Merge remote-tracking branch 'upstream/develop' into gktplus3-deps

.travis.yml

@@ -1,7 +1,17 @@
 language: python
+
 python:
   - "2.6"
   - "2.7"
+env:
+  - TEST_TYPE=unit
+  - TEST_TYPE=flake8
+
+# Exclude flake8 from python 2.6
+matrix:
+  exclude:
+  - python: "2.6"
+    env: TEST_TYPE=flake8
 
 # Use new Travis infrastructure (Docker can't sudo yet)
 sudo: false
@@ -20,20 +30,13 @@ before_install:
   - git fetch origin develop:develop
 
 script:
-  # Regular spack setup and tests
+  # Run unit tests with code coverage plus install libdwarf
-  - . share/spack/setup-env.sh
+  - 'if [ "$TEST_TYPE" = "unit" ]; then share/spack/qa/run-unit-tests; fi'
-  - spack compilers
-  - spack config get compilers
-  - spack install -v libdwarf
-
-  # Run unit tests with code coverage
-  - coverage run bin/spack test
-
   # Run flake8 code style checks.
-  - share/spack/qa/run-flake8
+  - 'if [ "$TEST_TYPE" = "flake8" ]; then share/spack/qa/run-flake8; fi'
 
 after_success:
-  - coveralls
+  - 'if [ "$TEST_TYPE" = "unit" ] && [ "$TRAVIS_PYTHON_VERSION" = "2.7" ]; then coveralls; fi'
 
 notifications:
   email:

lib/spack/llnl/util/filesystem.py

@@ -29,8 +29,9 @@
 import stat
 import errno
 import getpass
-from contextlib import contextmanager, closing
+from contextlib import contextmanager
 import subprocess
+import fileinput
 
 import llnl.util.tty as tty
 
@@ -85,13 +86,14 @@ def groupid_to_group(x):
         if ignore_absent and not os.path.exists(filename):
             continue
 
+        # Create backup file. Don't overwrite an existing backup
+        # file in case this file is being filtered multiple times.
+        if not os.path.exists(backup_filename):
             shutil.copy(filename, backup_filename)
+
         try:
-            with closing(open(backup_filename)) as infile:
+            for line in fileinput.input(filename, inplace=True):
-                with closing(open(filename, 'w')) as outfile:
+                print(re.sub(regex, repl, line.rstrip()))
-                    for line in infile:
-                        foo = re.sub(regex, repl, line)
-                        outfile.write(foo)
         except:
             # clean up the original file on failure.
             shutil.move(backup_filename, filename)
@@ -189,7 +191,7 @@ def install(src, dest):
 
 
 def install_tree(src, dest, **kwargs):
-    """Manually install a file to a particular location."""
+    """Manually install a directory tree to a particular location."""
     tty.debug("Installing %s to %s" % (src, dest))
     shutil.copytree(src, dest, **kwargs)
 

lib/spack/spack/concretize.py

@@ -336,14 +336,18 @@ def _proper_compiler_style(cspec, arch):
             spack.pkgsort.compiler_compare, other_spec.name)
         matches = sorted(compiler_list, cmp=cmp_compilers)
         if not matches:
-            raise UnavailableCompilerVersionError(other_compiler)
+            arch = spec.architecture
+            raise UnavailableCompilerVersionError(other_compiler,
+                                                  arch.platform_os)
 
         # copy concrete version into other_compiler
         index = 0
         while not _proper_compiler_style(matches[index], spec.architecture):
             index += 1
             if index == len(matches) - 1:
-                raise NoValidVersionError(spec)
+                arch = spec.architecture
+                raise UnavailableCompilerVersionError(spec.compiler,
+                                                      arch.platform_os)
         spec.compiler = matches[index].copy()
         assert(spec.compiler.concrete)
         return True  # things changed.
@@ -489,9 +493,9 @@ class UnavailableCompilerVersionError(spack.error.SpackError):
     """Raised when there is no available compiler that satisfies a
        compiler spec."""
 
-    def __init__(self, compiler_spec):
+    def __init__(self, compiler_spec, operating_system):
         super(UnavailableCompilerVersionError, self).__init__(
-            "No available compiler version matches '%s'" % compiler_spec,
+            "No available compiler version matches '%s' on operating_system %s" % compiler_spec, operating_system,  # NOQA: ignore=E501
             "Run 'spack compilers' to see available compiler Options.")
 
 

lib/spack/spack/config.py

@@ -266,6 +266,19 @@
                                     ], },
                         },},},},},},
 
+    'targets': {
+        '$schema': 'http://json-schema.org/schema#',
+        'title': 'Spack target configuration file schema',
+        'type': 'object',
+        'additionalProperties': False,
+        'patternProperties': {
+            r'targets:?': {
+                'type': 'object',
+                'default': {},
+                'additionalProperties': False,
+                'patternProperties': {
+                    r'\w[\w-]*': { # target name
+                        'type': 'string' ,},},},},},
     'modules': {
         '$schema': 'http://json-schema.org/schema#',
         'title': 'Spack module file configuration file schema',

lib/spack/spack/operating_systems/cnl.py

@@ -7,6 +7,7 @@
 from spack.util.multiproc import parmap
 import spack.compilers
 
+
 class Cnl(OperatingSystem):
     """ Compute Node Linux (CNL) is the operating system used for the Cray XC
     series super computers. It is a very stripped down version of GNU/Linux.
@@ -19,17 +20,19 @@ def __init__(self):
         version = '10'
         super(Cnl, self).__init__(name, version)
 
+    def __str__(self):
+        return self.name
 
     def find_compilers(self, *paths):
         types = spack.compilers.all_compiler_types()
-        compiler_lists = parmap(lambda cmp_cls: self.find_compiler(cmp_cls, *paths), types)
+        compiler_lists = parmap(
+            lambda cmp_cls: self.find_compiler(cmp_cls, *paths), types)
 
         # ensure all the version calls we made are cached in the parent
         # process, as well.  This speeds up Spack a lot.
         clist = reduce(lambda x, y: x + y, compiler_lists)
         return clist
 
-
     def find_compiler(self, cmp_cls, *paths):
         compilers = []
         if cmp_cls.PrgEnv:
@@ -46,11 +49,14 @@ def find_compiler(self, cmp_cls, *paths):
                 module_paths = ':' + ':'.join(p for p in paths)
                 os.environ['MODULEPATH'] = module_paths
 
-            output = modulecmd('avail', cmp_cls.PrgEnv_compiler, output=str, error=str)
+            output = modulecmd(
-            matches = re.findall(r'(%s)/([\d\.]+[\d])' % cmp_cls.PrgEnv_compiler, output)
+                'avail', cmp_cls.PrgEnv_compiler, output=str, error=str)
+            matches = re.findall(
+                r'(%s)/([\d\.]+[\d])' % cmp_cls.PrgEnv_compiler, output)
             for name, version in matches:
                 v = version
-                comp = cmp_cls(spack.spec.CompilerSpec(name + '@' + v), self,
+                comp = cmp_cls(
+                    spack.spec.CompilerSpec(name + '@' + v), self,
                     ['cc', 'CC', 'ftn'], [cmp_cls.PrgEnv, name + '/' + v])
 
                 compilers.append(comp)

lib/spack/spack/platforms/cray.py

@@ -0,0 +1,105 @@
+import os
+import re
+import spack.config
+import llnl.util.tty as tty
+from spack.util.executable import which
+from spack.architecture import Platform, Target, NoPlatformError
+from spack.operating_systems.linux_distro import LinuxDistro
+from spack.operating_systems.cnl import Cnl
+from llnl.util.filesystem import join_path
+
+# Craype- module prefixes that are not valid CPU targets.
+NON_TARGETS = ('hugepages', 'network', 'target', 'accel', 'xtpe')
+
+
+def _target_from_clean_env(name):
+    '''Return the default back_end target as loaded in a clean login session.
+
+    A bash subshell is launched with a wiped environment and the list of loaded
+    modules is parsed for the first acceptable CrayPE target.
+    '''
+    # Based on the incantation:
+    # echo "$(env - USER=$USER /bin/bash -l -c 'module list -lt')"
+    targets = []
+    if name != 'front_end':
+        env = which('env')
+        env.add_default_arg('-')
+        # CAUTION - $USER is generally needed to initialize the environment.
+        # There may be other variables needed for general success.
+        output = env('USER=%s' % os.environ['USER'],
+                     '/bin/bash', '--noprofile', '--norc', '-c',
+                     '. /etc/profile; module list -lt',
+                     output=str, error=str)
+        default_modules = [i for i in output.splitlines()
+                           if len(i.split()) == 1]
+        tty.debug("Found default modules:",
+                  *["      " + mod for mod in default_modules])
+        pattern = 'craype-(?!{0})(\S*)'.format('|'.join(NON_TARGETS))
+        for mod in default_modules:
+            if 'craype-' in mod:
+                targets.extend(re.findall(pattern, mod))
+    return targets[0] if targets else None
+
+
+class Cray(Platform):
+    priority = 10
+
+    def __init__(self):
+        ''' Create a Cray system platform.
+
+        Target names should use craype target names but not include the
+        'craype-' prefix. Uses first viable target from:
+          self
+          envars [SPACK_FRONT_END, SPACK_BACK_END]
+          configuration file "targets.yaml" with keys 'front_end', 'back_end'
+          scanning /etc/bash/bashrc.local for back_end only
+        '''
+        super(Cray, self).__init__('cray')
+
+        # Get targets from config or make best guess from environment:
+        conf = spack.config.get_config('targets')
+        for name in ('front_end', 'back_end'):
+            _target = getattr(self, name, None)
+            if _target is None:
+                _target = os.environ.get('SPACK_' + name.upper())
+            if _target is None:
+                _target = conf.get(name)
+            if _target is None:
+                _target = _target_from_clean_env(name)
+            setattr(self, name, _target)
+
+            if _target is not None:
+                self.add_target(name, Target(_target, 'craype-' + _target))
+                self.add_target(_target, Target(_target, 'craype-' + _target))
+
+        if self.back_end is not None:
+            self.default = self.back_end
+            self.add_target(
+                'default', Target(self.default, 'craype-' + self.default))
+        else:
+            raise NoPlatformError()
+
+        front_distro = LinuxDistro()
+        back_distro = Cnl()
+
+        self.default_os = str(back_distro)
+        self.back_os = self.default_os
+        self.front_os = str(front_distro)
+
+        self.add_operating_system(self.back_os, back_distro)
+        self.add_operating_system(self.front_os, front_distro)
+
+    @classmethod
+    def setup_platform_environment(self, pkg, env):
+        """ Change the linker to default dynamic to be more
+            similar to linux/standard linker behavior
+        """
+        env.set('CRAYPE_LINK_TYPE', 'dynamic')
+        cray_wrapper_names = join_path(spack.build_env_path, 'cray')
+        if os.path.isdir(cray_wrapper_names):
+            env.prepend_path('PATH', cray_wrapper_names)
+            env.prepend_path('SPACK_ENV_PATHS', cray_wrapper_names)
+
+    @classmethod
+    def detect(self):
+        return os.environ.get('CRAYPE_VERSION') is not None

