Merge remote branch 'origin/develop' into develop

.travis.yml

@@ -71,12 +71,14 @@ addons:
       - gfortran
       - mercurial
       - graphviz
+      - gnupg2
 
 # Work around Travis's lack of support for Python on OSX
 before_install:
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions python > /dev/null || brew install python; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions gcc    > /dev/null || brew install gcc;    fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew ls --versions gnupg2 > /dev/null || brew install gnupg2; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then virtualenv venv; fi
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then source venv/bin/activate; fi
 

lib/spack/docs/basic_usage.rst

@@ -276,6 +276,70 @@ Seeing installed packages
 We know that ``spack list`` shows you the names of available packages,
 but how do you figure out which are already installed?
 
+.. _cmd-spack-gpg:
+
+^^^^^^^^^^^^^
+``spack gpg``
+^^^^^^^^^^^^^
+
+Spack has support for signing and verifying packages using GPG keys. A
+separate keyring is used for Spack, so any keys available in the user's home
+directory are not used.
+
+^^^^^^^^^^^^^^^^^^
+``spack gpg init``
+^^^^^^^^^^^^^^^^^^
+
+When Spack is first installed, its keyring is empty. Keys stored in
+:file:`var/spack/gpg` are the default keys for a Spack installation. These
+keys may be imported by running ``spack gpg init``. This will import the
+default keys into the keyring as trusted keys.
+
+-------------
+Trusting keys
+-------------
+
+Additional keys may be added to the keyring using
+``spack gpg trust <keyfile>``. Once a key is trusted, packages signed by the
+owner of they key may be installed.
+
+-------------
+Creating keys
+-------------
+
+You may also create your own key so that you may sign your own packages using
+``spack gpg create <name> <email>``. By default, the key has no expiration,
+but it may be set with the ``--expires <date>`` flag (see the ``gnupg2``
+documentation for accepted date formats). It is also recommended to add a
+comment as to the use of the key using the ``--comment <comment>`` flag. The
+public half of the key can also be exported for sharing with others so that
+they may use packages you have signed using the ``--export <keyfile>`` flag.
+Secret keys may also be later exported using the
+``spack gpg export <location> [<key>...]`` command.
+
+------------
+Listing keys
+------------
+
+In order to list the keys available in the keyring, the
+``spack gpg list`` command will list trusted keys with the ``--trusted`` flag
+and keys available for signing using ``--signing``. If you would like to
+remove keys from your keyring, ``spack gpg untrust <keyid>``. Key IDs can be
+email addresses, names, or (best) fingerprints.
+
+------------------------------
+Signing and Verifying Packages
+------------------------------
+
+In order to sign a package, ``spack gpg sign <file>`` should be used. By
+default, the signature will be written to ``<file>.asc``, but that may be
+changed by using the ``--output <file>`` flag. If there is only one signing
+key available, it will be used, but if there is more than one, the key to use
+must be specified using the ``--key <keyid>`` flag. The ``--clearsign`` flag
+may also be used to create a signed file which contains the contents, but it
+is not recommended. Signed packages may be verified by using
+``spack gpg verify <file>``.
+
 .. _cmd-spack-find:
 
 ^^^^^^^^^^^^^^

lib/spack/docs/getting_started.rst

@@ -14,6 +14,7 @@ before Spack is run:
 1. Python 2 (2.6 or 2.7) or 3 (3.3 - 3.6)
 2. A C/C++ compiler
 3. The ``git`` and ``curl`` commands.
+4. If using the ``gpg`` subcommand, ``gnupg2`` is required.
 
 These requirements can be easily installed on most modern Linux systems;
 on Macintosh, XCode is required.  Spack is designed to run on HPC

lib/spack/docs/known_issues.rst

@@ -37,6 +37,46 @@ A workaround is to explicitly activate the variant related to the dependency:
 See https://github.com/LLNL/spack/issues/397 for further details.
 
 
+---------------------------------------------------
+Variants are not properly forwarded to dependencies
+---------------------------------------------------
+
+**Status:** Expected to be fixed in the next release
+
+Sometimes, a variant of a package can also affect how its dependencies are
+built. For example, in order to build MPI support for a package, it may
+require that its dependencies are also built with MPI support. In the
+``package.py``, this looks like:
+
+.. code-block:: python
+
+   depends_on('hdf5~mpi', when='~mpi')
+   depends_on('hdf5+mpi', when='+mpi')
+
+Spack handles this situation properly for *immediate* dependencies, and
+builds ``hdf5`` with the same variant you used for the package that
+depends on it. However, for *indirect* dependencies (dependencies of
+dependencies), Spack does not backtrack up the DAG far enough to handle
+this. Users commonly run into this situation when trying to build R with
+X11 support:
+
+.. code-block:: console
+
+   $ spack install r+X
+   ...
+   ==> Error: Invalid spec: 'cairo@1.14.8%gcc@6.2.1+X arch=linux-fedora25-x86_64 ^bzip2@1.0.6%gcc@6.2.1+shared arch=linux-fedora25-x86_64 ^font-util@1.3.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^fontconfig@2.12.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^freetype@2.7.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^gettext@0.19.8.1%gcc@6.2.1+bzip2+curses+git~libunistring+libxml2+tar+xz arch=linux-fedora25-x86_64 ^glib@2.53.1%gcc@6.2.1~libmount arch=linux-fedora25-x86_64 ^inputproto@2.3.2%gcc@6.2.1 arch=linux-fedora25-x86_64 ^kbproto@1.0.7%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libffi@3.2.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libpng@1.6.29%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libpthread-stubs@0.4%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libx11@1.6.5%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxau@1.0.8%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxcb@1.12%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxdmcp@1.1.2%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxext@1.3.3%gcc@6.2.1 arch=linux-fedora25-x86_64 ^libxml2@2.9.4%gcc@6.2.1~python arch=linux-fedora25-x86_64 ^libxrender@0.9.10%gcc@6.2.1 arch=linux-fedora25-x86_64 ^ncurses@6.0%gcc@6.2.1~symlinks arch=linux-fedora25-x86_64 ^openssl@1.0.2k%gcc@6.2.1 arch=linux-fedora25-x86_64 ^pcre@8.40%gcc@6.2.1+utf arch=linux-fedora25-x86_64 ^pixman@0.34.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^pkg-config@0.29.2%gcc@6.2.1+internal_glib arch=linux-fedora25-x86_64 ^python@2.7.13%gcc@6.2.1+shared~tk~ucs4 arch=linux-fedora25-x86_64 ^readline@7.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^renderproto@0.11.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^sqlite@3.18.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^tar^util-macros@1.19.1%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xcb-proto@1.12%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xextproto@7.3.0%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xproto@7.0.31%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xtrans@1.3.5%gcc@6.2.1 arch=linux-fedora25-x86_64 ^xz@5.2.3%gcc@6.2.1 arch=linux-fedora25-x86_64 ^zlib@1.2.11%gcc@6.2.1+pic+shared arch=linux-fedora25-x86_64'.
+   Package cairo requires variant ~X, but spec asked for +X
+
+A workaround is to explicitly activate the variants of dependencies as well:
+
+.. code-block:: console
+
+   $ spack install r+X ^cairo+X ^pango+X
+
+See https://github.com/LLNL/spack/issues/267 and
+https://github.com/LLNL/spack/issues/2546 for further details.
+
+
 ---------------------------------
 ``spack extensions`` doesn't work
 ---------------------------------

lib/spack/spack/__init__.py

@@ -68,6 +68,13 @@
 etc_path       = join_path(prefix, "etc")
 
 
+# GPG paths.
+gpg_keys_path      = join_path(var_path, "gpg")
+mock_gpg_data_path = join_path(var_path, "gpg.mock", "data")
+mock_gpg_keys_path = join_path(var_path, "gpg.mock", "keys")
+gpg_path           = join_path(opt_path, "spack", "gpg")
+
+
 #-----------------------------------------------------------------------------
 # Initial imports (only for use in this file -- see __all__ below.)
 #-----------------------------------------------------------------------------

lib/spack/spack/build_systems/r.py

@@ -30,7 +30,10 @@
 
 
 class RPackage(PackageBase):
-    """Specialized class for packages that are built using R
+    """Specialized class for packages that are built using R.
+
+    For more information on the R build system, see:
+    https://stat.ethz.ch/R-manual/R-devel/library/utils/html/INSTALL.html
 
