3202 files changed, 57801 insertions, 60419 deletions

diff --git a/var/spack/repos/builtin.mock/packages/a/package.py b/var/spack/repos/builtin.mock/packages/a/package.py
index 468e839dec..a9197c94b0 100644
--- a/var/spack/repos/builtin.mock/packages/a/package.py
+++ b/var/spack/repos/builtin.mock/packages/a/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/archive-files/package.py b/var/spack/repos/builtin.mock/packages/archive-files/package.py
new file mode 100644
index 0000000000..5025d70d6b
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/archive-files/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class ArchiveFiles(AutotoolsPackage):
+    """Simple package with one optional dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/a-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+    version('2.0', '2.0_a_hash')
+
+    @property
+    def archive_files(self):
+        return super(ArchiveFiles, self).archive_files + ['../../outside.log']
+
+    def autoreconf(self, spec, prefix):
+        pass
+
+    def configure(self, spec, prefix):
+        pass
+
+    def build(self, spec, prefix):
+        mkdirp(self.build_directory)
+        config_log = join_path(self.build_directory, 'config.log')
+        touch(config_log)
+
+    def install(self, spec, prefix):
+        touch(join_path(prefix, 'deleteme'))
diff --git a/var/spack/repos/builtin.mock/packages/b/package.py b/var/spack/repos/builtin.mock/packages/b/package.py
index b352fa6f80..776240a31c 100644
--- a/var/spack/repos/builtin.mock/packages/b/package.py
+++ b/var/spack/repos/builtin.mock/packages/b/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/boost/package.py b/var/spack/repos/builtin.mock/packages/boost/package.py
index df50e18574..4398d445df 100644
--- a/var/spack/repos/builtin.mock/packages/boost/package.py
+++ b/var/spack/repos/builtin.mock/packages/boost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/build-error/package.py b/var/spack/repos/builtin.mock/packages/build-error/package.py
index e0c1a9ee83..191cfe3b14 100644
--- a/var/spack/repos/builtin.mock/packages/build-error/package.py
+++ b/var/spack/repos/builtin.mock/packages/build-error/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/build-warnings/package.py b/var/spack/repos/builtin.mock/packages/build-warnings/package.py
new file mode 100644
index 0000000000..1ea58a2a1a
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/build-warnings/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class BuildWarnings(Package):
+    """This package's install fails but only emits warnings."""
+
+    homepage = "http://www.example.com/trivial_install"
+    url      = "http://www.unit-test-should-replace-this-url/trivial_install-1.0.tar.gz"
+
+    version('1.0', 'foobarbaz')
+
+    def install(self, spec, prefix):
+        with open('configure', 'w') as f:
+            f.write("""#!/bin/sh\n
+echo 'checking for gcc... /Users/gamblin2/src/spack/lib/spack/env/clang/clang'
+echo 'checking whether the C compiler works... yes'
+echo 'checking for C compiler default output file name... a.out'
+echo 'WARNING: ALL CAPITAL WARNING!'
+echo 'checking for suffix of executables...'
+echo 'foo.c:89: warning: some weird warning!'
+exit 1
+""")
+        configure()
diff --git a/var/spack/repos/builtin.mock/packages/c/package.py b/var/spack/repos/builtin.mock/packages/c/package.py
index 22132dd00d..5687635f7c 100644
--- a/var/spack/repos/builtin.mock/packages/c/package.py
+++ b/var/spack/repos/builtin.mock/packages/c/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/callpath/package.py b/var/spack/repos/builtin.mock/packages/callpath/package.py
index 19438e6277..27214741b7 100644
--- a/var/spack/repos/builtin.mock/packages/callpath/package.py
+++ b/var/spack/repos/builtin.mock/packages/callpath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/canfail/package.py b/var/spack/repos/builtin.mock/packages/canfail/package.py
index b49bb3ce3e..777a9bd023 100644
--- a/var/spack/repos/builtin.mock/packages/canfail/package.py
+++ b/var/spack/repos/builtin.mock/packages/canfail/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/cmake-client/package.py b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
index 2fde961376..4082d77055 100644
--- a/var/spack/repos/builtin.mock/packages/cmake-client/package.py
+++ b/var/spack/repos/builtin.mock/packages/cmake-client/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 from spack import *
diff --git a/var/spack/repos/builtin.mock/packages/cmake/package.py b/var/spack/repos/builtin.mock/packages/cmake/package.py
index 15ad5606b4..a589797d69 100644
--- a/var/spack/repos/builtin.mock/packages/cmake/package.py
+++ b/var/spack/repos/builtin.mock/packages/cmake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin.mock/packages/conflict-parent/package.py b/var/spack/repos/builtin.mock/packages/conflict-parent/package.py
index b8aaf55def..8f27d59ff5 100644
--- a/var/spack/repos/builtin.mock/packages/conflict-parent/package.py
+++ b/var/spack/repos/builtin.mock/packages/conflict-parent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/conflict/package.py b/var/spack/repos/builtin.mock/packages/conflict/package.py
index 26f09d77ee..08d8c5df4b 100644
--- a/var/spack/repos/builtin.mock/packages/conflict/package.py
+++ b/var/spack/repos/builtin.mock/packages/conflict/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py b/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py
index 620d398d35..efa8ae9596 100644
--- a/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py
+++ b/var/spack/repos/builtin.mock/packages/conflicting-dependent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dependency-install/package.py b/var/spack/repos/builtin.mock/packages/dependency-install/package.py
index eeaf2ada11..2e40b8dc8d 100644
--- a/var/spack/repos/builtin.mock/packages/dependency-install/package.py
+++ b/var/spack/repos/builtin.mock/packages/dependency-install/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dependent-install/package.py b/var/spack/repos/builtin.mock/packages/dependent-install/package.py
index 9bcc73d056..01a955d744 100644
--- a/var/spack/repos/builtin.mock/packages/dependent-install/package.py
+++ b/var/spack/repos/builtin.mock/packages/dependent-install/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/develop-test/package.py b/var/spack/repos/builtin.mock/packages/develop-test/package.py
index c546f701fd..7a28cc25be 100644
--- a/var/spack/repos/builtin.mock/packages/develop-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/develop-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/direct-mpich/package.py b/var/spack/repos/builtin.mock/packages/direct-mpich/package.py
index 737570ffe8..44bd7d16b1 100644
--- a/var/spack/repos/builtin.mock/packages/direct-mpich/package.py
+++ b/var/spack/repos/builtin.mock/packages/direct-mpich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py
index 7f55beb542..1c6b8d624d 100644
--- a/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py
+++ b/var/spack/repos/builtin.mock/packages/dt-diamond-bottom/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py
index 262008079c..f54086e8b3 100644
--- a/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py
+++ b/var/spack/repos/builtin.mock/packages/dt-diamond-left/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py
index cc0db5bff1..2a915a1f10 100644
--- a/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py
+++ b/var/spack/repos/builtin.mock/packages/dt-diamond-right/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dt-diamond/package.py b/var/spack/repos/builtin.mock/packages/dt-diamond/package.py
index c3b0b9db57..a4dcdfd04b 100644
--- a/var/spack/repos/builtin.mock/packages/dt-diamond/package.py
+++ b/var/spack/repos/builtin.mock/packages/dt-diamond/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtbuild1/package.py b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py
index bc00d4ed03..dfc71d5f89 100644
--- a/var/spack/repos/builtin.mock/packages/dtbuild1/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtbuild1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtbuild2/package.py b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py
index 1a3eb57835..b91aa8bba3 100644
--- a/var/spack/repos/builtin.mock/packages/dtbuild2/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtbuild2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtbuild3/package.py b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py
index a03a04a523..8102ca80f0 100644
--- a/var/spack/repos/builtin.mock/packages/dtbuild3/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtbuild3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink1/package.py b/var/spack/repos/builtin.mock/packages/dtlink1/package.py
index 9c7e4bdebf..05885a00e0 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink1/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink2/package.py b/var/spack/repos/builtin.mock/packages/dtlink2/package.py
index 1a78a4879c..06bcb7bda7 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink2/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink3/package.py b/var/spack/repos/builtin.mock/packages/dtlink3/package.py
index 8c53f3e2a0..58a9e9f995 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink3/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink4/package.py b/var/spack/repos/builtin.mock/packages/dtlink4/package.py
index 4d7a57b2da..10fbf0b033 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink4/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtlink5/package.py b/var/spack/repos/builtin.mock/packages/dtlink5/package.py
index 914e7655fb..a573555274 100644
--- a/var/spack/repos/builtin.mock/packages/dtlink5/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtlink5/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtrun1/package.py b/var/spack/repos/builtin.mock/packages/dtrun1/package.py
index 738540ea52..865d8ee633 100644
--- a/var/spack/repos/builtin.mock/packages/dtrun1/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtrun1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtrun2/package.py b/var/spack/repos/builtin.mock/packages/dtrun2/package.py
index 84129c1732..6e207ba5ae 100644
--- a/var/spack/repos/builtin.mock/packages/dtrun2/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtrun2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtrun3/package.py b/var/spack/repos/builtin.mock/packages/dtrun3/package.py
index ee0c4272e4..3d834c2749 100644
--- a/var/spack/repos/builtin.mock/packages/dtrun3/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtrun3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dttop/package.py b/var/spack/repos/builtin.mock/packages/dttop/package.py
index 9bb83fff89..b68c3e1cd4 100644
--- a/var/spack/repos/builtin.mock/packages/dttop/package.py
+++ b/var/spack/repos/builtin.mock/packages/dttop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dtuse/package.py b/var/spack/repos/builtin.mock/packages/dtuse/package.py
index 3f8b0c9e98..c87d9e145d 100644
--- a/var/spack/repos/builtin.mock/packages/dtuse/package.py
+++ b/var/spack/repos/builtin.mock/packages/dtuse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/dyninst/package.py b/var/spack/repos/builtin.mock/packages/dyninst/package.py
index d00f604d61..f6fdc5a432 100644
--- a/var/spack/repos/builtin.mock/packages/dyninst/package.py
+++ b/var/spack/repos/builtin.mock/packages/dyninst/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/e/package.py b/var/spack/repos/builtin.mock/packages/e/package.py
index a00d459e9f..12fc145e17 100644
--- a/var/spack/repos/builtin.mock/packages/e/package.py
+++ b/var/spack/repos/builtin.mock/packages/e/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/extendee/package.py b/var/spack/repos/builtin.mock/packages/extendee/package.py
index cae5f93bf3..ead0d8c9ec 100644
--- a/var/spack/repos/builtin.mock/packages/extendee/package.py
+++ b/var/spack/repos/builtin.mock/packages/extendee/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/extension1/package.py b/var/spack/repos/builtin.mock/packages/extension1/package.py
index f4999e9963..abb526459e 100644
--- a/var/spack/repos/builtin.mock/packages/extension1/package.py
+++ b/var/spack/repos/builtin.mock/packages/extension1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin.mock/packages/extension2/package.py b/var/spack/repos/builtin.mock/packages/extension2/package.py
index 01f3f94636..0d4ce8b374 100644
--- a/var/spack/repos/builtin.mock/packages/extension2/package.py
+++ b/var/spack/repos/builtin.mock/packages/extension2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin.mock/packages/externalmodule/package.py b/var/spack/repos/builtin.mock/packages/externalmodule/package.py
index 5e9f8fda44..84b152a93b 100644
--- a/var/spack/repos/builtin.mock/packages/externalmodule/package.py
+++ b/var/spack/repos/builtin.mock/packages/externalmodule/package.py
@@ -1,28 +1,8 @@
-
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/externalprereq/package.py b/var/spack/repos/builtin.mock/packages/externalprereq/package.py
index 1890ab72d8..b14045afd2 100644
--- a/var/spack/repos/builtin.mock/packages/externalprereq/package.py
+++ b/var/spack/repos/builtin.mock/packages/externalprereq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/externaltest/package.py b/var/spack/repos/builtin.mock/packages/externaltest/package.py
index 00cc553cbe..69484f5d54 100644
--- a/var/spack/repos/builtin.mock/packages/externaltest/package.py
+++ b/var/spack/repos/builtin.mock/packages/externaltest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/externaltool/package.py b/var/spack/repos/builtin.mock/packages/externaltool/package.py
index c47c31ac66..6e8cb30f09 100644
--- a/var/spack/repos/builtin.mock/packages/externaltool/package.py
+++ b/var/spack/repos/builtin.mock/packages/externaltool/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Externaltool(Package):
     url      = "http://somewhere.com/tool-1.0.tar.gz"
 
     version('1.0', '1234567890abcdef1234567890abcdef')
+    version('0.9', '1234567890abcdef1234567890abcdef')
 
     depends_on('externalprereq')
 
