/v%s/ParaView-v%s-source.tar.gz'
 
-    version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378', url='http://www.paraview.org/files/v4.4/ParaView-v4.4.0-source.tar.gz')
+    version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378')
+    version('5.0.0', '4598f0b421460c8bbc635c9a1c3bdbee')
 
     variant('python', default=False, description='Enable Python support')
 
@@ -25,8 +27,8 @@ class Paraview(Package):
 
     depends_on('bzip2')
     depends_on('freetype')
-    depends_on('hdf5')
     depends_on('hdf5+mpi', when='+mpi')
+    depends_on('hdf5~mpi', when='~mpi')
     depends_on('jpeg')
     depends_on('libpng')
     depends_on('libtiff')
@@ -35,6 +37,11 @@ class Paraview(Package):
     #depends_on('protobuf') # version mismatches?
     #depends_on('sqlite') # external version not supported
     depends_on('zlib')
+    
+    def url_for_version(self, version):
+        """Handle ParaView version-based custom URLs."""
+        return self._url_str % (version.up_to(2), version)
+    
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
-- 
cgit v1.2.3-70-g09d2


From 67f327f805868d369eec0392631392281b68c39d Mon Sep 17 00:00:00 2001
From: Ian Lee <lee1001@llnl.gov>
Date: Sun, 28 Feb 2016 19:47:19 -0800
Subject: Updated links to use new llnl.gov address

---
 README.md                                           | 4 ++--
 lib/spack/docs/getting_started.rst                  | 2 +-
 lib/spack/spack/cmd/repo.py                         | 2 +-
 lib/spack/spack/repository.py                       | 2 +-
 lib/spack/spack/resource.py                         | 2 +-
 lib/spack/spack/test/namespace_trie.py              | 2 +-
 lib/spack/spack/test/tally_plugin.py                | 8 ++++----
 var/spack/repos/builtin/packages/gdb/package.py     | 2 +-
 var/spack/repos/builtin/packages/texinfo/package.py | 2 +-
 9 files changed, 13 insertions(+), 13 deletions(-)

(limited to 'var')

diff --git a/README.md b/README.md
index bdce345764..8664953c0c 100644
--- a/README.md
+++ b/README.md
@@ -19,7 +19,7 @@ written in pure Python, and specs allow package authors to write a
 single build script for many different builds of the same package.
 
 See the
-[Feature Overview](http://llnl.github.io/spack/features.html)
+[Feature Overview](http://software.llnl.gov/spack/features.html)
 for examples and highlights.
 
 To install spack and install your first package:
@@ -31,7 +31,7 @@ To install spack and install your first package:
 Documentation
 ----------------
 
-[**Full documentation**](http://llnl.github.io/spack) for Spack is
+[**Full documentation**](http://software.llnl.gov/spack) for Spack is
 the first place to look.
 
 See also:
diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst
index 67ca18e71a..2c5b68ea65 100644
--- a/lib/spack/docs/getting_started.rst
+++ b/lib/spack/docs/getting_started.rst
@@ -22,7 +22,7 @@ go:
    $ spack install libelf
 
 For a richer experience, use Spack's `shell support
-<http://llnl.github.io/spack/basic_usage.html#environment-modules>`_:
+<http://software.llnl.gov/spack/basic_usage.html#environment-modules>`_:
 
 .. code-block:: sh
 
diff --git a/lib/spack/spack/cmd/repo.py b/lib/spack/spack/cmd/repo.py
index 34c755fb67..908f5400ab 100644
--- a/lib/spack/spack/cmd/repo.py
+++ b/lib/spack/spack/cmd/repo.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
diff --git a/lib/spack/spack/repository.py b/lib/spack/spack/repository.py
index f58cd52125..e8d0cc09ec 100644
--- a/lib/spack/spack/repository.py
+++ b/lib/spack/spack/repository.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
diff --git a/lib/spack/spack/resource.py b/lib/spack/spack/resource.py
index 2bf92947fd..ddfaaf4cb0 100644
--- a/lib/spack/spack/resource.py
+++ b/lib/spack/spack/resource.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
diff --git a/lib/spack/spack/test/namespace_trie.py b/lib/spack/spack/test/namespace_trie.py
index d0d809004d..647976df21 100644
--- a/lib/spack/spack/test/namespace_trie.py
+++ b/lib/spack/spack/test/namespace_trie.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
diff --git a/lib/spack/spack/test/tally_plugin.py b/lib/spack/spack/test/tally_plugin.py
index 9ca898c47c..e0b9618e0c 100644
--- a/lib/spack/spack/test/tally_plugin.py
+++ b/lib/spack/spack/test/tally_plugin.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://scalability-llnl.github.io/spack
+# For details, see https://scalability-software.llnl.gov/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
@@ -34,7 +34,7 @@ class Tally(Plugin):
         self.successCount = 0
         self.failCount = 0
         self.errorCount = 0
-    
+
     @property
     def numberOfTestsRun(self):
         """Excludes skipped tests"""
@@ -48,10 +48,10 @@ class Tally(Plugin):
 
     def addSuccess(self, test):
         self.successCount += 1
-        
+
     def addError(self, test, err):
         self.errorCount += 1
-            
+
     def addFailure(self, test, err):
         self.failCount += 1
 
diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py
index dd02b426b9..b346fe80c2 100644
--- a/var/spack/repos/builtin/packages/gdb/package.py
+++ b/var/spack/repos/builtin/packages/gdb/package.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
diff --git a/var/spack/repos/builtin/packages/texinfo/package.py b/var/spack/repos/builtin/packages/texinfo/package.py
index a83c10c0c1..6cf8d79072 100644
--- a/var/spack/repos/builtin/packages/texinfo/package.py
+++ b/var/spack/repos/builtin/packages/texinfo/package.py
@@ -6,7 +6,7 @@
 # Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
 # LLNL-CODE-647188
 #
-# For details, see https://llnl.github.io/spack
+# For details, see https://software.llnl.gov/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
-- 
cgit v1.2.3-70-g09d2


From e414c5fdfbc91e5934ee59233475f8f862e2e0ce Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Mon, 29 Feb 2016 22:31:18 -0500
Subject: Added missing cmake dependencies

---
 var/spack/repos/builtin/packages/cgal/package.py  | 1 +
 var/spack/repos/builtin/packages/curl/package.py  | 6 +++---
 var/spack/repos/builtin/packages/expat/package.py | 1 +
 3 files changed, 5 insertions(+), 3 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py
index 97356433be..ef4a2736db 100644
--- a/var/spack/repos/builtin/packages/cgal/package.py
+++ b/var/spack/repos/builtin/packages/cgal/package.py
@@ -46,6 +46,7 @@ class Cgal(Package):
     depends_on('mpfr')
     depends_on('gmp')
     depends_on('zlib')
+    depends_on('cmake')
 
     # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL)
     # FIXME : Optional third party libraries missing
diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py
index 9e684445c7..6c302281a7 100644
--- a/var/spack/repos/builtin/packages/curl/package.py
+++ b/var/spack/repos/builtin/packages/curl/package.py
@@ -13,13 +13,13 @@ class Curl(Package):
     version('7.43.0', '11bddbb452a8b766b932f859aaeeed39')
     version('7.42.1', '296945012ce647b94083ed427c1877a8')
 
-    depends_on("openssl")
+#    depends_on("openssl")
     depends_on("zlib")
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix,
-                  '--with-zlib=%s' % spec['zlib'].prefix,
-                  '--with-ssl=%s' % spec['openssl'].prefix)
+                  '--with-zlib=%s' % spec['zlib'].prefix)
+#                  '--with-ssl=%s' % spec['openssl'].prefix)
 
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py
index 082da5bf0b..3f925c6546 100644
--- a/var/spack/repos/builtin/packages/expat/package.py
+++ b/var/spack/repos/builtin/packages/expat/package.py
@@ -7,6 +7,7 @@ class Expat(Package):
 
     version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd')
 
+    depends_on('cmake')
 
     def install(self, spec, prefix):
 
-- 
cgit v1.2.3-70-g09d2


From 15ae92aae9c8ac521bb5d7ee5f210d265494d87a Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Mon, 29 Feb 2016 22:59:28 -0500
Subject: New packages added: blitz, netcdf-cxx4, netcdf-fortran, proj,
 udunits2

---
 var/spack/repos/builtin/packages/blitz/package.py  | 40 +++++++++++++++++++++
 .../repos/builtin/packages/netcdf-cxx4/package.py  | 41 ++++++++++++++++++++++
 .../builtin/packages/netcdf-fortran/package.py     | 21 +++++++++++
 var/spack/repos/builtin/packages/proj/package.py   | 37 +++++++++++++++++++
 .../repos/builtin/packages/udunits2/package.py     | 16 +++++++++
 5 files changed, 155 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/blitz/package.py
 create mode 100644 var/spack/repos/builtin/packages/netcdf-cxx4/package.py
 create mode 100644 var/spack/repos/builtin/packages/netcdf-fortran/package.py
 create mode 100644 var/spack/repos/builtin/packages/proj/package.py
 create mode 100644 var/spack/repos/builtin/packages/udunits2/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/blitz/package.py b/var/spack/repos/builtin/packages/blitz/package.py
new file mode 100644
index 0000000000..82ff634925
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blitz/package.py
@@ -0,0 +1,40 @@
+# FIXME:
+# This is a template package file for Spack.  We've conveniently
+# put "FIXME" labels next to all the things you'll want to change.
+#
+# Once you've edited all the FIXME's, delete this whole message,
+# save this file, and test out your package like this:
+#
+#     spack install blitz
+#
+# You can always get back here to change things with:
+#
+#     spack edit blitz
+#
+# See the spack documentation for more information on building
+# packages.
+#
+from spack import *
+
+class Blitz(Package):
+    """N-dimensional arrays for C++"""
+    homepage = "http://github.com/blitzpp/blitz"
+
+# This version doesn't have the configure script generated yet.
+    url      = "https://github.com/blitzpp/blitz/tarball/1.0.0"
+#http://prdownloads.sourceforge.net/%(namelower)s
+
+    version('1.0.0', '9f040b9827fe22228a892603671a77af')
+
+    # FIXME: Add dependencies if this package requires them.
+    # depends_on("foo")
+
+    def install(self, spec, prefix):
+        # FIXME: Modify the configure line to suit your build system here.
+        # FIXME: Spack couldn't guess one, so here are some options:
+        configure('--prefix=%s' % prefix)
+        # cmake('.', *std_cmake_args)
+
+        # FIXME: Add logic to build and install here
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
new file mode 100644
index 0000000000..9d70eab05f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -0,0 +1,41 @@
+# FIXME:
+# This is a template package file for Spack.  We've conveniently
+# put "FIXME" labels next to all the things you'll want to change.
+#
+# Once you've edited all the FIXME's, delete this whole message,
+# save this file, and test out your package like this:
+#
+#     spack install netcdf-cxx4
+#
+# You can always get back here to change things with:
+#
+#     spack edit netcdf-cxx4
+#
+# See the spack documentation for more information on building
+# packages.
+#
+from spack import *
+
+class NetcdfCxx4(Package):
+    """C++ interface for NetCDF4"""
+    homepage = "http://www.unidata.ucar.edu/downloads/netcdf/netcdf-cxx/index.jsp"
+    url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.2.tar.gz"
+
+    version('4.2', 'd019853802092cf686254aaba165fc81')
+
+
+    variant('mpi', default=True, description='Enables MPI parallelism')
+#    variant('hdf4',    default=False, description="Enable HDF4 support")
+
+    # NetCDF-CXX4 doesn't really depend (directly) on MPI.  However... this
+    # depndency ensures taht the right version of MPI is selected (eg: ^openmpi)
+    depends_on('mpi', when='+mpi')
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        # FIXME: Modify the configure line to suit your build system here.
+        configure('--prefix=%s' % prefix)
+
+        # FIXME: Add logic to build and install here
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
new file mode 100644
index 0000000000..8e5c8ecc3a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -0,0 +1,21 @@
+from spack import *
+
+class NetcdfFortran(Package):
+    """Fortran interface for NetCDF4"""
+
+    homepage = "http://www.unidata.ucar.edu/downloads/netcdf/netcdf-cxx/index.jsp"
+    url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz"
+
+    version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
+
+    variant('mpi', default=True, description='Enables MPI parallelism')
+
+    # NetCDF-CXX4 doesn't really depend (directly) on MPI.  However... this
+    # depndency ensures taht the right version of MPI is selected (eg: ^openmpi)
+    depends_on('mpi', when='+mpi')
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py
new file mode 100644
index 0000000000..4a0d3feac7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/proj/package.py
@@ -0,0 +1,37 @@
+# FIXME:
+# This is a template package file for Spack.  We've conveniently
+# put "FIXME" labels next to all the things you'll want to change.
+#
+# Once you've edited all the FIXME's, delete this whole message,
+# save this file, and test out your package like this:
+#
+#     spack install proj
+#
+# You can always get back here to change things with:
+#
+#     spack edit proj
+#
+# See the spack documentation for more information on building
+# packages.
+#
+from spack import *
+
+class Proj(Package):
+    """Cartographic Projections"""
+    homepage = "https://github.com/OSGeo/proj.4/wiki"
+    url      = "http://download.osgeo.org/proj/proj-4.9.2.tar.gz"
+
+    version('4.9.2', '9843131676e31bbd903d60ae7dc76cf9')
+    version('4.9.1', '3cbb2a964fd19a496f5f4265a717d31c')
+    version('4.8.0', 'd815838c92a29179298c126effbb1537')
+    version('4.7.0', '927d34623b52e0209ba2bfcca18fe8cd')
+    version('4.6.1', '7dbaab8431ad50c25669fd3fb28dc493')
+
+    # FIXME: Add dependencies if this package requires them.
+    # depends_on("foo")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits2/package.py
new file mode 100644
index 0000000000..9954a733bb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/udunits2/package.py
@@ -0,0 +1,16 @@
+from spack import *
+
+class Udunits2(Package):
+    """Automated units conversion"""
+
+    homepage = "http://www.unidata.ucar.edu/software/udunits"
+    url      = "ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.20.tar.gz"
+
+    version('2.2.20', '1586b70a49dfe05da5fcc29ef239dce0')
+
+    depends_on('expat')
+
+    def install(self, spec, prefix):
+        configure("--prefix=%s" % prefix)
+        make()
+        make("install")
-- 
cgit v1.2.3-70-g09d2


From eb1d90a8cfadeb556754b57e5d21e5605b9a0e9d Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Mon, 29 Feb 2016 23:31:54 -0500
Subject: Undid accidental change on this branch.