     This class provides a single phase that can be overridden:
 
@@ -49,12 +52,37 @@ class RPackage(PackageBase):
 
     depends_on('r', type=('build', 'run'))
 
+    def configure_args(self, spec, prefix):
+        """Arguments to pass to install via ``--configure-args``."""
+        return []
+
+    def configure_vars(self, spec, prefix):
+        """Arguments to pass to install via ``--configure-vars``."""
+        return []
+
     def install(self, spec, prefix):
         """Installs an R package."""
-        inspect.getmodule(self).R(
+
-            'CMD', 'INSTALL',
+        config_args = self.configure_args(spec, prefix)
+        config_vars = self.configure_vars(spec, prefix)
+
+        args = [
+            'CMD',
+            'INSTALL'
+        ]
+
+        if config_args:
+            args.append('--configure-args={0}'.format(' '.join(config_args)))
+
+        if config_vars:
+            args.append('--configure-vars={0}'.format(' '.join(config_vars)))
+
+        args.extend([
             '--library={0}'.format(self.module.r_lib_dir),
-            self.stage.source_path)
+            self.stage.source_path
+        ])
+
+        inspect.getmodule(self).R(*args)
 
     # Check that self.prefix is there after installation
     run_after('install')(PackageBase.sanity_check_prefix)

lib/spack/spack/cmd/create.py

@@ -265,7 +265,11 @@ class RPackageTemplate(PackageTemplate):
     # depends_on('r-foo', type=('build', 'run'))"""
 
     body = """\
-    # FIXME: Override install() if necessary."""
+    def configure_args(self, spec, prefix):
+        # FIXME: Add arguments to pass to install via --configure-args
+        # FIXME: If not needed delete this function
+        args = []
+        return args"""
 
     def __init__(self, name, *args):
         # If the user provided `--name r-rcpp`, don't rename it r-r-rcpp

lib/spack/spack/cmd/gpg.py

@@ -0,0 +1,168 @@
+##############################################################################
+# 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.util.gpg import Gpg
+import spack
+import os
+
+description = "handle GPG actions for spack"
+section = "developer"
+level = "long"
+
+
+def setup_parser(subparser):
+    setup_parser.parser = subparser
+    subparsers = subparser.add_subparsers(help='GPG sub-commands')
+
+    verify = subparsers.add_parser('verify')
+    verify.add_argument('package', type=str,
+                        help='the package to verify')
+    verify.add_argument('signature', type=str, nargs='?',
+                        help='the signature file')
+    verify.set_defaults(func=gpg_verify)
+
+    trust = subparsers.add_parser('trust')
+    trust.add_argument('keyfile', type=str,
+                       help='add a key to the trust store')
+    trust.set_defaults(func=gpg_trust)
+
+    untrust = subparsers.add_parser('untrust')
+    untrust.add_argument('--signing', action='store_true',
+                         help='allow untrusting signing keys')
+    untrust.add_argument('keys', nargs='+', type=str,
+                         help='remove keys from the trust store')
+    untrust.set_defaults(func=gpg_untrust)
+
+    sign = subparsers.add_parser('sign')
+    sign.add_argument('--output', metavar='DEST', type=str,
+                      help='the directory to place signatures')
+    sign.add_argument('--key', metavar='KEY', type=str,
+                      help='the key to use for signing')
+    sign.add_argument('--clearsign', action='store_true',
+                      help='if specified, create a clearsign signature')
+    sign.add_argument('package', type=str,
+                      help='the package to sign')
+    sign.set_defaults(func=gpg_sign)
+
+    create = subparsers.add_parser('create')
+    create.add_argument('name', type=str,
+                        help='the name to use for the new key')
+    create.add_argument('email', type=str,
+                        help='the email address to use for the new key')
+    create.add_argument('--comment', metavar='COMMENT', type=str,
+                        default='GPG created for Spack',
+                        help='a description for the intended use of the key')
+    create.add_argument('--expires', metavar='EXPIRATION', type=str,
+                        default='0', help='when the key should expire')
+    create.add_argument('--export', metavar='DEST', type=str,
+                        help='export the public key to a file')
+    create.set_defaults(func=gpg_create)
+
+    list = subparsers.add_parser('list')
+    list.add_argument('--trusted', action='store_true',
+                      help='list trusted keys')
+    list.add_argument('--signing', action='store_true',
+                      help='list keys which may be used for signing')
+    list.set_defaults(func=gpg_list)
+
+    init = subparsers.add_parser('init')
+    init.set_defaults(func=gpg_init)
+    init.set_defaults(import_dir=spack.gpg_keys_path)
+
+    export = subparsers.add_parser('export')
+    export.add_argument('location', type=str,
+                        help='where to export keys')
+    export.add_argument('keys', nargs='*',
+                        help='the keys to export; '
+                             'all secret keys if unspecified')
+    export.set_defaults(func=gpg_export)
+
+
+def gpg_create(args):
+    if args.export:
+        old_sec_keys = Gpg.signing_keys()
+    Gpg.create(name=args.name, email=args.email,
+               comment=args.comment, expires=args.expires)
+    if args.export:
+        new_sec_keys = set(Gpg.signing_keys())
+        new_keys = new_sec_keys.difference(old_sec_keys)
+        Gpg.export_keys(args.export, *new_keys)
+
+
+def gpg_export(args):
+    keys = args.keys
+    if not keys:
+        keys = Gpg.signing_keys()
+    Gpg.export_keys(args.location, *keys)
+
+
+def gpg_list(args):
+    Gpg.list(args.trusted, args.signing)
+
+
+def gpg_sign(args):
+    key = args.key
+    if key is None:
+        keys = Gpg.signing_keys()
+        if len(keys) == 1:
+            key = keys[0]
+        elif not keys:
+            raise RuntimeError('no signing keys are available')
+        else:
+            raise RuntimeError('multiple signing keys are available; '
+                               'please choose one')
+    output = args.output
+    if not output:
+        output = args.package + '.asc'
+    # TODO: Support the package format Spack creates.
+    Gpg.sign(key, args.package, output, args.clearsign)
+
+
+def gpg_trust(args):
+    Gpg.trust(args.keyfile)
+
+
+def gpg_init(args):
+    for root, _, filenames in os.walk(args.import_dir):
+        for filename in filenames:
+            if not filename.endswith('.key'):
+                continue
+            Gpg.trust(os.path.join(root, filename))
+
+
+def gpg_untrust(args):
+    Gpg.untrust(args.signing, *args.keys)
+
+
+def gpg_verify(args):
+    # TODO: Support the package format Spack creates.
+    signature = args.signature
+    if signature is None:
+        signature = args.package + '.asc'
+    Gpg.verify(signature, args.package)
+
+
+def gpg(parser, args):
+    if args.func:
+        args.func(args)

lib/spack/spack/cmd/info.py

@@ -25,7 +25,7 @@
 from __future__ import print_function
 
 import textwrap
-import itertools
+from six.moves import zip_longest
 from llnl.util.tty.colify import *
 import spack
 import spack.fetch_strategy as fs
@@ -119,7 +119,7 @@ def lines(self):
                     v.description,
                     width=self.column_widths[2]
                 )
-                for t in itertools.izip_longest(
+                for t in zip_longest(
                         name, allowed, description, fillvalue=''
                 ):
                     yield "    " + self.fmt % t