diff --git a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py
index d0b814d83b..a23743ca66 100644
--- a/var/spack/repos/builtin.mock/packages/externalvirtual/package.py
+++ b/var/spack/repos/builtin.mock/packages/externalvirtual/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/failing-build/package.py b/var/spack/repos/builtin.mock/packages/failing-build/package.py
index e61451253a..f332b86323 100644
--- a/var/spack/repos/builtin.mock/packages/failing-build/package.py
+++ b/var/spack/repos/builtin.mock/packages/failing-build/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/fake/package.py b/var/spack/repos/builtin.mock/packages/fake/package.py
index 6b264a4d55..6d6e133cb5 100644
--- a/var/spack/repos/builtin.mock/packages/fake/package.py
+++ b/var/spack/repos/builtin.mock/packages/fake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/flake8/package.py b/var/spack/repos/builtin.mock/packages/flake8/package.py
index 4f2e9bd475..a38ede73f9 100644
--- a/var/spack/repos/builtin.mock/packages/flake8/package.py
+++ b/var/spack/repos/builtin.mock/packages/flake8/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py
new file mode 100644
index 0000000000..9864269a21
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/git-svn-top-level/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitSvnTopLevel(Package):
+    """Mock package that uses git for fetching."""
+    homepage = "http://www.git-fetch-example.com"
+
+    # can't have two VCS fetchers.
+    git = 'https://example.com/some/git/repo'
+    svn = 'https://example.com/some/svn/repo'
+
+    version('2.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/git-test/package.py b/var/spack/repos/builtin.mock/packages/git-test/package.py
index 9378f72195..544168d53b 100644
--- a/var/spack/repos/builtin.mock/packages/git-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/git-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/git-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-top-level/package.py
new file mode 100644
index 0000000000..36a2852f32
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/git-top-level/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitTopLevel(Package):
+    """Mock package that uses git for fetching."""
+    homepage = "http://www.git-fetch-example.com"
+
+    git = 'https://example.com/some/git/repo'
+    version('1.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py
new file mode 100644
index 0000000000..c737284fff
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/git-url-svn-top-level/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitUrlSvnTopLevel(Package):
+    """Mock package that uses git for fetching."""
+    homepage = "http://www.git-fetch-example.com"
+
+    # can't have two VCS fetchers.
+    url = 'https://example.com/some/tarball-1.0.tar.gz'
+    git = 'https://example.com/some/git/repo'
+    svn = 'https://example.com/some/svn/repo'
+
+    version('2.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py b/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py
new file mode 100644
index 0000000000..8b41eda0eb
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/git-url-top-level/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitUrlTopLevel(Package):
+    """Mock package that top-level git and url attributes.
+
+    This demonstrates how Spack infers fetch mechanisms from parameters
+    to the ``version`` directive.
+
+    """
+    homepage = "http://www.git-fetch-example.com"
+
+    git = 'https://example.com/some/git/repo'
+    url = 'https://example.com/some/tarball-1.0.tar.gz'
+
+    # These resolve to git fetchers
+    version('develop', branch='develop')
+    version('submodules', submodules=True)
+    version('3.4', commit='abc34')
+    version('3.3', branch='releases/v3.3', commit='abc33')
+    version('3.2', branch='releases/v3.2')
+    version('3.1', tag='v3.1', commit='abc31')
+    version('3.0', tag='v3.0')
+
+    # These resolve to URL fetchers
+    version('2.3', 'abc23', url='https://www.example.com/foo2.3.tar.gz')
+    version('2.2', sha256='abc22', url='https://www.example.com/foo2.2.tar.gz')
+    version('2.1', sha256='abc21')
+    version('2.0', 'abc20')
+
+    # These result in a FetcherConflict b/c we can't tell what to use
+    version('1.3', sha256='abc13', commit='abc13')
+    version('1.2', sha512='abc12', branch='releases/v1.2')
+    version('1.1', md5='abc11', tag='v1.1')
+    version('1.0', 'abc11', tag='abc123')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/hash-test1/package.py b/var/spack/repos/builtin.mock/packages/hash-test1/package.py
new file mode 100644
index 0000000000..2fd44f07e4
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test1/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import os
+
+
+class HashTest1(Package):
+    """Used to test package hashing
+    """
+
+    homepage = "http://www.hashtest1.org"
+    url = "http://www.hashtest1.org/downloads/hashtest1-1.1.tar.bz2"
+
+    version('1.1', 'a' * 32)
+    version('1.2', 'b' * 32)
+    version('1.3', 'c' * 32)
+    version('1.4', 'd' * 32)
+
+    patch('patch1.patch', when="@1.1")
+    patch('patch2.patch', when="@1.4")
+
+    variant('variantx', default=False, description='Test variant X')
+    variant('varianty', default=False, description='Test variant Y')
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        pass
+
+    @when('@:1.4')
+    def install(self, spec, prefix):
+        print("install 1")
+        os.listdir(os.getcwd())
+
+    @when('@1.5')
+    def install(self, spec, prefix):
+        os.listdir(os.getcwd())
diff --git a/var/spack/repos/builtin.mock/packages/hash-test1/patch1.patch b/var/spack/repos/builtin.mock/packages/hash-test1/patch1.patch
new file mode 100644
index 0000000000..a333c82dfd
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test1/patch1.patch
@@ -0,0 +1 @@
+the contents of patch 1 (not a valid diff, but sufficient for testing)
diff --git a/var/spack/repos/builtin.mock/packages/hash-test1/patch2.patch b/var/spack/repos/builtin.mock/packages/hash-test1/patch2.patch
new file mode 100644
index 0000000000..9e292a10fe
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test1/patch2.patch
@@ -0,0 +1 @@
+the contents of patch 2 (not a valid diff, but sufficient for testing)
diff --git a/var/spack/repos/builtin.mock/packages/hash-test2/package.py b/var/spack/repos/builtin.mock/packages/hash-test2/package.py
new file mode 100644
index 0000000000..de08125bf6
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test2/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import os
+
+
+class HashTest2(Package):
+    """Used to test package hashing
+    """
+
+    homepage = "http://www.hashtest2.org"
+    url = "http://www.hashtest1.org/downloads/hashtest2-1.1.tar.bz2"
+
+    version('1.1', 'a' * 32)
+    version('1.2', 'b' * 32)
+    version('1.3', 'c' * 31 + 'x')  # Source hash differs from hash-test1@1.3
+    version('1.4', 'd' * 32)
+
+    patch('patch1.patch', when="@1.1")
+
+    variant('variantx', default=False, description='Test variant X')
+    variant('varianty', default=False, description='Test variant Y')
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        pass
+
+    def install(self, spec, prefix):
+        print("install 1")
+        os.listdir(os.getcwd())
diff --git a/var/spack/repos/builtin.mock/packages/hash-test2/patch1.patch b/var/spack/repos/builtin.mock/packages/hash-test2/patch1.patch
new file mode 100644
index 0000000000..bbfa868935
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hash-test2/patch1.patch
@@ -0,0 +1,2 @@
+the different contents of patch 1 (not a valid diff, but sufficient for testing,
+and different from patch 1 of hash-test1)
diff --git a/var/spack/repos/builtin.mock/packages/hg-test/package.py b/var/spack/repos/builtin.mock/packages/hg-test/package.py
index 17d8379d1c..89a3286bea 100644
--- a/var/spack/repos/builtin.mock/packages/hg-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/hg-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/hg-top-level/package.py b/var/spack/repos/builtin.mock/packages/hg-top-level/package.py
new file mode 100644
index 0000000000..225a2e852c
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/hg-top-level/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class HgTopLevel(Package):
+    """Test package that does fetching with mercurial."""
+    homepage = "http://www.hg-fetch-example.com"
+
+    hg = 'https://example.com/some/hg/repo'
+    version('1.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/hypre/package.py b/var/spack/repos/builtin.mock/packages/hypre/package.py
index c815aca191..62133f48ac 100644
--- a/var/spack/repos/builtin.mock/packages/hypre/package.py
+++ b/var/spack/repos/builtin.mock/packages/hypre/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py b/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py
index 3b9b9caec1..902a8f7345 100644
--- a/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py
+++ b/var/spack/repos/builtin.mock/packages/indirect-mpich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/libdwarf/package.py b/var/spack/repos/builtin.mock/packages/libdwarf/package.py
index 726cb756a6..302e7f1eeb 100644
--- a/var/spack/repos/builtin.mock/packages/libdwarf/package.py
+++ b/var/spack/repos/builtin.mock/packages/libdwarf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 # Only build certain parts of dwarf because the other ones break.
diff --git a/var/spack/repos/builtin.mock/packages/libelf/package.py b/var/spack/repos/builtin.mock/packages/libelf/package.py
index 9cf8d152df..4fdd90e935 100644
--- a/var/spack/repos/builtin.mock/packages/libelf/package.py
+++ b/var/spack/repos/builtin.mock/packages/libelf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/mixedversions/package.py b/var/spack/repos/builtin.mock/packages/mixedversions/package.py
index 6e01fbc13b..ff564d5cb9 100644
--- a/var/spack/repos/builtin.mock/packages/mixedversions/package.py
+++ b/var/spack/repos/builtin.mock/packages/mixedversions/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/module-path-separator/package.py b/var/spack/repos/builtin.mock/packages/module-path-separator/package.py
new file mode 100644
index 0000000000..a7a4baabb7
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/module-path-separator/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class ModulePathSeparator(Package):
+    homepage = "http://www.llnl.gov"
+    url      = "http://www.llnl.gov/module-path-separator-1.0.tar.gz"
+
+    version(1.0, 'foobarbaz')
+
+    def install(self, spec, prefix):
+        pass
+
+    def setup_environment(self, senv, renv):
+        renv.append_path("COLON", "foo")
+        renv.prepend_path("COLON", "foo")
+        renv.remove_path("COLON", "foo")
+
+        renv.append_path("SEMICOLON", "bar", separator=";")
+        renv.prepend_path("SEMICOLON", "bar", separator=";")
+        renv.remove_path("SEMICOLON", "bar", separator=";")
diff --git a/var/spack/repos/builtin.mock/packages/mpich/package.py b/var/spack/repos/builtin.mock/packages/mpich/package.py
index f9dbf572c5..1ba68925d5 100644
--- a/var/spack/repos/builtin.mock/packages/mpich/package.py
+++ b/var/spack/repos/builtin.mock/packages/mpich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/mpich2/package.py b/var/spack/repos/builtin.mock/packages/mpich2/package.py
index 92e72daa4a..9f7df9696f 100644
--- a/var/spack/repos/builtin.mock/packages/mpich2/package.py
+++ b/var/spack/repos/builtin.mock/packages/mpich2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/mpileaks/package.py b/var/spack/repos/builtin.mock/packages/mpileaks/package.py
index 6b5afafdb2..478da9f9b9 100644
--- a/var/spack/repos/builtin.mock/packages/mpileaks/package.py
+++ b/var/spack/repos/builtin.mock/packages/mpileaks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py b/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py
index 9240671ba2..1b3e044f22 100644
--- a/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py
+++ b/var/spack/repos/builtin.mock/packages/multi-provider-mpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/multimethod-base/package.py b/var/spack/repos/builtin.mock/packages/multimethod-base/package.py
index 454f658adf..7b7d00b43b 100644
--- a/var/spack/repos/builtin.mock/packages/multimethod-base/package.py
+++ b/var/spack/repos/builtin.mock/packages/multimethod-base/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/multimethod/package.py b/var/spack/repos/builtin.mock/packages/multimethod/package.py
index 25a7ec7fca..3224d73fe9 100644
--- a/var/spack/repos/builtin.mock/packages/multimethod/package.py
+++ b/var/spack/repos/builtin.mock/packages/multimethod/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from six import string_types
 