---
 var/spack/repos/builtin/packages/curl/package.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py
index 6c302281a7..9e684445c7 100644
--- a/var/spack/repos/builtin/packages/curl/package.py
+++ b/var/spack/repos/builtin/packages/curl/package.py
@@ -13,13 +13,13 @@ class Curl(Package):
     version('7.43.0', '11bddbb452a8b766b932f859aaeeed39')
     version('7.42.1', '296945012ce647b94083ed427c1877a8')
 
-#    depends_on("openssl")
+    depends_on("openssl")
     depends_on("zlib")
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix,
-                  '--with-zlib=%s' % spec['zlib'].prefix)
-#                  '--with-ssl=%s' % spec['openssl'].prefix)
+                  '--with-zlib=%s' % spec['zlib'].prefix,
+                  '--with-ssl=%s' % spec['openssl'].prefix)
 
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 8174489787c56cee1726ca36799c236e4869f471 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Tue, 1 Mar 2016 15:25:57 -0700
Subject: + Provide two new variants for cmake:   1) +qt          - build the
 cmake-gui Qt application.                   - adds a dependency on Qt.   2)
 +sphinxbuild - build the html CMake documentation.                   - adds a
 dependency on python and py-sphinx

---
 var/spack/repos/builtin/packages/cmake/package.py | 26 +++++++++++++++++++----
 1 file changed, 22 insertions(+), 4 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index e20c1e4aeb..f39a681284 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -37,16 +37,34 @@ class Cmake(Package):
     version('2.8.10.2', '097278785da7182ec0aea8769d06860c')
 
     variant('ncurses', default=True, description='Enables the build of the ncurses gui')
+    variant('qt', default=False, description='Enables the build of cmake-gui')
+    variant('sphinxbuild', default=False, description='Enables the generation of html and man page documentation')
+
     depends_on('ncurses', when='+ncurses')
+    depends_on('qt', when='+qt')
+    depends_on('python@2.7.11:', when='+sphinxbuild')
+    depends_on('py-sphinx', when='+sphinxbuild')
 
     def url_for_version(self, version):
         """Handle CMake's version-based custom URLs."""
         return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version)
 
-
     def install(self, spec, prefix):
-        configure('--prefix='   + prefix,
-                  '--parallel=' + str(make_jobs),
-                  '--', '-DCMAKE_USE_OPENSSL=ON')
+
+        options = ['--prefix=%s' % prefix]
+        options.append('--parallel=%s' % str(make_jobs))
+
+        if '+qt' in spec:
+            options.append('--qt-gui')
+
+        if '+sphinxbuild' in spec:
+            options.append('--sphinx-html')
+            options.append('--sphinx-man')
+
+        options.append('--')
+        options.append('-DCMAKE_USE_OPENSSL=ON')
+
+        configure(*options)
+
         make()
         make('install')
-- 
cgit v1.2.3-70-g09d2


From 976d0240c467b9ff74333fafcd2ac1e896819a80 Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Wed, 2 Mar 2016 18:58:47 -0500
Subject: Removed FIXMEs.

---
 var/spack/repos/builtin/packages/blitz/package.py  | 27 +---------------------
 .../repos/builtin/packages/netcdf-cxx4/package.py  | 21 +----------------
 .../builtin/packages/netcdf-fortran/package.py     |  2 +-
 var/spack/repos/builtin/packages/proj/package.py   | 19 +--------------
 4 files changed, 4 insertions(+), 65 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/blitz/package.py b/var/spack/repos/builtin/packages/blitz/package.py
index 82ff634925..9413b276fe 100644
--- a/var/spack/repos/builtin/packages/blitz/package.py
+++ b/var/spack/repos/builtin/packages/blitz/package.py
@@ -1,40 +1,15 @@
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-#     spack install blitz
-#
-# You can always get back here to change things with:
-#
-#     spack edit blitz
-#
-# See the spack documentation for more information on building
-# packages.
-#
 from spack import *
 
 class Blitz(Package):
     """N-dimensional arrays for C++"""
     homepage = "http://github.com/blitzpp/blitz"
-
-# This version doesn't have the configure script generated yet.
     url      = "https://github.com/blitzpp/blitz/tarball/1.0.0"
-#http://prdownloads.sourceforge.net/%(namelower)s
 
     version('1.0.0', '9f040b9827fe22228a892603671a77af')
 
-    # FIXME: Add dependencies if this package requires them.
-    # depends_on("foo")
+    # No dependencies
 
     def install(self, spec, prefix):
-        # FIXME: Modify the configure line to suit your build system here.
-        # FIXME: Spack couldn't guess one, so here are some options:
         configure('--prefix=%s' % prefix)
-        # cmake('.', *std_cmake_args)
-
-        # FIXME: Add logic to build and install here
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
index 9d70eab05f..8d51a10679 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -1,19 +1,3 @@
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-#     spack install netcdf-cxx4
-#
-# You can always get back here to change things with:
-#
-#     spack edit netcdf-cxx4
-#
-# See the spack documentation for more information on building
-# packages.
-#
 from spack import *
 
 class NetcdfCxx4(Package):
@@ -25,17 +9,14 @@ class NetcdfCxx4(Package):
 
 
     variant('mpi', default=True, description='Enables MPI parallelism')
-#    variant('hdf4',    default=False, description="Enable HDF4 support")
 
-    # NetCDF-CXX4 doesn't really depend (directly) on MPI.  However... this
+    # netcdf-cxx4 doesn't really depend (directly) on MPI.  However... this
     # depndency ensures taht the right version of MPI is selected (eg: ^openmpi)
     depends_on('mpi', when='+mpi')
     depends_on('netcdf')
 
     def install(self, spec, prefix):
-        # FIXME: Modify the configure line to suit your build system here.
         configure('--prefix=%s' % prefix)
 
-        # FIXME: Add logic to build and install here
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index 8e5c8ecc3a..9e4aee95fb 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -10,7 +10,7 @@ class NetcdfFortran(Package):
 
     variant('mpi', default=True, description='Enables MPI parallelism')
 
-    # NetCDF-CXX4 doesn't really depend (directly) on MPI.  However... this
+    # netcdf-fortran doesn't really depend (directly) on MPI.  However... this
     # depndency ensures taht the right version of MPI is selected (eg: ^openmpi)
     depends_on('mpi', when='+mpi')
     depends_on('netcdf')
diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py
index 4a0d3feac7..797772f4f6 100644
--- a/var/spack/repos/builtin/packages/proj/package.py
+++ b/var/spack/repos/builtin/packages/proj/package.py
@@ -1,19 +1,3 @@
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-#     spack install proj
-#
-# You can always get back here to change things with:
-#
-#     spack edit proj
-#
-# See the spack documentation for more information on building
-# packages.
-#
 from spack import *
 
 class Proj(Package):
@@ -27,8 +11,7 @@ class Proj(Package):
     version('4.7.0', '927d34623b52e0209ba2bfcca18fe8cd')
     version('4.6.1', '7dbaab8431ad50c25669fd3fb28dc493')
 
-    # FIXME: Add dependencies if this package requires them.
-    # depends_on("foo")
+    # No dependencies
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
-- 
cgit v1.2.3-70-g09d2


From 7183db1b7df3bce7e5f174ce38a50476c2e3b218 Mon Sep 17 00:00:00 2001
From: Scott Pakin <pakin@lanl.gov>
Date: Thu, 3 Mar 2016 11:30:57 -0700
Subject: Added LLVM 3.7.1 support

---
 var/spack/repos/builtin/packages/llvm/package.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 934d994bd3..280e400f69 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -1,5 +1,5 @@
 ##############################################################################
-# Copyright (c) 2013, Lawrence Livermore National Security, LLC.
+# Copyright (c) 2016, Lawrence Livermore National Security, LLC.
 # Produced at the Lawrence Livermore National Laboratory.
 #
 # This file is part of Spack.
@@ -34,7 +34,7 @@ class Llvm(Package):
        it is the full name of the project.
     """
     homepage = 'http://llvm.org/'
-    url = 'http://llvm.org/releases/3.7.0/llvm-3.7.0.src.tar.xz'
+    url = 'http://llvm.org/releases/3.7.1/llvm-3.7.1.src.tar.xz'
 
     version('3.0', 'a8e5f5f1c1adebae7b4a654c376a6005', url='http://llvm.org/releases/3.0/llvm-3.0.tar.gz') # currently required by mesa package
 
@@ -132,6 +132,21 @@ class Llvm(Package):
                         'llvm-libunwind' : 'http://llvm.org/svn/llvm-project/libunwind/trunk',
                         }
                   },
+                  {
+                    'version' : '3.7.1',
+                    'md5':'bf8b3a2c79e61212c5409041dfdbd319',
+                    'resources' : {
+                        'compiler-rt' : '1c6975daf30bb3b0473b53c3a1a6ff01',
+                        'openmp' : 'b4ad08cda4e5c22e42b66062b140438e',
+                        'polly' : '3a2a7367002740881637f4d47bca4dc3',
+                        'libcxx' : 'f9c43fa552a10e14ff53b94d04bea140',
+                        'libcxxabi' : '52d925afac9f97e9dcac90745255c169',
+                        'clang' : '0acd026b5529164197563d135a8fd83e',
+                        'clang-tools-extra' : '5d49ff745037f061a7c86aeb6a24c3d2',
+                        'lldb' : 'a106d8a0d21fc84d76953822fbaf3398',
+                        'llvm-libunwind' : '814bd52c9247c5d04629658fbcb3ab8c',
+                        }
+                  },
                   {
                     'version' : '3.7.0',
                     'md5':'b98b9495e5655a672d6cb83e1a180f8e',
-- 
cgit v1.2.3-70-g09d2


From 0eb6ef2cd031d1668e1891425bdc6234df0594df Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Fri, 4 Mar 2016 11:09:40 -0500
Subject: 1. Removed fake MPI dependency from netcdf-cxx4 and netcdf-fortran.

2. Removed Fortran bootstrap variant from netcdf.  Users who need NetCDF Fortran interface should install netcdf-fortran.

3. Added result of ./configure --help on the netcdf-fortran.  Verified  the package has no additional options that should be exposed through Spack.
---
 .../repos/builtin/packages/netcdf-cxx4/package.py  |   6 -
 .../builtin/packages/netcdf-fortran/package.py     | 156 ++++++++++++++++++++-
 var/spack/repos/builtin/packages/netcdf/package.py |  12 +-
 3 files changed, 154 insertions(+), 20 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
index 8d51a10679..fb4c2886cd 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -7,12 +7,6 @@ class NetcdfCxx4(Package):
 
     version('4.2', 'd019853802092cf686254aaba165fc81')
 
-
-    variant('mpi', default=True, description='Enables MPI parallelism')
-
-    # netcdf-cxx4 doesn't really depend (directly) on MPI.  However... this
-    # depndency ensures taht the right version of MPI is selected (eg: ^openmpi)
-    depends_on('mpi', when='+mpi')
     depends_on('netcdf')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index 9e4aee95fb..4e0b14d012 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -10,12 +10,162 @@ class NetcdfFortran(Package):
 
     variant('mpi', default=True, description='Enables MPI parallelism')
 
-    # netcdf-fortran doesn't really depend (directly) on MPI.  However... this
-    # depndency ensures taht the right version of MPI is selected (eg: ^openmpi)
-    depends_on('mpi', when='+mpi')
     depends_on('netcdf')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
         make("install")
+
+
+
+
+# netcdf-fortran configure parameters are below
+# ---------------------------------------------
+#
+# `configure' configures netCDF-Fortran 4.4.3 to adapt to many kinds of systems.
+# 
+# Usage: ./configure [OPTION]... [VAR=VALUE]...
+# 
+# To assign environment variables (e.g., CC, CFLAGS...), specify them as
+# VAR=VALUE.  See below for descriptions of some of the useful variables.
+# 
+# Defaults for the options are specified in brackets.
+# 
+# Configuration:
+#   -h, --help              display this help and exit
+#       --help=short        display options specific to this package
+#       --help=recursive    display the short help of all the included packages
+#   -V, --version           display version information and exit
+#   -q, --quiet, --silent   do not print `checking ...' messages
+#       --cache-file=FILE   cache test results in FILE [disabled]
+#   -C, --config-cache      alias for `--cache-file=config.cache'
+#   -n, --no-create         do not create output files
+#       --srcdir=DIR        find the sources in DIR [configure dir or `..']
+# 
+# Installation directories:
+#   --prefix=PREFIX         install architecture-independent files in PREFIX
+#                           [/usr/local]
+#   --exec-prefix=EPREFIX   install architecture-dependent files in EPREFIX
+#                           [PREFIX]
+# 
+# By default, `make install' will install all the files in
+# `/usr/local/bin', `/usr/local/lib' etc.  You can specify
+# an installation prefix other than `/usr/local' using `--prefix',
+# for instance `--prefix=$HOME'.
+# 
+# For better control, use the options below.
+# 
+# Fine tuning of the installation directories:
+#   --bindir=DIR            user executables [EPREFIX/bin]
+#   --sbindir=DIR           system admin executables [EPREFIX/sbin]
+#   --libexecdir=DIR        program executables [EPREFIX/libexec]
+#   --sysconfdir=DIR        read-only single-machine data [PREFIX/etc]
+#   --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com]
+#   --localstatedir=DIR     modifiable single-machine data [PREFIX/var]
+#   --libdir=DIR            object code libraries [EPREFIX/lib]
+#   --includedir=DIR        C header files [PREFIX/include]
+#   --oldincludedir=DIR     C header files for non-gcc [/usr/include]
+#   --datarootdir=DIR       read-only arch.-independent data root [PREFIX/share]
+#   --datadir=DIR           read-only architecture-independent data [DATAROOTDIR]
+#   --infodir=DIR           info documentation [DATAROOTDIR/info]
+#   --localedir=DIR         locale-dependent data [DATAROOTDIR/locale]
+#   --mandir=DIR            man documentation [DATAROOTDIR/man]
+#   --docdir=DIR            documentation root [DATAROOTDIR/doc/netcdf-fortran]
+#   --htmldir=DIR           html documentation [DOCDIR]
+#   --dvidir=DIR            dvi documentation [DOCDIR]
+#   --pdfdir=DIR            pdf documentation [DOCDIR]
+#   --psdir=DIR             ps documentation [DOCDIR]
+# 
+# Program names:
+#   --program-prefix=PREFIX            prepend PREFIX to installed program names
+#   --program-suffix=SUFFIX            append SUFFIX to installed program names
+#   --program-transform-name=PROGRAM   run sed PROGRAM on installed program names
+# 
+# System types:
+#   --build=BUILD     configure for building on BUILD [guessed]
+#   --host=HOST       cross-compile to build programs to run on HOST [BUILD]
+#   --target=TARGET   configure for building compilers for TARGET [HOST]
+# 
+# Optional Features:
+#   --disable-option-checking  ignore unrecognized --enable/--with options
+#   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
+#   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
+#   --enable-silent-rules   less verbose build output (undo: "make V=1")
+#   --disable-silent-rules  verbose build output (undo: "make V=0")
+#   --enable-maintainer-mode
+#                           enable make rules and dependencies not useful (and
+#                           sometimes confusing) to the casual installer
+#   --enable-valgrind-tests build with valgrind-tests (valgrind is required,
+#                           static builds only)
+#   --enable-parallel-tests Run extra parallel IO tests. Ignored if netCDF-4 is
+#                           not enabled, or built on a system without parallel
+#                           I/O support.
+#   --enable-extra-tests    run some extra tests that may not pass because of
+#                           known issues
+#   --enable-doxygen        Enable generation of documentation with doxygen.
+#   --enable-dot            Use dot (provided by graphviz) to generate charts
+#                           and graphs in the doxygen-based documentation.
+#   --enable-internal-docs  Include documentation of library internals. This is
+#                           of interest only to those developing the netCDF
+#                           library.
+#   --enable-dependency-tracking
+#                           do not reject slow dependency extractors
+#   --disable-dependency-tracking
+#                           speeds up one-time build
+#   --disable-f03-compiler-check
+#                           disable check of ISO_C_BINDING support in Fortran
+#                           compiler
+#   --disable-f03           suppress netCDF Fortran 2003 native code
+#   --disable-fortran-type-check
+#                           cause the Fortran type sizes checks to be skipped
+#   --enable-large-file-tests
+#                           Run tests which create very large data files (~13 GB
+#                           disk space required, but it will be recovered when
+#                           tests are complete). See option --with-temp-large to
+#                           specify temporary directory
+#   --enable-benchmarks     Run benchmarks. This is an experimental feature.
+#   --enable-shared[=PKGS]  build shared libraries [default=yes]
+#   --enable-static[=PKGS]  build static libraries [default=yes]
+#   --enable-fast-install[=PKGS]
+#                           optimize for fast installation [default=yes]
+#   --disable-libtool-lock  avoid locking (might break parallel builds)
+#   --disable-largefile     omit support for large files
+#   --enable-extra-example-tests
+#                           Run extra example tests; requires GNU sed. Ignored
+#                           if netCDF-4 is not enabled.
+#   --enable-dll            build a win32 DLL (only works on mingw)
+# 
+# Optional Packages:
+#   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
+#   --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
+#   --with-temp-large=<directory>
+#                           specify directory where large files (i.e. >2 GB)
+#                           will be written, if large files tests are run with
+#                           --enable-large-file-tests
+#   --with-pic[=PKGS]       try to use only PIC/non-PIC objects [default=use
+#                           both]
+#   --with-gnu-ld           assume the C compiler uses GNU ld [default=no]
+#   --with-sysroot=DIR Search for dependent libraries within DIR
+#                         (or the compiler's sysroot if not specified).
+# 
+# Some influential environment variables:
+#   CC          C compiler command
+#   CFLAGS      C compiler flags
+#   LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
+#               nonstandard directory <lib dir>
+#   LIBS        libraries to pass to the linker, e.g. -l<library>
+#   CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
+#               you have headers in a nonstandard directory <include dir>
+#   FC          Fortran compiler command
+#   FCFLAGS     Fortran compiler flags
+#   F77         Fortran 77 compiler command
+#   FFLAGS      Fortran 77 compiler flags
+#   CPP         C preprocessor
+# 
+# Use these variables to override the choices made by `configure' or to help
+# it to find libraries and programs with nonstandard names/locations.
+# 
+# Report bugs to <support-netcdf@unidata.ucar.edu>.
+# 
+# from spack import *
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index 41a0d2b6f9..0b112a59ce 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -13,7 +13,6 @@ class Netcdf(Package):
     version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae')
 