lib/spack/spack/test/cmd/gpg.py

@@ -0,0 +1,181 @@
+##############################################################################
+# 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 argparse
+import os.path
+
+import pytest
+import spack
+import spack.cmd.gpg as gpg
+import spack.util.gpg as gpg_util
+from spack.util.executable import ProcessError
+
+
+@pytest.fixture(scope='function')
+def testing_gpg_directory(tmpdir):
+    old_gpg_path = gpg_util.GNUPGHOME
+    gpg_util.GNUPGHOME = str(tmpdir.join('gpg'))
+    yield
+    gpg_util.GNUPGHOME = old_gpg_path
+
+
+def has_gnupg2():
+    try:
+        gpg_util.Gpg.gpg()('--version')
+        return True
+    except Exception:
+        return False
+
+
+@pytest.mark.usefixtures('testing_gpg_directory')
+@pytest.mark.skipif(not has_gnupg2(),
+                    reason='These tests require gnupg2')
+def test_gpg(tmpdir):
+    parser = argparse.ArgumentParser()
+    gpg.setup_parser(parser)
+
+    # Verify a file with an empty keyring.
+    args = parser.parse_args(['verify', os.path.join(
+        spack.mock_gpg_data_path, 'content.txt')])
+    with pytest.raises(ProcessError):
+        gpg.gpg(parser, args)
+
+    # Import the default key.
+    args = parser.parse_args(['init'])
+    args.import_dir = spack.mock_gpg_keys_path
+    gpg.gpg(parser, args)
+
+    # List the keys.
+    # TODO: Test the output here.
+    args = parser.parse_args(['list', '--trusted'])
+    gpg.gpg(parser, args)
+    args = parser.parse_args(['list', '--signing'])
+    gpg.gpg(parser, args)
+
+    # Verify the file now that the key has been trusted.
+    args = parser.parse_args(['verify', os.path.join(
+        spack.mock_gpg_data_path, 'content.txt')])
+    gpg.gpg(parser, args)
+
+    # Untrust the default key.
+    args = parser.parse_args(['untrust', 'Spack testing'])
+    gpg.gpg(parser, args)
+
+    # Now that the key is untrusted, verification should fail.
+    args = parser.parse_args(['verify', os.path.join(
+        spack.mock_gpg_data_path, 'content.txt')])
+    with pytest.raises(ProcessError):
+        gpg.gpg(parser, args)
+
+    # Create a file to test signing.
+    test_path = tmpdir.join('to-sign.txt')
+    with open(str(test_path), 'w+') as fout:
+        fout.write('Test content for signing.\n')
+
+    # Signing without a private key should fail.
+    args = parser.parse_args(['sign', str(test_path)])
+    with pytest.raises(RuntimeError) as exc_info:
+        gpg.gpg(parser, args)
+    assert exc_info.value.args[0] == 'no signing keys are available'
+
+    # Create a key for use in the tests.
+    keypath = tmpdir.join('testing-1.key')
+    args = parser.parse_args(['create',
+                              '--comment', 'Spack testing key',
+                              '--export', str(keypath),
+                              'Spack testing 1',
+                              'spack@googlegroups.com'])
+    gpg.gpg(parser, args)
+    keyfp = gpg_util.Gpg.signing_keys()[0]
+
+    # List the keys.
+    # TODO: Test the output here.
+    args = parser.parse_args(['list', '--trusted'])
+    gpg.gpg(parser, args)
+    args = parser.parse_args(['list', '--signing'])
+    gpg.gpg(parser, args)
+
+    # Signing with the default (only) key.
+    args = parser.parse_args(['sign', str(test_path)])
+    gpg.gpg(parser, args)
+
+    # Verify the file we just verified.
+    args = parser.parse_args(['verify', str(test_path)])
+    gpg.gpg(parser, args)
+
+    # Export the key for future use.
+    export_path = tmpdir.join('export.testing.key')
+    args = parser.parse_args(['export', str(export_path)])
+    gpg.gpg(parser, args)
+
+    # Create a second key for use in the tests.
+    args = parser.parse_args(['create',
+                              '--comment', 'Spack testing key',
+                              'Spack testing 2',
+                              'spack@googlegroups.com'])
+    gpg.gpg(parser, args)
+
+    # List the keys.
+    # TODO: Test the output here.
+    args = parser.parse_args(['list', '--trusted'])
+    gpg.gpg(parser, args)
+    args = parser.parse_args(['list', '--signing'])
+    gpg.gpg(parser, args)
+
+    test_path = tmpdir.join('to-sign-2.txt')
+    with open(str(test_path), 'w+') as fout:
+        fout.write('Test content for signing.\n')
+
+    # Signing with multiple signing keys is ambiguous.
+    args = parser.parse_args(['sign', str(test_path)])
+    with pytest.raises(RuntimeError) as exc_info:
+        gpg.gpg(parser, args)
+    assert exc_info.value.args[0] == \
+        'multiple signing keys are available; please choose one'
+
+    # Signing with a specified key.
+    args = parser.parse_args(['sign', '--key', keyfp, str(test_path)])
+    gpg.gpg(parser, args)
+
+    # Untrusting signing keys needs a flag.
+    args = parser.parse_args(['untrust', 'Spack testing 1'])
+    with pytest.raises(ProcessError):
+        gpg.gpg(parser, args)
+
+    # Untrust the key we created.
+    args = parser.parse_args(['untrust', '--signing', keyfp])
+    gpg.gpg(parser, args)
+
+    # Verification should now fail.
+    args = parser.parse_args(['verify', str(test_path)])
+    with pytest.raises(ProcessError):
+        gpg.gpg(parser, args)
+
+    # Trust the exported key.
+    args = parser.parse_args(['trust', str(export_path)])
+    gpg.gpg(parser, args)
+
+    # Verification should now succeed again.
+    args = parser.parse_args(['verify', str(test_path)])
+    gpg.gpg(parser, args)

lib/spack/spack/util/gpg.py

@@ -0,0 +1,120 @@
+##############################################################################
+# 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 spack
+from spack.util.executable import Executable
+
+
+GNUPGHOME = spack.gpg_path
+
+
+class Gpg(object):
+    @staticmethod
+    def gpg():
+        # TODO: Support loading up a GPG environment from a built gpg.
+        gpg = Executable('gpg2')
+        if not os.path.exists(GNUPGHOME):
+            os.makedirs(GNUPGHOME)
+            os.chmod(GNUPGHOME, 0o700)
+        gpg.add_default_env('GNUPGHOME', GNUPGHOME)
+        return gpg
+
+    @classmethod
+    def create(cls, **kwargs):
+        r, w = os.pipe()
+        r = os.fdopen(r, 'r')
+        w = os.fdopen(w, 'w')
+        w.write('''
+        Key-Type: rsa
+        Key-Length: 4096
+        Key-Usage: sign
+        Name-Real: %(name)s
+        Name-Email: %(email)s
+        Name-Comment: %(comment)s
+        Expire-Date: %(expires)s
+        %%no-protection
+        %%commit
+        ''' % kwargs)
+        w.close()
+        cls.gpg()('--gen-key', '--batch', input=r)
+        r.close()
+
+    @classmethod
+    def signing_keys(cls):
+        keys = []
+        output = cls.gpg()('--list-secret-keys', '--with-colons',
+                           '--fingerprint', output=str)
+        for line in output.split('\n'):
+            if line.startswith('fpr'):
+                keys.append(line.split(':')[9])
+        return keys
+
+    @classmethod
+    def export_keys(cls, location, *keys):
+        cls.gpg()('--armor', '--export', '--output', location, *keys)
+
+    @classmethod
+    def trust(cls, keyfile):
+        cls.gpg()('--import', keyfile)
+
+    @classmethod
+    def untrust(cls, signing, *keys):
+        args = [
+            '--yes',
+            '--batch',
+        ]
+        if signing:
+            signing_args = args + ['--delete-secret-keys'] + list(keys)
+            cls.gpg()(*signing_args)
+        args.append('--delete-keys')
+        args.extend(keys)
+        cls.gpg()(*args)
+
+    @classmethod
+    def sign(cls, key, file, output, clearsign=False):
+        args = [
+            '--armor',
+            '--default-key', key,
+            '--output', output,
+            file,
+        ]
+        if clearsign:
+            args.insert(0, '--clearsign')
+        else:
+            args.insert(0, '--detach-sign')
+        cls.gpg()(*args)
+
+    @classmethod
+    def verify(cls, signature, file):
+        cls.gpg()('--verify', signature, file)
+
+    @classmethod
+    def list(cls, trusted, signing):
+        if trusted:
+            cls.gpg()('--list-public-keys')
+        if signing:
+            cls.gpg()('--list-secret-keys')

lib/spack/spack/util/naming.py

@@ -57,7 +57,7 @@ def mod_to_class(mod_name):
           * Class names use the CapWords convention.
 