 from spack import *
diff --git a/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py b/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py
index 0d27e31e44..1077f5f978 100644
--- a/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py
+++ b/var/spack/repos/builtin.mock/packages/multivalue_variant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py
index 48c99ba9d6..07bdbcb801 100644
--- a/var/spack/repos/builtin.mock/packages/netlib-blas/package.py
+++ b/var/spack/repos/builtin.mock/packages/netlib-blas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
index 9108e70cf0..2b12ee77ce 100644
--- a/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin.mock/packages/netlib-lapack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
index c73e65ac2b..5480507e1b 100644
--- a/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
+++ b/var/spack/repos/builtin.mock/packages/openblas-with-lapack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/openblas/package.py b/var/spack/repos/builtin.mock/packages/openblas/package.py
index 8d41c8958a..d10b423626 100644
--- a/var/spack/repos/builtin.mock/packages/openblas/package.py
+++ b/var/spack/repos/builtin.mock/packages/openblas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
index 51bbb9761f..6f988410fa 100644
--- a/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
+++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
index 48bf3820af..d1bf81a7fa 100644
--- a/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
+++ b/var/spack/repos/builtin.mock/packages/optional-dep-test-3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
index 48ffbf6765..af30815bc7 100644
--- a/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/optional-dep-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/othervirtual/package.py b/var/spack/repos/builtin.mock/packages/othervirtual/package.py
index c7b0e72a01..db9a218767 100644
--- a/var/spack/repos/builtin.mock/packages/othervirtual/package.py
+++ b/var/spack/repos/builtin.mock/packages/othervirtual/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/override-context-templates/package.py b/var/spack/repos/builtin.mock/packages/override-context-templates/package.py
index 9f59ad0e7e..6ec1b26dfa 100644
--- a/var/spack/repos/builtin.mock/packages/override-context-templates/package.py
+++ b/var/spack/repos/builtin.mock/packages/override-context-templates/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/override-module-templates/package.py b/var/spack/repos/builtin.mock/packages/override-module-templates/package.py
index 6d877c7a76..090a889448 100644
--- a/var/spack/repos/builtin.mock/packages/override-module-templates/package.py
+++ b/var/spack/repos/builtin.mock/packages/override-module-templates/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/patch-a-dependency/foo.patch b/var/spack/repos/builtin.mock/packages/patch-a-dependency/foo.patch
deleted file mode 100644
index 257cc5642c..0000000000
--- a/var/spack/repos/builtin.mock/packages/patch-a-dependency/foo.patch
+++ /dev/null
@@ -1 +0,0 @@
-foo
diff --git a/var/spack/repos/builtin.mock/packages/patch-a-dependency/libelf.patch b/var/spack/repos/builtin.mock/packages/patch-a-dependency/libelf.patch
new file mode 100644
index 0000000000..02bfad9103
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/patch-a-dependency/libelf.patch
@@ -0,0 +1,11 @@
+--- patch-a-dependency/configure	2018-08-13 23:13:51.000000000 -0700
++++ patch-a-dependency/configure.patched	2018-08-13 23:14:15.000000000 -0700
+@@ -2,7 +2,7 @@
+ prefix=$(echo $1 | sed 's/--prefix=//')
+ cat > Makefile <<EOF
+ all:
+-	echo Building...
++	echo Patched!
+ 
+ install:
+ 	mkdir -p $prefix
diff --git a/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py b/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py
index fea0b27195..4b4f044504 100644
--- a/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py
+++ b/var/spack/repos/builtin.mock/packages/patch-a-dependency/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class PatchADependency(Package):
 
     version('1.0', '0123456789abcdef0123456789abcdef')
 
-    depends_on('libelf', patches=patch('foo.patch'))
+    depends_on('libelf', patches=patch('libelf.patch'))
 
     def install(self, spec, prefix):
         pass
diff --git a/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py b/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py
index 73837449c6..fdd5cc30e7 100644
--- a/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py
+++ b/var/spack/repos/builtin.mock/packages/patch-several-dependencies/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/patch/package.py b/var/spack/repos/builtin.mock/packages/patch/package.py
index 79b0943b24..cf0d2f1c63 100644
--- a/var/spack/repos/builtin.mock/packages/patch/package.py
+++ b/var/spack/repos/builtin.mock/packages/patch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/patchelf/package.py b/var/spack/repos/builtin.mock/packages/patchelf/package.py
index d499199d3e..6b7205cb9a 100644
--- a/var/spack/repos/builtin.mock/packages/patchelf/package.py
+++ b/var/spack/repos/builtin.mock/packages/patchelf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/printing-package/package.py b/var/spack/repos/builtin.mock/packages/printing-package/package.py
index 815972f9eb..580e9727f1 100644
--- a/var/spack/repos/builtin.mock/packages/printing-package/package.py
+++ b/var/spack/repos/builtin.mock/packages/printing-package/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/python/package.py b/var/spack/repos/builtin.mock/packages/python/package.py
index f402be3b56..053c6d24f1 100644
--- a/var/spack/repos/builtin.mock/packages/python/package.py
+++ b/var/spack/repos/builtin.mock/packages/python/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/raiser/package.py b/var/spack/repos/builtin.mock/packages/raiser/package.py
new file mode 100644
index 0000000000..bbd4cb329b
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/raiser/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from six.moves import builtins
+
+from spack import *
+
+
+class Raiser(Package):
+    """A package that can raise a built-in exception
+    of any kind with any message
+    """
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/a-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+    version('2.0', '2.0_a_hash')
+
+    variant(
+        'exc_type',
+        values=lambda x: isinstance(x, str),
+        default='RuntimeError',
+        description='type of the exception to be raised',
+        multi=False
+    )
+
+    variant(
+        'msg',
+        values=lambda x: isinstance(x, str),
+        default='Unknown Exception',
+        description='message that will be tied to the exception',
+        multi=False
+    )
+
+    def install(self, spec, prefix):
+        print('Raiser will raise ')
+        exc_typename = self.spec.variants['exc_type'].value
+        exc_type = getattr(builtins, exc_typename)
+        msg = self.spec.variants['msg'].value
+        raise exc_type(msg)
diff --git a/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py b/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py
index 3f135b002e..cd43575a01 100644
--- a/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py
+++ b/var/spack/repos/builtin.mock/packages/simple-inheritance/package.py
@@ -1,3 +1,8 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py b/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py
index 60530e8202..c9cc385b6a 100644
--- a/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py
+++ b/var/spack/repos/builtin.mock/packages/singlevalue-variant-dependent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/svn-test/package.py b/var/spack/repos/builtin.mock/packages/svn-test/package.py
index 1c4424dab5..b0ad42542b 100644
--- a/var/spack/repos/builtin.mock/packages/svn-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/svn-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class SvnTest(Package):
     """Mock package that uses svn for fetching."""
     url      = "http://www.example.com/svn-test-1.0.tar.gz"
 
-    version('svn', 'to-be-filled-in-by-test')
+    version('svn', svn='to-be-filled-in-by-test')
 
     def install(self, spec, prefix):
         pass
diff --git a/var/spack/repos/builtin.mock/packages/svn-top-level/package.py b/var/spack/repos/builtin.mock/packages/svn-top-level/package.py
new file mode 100644
index 0000000000..8acd54b66a
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/svn-top-level/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SvnTopLevel(Package):
+    """Mock package that uses svn for fetching."""
+
+    svn = 'https://example.com/some/svn/repo'
+    version('1.0')
+
+    def install(self, spec, prefix):
+        pass
diff --git a/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py b/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py
index eadba7064c..aad58f08e3 100644
--- a/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py
+++ b/var/spack/repos/builtin.mock/packages/trivial-install-test-package/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/url-list-test/package.py b/var/spack/repos/builtin.mock/packages/url-list-test/package.py
index e77d203707..98d7af8425 100644
--- a/var/spack/repos/builtin.mock/packages/url-list-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/url-list-test/package.py
@@ -1,49 +1,30 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import os
-import spack
+import spack.paths
 
 
 class UrlListTest(Package):
     """Mock package with url_list."""
     homepage = "http://www.url-list-example.com"
 
-    web_data_path = os.path.join(spack.test_path, 'data', 'web')
+    web_data_path = os.path.join(spack.paths.test_path, 'data', 'web')
     url = 'file://' + web_data_path + '/foo-0.0.0.tar.gz'
     list_url = 'file://' + web_data_path + '/index.html'
     list_depth = 3
 
-    version('0.0.0')
-    version('1.0.0')
-    version('3.0')
-    version('4.5')
-    version('2.0.0b2')
-    version('3.0a1')
-    version('4.5-rc5')
+    version('0.0.0',   'abc000')
+    version('1.0.0',   'abc100')
+    version('3.0',     'abc30')
+    version('4.5',     'abc45')
+    version('2.0.0b2', 'abc200b2')
+    version('3.0a1',   'abc30a1')
+    version('4.5-rc5', 'abc45rc5')
 
     def install(self, spec, prefix):
         pass
diff --git a/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py b/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py
new file mode 100644
index 0000000000..bee39c0c72
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/url-only-override-with-gaps/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UrlOnlyOverrideWithGaps(Package):
+    homepage = 'http://www.example.com'
+
+    version('1.0.5', 'abcdef0')
+    version('1.0.0', 'bcdef0a', url='http://a.example.com/url_override-1.0.0.tar.gz')
+    version('0.9.5', 'cdef0ab')
+    version('0.9.0', 'def0abc', url='http://b.example.com/url_override-0.9.0.tar.gz')
+    version('0.8.5', 'ef0abcd')
+    version('0.8.1', 'f0abcde', url='http://c.example.com/url_override-0.8.1.tar.gz')
+    version('0.7.0', '0abcdef')
diff --git a/var/spack/repos/builtin.mock/packages/url-only-override/package.py b/var/spack/repos/builtin.mock/packages/url-only-override/package.py
new file mode 100644
index 0000000000..e145285985
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/url-only-override/package.py
@@ -0,0 +1,14 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UrlOnlyOverride(Package):
+    homepage = 'http://www.example.com'
+
+    version('1.0.0', 'cxyzab', url='http://a.example.com/url_override-1.0.0.tar.gz')
+    version('0.9.0', 'bcxyza', url='http://b.example.com/url_override-0.9.0.tar.gz')
+    version('0.8.1', 'cxyzab', url='http://c.example.com/url_override-0.8.1.tar.gz')
diff --git a/var/spack/repos/builtin.mock/packages/url-test/package.py b/var/spack/repos/builtin.mock/packages/url-test/package.py
index 113dc0714b..c16f345980 100644
--- a/var/spack/repos/builtin.mock/packages/url-test/package.py
+++ b/var/spack/repos/builtin.mock/packages/url-test/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin.mock/packages/url_override/package.py b/var/spack/repos/builtin.mock/packages/url_override/package.py
new file mode 100644
index 0000000000..803afe5e33
--- /dev/null
+++ b/var/spack/repos/builtin.mock/packages/url_override/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UrlOverride(Package):
+    homepage = 'http://www.doesnotexist.org'
+    url      = 'http://www.doesnotexist.org/url_override-1.0.0.tar.gz'
+
+    version('1.0.0', 'cxyzab')
+    version('0.9.0', 'bcxyza', url='http://www.anothersite.org/uo-0.9.0.tgz')
+    version('0.8.1', 'cxyzab')
diff --git a/var/spack/repos/builtin.mock/packages/zmpi/package.py b/var/spack/repos/builtin.mock/packages/zmpi/package.py
index 99a750afc1..4546ed7335 100644
--- a/var/spack/repos/builtin.mock/packages/zmpi/package.py
+++ b/var/spack/repos/builtin.mock/packages/zmpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/abinit/package.py b/var/spack/repos/builtin/packages/abinit/package.py
index 59040cd0d8..4902509d4e 100644
--- a/var/spack/repos/builtin/packages/abinit/package.py
+++ b/var/spack/repos/builtin/packages/abinit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # Author: Matteo Giantomassi <matteo.giantomassiNOSPAM AT uclouvain.be>
 # Date: October 11, 2016
@@ -47,8 +28,10 @@ class Abinit(AutotoolsPackage):
     """
 
     homepage = 'http://www.abinit.org'
-    url      = 'http://ftp.abinit.org/abinit-8.0.8b.tar.gz'
+    url      = 'https://www.abinit.org/sites/default/files/packages/abinit-8.6.3.tar.gz'
 
+    version('8.8.2', '72d7046c7ff31b9f17afe050ecdfb3a5')
+    version('8.6.3', '6c34d2cec0cf0008dd25b8ec1b6d3ee8')
     version('8.2.2', '5f25250e06fdc0815c224ffd29858860')
     # Versions before 8.0.8b are not supported.
     version('8.0.8b', 'abc9e303bfa7f9f43f95598f87d84d5d')
diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py
index 4a8aa0fb03..aabaf94400 100644
--- a/var/spack/repos/builtin/packages/abyss/package.py
+++ b/var/spack/repos/builtin/packages/abyss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,15 @@ class Abyss(AutotoolsPackage):
        is useful for assembling genomes up to 100 Mbases in size."""
 
     homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss"
-    url      = "https://github.com/bcgsc/abyss/archive/2.0.2.tar.gz"
+    url      = "https://github.com/bcgsc/abyss/releases/download/1.5.2/abyss-1.5.2.tar.gz"
 
-    version('2.0.2', 'bb3f8cebf121312bf81789d963b4ecc5')
+    version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798')
     version('1.5.2', '10d6d72d1a915e618d41a5cbbcf2364c')
 
+    variant('maxk', values=int, default=0, 
+            description='''set the maximum k-mer length.
+            This value must be a multiple of 32''')
+
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
 