     variant('mpi', default=True, description='Enables MPI parallelism')
-    variant('fortran', default=False, description="Download and install NetCDF-Fortran")
     variant('hdf4',    default=False, description="Enable HDF4 support")
 
     # Dependencies:
@@ -66,11 +65,7 @@ class Netcdf(Package):
 
         # Fortran support
         # In version 4.2+, NetCDF-C and NetCDF-Fortran have split.
-        # They can be installed separately, but this bootstrap procedure
-        # should be able to install both at the same time.
-        # Note: this is a new experimental feature.
-        if '+fortran' in spec:
-            config_args.append("--enable-remote-fortran-bootstrap")
+        # Use the netcdf-fortran package to install Fortran support.
 
         config_args.append('CPPFLAGS=%s' % ' '.join(CPPFLAGS))
         config_args.append('LDFLAGS=%s'  % ' '.join(LDFLAGS))
@@ -79,8 +74,3 @@ class Netcdf(Package):
         configure(*config_args)
         make()
         make("install")
-
-        # After installing NetCDF-C, install NetCDF-Fortran
-        if '+fortran' in spec:
-            make("build-netcdf-fortran")
-            make("install-netcdf-fortran")
-- 
cgit v1.2.3-70-g09d2


From b043c4a5b83f36ad4837fc7302f0919a3d759940 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Fri, 4 Mar 2016 12:04:41 -0500
Subject: Update package.py

Removed comments on configure options.
---
 .../builtin/packages/netcdf-fortran/package.py     | 153 ---------------------
 1 file changed, 153 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index 4e0b14d012..954e7dc3e8 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -16,156 +16,3 @@ class NetcdfFortran(Package):
         configure("--prefix=%s" % prefix)
         make()
         make("install")
-
-
-
-
-# netcdf-fortran configure parameters are below
-# ---------------------------------------------
-#
-# `configure' configures netCDF-Fortran 4.4.3 to adapt to many kinds of systems.
-# 
-# Usage: ./configure [OPTION]... [VAR=VALUE]...
-# 
-# To assign environment variables (e.g., CC, CFLAGS...), specify them as
-# VAR=VALUE.  See below for descriptions of some of the useful variables.
-# 
-# Defaults for the options are specified in brackets.
-# 
-# Configuration:
-#   -h, --help              display this help and exit
-#       --help=short        display options specific to this package
-#       --help=recursive    display the short help of all the included packages
-#   -V, --version           display version information and exit
-#   -q, --quiet, --silent   do not print `checking ...' messages
-#       --cache-file=FILE   cache test results in FILE [disabled]
-#   -C, --config-cache      alias for `--cache-file=config.cache'
-#   -n, --no-create         do not create output files
-#       --srcdir=DIR        find the sources in DIR [configure dir or `..']
-# 
-# Installation directories:
-#   --prefix=PREFIX         install architecture-independent files in PREFIX
-#                           [/usr/local]
-#   --exec-prefix=EPREFIX   install architecture-dependent files in EPREFIX
-#                           [PREFIX]
-# 
-# By default, `make install' will install all the files in
-# `/usr/local/bin', `/usr/local/lib' etc.  You can specify
-# an installation prefix other than `/usr/local' using `--prefix',
-# for instance `--prefix=$HOME'.
-# 
-# For better control, use the options below.
-# 
-# Fine tuning of the installation directories:
-#   --bindir=DIR            user executables [EPREFIX/bin]
-#   --sbindir=DIR           system admin executables [EPREFIX/sbin]
-#   --libexecdir=DIR        program executables [EPREFIX/libexec]
-#   --sysconfdir=DIR        read-only single-machine data [PREFIX/etc]
-#   --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com]
-#   --localstatedir=DIR     modifiable single-machine data [PREFIX/var]
-#   --libdir=DIR            object code libraries [EPREFIX/lib]
-#   --includedir=DIR        C header files [PREFIX/include]
-#   --oldincludedir=DIR     C header files for non-gcc [/usr/include]
-#   --datarootdir=DIR       read-only arch.-independent data root [PREFIX/share]
-#   --datadir=DIR           read-only architecture-independent data [DATAROOTDIR]
-#   --infodir=DIR           info documentation [DATAROOTDIR/info]
-#   --localedir=DIR         locale-dependent data [DATAROOTDIR/locale]
-#   --mandir=DIR            man documentation [DATAROOTDIR/man]
-#   --docdir=DIR            documentation root [DATAROOTDIR/doc/netcdf-fortran]
-#   --htmldir=DIR           html documentation [DOCDIR]
-#   --dvidir=DIR            dvi documentation [DOCDIR]
-#   --pdfdir=DIR            pdf documentation [DOCDIR]
-#   --psdir=DIR             ps documentation [DOCDIR]
-# 
-# Program names:
-#   --program-prefix=PREFIX            prepend PREFIX to installed program names
-#   --program-suffix=SUFFIX            append SUFFIX to installed program names
-#   --program-transform-name=PROGRAM   run sed PROGRAM on installed program names
-# 
-# System types:
-#   --build=BUILD     configure for building on BUILD [guessed]
-#   --host=HOST       cross-compile to build programs to run on HOST [BUILD]
-#   --target=TARGET   configure for building compilers for TARGET [HOST]
-# 
-# Optional Features:
-#   --disable-option-checking  ignore unrecognized --enable/--with options
-#   --disable-FEATURE       do not include FEATURE (same as --enable-FEATURE=no)
-#   --enable-FEATURE[=ARG]  include FEATURE [ARG=yes]
-#   --enable-silent-rules   less verbose build output (undo: "make V=1")
-#   --disable-silent-rules  verbose build output (undo: "make V=0")
-#   --enable-maintainer-mode
-#                           enable make rules and dependencies not useful (and
-#                           sometimes confusing) to the casual installer
-#   --enable-valgrind-tests build with valgrind-tests (valgrind is required,
-#                           static builds only)
-#   --enable-parallel-tests Run extra parallel IO tests. Ignored if netCDF-4 is
-#                           not enabled, or built on a system without parallel
-#                           I/O support.
-#   --enable-extra-tests    run some extra tests that may not pass because of
-#                           known issues
-#   --enable-doxygen        Enable generation of documentation with doxygen.
-#   --enable-dot            Use dot (provided by graphviz) to generate charts
-#                           and graphs in the doxygen-based documentation.
-#   --enable-internal-docs  Include documentation of library internals. This is
-#                           of interest only to those developing the netCDF
-#                           library.
-#   --enable-dependency-tracking
-#                           do not reject slow dependency extractors
-#   --disable-dependency-tracking
-#                           speeds up one-time build
-#   --disable-f03-compiler-check
-#                           disable check of ISO_C_BINDING support in Fortran
-#                           compiler
-#   --disable-f03           suppress netCDF Fortran 2003 native code
-#   --disable-fortran-type-check
-#                           cause the Fortran type sizes checks to be skipped
-#   --enable-large-file-tests
-#                           Run tests which create very large data files (~13 GB
-#                           disk space required, but it will be recovered when
-#                           tests are complete). See option --with-temp-large to
-#                           specify temporary directory
-#   --enable-benchmarks     Run benchmarks. This is an experimental feature.
-#   --enable-shared[=PKGS]  build shared libraries [default=yes]
-#   --enable-static[=PKGS]  build static libraries [default=yes]
-#   --enable-fast-install[=PKGS]
-#                           optimize for fast installation [default=yes]
-#   --disable-libtool-lock  avoid locking (might break parallel builds)
-#   --disable-largefile     omit support for large files
-#   --enable-extra-example-tests
-#                           Run extra example tests; requires GNU sed. Ignored
-#                           if netCDF-4 is not enabled.
-#   --enable-dll            build a win32 DLL (only works on mingw)
-# 
-# Optional Packages:
-#   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
-#   --without-PACKAGE       do not use PACKAGE (same as --with-PACKAGE=no)
-#   --with-temp-large=<directory>
-#                           specify directory where large files (i.e. >2 GB)
-#                           will be written, if large files tests are run with
-#                           --enable-large-file-tests
-#   --with-pic[=PKGS]       try to use only PIC/non-PIC objects [default=use
-#                           both]
-#   --with-gnu-ld           assume the C compiler uses GNU ld [default=no]
-#   --with-sysroot=DIR Search for dependent libraries within DIR
-#                         (or the compiler's sysroot if not specified).
-# 
-# Some influential environment variables:
-#   CC          C compiler command
-#   CFLAGS      C compiler flags
-#   LDFLAGS     linker flags, e.g. -L<lib dir> if you have libraries in a
-#               nonstandard directory <lib dir>
-#   LIBS        libraries to pass to the linker, e.g. -l<library>
-#   CPPFLAGS    (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if
-#               you have headers in a nonstandard directory <include dir>
-#   FC          Fortran compiler command
-#   FCFLAGS     Fortran compiler flags
-#   F77         Fortran 77 compiler command
-#   FFLAGS      Fortran 77 compiler flags
-#   CPP         C preprocessor
-# 
-# Use these variables to override the choices made by `configure' or to help
-# it to find libraries and programs with nonstandard names/locations.
-# 
-# Report bugs to <support-netcdf@unidata.ucar.edu>.
-# 
-# from spack import *
-- 
cgit v1.2.3-70-g09d2


From 648d08eb305e04d95ee702b819923f31fd829955 Mon Sep 17 00:00:00 2001
From: Elizabeth Fischer <rpf2116@columbia.edu>
Date: Fri, 4 Mar 2016 12:05:43 -0500
Subject: Update package.py

Updated homepage URL to general NetCDF homepage.
---
 var/spack/repos/builtin/packages/netcdf-cxx4/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
index fb4c2886cd..ab717ac6ff 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -2,7 +2,7 @@ from spack import *
 
 class NetcdfCxx4(Package):
     """C++ interface for NetCDF4"""
-    homepage = "http://www.unidata.ucar.edu/downloads/netcdf/netcdf-cxx/index.jsp"
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.2.tar.gz"
 
     version('4.2', 'd019853802092cf686254aaba165fc81')
-- 
cgit v1.2.3-70-g09d2


From a7b918837eab02ebff5af783d06e56ec7f868d9e Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 4 Mar 2016 15:22:28 -0600
Subject: GNU m4 depends on libsigsegv

---
 var/spack/repos/builtin/packages/libsigsegv/package.py | 15 +++++++++++++++
 var/spack/repos/builtin/packages/m4/package.py         |  2 ++
 2 files changed, 17 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/libsigsegv/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py
new file mode 100644
index 0000000000..4b486198ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libsigsegv/package.py
@@ -0,0 +1,15 @@
+from spack import *
+
+class Libsigsegv(Package):
+    """GNU libsigsegv is a library for handling page faults in user mode."""
+    homepage = "https://www.gnu.org/software/libsigsegv/"
+    url      = "ftp://ftp.gnu.org/gnu/libsigsegv/libsigsegv-2.10.tar.gz"
+
+    version('2.10', '7f96fb1f65b3b8cbc1582fb7be774f0f')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix,
+                  '--enable-shared')
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index 5d76d8866b..3890663ad1 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -7,6 +7,8 @@ class M4(Package):
 
     version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76')
 
+    depends_on('libsigsegv')
+
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
-- 
cgit v1.2.3-70-g09d2


From f90eaa5f46bfd64b9b0adb4ab5a58d169efe3c69 Mon Sep 17 00:00:00 2001
From: Alfredo Gimenez <gimenez1@llnl.gov>
Date: Fri, 4 Mar 2016 14:53:08 -0800
Subject: Fixed unmatched function signature for do_fetch in jdk package

---
 var/spack/repos/builtin/packages/jdk/package.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index f8f5fc21bd..cbcc53ac0a 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -28,7 +28,7 @@ class Jdk(Package):
         '-H', # specify required License Agreement cookie
         'Cookie: oraclelicense=accept-securebackup-cookie']
 
-    def do_fetch(self):
+    def do_fetch(self, mirror_only=False):
         # Add our custom curl commandline options
         tty.msg(
             "[Jdk] Adding required commandline options to curl " +
@@ -39,7 +39,7 @@ class Jdk(Package):
             spack.curl.add_default_arg(option)
 
         # Now perform the actual fetch
-        super(Jdk, self).do_fetch()
+        super(Jdk, self).do_fetch(mirror_only)
 
 
     def install(self, spec, prefix):
-- 
cgit v1.2.3-70-g09d2


From f663d37da75e4ef0f266c63707e77d29a651e07d Mon Sep 17 00:00:00 2001
From: Mark Miller <miller86@llnl.gov>
Date: Fri, 4 Mar 2016 17:08:11 -0800
Subject: Adding zfp package.