        Regular source code follows these convetions.  Spack is a bit
-       more liberal with its Package names nad Compiler names:
+       more liberal with its Package names and Compiler names:
 
           * They can contain '-' as well as '_', but cannot start with '-'.
           * They can start with numbers, e.g. "3proxy".

var/spack/gpg.mock/README.md

@@ -0,0 +1,3 @@
+# Mock GPG directory
+
+This directory contains keys and data used in the testing Spack.

var/spack/gpg.mock/data/content.txt

@@ -0,0 +1 @@
+This file has a signature signed by an external key.

var/spack/gpg.mock/data/content.txt.asc

@@ -0,0 +1,17 @@
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2
+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+=kwo9
+-----END PGP SIGNATURE-----

var/spack/gpg.mock/keys/external.key

@@ -0,0 +1,30 @@
+-----BEGIN PGP PUBLIC KEY BLOCK-----
+Version: GnuPG v2
+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+=yVqw
+-----END PGP PUBLIC KEY BLOCK-----

var/spack/gpg/README.md

@@ -0,0 +1,5 @@
+# GPG Keys
+
+This directory contains keys that should be trusted by this installation of
+Spack.  They are imported when running `spack gpg init`, but may also be
+imported manually with `spack gpg trust path/to/key`.

var/spack/repos/builtin/packages/arpack-ng/package.py

@@ -56,6 +56,7 @@ class ArpackNg(Package):
     homepage = 'https://github.com/opencollab/arpack-ng'
     url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz'
 
+    version('3.5.0', '9762c9ae6d739a9e040f8201b1578874')
     version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4')
     version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5')
 

var/spack/repos/builtin/packages/bamutil/libstatgen-issue-9.patch

@@ -0,0 +1,11 @@
+--- a/libStatGen/general/PedigreeLoader.cpp	2017-05-29 11:08:07.627528417 -0700
++++ b/libStatGen/general/PedigreeLoader.cpp	2017-05-29 11:08:36.247547411 -0700
+@@ -636,7 +636,7 @@
+             return 2;
+         default :
+         {
+-            bool result = atoi(code);
++            int result = atoi(code);
+ 
+             if (result != 0 && result != 1 && result != 2)
+             {

var/spack/repos/builtin/packages/bamutil/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 Bamutil(MakefilePackage):
+    """bamUtil is a repository that contains several programs
+       that perform operations on SAM/BAM files. All of these programs
+       are built into a single executable, bam.
+    """
+
+    homepage = "http://genome.sph.umich.edu/wiki/BamUtil"
+    url      = "http://genome.sph.umich.edu/w/images/7/70/BamUtilLibStatGen.1.0.13.tgz"
+
+    version('1.0.13', '08b7d0bb1d60be104a11f0e54ddf4a79')
+
+    # Looks like this will be fixed in 1.0.14.
+    # https://github.com/statgen/libStatGen/issues/9
+    patch('libstatgen-issue-9.patch', when='@1.0.13:')
+
+    @property
+    def install_targets(self):
+        return ['install', 'INSTALLDIR={0}'.format(self.prefix.bin)]

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

@@ -31,7 +31,8 @@ class Bwa(Package):
     homepage = "http://github.com/lh3/bwa"
     url      = "https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2"
 
-    version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554')
+    version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554',
+            url="https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2")
     version('0.7.12', 'e24a587baaad411d5da89516ad7a261a',
             url='https://github.com/lh3/bwa/archive/0.7.12.tar.gz')
 

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

@@ -34,6 +34,7 @@ class Fastqc(Package):
     url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
 
     version('0.11.5', '3524f101c0ab0bae77c7595983170a76')
+    version('0.11.4', '104ff2e0e9aebf5bee1f6b068a059b0d')
 
     depends_on('jdk', type='run')
     depends_on('perl')          # for fastqc "script", any perl will do

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

@@ -36,7 +36,7 @@ class Hypre(Package):
     url      = "http://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz"
 
     version('develop', git='https://github.com/LLNL/hypre', tag='master')
-    version('xsdk-0.2.0', git='https://github.com/LLNL/hypre', tag='xsdk-0.2.0')        
+    version('xsdk-0.2.0', git='https://github.com/LLNL/hypre', tag='xsdk-0.2.0')
     version('2.11.2', 'd507943a1a3ce5681c3308e2f3a6dd34')
     version('2.11.1', '3f02ef8fd679239a6723f60b7f796519')
     version('2.10.1', 'dc048c4cabb3cd549af72591474ad674')

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

@@ -54,6 +54,10 @@ class Jdk(Package):
     version('8u66', '88f31f3d642c3287134297b8c10e61bf',
             url="http://download.oracle.com/otn-pub/java/jdk/8u66-b17/jdk-8u66-linux-x64.tar.gz",
             curl_options=curl_options)
+    # The 7u80 tarball is not readily available from Oracle.  If you have
+    # the tarball, add it to your mirror as mirror/jdk/jdk-7u80.tar.gz and
+    # away you go.
+    version('7u80', '6152f8a7561acf795ca4701daa10a965')
 
     def install(self, spec, prefix):
         distutils.dir_util.copy_tree(".", prefix)

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

@@ -28,10 +28,10 @@
 class Libaio(Package):
     """This is the linux native Asynchronous I/O interface library."""
 
-    homepage = "https://git.fedorahosted.org/cgit/libaio.git"
+    homepage = "http://lse.sourceforge.net/io/aio.html"
-    url      = "https://git.fedorahosted.org/cgit/libaio.git/snapshot/libaio-0.3.110-1.tar.gz"
+    url      = "https://ftp.de.debian.org/debian/pool/main/liba/libaio/libaio_0.3.110.orig.tar.gz"
 
-    version('0.3.110-1', 'eb6b1b435afadb5b80c5dd80984249f6')
+    version('0.3.110', '2a35602e43778383e2f4907a4ca39ab8')
 
     def install(self, spec, prefix):
         # libaio is not supported on OS X

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

@@ -34,6 +34,7 @@ class Libdrm(Package):
     homepage = "http://dri.freedesktop.org/libdrm/"
     url      = "http://dri.freedesktop.org/libdrm/libdrm-2.4.59.tar.gz"
 
+    version('2.4.75', '743c16109d91a2539dfc9cc56130d695')
     version('2.4.70', 'a8c275bce5f3d71a5ca25e8fb60df084')
     version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
     version('2.4.33', '86e4e3debe7087d5404461e0032231c8')

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

@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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 *
+import os
+
+
+class Libharu(AutotoolsPackage):
+    """libharu - free PDF library.
+
+    Haru is a free, cross platform, open-sourced software library for
+    generating PDF."""
+
+    homepage = "http://libharu.org"
+    url      = "https://github.com/libharu/libharu/archive/RELEASE_2_3_0.tar.gz"
+
+    version('2.3.0', '4f916aa49c3069b3a10850013c507460')
+    version('2.2.0', 'b65a6fc33a0bdad89bec6b7def101f01')
+    version('master', branch='master',
+            git='https://github.com/libharu/libharu.git')
+
+    def autoreconf(self, spec, prefix):
+        """execute their autotools wrapper script"""
+        if os.path.exists('./buildconf.sh'):
+            bash = which('bash')
+            bash('./buildconf.sh', '--force')
+
+    def url_for_version(self, version):
+        url = 'https://github.com/libharu/libharu/archive/RELEASE_{0}.tar.gz'
+        return url.format(version.underscored)

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

@@ -50,6 +50,10 @@ class Mfem(Package):
     # If this quick verification procedure fails, additional discussion
     # will be required to verify the new version.
 