lib/spack/spack/platforms/cray_xc.py

@@ -1,72 +0,0 @@
-import os
-import spack
-from spack.architecture import Platform, Target
-from spack.operating_systems.linux_distro import LinuxDistro
-from spack.operating_systems.cnl import Cnl
-from spack.util.executable import which
-from llnl.util.filesystem import join_path
-
-
-class CrayXc(Platform):
-    priority    = 20
-    front_end   = 'sandybridge'
-    back_end    = 'ivybridge'
-    default     = 'ivybridge'
-
-    back_os     = "CNL10"
-    default_os  = "CNL10"
-
-    def __init__(self):
-        ''' Since cori doesn't have ivybridge as a front end it's better
-            if we use CRAY_CPU_TARGET as the default. This will ensure
-            that if we're on a XC-40 or XC-30 then we can detect the target
-        '''
-        super(CrayXc, self).__init__('cray_xc')
-
-        # Handle the default here so we can check for a key error
-        if 'CRAY_CPU_TARGET' in os.environ:
-            self.default = os.environ['CRAY_CPU_TARGET']
-
-        # Change the defaults to haswell if we're on an XC40
-        if self.default == 'haswell':
-            self.front_end = self.default
-            self.back_end = self.default
-
-        # Could switch to use modules and fe targets for front end
-        # Currently using compilers by path for front end.
-        self.add_target('sandybridge', Target('sandybridge'))
-        self.add_target('ivybridge',
-                        Target('ivybridge', 'craype-ivybridge'))
-        self.add_target('haswell',
-                        Target('haswell', 'craype-haswell'))
-
-        # Front end of the cray platform is a linux distro.
-        linux_dist = LinuxDistro()
-        self.front_os = str(linux_dist)
-        self.add_operating_system(str(linux_dist), linux_dist)
-        self.add_operating_system('CNL10', Cnl())
-
-    @classmethod
-    def setup_platform_environment(self, pkg, env):
-        """ Change the linker to default dynamic to be more
-            similar to linux/standard linker behavior
-        """
-        env.set('CRAYPE_LINK_TYPE', 'dynamic')
-        cray_wrapper_names = join_path(spack.build_env_path, 'cray')
-        if os.path.isdir(cray_wrapper_names):
-            env.prepend_path('PATH', cray_wrapper_names)
-            env.prepend_path('SPACK_ENV_PATHS', cray_wrapper_names)
-
-    @classmethod
-    def detect(self):
-        try:
-            cc_verbose = which('ftn')
-            text = cc_verbose('-craype-verbose',
-                              output=str, error=str,
-                              ignore_errors=True).split()
-            if '-D__CRAYXC' in text:
-                return True
-            else:
-                return False
-        except:
-            return False

lib/spack/spack/stage.py

@@ -37,6 +37,7 @@
 import spack.config
 import spack.fetch_strategy as fs
 import spack.error
+from spack.version import *
 
 STAGE_PREFIX = 'spack-stage-'
 
@@ -51,10 +52,12 @@ class Stage(object):
     lifecycle looks like this:
 
     ```
-    with Stage() as stage:      # Context manager creates and destroys the stage directory
+    with Stage() as stage:      # Context manager creates and destroys the
+                                # stage directory
         stage.fetch()           # Fetch a source archive into the stage.
         stage.expand_archive()  # Expand the source archive.
-        <install>               # Build and install the archive. (handled by user of Stage)
+        <install>               # Build and install the archive. (handled by
+                                # user of Stage)
     ```
 
     When used as a context manager, the stage is automatically
@@ -71,7 +74,8 @@ class Stage(object):
         stage.create()          # Explicitly create the stage directory.
         stage.fetch()           # Fetch a source archive into the stage.
         stage.expand_archive()  # Expand the source archive.
-        <install>               # Build and install the archive. (handled by user of Stage)
+        <install>               # Build and install the archive. (handled by
+                                # user of Stage)
     finally:
         stage.destroy()         # Explicitly destroy the stage directory.
     ```
@@ -120,13 +124,17 @@ def __init__(self, url_or_fetch_strategy,
         elif isinstance(url_or_fetch_strategy, fs.FetchStrategy):
             self.fetcher = url_or_fetch_strategy
         else:
-            raise ValueError("Can't construct Stage without url or fetch strategy")
+            raise ValueError(
+                "Can't construct Stage without url or fetch strategy")
         self.fetcher.set_stage(self)
-        self.default_fetcher = self.fetcher  # self.fetcher can change with mirrors.
+        # self.fetcher can change with mirrors.
-        self.skip_checksum_for_mirror = True  # used for mirrored archives of repositories.
+        self.default_fetcher = self.fetcher
+        # used for mirrored archives of repositories.
+        self.skip_checksum_for_mirror = True
 
-        # TODO : this uses a protected member of tempfile, but seemed the only way to get a temporary name
+        # TODO : this uses a protected member of tempfile, but seemed the only
-        # TODO : besides, the temporary link name won't be the same as the temporary stage area in tmp_root
+        # TODO : way to get a temporary name besides, the temporary link name
+        # TODO : won't be the same as the temporary stage area in tmp_root
         self.name = name
         if name is None:
             self.name = STAGE_PREFIX + next(tempfile._get_candidate_names())
@@ -143,7 +151,6 @@ def __init__(self, url_or_fetch_strategy,
         # Flag to decide whether to delete the stage folder on exit or not
         self.keep = keep
 
-
     def __enter__(self):
         """
         Entering a stage context will create the stage directory
@@ -154,7 +161,6 @@ def __enter__(self):
         self.create()
         return self
 
-
     def __exit__(self, exc_type, exc_val, exc_tb):
         """
         Exiting from a stage context will delete the stage directory unless:
@@ -173,12 +179,10 @@ def __exit__(self, exc_type, exc_val, exc_tb):
         if exc_type is None and not self.keep:
             self.destroy()
 
-
     def _need_to_create_path(self):
         """Makes sure nothing weird has happened since the last time we
            looked at path.  Returns True if path already exists and is ok.
-           Returns False if path needs to be created.
+           Returns False if path needs to be created."""
-        """
         # Path doesn't exist yet.  Will need to create it.
         if not os.path.exists(self.path):
             return True
@@ -196,7 +200,8 @@ def _need_to_create_path(self):
             if spack.use_tmp_stage:
                 # If we're using a tmp dir, it's a link, and it points at the
                 # right spot, then keep it.
-                if (real_path.startswith(real_tmp) and os.path.exists(real_path)):
+                if (real_path.startswith(real_tmp) and
+                        os.path.exists(real_path)):
                     return False
                 else:
                     # otherwise, just unlink it and start over.
@@ -204,7 +209,8 @@ def _need_to_create_path(self):
                     return True
 
             else:
-                # If we're not tmp mode, then it's a link and we want a directory.
+                # If we're not tmp mode, then it's a link and we want a
+                # directory.
                 os.unlink(self.path)
                 return True
 
@@ -215,10 +221,12 @@ def expected_archive_files(self):
         """Possible archive file paths."""
         paths = []
         if isinstance(self.fetcher, fs.URLFetchStrategy):
-            paths.append(os.path.join(self.path, os.path.basename(self.fetcher.url)))
+            paths.append(os.path.join(
+                self.path, os.path.basename(self.fetcher.url)))
 
         if self.mirror_path:
-            paths.append(os.path.join(self.path, os.path.basename(self.mirror_path)))
+            paths.append(os.path.join(
+                self.path, os.path.basename(self.mirror_path)))
 
         return paths
 
@@ -227,10 +235,12 @@ def archive_file(self):
         """Path to the source archive within this stage directory."""
         paths = []
         if isinstance(self.fetcher, fs.URLFetchStrategy):
-            paths.append(os.path.join(self.path, os.path.basename(self.fetcher.url)))
+            paths.append(os.path.join(
+                self.path, os.path.basename(self.fetcher.url)))
 
         if self.mirror_path:
-            paths.append(os.path.join(self.path, os.path.basename(self.mirror_path)))
+            paths.append(os.path.join(
+                self.path, os.path.basename(self.mirror_path)))
 
         for path in paths:
             if os.path.exists(path):
@@ -262,7 +272,8 @@ def source_path(self):
         return None
 
     def chdir(self):
-        """Changes directory to the stage path.  Or dies if it is not set up."""
+        """Changes directory to the stage path. Or dies if it is not set
+        up."""
         if os.path.isdir(self.path):
             os.chdir(self.path)
         else:
@@ -306,6 +317,19 @@ def fetch(self, mirror_only=False):
                 fetchers.insert(0, fs.URLFetchStrategy(url, digest))
             fetchers.insert(0, spack.cache.fetcher(self.mirror_path, digest))
 
+            # Look for the archive in list_url
+            archive_version = spack.url.parse_version(self.default_fetcher.url)
+            package_name = os.path.dirname(self.mirror_path)
+            pkg = spack.repo.get(package_name)
+            if pkg.list_url is not None and pkg.url is not None:
+                versions = pkg.fetch_remote_versions()
+                try:
+                    url_from_list = versions[Version(archive_version)]
+                    fetchers.append(fs.URLFetchStrategy(url_from_list, digest))
+                except KeyError:
+                    tty.msg("Can not find version %s in url_list" %
+                            archive_version)
+
         for fetcher in fetchers:
             try:
                 fetcher.set_stage(self)
@@ -321,11 +345,11 @@ def fetch(self, mirror_only=False):
             self.fetcher = self.default_fetcher
             raise fs.FetchError(errMessage, None)
 
-
     def check(self):
         """Check the downloaded archive against a checksum digest.
            No-op if this stage checks code out of a repository."""
-        if self.fetcher is not self.default_fetcher and self.skip_checksum_for_mirror:
+        if self.fetcher is not self.default_fetcher and \
+           self.skip_checksum_for_mirror:
             tty.warn("Fetching from mirror without a checksum!",
                      "This package is normally checked out from a version "
                      "control system, but it has been archived on a spack "
@@ -335,16 +359,13 @@ def check(self):
         else:
             self.fetcher.check()
 