---
 var/spack/repos/builtin/packages/zfp/package.py | 26 +++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/zfp/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py
new file mode 100644
index 0000000000..620fe9d456
--- /dev/null
+++ b/var/spack/repos/builtin/packages/zfp/package.py
@@ -0,0 +1,26 @@
+from spack import *
+
+class Zfp(Package):
+    """zfp is an open source C library for compressed floating-point arrays that supports
+       very high throughput read and write random acces, target error bounds or bit rates.
+       Although bit-for-bit lossless compression is not always possible, zfp is usually
+       accurate to within machine epsilon in near-lossless mode, and is often orders of
+       magnitude more accurate than other lossy compressors.
+    """
+
+    homepage = "http://computation.llnl.gov/projects/floating-point-compression"
+    url      = "http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.0.tar.gz"
+
+    version('0.5.0', '2ab29a852e65ad85aae38925c5003654')
+
+    def install(self, spec, prefix):
+        make("shared")
+
+        # No install provided
+        mkdirp(prefix.lib)
+        mkdirp(prefix.include)
+        install('lib/libzfp.so', prefix.lib)
+        install('inc/zfp.h', prefix.include)
+        install('inc/types.h', prefix.include)
+        install('inc/bitstream.h', prefix.include)
+        install('inc/system.h', prefix.include)
-- 
cgit v1.2.3-70-g09d2


From 3dd630d0a567964acd11bee23ebbc52c7d1c61c5 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 5 Mar 2016 14:33:23 -0800
Subject: Make openssl a variant in libevent.

---
 var/spack/repos/builtin/packages/libevent/package.py | 12 ++++++++----
 1 file changed, 8 insertions(+), 4 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py
index 2a44c49325..714a155dc0 100644
--- a/var/spack/repos/builtin/packages/libevent/package.py
+++ b/var/spack/repos/builtin/packages/libevent/package.py
@@ -22,12 +22,16 @@ class Libevent(Package):
     version('2.0.13', 'af786b4b3f790c9d3279792edf7867fc')
     version('2.0.12', '42986228baf95e325778ed328a93e070')
 
-
-    depends_on('openssl')
-
+    variant('openssl', default=True, description="Build with encryption enabled at the libevent level.")
+    depends_on('openssl', when='+openssl')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure_args = []
+        if '+openssl' in spec:
+            configure_args.append('--enable-openssl')
+        else:
+            configure_args.append('--enable-openssl')
 
+        configure("--prefix=%s" % prefix, *configure_args)
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 220b6a9fee0f307d4de1e48b29093812f7dd10ec Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Sat, 5 Mar 2016 16:46:32 -0600
Subject: Make libsigsegv an optional dependency

---
 var/spack/repos/builtin/packages/m4/package.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index 3890663ad1..9d522dfccf 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -7,7 +7,9 @@ class M4(Package):
 
     version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76')
 
-    depends_on('libsigsegv')
+    variant('sigsegv', default=True, description="Build the libsigsegv dependency")
+
+    depends_on('libsigsegv', when='+sigsegv')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
-- 
cgit v1.2.3-70-g09d2


From 7d847f4dc4f8895d57e492c11cfd7c3fbb794945 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Sat, 5 Mar 2016 15:14:21 -0800
Subject: Minor tweaks to m4 -- be sure to add sigsegv args explicitly.

---
 var/spack/repos/builtin/packages/m4/package.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index 9d522dfccf..d6829dbcd4 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -12,6 +12,12 @@ class M4(Package):
     depends_on('libsigsegv', when='+sigsegv')
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix)
+        configure_args = []
+        if 'libsigsegv' in spec:
+            configure_args.append('--with-libsigsegv-prefix=%s' % spec['libsigsegv'].prefix)
+        else:
+            configure_args.append('--without-libsigsegv-prefix')
+
+        configure("--prefix=%s" % prefix, *configure_args)
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From ae87948a232c17982a7987e5423ac77acdc59194 Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Sat, 5 Mar 2016 23:05:45 -0500
Subject: Fixed URLs Removed vestigal mpi variant in netcdf-fortran

---
 var/spack/repos/builtin/packages/netcdf-cxx4/package.py    | 1 -
 var/spack/repos/builtin/packages/netcdf-fortran/package.py | 4 +---
 var/spack/repos/builtin/packages/netcdf/package.py         | 2 +-
 3 files changed, 2 insertions(+), 5 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
index ab717ac6ff..b83e964b00 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -11,6 +11,5 @@ class NetcdfCxx4(Package):
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
-
         make()
         make("install")
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index 954e7dc3e8..e4e33445e5 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -3,13 +3,11 @@ from spack import *
 class NetcdfFortran(Package):
     """Fortran interface for NetCDF4"""
 
-    homepage = "http://www.unidata.ucar.edu/downloads/netcdf/netcdf-cxx/index.jsp"
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.4.3.tar.gz"
 
     version('4.4.3', 'bfd4ae23a34635b273d3eb0d91cbde9e')
 
-    variant('mpi', default=True, description='Enables MPI parallelism')
-
     depends_on('netcdf')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index 0b112a59ce..227362399a 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -6,7 +6,7 @@ class Netcdf(Package):
     data formats that support the creation, access, and sharing of array-oriented
     scientific data."""
 
-    homepage = "http://www.unidata.ucar.edu/software/netcdf/"
+    homepage = "http://www.unidata.ucar.edu/software/netcdf"
     url      = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz"
 
     version('4.4.0', 'cffda0cbd97fdb3a06e9274f7aef438e')
-- 
cgit v1.2.3-70-g09d2


From a399451e1e32c9a294f5b735237cef93ddbd4131 Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Sun, 6 Mar 2016 23:34:48 -0500
Subject: Update OpenSSL to 1.0.2g

---
 var/spack/repos/builtin/packages/openssl/package.py | 1 +
 1 file changed, 1 insertion(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index c73102f05d..70afaf4038 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -17,6 +17,7 @@ class Openssl(Package):
     version('1.0.2d', '38dd619b2e77cbac69b99f52a053d25a')
     version('1.0.2e', '5262bfa25b60ed9de9f28d5d52d77fc5')
     version('1.0.2f', 'b3bf73f507172be9292ea2a8c28b659d')
+    version('1.0.2g', 'f3c710c045cdee5fd114feb69feba7aa')
 
     depends_on("zlib")
     parallel = False
-- 
cgit v1.2.3-70-g09d2


From 1e7d946d9116dee4900b95def1614bd3f788f6f0 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 7 Mar 2016 12:37:51 -0600
Subject: Add patch to allow PGI to build M4

---
 var/spack/repos/builtin/packages/m4/inline-pgi.patch | 10 ++++++++++
 var/spack/repos/builtin/packages/m4/package.py       |  2 ++
 2 files changed, 12 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/m4/inline-pgi.patch

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/m4/inline-pgi.patch b/var/spack/repos/builtin/packages/m4/inline-pgi.patch
new file mode 100644
index 0000000000..da5eb57a93
--- /dev/null
+++ b/var/spack/repos/builtin/packages/m4/inline-pgi.patch
@@ -0,0 +1,10 @@
+--- a/m4/extern-inline.m4
++++ b/m4/extern-inline.m4
+@@ -34,6 +34,7 @@
+       ? defined __GNUC_STDC_INLINE__ && __GNUC_STDC_INLINE__ \
+       : (199901L <= __STDC_VERSION__ \
+          && !defined __HP_cc \
++         && !defined __PGI \
+          && !(defined __SUNPRO_C && __STDC__))) \
+      && !defined _GL_EXTERN_INLINE_STDHEADER_BUG)
+ # define _GL_INLINE inline
diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index d6829dbcd4..ef70add18a 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -7,6 +7,8 @@ class M4(Package):
 
     version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76')
 
+    patch('inline-pgi.patch', when='@1.4.17')
+
     variant('sigsegv', default=True, description="Build the libsigsegv dependency")
 
     depends_on('libsigsegv', when='+sigsegv')
-- 
cgit v1.2.3-70-g09d2


From b7750cf61c51704d87d679efeba9ca8cb8c2b768 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 7 Mar 2016 15:52:22 -0600
Subject: Autoreconf is necessary after patch

---
 var/spack/repos/builtin/packages/m4/inline-pgi.patch | 12 ++++++++++++
 var/spack/repos/builtin/packages/m4/package.py       |  4 ++++
 2 files changed, 16 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/m4/inline-pgi.patch b/var/spack/repos/builtin/packages/m4/inline-pgi.patch
index da5eb57a93..bc31ad918e 100644
--- a/var/spack/repos/builtin/packages/m4/inline-pgi.patch
+++ b/var/spack/repos/builtin/packages/m4/inline-pgi.patch
@@ -8,3 +8,15 @@
           && !(defined __SUNPRO_C && __STDC__))) \
       && !defined _GL_EXTERN_INLINE_STDHEADER_BUG)
  # define _GL_INLINE inline
+--- a/configure.ac
++++ b/configure.ac
+@@ -22,7 +22,7 @@
+   [bug-m4@gnu.org])
+ AC_CONFIG_AUX_DIR([build-aux])
+ 
+-AM_INIT_AUTOMAKE([1.11.6 dist-bzip2 dist-xz color-tests parallel-tests
++AM_INIT_AUTOMAKE([dist-bzip2 dist-xz color-tests parallel-tests
+ silent-rules subdir-objects gnu])
+ 
+ m4_pattern_forbid([^M4_[A-Z]])
+
diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index ef70add18a..aa0c775f08 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -14,6 +14,10 @@ class M4(Package):
     depends_on('libsigsegv', when='+sigsegv')
 
     def install(self, spec, prefix):
+        # After patch, update generated configuration files that depend on extern-inline.m4
+        autoreconf = which('autoreconf')
+        autoreconf()
+
         configure_args = []
         if 'libsigsegv' in spec:
             configure_args.append('--with-libsigsegv-prefix=%s' % spec['libsigsegv'].prefix)
-- 
cgit v1.2.3-70-g09d2


From 18ce5ccf8fb31dae71848f541f3e139bd582953c Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 8 Mar 2016 02:49:11 -0800
Subject: Avoid race in pango's `make install`, set parallel=False

---
 var/spack/repos/builtin/packages/pango/package.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py
index df43625bf5..79dad3a3d2 100644
--- a/var/spack/repos/builtin/packages/pango/package.py
+++ b/var/spack/repos/builtin/packages/pango/package.py
@@ -16,4 +16,4 @@ class Pango(Package):
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
         make()
-        make("install")
+        make("install", parallel=False)
-- 
cgit v1.2.3-70-g09d2


From e0e545774aaddb5386367bd900a31b85692abc51 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Tue, 8 Mar 2016 12:15:40 -0600
Subject: Add more versions to Autotools

---
 var/spack/repos/builtin/packages/autoconf/package.py | 1 +
 var/spack/repos/builtin/packages/automake/package.py | 2 ++
 2 files changed, 3 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py
index 5189faf054..6412e810a6 100644
--- a/var/spack/repos/builtin/packages/autoconf/package.py
+++ b/var/spack/repos/builtin/packages/autoconf/package.py
@@ -6,6 +6,7 @@ class Autoconf(Package):
     url      = "http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz"
 
     version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
+    version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)
diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py
index 9115822730..2172a42030 100644
--- a/var/spack/repos/builtin/packages/automake/package.py
+++ b/var/spack/repos/builtin/packages/automake/package.py
@@ -5,7 +5,9 @@ class Automake(Package):
     homepage = "http://www.gnu.org/software/automake/"
     url      = "http://ftp.gnu.org/gnu/automake/automake-1.14.tar.gz"
 
+    version('1.15',   '716946a105ca228ab545fc37a70df3a3')
     version('1.14.1', 'd052a3e884631b9c7892f2efce542d75')
+    version('1.11.6', '0286dc30295b62985ca51919202ecfcc')
 
     depends_on('autoconf')
 
-- 
cgit v1.2.3-70-g09d2


From 0c7d0c0b6c650cd0fd6f4814a255613e3efa1814 Mon Sep 17 00:00:00 2001
From: Alfredo Gimenez <gimenez1@llnl.gov>
Date: Tue, 8 Mar 2016 12:26:40 -0800
Subject: Variants and fixes to thrift package

---
 var/spack/repos/builtin/packages/thrift/package.py | 64 +++++++++++++---------
 1 file changed, 38 insertions(+), 26 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py
index 0e15052f64..ec3b13e563 100644
--- a/var/spack/repos/builtin/packages/thrift/package.py
+++ b/var/spack/repos/builtin/packages/thrift/package.py
@@ -12,33 +12,45 @@ class Thrift(Package):
 
     version('0.9.2', '89f63cc4d0100912f4a1f8a9dee63678')
 
-    extends("python")
-
-    depends_on("autoconf")
-    depends_on("automake")
-    depends_on("bison")
-    depends_on("boost")
-    depends_on("flex")
-    depends_on("jdk")
-    depends_on("libtool")
-    depends_on("openssl")
-    depends_on("python")
-
-    # Compilation fails for most languages, fortunately cpp installs fine
-    # All other languages (yes, including C) are omitted until someone needs them
+    # Currently only support for c-family and python
+    variant('c', default=True, description="Build support for C-family languages")
+    variant('python', default=True, description="Build support for python")
+
+    depends_on('jdk')
+    depends_on('autoconf')
+    depends_on('automake')
+    depends_on('libtool')
+    depends_on('boost@1.53:')
+    depends_on('bison')
+    depends_on('flex')
+    depends_on('openssl')
+
+    # Variant dependencies
+    extends('python', when='+python')
+    depends_on('python', when='+python')
+
+    depends_on('zlib', when='+c')
+    depends_on('libevent', when='+c')
+
     def install(self, spec, prefix):
-        env["PY_PREFIX"]   = prefix
-        env["JAVA_PREFIX"] = prefix
-
-        configure("--prefix=%s" % prefix,
-                  "--with-boost=%s" % spec['boost'].prefix,
-                  "--with-c=no",
-                  "--with-go=no",
-                  "--with-python=yes",
-                  "--with-lua=no",
-                  "--with-php=no",
-                  "--with-qt4=no",
-                  "--enable-tests=no")
+        env['PY_PREFIX'] = prefix
+        env['JAVA_HOME'] = spec['jdk'].prefix
+
+        # configure options
+        options = ['--prefix=%s' % prefix]
+
+        options.append('--with-boost=%s' % spec['boost'].prefix)
+        options.append('--enable-tests=no')
+
+        options.append('--with-c=%s' % ('yes' if '+c' in spec else 'no'))
+        options.append('--with-python=%s' % ('yes' if '+python' in spec else 'no'))
+        options.append('--with-java=%s' % ('yes' if '+java' in spec else 'no'))
+        options.append('--with-go=%s' % ('yes' if '+go' in spec else 'no'))
+        options.append('--with-lua=%s' % ('yes' if '+lua' in spec else 'no'))
+        options.append('--with-php=%s' % ('yes' if '+php' in spec else 'no'))
+        options.append('--with-qt4=%s' % ('yes' if '+qt4' in spec else 'no'))
+
+        configure(*options)
 
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 5b22873b3dce37c0d7bad418bf6e0b73d381d19e Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Wed, 9 Mar 2016 00:18:20 -0500
Subject: Fixed issues with hypre:

1. --with-lapack-lib was wrong.
2. --with-MPI was wrong; set env vars for MPI wrappers instead.
3. Added version 2.10.1
4. Added shared library variant (True by default).  Hypre can build shared or static libraries, but not both in the same build.
---
 var/spack/repos/builtin/packages/hypre/package.py | 28 +++++++++++++++++------
 1 file changed, 21 insertions(+), 7 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 0f7f14dd89..242ee100d7 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import os
 
 class Hypre(Package):
     """Hypre is a library of high performance preconditioners that
@@ -8,8 +9,11 @@ class Hypre(Package):
     homepage = "http://computation.llnl.gov/project/linear_solvers/software.php"
     url      = "http://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz"
 
+    version('2.10.1', 'dc048c4cabb3cd549af72591474ad674')
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
 
+    variant('shared', default=True, description="Build shared library version (disables static library)")
+
     depends_on("mpi")
     depends_on("blas")
     depends_on("lapack")
@@ -17,16 +21,26 @@ class Hypre(Package):
     def install(self, spec, prefix):
         blas_dir = spec['blas'].prefix
         lapack_dir = spec['lapack'].prefix
+        mpi_dir = spec['mpi'].prefix
+
+        os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc')
+        os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx')
+        os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77')
+
+
+        configure_args = [
+                "--prefix=%s" % prefix,
+                "--with-lapack-libs=lapack",
+                "--with-lapack-lib-dirs=%s/lib" % lapack_dir,
+                "--with-blas-libs=blas",
+                "--with-blas-lib-dirs=%s/lib" % blas_dir]
+        if '+shared' in self.spec:
+            configure_args.append("--enable-shared")
 
         # Hypre's source is staged under ./src so we'll have to manually
         # cd into it.
         with working_dir("src"):
-            configure(
-                "--prefix=%s" % prefix,
-                "--with-blas-libs=blas",
-                "--with-blas-lib-dirs=%s/lib" % blas_dir,
-                "--with-lapack-libs=\"lapack blas\"",
-                "--with-lapack-lib-dirs=%s/lib" % lapack_dir,
-                "--with-MPI")
+            configure(*configure_args)
+
             make()
             make("install")
-- 
cgit v1.2.3-70-g09d2


From c67b922185ebf5b7686d5b4958e2b31b8f0f1469 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Wed, 9 Mar 2016 00:34:08 -0500
Subject: Added shared library capability.