+    version('3.3',
+            'b17bd452593aada93dc0fee748fcfbbf4f04ce3e7d77fdd0341cc9103bcacd0b',
+            url='http://goo.gl/Vrpsns', extension='.tar.gz')
+
     version('3.2',
             '2938c3deed4ec4f7fd5b5f5cfe656845282e86e2dcd477d292390058b7b94340',
             url='http://goo.gl/Y9T75B', extension='.tar.gz')
@@ -173,9 +177,7 @@ def install(self, spec, prefix):
             ss_lib += (' -lumfpack -lcholmod -lcolamd' +
                        ' -lamd -lcamd -lccolamd -lsuitesparseconfig')
 
-            no_librt_archs = ['darwin-i686', 'darwin-x86_64']
+            no_rt = spec.satisfies('platform=darwin')
-            no_rt = any(map(lambda a: spec.satisfies('=' + a),
-                            no_librt_archs))
             if not no_rt:
                 ss_lib += ' -lrt'
             ss_lib += (' ' + metis_lib + ' ' + lapack_lib)

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

@@ -39,6 +39,14 @@ class Mummer(Package):
     patch('Makefile.patch')
     patch('scripts-Makefile.patch')
 
+    def patch(self):
+        """Fix mummerplot's use of defined on hashes (deprecated
+           since perl@5.10, made illegal in perl@5.20."""
+
+        kwargs = {'string': True}
+        filter_file('defined (%', '(%', 'scripts/mummerplot.pl',
+                    **kwargs)
+
     def install(self, spec, prefix):
         if self.run_tests:
             make('check')

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

@@ -178,8 +178,8 @@ def write_makefile_inc(self):
 
         # TODO: change the value to the correct one according to the
         # compiler possible values are -DAdd_, -DAdd__ and/or -DUPPER
-        if self.compiler.name == 'intel':
+        if self.compiler.name == 'intel' or self.compiler.name == 'pgi':
-            # Intel Fortran compiler provides the main() function so
+            # Intel & PGI Fortran compiler provides the main() function so
             # C examples linked with the Fortran compiler require a
             # hack defined by _DMAIN_COMP (see examples/c_example.c)
             makefile_conf.append("CDEFS   = -DAdd_ -DMAIN_COMP")

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

@@ -30,8 +30,9 @@ class Nco(AutotoolsPackage):
     netCDF-accessible formats"""
 
     homepage = "http://nco.sourceforge.net/"
-    url      = "https://github.com/nco/nco/archive/4.6.6.tar.gz"
+    url      = "https://github.com/nco/nco/archive/4.6.7.tar.gz"
 
+    version('4.6.7', 'b04c92aa715d3fad3ebebd1fd178ce32')
     version('4.6.6', 'df6fa47aaf6e41adfc0631912a7a341f')
     version('4.6.5', '2afd34a6bb5ff6c7ed39cf40c917b6e4')
     version('4.6.4', '22f4e779d0011a9c0db90fda416c8e45')

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

@@ -34,6 +34,7 @@ class Oce(Package):
     homepage = "https://github.com/tpaviot/oce"
     url      = "https://github.com/tpaviot/oce/archive/OCE-0.18.tar.gz"
 
+    version('0.18.1', '2a7597f4243ee1f03245aeeb02d00956')
     version('0.18',   '226e45e77c16a4a6e127c71fefcd171410703960ae75c7ecc7eb68895446a993')
     version('0.17.2', 'bf2226be4cd192606af677cf178088e5')
     version('0.17.1', '36c67b87093c675698b483454258af91')
@@ -59,7 +60,7 @@ class Oce(Package):
     # reported 27 Sep 2016 https://github.com/tpaviot/oce/issues/643
     if (platform.system() == "Darwin") and (
        '.'.join(platform.mac_ver()[0].split('.')[:2]) == '10.12'):
-        patch('sierra.patch', when='@0.17.2:0.18')
+        patch('sierra.patch', when='@0.17.2:0.18.0')
 
     def install(self, spec, prefix):
         options = []

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

@@ -66,26 +66,96 @@ class Openmpi(AutotoolsPackage):
     homepage = "http://www.open-mpi.org"
     url = "https://www.open-mpi.org/software/ompi/v2.1/downloads/openmpi-2.1.1.tar.bz2"
     list_url = "http://www.open-mpi.org/software/ompi/"
-    list_depth = 2
 