-
     def cache_local(self):
         spack.cache.store(self.fetcher, self.mirror_path)
 
-
     def expand_archive(self):
         """Changes to the stage directory and attempt to expand the downloaded
         archive.  Fail if the stage is not set up or if the archive is not yet
-           downloaded.
+        downloaded."""
-        """
         archive_dir = self.source_path
         if not archive_dir:
             self.fetcher.expand()
@@ -386,8 +407,8 @@ def create(self):
         # Create the top-level stage directory
         mkdirp(spack.stage_path)
         remove_dead_links(spack.stage_path)
-        # If a tmp_root exists then create a directory there and then link it in the stage area,
+        # If a tmp_root exists then create a directory there and then link it
-        # otherwise create the stage directory in self.path
+        # in the stage area, otherwise create the stage directory in self.path
         if self._need_to_create_path():
             if self.tmp_root:
                 tmp_dir = tempfile.mkdtemp('', STAGE_PREFIX, self.tmp_root)
@@ -409,6 +430,7 @@ def destroy(self):
 
 
 class ResourceStage(Stage):
+
     def __init__(self, url_or_fetch_strategy, root, resource, **kwargs):
         super(ResourceStage, self).__init__(url_or_fetch_strategy, **kwargs)
         self.root_stage = root
@@ -418,12 +440,15 @@ def expand_archive(self):
         super(ResourceStage, self).expand_archive()
         root_stage = self.root_stage
         resource = self.resource
-        placement = os.path.basename(self.source_path) if resource.placement is None else resource.placement
+        placement = os.path.basename(self.source_path) \
+            if resource.placement is None \
+            else resource.placement
         if not isinstance(placement, dict):
             placement = {'': placement}
         # Make the paths in the dictionary absolute and link
         for key, value in placement.iteritems():
-            target_path = join_path(root_stage.source_path, resource.destination)
+            target_path = join_path(
+                root_stage.source_path, resource.destination)
             destination_path = join_path(target_path, value)
             source_path = join_path(self.source_path, key)
 
@@ -437,21 +462,23 @@ def expand_archive(self):
 
             if not os.path.exists(destination_path):
                 # Create a symlink
-                tty.info('Moving resource stage\n\tsource : {stage}\n\tdestination : {destination}'.format(
+                tty.info('Moving resource stage\n\tsource : '
+                         '{stage}\n\tdestination : {destination}'.format(
                              stage=source_path, destination=destination_path
                          ))
                 shutil.move(source_path, destination_path)
 
 
-@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive',  'restage', 'destroy', 'cache_local'])
+@pattern.composite(method_list=['fetch', 'create', 'check', 'expand_archive',
+                                'restage', 'destroy', 'cache_local'])
 class StageComposite:
-    """
+    """Composite for Stage type objects. The first item in this composite is
-    Composite for Stage type objects. The first item in this composite is considered to be the root package, and
+    considered to be the root package, and operations that return a value are
-    operations that return a value are forwarded to it.
+    forwarded to it."""
-    """
     #
     # __enter__ and __exit__ delegate to all stages in the composite.
     #
+
     def __enter__(self):
         for item in self:
             item.__enter__()
@@ -496,8 +523,11 @@ def chdir(self):
             raise ChdirError("Setup failed: no such directory: " + self.path)
 
     # DIY stages do nothing as context managers.
-    def __enter__(self): pass
+    def __enter__(self):
-    def __exit__(self, exc_type, exc_val, exc_tb): pass
+        pass
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        pass
 
     def chdir_to_source(self):
         self.chdir()

lib/spack/spack/test/architecture.py

@@ -31,7 +31,7 @@
 import spack
 import spack.architecture
 from spack.spec import *
-from spack.platforms.cray_xc import CrayXc
+from spack.platforms.cray import Cray
 from spack.platforms.linux import Linux
 from spack.platforms.bgq import Bgq
 from spack.platforms.darwin import Darwin
@@ -76,7 +76,7 @@ def test_dict_functions_for_architecture(self):
     def test_platform(self):
         output_platform_class = spack.architecture.platform()
         if os.path.exists('/opt/cray/craype'):
-            my_platform_class = CrayXc()
+            my_platform_class = Cray()
         elif os.path.exists('/bgsys'):
             my_platform_class = Bgq()
         elif 'Linux' in py_platform.system():

share/spack/qa/run-unit-tests

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+#
+# This script runs Spack unit tests.
+#
+# It should be executed from the top-level directory of the repo,
+# e.g.:
+#
+#    share/spack/qa/run-unit-tests
+#
+# To run it, you'll need to have the Python coverage installed locally.
+#
+
+# Regular spack setup and tests
+. ./share/spack/setup-env.sh
+spack compilers
+spack config get compilers
+spack install -v libdwarf
+
+# Run unit tests with code coverage
+coverage run bin/spack test

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

@@ -22,10 +22,9 @@
 # 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
-
 from spack import *
 from spack.util.environment import *
+import shutil
 
 
 class R(Package):
@@ -74,6 +73,10 @@ class R(Package):
     depends_on('pcre')
     depends_on('jdk')
 
+    @property
+    def etcdir(self):
+        return join_path(prefix, 'rlib', 'R', 'etc')
+
     def install(self, spec, prefix):
         rlibdir = join_path(prefix, 'rlib')
         configure_args = ['--prefix=%s' % prefix,
@@ -88,6 +91,12 @@ def install(self, spec, prefix):
         make()
         make('install')
 
+        # Make a copy of Makeconf because it will be needed to properly build R
+        # dependencies in Spack.
+        src_makeconf = join_path(self.etcdir, 'Makeconf')
+        dst_makeconf = join_path(self.etcdir, 'Makeconf.spack')
+        shutil.copy(src_makeconf, dst_makeconf)
+
         self.filter_compilers(spec, prefix)
 
     def filter_compilers(self, spec, prefix):
@@ -98,18 +107,16 @@ def filter_compilers(self, spec, prefix):
         cc and c++. We want them to be bound to whatever compiler
         they were built with."""
 
-        etcdir = join_path(prefix, 'rlib', 'R', 'etc')
-
         kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
 
         filter_file(env['CC'], self.compiler.cc,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
         filter_file(env['CXX'], self.compiler.cxx,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
         filter_file(env['F77'], self.compiler.f77,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
         filter_file(env['FC'], self.compiler.fc,
-                    join_path(etcdir, 'Makeconf'), **kwargs)
+                    join_path(self.etcdir, 'Makeconf'), **kwargs)
 
     # ========================================================================
     # Set up environment to make install easy for R extensions.
@@ -117,7 +124,7 @@ def filter_compilers(self, spec, prefix):
 
     @property
     def r_lib_dir(self):
-        return os.path.join('rlib', 'R', 'library')
+        return join_path('rlib', 'R', 'library')
 
     def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         # Set R_LIBS to include the library dir for the
@@ -125,15 +132,21 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         r_libs_path = []
         for d in extension_spec.traverse(deptype=nolink, deptype_query='run'):
             if d.package.extends(self.spec):
-                r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir))
+                r_libs_path.append(join_path(d.prefix, self.r_lib_dir))
 
         r_libs_path = ':'.join(r_libs_path)
         spack_env.set('R_LIBS', r_libs_path)
+        spack_env.set('R_MAKEVARS_SITE',
+                      join_path(self.etcdir, 'Makeconf.spack'))
+
+        # Use the number of make_jobs set in spack. The make program will
+        # determine how many jobs can actually be started.
+        spack_env.set('MAKEFLAGS', '-j{0}'.format(make_jobs))
 
         # For run time environment set only the path for extension_spec and
         # prepend it to R_LIBS
         if extension_spec.package.extends(self.spec):
-            run_env.prepend_path('R_LIBS', os.path.join(
+            run_env.prepend_path('R_LIBS', join_path(
                 extension_spec.prefix, self.r_lib_dir))
 
     def setup_environment(self, spack_env, run_env):
@@ -147,13 +160,14 @@ def setup_environment(self, spack_env, run_env):
     def setup_dependent_package(self, module, ext_spec):
         """Called before R modules' install() methods. In most cases,
         extensions will only need to have one line:
-            R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' %
+            R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
               self.stage.source_path)"""
+
         # R extension builds can have a global R executable function
         module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
 
         # Add variable for library directry
-        module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir)
+        module.r_lib_dir = join_path(ext_spec.prefix, self.r_lib_dir)
 
         # Make the site packages directory for extensions, if it does not exist
         # already.

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

@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+#
+# Based on Homebrew's formula:
+# https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb
+#
+from spack import *
+from glob import glob
+
+
+class Cask(Package):
+    """Cask is a project management tool for Emacs Lisp to automate the package
+       development cycle; development, dependencies, testing, building,
+       packaging and more."""
+    homepage = "http://cask.readthedocs.io/en/latest/"
+    url      = "https://github.com/cask/cask/archive/v0.7.4.tar.gz"
+
+    version('0.7.4', 'c973a7db43bc980dd83759a5864a1260')
+
+    depends_on('emacs', type=nolink)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('bin/cask', prefix.bin)
+        install_tree('templates', join_path(prefix, 'templates'))
+        for el_file in glob("*.el"):
+            install(el_file, prefix)
+        for misc_file in ['COPYING', 'cask.png', 'README.md']:
+            install(misc_file, prefix)
+        # disable cask's automatic upgrading feature
+        touch(join_path(prefix, ".no-upgrade"))