@@ -44,6 +29,7 @@ class Abyss(AutotoolsPackage):
     depends_on('boost@:1.50.0,1.53.0:1.59.0', when='@:1.5.2')
     depends_on('sparsehash')
     depends_on('sqlite')
+    depends_on('libtool')
 
     conflicts('^intel-mpi')
     conflicts('^intel-parallel-studio+mpi')
@@ -51,9 +37,12 @@ class Abyss(AutotoolsPackage):
     conflicts('^spectrum-mpi')
 
     def configure_args(self):
+        maxk = int(self.spec.variants['maxk'].value)
         args = ['--with-boost=%s' % self.spec['boost'].prefix,
                 '--with-sqlite=%s' % self.spec['sqlite'].prefix,
                 '--with-mpi=%s' % self.spec['mpi'].prefix]
+        if maxk:
+                args.append('--enable-maxk=%s' % maxk)
         if self.spec['mpi'].name == 'mpich':
                 args.append('--enable-mpich')
         return args
diff --git a/var/spack/repos/builtin/packages/accfft/package.py b/var/spack/repos/builtin/packages/accfft/package.py
new file mode 100644
index 0000000000..3a59f11f27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/accfft/package.py
@@ -0,0 +1,47 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Accfft(CMakePackage, CudaPackage):
+    """AccFFT extends existing FFT libraries for CUDA-enabled
+    Graphics Processing Units (GPUs) to distributed memory clusters
+    """
+
+    homepage = "http://accfft.org"
+    git      = "https://github.com/amirgholami/accfft.git"
+
+    version('develop', branch='master')
+
+    variant('pnetcdf', default=True, description='Add support for parallel NetCDF')
+    variant('shared', default=True, description='Enables the build of shared libraries')
+
+    # See: http://accfft.org/articles/install/#installing-dependencies
+    depends_on('fftw+float+double~mpi+openmp')
+
+    depends_on('parallel-netcdf', when='+pnetcdf')
+
+    parallel = False
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DFFTW_ROOT={0}'.format(spec['fftw'].prefix),
+            '-DFFTW_USE_STATIC_LIBS=false',
+            '-DBUILD_GPU={0}'.format('true' if '+cuda' in spec else 'false'),
+            '-DBUILD_SHARED={0}'.format(
+                'true' if '+shared' in spec else 'false'
+            ),
+        ]
+
+        if '+cuda' in spec:
+            cuda_arch = [x for x in spec.variants['cuda_arch'].value if x]
+            if cuda_arch:
+                args.append('-DCUDA_NVCC_FLAGS={0}'.format(
+                    ' '.join(self.cuda_flags(cuda_arch))
+                ))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/ack/package.py b/var/spack/repos/builtin/packages/ack/package.py
index ec1b6d2a22..c889d1f31e 100644
--- a/var/spack/repos/builtin/packages/ack/package.py
+++ b/var/spack/repos/builtin/packages/ack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Ack(Package):
     homepage = "http://beyondgrep.com/"
     url      = "http://beyondgrep.com/ack-2.14-single-file"
 
+    version('2.22', 'eea9d4daef7c262751f15ca9b3b70317', expand=False)
     version('2.18', 'e8ebfd7a7ec8476bffd4686bf7b14fd7', expand=False)
     version('2.16', '7085b5a5c76fda43ff049410870c8535', expand=False)
     version('2.14', 'e74150a1609d28a70b450ef9cc2ed56b', expand=False)
diff --git a/var/spack/repos/builtin/packages/activeharmony/package.py b/var/spack/repos/builtin/packages/activeharmony/package.py
index d03d3f99eb..7c90f24a0d 100644
--- a/var/spack/repos/builtin/packages/activeharmony/package.py
+++ b/var/spack/repos/builtin/packages/activeharmony/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/adept-utils/package.py b/var/spack/repos/builtin/packages/adept-utils/package.py
index 3f704a4893..fcac87759a 100644
--- a/var/spack/repos/builtin/packages/adept-utils/package.py
+++ b/var/spack/repos/builtin/packages/adept-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py
index 1b0b88d167..2b93379129 100644
--- a/var/spack/repos/builtin/packages/adios/package.py
+++ b/var/spack/repos/builtin/packages/adios/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,15 +14,19 @@ class Adios(AutotoolsPackage):
     """
 
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
-    url = "https://github.com/ornladios/ADIOS/archive/v1.12.0.tar.gz"
+    url      = "https://github.com/ornladios/ADIOS/archive/v1.12.0.tar.gz"
+    git      = "https://github.com/ornladios/ADIOS.git"
+
+    maintainers = ['ax3l']
 
-    version('develop', git='https://github.com/ornladios/ADIOS.git',
-            branch='master')
+    version('develop', branch='master')
+    version('1.13.1', '958aed11240d7f5a065ab5ee271ecb44')
+    version('1.13.0', '68af36b821debbdf4748b20320a990ce')
     version('1.12.0', '84a1c71b6698009224f6f748c5257fc9')
     version('1.11.1', '5639bfc235e50bf17ba9dafb14ea4185')
     version('1.11.0', '5eead5b2ccf962f5e6d5f254d29d5238')
     version('1.10.0', 'eff450a4c0130479417cfd63186957f3')
-    version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
+    version('1.9.0',  '310ff02388bbaa2b1c1710ee970b5678')
 
     variant('shared', default=True,
             description='Builds a shared version of the library')
@@ -65,6 +50,10 @@ class Adios(AutotoolsPackage):
             description='Enable ZFP transform support')
     variant('sz', default=True,
             description='Enable SZ transform support')
+    variant('lz4', default=True,
+            description='Enable LZ4 transform support')
+    variant('blosc', default=True,
+            description='Enable Blosc transform support')
     # transports and serial file converters
     variant('hdf5', default=False,
             description='Enable parallel HDF5 transport and serial bp2h5 ' +
@@ -90,8 +79,12 @@ class Adios(AutotoolsPackage):
     depends_on('zlib', when='+zlib')
     depends_on('bzip2', when='+bzip2')
     depends_on('szip', when='+szip')
-    depends_on('sz@:1.4.10', when='+sz')
+    depends_on('sz@:1.4.10', when='@:1.12.0 +sz')
+    depends_on('sz@1.4.11.0:1.4.11.99', when='@1.13.0 +sz')
+    depends_on('sz@1.4.12.3:1.4.12.99', when='@1.13.1: +sz')
     depends_on('zfp@:0.5.0', when='+zfp')
+    depends_on('lz4', when='+lz4')
+    depends_on('c-blosc@1.12.0:', when='+blosc')
     # optional transports & file converters
     depends_on('hdf5@1.8:+hl+mpi', when='+hdf5')
     depends_on('netcdf', when='+netcdf')
@@ -153,7 +146,16 @@ class Adios(AutotoolsPackage):
         extra_args += self.with_or_without('infiniband')
 
         # Transforms
-        variants = ['zlib', 'bzip2', 'szip', 'zfp', 'sz']
+        variants = ['zlib', 'bzip2', 'szip']
+        if spec.satisfies('@1.11.0:'):
+            variants += ['zfp']
+        if spec.satisfies('@1.12.0:'):
+            variants += ['sz', 'lz4']
+        if spec.satisfies('@1.13.0:'):
+            extra_args += self.with_or_without(
+                'blosc',
+                activation_value=lambda x: spec['c-blosc'].prefix
+            )
 
         # External I/O libraries
         variants += ['hdf5', 'netcdf']
diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py
index a222477c2d..a7ba1eec0b 100644
--- a/var/spack/repos/builtin/packages/adios2/package.py
+++ b/var/spack/repos/builtin/packages/adios2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,21 +11,27 @@ class Adios2(CMakePackage):
 
     homepage = "https://www.olcf.ornl.gov/center-projects/adios/"
     url      = "https://github.com/ornladios/ADIOS2/archive/v2.0.0.tar.gz"
+    git      = "https://github.com/ornladios/ADIOS2.git"
 
-    version('develop', branch='master',
-            git='https://github.com/ornladios/ADIOS2.git')
+    maintainers = ['ax3l']
 
+    version('develop', branch='master')
+    version('2.2.0', sha256='77058ea2ff7224dc02ea519733de42d89112cf21ffe7474fb2fa3c5696152948')
+    version('2.1.0', '431fa5b015349f1838b96b8f5a1cc8f8')
     version('2.0.0', 'da39655b51745d2c5f3f1e46c5abc4d7')
 
     variant('shared', default=True,
             description='Also build shared libraries')
     variant('mpi', default=True,
             description='Enable MPI')
-    # transforms (not yet implemented)
-    # variant('bzip2', default=True,
-    #         description='Enable BZip2 compression')
-    # variant('zfp', default=True,
-    #         description='Enable ZFP compression')
+    # transforms
+    variant('bzip2', default=True,
+            description='Enable BZip2 compression')
+    variant('zfp', default=True,
+            description='Enable ZFP compression')
+    # sz is broken in 2.2.0: https://github.com/ornladios/ADIOS2/issues/705
+    # variant('sz', default=True,
+    #         description='Enable SZ compression')
     # transport engines
     variant('dataman', default=True,
             description='Enable the DataMan engine for WAN transports')
@@ -58,6 +45,8 @@ class Adios2(CMakePackage):
     # language bindings
     variant('python', default=True,
             description='Enable the Python >= 2.7 bindings')
+    variant('fortran', default=True,
+            description='Enable the Fortran bindings')
 
     # requires mature C++11 implementations
     conflicts('%gcc@:4.7')
@@ -68,12 +57,17 @@ class Adios2(CMakePackage):
     conflicts('+dataman', when='~shared')
 
     depends_on('cmake@3.5.0:', type='build')
+    depends_on('pkgconfig', type='build', when='@2.2.0:')
+    # The included ffs requires bison and flex but using them makes
+    # the build fail due to an undefined reference.
+    # depends_on('bison', type='build', when='@2.2.0:')
+    # depends_on('flex', when='@2.2.0:')
 
     # contained in thirdparty/
     # depends_on('googletest')
     # depends_on('pugixml')
     # depends_on('kwsys')
-    # depends_on('nlohmannjson')
+    # depends_on('nlohmann-json')
     # depends_on('pybind11@2.1.1:', when='+python')
 
     depends_on('mpi', when='+mpi')
@@ -86,6 +80,7 @@ class Adios2(CMakePackage):
 
     depends_on('bzip2', when='+bzip2')
     depends_on('zfp', when='+zfp')
+    # depends_on('sz@:1.4.12', when='+sz')
 
     extends('python', when='+python')
     depends_on('python@2.7:', type=('build', 'run'), when='+python')
@@ -96,24 +91,31 @@ class Adios2(CMakePackage):
         spec = self.spec
 
         args = [
-            '-DADIOS2_BUILD_SHARED_LIBS:BOOL={0}'.format((
-                'ON' if '+shared' in spec else 'OFF')),
+            '-DADIOS2_BUILD_SHARED_LIBS:BOOL={0}'.format(
+                'ON' if '+shared' in spec else 'OFF'),
             '-DADIOS2_BUILD_TESTING=OFF',
-            '-DADIOS2_USE_MPI={0}'.format((
-                'ON' if '+mpi' in spec else 'OFF')),
-            '-DADIOS2_USE_BZip2={0}'.format((
-                'ON' if '+bzip2' in spec else 'OFF')),
-            '-DADIOS2_USE_ZFP={0}'.format((
-                'ON' if '+zfp' in spec else 'OFF')),
-            '-DADIOS2_USE_DataMan={0}'.format((
-                'ON' if '+dataman' in spec else 'OFF')),
-            '-DADIOS2_USE_ZeroMQ={0}'.format((
-                'ON' if '+dataman' in spec else 'OFF')),
-            '-DADIOS2_USE_HDF5={0}'.format((
-                'ON' if '+hdf5' in spec else 'OFF')),
-            '-DADIOS2_USE_ADIOS1={0}'.format((
-                'ON' if '+adios1' in spec else 'OFF')),
-            '-DADIOS2_USE_Python={0}'.format((
-                'ON' if '+python' in spec else 'OFF'))
+            '-DADIOS2_USE_MPI={0}'.format(
+                'ON' if '+mpi' in spec else 'OFF'),
+            '-DADIOS2_USE_BZip2={0}'.format(
+                'ON' if '+bzip2' in spec else 'OFF'),
+            '-DADIOS2_USE_ZFP={0}'.format(
+                'ON' if '+zfp' in spec else 'OFF'),
+            '-DADIOS2_USE_SZ={0}'.format(
+                'ON' if '+sz' in spec else 'OFF'),
+            '-DADIOS2_USE_DataMan={0}'.format(
+                'ON' if '+dataman' in spec else 'OFF'),
+            '-DADIOS2_USE_ZeroMQ={0}'.format(
+                'ON' if '+dataman' in spec else 'OFF'),
+            '-DADIOS2_USE_HDF5={0}'.format(
+                'ON' if '+hdf5' in spec else 'OFF'),
+            '-DADIOS2_USE_ADIOS1={0}'.format(
+                'ON' if '+adios1' in spec else 'OFF'),
+            '-DADIOS2_USE_Python={0}'.format(
+                'ON' if '+python' in spec else 'OFF'),
+            '-DADIOS2_USE_Fortran={0}'.format(
+                'ON' if '+fortran' in spec else 'OFF')
         ]
+        if spec.satisfies('+python'):
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s'
+                        % self.spec['python'].command.path)
         return args
diff --git a/var/spack/repos/builtin/packages/adlbx/package.py b/var/spack/repos/builtin/packages/adlbx/package.py
index dfe6dffb03..4f7e06d2c9 100644
--- a/var/spack/repos/builtin/packages/adlbx/package.py
+++ b/var/spack/repos/builtin/packages/adlbx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,12 +11,21 @@ class Adlbx(AutotoolsPackage):
     """ADLB/X: Master-worker library + work stealing and data dependencies"""
 
     homepage = 'http://swift-lang.org/Swift-T'
-    url      = 'http://swift-lang.github.io/swift-t-downloads/adlbx-0.8.0.tar.gz'
+    url      = 'http://swift-lang.github.io/swift-t-downloads/spack/adlbx-0.0.0.tar.gz'
+
+    version('0.9.1', '07151ddef5fb83d8f4b40700013d9daf')
     version('0.8.0', '34ade59ce3be5bc296955231d47a27dd')
 