---
 var/spack/repos/builtin/packages/petsc/package.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 87f700629d..e42425bcef 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -11,8 +11,11 @@ class Petsc(Package):
     version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f')
     version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13')
     version('3.5.1', 'a557e029711ebf425544e117ffa44d8f')
+    version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d')
 
-    depends_on("python @2.6:2.9")   # requires Python for building
+    variant('shared', default=True, description="Build shared library version")
+
+    depends_on("python @2.6:2.7")   # requires Python for building
 
     depends_on("boost")
     depends_on("blas")
@@ -33,7 +36,7 @@ class Petsc(Package):
                   "--with-metis-dir=%s"              % spec['metis'].prefix,
                   "--with-hdf5-dir=%s"               % spec['hdf5'].prefix,
                   "--with-mpi-dir=%s"                % spec['mpi'].prefix,
-                  "--with-shared-libraries=0")
+                  "--with-shared-libraries=%d"       % (1 if '+shared' in self.spec else 0))
 
         # PETSc has its own way of doing parallel make.
         make('MAKE_NP=%s' % make_jobs, parallel=False)
-- 
cgit v1.2.3-70-g09d2


From f01d1c4385f05dd7bda7efb3a9e7f2c8008e177a Mon Sep 17 00:00:00 2001
From: alalazo <massimiliano.culpo@googlemail.com>
Date: Wed, 9 Mar 2016 14:36:37 +0100
Subject: petsc : added variants and logic to build various flavors

---
 var/spack/repos/builtin/packages/petsc/package.py | 92 +++++++++++++++++------
 1 file changed, 69 insertions(+), 23 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 87f700629d..5be187f348 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -1,40 +1,86 @@
+import os
 from spack import *
 
+
 class Petsc(Package):
-    """PETSc is a suite of data structures and routines for the
-       scalable (parallel) solution of scientific applications modeled by
-       partial differential equations."""
+    """
+    PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications
+    modeled by partial differential equations.
+    """
 
     homepage = "http://www.mcs.anl.gov/petsc/index.html"
-    url      = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
+    url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
 
+    version('3.6.3', '91dd3522de5a5ef039ff8f50800db606')
     version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f')
     version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13')
     version('3.5.1', 'a557e029711ebf425544e117ffa44d8f')
 
-    depends_on("python @2.6:2.9")   # requires Python for building
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('mpi', default=True, description='Activates MPI support')
+    variant('double', default=True, description='Switches between single and double precision')
+
+    variant('metis', default=True, description='Activates support for metis and parmetis')
+    variant('hdf5', default=True, description='Activates support for HDF5 (only parallel)')
+    variant('boost', default=True, description='Activates support for Boost')
+    variant('hypre', default=True, description='Activates support for Hypre')
+
+    # Build dependencies
+    depends_on('python @2.6:2.9')  # requires Python for building
+
+    # Virtual dependencies
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('mpi', when='+mpi')
 
-    depends_on("boost")
-    depends_on("blas")
-    depends_on("lapack")
-    depends_on("hypre")
-    depends_on("parmetis")
-    depends_on("metis")
-    depends_on("hdf5+mpi")
-    depends_on("mpi")
+    # Other dependencies
+    depends_on('boost', when='+boost')
+    depends_on('metis', when='+metis')
+
+    depends_on('hdf5~cxx~unsupported+mpi', when='+hdf5+mpi')
+    depends_on('parmetis', when='+metis+mpi')
+    depends_on('hypre', when='+hypre+mpi')
+
+    def mpi_dependent_options(self):
+        if '~mpi' in self.spec:
+            compiler_opts = [
+                '--with-cc=%s' % os.environ['CC'],
+                '--with-cxx=%s' % (os.environ['CXX'] if self.compiler.cxx is not None else '0'),
+                '--with-fc=%s' % (os.environ['FC'] if self.compiler.fc is not None else '0'),
+                '--with-mpi=0'
+            ]
+            error_message_fmt = '\t{library} support requires "+mpi" to be activated'
+            errors = [error_message_fmt.format(library=x) for x in ('hdf5', 'hypre') if ('+'+x) in self.spec]
+            if errors:
+                errors = ['incompatible variants given'] + errors
+                raise RuntimeError('\n'.join(errors))
+        else:
+            compiler_opts = [
+                '--with-mpi=1',
+                '--with-mpi-dir=%s' % self.spec['mpi'].prefix,
+            ]
+        return compiler_opts
 
     def install(self, spec, prefix):
-        configure("--prefix=%s" % prefix,
-                  "--with-blas-lib=%s/libblas.a"     % spec['blas'].prefix.lib,
-                  "--with-lapack-lib=%s/liblapack.a" % spec['lapack'].prefix.lib,
-                  "--with-boost-dir=%s"              % spec['boost'].prefix,
-                  "--with-hypre-dir=%s"              % spec['hypre'].prefix,
-                  "--with-parmetis-dir=%s"           % spec['parmetis'].prefix,
-                  "--with-metis-dir=%s"              % spec['metis'].prefix,
-                  "--with-hdf5-dir=%s"               % spec['hdf5'].prefix,
-                  "--with-mpi-dir=%s"                % spec['mpi'].prefix,
-                  "--with-shared-libraries=0")
+        options = []
+        options.extend(self.mpi_dependent_options())
+        options.extend([
+            '--with-precision=%s' % ('double' if '+double' in spec else 'single'),
+            '--with-shared-libraries=%s' % ('1' if '+shared' in spec else '0'),
+            '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
+        ])
+        # Activates library support if needed
+        for library in ('metis', 'boost', 'hfd5', 'hypre', 'parmetis'):
+            options.append(
+                '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
+            )
+            if library in spec:
+                options.append(
+                    '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
+                )
+
 
+        configure('--prefix=%s' % prefix, *options)
         # PETSc has its own way of doing parallel make.
         make('MAKE_NP=%s' % make_jobs, parallel=False)
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 8e76cda200bb3da159cdc27726c7812f66c5a5ed Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Wed, 9 Mar 2016 10:41:31 -0600
Subject: Patch config.hin, not extern-inline.m4

---
 .../repos/builtin/packages/m4/inline-pgi.patch     | 22 ----------------------
 var/spack/repos/builtin/packages/m4/package.py     |  6 +-----
 var/spack/repos/builtin/packages/m4/pgi.patch      | 10 ++++++++++
 3 files changed, 11 insertions(+), 27 deletions(-)
 delete mode 100644 var/spack/repos/builtin/packages/m4/inline-pgi.patch
 create mode 100644 var/spack/repos/builtin/packages/m4/pgi.patch

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/m4/inline-pgi.patch b/var/spack/repos/builtin/packages/m4/inline-pgi.patch
deleted file mode 100644
index bc31ad918e..0000000000
--- a/var/spack/repos/builtin/packages/m4/inline-pgi.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/m4/extern-inline.m4
-+++ b/m4/extern-inline.m4
-@@ -34,6 +34,7 @@
-       ? defined __GNUC_STDC_INLINE__ && __GNUC_STDC_INLINE__ \
-       : (199901L <= __STDC_VERSION__ \
-          && !defined __HP_cc \
-+         && !defined __PGI \
-          && !(defined __SUNPRO_C && __STDC__))) \
-      && !defined _GL_EXTERN_INLINE_STDHEADER_BUG)
- # define _GL_INLINE inline
---- a/configure.ac
-+++ b/configure.ac
-@@ -22,7 +22,7 @@
-   [bug-m4@gnu.org])
- AC_CONFIG_AUX_DIR([build-aux])
- 
--AM_INIT_AUTOMAKE([1.11.6 dist-bzip2 dist-xz color-tests parallel-tests
-+AM_INIT_AUTOMAKE([dist-bzip2 dist-xz color-tests parallel-tests
- silent-rules subdir-objects gnu])
- 
- m4_pattern_forbid([^M4_[A-Z]])
-
diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index aa0c775f08..a4b9dcb623 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -7,17 +7,13 @@ class M4(Package):
 
     version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76')
 
-    patch('inline-pgi.patch', when='@1.4.17')
+    patch('pgi.patch', when='@1.4.17')
 
     variant('sigsegv', default=True, description="Build the libsigsegv dependency")
 
     depends_on('libsigsegv', when='+sigsegv')
 
     def install(self, spec, prefix):
-        # After patch, update generated configuration files that depend on extern-inline.m4
-        autoreconf = which('autoreconf')
-        autoreconf()
-
         configure_args = []
         if 'libsigsegv' in spec:
             configure_args.append('--with-libsigsegv-prefix=%s' % spec['libsigsegv'].prefix)
diff --git a/var/spack/repos/builtin/packages/m4/pgi.patch b/var/spack/repos/builtin/packages/m4/pgi.patch
new file mode 100644
index 0000000000..1ad63e2cf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/m4/pgi.patch
@@ -0,0 +1,10 @@
+--- a/lib/config.hin
++++ b/lib/config.hin
+@@ -1510,6 +1510,7 @@
+       ? defined __GNUC_STDC_INLINE__ && __GNUC_STDC_INLINE__ \
+       : (199901L <= __STDC_VERSION__ \
+          && !defined __HP_cc \
++         && !defined __PGI \
+          && !(defined __SUNPRO_C && __STDC__))) \
+      && !defined _GL_EXTERN_INLINE_APPLE_BUG)
+ # define _GL_INLINE inline
-- 
cgit v1.2.3-70-g09d2


From b43c277dc617020d7aaa1e292e01e79d0840999e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 9 Mar 2016 10:55:50 -0800
Subject: Merge @citibeth and @alalazo's petsc fixes from #515 and #517

---
 var/spack/repos/builtin/packages/petsc/package.py | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 5be187f348..41fd859945 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -15,6 +15,7 @@ class Petsc(Package):
     version('3.5.3', 'd4fd2734661e89f18ac6014b5dd1ef2f')
     version('3.5.2', 'ad170802b3b058b5deb9cd1f968e7e13')
     version('3.5.1', 'a557e029711ebf425544e117ffa44d8f')
+    version('3.4.4', '7edbc68aa6d8d6a3295dd5f6c2f6979d')
 
     variant('shared', default=True, description='Enables the build of shared libraries')
     variant('mpi', default=True, description='Activates MPI support')
@@ -25,21 +26,21 @@ class Petsc(Package):
     variant('boost', default=True, description='Activates support for Boost')
     variant('hypre', default=True, description='Activates support for Hypre')
 
-    # Build dependencies
-    depends_on('python @2.6:2.9')  # requires Python for building
-
     # Virtual dependencies
     depends_on('blas')
     depends_on('lapack')
     depends_on('mpi', when='+mpi')
 
+    # Build dependencies
+    depends_on('python @2.6:2.7')
+
     # Other dependencies
     depends_on('boost', when='+boost')
     depends_on('metis', when='+metis')
 
-    depends_on('hdf5~cxx~unsupported+mpi', when='+hdf5+mpi')
+    depends_on('hdf5+mpi', when='+hdf5+mpi')
     depends_on('parmetis', when='+metis+mpi')
-    depends_on('hypre', when='+hypre+mpi')
+    depends_on('hypre',    when='+hypre+mpi')
 
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
@@ -50,7 +51,9 @@ class Petsc(Package):
                 '--with-mpi=0'
             ]
             error_message_fmt = '\t{library} support requires "+mpi" to be activated'
-            errors = [error_message_fmt.format(library=x) for x in ('hdf5', 'hypre') if ('+'+x) in self.spec]
+            errors = [error_message_fmt.format(library=x)
+                      for x in ('hdf5', 'hypre', 'parmetis')
+                      if ('+'+x) in self.spec]
             if errors:
                 errors = ['incompatible variants given'] + errors
                 raise RuntimeError('\n'.join(errors))
@@ -70,7 +73,7 @@ class Petsc(Package):
             '--with-blas-lapack-dir=%s' % spec['lapack'].prefix
         ])
         # Activates library support if needed
-        for library in ('metis', 'boost', 'hfd5', 'hypre', 'parmetis'):
+        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis'):
             options.append(
                 '--with-{library}={value}'.format(library=library, value=('1' if library in spec else '0'))
             )
@@ -79,8 +82,8 @@ class Petsc(Package):
                     '--with-{library}-dir={path}'.format(library=library, path=spec[library].prefix)
                 )
 
-
         configure('--prefix=%s' % prefix, *options)
+
         # PETSc has its own way of doing parallel make.
         make('MAKE_NP=%s' % make_jobs, parallel=False)
         make("install")
-- 
cgit v1.2.3-70-g09d2


From d06ebf23d4ffe3499edca3f34f60be9b561f5f8c Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 9 Mar 2016 11:16:35 -0800
Subject: Removing `unsupported` variant from HDF5.