var/spack/repos/builtin/packages/cp2k/package.py

@@ -0,0 +1,161 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+import os
+import shutil
+import copy
+
+from spack import *
+
+
+class Cp2k(Package):
+    """CP2K is a quantum chemistry and solid state physics software package
+    that can perform atomistic simulations of solid state, liquid, molecular,
+    periodic, material, crystal, and biological systems
+    """
+    homepage = 'https://www.cp2k.org'
+    url = 'https://sourceforge.net/projects/cp2k/files/cp2k-3.0.tar.bz2'
+
+    version('3.0', 'c05bc47335f68597a310b1ed75601d35')
+
+    variant('mpi', default=True, description='Enable MPI support')
+
+    depends_on('python')  # Build dependency
+
+    depends_on('lapack')
+    depends_on('blas')
+    depends_on('fftw')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('scalapack', when='+mpi')
+
+    # TODO : add dependency on libint
+    # TODO : add dependency on libsmm, libxsmm
+    # TODO : add dependency on elpa
+    # TODO : add dependency on CUDA
+    # TODO : add dependency on PEXSI
+    # TODO : add dependency on QUIP
+    # TODO : add dependency on plumed
+    # TODO : add dependency on libwannier90
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        # Construct a proper filename for the architecture file
+        cp2k_architecture = '{0.architecture}-{0.compiler.name}'.format(spec)
+        cp2k_version = 'sopt' if '~mpi' in spec else 'popt'
+        makefile_basename = '.'.join([cp2k_architecture, cp2k_version])
+        makefile = join_path('arch', makefile_basename)
+
+        # Write the custom makefile
+        with open(makefile, 'w') as mkf:
+            mkf.write('CC = {0.compiler.cc}\n'.format(self))
+            if '%intel' in self.spec:
+                # CPP is a commented command in Intel arch of CP2K
+                # This is the hack through which cp2k developers avoid doing :
+                #
+                # ${CPP} <file>.F > <file>.f90
+                #
+                # and use `-fpp` instead
+                mkf.write('CPP = # {0.compiler.cc} -P\n'.format(self))
+                mkf.write('AR = xiar -r\n')
+            else:
+                mkf.write('CPP = {0.compiler.cc} -E\n'.format(self))
+                mkf.write('AR = ar -r\n')
+            fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc
+            mkf.write('FC = {0}\n'.format(fc))
+            mkf.write('LD = {0}\n'.format(fc))
+            # Optimization flags
+            optflags = {
+                'gcc': ['-O2',
+                        '-ffast-math',
+                        '-ffree-form',
+                        '-ffree-line-length-none',
+                        '-ftree-vectorize',
+                        '-funroll-loops',
+                        '-mtune=native'],
+                'intel': ['-O2',
+                          '-pc64',
+                          '-unroll',
+                          '-heap-arrays 64']
+            }
+            cppflags = [
+                '-D__FFTW3',
+                '-I' + spec['fftw'].prefix.include
+            ]
+            fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
+            fcflags.extend([
+                '-I' + spec['fftw'].prefix.include
+            ])
+            ldflags = ['-L' + spec['fftw'].prefix.lib]
+            libs = []
+            # Intel
+            if '%intel' in self.spec:
+                cppflags.extend([
+                    '-D__INTEL_COMPILER',
+                    '-D__MKL'
+                ])
+                fcflags.extend([
+                    '-diag-disable 8290,8291,10010,10212,11060',
+                    '-free',
+                    '-fpp'
+                ])
+            # MPI
+            if '+mpi' in self.spec:
+                cppflags.extend([
+                    '-D__parallel',
+                    '-D__SCALAPACK'
+                ])
+                ldflags.extend([
+                    '-L' + spec['scalapack'].prefix.lib
+                ])
+                libs.extend(spec['scalapack'].scalapack_shared_libs)
+
+            # LAPACK / BLAS
+            ldflags.extend([
+                '-L' + spec['lapack'].prefix.lib,
+                '-L' + spec['blas'].prefix.lib
+            ])
+            libs.extend([
+                join_path(spec['fftw'].prefix.lib, 'libfftw3.so'),
+                spec['lapack'].lapack_shared_lib,
+                spec['blas'].blas_shared_lib
+            ])
+
+            # Write compiler flags to file
+            mkf.write('CPPFLAGS = {0}\n'.format(' '.join(cppflags)))
+            mkf.write('FCFLAGS = {0}\n'.format(' '.join(fcflags)))
+            mkf.write('LDFLAGS = {0}\n'.format(' '.join(ldflags)))
+            mkf.write('LIBS = {0}\n'.format(' '.join(libs)))
+
+        with working_dir('makefiles'):
+            # Apparently the Makefile bases its paths on PWD
+            # so we need to set PWD = os.getcwd()
+            pwd_backup = env['PWD']
+            env['PWD'] = os.getcwd()
+            make('ARCH={0}'.format(cp2k_architecture),
+                 'VERSION={0}'.format(cp2k_version))
+            env['PWD'] = pwd_backup
+        exe_dir = join_path('exe', cp2k_architecture)
+        shutil.copytree(exe_dir, self.prefix.bin)

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

@@ -62,10 +62,10 @@ def install(self, spec, prefix):
             '--prefix=%s' % prefix,
             '--with-lapack-libs=%s' % to_lib_name(
                 spec['lapack'].lapack_shared_lib),
-            '--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix,
+            '--with-lapack-lib-dirs=%s' % spec['lapack'].prefix.lib,
             '--with-blas-libs=%s' % to_lib_name(
                 spec['blas'].blas_shared_lib),
-            '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix
+            '--with-blas-lib-dirs=%s' % spec['blas'].prefix.lib
         ]
 
         if '+shared' in self.spec:

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

@@ -25,7 +25,7 @@
 #
 # Author: Justin Too <too1@llnl.gov>
 #
-import distutils
+import distutils.dir_util
 
 import spack
 from spack import *

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

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libhio(Package):
+    """
+    A library for writing to hierarchical data store systems.
+    """
+
+    homepage = "https://github.com/hpc/libhio/"
+    url      = "https://github.com/hpc/libhio/releases/download/hio.1.3.0.1/libhio-1.3.0.1.tar.gz"
+
+    version('1.3.0.1', 'c073541de8dd70aeb8878bd00d6d877f')
+
+    depends_on("libjson-c")
+    depends_on("bzip2")
+    depends_on("pkg-config", type="build")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")

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

@@ -0,0 +1,66 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Libxsmm(Package):
+    '''LIBXSMM is a library for small dense and small sparse matrix-matrix
+    multiplications targeting Intel Architecture (x86).'''
+
+    homepage = 'https://github.com/hfp/libxsmm'
+    url      = 'https://github.com/hfp/libxsmm/archive/1.4.3.tar.gz'
+
+    version('1.4.3', '9839bf0fb8be7badf1e97ce4c817149b')
+    version('1.4.2', 'ea025761437f3b5c936821b9ca21ec31')
+    version('1.4.1', '71648500ea4510529845d329091917df')
+    version('1.4',   'b42f91bf5285e7ad0463446e55ebdc2b')
+
+    def patch(self):
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': True}
+        makefile = FileFilter('Makefile.inc')
+
+        # Spack sets CC, CXX, and FC to point to the compiler wrappers
+        # Don't let Makefile.inc overwrite these
+        makefile.filter('CC = icc',         'CC ?= icc', **kwargs)
+        makefile.filter('CC = gcc',         'CC ?= gcc', **kwargs)
+        makefile.filter('CXX = icpc',       'CXX ?= icpc', **kwargs)
+        makefile.filter('CXX = g++',        'CXX ?= g++', **kwargs)
+        makefile.filter('FC = ifort',       'FC ?= ifort', **kwargs)
+        makefile.filter('FC = gfortran',    'FC ?= gfortran', **kwargs)
+
+    def manual_install(self, prefix):
+        install_tree('include', prefix.include)
+        install_tree('lib', prefix.lib)
+        install_tree('documentation', prefix.share + '/libxsmm/doc')
+
+    def install(self, spec, prefix):
+        make_args = [
+            'ROW_MAJOR=0',
+            'INDICES_M={0}'.format(' '.join(str(i) for i in range(1, 25))),
+            'INDICES_N={0}'.format(' '.join(str(i) for i in range(1, 25))),
+            'INDICES_K={0}'.format(' '.join(str(i) for i in range(1, 25)))
+        ]
+        make(*make_args)
+        self.manual_install(prefix)

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

@@ -12,9 +12,9 @@ class Mkl(IntelInstaller):
     mirror, see http://software.llnl.gov/spack/mirrors.html.
 
     To set the threading layer at run time set MKL_THREADING_LAYER
-    variable to one of the following values: INTEL, SEQUENTIAL, PGI.
+    variable to one of the following values: INTEL (default), SEQUENTIAL, PGI.
     To set interface layer at run time, use set the MKL_INTERFACE_LAYER
-    variable to LP64 or ILP64.
+    variable to LP64 (default) or ILP64.
     """
 
     homepage = "https://software.intel.com/en-us/intel-mkl"
@@ -38,6 +38,13 @@ def install(self, spec, prefix):
         for f in os.listdir(mkl_dir):
             os.symlink(os.path.join(mkl_dir, f), os.path.join(self.prefix, f))
 
+        # Unfortunately MKL libs are natively distrubted in prefix/lib/intel64.
+        # To make MKL play nice with Spack, symlink all files to prefix/lib:
+        mkl_lib_dir = os.path.join(prefix, "lib", "intel64")
+        for f in os.listdir(mkl_lib_dir):
+            os.symlink(os.path.join(mkl_lib_dir, f),
+                       os.path.join(self.prefix, "lib", f))
+
     def setup_dependent_package(self, module, dspec):
         # For now use Single Dynamic Library:
         # To set the threading layer at run time, use the
@@ -53,6 +60,7 @@ def setup_dependent_package(self, module, dspec):
         name = 'libmkl_rt.%s' % dso_suffix
         libdir = find_library_path(name, self.prefix.lib64, self.prefix.lib)
 
+        # Now set blas/lapack libs:
         self.spec.blas_shared_lib   = join_path(libdir, name)
         self.spec.lapack_shared_lib = self.spec.blas_shared_lib
 

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

@@ -23,51 +23,186 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
+from glob import glob
 
 
 class Opencv(Package):
+    """OpenCV is released under a BSD license and hence it's free for both
+    academic and commercial use. It has C++, C, Python and Java interfaces and
+    supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for
+    computational efficiency and with a strong focus on real-time applications.
+    Written in optimized C/C++, the library can take advantage of multi-core
+    processing. Enabled with OpenCL, it can take advantage of the hardware
+    acceleration of the underlying heterogeneous compute platform. Adopted all
+    around the world, OpenCV has more than 47 thousand people of user community
+    and estimated number of downloads exceeding 9 million. Usage ranges from
+    interactive art, to mines inspection, stitching maps on the web or through
+    advanced robotics.
     """
-    OpenCV is released under a BSD license and hence it's free for both academic and commercial use. It has C++, C,
+
-    Python and Java interfaces and supports Windows, Linux, Mac OS, iOS and Android. OpenCV was designed for
-    computational efficiency and with a strong focus on real-time applications. Written in optimized C/C++, the library
-    can take advantage of multi-core processing. Enabled with OpenCL, it can take advantage of the hardware
-    acceleration of the underlying heterogeneous compute platform. Adopted all around the world, OpenCV has more than
-    47 thousand people of user community and estimated number of downloads exceeding 9 million. Usage ranges from
-    interactive art, to mines inspection, stitching maps on the web or through advanced robotics.
-    """
     homepage = 'http://opencv.org/'
     url = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz'
 
     version('3.1.0', '70e1dd07f0aa06606f1bc0e3fa15abd3')
 