-    depends_on('exmcutils')
+    depends_on('exmcutils@:0.5.3', when='@:0.8.0')
+    depends_on('exmcutils', when='@0.9.1:')
     depends_on('mpi')
 
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+        spack_env.set('CC', spec['mpi'].mpicc)
+        spack_env.set('CXX', spec['mpi'].mpicxx)
+        spack_env.set('CXXLD', spec['mpi'].mpicxx)
+
     def configure_args(self):
         args = ['--with-c-utils=' + self.spec['exmcutils'].prefix]
         return args
diff --git a/var/spack/repos/builtin/packages/adol-c/package.py b/var/spack/repos/builtin/packages/adol-c/package.py
index 953cade297..7769dc13b7 100644
--- a/var/spack/repos/builtin/packages/adol-c/package.py
+++ b/var/spack/repos/builtin/packages/adol-c/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,14 +10,16 @@ class AdolC(AutotoolsPackage):
     """A package for the automatic differentiation of first and higher
     derivatives of vector functions in C and C++ programs by operator
     overloading."""
+
     homepage = "https://projects.coin-or.org/ADOL-C"
     url      = "http://www.coin-or.org/download/source/ADOL-C/ADOL-C-2.6.1.tgz"
+    git      = "https://gitlab.com/adol-c/adol-c.git"
 
-    version('develop',  git='https://gitlab.com/adol-c/adol-c.git',
-            branch='master')
+    version('develop',  branch='master')
     version('2.6.3', 'f78f67f70d5874830a1ad1c0f54e54f7')
     version('2.6.2', '0f9547584c99c0673e4f81cf64e8d865')
     version('2.6.1', '1032b28427d6e399af4610e78c0f087b')
+    version('2.5.2', '96f81b80e93cca57398066ea4afe28f0')
 
     variant('advanced_branching', default=False,
             description='Enable advanced branching to reduce retaping')
@@ -46,6 +29,7 @@ class AdolC(AutotoolsPackage):
     variant('openmp',   default=False, description='Enable OpenMP support')
     variant('sparse',   default=False, description='Enable sparse drivers')
     variant('examples', default=True,  description='Install examples')
+    variant('boost',    default=False, description='Enable boost')
 
     # Build dependencies
     depends_on('automake', type='build', when='@develop')
@@ -53,6 +37,18 @@ class AdolC(AutotoolsPackage):
     depends_on('libtool',  type='build', when='@develop')
     depends_on('m4',       type='build', when='@develop')
 
+    # Link dependencies
+    depends_on('boost+system', when='+boost')
+
+    # FIXME: add
+    #  --with-colpack=DIR      path to the colpack library and headers
+    #                       [default=system libraries]
+    #  --with-mpi-root=MPIROOT absolute path to the MPI root directory
+    #  --with-mpicc=MPICC      name of the MPI C++ compiler (default mpicc)
+    #  --with-mpicxx=MPICXX    name of the MPI C++ compiler (default mpicxx)
+    #  --with-ampi=AMPI_DIR    full path to the installation of adjoinable MPI
+    #                           (AMPI)
+
     patch('openmp_exam_261.patch', when='@2.6.1')
 
     def configure_args(self):
@@ -60,25 +56,34 @@ class AdolC(AutotoolsPackage):
 
         configure_args = []
 
+        if '+boost' in spec:
+            configure_args.append(
+                '--with-boost={0}'.format(spec['boost'].prefix)
+            )
+        else:
+            configure_args.append(
+                '--with-boost=no'
+            )
+
         if '+advanced_branching' in spec:
-            configure_args.extend([
+            configure_args.append(
                 '--enable-advanced-branching'
-            ])
+            )
 
         if '+atrig_erf' in spec:
-            configure_args.extend([
+            configure_args.append(
                 '--enable-atrig-erf'
-            ])
+            )
 
         if '+openmp' in spec:
-            configure_args.extend([
+            configure_args.append(
                 '--with-openmp-flag={0}'.format(self.compiler.openmp_flag)
-            ])
+            )
 
         if '+sparse' in spec:
-            configure_args.extend([
+            configure_args.append(
                 '--enable-sparse'
-            ])
+            )
 
         # We can simply use the bundled examples to check
         # whether Adol-C works as expected
@@ -88,9 +93,9 @@ class AdolC(AutotoolsPackage):
                 '--enable-addexa'  # Additional examples
             ])
             if '+openmp' in spec:
-                configure_args.extend([
+                configure_args.append(
                     '--enable-parexa'  # Parallel examples
-                ])
+                )
 
         return configure_args
 
diff --git a/var/spack/repos/builtin/packages/aegean/package.py b/var/spack/repos/builtin/packages/aegean/package.py
new file mode 100644
index 0000000000..a66c4d1e72
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aegean/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aegean(MakefilePackage):
+    """The AEGeAn Toolkit is designed for the Analysis and Evaluation of
+       Genome Annotations. The toolkit includes a variety of analysis programs
+       as well as a C library whose API provides access to AEGeAn's core
+       functions and data structures."""
+
+    homepage = "http://brendelgroup.github.io/AEGeAn/"
+    url      = "https://github.com/BrendelGroup/AEGeAn/archive/v0.15.2.tar.gz"
+
+    version('0.15.2', 'd7d73f5f132ff52340975b636564e949')
+
+    depends_on('genometools')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('/usr/local', prefix)
diff --git a/var/spack/repos/builtin/packages/aida/package.py b/var/spack/repos/builtin/packages/aida/package.py
new file mode 100644
index 0000000000..d2b2a22d72
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aida/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aida(Package):
+    """Abstract Interfaces for Data Analysis"""
+
+    homepage = "http://aida.freehep.org/"
+    url      = "ftp://ftp.slac.stanford.edu/software/freehep/AIDA/v3.2.1/aida-3.2.1.tar.gz"
+
+    version('3.2.1', sha256='c51da83e99c0985a7ef3e8bc5a60c3ae61f3ca603b61100c2438b4cdadd5bb2e')
+
+    def install(self, spec, prefix):
+        install_tree('src/cpp', prefix.include)
+        install_tree('lib', prefix)
diff --git a/var/spack/repos/builtin/packages/albany/package.py b/var/spack/repos/builtin/packages/albany/package.py
new file mode 100644
index 0000000000..ae8613d361
--- /dev/null
+++ b/var/spack/repos/builtin/packages/albany/package.py
@@ -0,0 +1,102 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Albany(CMakePackage):
+    """Albany is an implicit, unstructured grid, finite element code for the
+       solution and analysis of multiphysics problems.  The Albany repository
+       on the GitHub site contains hundreds of regression tests and examples
+       that demonstrate the code's capabilities on a wide variety of problems
+       including fluid mechanics, solid mechanics (elasticity and plasticity),
+       ice-sheet flow, quantum device modeling, and many other applications."""
+
+    homepage = "http://gahansen.github.io/Albany"
+    git      = "https://github.com/gahansen/Albany.git"
+
+    maintainers = ['gahansen']
+
+    version('develop', branch='master')
+
+    variant('lcm',          default=True,
+            description='Enable LCM')
+    variant('aeras',          default=False,
+            description='Enable AERAS')
+    variant('qcad',          default=False,
+            description='Enable QCAD')
+    variant('hydride',          default=False,
+            description='Enable HYDRIDE')
+    variant('lcm_spec',          default=False,
+            description='Enable LCM_SPECULATIVE')
+    variant('lame',          default=False,
+            description='Enable LAME')
+    variant('debug',          default=False,
+            description='Enable DEBUGGING')
+    variant('fpe',          default=False,
+            description='Enable CHECK_FPE')
+    variant('scorec',          default=False,
+            description='Enable SCOREC')
+    variant('felix',          default=False,
+            description='Enable FELIX')
+    variant('mor',          default=False,
+            description='Enable MOR')
+    variant('confgui',          default=False,
+            description='Enable Albany configuration (CI) GUI')
+    variant('ascr',          default=False,
+            description='Enable ALBANY_ASCR')
+    variant('perf',          default=False,
+            description='Enable PERFORMANCE_TESTS')
+    variant('64bit',          default=True,
+            description='Enable 64BIT')
+
+    # Add dependencies
+    depends_on('mpi')
+    depends_on('trilinos~superlu-dist+isorropia+tempus+rythmos+teko+intrepid+intrepid2+minitensor+phalanx+pnetcdf+nox+piro+rol+shards+stk+superlu@master,develop')
+
+    def cmake_args(self):
+        spec = self.spec
+        trilinos_dir = spec['trilinos'].prefix
+        options = []
+
+        options.extend([
+            '-DALBANY_TRILINOS_DIR:FILEPATH={0}'.format(trilinos_dir),
+            '-DINSTALL_ALBANY:BOOL=ON'
+        ])
+
+        options.extend([
+                       '-DENABLE_LCM:BOOL=%s' % (
+                           'ON' if '+lcm' in spec else 'OFF'),
+                       '-DENABLE_AERAS:BOOL=%s' % (
+                           'ON' if '+aeras' in spec else 'OFF'),
+                       '-DENABLE_QCAD:BOOL=%s' % (
+                           'ON' if '+qcad' in spec else 'OFF'),
+                       '-DENABLE_HYDRIDE:BOOL=%s' % (
+                           'ON' if '+hydride' in spec else 'OFF'),
+                       '-DENABLE_LCM_SPECULATIVE:BOOL=%s' % (
+                           'ON' if '+lcm_spec' in spec else 'OFF'),
+                       '-DENABLE_LAME:BOOL=%s' % (
+                           'ON' if '+lame' in spec else 'OFF'),
+                       '-DENABLE_DEBUGGING:BOOL=%s' % (
+                           'ON' if '+debug' in spec else 'OFF'),
+                       '-DENABLE_CHECK_FPE:BOOL=%s' % (
+                           'ON' if '+fpe' in spec else 'OFF'),
+                       '-DENABLE_SCOREC:BOOL=%s' % (
+                           'ON' if '+scorec' in spec else 'OFF'),
+                       '-DENABLE_FELIX:BOOL=%s' % (
+                           'ON' if '+felix' in spec else 'OFF'),
+                       '-DENABLE_MOR:BOOL=%s' % (
+                           'ON' if '+mor' in spec else 'OFF'),
+                       '-DENABLE_ALBANY_CI:BOOL=%s' % (
+                           'ON' if '+ci' in spec else 'OFF'),
+                       '-DENABLE_ASCR:BOOL=%s' % (
+                           'ON' if '+ascr' in spec else 'OFF'),
+                       '-DENABLE_PERFORMANCE_TESTS:BOOL=%s' % (
+                           'ON' if '+perf' in spec else 'OFF'),
+                       '-DENABLE_64BIT_INT:BOOL=%s' % (
+                           'ON' if '+64bit' in spec else 'OFF')
+                       ])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/albert/package.py b/var/spack/repos/builtin/packages/albert/package.py
index d720f04650..c2d432fd36 100644
--- a/var/spack/repos/builtin/packages/albert/package.py
+++ b/var/spack/repos/builtin/packages/albert/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/alglib/package.py b/var/spack/repos/builtin/packages/alglib/package.py
index e470dba292..6842cbd8ad 100644
--- a/var/spack/repos/builtin/packages/alglib/package.py
+++ b/var/spack/repos/builtin/packages/alglib/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
-import shutil
+import sys
 