-    version('2.1.1', 'ae542f5cf013943ffbbeb93df883731b')
+    # Current
-    version('2.1.0', '4838a5973115c44e14442c01d3f21d52')
+    version('2.1.1', 'ae542f5cf013943ffbbeb93df883731b')  # libmpi.so.20.10.1
-    version('2.0.2', 'ecd99aa436a1ca69ce936a96d6a3fa48')
+    version('2.1.0', '4838a5973115c44e14442c01d3f21d52')  # libmpi.so.20.10.0
-    version('2.0.1', '6f78155bd7203039d2448390f3b51c96')
+
-    version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674')
+    # Still supported
-    version('1.10.6', '2e65008c1867b1f47c32f9f814d41706')
+    version('2.0.2', 'ecd99aa436a1ca69ce936a96d6a3fa48')  # libmpi.so.20.0.2
-    version('1.10.5', 'd32ba9530a869d9c1eae930882ea1834')
+    version('2.0.1', '6f78155bd7203039d2448390f3b51c96')  # libmpi.so.20.0.1
-    version('1.10.4', '9d2375835c5bc5c184ecdeb76c7c78ac')
+    version('2.0.0', 'cdacc800cb4ce690c1f1273cb6366674')  # libmpi.so.20.0.0
-    version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b')
+
-    version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c')
+    version('1.10.7', 'c87c613f9acb1a4eee21fa1ac8042579')  # libmpi.so.12.0.7
-    version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e')
+    version('1.10.6', '2e65008c1867b1f47c32f9f814d41706')  # libmpi.so.12.0.6
-    version('1.10.0', '280cf952de68369cebaca886c5ce0304')
+    version('1.10.5', 'd32ba9530a869d9c1eae930882ea1834')  # libmpi.so.12.0.5
-    version('1.8.8', '0dab8e602372da1425e9242ae37faf8c')
+    version('1.10.4', '9d2375835c5bc5c184ecdeb76c7c78ac')  # libmpi.so.12.0.4
-    version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475')
+    version('1.10.3', 'e2fe4513200e2aaa1500b762342c674b')  # libmpi.so.12.0.3
+    version('1.10.2', 'b2f43d9635d2d52826e5ef9feb97fd4c')  # libmpi.so.12.0.2
+    version('1.10.1', 'f0fcd77ed345b7eafb431968124ba16e')  # libmpi.so.12.0.1
+    version('1.10.0', '280cf952de68369cebaca886c5ce0304')  # libmpi.so.12.0.0
+
+    # Retired
+    version('1.8.8', '0dab8e602372da1425e9242ae37faf8c')  # libmpi.so.1.6.3
+    version('1.8.7', '2485ed6fa0fab9bb5b4e7a9f63718630')  # libmpi.so.1.6.2
+    version('1.8.6', 'eb569e7dc97eeaa5b1876cccf114f377')  # libmpi.so.1.6.1
+    version('1.8.5', '93e958914ff0e4d9634d668d2d48c793')  # libmpi.so.1.6.0
+    version('1.8.4', '93b7ea2c4ebae76947f942579608ae4a')  # libmpi.so.1.6.0
+    version('1.8.3', '2067d00853e0c33d498153fc7d268d2b')  # libmpi.so.1.6.0
+    version('1.8.2', '339a9fc199563bacbb359875ce8c9e20')  # libmpi.so.1.5.2
+    version('1.8.1', '0e12c24a28a605f681ff9a19a1aca2f1')  # libmpi.so.1.5.0
+    version('1.8',   '5999cfb177a50c480b5d0bced379aff1')  # libmpi.so.1.5.0
+
+    version('1.7.5', '321ab81147ac69a5bbca72652fb3b468')  # libmpi.so.1.4.0
+    version('1.7.4', '4aea4fb00f8956dd56ccf50e5784e03f')  # libmpi.so.1.3.0
+    version('1.7.3', '7d0779f73c43eb1d098ad037d60649bc')  # libmpi.so.1.2.0
+    version('1.7.2', 'b897b92100bd13b367e651df483421d5')  # libmpi.so.1.1.2
+    version('1.7.1', 'f25b446a9dcbbd6a105a99d926d34441')  # libmpi.so.1.1.1
+    version('1.7',   'c0e3c4b3bfcd8b8bbd027f6f4c164acb')  # libmpi.so.1.1.0
+
+    version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475')  # libmpi.so.1.0.8
+    version('1.6.4', '62119579ab92b2592cd96b6a9d2a8cc3')  # libmpi.so.1.0.7
+    version('1.6.3', 'eedb73155a7a40b0b07718494298fb25')  # libmpi.so.1.0.6
+    version('1.6.2', '219754715a8e40beb468bbc8f0b3251a')  # libmpi.so.1.0.3
+    version('1.6.1', '33d2782c20ff6be79130a703b85da8f0')  # libmpi.so.1.0.3
+    version('1.6',   'dd6f5bd4b3cb14d93bbf530e50e46e60')  # libmpi.so.1.0.3
+
+    # Ancient
+    version('1.5.5', 'f882fd61ff89db856bfd8f0dfa42e1bd')  # libmpi.so.1.0.3
+    version('1.5.4', '51153d794c49ce6d275dba2793ab0c68')  # libmpi.so.1.0.2
+    version('1.5.3', '0eb8ec2aa05c74a4bc7602b01847131e')  # libmpi.so.1.0.1
+    version('1.5.2', 'faaee6a2777bf607d7fa1297c0b3a9ed')  # libmpi.so.1.0.1
+    version('1.5.1', '3f9409f5d3b617c04dea48ba8fbd703a')  # libmpi.so.1.0.0
+    version('1.5',   '86bf5f9ef7337231abbca3350b31f112')  # libmpi.so.1.0.0
+
+    version('1.4.5', '84ddd2772f46d35da79e1db8a274c99d')  # libmpi.so.0.0.4
+    version('1.4.4', 'e58a1ea7b8af62453aaa0ddaee5f26a0')  # libmpi.so.0.0.3
+    version('1.4.3', 'd2ead141c43b915343f5c5a18f3b5016')  # libmpi.so.0.0.2
+    version('1.4.2', '53b26fa2586aedaf73cf40effbfcc2f3')  # libmpi.so.0.0.2
+    version('1.4.1', '28a820c85e02973809df881fdeddd15e')  # libmpi.so.0.0.1
+    version('1.4',   '9786ec0698afed9498ce43dc3978a435')  # libmpi.so.0.0.1
+
+    version('1.3.4', '978c29f3b671856daa0fc67459b73e01')  # libmpi.so.0.0.1
+    version('1.3.3', 'f6cdc9c195daa8571b2e509e952d6755')  # libmpi.so.0.0.0
+    version('1.3.2', '75781dc31255cd841701c065e239d994')  # libmpi.so.0.0.0
+    version('1.3.1', 'd759523b0752139872c534714d641d64')  # libmpi.so.0.0.0
+    version('1.3',   'efbba7d652d1e430d456f65d7a2e339b')  # libmpi.so.0.0.0
+
+    version('1.2.9', '78c2aebbb746610ed12bdedcc2b6ec0e')  # libmpi.so.0.0.0
+    version('1.2.8', '7f2d5af02101c5f01173f4f6de296549')  # libmpi.so.0.0.0
+    version('1.2.7', 'b5ae3059fba71eba4a89a2923da8223f')  # libmpi.so.0.0.0
+    version('1.2.6', 'f126793b68e71f5ec4a192c40675af2d')  # libmpi.so.0.0.0
+    version('1.2.5', 'c6e82aab6cdcd425bf29217e8317d7dc')  # libmpi.so.0.0.0
+    version('1.2.4', '311b38c597f54d8d6b277225ef458666')  # libmpi.so.0.0.0
+    version('1.2.3', 'ae980bb00f9686934a1143701cc041e4')  # libmpi.so.0.0.0
+    version('1.2.2', '7f553317e388c4efe479e908b66f910d')  # libmpi.so.0.0.0
+    version('1.2.1', 'ceaa42891edba2324a94fdd0b87e46ca')  # libmpi.so.0.0.0
+    version('1.2',   '37e8d4edad54a8d8c3127fbef87ebda1')  # libmpi.so.0.0.0
+
+    version('1.1.5', '6aada92896a1830ece6d3ba1e66a17fa')  # libmpi.so.0.0.0
+    version('1.1.4', '28940b182156478fa442397b0c9660e1')  # libmpi.so.0.0.0
+    version('1.1.3', 'bbaa7fe9d556212d877d872544a31569')  # libmpi.so.0.0.0
+    version('1.1.2', '53877ec8bca5f6e505496b6b94b1d850')  # libmpi.so.0.0.0
+    version('1.1.1', '498b9322ae0ad512026a008a30c7e0b5')  # libmpi.so.0.0.0
+    version('1.1',   '821af8bbb7a8e85ec707cb4c3b6bcbf6')  # libmpi.so.0.0.0
+
+    version('1.0.2', 'fd32861d643f9fe539a01d0d5b836f41')  # libmpi.so.0.0.0
+    version('1.0.1', '8abccca5cdddc81a6d9d9e22b3bb6db9')  # libmpi.so.0.0.0
+    version('1.0',   'f5dcb5d3a98f2e5a9c2a0caaef54d806')  # libmpi.so.0.0.0
 
     patch('ad_lustre_rwcontig_open_source.patch', when="@1.6.5")
     patch('llnl-platforms.patch', when="@1.6.5")
-    patch('configure.patch', when="@1.10.0:1.10.1")
+    patch('configure.patch', when="@1.10.1")
     patch('fix_multidef_pmi_class.patch', when="@2.0.0:2.0.1")
 
     variant(
@@ -120,6 +190,10 @@ class Openmpi(AutotoolsPackage):
     depends_on('jdk', when='+java')
     depends_on('sqlite', when='+sqlite3@:1.11')
 
+    conflicts('fabrics=psm2', when='@:1.8')  # PSM2 support was added in 1.10.0
+    conflicts('fabrics=pmi', when='@:1.5.4')  # PMI support was added in 1.5.5
+    conflicts('fabrics=mxm', when='@:1.5.3')  # MXM support was added in 1.5.4
+
     def url_for_version(self, version):
         return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (
             version.up_to(2), version)
@@ -236,7 +310,7 @@ def configure_args(self):
                 config_args.append('--disable-mpi-thread-multiple')
 
         # CUDA support
-        if spec.satisfies('@1.6:'):
+        if spec.satisfies('@1.7:'):
             if '+cuda' in spec:
                 config_args.append('--with-cuda={0}'.format(
                     spec['cuda'].prefix))

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

@@ -70,7 +70,9 @@ def install(self, spec, prefix):
             '-DGKLIB_PATH:PATH=%s/GKlib' % spec['metis'].prefix.include,
             '-DMETIS_PATH:PATH=%s' % spec['metis'].prefix,
             '-DCMAKE_C_COMPILER:STRING=%s' % spec['mpi'].mpicc,
-            '-DCMAKE_CXX_COMPILER:STRING=%s' % spec['mpi'].mpicxx
+            '-DCMAKE_CXX_COMPILER:STRING=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_C_FLAGS:STRING=%s' % (
+                '-c11' if '%pgi' in spec else ''),
         ])
 
         if '+shared' in spec:

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

@@ -31,6 +31,7 @@
 # Date: September 6, 2015
 #
 from spack import *
+import os
 
 
 class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
@@ -160,3 +161,33 @@ def setup_dependent_package(self, module, dependent_spec):
         # if it does not exist already.
         if dependent_spec.package.is_extension:
             mkdirp(module.perl_lib_dir)
+
+    @run_after('install')
+    def filter_config_dot_pm(self):
+        """Run after install so that Config.pm records the compiler that Spack
+        built the package with.  If this isn't done, $Config{cc} will
+        be set to Spack's cc wrapper script.
+        """
+
+        kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
+
+        # Find the actual path to the installed Config.pm file.
+        perl = Executable(join_path(prefix.bin, 'perl'))
+        config_dot_pm = perl('-MModule::Loaded', '-MConfig', '-e',
+                             'print is_loaded(Config)', output=str)
+
+        match = 'cc *=>.*'
+        substitute = "cc => '{cc}',".format(cc=self.compiler.cc)
+        filter_file(match, substitute, config_dot_pm, **kwargs)
+
+        # And the path Config_heavy.pl
+        d = os.path.dirname(config_dot_pm)
+        config_heavy = join_path(d, 'Config_heavy.pl')
+
+        match = '^cc=.*'
+        substitute = "cc='{cc}'".format(cc=self.compiler.cc)
+        filter_file(match, substitute, config_heavy, **kwargs)
+
+        match = '^ld=.*'
+        substitute = "ld='{ld}'".format(ld=self.compiler.cc)
+        filter_file(match, substitute, config_heavy, **kwargs)

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

@@ -40,6 +40,7 @@ class Petsc(Package):
     version('develop', git='https://bitbucket.org/petsc/petsc.git', tag='master')
     version('xsdk-0.2.0', git='https://bitbucket.org/petsc/petsc.git', tag='xsdk-0.2.0')
 
+    version('3.7.6', '977aa84b85aa3146c695592cd0a11057')
     version('3.7.5', 'f00f6e6a3bac39052350dd47194b58a3')
     version('3.7.4', 'aaf94fa54ef83022c14091f10866eedf')
     version('3.7.2', '50da49867ce7a49e7a0c1b37f4ec7b34')

var/spack/repos/builtin/packages/python/cray-rpath-2.3.patch

@@ -0,0 +1,12 @@
+--- a/Lib/distutils/unixccompiler.py	2003-06-02 05:27:40.000000000 +1000
++++ b/Lib/distutils/unixccompiler.py	2017-05-13 13:52:45.554213616 +1000
+@@ -208,7 +208,8 @@
+         elif compiler[:3] == "gcc" or compiler[:3] == "g++":
+           return "-Wl,-R" + dir
+         else:
+-            return "-R" + dir
++            # Patched by spack to use gcc syntax by default:
++            return "-Wl,-R" + dir
+ 
+     def library_option(self, lib):
+         return "-l" + lib

var/spack/repos/builtin/packages/python/cray-rpath-3.1.patch

@@ -0,0 +1,15 @@
+--- a/Lib/distutils/unixccompiler.py	2009-05-09 21:55:12.000000000 +1000
++++ b/Lib/distutils/unixccompiler.py	2017-05-13 14:30:18.077518999 +1000
+@@ -299,10 +299,8 @@
+                 else:
+                     return "-Wl,-R" + dir
+             else:
+-                # No idea how --enable-new-dtags would be passed on to
+-                # ld if this system was using GNU ld.  Don't know if a
+-                # system like this even exists.
+-                return "-R" + dir
++                # Patched by spack to use gcc syntax by default:
++                return "-Wl,-R" + dir
+ 
+     def library_option(self, lib):
+         return "-l" + lib

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

@@ -92,6 +92,10 @@ class Python(AutotoolsPackage):
     # Patch does not work for Python 3.1
     patch('ncurses.patch', when='@:2.8,3.2:')
 
+    # Ensure that distutils chooses correct compiler option for RPATH on cray:
+    patch('cray-rpath-2.3.patch', when="@2.3:3.0.1 platform=cray")
+    patch('cray-rpath-3.1.patch', when="@3.1:3.99  platform=cray")
+
     _DISTUTIL_VARS_TO_SAVE = ['LDSHARED']
     _DISTUTIL_CACHE_FILENAME = 'sysconfig.json'
     _distutil_vars = None

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

@@ -38,18 +38,25 @@ class RRmpi(RPackage):
     depends_on('mpi')
     depends_on('r@2.15.1:')
 
-    def install(self, spec, prefix):
+    # The following MPI types are not supported
-        if 'mpich' in spec:
+    conflicts('^intel-mpi')
-            Rmpi_type = 'MPICH'
+    conflicts('^intel-parallel-studio')
-        elif 'mvapich' in spec:
+    conflicts('^mvapich2')
-            Rmpi_type = 'MVAPICH'
+    conflicts('^spectrum-mpi')
-        else:
+
+    def configure_args(self, spec, prefix):
+        mpi_name = spec['mpi'].name
+
+        # The type of MPI. Supported values are:
+        # OPENMPI, LAM, MPICH, MPICH2, or CRAY
+        if mpi_name == 'openmpi':
             Rmpi_type = 'OPENMPI'
+        elif mpi_name == 'mpich':
+            Rmpi_type = 'MPICH2'
+        else:
+            raise InstallError('Unsupported MPI type')
 
-        my_mpi = spec['mpi']
+        return [
-
+            '--with-Rmpi-type={0}'.format(Rmpi_type),
-        R('CMD', 'INSTALL',
+            '--with-mpi={0}'.format(spec['mpi'].prefix),
-          '--configure-args=--with-Rmpi-type=%s' % Rmpi_type +
+        ]
-          ' --with-mpi=%s' % my_mpi.prefix,
-          '--library={0}'.format(self.module.r_lib_dir),
-          self.stage.source_path)

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

@@ -74,6 +74,8 @@ class R(AutotoolsPackage):
     depends_on('cairo+X', when='+X')
     depends_on('cairo~X', when='~X')
     depends_on('pango')
+    depends_on('pango+X', when='+X')
+    depends_on('pango~X', when='~X')
     depends_on('freetype')
     depends_on('tcl')
     depends_on('tk')

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

@@ -34,6 +34,7 @@ class Slepc(Package):
     homepage = "http://www.grycap.upv.es/slepc"
     url = "http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz"
 
+    version('3.7.4', '2fb782844e3bc265a8d181c3c3e2632a4ca073111c874c654f1365d33ca2eb8a')
     version('3.7.3', '3ef9bcc645a10c1779d56b3500472ceb66df692e389d635087d30e7c46424df9')
     version('3.7.1', '670216f263e3074b21e0623c01bc0f562fdc0bffcd7bd42dd5d8edbe73a532c2')
     version('3.6.3', '384939d009546db37bc05ed81260c8b5ba451093bf891391d32eb7109ccff876')

var/spack/repos/builtin/packages/star/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 Star(Package):
+    """STAR is an ultrafast universal RNA-seq aligner."""
+
+    homepage = "https://github.com/alexdobin/STAR"
+    url      = "https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz"
+
+    version('2.5.3a', 'baf8d1b62a50482cfa13acb7652dc391',
+            url='https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz')
+    version('2.4.2a', '8b9345f2685a5ec30731e0868e86d506',
+            url='https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.tar.gz')
+
+    def install(self, spec, prefix):
+        with working_dir('source'):
+            make('STAR', 'STARlong')
+            mkdirp(prefix.bin)
+            install('STAR', prefix.bin)
+            install('STARlong', prefix.bin)

var/spack/repos/builtin/packages/suite-sparse/package.py

@@ -53,6 +53,9 @@ class SuiteSparse(Package):
 
     patch('tbb_453.patch', when='@4.5.3:+tbb')
 
+    # This patch removes unsupported flags for pgi compiler
+    patch('pgi.patch', when='%pgi')
+
     def install(self, spec, prefix):
         # The build system of SuiteSparse is quite old-fashioned.
         # It's basically a plain Makefile which include an header
@@ -74,7 +77,8 @@ def install(self, spec, prefix):
             'CUDA=no',
             'CUDA_PATH={0}'.format(
                 spec['cuda'].prefix if '+cuda' in spec else ''
-            )
+            ),
+            'CFOPENMP={0}'.format(self.compiler.openmp_flag)
         ])
 
         if '+pic' in spec:

var/spack/repos/builtin/packages/suite-sparse/pgi.patch

@@ -0,0 +1,12 @@
+--- a/SuiteSparse_config/SuiteSparse_config.mk
++++ b/SuiteSparse_config/SuiteSparse_config.mk
+@@ -89,7 +89,8 @@
+ 
+     # The CF macro is used by SuiteSparse Makefiles as a combination of
+     # CFLAGS, CPPFLAGS, TARGET_ARCH, and system-dependent settings.
+-    CF ?= $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) $(OPTIMIZATION) -fexceptions -fPIC
++    #CF ?= $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) $(OPTIMIZATION) -fexceptions -fPIC
++    CF ?= $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) $(OPTIMIZATION) -fPIC
+ 
+     #---------------------------------------------------------------------------
+     # OpenMP is used in CHOLMOD