- `unsupported` shouldn't be a variant.
---
 var/spack/repos/builtin/packages/hdf5/package.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index ed4e7c35c9..513a38ee8a 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -46,7 +46,6 @@ class Hdf5(Package):
 
     variant('cxx', default=True, description='Enable C++ support')
     variant('fortran', default=True, description='Enable Fortran support')
-    variant('unsupported', default=True, description='Enables unsupported configuration options')
 
     variant('mpi', default=False, description='Enable MPI support')
     variant('szip', default=False, description='Enable szip support')
@@ -74,6 +73,13 @@ class Hdf5(Package):
         self.validate(spec)
         # Handle compilation after spec validation
         extra_args = []
+
+        # Always enable this option. This does not actually enable any
+        # features: it only *allows* the user to specify certain
+        # combinations of other arguments. Enabling it just skips a
+        # sanity check in configure, so this doesn't merit a variant.
+        extra_args.append("--enable-unsupported")
+
         if '+debug' in spec:
             extra_args.append('--enable-debug=all')
         else:
@@ -84,9 +90,6 @@ class Hdf5(Package):
         else:
             extra_args.append('--enable-static-exec')
 
-        if '+unsupported' in spec:
-            extra_args.append("--enable-unsupported")
-
         if '+cxx' in spec:
             extra_args.append('--enable-cxx')
 
-- 
cgit v1.2.3-70-g09d2


From 383e73a5f53e0ab3d1f448789bc5a1b4a7c85292 Mon Sep 17 00:00:00 2001
From: Alfredo Adolfo Gimenez <alfredo.gimenez@gmail.com>
Date: Wed, 9 Mar 2016 11:25:51 -0800
Subject: Remove unneccessary depends_on

---
 var/spack/repos/builtin/packages/thrift/package.py | 1 -
 1 file changed, 1 deletion(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py
index ec3b13e563..6430f40e80 100644
--- a/var/spack/repos/builtin/packages/thrift/package.py
+++ b/var/spack/repos/builtin/packages/thrift/package.py
@@ -27,7 +27,6 @@ class Thrift(Package):
 
     # Variant dependencies
     extends('python', when='+python')
-    depends_on('python', when='+python')
 
     depends_on('zlib', when='+c')
     depends_on('libevent', when='+c')
-- 
cgit v1.2.3-70-g09d2


From 45ef496dd553e023903b8b4d5bcace59c56eb486 Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 9 Mar 2016 11:26:37 -0800
Subject: Add some descriptive language to a list comprehension.

---
 var/spack/repos/builtin/packages/petsc/package.py | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 41fd859945..efe172fc08 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -51,6 +51,9 @@ class Petsc(Package):
                 '--with-mpi=0'
             ]
             error_message_fmt = '\t{library} support requires "+mpi" to be activated'
+
+            # If mpi is disabled (~mpi), it's an error to have any of these enabled.
+            # This generates a list of any such errors.
             errors = [error_message_fmt.format(library=x)
                       for x in ('hdf5', 'hypre', 'parmetis')
                       if ('+'+x) in self.spec]
-- 
cgit v1.2.3-70-g09d2


From 6e82ab1f1501c8b64383f1d9a26d743284f4054f Mon Sep 17 00:00:00 2001
From: Nicolas Richart <nicolas.richart@epfl.ch>
Date: Wed, 9 Mar 2016 21:18:44 +0100
Subject: change of url for mpfr

---
 var/spack/repos/builtin/packages/mpfr/package.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py
index a1bd7529cf..7e6e7d5bb6 100644
--- a/var/spack/repos/builtin/packages/mpfr/package.py
+++ b/var/spack/repos/builtin/packages/mpfr/package.py
@@ -28,8 +28,9 @@ class Mpfr(Package):
     """The MPFR library is a C library for multiple-precision
        floating-point computations with correct rounding."""
     homepage = "http://www.mpfr.org"
-    url      = "http://www.mpfr.org/mpfr-current/mpfr-3.1.3.tar.bz2"
+    url      = "https://gforge.inria.fr/frs/download.php/latestfile/159/mpfr-3.1.2.tar.bz2"
 
+    version('3.1.4', 'b8a2f6b0e68bef46e53da2ac439e1cf4')
     version('3.1.3', '5fdfa3cfa5c86514ee4a241a1affa138')
     version('3.1.2', 'ee2c3ac63bf0c2359bf08fc3ee094c19')
 
-- 
cgit v1.2.3-70-g09d2


From 23cbc2b1d9dc5816c63f330640105c5435ccdc22 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Tue, 8 Mar 2016 09:44:21 -0700
Subject: + Provide download/build instructions for qt/5.4.2.   - This version
 provides updates to provided cmake scripts that are required     for building
 cmake-gui. + Provide download/build instructions for version 3.5.0.   - When
 building the +qt variant, add a validate function to ensure that     qt-5.4.0
 is not used (this version of qt has errors related to cmake).

---
 var/spack/repos/builtin/packages/cmake/package.py | 19 ++++++++++++++++++-
 var/spack/repos/builtin/packages/qt/package.py    |  3 +++
 2 files changed, 21 insertions(+), 1 deletion(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index f39a681284..806c37a68c 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -30,6 +30,7 @@ class Cmake(Package):
     homepage  = 'https://www.cmake.org'
     url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
 
+    version('3.5.0',    '33c5d09d4c33d4ffcc63578a6ba8777e')
     version('3.4.3',    '4cb3ff35b2472aae70f542116d616e63')
     version('3.4.0',    'cd3034e0a44256a0917e254167217fc8')
     version('3.3.1',    '52638576f4e1e621fed6c3410d3a1b12')
@@ -49,8 +50,25 @@ class Cmake(Package):
         """Handle CMake's version-based custom URLs."""
         return 'https://cmake.org/files/v%s/cmake-%s.tar.gz' % (version.up_to(2), version)
 
+    def validate(self, spec):
+        """
+        Checks if incompatible versions of qt were specified
+
+        :param spec: spec of the package
+        :raises RuntimeError: in case of inconsistencies
+        """
+
+        print spec
+
+        if '+qt' in spec and spec.satisfies('^qt@5.4.0'):
+            msg = 'qt-5.4.0 has broken CMake modules.'
+            raise RuntimeError(msg)
+
     def install(self, spec, prefix):
+        # Consistency check
+        self.validate(spec)
 
+        # configure, build, install:
         options = ['--prefix=%s' % prefix]
         options.append('--parallel=%s' % str(make_jobs))
 
@@ -65,6 +83,5 @@ class Cmake(Package):
         options.append('-DCMAKE_USE_OPENSSL=ON')
 
         configure(*options)
-
         make()
         make('install')
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index 91afa420c1..ef5f05601f 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -8,6 +8,9 @@ class Qt(Package):
     list_url   = 'http://download.qt-project.org/official_releases/qt/'
     list_depth = 2
 
+    version('5.4.2', 'fa1c4d819b401b267eb246a543a63ea5',
+            url='http://download.qt-project.org/official_releases/qt/5.4/5.4.2/single/qt-everywhere-opensource-src-5.4.2.tar.gz')
+
     version('5.4.0', 'e8654e4b37dd98039ba20da7a53877e6',
             url='http://download.qt-project.org/official_releases/qt/5.4/5.4.0/single/qt-everywhere-opensource-src-5.4.0.tar.gz')
 
-- 
cgit v1.2.3-70-g09d2


From 267e83d8a70324d9b8a70a86085853dd762c7f93 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Wed, 9 Mar 2016 21:12:11 -0500
Subject: Added emacs package.

---
 var/spack/repos/builtin/packages/emacs/package.py | 36 +++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/emacs/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py
new file mode 100644
index 0000000000..e496ffc3d1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/emacs/package.py
@@ -0,0 +1,36 @@
+# FIXME:
+# This is a template package file for Spack.  We've conveniently
+# put "FIXME" labels next to all the things you'll want to change.
+#
+# Once you've edited all the FIXME's, delete this whole message,
+# save this file, and test out your package like this:
+#
+#     spack install emacs
+#
+# You can always get back here to change things with:
+#
+#     spack edit emacs
+#
+# See the spack documentation for more information on building
+# packages.
+#
+from spack import *
+
+class Emacs(Package):
+    """FIXME: put a proper description of your package here."""
+    # FIXME: add a proper url for your package's homepage here.
+    homepage = "http://www.example.com"
+    url      = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz"
+
+    version('24.5', 'd74b597503a68105e61b5b9f6d065b44')
+
+    # FIXME: Add dependencies if this package requires them.
+    depends_on('ncurses')
+
+    def install(self, spec, prefix):
+        # FIXME: Modify the configure line to suit your build system here.
+        configure('--prefix=%s' % prefix)
+
+        # FIXME: Add logic to build and install here
+        make()
+        make("install")
-- 
cgit v1.2.3-70-g09d2


From b701aa10d4b40eda3d5ea3f0c96b5aed7493c7a7 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Wed, 9 Mar 2016 21:21:25 -0500
Subject: Fixed up

---
 var/spack/repos/builtin/packages/emacs/package.py | 29 +++++------------------
 1 file changed, 6 insertions(+), 23 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py
index e496ffc3d1..09eb05d5a7 100644
--- a/var/spack/repos/builtin/packages/emacs/package.py
+++ b/var/spack/repos/builtin/packages/emacs/package.py
@@ -1,36 +1,19 @@
-# FIXME:
-# This is a template package file for Spack.  We've conveniently
-# put "FIXME" labels next to all the things you'll want to change.
-#
-# Once you've edited all the FIXME's, delete this whole message,
-# save this file, and test out your package like this:
-#
-#     spack install emacs
-#
-# You can always get back here to change things with:
-#
-#     spack edit emacs
-#
-# See the spack documentation for more information on building
-# packages.
-#
 from spack import *
 
 class Emacs(Package):
-    """FIXME: put a proper description of your package here."""
-    # FIXME: add a proper url for your package's homepage here.
-    homepage = "http://www.example.com"
+    """The Emacs programmable text editor."""
+    homepage = "https://www.gnu.org/software/emacs"
     url      = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz"
 
     version('24.5', 'd74b597503a68105e61b5b9f6d065b44')
 
-    # FIXME: Add dependencies if this package requires them.
     depends_on('ncurses')
+    # Emacs also depends on:
+    #     GTK or other widget library
+    #     libtiff, png, etc.
+    # For now, we assume the system provides all that stuff.
 
     def install(self, spec, prefix):
-        # FIXME: Modify the configure line to suit your build system here.
         configure('--prefix=%s' % prefix)
-
-        # FIXME: Add logic to build and install here
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2


From 1fe196f95cc26cac73abe64752ff67b150f4d50a Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Wed, 2 Mar 2016 22:38:21 -0800
Subject: whitespace and formatting

---
 lib/spack/spack/preferred_packages.py              | 38 +++++++++++-----------
 lib/spack/spack/spec.py                            |  8 ++---
 var/spack/repos/builtin/packages/python/package.py |  5 +--
 3 files changed, 26 insertions(+), 25 deletions(-)

(limited to 'var')

diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py
index eaea016a85..4ff0f18b31 100644
--- a/lib/spack/spack/preferred_packages.py
+++ b/lib/spack/spack/preferred_packages.py
@@ -33,8 +33,8 @@ class PreferredPackages(object):
         self.preferred = spack.config.get_config('packages')
         self._spec_for_pkgname_cache = {}
 
-    #Given a package name, sort component (e.g, version, compiler, ...), and
-    # a second_key (used by providers), return the list 
+    # Given a package name, sort component (e.g, version, compiler, ...), and
+    # a second_key (used by providers), return the list
     def _order_for_package(self, pkgname, component, second_key, test_all=True):
         pkglist = [pkgname]
         if test_all:
@@ -47,10 +47,10 @@ class PreferredPackages(object):
                 continue
             return [str(s).strip() for s in order]
         return []
-            
 
-    # A generic sorting function. Given a package name and sort 
-    # component, return less-than-0, 0, or greater-than-0 if 
+
+    # A generic sorting function. Given a package name and sort
+    # component, return less-than-0, 0, or greater-than-0 if
     # a is respectively less-than, equal to, or greater than b.
     def _component_compare(self, pkgname, component, a, b, reverse_natural_compare, second_key):
         if a is None:
@@ -76,7 +76,7 @@ class PreferredPackages(object):
             cmp_a = orderlist.index(str(a))
             cmp_b = orderlist.index(str(b))
             reverse = 1
-        
+
         if cmp_a < cmp_b:
             return -1 * reverse
         elif cmp_a > cmp_b:
@@ -87,7 +87,7 @@ class PreferredPackages(object):
 
     # A sorting function for specs.  Similar to component_compare, but
     # a and b are considered to match entries in the sorting list if they
-    # satisfy the list component.  
+    # satisfy the list component.
     def _spec_compare(self, pkgname, component, a, b, reverse_natural_compare, second_key):
         if not a or not a.concrete:
             return -1
@@ -121,7 +121,7 @@ class PreferredPackages(object):
         key = (pkgname, component, second_key)
         if not key in self._spec_for_pkgname_cache:
             pkglist = self._order_for_package(pkgname, component, second_key)
-            if not pkglist: 
+            if not pkglist:
                 if component in self._default_order:
                     pkglist = self._default_order[component]
             if component == 'compiler':
@@ -132,9 +132,9 @@ class PreferredPackages(object):
                 self._spec_for_pkgname_cache[key] = [spack.spec.Spec(s) for s in pkglist]
         return self._spec_for_pkgname_cache[key]
 
-    
+
     def provider_compare(self, pkgname, provider_str, a, b):
-        """Return less-than-0, 0, or greater than 0 if a is respecively less-than, equal-to, or 
+        """Return less-than-0, 0, or greater than 0 if a is respecively less-than, equal-to, or
            greater-than b. A and b are possible implementations of provider_str.
            One provider is less-than another if it is preferred over the other.
            For example, provider_compare('scorep', 'mpi', 'mvapich', 'openmpi') would return -1 if
@@ -148,28 +148,28 @@ class PreferredPackages(object):
 
 
     def version_compare(self, pkgname, a, b):
-        """Return less-than-0, 0, or greater than 0 if version a of pkgname is 
-           respecively less-than, equal-to, or greater-than version b of pkgname. 
+        """Return less-than-0, 0, or greater than 0 if version a of pkgname is
+           respecively less-than, equal-to, or greater-than version b of pkgname.
            One version is less-than another if it is preferred over the other."""
         return self._spec_compare(pkgname, 'version', a, b, True, None)
 
-    
+
     def variant_compare(self, pkgname, a, b):
-        """Return less-than-0, 0, or greater than 0 if variant a of pkgname is 
-           respecively less-than, equal-to, or greater-than variant b of pkgname. 
+        """Return less-than-0, 0, or greater than 0 if variant a of pkgname is
+           respecively less-than, equal-to, or greater-than variant b of pkgname.
            One variant is less-than another if it is preferred over the other."""
         return self._component_compare(pkgname, 'variant', a, b, False, None)
 
 
     def architecture_compare(self, pkgname, a, b):
-        """Return less-than-0, 0, or greater than 0 if architecture a of pkgname is 
-           respecively less-than, equal-to, or greater-than architecture b of pkgname. 
+        """Return less-than-0, 0, or greater than 0 if architecture a of pkgname is
+           respecively less-than, equal-to, or greater-than architecture b of pkgname.
            One architecture is less-than another if it is preferred over the other."""
         return self._component_compare(pkgname, 'architecture', a, b, False, None)
 
 
     def compiler_compare(self, pkgname, a, b):
-        """Return less-than-0, 0, or greater than 0 if compiler a of pkgname is 
-           respecively less-than, equal-to, or greater-than compiler b of pkgname. 
+        """Return less-than-0, 0, or greater than 0 if compiler a of pkgname is
+           respecively less-than, equal-to, or greater-than compiler b of pkgname.
            One compiler is less-than another if it is preferred over the other."""
         return self._spec_compare(pkgname, 'compiler', a, b, False, None)
diff --git a/lib/spack/spack/spec.py b/lib/spack/spack/spec.py
index 6f55065f01..b8c0d0ef9c 100644
--- a/lib/spack/spack/spec.py
+++ b/lib/spack/spack/spec.py
@@ -428,7 +428,7 @@ class Spec(object):
         for dep in dep_like:
             spec = dep if isinstance(dep, Spec) else Spec(dep)
             self._add_dependency(spec)
-        
+
 