-    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('shared', default=True,
-    variant('debug', default=False, description='Builds a debug version of the libraries')
+            description='Enables the build of shared libraries')
+    variant('debug', default=False,
+            description='Builds a debug version of the libraries')
 
     variant('eigen', default=True, description='Activates support for eigen')
     variant('ipp', default=True, description='Activates support for IPP')
+    variant('jasper', default=True, description='Activates support for JasPer')
+    variant('cuda', default=False, description='Activates support for CUDA')
+    variant('gtk', default=False, description='Activates support for GTK')
+    variant('vtk', default=False, description='Activates support for VTK')
+    variant('qt', default=False, description='Activates support for QT')
+    variant('python', default=False,
+            description='Enables the build of Python extensions')
+    variant('java', default=False,
+            description='Activates support for Java')
+
+    depends_on('cmake', type='build')
+    depends_on('eigen', when='+eigen', type='build')
 
     depends_on('zlib')
     depends_on('libpng')
     depends_on('libjpeg-turbo')
     depends_on('libtiff')
 
-    depends_on('python')
+    depends_on('jasper', when='+jasper')
-    depends_on('py-numpy')
+    depends_on('cuda', when='+cuda')
+    depends_on('gtkplus', when='+gtk')
+    depends_on('vtk', when='+vtk')
+    depends_on('qt', when='+qt')
+    depends_on('jdk', when='+java')
+    depends_on('py-numpy', when='+python')
 
-    depends_on('eigen', when='+eigen', type='build')
+    extends('python', when='+python')
-    depends_on('cmake', type='build')
-
-    # FIXME : GUI extensions missing
-    # FIXME : CUDA extensions still missing
 
     def install(self, spec, prefix):
         cmake_options = []
         cmake_options.extend(std_cmake_args)
 
-        cmake_options.extend(['-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'),
+        cmake_options.extend([
-                              '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if '+shared' in spec else 'OFF'),
+            '-DCMAKE_BUILD_TYPE:STRING={0}'.format((
+                'Debug' if '+debug' in spec else 'Release')),
+            '-DBUILD_SHARED_LIBS:BOOL={0}'.format((
+                'ON' if '+shared' in spec else 'OFF')),
             '-DENABLE_PRECOMPILED_HEADERS:BOOL=OFF',
-                              '-DWITH_IPP:BOOL=%s' % ('ON' if '+ipp' in spec else 'OFF')])
+            '-DWITH_IPP:BOOL={0}'.format((
+                'ON' if '+ipp' in spec else 'OFF')),
+            '-DWITH_CUDA:BOOL={0}'.format((
+                'ON' if '+cuda' in spec else 'OFF')),
+            '-DWITH_QT:BOOL={0}'.format((
+                'ON' if '+qt' in spec else 'OFF')),
+            '-DWITH_VTK:BOOL={0}'.format((
+                'ON' if '+vtk' in spec else 'OFF')),
+            '-DBUILD_opencv_java:BOOL={0}'.format((
+                'ON' if '+java' in spec else 'OFF')),
+        ])
+
+        # Media I/O
+        zlib = spec['zlib']
+        cmake_options.extend([
+            '-DZLIB_LIBRARY_{0}:FILEPATH={1}'.format((
+                'DEBUG' if '+debug' in spec else 'RELEASE'),
+                join_path(zlib.prefix.lib,
+                          'libz.{0}'.format(dso_suffix))),
+            '-DZLIB_INCLUDE_DIR:PATH={0}'.format(zlib.prefix.include)
+        ])
+
+        libpng = spec['libpng']
+        cmake_options.extend([
+            '-DPNG_LIBRARY_{0}:FILEPATH={1}'.format((
+                'DEBUG' if '+debug' in spec else 'RELEASE'),
+                join_path(libpng.prefix.lib,
+                          'libpng.{0}'.format(dso_suffix))),
+            '-DPNG_INCLUDE_DIR:PATH={0}'.format(libpng.prefix.include)
+        ])
+
+        libjpeg = spec['libjpeg-turbo']
+        cmake_options.extend([
+            '-DJPEG_LIBRARY:FILEPATH={0}'.format(
+                join_path(libjpeg.prefix.lib,
+                          'libjpeg.{0}'.format(dso_suffix))),
+            '-DJPEG_INCLUDE_DIR:PATH={0}'.format(libjpeg.prefix.include)
+        ])
+
+        libtiff = spec['libtiff']
+        cmake_options.extend([
+            '-DTIFF_LIBRARY_{0}:FILEPATH={1}'.format((
+                'DEBUG' if '+debug' in spec else 'RELEASE'),
+                join_path(libtiff.prefix.lib,
+                          'libtiff.{0}'.format(dso_suffix))),
+            '-DTIFF_INCLUDE_DIR:PATH={0}'.format(libtiff.prefix.include)
+        ])
+
+        jasper = spec['jasper']
+        cmake_options.extend([
+            '-DJASPER_LIBRARY_{0}:FILEPATH={1}'.format((
+                'DEBUG' if '+debug' in spec else 'RELEASE'),
+                join_path(jasper.prefix.lib,
+                          'libjasper.{0}'.format(dso_suffix))),
+            '-DJASPER_INCLUDE_DIR:PATH={0}'.format(jasper.prefix.include)
+        ])
+
+        # GUI
+        if '+gtk' not in spec:
+            cmake_options.extend([
+                '-DWITH_GTK:BOOL=OFF',
+                '-DWITH_GTK_2_X:BOOL=OFF'
+            ])
+        elif '^gtkplus@3:' in spec:
+            cmake_options.extend([
+                '-DWITH_GTK:BOOL=ON',
+                '-DWITH_GTK_2_X:BOOL=OFF'
+            ])
+        elif '^gtkplus@2:3' in spec:
+            cmake_options.extend([
+                '-DWITH_GTK:BOOL=OFF',
+                '-DWITH_GTK_2_X:BOOL=ON'
+            ])
+
+        # Python
+        if '+python' in spec:
+            python = spec['python']
+
+            try:
+                python_lib = glob(join_path(
+                    python.prefix.lib, 'libpython*.{0}'.format(dso_suffix)))[0]
+            except KeyError:
+                raise InstallError('Cannot find libpython')
+
+            try:
+                python_include_dir = glob(join_path(python.prefix.include,
+                                                    'python*'))[0]
+            except KeyError:
+                raise InstallError('Cannot find python include directory')
+
+            if '^python@3:' in spec:
+                python_exe = join_path(python.prefix.bin, 'python3')
+                cmake_options.extend([
+                    '-DBUILD_opencv_python3=ON',
+                    '-DPYTHON3_EXECUTABLE={0}'.format(python_exe),
+                    '-DPYTHON3_LIBRARY={0}'.format(python_lib),
+                    '-DPYTHON3_INCLUDE_DIR={0}'.format(python_include_dir),
+                    '-DBUILD_opencv_python2=OFF',
+                ])
+            elif '^python@2:3' in spec:
+                python_exe = join_path(python.prefix.bin, 'python2')
+                cmake_options.extend([
+                    '-DBUILD_opencv_python2=ON',
+                    '-DPYTHON2_EXECUTABLE={0}'.format(python_exe),
+                    '-DPYTHON2_LIBRARY={0}'.format(python_lib),
+                    '-DPYTHON2_INCLUDE_DIR={0}'.format(python_include_dir),
+                    '-DBUILD_opencv_python3=OFF',
+                ])
+        else:
+            cmake_options.extend([
+                '-DBUILD_opencv_python2=OFF',
+                '-DBUILD_opencv_python3=OFF'
+            ])
 
         with working_dir('spack_build', create=True):
             cmake('..', *cmake_options)

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

@@ -41,6 +41,7 @@ class Pgi(Package):
     homepage = "http://www.pgroup.com/"
     url = "file://%s/pgi-16.3.tar.gz" % os.getcwd()
 
+    version('16.5', 'a40e8852071b5d600cb42f31631b3de1')
     version('16.3', '618cb7ddbc57d4e4ed1f21a0ab25f427')
 
     variant('network', default=True,

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

@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RBoot(Package):
+    """Functions and datasets for bootstrapping from the book "Bootstrap
+    Methods and Their Application" by A. C. Davison and D. V. Hinkley (1997,
+    CUP), originally written by Angelo Canty for S."""
+
+    homepage = "https://cran.r-project.org/package=boot"
+    url      = "https://cran.r-project.org/src/contrib/boot_1.3-18.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/boot"
+
+    version('1.3-18', '711dd58af14e1027eb8377d9202e9b6f')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RBrew(Package):
+    """brew implements a templating framework for mixing text and R code for
+    report generation. brew template syntax is similar to PHP, Ruby's erb
+    module, Java Server Pages, and Python's psp module."""
+
+    homepage = "https://cran.r-project.org/package=brew"
+    url      = "https://cran.r-project.org/src/contrib/brew_1.0-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/brew"
+
+    version('1.0-6', '4aaca5e6ec145e0fc0fe6375ce1f3806')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCar(Package):
+    """Functions and Datasets to Accompany J. Fox and S. Weisberg, An R
+    Companion to Applied Regression, Second Edition, Sage, 2011."""
+
+    homepage = "https://r-forge.r-project.org/projects/car/"
+    url      = "https://cran.r-project.org/src/contrib/car_2.1-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/car"
+
+    version('2.1-2', '0f78ad74ef7130126d319acec23951a0')
+
+    extends('R')
+
+    depends_on('r-mass', type=nolink)
+    depends_on('r-mgcv', type=nolink)
+    depends_on('r-nnet', type=nolink)
+    depends_on('r-pbkrtest', type=nolink)
+    depends_on('r-quantreg', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCaret(Package):
+    """Misc functions for training and plotting classification and regression
+    models."""
+
+    homepage = "https://github.com/topepo/caret/"
+    url      = "https://cran.r-project.org/src/contrib/caret_6.0-70.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/caret"
+
+    version('6.0-70', '202d7abb6a679af716ea69fb2573f108')
+
+    extends('R')
+
+    depends_on('r-lattice', type=nolink)
+    depends_on('r-ggplot2', type=nolink)
+    depends_on('r-car', type=nolink)
+    depends_on('r-foreach', type=nolink)
+    depends_on('r-plyr', type=nolink)
+    depends_on('r-nlme', type=nolink)
+    depends_on('r-reshape2', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RChron(Package):
+    """Chronological objects which can handle dates and times."""
+
+    homepage = "https://cran.r-project.org/package=chron"
+    url      = "https://cran.r-project.org/src/contrib/chron_2.3-47.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/chron"
+
+    version('2.3-47', 'b8890cdc5f2337f8fd775b0becdcdd1f')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RClass(Package):
+    """Various functions for classification, including k-nearest neighbour,
+    Learning Vector Quantization and Self-Organizing Maps."""
+
+    homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
+    url      = "https://cran.r-project.org/src/contrib/class_7.3-14.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/class"
+
+    version('7.3-14', '6a21dd206fe4ea29c55faeb65fb2b71e')
+
+    extends('R')
+
+    depends_on('r-mass', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCrayon(Package):
+    """Colored terminal output on terminals that support 'ANSI' color and
+    highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is
+    automatically detected. Colors and highlighting can be combined and nested.
+    New styles can also be created easily. This package was inspired by the
+    'chalk' 'JavaScript' project."""
+
+    homepage = "https://github.com/gaborcsardi/crayon"
+    url      = "https://cran.r-project.org/src/contrib/crayon_1.3.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/crayon"
+
+    version('1.3.2', 'fe29c6204d2d6ff4c2f9d107a03d0cb9')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RCubature(Package):
+    """Adaptive multivariate integration over hypercubes"""
+
+    homepage = "https://cran.r-project.org/package=cubature"
+    url      = "https://cran.r-project.org/src/contrib/cubature_1.1-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/cubature"
+
+    version('1.1-2', '5617e1d82baa803a3814d92461da45c9')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -38,8 +38,9 @@ class RCurl(Package):
 