 
 class Alglib(MakefilePackage):
@@ -47,7 +28,7 @@ class Alglib(MakefilePackage):
         make_file_src = join_path(os.path.dirname(self.module.__file__),
                                   'Makefile')
         make_file = join_path(self.stage.source_path, 'src', 'Makefile')
-        shutil.copy(make_file_src, make_file)
+        copy(make_file_src, make_file)
         filter_file(r'so', dso_suffix, make_file)
 
     def install(self, spec, prefix):
@@ -59,3 +40,9 @@ class Alglib(MakefilePackage):
             headers = glob.glob('*.h')
             for h in headers:
                 install(h, prefix.include)
+
+    @run_after('install')
+    def fix_darwin_install(self):
+        # The shared libraries are not installed correctly on Darwin:
+        if sys.platform == 'darwin':
+            fix_darwin_install_name(self.spec.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/allinea-forge/package.py b/var/spack/repos/builtin/packages/allinea-forge/package.py
index a4a821737d..c0519014a8 100644
--- a/var/spack/repos/builtin/packages/allinea-forge/package.py
+++ b/var/spack/repos/builtin/packages/allinea-forge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/allinea-reports/package.py b/var/spack/repos/builtin/packages/allinea-reports/package.py
index 69c881c369..a1da29ba47 100644
--- a/var/spack/repos/builtin/packages/allinea-reports/package.py
+++ b/var/spack/repos/builtin/packages/allinea-reports/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/allpaths-lg/package.py b/var/spack/repos/builtin/packages/allpaths-lg/package.py
index 69731045aa..3ec1e99418 100644
--- a/var/spack/repos/builtin/packages/allpaths-lg/package.py
+++ b/var/spack/repos/builtin/packages/allpaths-lg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/alquimia/package.py b/var/spack/repos/builtin/packages/alquimia/package.py
index 983bab23f7..2b42e89db2 100644
--- a/var/spack/repos/builtin/packages/alquimia/package.py
+++ b/var/spack/repos/builtin/packages/alquimia/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,17 +11,21 @@ class Alquimia(CMakePackage):
     of mature geochemistry codes such as CrunchFlow and PFLOTRAN"""
 
     homepage = "https://github.com/LBL-EESA/alquimia-dev"
+    git      = "https://github.com/LBL-EESA/alquimia-dev.git"
 
-    version('xsdk-0.2.0', git='https://github.com/LBL-EESA/alquimia-dev.git', tag='xsdk-0.2.0')
-    version('develop', git='https://github.com/LBL-EESA/alquimia-dev.git')
+    version('develop')
+    version('xsdk-0.3.0', tag='xsdk-0.3.0')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
 
     variant('shared', default=True,
             description='Enables the build of shared libraries')
 
     depends_on('mpi')
     depends_on('hdf5')
+    depends_on('pflotran@xsdk-0.3.0', when='@xsdk-0.3.0')
     depends_on('pflotran@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('pflotran@develop', when='@develop')
+    depends_on('petsc@3.8.0:', when='@xsdk-0.3.0')
     depends_on('petsc@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('petsc@develop', when='@develop')
 
diff --git a/var/spack/repos/builtin/packages/alsa-lib/package.py b/var/spack/repos/builtin/packages/alsa-lib/package.py
index 8e469e9ae7..48cf792548 100644
--- a/var/spack/repos/builtin/packages/alsa-lib/package.py
+++ b/var/spack/repos/builtin/packages/alsa-lib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/aluminum/package.py b/var/spack/repos/builtin/packages/aluminum/package.py
new file mode 100644
index 0000000000..9700988217
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aluminum/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aluminum(CMakePackage):
+    """Aluminum provides a generic interface to high-performance
+    communication libraries, with a focus on allreduce
+    algorithms. Blocking and non-blocking algorithms and GPU-aware
+    algorithms are supported. Aluminum also contains custom
+    implementations of select algorithms to optimize for certain
+    situations."""
+
+    homepage = "https://github.com/LLNL/Aluminum"
+    url      = "https://github.com/LLNL/Aluminum/archive/v0.1.tar.gz"
+    git      = "https://github.com/LLNL/Aluminum.git"
+
+    version('master', branch='master')
+    version('0.1', sha256='3880b736866e439dd94e6a61eeeb5bb2abccebbac82b82d52033bc6c94950bdb')
+
+    variant('gpu', default=False, description='Builds with support for GPUs via CUDA and cuDNN')
+    variant('nccl', default=False, description='Builds with support for NCCL communication lib')
+    variant('mpi_cuda', default=False, description='Builds with support for MPI-CUDA enabled library')
+
+    depends_on('cmake@3.9.0:', type='build')
+    depends_on('cuda', when='+gpu')
+    depends_on('cudnn', when='+gpu')
+    depends_on('cub', when='+gpu')
+    depends_on('mpi', when='~mpi_cuda')
+    depends_on('mpi +cuda', when='+mpi_cuda')
+    depends_on('nccl', when='+nccl')
+    depends_on('hwloc')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DALUMINUM_ENABLE_CUDA:BOOL=%s' % ('+gpu' in spec),
+            '-DALUMINUM_ENABLE_MPI_CUDA:BOOL=%s' % ('+mpi_cuda' in spec),
+            '-DALUMINUM_ENABLE_NCCL:BOOL=%s' % ('+nccl' in spec)]
+        return args
diff --git a/var/spack/repos/builtin/packages/amg/package.py b/var/spack/repos/builtin/packages/amg/package.py
index 5167347dc9..5a16aac3e0 100644
--- a/var/spack/repos/builtin/packages/amg/package.py
+++ b/var/spack/repos/builtin/packages/amg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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 0s2111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,11 +13,12 @@ class Amg(MakefilePackage):
     """
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    homepage = "https://codesign.llnl.gov/amg2013.php"
-    git      = "https://github.com/LLNL/AMG"
+    homepage = "https://computation.llnl.gov/projects/co-design/amg2013"
+    git      = "https://github.com/LLNL/AMG.git"
 
-    version('1.0', git=git, tag='1.0')
-    version('develop', git=git, branch='master')
+    version('develop', branch='master')
+    version('1.1', tag='1.1')
+    version('1.0', tag='1.0')
 
     variant('openmp', default=True, description='Build with OpenMP support')
     variant('optflags', default=False, description='Additional optimizations')
diff --git a/var/spack/repos/builtin/packages/amg2013/package.py b/var/spack/repos/builtin/packages/amg2013/package.py
index 43e9277805..78a3ac71c9 100644
--- a/var/spack/repos/builtin/packages/amg2013/package.py
+++ b/var/spack/repos/builtin/packages/amg2013/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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 0s2111-1307 USA
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,11 @@ class Amg2013(MakefilePackage):
     in the Center for Applied Scientific Computing (CASC) at LLNL.
     """
     tags = ['proxy-app']
-    homepage = "https://codesign.llnl.gov/amg2013.php"
-    url      = "https://codesign.llnl.gov/amg2013/amg2013.tgz"
+    homepage = "https://computation.llnl.gov/projects/co-design/amg2013"
+    url      = "https://computation.llnl.gov/projects/co-design/download/amg2013.tgz"
 
     version('master', '9d918d2a69528b83e6e0aba6ba601fef',
-            url='https://codesign.llnl.gov/amg2013/amg2013.tgz')
+            url='https://computation.llnl.gov/projects/co-design/download/amg2013.tgz')
 
     variant('openmp', default=True, description='Build with OpenMP support')
     variant('assumedpartition', default=False, description='Use assumed partition (for thousands of processors)')
diff --git a/var/spack/repos/builtin/packages/amp/package.py b/var/spack/repos/builtin/packages/amp/package.py
new file mode 100644
index 0000000000..c56d101a3a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/amp/package.py
@@ -0,0 +1,140 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Amp(CMakePackage):
+    """The Advanced Multi-Physics (AMP) package is an open source parallel
+    object-oriented computational framework that is designed with single
+    and multi-domain multi-physics applications in mind. AMP can be used
+    to build powerful and flexible multi-physics simulation algorithms
+    from lightweight operator, solver, linear algebra, material database,
+    discretization, and meshing components. The AMP design is meant to
+    enable existing investments in application codes to be leveraged without
+    having to adopt dramatically different data structures while developing
+    new computational science applications. Application components are
+    represented as discrete mathematical operators that only require a
+    minimal interface and through operator composition the incremental
+    development of complex parallel applications is enabled. AMP is meant
+    to allow application domain scientists, computer scientists and
+    mathematicians to simulate, collaborate, and conduct research on
+    various aspects of massively parallel simulation algorithms."""
+
+    homepage = "https://bitbucket.org/AdvancedMultiPhysics/amp"
+    hg       = homepage
+
+    version('develop')
+
+    # Everything should be compiled position independent (-fpic)
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('boost', when='+boost')
+    depends_on('petsc', when='+petsc')
+    depends_on('trilinos', when='+trilinos')
+    depends_on('hdf5', when='+hdf5')
+    depends_on('hdf5', when='+silo')
+    depends_on('silo', when='+silo')
+    depends_on('zlib', when="+zlib")
+
+    # MPI related dependencies
+    depends_on('mpi', when='+mpi')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        # #################### Base Settings #######################
+
+        options.extend([
+            '-DTPL_URL=https://bitbucket.org/AdvancedMultiPhysics/tpl-builder',
+            '-DAMP_DATA_URL=https://bitbucket.org/AdvancedMultiPhysics/amp/downloads/AMP-Data.tar.gz',
+            '-DAMP_ENABLE_TESTS:BOOL=OFF',
+            '-DAMP_ENABLE_EXAMPLES:BOOL=OFF',
+            '-DAMP_ENABLE_CXX11:BOOL=ON',
+            '-DCXX_STD=11',
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in spec else 'OFF'),
+        ])
+
+        # #################### Compiler Settings #######################
+
+        if '+mpi' in spec:
+            options.extend([
+                '-DCMAKE_C_COMPILER=%s'       % spec['mpi'].mpicc,
+                '-DCMAKE_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
+                '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+                '-DUSE_MPI=0',
+                '-DMPI_COMPILER=1',
+                '-DMPIEXEC=$s'                % spec['mpi'].prefix.bin,
+            ])
+        else:
+            options.extend([
+                '-DCMAKE_C_COMPILER=%s'       % self.compiler.cc,
+                '-DCMAKE_CXX_COMPILER=%s'     % self.compiler.cxx,
+                '-DCMAKE_Fortran_COMPILER=%s' % self.compiler.fc,
+                '-DUSE_MPI=0',
+            ])
+
+        # ################## Third Party Libraries #####################
+
+        tpl_list = "LAPACK"
+        blas = spec['blas'].libs
+        lapack = spec['lapack'].libs
+        options.extend([
+            '-DTPL_LAPACK_INSTALL_DIR=%s' % spec['lapack'].prefix,
+            '-DTPL_BLAS_LIBRARY_NAMES=%s' % ';'.join(blas.names),
+            '-DTPL_BLAS_LIBRARY_DIRS=%s' % ';'.join(blas.directories),
+            '-DTPL_LAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names),
+            '-DTPL_LAPACK_LIBRARY_DIRS=%s' % ';'.join(lapack.directories),
+        ])
+        if '+boost' in spec:
+            tpl_list = tpl_list + ";BOOST"
+            options.extend(['-DTPL_BOOST_INSTALL_DIR=%s' %
+                            spec['boost'].prefix, ])
+        if '+zlib' in spec:
+            tpl_list = tpl_list + ";ZLIB"
+            options.extend(['-DTPL_ZLIB_INSTALL_DIR=%s' %
+                            spec['zlib'].prefix, ])
+        if '+hdf5' in spec:
+            tpl_list = tpl_list + ";HDF5"
+            options.extend(['-DTPL_HDF5_INSTALL_DIR=%s' %
+                            spec['hdf5'].prefix, ])
+        if '+silo' in spec:
+            tpl_list = tpl_list + ";SILO"
+            options.extend(['-DTPL_SILO_INSTALL_DIR=%s' %
+                            spec['silo'].prefix, ])
+        if '+netcdf' in spec:
+            tpl_list = tpl_list + ";NETCDF"
+            options.extend(['-DTPL_NETCDF_INSTALL_DIR=%s' %
+                            spec['netcdf'].prefix, ])
+        if '+hypre' in spec:
+            tpl_list = tpl_list + ";HYPRE"
+            options.extend(['-DTPL_HYPRE_INSTALL_DIR=%s' %
+                            spec['hypre'].prefix, ])
+        if '+petsc' in spec:
+            tpl_list = tpl_list + ";PETSC"
+            options.extend(['-DTPL_PETSC_INSTALL_DIR=%s' %
+                            spec['petsc'].prefix, ])
+        if '+trilinos' in spec:
+            tpl_list = tpl_list + ";TRILINOS"
+            options.extend(['-DTPL_TRILINOS_INSTALL_DIR=%s' %
+                            spec['trilinos'].prefix, ])
+        if '+libmesh' in spec:
+            tpl_list = tpl_list + ";LIBMESH"
+            options.extend(['-DTPL_LIBMESH_INSTALL_DIR=%s' %
+                            spec['libmesh'].prefix, ])
+        if '+sundials' in spec:
+            tpl_list = tpl_list + ";SUNDIALS"
+            options.extend(['-DTPL_SUNDIALS_INSTALL_DIR=%s' %
+                            spec['sundials'].prefix, ])
+        if '+amp-timer' in spec:
+            tpl_list = tpl_list + ";TIMER"
+            options.extend(['-DTPL_TIMER_INSTALL_DIR=%s' %
+                            spec['amp-timer'].prefix, ])
+        options.extend(['-DTPL_LIST=%s' % tpl_list, ])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/ampliconnoise/package.py b/var/spack/repos/builtin/packages/ampliconnoise/package.py
index 626ac16678..e70328fa1e 100644
--- a/var/spack/repos/builtin/packages/ampliconnoise/package.py
+++ b/var/spack/repos/builtin/packages/ampliconnoise/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/amr-exp-parabolic/package.py b/var/spack/repos/builtin/packages/amr-exp-parabolic/package.py
deleted file mode 100644
index 14d393ed27..0000000000
--- a/var/spack/repos/builtin/packages/amr-exp-parabolic/package.py
+++ /dev/null
@@ -1,95 +0,0 @@
-##############################################################################
-# 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/spack/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 glob
-
-
-class AmrExpParabolic(MakefilePackage):
-    """Simplified block-structured adaptive mesh refinement algorithm
-    in two and three dimensions with subcycling in time.
-    The algorithm solves a linear advection diffusion equation
-    with a simple numerical method. This proxy app is intended to
-    capture the communication pattern of an explicit AMR algorithm
-    but does not represent an accurate characterization of
-    floating point effort or
-    relative costs of communication to computation."""
-
-    homepage = "https://ccse.lbl.gov/ExaCT/index.html"
-    url      = "https://ccse.lbl.gov/ExaCT/AMR_Exp_Parabolic.tgz"
-    tags     = ['proxy-app']
-
-    version(
-        'release', '330604d9cc755dad8a2cdfaa7ff8f6a4',
-        url='https://ccse.lbl.gov/ExaCT/AMR_Exp_Parabolic.tgz')
-
-    variant(
-        'debug', default=False, description='Turn on debugging')
-    variant(
-        'mpi', default=True, description='Build with MPI support')
-    variant(
-        'openmp', default=False,
-        description='Build with OpenMP support')
-    variant(
-        'prof', default=False, description='Use profiler')
-
-    depends_on('mpi', when='+mpi')
-    depends_on('gmake', type='build')
-
-    build_directory = 'MiniApps/AMR_Adv_Diff_F90'
-
-    def edit(self, spec, prefix):
-        def_file = FileFilter('Tools/F_mk/GMakedefs.mak')
-        def_file.filter('tdir = t/.*', 'tdir := t/$(suf)')
-        def_file.filter('hdir = t/.*', 'hdir := t/html')
-        def_file.filter('include $(BOXLIB_HOME)/Tools/F_mk/GMakeMPI.mak', '#')
-
-        if '+mpi' in spec:
-            def_file.filter('FC.*:=.*', 'FC = {0}'.format(spec['mpi'].mpifc))
-            def_file.filter('F90.*:=.*', 'F90 = {0}'.format(spec['mpi'].mpifc))
-            def_file.filter(
-                'mpi_include_dir =.*',
-                'mpi_include_dir = {0}'.format(spec['mpi'].prefix.include))
-            def_file.filter(
-                'mpi_lib_dir =.*',
-                'mpi_lib_dir = {0}'.format(spec['mpi'].prefix.lib))
-
-        with working_dir(self.build_directory):
-            makefile = FileFilter('GNUmakefile')
-            if '+debug' in spec:
-                makefile.filter('NDEBUG.*:= t', '#')
-            if '~mpi' in spec:
-                makefile.filter('MPI.*:= t', '#')
-            if '+openmp' in spec:
-                makefile.filter('OMP.*:=', 'OMP := t')
-            if '+prof' in spec:
-                makefile.filter('PROF.*:=', 'PROF := t')
-
-    def install(self, spec, prefix):
-        mkdirp(prefix.bin)
-        files = glob.glob(join_path(self.build_directory, '*.exe'))
-        for f in files:
-            install(f, prefix.bin)
-        install('README.txt', prefix)
-        install('license.txt', prefix)
diff --git a/var/spack/repos/builtin/packages/amrex/package.py b/var/spack/repos/builtin/packages/amrex/package.py
index 89533db2e6..abf1e54968 100644
--- a/var/spack/repos/builtin/packages/amrex/package.py
+++ b/var/spack/repos/builtin/packages/amrex/package.py
@@ -1,86 +1,73 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Amrex(CMakePackage):
-    """AMReX is the successor to BoxLib.
-       It is a Block-Structured AMR Framework.
-    """
-
-    homepage = "https://ccse.lbl.gov/AMReX/index.html"
-    url      = "https://github.com/AMReX-Codes/amrex.git"
+    """AMReX is a publicly available software framework designed
+    for building massively parallel block- structured adaptive
+    mesh refinement (AMR) applications."""
 