     #
     # Private routines here are called by the parser when building a spec.
@@ -1410,7 +1410,7 @@ class Spec(object):
                        self.architecture != other.architecture and self.compiler != other.compiler and \
                        self.variants != other.variants and self._normal != other._normal and \
                        self.concrete != other.concrete and self.external != other.external)
-                                       
+
         # Local node attributes get copied first.
         self.name = other.name
         self.versions = other.versions.copy()
@@ -1585,7 +1585,7 @@ class Spec(object):
                $@   Version with '@' prefix
                $%   Compiler with '%' prefix
                $%@  Compiler with '%' prefix & compiler version with '@' prefix
-               $+   Options 
+               $+   Options
                $=   Architecture with '=' prefix
                $#   7-char prefix of DAG hash with '-' prefix
                $$   $
@@ -1738,7 +1738,7 @@ class Spec(object):
         #Package name sort order is not configurable, always goes alphabetical
         if self.name != other.name:
             return cmp(self.name, other.name)
-        
+
         #Package version is second in compare order
         pkgname = self.name
         if self.versions != other.versions:
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index 58d401244e..dd240d1ea0 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -34,8 +34,9 @@ class Python(Package):
         env['PYTHONHOME'] = prefix
         env['MACOSX_DEPLOYMENT_TARGET'] = '10.6'
 
-        # Rest of install is pretty standard except setup.py needs to be able to read the CPPFLAGS
-        # and LDFLAGS as it scans for the library and headers to build
+        # Rest of install is pretty standard except setup.py needs to
+        # be able to read the CPPFLAGS and LDFLAGS as it scans for the
+        # library and headers to build
         configure_args= [
                   "--prefix=%s" % prefix,
                   "--with-threads",
-- 
cgit v1.2.3-70-g09d2


From f5e8857c5e44719778e531bcc149c9fe228240b3 Mon Sep 17 00:00:00 2001
From: "Kelly (KT) Thompson" <kgt@lanl.gov>
Date: Fri, 11 Mar 2016 09:51:12 -0700
Subject: + Rename variant 'sphinxbuild' to 'doc' as recommended in the
 discussion of   PR#526. Also, remove a debug print statement that was
 accidentally committed.

---
 var/spack/repos/builtin/packages/cmake/package.py | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index 806c37a68c..cc93c7067c 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -39,12 +39,12 @@ class Cmake(Package):
 
     variant('ncurses', default=True, description='Enables the build of the ncurses gui')
     variant('qt', default=False, description='Enables the build of cmake-gui')
-    variant('sphinxbuild', default=False, description='Enables the generation of html and man page documentation')
+    variant('doc', default=False, description='Enables the generation of html and man page documentation')
 
     depends_on('ncurses', when='+ncurses')
     depends_on('qt', when='+qt')
-    depends_on('python@2.7.11:', when='+sphinxbuild')
-    depends_on('py-sphinx', when='+sphinxbuild')
+    depends_on('python@2.7.11:', when='+doc')
+    depends_on('py-sphinx', when='+doc')
 
     def url_for_version(self, version):
         """Handle CMake's version-based custom URLs."""
@@ -58,8 +58,6 @@ class Cmake(Package):
         :raises RuntimeError: in case of inconsistencies
         """
 
-        print spec
-
         if '+qt' in spec and spec.satisfies('^qt@5.4.0'):
             msg = 'qt-5.4.0 has broken CMake modules.'
             raise RuntimeError(msg)
@@ -75,7 +73,7 @@ class Cmake(Package):
         if '+qt' in spec:
             options.append('--qt-gui')
 
-        if '+sphinxbuild' in spec:
+        if '+doc' in spec:
             options.append('--sphinx-html')
             options.append('--sphinx-man')
 
-- 
cgit v1.2.3-70-g09d2


From 6ec65cd4ca1e6c2d346c949e21902680f27364c5 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 11 Mar 2016 15:03:37 -0600
Subject: Add GNU Octave package

---
 var/spack/repos/builtin/packages/octave/package.py | 182 +++++++++++++++++++++
 1 file changed, 182 insertions(+)
 create mode 100644 var/spack/repos/builtin/packages/octave/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
new file mode 100644
index 0000000000..6810da6d98
--- /dev/null
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -0,0 +1,182 @@
+from spack import *
+
+class Octave(Package):
+    """GNU Octave is a high-level language, primarily intended for numerical
+    computations. It provides a convenient command line interface for solving
+    linear and nonlinear problems numerically, and for performing other
+    numerical experiments using a language that is mostly compatible with
+    Matlab. It may also be used as a batch-oriented language."""
+
+    homepage = "https://www.gnu.org/software/octave/"
+    url      = "ftp://ftp.gnu.org/gnu/octave/octave-4.0.0.tar.gz"
+
+    version('4.0.0' , 'a69f8320a4f20a8480c1b278b1adb799')
+
+    variant('readline',   default=True)
+    variant('arpack',     default=False)
+    variant('curl',       default=False)
+    variant('fftw',       default=False)
+    variant('fltk',       default=False)
+    variant('fontconfig', default=False)
+    variant('freetype',   default=False)
+    variant('glpk',       default=False)
+    variant('gl2ps',      default=False)
+    variant('gnuplot',    default=False)
+    variant('magick',     default=False)
+    variant('hdf5',       default=False)
+    variant('jdk',        default=False)
+    variant('llvm',       default=False)
+    variant('opengl',     default=False)
+    variant('qhull',      default=False)
+    variant('qrupdate',   default=False)
+    variant('qscintilla', default=False)
+    variant('qt',         default=False)
+    variant('suiteparse', default=False)
+    variant('zlib',       default=False)
+
+    # Required dependencies
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('pcre')
+
+    # Strongly recommended dependencies
+    depends_on('readline',    when='+readline')
+
+    # Optional dependencies
+    depends_on('arpack',      when='+arpack')
+    depends_on('curl',        when='+curl')
+    depends_on('fftw@3',      when='+fftw')
+    depends_on('fltk',        when='+fltk')
+    depends_on('fontconfig',  when='+fontconfig')
+    depends_on('freetype',    when='+freetype')
+    depends_on('glpk',        when='+glpk')
+    #depends_on('gl2ps',       when='+gl2ps')
+    depends_on('gnuplot',     when='+gnuplot')
+    depends_on('ImageMagick', when='+magick')
+    depends_on('hdf5',        when='+hdf5')
+    depends_on('jdk',         when='+jdk')
+    depends_on('llvm',        when='+llvm')
+    #depends_on('opengl',      when='+opengl')
+    depends_on('qhull',       when='+qhull')
+    #depends_on('qrupdate',    when='+qrupdate')
+    #depends_on('qscintilla',  when='+qscintilla)
+    depends_on('qt',          when='+qt')
+    depends_on('SuiteSparse', when='suitesparse')
+    depends_on('zlib',        when='+zlib')
+
+
+    def install(self, spec, prefix):
+        config_args = [
+            "--prefix=%s" % prefix
+        ]
+
+        # Required dependencies
+        config_args.extend([
+            "--with-blas=%s" % spec['blas'].prefix.lib,
+            "--with-lapack=%s" % spec['lapack'].prefix.lib
+        ])
+
+        # Strongly recommended dependencies
+        if '+readline' in spec:
+            config_args.append('--enable-readline')
+        else:
+            config_args.append('--disable-readline')
+
+        # Optional dependencies
+        if '+arpack' in spec:
+            config_args.extend([
+                "--with-arpack-includedir=%s" % spec['arpack'].prefix.include,
+                "--with-arpack-libdir=%s"     % spec['arpack'].prefix.lib
+            ])
+        else:
+            config_args.append("--without-arpack")
+
+        if '+curl' in spec:
+            config_args.extend([
+                "--with-curl-includedir=%s" % spec['curl'].prefix.include,
+                "--with-curl-libdir=%s"     % spec['curl'].prefix.lib
+            ])
+        else:
+            config_args.append("--without-curl")
+
+        if '+fftw' in spec:
+            config_args.extend([
+                "--with-fftw3-includedir=%s"  % spec['fftw'].prefix.include,
+                "--with-fftw3-libdir=%s"      % spec['fftw'].prefix.lib,
+                "--with-fftw3f-includedir=%s" % spec['fftw'].prefix.include,
+                "--with-fftw3f-libdir=%s"     % spec['fftw'].prefix.lib
+            ])
+        else:
+            config_args.extend([
+                "--without-fftw3",
+                "--without-fftw3f"
+            ])
+
+        if '+fltk' in spec:
+            config_args.extend([
+                "--with-fltk-prefix=%s"      % spec['fltk'].prefix,
+                "--with-fltk-exec-prefix=%s" % spec['fltk'].prefix
+            ])
+        else:
+            config_args.append("--without-fltk")
+
+        if '+glpk' in spec:
+            config_args.extend([
+                "--with-glpk-includedir=%s" % spec['glpk'].prefix.include
+                "--with-glpk-libdir=%s"     % spec['glpk'].prefix.lib
+            ])
+        else:
+            config_args.append("--without-glpk")
+
+        if '+magick' in spec:
+            config_args.append("--with-magick=%s" % spec['ImageMagick'].prefix.lib)
+
+        if '+hdf5' in spec:
+            config_args.extend([
+                "--with-hdf5-includedir=%s" % spec['hdf5'].prefix.include,
+                "--with-hdf5-libdir=%s"     % spec['hdf5'].prefix.lib
+            ])
+        else:
+            config_args.append("--without-hdf5")
+
+        if '+jdk' in spec:
+            config_args.extend([
+                "--with-java-homedir=%s"    % spec['jdk'].prefix,
+                "--with-java-includedir=%s" % spec['jdk'].prefix.include,
+                "--with-java-libdir=%s"     % spec['jdk'].prefix.lib
+            ])
+
+        #if '~opengl' in spec:
+        #    config_args.extend([
+        #        "--without-opengl",
+        #        "--without-framework-opengl"
+        #    ])
+
+        if '+qhull' in spec:
+            config_args.extend([
+                "--with-qhull-includedir=%s" % spec['qhull'].prefix.include,
+                "--with-qhull-libdir=%s"     % spec['qhull'].prefix.lib
+            ])
+        else:
+            config_args.append("--without-qhull")
+
+        #if '+qrupdate' in spec:
+        #    config_args.extend([
+        #        "--with-qrupdate-includedir=%s" % spec['qrupdate'].prefix.include,
+        #        "--with-qrupdate-libdir=%s"     % spec['qrupdate'].prefix.lib
+        #    ])
+        #else:
+        #    config_args.append("--without-qrupdate")
+
+        if '+zlib' in spec:
+            config_args.extend([
+                "--with-z-includedir=%s" % spec['zlib'].prefix.include,
+                "--with-z-libdir=%s"     % spec['zlib'].prefix.lib
+            ])
+        else:
+            config_args.append("--without-z")
+
+        configure(*config_args)
+
+        make()
+        make("install")
-- 
cgit v1.2.3-70-g09d2


From 145390c7f3a9de6e679f56dc9b275973a459de91 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Fri, 11 Mar 2016 16:57:37 -0600
Subject: Add gl2ps and qrupdate packages

---
 var/spack/repos/builtin/packages/gl2ps/package.py  | 18 ++++++++++++++++
 var/spack/repos/builtin/packages/octave/package.py | 24 +++++++++++-----------
 .../repos/builtin/packages/qrupdate/package.py     | 18 ++++++++++++++++
 3 files changed, 48 insertions(+), 12 deletions(-)
 create mode 100644 var/spack/repos/builtin/packages/gl2ps/package.py
 create mode 100644 var/spack/repos/builtin/packages/qrupdate/package.py

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/gl2ps/package.py b/var/spack/repos/builtin/packages/gl2ps/package.py
new file mode 100644
index 0000000000..cb376b3f03
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gl2ps/package.py
@@ -0,0 +1,18 @@
+from spack import *
+
+class Gl2ps(Package):
+    """GL2PS is a C library providing high quality vector output for any
+    OpenGL application."""
+
+    homepage = "http://www.geuz.org/gl2ps/"
+    url      = "http://geuz.org/gl2ps/src/gl2ps-1.3.9.tgz"
+
+    version('1.3.9', '377b2bcad62d528e7096e76358f41140')
+
+    depends_on("libpng")
+
+    def install(self, spec, prefix):
+        cmake('.', *std_cmake_args)
+
+        make()
+        make("install")
diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
index 6810da6d98..99847e1dbe 100644
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -50,7 +50,7 @@ class Octave(Package):
     depends_on('fontconfig',  when='+fontconfig')
     depends_on('freetype',    when='+freetype')
     depends_on('glpk',        when='+glpk')
-    #depends_on('gl2ps',       when='+gl2ps')
+    depends_on('gl2ps',       when='+gl2ps')
     depends_on('gnuplot',     when='+gnuplot')
     depends_on('ImageMagick', when='+magick')
     depends_on('hdf5',        when='+hdf5')
@@ -58,10 +58,10 @@ class Octave(Package):
     depends_on('llvm',        when='+llvm')
     #depends_on('opengl',      when='+opengl')
     depends_on('qhull',       when='+qhull')
-    #depends_on('qrupdate',    when='+qrupdate')
+    depends_on('qrupdate',    when='+qrupdate')
     #depends_on('qscintilla',  when='+qscintilla)
     depends_on('qt',          when='+qt')
-    depends_on('SuiteSparse', when='suitesparse')
+    depends_on('SuiteSparse', when='+suitesparse')
     depends_on('zlib',        when='+zlib')
 
 
@@ -72,7 +72,7 @@ class Octave(Package):
 
         # Required dependencies
         config_args.extend([
-            "--with-blas=%s" % spec['blas'].prefix.lib,
+            "--with-blas=%s"   % spec['blas'].prefix.lib,
             "--with-lapack=%s" % spec['lapack'].prefix.lib
         ])
 
@@ -122,7 +122,7 @@ class Octave(Package):
 
         if '+glpk' in spec:
             config_args.extend([
-                "--with-glpk-includedir=%s" % spec['glpk'].prefix.include
+                "--with-glpk-includedir=%s" % spec['glpk'].prefix.include,
                 "--with-glpk-libdir=%s"     % spec['glpk'].prefix.lib
             ])
         else:
@@ -160,13 +160,13 @@ class Octave(Package):
         else:
             config_args.append("--without-qhull")
 
-        #if '+qrupdate' in spec:
-        #    config_args.extend([
-        #        "--with-qrupdate-includedir=%s" % spec['qrupdate'].prefix.include,
-        #        "--with-qrupdate-libdir=%s"     % spec['qrupdate'].prefix.lib
-        #    ])
-        #else:
-        #    config_args.append("--without-qrupdate")
+        if '+qrupdate' in spec:
+            config_args.extend([
+                "--with-qrupdate-includedir=%s" % spec['qrupdate'].prefix.include,
+                "--with-qrupdate-libdir=%s"     % spec['qrupdate'].prefix.lib
+            ])
+        else:
+            config_args.append("--without-qrupdate")
 
         if '+zlib' in spec:
             config_args.extend([
diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py
new file mode 100644
index 0000000000..aff44bb2d8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qrupdate/package.py
@@ -0,0 +1,18 @@
+from spack import *
+
+class Qrupdate(Package):
+    """qrupdate is a Fortran library for fast updates of QR and
+    Cholesky decompositions."""
+
+    homepage = "http://sourceforge.net/projects/qrupdate/"
+    url      = "https://downloads.sourceforge.net/qrupdate/qrupdate-1.1.2.tar.gz"
+
+    version('1.1.2', '6d073887c6e858c24aeda5b54c57a8c4')
+
+    depends_on("openblas")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+
+        make()
+        make("install")
-- 
cgit v1.2.3-70-g09d2


From 90f2e40ff92077da1f1b9b4d9aa317b89aa07960 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Fri, 11 Mar 2016 23:28:16 -0500
Subject: Added comment to Emacs.