     homepage = "https://github.com/jeroenooms/curl"
     url      = "https://cran.r-project.org/src/contrib/curl_0.9.7.tar.gz"
-    list_url = "https://cran.r-project.org/src/contrib/Archive/RCurl"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/curl"
 
+    version('1.0', '93d34926d6071e1fba7e728b482f0dd9')
     version('0.9.7', 'a101f7de948cb828fef571c730f39217')
 
     extends('R')

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

@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RDatatable(Package):
+    """Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins,
+    fast add/modify/delete of columns by group using no copies at all, list
+    columns and a fast file reader (fread). Offers a natural and flexible
+    syntax, for faster development."""
+
+    homepage = "https://github.com/Rdatatable/data.table/wiki"
+    url      = "https://cran.r-project.org/src/contrib/data.table_1.9.6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/data.table"
+
+    version('1.9.6', 'b1c0c7cce490bdf42ab288541cc55372')
+
+    extends('R')
+
+    depends_on('r-chron')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-e1071/package.py

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RE1071(Package):
+    """Functions for latent class analysis, short time Fourier transform, fuzzy
+    clustering, support vector machines, shortest path computation, bagged
+    clustering, naive Bayes classifier, ..."""
+
+    homepage = "https://cran.r-project.org/package=e1071"
+    url      = "https://cran.r-project.org/src/contrib/e1071_1.6-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/e1071"
+
+    version('1.6-7', 'd109a7e3dd0c905d420e327a9a921f5a')
+
+    extends('R')
+
+    depends_on('r-class', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,59 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGdata(Package):
+    """Various R programming tools for data manipulation, including: - medical
+    unit conversions ('ConvertMedUnits', 'MedUnits'), - combining objects
+    ('bindData', 'cbindX', 'combine', 'interleave'), - character vector
+    operations ('centerText', 'startsWith', 'trim'), - factor manipulation
+    ('levels', 'reorder.factor', 'mapLevels'), - obtaining information about R
+    objects ('object.size', 'elem', 'env', 'humanReadable', 'is.what', 'll',
+    'keep', 'ls.funs', 'Args','nPairs', 'nobs'), - manipulating MS-Excel
+    formatted files ('read.xls', 'installXLSXsupport', 'sheetCount',
+    'xlsFormats'), - generating fixed-width format files ('write.fwf'), -
+    extricating components of date & time objects ('getYear', 'getMonth',
+    'getDay', 'getHour', 'getMin', 'getSec'), - operations on columns of data
+    frames ('matchcols', 'rename.vars'), - matrix operations ('unmatrix',
+    'upperTriangle', 'lowerTriangle'), - operations on vectors ('case',
+    'unknownToNA', 'duplicated2', 'trimSum'), - operations on data frames
+    ('frameApply', 'wideByFactor'), - value of last evaluated expression
+    ('ans'), and - wrapper for 'sample' that ensures consistent behavior for
+    both scalar and vector arguments ('resample')."""
+
+    homepage = "https://cran.r-project.org/package=gdata"
+    url      = "https://cran.r-project.org/src/contrib/gdata_2.17.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gdata"
+
+    version('2.17.0', 'c716b663b9dc16ad8cafe6acc781a75f')
+
+    extends('R')
+
+    depends_on('r-gtools', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGeosphere(Package):
+    """Spherical trigonometry for geographic applications. That is, compute
+    distances and related measures for angular (longitude/latitude)
+    locations."""
+
+    homepage = "https://cran.r-project.org/package=geosphere"
+    url      = "https://cran.r-project.org/src/contrib/geosphere_1.5-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/geosphere"
+
+    version('1.5-5', '28efb7a8e266c7f076cdbcf642455f3e')
+
+    extends('R')
+
+    depends_on('r-sp', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,57 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGgmap(Package):
+    """A collection of functions to visualize spatial data and models on top of
+    static maps from various online sources (e.g Google Maps and Stamen Maps).
+    It includes tools common to those tasks, including functions for
+    geolocation and routing."""
+
+    homepage = "https://github.com/dkahle/ggmap"
+    url      = "https://cran.r-project.org/src/contrib/ggmap_2.6.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ggmap"
+
+    version('2.6.1', '25ad414a3a1c6d59a227a9f22601211a')
+
+    extends('R')
+
+    depends_on('r-ggplot2', type=nolink)
+    depends_on('r-proto', type=nolink)
+    depends_on('r-rgooglemaps', type=nolink)
+    depends_on('r-png', type=nolink)
+    depends_on('r-plyr', type=nolink)
+    depends_on('r-reshape2', type=nolink)
+    depends_on('r-rjson', type=nolink)
+    depends_on('r-mapproj', type=nolink)
+    depends_on('r-jpeg', type=nolink)
+    depends_on('r-geosphere', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-scales', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGlmnet(Package):
+    """Extremely efficient procedures for fitting the entire lasso or
+    elastic-net regularization path for linear regression, logistic and
+    multinomial regression models, Poisson regression and the Cox model. Two
+    recent additions are the multiple-response Gaussian, and the grouped
+    multinomial. The algorithm uses cyclical coordinate descent in a path-wise
+    fashion, as described in the paper linked to via the URL below."""
+
+    homepage = "http://www.jstatsoft.org/v33/i01/"
+    url      = "https://cran.r-project.org/src/contrib/glmnet_2.0-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/glmnet"
+
+    version('2.0-5', '049b18caa29529614cd684db3beaec2a')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-foreach', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,60 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGtools(Package):
+    """Functions to assist in R programming, including: - assist in developing,
+    updating, and maintaining R and R packages ('ask', 'checkRVersion',
+    'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse
+    logit transformations ('logit', 'inv.logit'), - test if a value is missing,
+    empty or contains only NA and NULL values ('invalid'), - manipulate R's
+    .Last function ('addLast'), - define macros ('defmacro'), - detect odd and
+    even integers ('odd', 'even'), - convert strings containing non-ASCII
+    characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a
+    binary search ('binsearch'), - sort strings containing both numeric and
+    character components ('mixedsort'), - create a factor variable from the
+    quantiles of a continuous variable ('quantcut'), - enumerate permutations
+    and combinations ('combinations', 'permutation'), - calculate and convert
+    between fold-change and log-ratio ('foldchange', 'logratio2foldchange',
+    'foldchange2logratio'), - calculate probabilities and generate random
+    numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply
+    a function over adjacent subsets of a vector ('running'), - modify the
+    TCP\_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of
+    data frames, even if the column names don't match ('smartbind'), - generate
+    significance stars from p-values ('stars.pval'), - convert characters
+    to/from ASCII codes."""
+
+    homepage = "https://cran.r-project.org/package=gtools"
+    url      = "https://cran.r-project.org/src/contrib/gtools_3.5.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/gtools"
+
+    version('3.5.0', '45f8800c0336d35046641fbacc56bdbb')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RJpeg(Package):
+    """This package provides an easy and simple way to read, write and display
+    bitmap images stored in the JPEG format. It can read and write both files
+    and in-memory raw vectors."""
+
+    homepage = "http://www.rforge.net/jpeg/"
+    url      = "https://cran.r-project.org/src/contrib/jpeg_0.1-8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/jpeg"
+
+    version('0.1-8', '696007451d14395b1ed1d0e9af667a57')
+
+    extends('R')
+
+    depends_on('jpeg')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-lme4/package.py