-    version('17.06', git='https://github.com/AMReX-Codes/amrex.git', commit='836d3c7')
-    version('master', git='https://github.com/AMReX-Codes/amrex.git', tag='master')
-    version('develop', git='https://github.com/AMReX-Codes/amrex.git', tag='development')
+    homepage = "https://amrex-codes.github.io/amrex/"
+    git      = "https://github.com/AMReX-Codes/amrex.git"
 
-    variant('dims',
-        default='3',
-        values=('1', '2', '3'),
-        multi=False,
-        description='Number of spatial dimensions')
+    version('develop', branch='development')
+    version('18.10.1', commit='260b53169badaa760b91dfc60ea6b2ea3d9ccf06')  # tag:18.10.1
+    version('18.10', commit='d37a266c38092e1174096e245326e9eead1f4e03')  # tag:18.10
+    version('18.09.1', commit='88120db4736c325a2d3d2c291adacaffd3bf224b')  # tag:18.09.1
 
-    variant('prec',
-        default='DOUBLE',
-        values=('FLOAT', 'DOUBLE'),
-        multi=False,
-        description='Floating point precision')
-
-    variant('mpi', default=True, description='Enable MPI parallel support')
-    variant('openmp', default=False, description='Enable OpenMP parallel support')
-    variant('fortran', default=True, description='Enable Fortran support')
-    variant('debug', default=False, description='Enable debugging features')
-    variant('particles', default=False, description='Include particle classes in build')
+    # Config options
+    variant('dimensions', default='3',
+            description='Dimensionality', values=('2', '3'))
+    variant('shared',  default=False,
+            description='Build shared library')
+    variant('mpi',          default=True,
+            description='Build with MPI support')
+    variant('openmp',       default=False,
+            description='Build with OpenMP support')
+    variant('precision',  default='double',
+            description='Real precision (double/single)',
+            values=('single', 'double'))
+    variant('eb',  default=False,
+            description='Build Embedded Boundary classes')
+    variant('fortran',  default=False,
+            description='Build Fortran API')
+    variant('linear_solvers', default=True,
+            description='Build linear solvers')
+    variant('amrdata',    default=False,
+            description='Build data services')
+    variant('particles',  default=False,
+            description='Build particle classes')
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
 
+    # Build dependencies
     depends_on('mpi', when='+mpi')
+    depends_on('python@2.7:', type='build')
+    depends_on('cmake@3.5:',  type='build')
+    conflicts('%clang')
 
-    def cmake_args(self):
-        spec = self.spec
+    def cmake_is_on(self, option):
+        return 'ON' if option in self.spec else 'OFF'
 
-        cmake_args = [
-            '-DENABLE_POSITION_INDEPENDENT_CODE=ON',
-            '-DBL_SPACEDIM:INT=%d' % int(spec.variants['dims'].value),
-            '-DBL_PRECISION:STRING=%s' % spec.variants['prec'].value,
-            '-DENABLE_FMG=%s' % ('+fortran' in spec),
-            '-DENABLE_FBASELIB=%s' % ('+fortran' in spec),
-            '-DBL_DEBUG:INT=%d' % int('+debug' in spec),
-            '-DBL_USE_PARTICLES:INT=%d' % int('+particles' in spec),
-            '-DENABLE_MPI:INT=%d' % int('+mpi' in spec),
-            '-DENABLE_OpenMP:INT=%d' % int('+openmp' in spec),
+    def cmake_args(self):
+        args = [
+            '-DUSE_XSDK_DEFAULTS=ON',
+            '-DDIM:STRING=%s' % self.spec.variants['dimensions'].value,
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % self.cmake_is_on('+shared'),
+            '-DENABLE_MPI:BOOL=%s' % self.cmake_is_on('+mpi'),
+            '-DENABLE_OMP:BOOL=%s' % self.cmake_is_on('+openmp'),
+            '-DXSDK_PRECISION:STRING=%s' %
+            self.spec.variants['precision'].value.upper(),
+            '-DENABLE_EB:BOOL=%s' % self.cmake_is_on('+eb'),
+            '-DXSDK_ENABLE_Fortran:BOOL=%s' % self.cmake_is_on('+fortran'),
+            '-DENABLE_LINEAR_SOLVERS:BOOL=%s' %
+            self.cmake_is_on('+linear_solvers'),
+            '-DENABLE_AMRDATA:BOOL=%s' % self.cmake_is_on('+amrdata'),
+            '-DENABLE_PARTICLES:BOOL=%s' % self.cmake_is_on('+particles')
         ]
-
-        if '+mpi' in spec:
-            cmake_args += [
-                '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
-                '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx
-            ]
-            if '+fortran' in spec:
-                cmake_args += [
-                    '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc
-                ]
-            cmake_args += ['-DENABLE_FORTRAN_MPI=%s' % ('+fortran' in spec)]
-
-        return cmake_args
+        return args
diff --git a/var/spack/repos/builtin/packages/amrvis/package.py b/var/spack/repos/builtin/packages/amrvis/package.py
new file mode 100644
index 0000000000..b9e69466d7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/amrvis/package.py
@@ -0,0 +1,192 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Amrvis(MakefilePackage):
+    """Amrvis is a visualization package specifically designed to
+       read and display output and profiling data from codes built
+       on the AMReX framework.
+    """
+
+    homepage = "https://github.com/AMReX-Codes/Amrvis"
+    git      = "https://github.com/AMReX-Codes/Amrvis.git"
+
+    version('master', tag='master')
+
+    variant(
+        'dims',
+        default='3',
+        values=('1', '2', '3'),
+        multi=False,
+        description='Number of spatial dimensions'
+    )
+    variant(
+        'prec',
+        default='DOUBLE',
+        values=('FLOAT', 'DOUBLE'),
+        multi=False,
+        description='Floating point precision'
+    )
+    variant('mpi', default=True, description='Enable MPI parallel support')
+    variant('debug', default=False, description='Enable debugging features')
+    variant('profiling', default=False,
+            description='Enable AMReX profiling features')
+
+    depends_on('gmake', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('libsm')
+    depends_on('libice')
+    depends_on('libxpm')
+    depends_on('libx11')
+    depends_on('libxt')
+    depends_on('libxext')
+    depends_on('motif')
+    depends_on('flex')
+    depends_on('bison')
+
+    conflicts(
+        '+profiling', when='dims=1',
+        msg='Amrvis profiling support requires a 2D build'
+    )
+    conflicts(
+        '+profiling', when='dims=3',
+        msg='Amrvis profiling support requires a 2D build'
+    )
+
+    # Only doing gcc and clang at the moment.
+    # Intel currently fails searching for mpiicc, mpiicpc, etc.
+    for comp in ['%intel', '%cce', '%nag', '%pgi', '%xl', '%xl_r']:
+        conflicts(
+            comp,
+            msg='Amrvis currently only builds with gcc and clang'
+        )
+
+    # Need to clone AMReX into Amrvis because Amrvis uses AMReX's source
+    resource(name='amrex',
+             git='https://github.com/AMReX-Codes/amrex.git',
+             tag='master',
+             placement='amrex')
+
+    def edit(self, spec, prefix):
+        # Set all available makefile options to values we want
+        makefile = FileFilter('GNUmakefile')
+        makefile.filter(
+            r'^AMREX_HOME\s*\?=.*',
+            'AMREX_HOME = {0}'.format('./amrex')
+        )
+        makefile.filter(
+            r'^PRECISION\s*=.*',
+            'PRECISION = {0}'.format(spec.variants['prec'].value)
+        )
+        makefile.filter(
+            r'^DIM\s*=.*',
+            'DIM = {0}'.format(spec.variants['dims'].value)
+        )
+        makefile.filter(
+            r'^PROFILE\s*=.*',
+            'PROFILE = {0}'.format(
+                spec.variants['profiling'].value
+            ).upper()
+        )
+        makefile.filter(
+            r'^TRACE_PROFILE\s*=.*',
+            'TRACE_PROFILE = {0}'.format(
+                spec.variants['profiling'].value
+            ).upper()
+        )
+        makefile.filter(
+            r'^COMM_PROFILE\s*=.*',
+            'COMM_PROFILE = {0}'.format(
+                spec.variants['profiling'].value
+            ).upper()
+        )
+        makefile.filter(
+            r'^COMP\s*=.*',
+            'COMP = {0}'.format(self.compiler.name)
+        )
+        makefile.filter(
+            r'^DEBUG\s*=.*',
+            'DEBUG = {0}'.format(spec.variants['debug'].value).upper()
+        )
+        makefile.filter(
+            r'^USE_ARRAYVIEW\s*=.*',
+            'USE_ARRAY_VIEW = FALSE'
+        )
+        makefile.filter(
+            r'^USE_MPI\s*=.*',
+            'USE_MPI = {0}'.format(spec.variants['mpi'].value).upper()
+        )
+        makefile.filter(
+            r'^USE_CXX11\s*=.*',
+            'USE_CXX11 = TRUE'
+        )
+        makefile.filter(
+            r'^USE_VOLRENDER\s*=.*',
+            'USE_VOLRENDER = FALSE'
+        )
+        makefile.filter(
+            r'^USE_PARALLELVOLRENDER\s*=.*',
+            'USE_PARALLELVOLRENDER = FALSE'
+        )
+        makefile.filter(
+            r'^USE_PROFPARSER\s*=.*',
+            'USE_PROFPARSER = {0}'.format(
+                spec.variants['profiling'].value
+            ).upper()
+        )
+
+        # A bit risky here deleting all /usr and /opt X
+        # library default search paths in makefile
+        makefile.filter(
+            r'^.*\b(usr|opt)\b.*$',
+            '# Spack removed INCLUDE_LOCATIONS and LIBRARY_LOCATIONS'
+        )
+
+        # Read GNUmakefile into array
+        with open('GNUmakefile', 'r') as file:
+            contents = file.readlines()
+
+        # Edit GNUmakefile includes and libraries to point to Spack
+        # dependencies.
+        # The safest bet is to put the LIBRARY_LOCATIONS and
+        # INCLUDE_LOCATIONS at the beginning of the makefile.
+        line_offset = 0
+        count = 0
+        for lib in ['libsm', 'libice', 'libxpm', 'libx11',
+                    'libxt', 'libxext', 'motif']:
+            contents.insert(
+                line_offset + count,
+                'LIBRARY_LOCATIONS += {0}\n'.format(spec[lib].prefix.lib)
+            )
+            contents.insert(
+                line_offset + count + 1,
+                'INCLUDE_LOCATIONS += {0}\n'.format(spec[lib].prefix.include)
+            )
+            count += 1
+
+        # Write GNUmakefile
+        with open('GNUmakefile', 'w') as file:
+            file.writelines(contents)
+
+    def setup_environment(self, spack_env, run_env):
+        # We don't want an AMREX_HOME the user may have set already
+        spack_env.unset('AMREX_HOME')
+        # Help force Amrvis to not pick up random system compilers
+        if '+mpi' in self.spec:
+            spack_env.set('MPI_HOME', self.spec['mpi'].prefix)
+            spack_env.set('CC', self.spec['mpi'].mpicc)
+            spack_env.set('CXX', self.spec['mpi'].mpicxx)
+            spack_env.set('F77', self.spec['mpi'].mpif77)
+            spack_env.set('FC', self.spec['mpi'].mpifc)
+
+    def install(self, spec, prefix):
+        # Install exe manually
+        mkdirp(prefix.bin)
+        exes = glob.iglob('*.ex')
+        for exe in exes:
+            install(exe, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/andi/package.py b/var/spack/repos/builtin/packages/andi/package.py
index 44c2644507..091cdc80ef 100644
--- a/var/spack/repos/builtin/packages/andi/package.py
+++ b/var/spack/repos/builtin/packages/andi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/angsd/package.py b/var/spack/repos/builtin/packages/angsd/package.py
index eb3e5e58f5..e39cc5e5a9 100644
--- a/var/spack/repos/builtin/packages/angsd/package.py
+++ b/var/spack/repos/builtin/packages/angsd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,9 +16,11 @@ class Angsd(MakefilePackage):
     homepage = "https://github.com/ANGSD/angsd"
     url      = "https://github.com/ANGSD/angsd/archive/0.919.tar.gz"
 