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

@@ -36,6 +36,8 @@ class Tbb(Package):
 
     # Only version-specific URL's work for TBB
     # can also use https://github.com/01org/tbb/releases/
+    version('2017.6', '5b0909fbb1741724f7a0ce83232f50b166788af0',
+            url='https://github.com/01org/tbb/archive/2017_U6.tar.gz')
     version('2017.5', '26f720729d322913912e99d1e4a36bd10625d3ca',
             url='https://github.com/01org/tbb/archive/2017_U5.tar.gz')
     version('2017.3', '2c451a5bcf6fc31487b98b4b29651c369874277c',

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

@@ -0,0 +1,75 @@
+##############################################################################
+# 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 Vcftools(AutotoolsPackage):
+    """VCFtools is a program package designed for working with VCF files,
+       such as those generated by the 1000 Genomes Project. The aim of
+       VCFtools is to provide easily accessible methods for working
+       with complex genetic variation data in the form of VCF files.
+    """
+
+    homepage = "https://vcftools.github.io/"
+    url      = "https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz"
+
+    # this is "a pre-release"
+    # version('0.1.15', '61045197848dea20a0158d2faf02e5be')
+    version('0.1.14', 'a110662535651caa6cc8c876216a9f77')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('zlib')
+
+    # this needs to be in sync with what setup_environment adds to
+    # PERL5LIB below
+    def configure_args(self):
+        return ['--with-pmdir=lib']
+
+    @run_before('install')
+    def filter_sbang(self):
+        """Run before install so that the standard Spack sbang install hook
+           can fix up the path to the perl binary.
+        """
+
+        with working_dir('src/perl'):
+            match = '^#!/usr/bin/env perl'
+            perl = join_path(self.spec['perl'].prefix.bin, 'perl')
+            substitute = "#!{perl}".format(perl=perl)
+            # tab-to-vcf added in 0.1.15
+            files = ['fill-aa', 'fill-an-ac', 'fill-fs',
+                     'fill-ref-md5', 'tab-to-vcf', 'vcf-annotate',
+                     'vcf-compare', 'vcf-concat', 'vcf-consensus',
+                     'vcf-contrast', 'vcf-convert',
+                     'vcf-fix-newlines', 'vcf-fix-ploidy',
+                     'vcf-indel-stats', 'vcf-isec', 'vcf-merge',
+                     'vcf-phased-join', 'vcf-query',
+                     'vcf-shuffle-cols', 'vcf-sort', 'vcf-stats',
+                     'vcf-subset', 'vcf-to-tab', 'vcf-tstv',
+                     'vcf-validator', ]
+            kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
+            filter_file(match, substitute, *files, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PERL5LIB', join_path(self.prefix, 'lib'))

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

@@ -0,0 +1,95 @@
+##############################################################################
+# Copyright (c) 2013-2017, 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 Wt(CMakePackage):
+    """Wt, C++ Web Toolkit.
+
+    Wt is a C++ library for developing web applications."""
+
+    homepage = "http://www.webtoolkit.eu/wt"
+    url = "https://github.com/emweb/wt/archive/3.3.7.tar.gz"
+
+    version('3.3.7', '09858901f2dcf5c3d36a9237daba3e3f')
+    version('master', branch='master',
+            git='https://github.com/emweb/wt.git')
+
+    # wt builds in parallel, but requires more than 5 GByte RAM per -j <njob>
+    # which most machines do not provide and crash the build
+    parallel = False
+
+    variant('openssl', default=True,
+            description='SSL and WebSockets support in the built-in httpd, '
+                        'the HTTP(S) client, and additional cryptographic '
+                        'hashes in the authentication module')
+    variant('libharu', default=True, description='painting to PDF')
+    # variant('graphicsmagick', default=True,
+    #         description='painting to PNG, GIF')
+    variant('sqlite', default=False, description='create SQLite3 DBO')
+    variant('mariadb', default=False, description='create MariaDB/MySQL DBO')
+    variant('postgresql', default=False, description='create PostgreSQL DBO')
+    # variant('firebird', default=False, description='create Firebird DBO')
+    variant('pango', default=True,
+            description='improved font support in PDF and raster image '
+                        'painting')
+    variant('zlib', default=True,
+            description='compression in the built-in httpd')
+    # variant('fastcgi', default=False,
+    #         description='FastCGI connector via libfcgi++')
+
+    depends_on('boost@1.46.1:')
+    depends_on('openssl', when='+openssl')
+    depends_on('libharu', when='+libharu')
+    depends_on('sqlite', when='+sqlite')
+    depends_on('mariadb', when='+mariadb')
+    depends_on('postgresql', when='+postgresql')
+    depends_on('pango', when='+pango')
+    depends_on('zlib', when='+zlib')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        cmake_args = [
+            '-DBUILD_EXAMPLES:BOOL=OFF',
+            '-DCONNECTOR_FCGI:BOOL=OFF',
+            '-DENABLE_OPENGL:BOOL=OFF',
+            '-DENABLE_QT4:BOOL=OFF'
+        ]
+        cmake_args.extend([
+            '-DENABLE_SSL:BOOL={0}'.format((
+                'ON' if '+openssl' in spec else 'OFF')),
+            '-DENABLE_HARU:BOOL={0}'.format((
+                'ON' if '+libharu' in spec else 'OFF')),
+            '-DENABLE_PANGO:BOOL={0}'.format((
+                'ON' if '+pango' in spec else 'OFF')),
+            '-DENABLE_SQLITE:BOOL={0}'.format((
+                'ON' if '+sqlite' in spec else 'OFF')),
+            '-DENABLE_MYSQL:BOOL={0}'.format((
+                'ON' if '+mariadb' in spec else 'OFF')),
+            '-DENABLE_POSTGRES:BOOL={0}'.format((
+                'ON' if '+postgres' in spec else 'OFF'))
+        ])
+        return cmake_args

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

@@ -31,8 +31,8 @@ class Xmlto(AutotoolsPackage):
     without remembering many long options and searching for the syntax of the
     backends."""
 
-    homepage = "http://cyberelk.net/tim/software/xmlto/"
+    homepage = "https://pagure.io/xmlto"
-    url      = "https://fedorahosted.org/releases/x/m/xmlto/xmlto-0.0.28.tar.gz"
+    url      = "https://releases.pagure.org/xmlto/xmlto-0.0.28.tar.gz"
 
     version('0.0.28', 'a1fefad9d83499a15576768f60f847c6')
 

var/spack/repos/builtin/packages/yaml-cpp/package.py

@@ -32,6 +32,7 @@ class YamlCpp(CMakePackage):
     url      = "https://github.com/jbeder/yaml-cpp/archive/yaml-cpp-0.5.3.tar.gz"
 
     version('0.5.3', '4e47733d98266e46a1a73ae0a72954eb')
+    version('develop', git='https://github.com/jbeder/yaml-cpp', branch='master')
 
     variant('shared', default=True,
             description='Enable build of shared libraries')

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

@@ -41,4 +41,8 @@ class Zeromq(AutotoolsPackage):
     depends_on("libsodium@:1.0.3", when='@:4.1.2')
 
     def configure_args(self):
-        return ['--with-libsodium']
+        config_args = ['--with-libsodium']
+        if 'clang' in self.compiler.cc:
+            config_args.append("CFLAGS=-Wno-gnu")
+            config_args.append("CXXFLAGS=-Wno-gnu")
+        return config_args