@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RLme4(Package):
+    """Fit linear and generalized linear mixed-effects models. The models and
+    their components are represented using S4 classes and methods. The core
+    computational algorithms are implemented using the 'Eigen' C++ library for
+    numerical linear algebra and 'RcppEigen' "glue"."""
+
+    homepage = "https://github.com/lme4/lme4/"
+    url      = "https://cran.r-project.org/src/contrib/lme4_1.1-12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lme4"
+
+    version('1.1-12', 'da8aaebb67477ecb5631851c46207804')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-mass', type=nolink)
+    depends_on('r-lattice', type=nolink)
+    depends_on('r-nlme', type=nolink)
+    depends_on('r-minqa', type=nolink)
+    depends_on('r-nloptr', type=nolink)
+    depends_on('r-rcpp', type=nolink)
+    depends_on('r-rcppeigen', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RLmtest(Package):
+    """A collection of tests, data sets, and examples for diagnostic checking
+    in linear regression models. Furthermore, some generic tools for inference
+    in parametric models are provided."""
+
+    homepage = "https://cran.r-project.org/package=lmtest"
+    url      = "https://cran.r-project.org/src/contrib/lmtest_0.9-34.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lmtest"
+
+    version('0.9-34', 'fcdf7286bb5ccc2ca46be00bf25ac2fe')
+
+    extends('R')
+
+    depends_on('r-zoo', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMapproj(Package):
+    """Converts latitude/longitude into projected coordinates."""
+
+    homepage = "https://cran.r-project.org/package=mapproj"
+    url      = "https://cran.r-project.org/src/contrib/mapproj_1.2-4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mapproj"
+
+    version('1.2-4', '10e22bde1c790e1540672f15ddcaee71')
+
+    extends('R')
+
+    depends_on('r-maps', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMaps(Package):
+    """Display of maps. Projection code and larger maps are in separate
+    packages ('mapproj' and 'mapdata')."""
+
+    homepage = "https://cran.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/maps_3.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/maps"
+
+    version('3.1.1', 'ff045eccb6d5a658db5a539116ddf764')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMaptools(Package):
+    """Set of tools for manipulating and reading geographic data, in particular
+    ESRI shapefiles; C code used from shapelib. It includes binary access to
+    GSHHG shoreline files. The package also provides interface wrappers for
+    exchanging spatial objects with packages such as PBSmapping, spatstat,
+    maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others."""
+
+    homepage = "http://r-forge.r-project.org/projects/maptools/"
+    url      = "https://cran.r-project.org/src/contrib/maptools_0.8-39.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/maptools"
+
+    version('0.8-39', '3690d96afba8ef22c8e27ae540ffb836')
+
+    extends('R')
+
+    depends_on('r-sp', type=nolink)
+    depends_on('r-foreign', type=nolink)
+    depends_on('r-lattice', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMatrixmodels(Package):
+    """Modelling with sparse and dense 'Matrix' matrices, using modular
+    prediction and response module classes."""
+
+    homepage = "http://matrix.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/MatrixModels_0.4-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/MatrixModels"
+
+    version('0.4-1', '65b3ab56650c62bf1046a3eb1f1e19a0')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMgcv(Package):
+    """GAMs, GAMMs and other generalized ridge regression with multiple
+    smoothing parameter estimation by GCV, REML or UBRE/AIC. Includes a gam()
+    function, a wide variety of smoothers, JAGS support and distributions
+    beyond the exponential family."""
+
+    homepage = "https://cran.r-project.org/package=mgcv"
+    url      = "https://cran.r-project.org/src/contrib/mgcv_1.8-13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mgcv"
+
+    version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984')
+
+    extends('R')
+
+    depends_on('r-nlme', type=nolink)
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMinqa(Package):
+    """Derivative-free optimization by quadratic approximation based on an
+    interface to Fortran implementations by M. J. D. Powell."""
+
+    homepage = "http://optimizer.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/minqa_1.2.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/minqa"
+
+    version('1.2.4', 'bcaae4fdba60a33528f2116e2fd51105')
+
+    extends('R')
+
+    depends_on('r-rcpp', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMultcomp(Package):
+    """Simultaneous tests and confidence intervals for general linear
+    hypotheses in parametric models, including linear, generalized linear,
+    linear mixed effects, and survival models. The package includes demos
+    reproducing analyzes presented in the book "Multiple Comparisons Using R"
+    (Bretz, Hothorn, Westfall, 2010, CRC Press)."""
+
+    homepage = "http://multcomp.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/multcomp_1.4-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/multcomp"
+
+    version('1.4-6', 'f1353ede2ed78b23859a7f1f1f9ebe88')
+
+    extends('R')
+
+    depends_on('r-mvtnorm', type=nolink)
+    depends_on('r-survival', type=nolink)
+    depends_on('r-thdata', type=nolink)
+    depends_on('r-sandwich', type=nolink)
+    depends_on('r-codetools', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RMvtnorm(Package):
+    """Computes multivariate normal and t probabilities, quantiles, random
+    deviates and densities."""
+
+    homepage = "http://mvtnorm.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/mvtnorm_1.0-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mvtnorm"
+
+    version('1.0-5', '5894dd3969bbfa26f4862c45f9a48a52')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-ncdf4/package.py

@@ -0,0 +1,56 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNcdf4(Package):
+    """Provides a high-level R interface to data files written using Unidata's
+    netCDF library (version 4 or earlier), which are binary data files that are
+    portable across platforms and include metadata information in addition to
+    the data sets. Using this package, netCDF files (either version 4 or
+    "classic" version 3) can be opened and data sets read in easily. It is also
+    easy to create new netCDF dimensions, variables, and files, in either
+    version 3 or 4 format, and manipulate existing netCDF files. This package
+    replaces the former ncdf package, which only worked with netcdf version 3
+    files. For various reasons the names of the functions have had to be
+    changed from the names in the ncdf package. The old ncdf package is still
+    available at the URL given below, if you need to have backward
+    compatibility. It should be possible to have both the ncdf and ncdf4
+    packages installed simultaneously without a problem. However, the ncdf
+    package does not provide an interface for netcdf version 4 files."""
+
+    homepage = "http://cirrus.ucsd.edu/~pierce/ncdf"
+    url      = "https://cran.r-project.org/src/contrib/ncdf4_1.15.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ncdf4"
+
+    version('1.15', 'cd60dadbae3be31371e1ed40ddeb420a')
+
+    extends('R')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNlme(Package):
+    """Fit and compare Gaussian linear and nonlinear mixed-effects models."""
+
+    homepage = "https://cran.r-project.org/package=nlme"
+    url      = "https://cran.r-project.org/src/contrib/nlme_3.1-128.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nlme"
+
+    version('3.1-128', '3d75ae7380bf123761b95a073eb55008')
+
+    extends('R')
+
+    depends_on('r-lattice', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNloptr(Package):
+    """nloptr is an R interface to NLopt. NLopt is a free/open-source library
+    for nonlinear optimization, providing a common interface for a number of
+    different free optimization routines available online as well as original
+    implementations of various other algorithms. See
+    http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction for more
+    information on the available algorithms. During installation on Unix the
+    NLopt code is downloaded and compiled from the NLopt website."""
+
+    homepage = "https://cran.r-project.org/package=nloptr"
+    url      = "https://cran.r-project.org/src/contrib/nloptr_1.0.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nloptr"
+
+    version('1.0.4', '9af69a613349b236fd377d0a107f484c')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNnet(Package):
+    """Software for feed-forward neural networks with a single hidden layer,
+    and for multinomial log-linear models."""
+
+    homepage = "http://www.stats.ox.ac.uk/pub/MASS4/"
+    url      = "https://cran.r-project.org/src/contrib/nnet_7.3-12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nnet"
+
+    version('7.3-12', 'dc7c6f0d0de53d8fc72b44554400a74e')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RNp(Package):
+    """This package provides a variety of nonparametric (and semiparametric)
+    kernel methods that seamlessly handle a mix of continuous, unordered, and
+    ordered factor data types. We would like to gratefully acknowledge support
+    from the Natural Sciences and Engineering Research Council of Canada
+    (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council
+    of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic
+    Research Computing Network (SHARCNET:www.sharcnet.ca)."""
+
+    homepage = "https://github.com/JeffreyRacine/R-Package-np/"
+    url      = "https://cran.r-project.org/src/contrib/np_0.60-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/np"
+
+    version('0.60-2', 'e094d52ddff7280272b41e6cb2c74389')
+
+    extends('R')
+
+    depends_on('r-boot', type=nolink)
+    depends_on('r-cubature', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,49 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RPbkrtest(Package):
+    """Test in mixed effects models. Attention is on mixed effects models as
+    implemented in the 'lme4' package. This package implements a parametric
+    bootstrap test and a Kenward Roger modification of F-tests for linear mixed
+    effects models and a parametric bootstrap test for generalized linear mixed
+    models."""
+
+    homepage = "http://people.math.aau.dk/~sorenh/software/pbkrtest/"
+    url      = "https://cran.r-project.org/src/contrib/pbkrtest_0.4-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/pbkrtest"
+
+    version('0.4-6', '0a7d9ff83b8d131af9b2335f35781ef9')
+
+    extends('R')
+
+    depends_on('r-lme4', type=nolink)
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-mass', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RPlotrix(Package):
+    """Lots of plots, various labeling, axis and color scaling functions."""
+
+    homepage = "https://cran.r-project.org/package=plotrix"
+    url      = "https://cran.r-project.org/src/contrib/plotrix_3.6-3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/plotrix"
+
+    version('3.6-3', '23e3e022a13a596e9b77b40afcb4a2ef')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RPraise(Package):
+    """Build friendly R packages that praise their users if they have done
+    something good, or they just need it to feel better."""
+
+    homepage = "https://github.com/gaborcsardi/praise"
+    url      = "https://cran.r-project.org/src/contrib/praise_1.0.0.tar.gz"
+
+    version('1.0.0', '9318724cec0454884b5f762bee2da6a1')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RProto(Package):
+    """An object oriented system using object-based, also called
+    prototype-based, rather than class-based object oriented ideas."""
+
+    homepage = "http://r-proto.googlecode.com/"
+    url      = "https://cran.r-project.org/src/contrib/proto_0.3-10.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/proto"
+
+    version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RQuantmod(Package):
+    """Specify, build, trade, and analyse quantitative financial trading
+    strategies."""
+
+    homepage = "http://www.quantmod.com/"
+    url      = "https://cran.r-project.org/src/contrib/quantmod_0.4-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/quantmod"
+
+    version('0.4-5', 'cab3c409e4de3df98a20f1ded60f3631')
+
+    extends('R')
+
+    depends_on('r-xts', type=nolink)
+    depends_on('r-zoo', type=nolink)
+    depends_on('r-ttr', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RQuantreg(Package):
+    """Estimation and inference methods for models of conditional quantiles:
+        Linear and nonlinear parametric and non-parametric (total variation
+        penalized) models for conditional quantiles of a univariate response
+        and several methods for handling censored survival data. Portfolio
+        selection methods based on expected shortfall risk are also
+        included."""
+
+    homepage = "https://cran.r-project.org/package=quantreg"
+    url      = "https://cran.r-project.org/src/contrib/quantreg_5.26.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/quantreg"
+
+    version('5.26', '1d89ed932fb4d67ae2d5da0eb8c2989f')
+
+    extends('R')
+
+    depends_on('r-sparsem', type=nolink)
+    depends_on('r-matrix', type=nolink)
+    depends_on('r-matrixmodels', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRandomforest(Package):
+    """Classification and regression based on a forest of trees using random
+    inputs."""
+
+    homepage = "https://www.stat.berkeley.edu/~breiman/RandomForests/"
+    url      = "https://cran.r-project.org/src/contrib/randomForest_4.6-12.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/randomForest"
+
+    version('4.6-12', '071c03af974198e861f1475c5bab9e7a')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRgooglemaps(Package):
+    """This package serves two purposes: (i) Provide a comfortable R interface
+    to query the Google server for static maps, and (ii) Use the map as a
+    background image to overlay plots within R. This requires proper coordinate
+    scaling."""
+
+    homepage = "https://cran.r-project.org/package=RgoogleMaps"
+    url      = "https://cran.r-project.org/src/contrib/RgoogleMaps_1.2.0.7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RgoogleMaps"
+
+    version('1.2.0.7', '2e1df804f0331b4122d841105f0c7ea5')
+
+    extends('R')
+
+    depends_on('r-png', type=nolink)
+    depends_on('r-rjsonio', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRjson(Package):
+    """Converts R object into JSON objects and vice-versa."""
+
+    homepage = "https://cran.r-project.org/package=rjson"
+    url      = "https://cran.r-project.org/src/contrib/rjson_0.2.15.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rjson"
+
+    version('0.2.15', '87d0e29bc179c6aeaf312b138089f8e9')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,55 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRjsonio(Package):
+    """This is a package that allows conversion to and from data in Javascript
+    object notation (JSON) format. This allows R objects to be inserted into
+    Javascript/ECMAScript/ActionScript code and allows R programmers to read
+    and convert JSON content to R objects. This is an alternative to rjson
+    package. Originally, that was too slow for converting large R objects to
+    JSON and was not extensible. rjson's performance is now similar to this
+    package, and perhaps slightly faster in some cases. This package uses
+    methods and is readily extensible by defining methods for different
+    classes, vectorized operations, and C code and callbacks to R functions for
+    deserializing JSON objects to R. The two packages intentionally share the
+    same basic interface. This package (RJSONIO) has many additional options to
+    allow customizing the generation and processing of JSON content. This
+    package uses libjson rather than implementing yet another JSON parser. The
+    aim is to support other general projects by building on their work,
+    providing feedback and benefit from their ongoing development."""
+
+    homepage = "https://cran.r-project.org/package=RJSONIO"
+    url      = "https://cran.r-project.org/src/contrib/RJSONIO_1.3-0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RJSONIO"
+
+    version('1.3-0', '72c395622ba8d1435ec43849fd32c830')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