---
 var/spack/repos/builtin/packages/emacs/package.py | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py
index 09eb05d5a7..caa264857e 100644
--- a/var/spack/repos/builtin/packages/emacs/package.py
+++ b/var/spack/repos/builtin/packages/emacs/package.py
@@ -12,6 +12,8 @@ class Emacs(Package):
     #     GTK or other widget library
     #     libtiff, png, etc.
     # For now, we assume the system provides all that stuff.
+    # For Ubuntu 14.04 LTS:
+    #     sudo apt-get install libgtk-3-dev libxpm-dev libtiff5-dev libjpeg8-dev libgif-dev libpng12-dev
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)
-- 
cgit v1.2.3-70-g09d2


From 7cd478418d5b8a204a8e6b9a5307ecf71ea83939 Mon Sep 17 00:00:00 2001
From: Elizabeth F <rpf2116@columbia.edu>
Date: Fri, 11 Mar 2016 23:28:36 -0500
Subject: New version of LAPACK

---
 var/spack/repos/builtin/packages/netlib-lapack/package.py | 1 +
 1 file changed, 1 insertion(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index fb6b99e27c..741f4af421 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -12,6 +12,7 @@ class NetlibLapack(Package):
     homepage = "http://www.netlib.org/lapack/"
     url      = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
 
+    version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101')
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
     version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478')
     version('3.4.1', '44c3869c38c8335c2b9c2a8bb276eb55')
-- 
cgit v1.2.3-70-g09d2


From 8b715d9c3fabdf4658ff4c0c500d01f74e7ed64e Mon Sep 17 00:00:00 2001
From: Erik Schnetter <schnetter@gmail.com>
Date: Sun, 13 Mar 2016 21:14:41 -0400
Subject: Update tmux

---
 var/spack/repos/builtin/packages/tmux/package.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py
index 23d36db427..f2067d1366 100644
--- a/var/spack/repos/builtin/packages/tmux/package.py
+++ b/var/spack/repos/builtin/packages/tmux/package.py
@@ -7,10 +7,11 @@ class Tmux(Package):
        do a lot more.
     """
 
-    homepage = "http://tmux.sourceforge.net"
-    url      = "http://downloads.sourceforge.net/project/tmux/tmux/tmux-1.9/tmux-1.9a.tar.gz"
+    homepage = "http://tmux.github.io"
+    url = "https://github.com/tmux/tmux/releases/download/2.1/tmux-2.1.tar.gz"
 
     version('1.9a', 'b07601711f96f1d260b390513b509a2d')
+    version('2.1', '74a2855695bccb51b6e301383ad4818c')
 
     depends_on('libevent')
     depends_on('ncurses')
-- 
cgit v1.2.3-70-g09d2


From f45b8b1083e5f628dd31fa4b7b873b6df7119d0e Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Mon, 14 Mar 2016 05:02:50 -0700
Subject: Add some tests for packages with multiple virtual dependencies.

- Added mock `hypre` package, depends on `lapack` and `blas`.

- test cases where some packages provide both `lapack` and `blas`, but
  others do not.
---
 lib/spack/spack/test/concretize.py                 | 29 +++++++++++++++-
 .../repos/builtin.mock/packages/hypre/package.py   | 39 ++++++++++++++++++++++
 .../packages/openblas-with-lapack/package.py       | 38 +++++++++++++++++++++
 3 files changed, 105 insertions(+), 1 deletion(-)
 create mode 100644 var/spack/repos/builtin.mock/packages/hypre/package.py
 create mode 100644 var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py

(limited to 'var')

diff --git a/lib/spack/spack/test/concretize.py b/lib/spack/spack/test/concretize.py
index 07828d8ea6..f264faf17a 100644
--- a/lib/spack/spack/test/concretize.py
+++ b/lib/spack/spack/test/concretize.py
@@ -142,6 +142,34 @@ class ConcretizeTest(MockPackagesTest):
                                 for spec in spack.repo.providers_for('mpi@3')))
 
 
+    def test_concretize_two_virtuals(self):
+        """Test a package with multiple virtual dependencies."""
+        s = Spec('hypre').concretize()
+
+
+    def test_concretize_two_virtuals_with_one_bound(self):
+        """Test a package with multiple virtual dependencies and one preset."""
+        s = Spec('hypre ^openblas').concretize()
+
+
+    def test_concretize_two_virtuals_with_two_bound(self):
+        """Test a package with multiple virtual dependencies and two of them preset."""
+        s = Spec('hypre ^openblas ^netlib-lapack').concretize()
+
+
+    def test_concretize_two_virtuals_with_dual_provider(self):
+        """Test a package with multiple virtual dependencies and force a provider
+           that provides both."""
+        s = Spec('hypre ^openblas-with-lapack').concretize()
+
+
+    def test_concretize_two_virtuals_with_dual_provider_and_a_conflict(self):
+        """Test a package with multiple virtual dependencies and force a provider
+           that provides both, and another conflicting package that provides one."""
+        s = Spec('hypre ^openblas-with-lapack ^netlib-lapack')
+        self.assertRaises(spack.spec.MultipleProviderError, s.concretize)
+
+
     def test_virtual_is_fully_expanded_for_callpath(self):
         # force dependence on fake "zmpi" by asking for MPI 10.0
         spec = Spec('callpath ^mpi@10.0')
@@ -281,4 +309,3 @@ class ConcretizeTest(MockPackagesTest):
                       Spec('d')),
                  Spec('e'))
         self.assertEqual(None, find_spec(s['b'], lambda s: '+foo' in s))
-
diff --git a/var/spack/repos/builtin.mock/packages/hypre/package.py b/var/spack/repos/builtin.mock/packages/hypre/package.py
new file mode 100644
index 0000000000..f69f16d2cc
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hypre/package.py
@@ -0,0 +1,39 @@
+##############################################################################
+# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class Hypre(Package):
+    """Hypre is included here as an example of a package that depends on
+       both LAPACK and BLAS."""
+    homepage = "http://www.openblas.net"
+    url      = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
+
+    version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
+
+    depends_on('lapack')
+    depends_on('blas')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
new file mode 100644
index 0000000000..509bfb71e5
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
@@ -0,0 +1,38 @@
+##############################################################################
+# Copyright (c) 2013-2015, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Written by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License (as published by
+# the Free Software Foundation) version 2.1 dated February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program; if not, write to the Free Software Foundation,
+# Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class OpenblasWithLapack(Package):
+    """Dummy version of OpenBLAS that also provides LAPACK, for testing."""
+    homepage = "http://www.openblas.net"
+    url      = "http://github.com/xianyi/OpenBLAS/archive/v0.2.15.tar.gz"
+
+    version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
+
+    provides('lapack')
+    provides('blas')
+
+    def install(self, spec, prefix):
+        pass
-- 
cgit v1.2.3-70-g09d2


From 0d9a6d3c25de2b8490622c49362b09f706459bc0 Mon Sep 17 00:00:00 2001
From: "Adam J. Stewart" <ajstewart426@gmail.com>
Date: Mon, 14 Mar 2016 14:19:30 -0500
Subject: Updates to qrupdate

---
 var/spack/repos/builtin/packages/octave/package.py   | 17 +++++++++--------
 var/spack/repos/builtin/packages/qrupdate/package.py | 10 +++++-----
 2 files changed, 14 insertions(+), 13 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
index 99847e1dbe..38b355159d 100644
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -12,6 +12,7 @@ class Octave(Package):
 
     version('4.0.0' , 'a69f8320a4f20a8480c1b278b1adb799')
 
+    # Variants
     variant('readline',   default=True)
     variant('arpack',     default=False)
     variant('curl',       default=False)
@@ -45,7 +46,7 @@ class Octave(Package):
     # Optional dependencies
     depends_on('arpack',      when='+arpack')
     depends_on('curl',        when='+curl')
-    depends_on('fftw@3',      when='+fftw')
+    depends_on('fftw',      when='+fftw')
     depends_on('fltk',        when='+fltk')
     depends_on('fontconfig',  when='+fontconfig')
     depends_on('freetype',    when='+freetype')
@@ -56,10 +57,10 @@ class Octave(Package):
     depends_on('hdf5',        when='+hdf5')
     depends_on('jdk',         when='+jdk')
     depends_on('llvm',        when='+llvm')
-    #depends_on('opengl',      when='+opengl')
+    #depends_on('opengl',      when='+opengl')    # TODO: add package
     depends_on('qhull',       when='+qhull')
     depends_on('qrupdate',    when='+qrupdate')
-    #depends_on('qscintilla',  when='+qscintilla)
+    #depends_on('qscintilla',  when='+qscintilla) # TODO: add package
     depends_on('qt',          when='+qt')
     depends_on('SuiteSparse', when='+suitesparse')
     depends_on('zlib',        when='+zlib')
@@ -146,11 +147,11 @@ class Octave(Package):
                 "--with-java-libdir=%s"     % spec['jdk'].prefix.lib
             ])
 
-        #if '~opengl' in spec:
-        #    config_args.extend([
-        #        "--without-opengl",
-        #        "--without-framework-opengl"
-        #    ])
+        if '~opengl' in spec:
+            config_args.extend([
+                "--without-opengl",
+                "--without-framework-opengl"
+            ])
 
         if '+qhull' in spec:
             config_args.extend([
diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py
index aff44bb2d8..5374d02c97 100644
--- a/var/spack/repos/builtin/packages/qrupdate/package.py
+++ b/var/spack/repos/builtin/packages/qrupdate/package.py
@@ -9,10 +9,10 @@ class Qrupdate(Package):
 
     version('1.1.2', '6d073887c6e858c24aeda5b54c57a8c4')
 
-    depends_on("openblas")
+    depends_on("blas")
+    depends_on("lapack")
 
     def install(self, spec, prefix):
-        configure('--prefix=%s' % prefix)
-
-        make()
-        make("install")
+        # Build static and dynamic libraries
+        make("lib", "solib")
+        make("install", "PREFIX=%s" % prefix)
-- 
cgit v1.2.3-70-g09d2


From 68d22253eca40bc4223234d6c26204f292be6a0c Mon Sep 17 00:00:00 2001
From: Todd Gamblin <tgamblin@llnl.gov>
Date: Tue, 15 Mar 2016 17:22:48 -0700
Subject: Add sanity checks to the libelf build.

---
 var/spack/repos/builtin/packages/libelf/package.py | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py
index 29bc21b65c..0fcb56c164 100644
--- a/var/spack/repos/builtin/packages/libelf/package.py
+++ b/var/spack/repos/builtin/packages/libelf/package.py
@@ -38,6 +38,9 @@ class Libelf(Package):
 
     provides('elf')
 
+    sanity_check_files = ['include/libelf.h']
+    sanity_check_dirs  = ['lib']
+
     def install(self, spec, prefix):
         configure("--prefix=" + prefix,
                   "--enable-shared",
-- 
cgit v1.2.3-70-g09d2


From 9c2996667433e4f69eb25cce2d74a94caeb1646c Mon Sep 17 00:00:00 2001
From: Nicolas Richart <nicolas.richart@epfl.ch>
Date: Wed, 16 Mar 2016 12:57:17 +0100
Subject: Change urls in binutils to help 'spack checksum/versions' + adding
 latest version

---
 var/spack/repos/builtin/packages/binutils/package.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index de04221e33..897539a439 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -4,10 +4,13 @@ class Binutils(Package):
     """GNU binutils, which contain the linker, assembler, objdump and others"""
     homepage = "http://www.gnu.org/software/binutils/"
 
-    version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2")
-    version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.24.tar.bz2")
-    version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.23.2.tar.bz2")
-    version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764',url="ftp://ftp.gnu.org/gnu/binutils/binutils-2.20.1.tar.bz2")
+    url="https://ftp.gnu.org/gnu/binutils/binutils-2.25.tar.bz2"
+
+    version('2.26', '64146a0faa3b411ba774f47d41de239f')
+    version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
+    version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
+    version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
+    version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
 
     # Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell
     variant('krellpatch', default=False, description="build with openspeedshop based patch.")
-- 
cgit v1.2.3-70-g09d2


From fa2a66db6721ef5d7b54b9cede69aa2f1b5b7531 Mon Sep 17 00:00:00 2001
From: citibeth <rpf2116@columbia.edu>
Date: Wed, 16 Mar 2016 15:46:59 -0400
Subject: 1. Disabled git versions known to have vulnerabilities. 2. Added
 autoconf command to allow building directly from GitHub source.

---
 var/spack/repos/builtin/packages/git/package.py | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

(limited to 'var')

diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index ddc5078c4d..586b6ce3c3 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -5,14 +5,22 @@ class Git(Package):
        system designed to handle everything from small to very large
        projects with speed and efficiency."""
     homepage = "http://git-scm.com"
-    url      = "https://www.kernel.org/pub/software/scm/git/git-2.2.1.tar.gz"
+    url      = "https://github.com/git/git/tarball/v2.7.1"
 
-    version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423')
-    version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8')
-    version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd')
-    version('2.6.0', 'eb76a07148d94802a1745d759716a57e')
-    version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b')
-    version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
+    version('2.8.0-rc2', 'c2cf9f2cc70e35f2fafbaf9258f82e4c')
+    version('2.7.3', 'fa1c008b56618c355a32ba4a678305f6')
+    version('2.7.1', 'bf0706b433a8dedd27a63a72f9a66060')
+
+
+    # See here for info on vulnerable Git versions:
+    # http://www.theregister.co.uk/2016/03/16/git_server_client_patch_now/
+    # All the following are vulnerable
+    #version('2.6.3', 'b711be7628a4a2c25f38d859ee81b423')
+    #version('2.6.2', 'da293290da69f45a86a311ad3cd43dc8')
+    #version('2.6.1', '4c62ee9c5991fe93d99cf2a6b68397fd')
+    #version('2.6.0', 'eb76a07148d94802a1745d759716a57e')
+    #version('2.5.4', '3eca2390cf1fa698b48e2a233563a76b')
+    #version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c')
 
 
     # Git compiles with curl support by default on but if your system
@@ -24,6 +32,7 @@ class Git(Package):
     variant("expat", default=False, description="Add the internal support of expat for https push")
 
     depends_on("openssl")
+    depends_on("autoconf")
     depends_on("curl", when="+curl")
     depends_on("expat", when="+expat")
 
@@ -47,6 +56,7 @@ class Git(Package):
         if '+expat' in spec:
             configure_args.append("--with-expat=%s" % spec['expat'].prefix)
 
+        which('autoreconf')('-i')
         configure(*configure_args)
         make()
         make("install")
-- 
cgit v1.2.3-70-g09d2