var/spack/repos/builtin/packages/r-roxygen2/package.py

@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RRoxygen2(Package):
+    """A 'Doxygen'-like in-source documentation system for Rd, collation, and
+    'NAMESPACE' files."""
+
+    homepage = "https://github.com/klutometis/roxygen"
+    url      = "https://cran.r-project.org/src/contrib/roxygen2_5.0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/roxygen2"
+
+    version('5.0.1', 'df5bdbc12fda372e427710ef1cd92ed7')
+
+    extends('R')
+
+    depends_on('r-stringr', type=nolink)
+    depends_on('r-stringi', type=nolink)
+    depends_on('r-brew', type=nolink)
+    depends_on('r-digest', type=nolink)
+    depends_on('r-rcpp', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RSandwich(Package):
+    """Model-robust standard error estimators for cross-sectional, time series,
+    and longitudinal data."""
+
+    homepage = "https://cran.r-project.org/package=sandwich"
+    url      = "https://cran.r-project.org/src/contrib/sandwich_2.3-4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/sandwich"
+
+    version('2.3-4', 'a621dbd8a57b6e1e036496642aadc2e5')
+
+    extends('R')
+
+    depends_on('r-zoo', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,43 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RSparsem(Package):
+    """Some basic linear algebra functionality for sparse matrices is provided:
+        including Cholesky decomposition and backsolving as well as standard R
+        subsetting and Kronecker products."""
+
+    homepage = "http://www.econ.uiuc.edu/~roger/research/sparse/sparse.html"
+    url      = "https://cran.r-project.org/src/contrib/SparseM_1.7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/SparseM"
+
+    version('1.7', '7b5b0ab166a0929ef6dcfe1d97643601')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,47 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RSurvey(Package):
+    """Summary statistics, two-sample tests, rank tests, generalised linear
+    models, cumulative link models, Cox models, loglinear models, and general
+    maximum pseudolikelihood estimation for multistage stratified,
+    cluster-sampled, unequally weighted survey samples. Variances by Taylor
+    series linearisation or replicate weights. Post-stratification,
+    calibration, and raking. Two-phase subsampling designs. Graphics. PPS
+    sampling without replacement. Principal components, factor analysis."""
+
+    homepage = "http://r-survey.r-forge.r-project.org/survey/"
+    url      = "https://cran.r-project.org/src/contrib/survey_3.30-3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/survey"
+
+    version('3.30-3', 'c70cdae9cb43d35abddd11173d64cad0')
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RSurvival(Package):
+    """Contains the core survival analysis routines, including definition of
+    Surv objects, Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox
+    models, and parametric accelerated failure time models."""
+
+    homepage = "https://cran.r-project.org/package=survival"
+    url      = "https://cran.r-project.org/src/contrib/survival_2.39-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/survival"
+
+    version('2.39-5', 'a3cc6b5762e8c5c0bb9e64a276710be2')
+
+    extends('R')
+
+    depends_on('r-matrix', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RTarifx(Package):
+    """A collection of various utility and convenience functions."""
+
+    homepage = "https://cran.r-project.org/package=taRifx"
+    url      = "https://cran.r-project.org/src/contrib/taRifx_1.0.6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/taRifx"
+
+    version('1.0.6', '7e782e04bd69d929b29f91553382e6a2')
+
+    extends('R')
+
+    depends_on('r-reshape2', type=nolink)
+    depends_on('r-plyr', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,48 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RTestthat(Package):
+    """A unit testing system designed to be fun, flexible and easy to set
+    up."""
+
+    homepage = "https://github.com/hadley/testthat"
+    url      = "https://cran.r-project.org/src/contrib/testthat_1.0.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/testthat"
+
+    version('1.0.2', '6c6a90c8db860292df5784a70e07b8dc')
+
+    extends('R')
+
+    depends_on('r-digest', type=nolink)
+    depends_on('r-crayon', type=nolink)
+    depends_on('r-praise', type=nolink)
+    depends_on('r-magrittr', type=nolink)
+    depends_on('r-R6', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RThdata(Package):
+    """Contains data sets used in other packages Torsten Hothorn maintains."""
+
+    homepage = "https://cran.r-project.org/package=TH.data"
+    url      = "https://cran.r-project.org/src/contrib/TH.data_1.0-7.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/TH.data"
+
+    version('1.0-7', '3e8b6b1a4699544f175215aed7039a94')
+
+    extends('R')
+
+    depends_on('r-survival', type=nolink)
+    depends_on('r-mass', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,44 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RTtr(Package):
+    """Functions and data to construct technical trading rules with R."""
+
+    homepage = "https://github.com/joshuaulrich/TTR"
+    url      = "https://cran.r-project.org/src/contrib/TTR_0.23-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/TTR"
+
+    version('0.23-1', '35f693ac0d97e8ec742ebea2da222986')
+
+    extends('R')
+
+    depends_on('r-xts', type=nolink)
+    depends_on('r-zoo', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,50 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RVcd(Package):
+    """Visualization techniques, data sets, summary and inference procedures
+    aimed particularly at categorical data. Special emphasis is given to highly
+    extensible grid graphics. The package was package was originally inspired
+    by the book "Visualizing Categorical Data" by Michael Friendly and is now
+    the main support package for a new book, "Discrete Data Analysis with R" by
+    Michael Friendly and David Meyer (2015)."""
+
+    homepage = "https://cran.r-project.org/package=vcd"
+    url      = "https://cran.r-project.org/src/contrib/vcd_1.4-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/vcd"
+
+    version('1.4-1', '7db150a77f173f85b69a1f86f73f8f02')
+
+    extends('R')
+
+    depends_on('r-mass', type=nolink)
+    depends_on('r-colorspace', type=nolink)
+    depends_on('r-lmtest', type=nolink)
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RXml(Package):
+    """Many approaches for both reading and creating XML (and HTML) documents
+    (including DTDs), both local and accessible via HTTP or FTP. Also offers
+    access to an 'XPath' "interpreter"."""
+
+    homepage = "http://www.omegahat.net/RSXML"
+    url      = "https://cran.r-project.org/src/contrib/XML_3.98-1.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/XML"
+
+    version('3.98-1', '1a7f3ce6f264eeb109bfa57bedb26c14')
+
+    extends('R')
+
+    depends_on('libxml2')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library={0}'.format(self.module.r_lib_dir),
+          self.stage.source_path)

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

@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Tree(Package):
+    """Tree is a recursive directory listing command that produces a depth
+       indented listing of files, which is colorized ala dircolors if
+       the LS_COLORS environment variable is set and output is to
+       tty. Tree has been ported and reported to work under the
+       following operating systems: Linux, FreeBSD, OS X, Solaris,
+       HP/UX, Cygwin, HP Nonstop and OS/2."""
+
+    homepage = "http://mama.indstate.edu/users/ice/tree/"
+    url      = "http://mama.indstate.edu/users/ice/tree/src/tree-1.7.0.tgz"
+
+    version('1.7.0', 'abe3e03e469c542d8e157cdd93f4d8a6')
+
+    def install(self, spec, prefix):
+        filter_file(r'^prefix =.*', 'prefix = %s' % prefix, 'Makefile')
+        filter_file(r'^CFLAGS', '# use spack settings instead... CFLAGS',
+                    'Makefile')
+        make()
+        make('install')

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

@@ -138,16 +138,23 @@ def install(self, spec, prefix):
             '-DTPL_ENABLE_LAPACK=ON',
             '-DLAPACK_LIBRARY_NAMES=%s' % to_lib_name(
                 spec['lapack'].lapack_shared_lib),
-            '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix,
+            '-DLAPACK_LIBRARY_DIRS=%s' % spec['lapack'].prefix.lib,
             '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
             '-DTrilinos_ENABLE_CXX11:BOOL=ON',
             '-DTPL_ENABLE_Netcdf:BOOL=ON',
             '-DTPL_ENABLE_HYPRE:BOOL=%s' % (
-                'ON' if '+hypre' in spec else 'OFF'),
+                'ON' if '+hypre' in spec else 'OFF')
-            '-DTPL_ENABLE_HDF5:BOOL=%s' % (
-                'ON' if '+hdf5' in spec else 'OFF'),
         ])
 
+        if '+hdf5' in spec:
+            options.extend([
+                '-DTPL_ENABLE_HDF5:BOOL=ON',
+                '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include,
+                '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib
+            ])
+        else:
+            options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
+
         if '+boost' in spec:
             options.extend([
                 '-DTPL_ENABLE_Boost:BOOL=ON',