+    version('0.921', '3702db035396db602c7f74728b1a5a1f')
     version('0.919', '79d342f49c24ac00d35934f2617048d4')
 
     depends_on('htslib')
+    conflicts('^htslib@1.6:', when='@0.919')
 
     def setup_environment(self, spack_env, run_env):
         run_env.set('R_LIBS', prefix.R)
diff --git a/var/spack/repos/builtin/packages/ant/package.py b/var/spack/repos/builtin/packages/ant/package.py
index 82478c481d..302ba94699 100644
--- a/var/spack/repos/builtin/packages/ant/package.py
+++ b/var/spack/repos/builtin/packages/ant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,8 +15,7 @@ class Ant(Package):
     homepage = "http://ant.apache.org/"
     url = "https://archive.apache.org/dist/ant/source/apache-ant-1.9.7-src.tar.gz"
 
-    # 1.10.0 requires newer Java, not yet tested....
-    # version('1.10.0', '2260301bb7734e34d8b96f1a5fd7979c')
+    version('1.10.0', '2260301bb7734e34d8b96f1a5fd7979c')
     version('1.9.9',  '22c9d40dabafbec348aaada226581239')
     version('1.9.8',  '16253d516d5c33c4af9ef8fafcf1004b')
     version('1.9.7',  'a2fd9458c76700b7be51ef12f07d4bb1')
@@ -46,4 +26,4 @@ class Ant(Package):
     def install(self, spec, prefix):
         env['ANT_HOME'] = self.prefix
         bash = which('bash')
-        bash('./build.sh', 'install')
+        bash('./build.sh', 'install-lite')
diff --git a/var/spack/repos/builtin/packages/antlr/package.py b/var/spack/repos/builtin/packages/antlr/package.py
index 50324dd82c..70a21cd0f9 100644
--- a/var/spack/repos/builtin/packages/antlr/package.py
+++ b/var/spack/repos/builtin/packages/antlr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -51,6 +32,7 @@ class Antlr(AutotoolsPackage):
         spec = self.spec
 
         return [
+            '--disable-csharp',
             '--{0}-cxx'.format('enable' if '+cxx' in spec else 'disable'),
             '--{0}-java'.format('enable' if '+java' in spec else 'disable'),
             '--{0}-python'.format('enable' if '+python' in spec else 'disable')
diff --git a/var/spack/repos/builtin/packages/ants/package.py b/var/spack/repos/builtin/packages/ants/package.py
new file mode 100644
index 0000000000..866301c1e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ants/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ants(CMakePackage):
+    """ANTs extracts information from complex datasets that include imaging.
+       Paired with ANTsR (answer), ANTs is useful for managing, interpreting
+       and visualizing multidimensional data. ANTs is popularly considered a
+       state-of-the-art medical image registration and segmentation toolkit.
+       ANTs depends on the Insight ToolKit (ITK), a widely used medical image
+       processing library to which ANTs developers contribute.
+    """
+
+    homepage = "http://stnava.github.io/ANTs/"
+    url      = "https://github.com/ANTsX/ANTs/archive/v2.2.0.tar.gz"
+
+    version('2.2.0', '5661b949268100ac0f7baf6d2702b4dd')
+
+    def install(self, spec, prefix):
+        with working_dir(join_path('spack-build', 'ANTS-build'), create=False):
+            make("install")
+        install_tree('Scripts', prefix.bin)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('ANTSPATH', self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/ape/package.py b/var/spack/repos/builtin/packages/ape/package.py
index dd24c84e5e..c054c06106 100644
--- a/var/spack/repos/builtin/packages/ape/package.py
+++ b/var/spack/repos/builtin/packages/ape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/aperture-photometry/APT.sh b/var/spack/repos/builtin/packages/aperture-photometry/APT.sh
new file mode 100644
index 0000000000..b51d30626b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aperture-photometry/APT.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+# convenience wrapper for the aperture jar file
+java -jar APT.jar "$@"
+
diff --git a/var/spack/repos/builtin/packages/aperture-photometry/package.py b/var/spack/repos/builtin/packages/aperture-photometry/package.py
new file mode 100644
index 0000000000..82d4af33b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aperture-photometry/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class AperturePhotometry(Package):
+    """Aperture Photometry Tool APT is software for astronomical research"""
+
+    homepage = "http://www.aperturephotometry.org/aptool/"
+    url      = "http://www.aperturephotometry.org/aptool/wp-content/plugins/download-monitor/download.php?id=1"
+
+    version('2.7.2', '2beca6aac14c5e0a94d115f81edf0caa9ec83dc9d32893ea00ee376c9360deb0', extension='tar.gz')
+
+    depends_on('java')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'APT.jar'
+        install(jar_file, prefix.bin)
+        java = join_path(self.spec['java'].prefix, 'bin', 'java')
+        script_sh = join_path(os.path.dirname(__file__), "APT.sh")
+        script = join_path(prefix.bin, "apt")
+        install(script_sh, script)
+        set_executable(script)
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('APT.jar', join_path(prefix.bin, 'APT.jar'),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/apex/package.py b/var/spack/repos/builtin/packages/apex/package.py
index 50f74f6220..b78b183021 100644
--- a/var/spack/repos/builtin/packages/apex/package.py
+++ b/var/spack/repos/builtin/packages/apex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/apple-libunwind/package.py b/var/spack/repos/builtin/packages/apple-libunwind/package.py
new file mode 100644
index 0000000000..ced31d20e8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/apple-libunwind/package.py
@@ -0,0 +1,79 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class AppleLibunwind(Package):
+    """Placeholder package for Apple's analogue to non-GNU libunwind"""
+
+    homepage = "https://opensource.apple.com/source/libunwind/libunwind-35.3/"
+
+    provides('unwind')
+
+    # The 'conflicts' directive only accepts valid spack specs;
+    # platforms cannot be negated -- 'platform!=darwin' is not a valid
+    # spec -- so expressing a conflict for any platform that isn't
+    # Darwin must be expressed by listing a conflict with every
+    # platform that isn't Darwin/macOS
+    conflicts('platform=linux')
+    conflicts('platform=bgq')
+    conflicts('platform=cray')
+
+    # Override the fetcher method to throw a useful error message;
+    # avoids GitHub issue (#7061) in which the opengl placeholder
+    # package threw a generic, uninformative error during the `fetch`
+    # step,
+    @property
+    def fetcher(self):
+        msg = """This package is intended to be a placeholder for Apple's
+        system-provided, non-GNU-compatible libunwind library.
+
+        Add to your packages.yaml:
+
+        packages:
+          apple-libunwind:
+            paths:
+              apple-libunwind@35.3: /usr
+            buildable: False
+
+        """
+        raise InstallError(msg)
+
+    def install(self, spec, prefix):
+        pass
+
+    @property
+    def libs(self):
+        """Export the Apple libunwind library. The Apple libunwind library
+        cannot be linked to directly using an absolute path; doing so
+        will cause the linker to throw an error 'cannot link directly
+        with /usr/lib/system/libunwind.dylib' and the linker will
+        suggest linking with System.framework instead. Linking to this
+        framework is equivalent to linking with libSystem.dylib, which
+        can be confirmed on a macOS system by executing at a terminal
+        the command `ls -l
+        /System/Library/Frameworks/System.Framework` -- the file
+        "System" is a symlink to `/usr/lib/libSystem.B.dylib`, and
+        `/usr/lib/libSystem.dylib` also symlinks to this file.
+
+        Running `otool -L /usr/lib/libSystem.dylib` confirms that
+        it will link dynamically to `/usr/lib/system/libunwind.dylib`.
+
+        """
+        libs = find_libraries('libSystem',
+                              self.prefix.lib,
+                              shared=True, recursive=False)
+        if libs:
+            return libs
+        return None
+
+    @property
+    def headers(self):
+        """ Export the Apple libunwind header
+        """
+        hdrs = HeaderList(find(self.prefix.include, 'libunwind.h',
+                               recursive=False))
+        return hdrs or None
diff --git a/var/spack/repos/builtin/packages/applewmproto/package.py b/var/spack/repos/builtin/packages/applewmproto/package.py
index 170df5d570..231becb6b2 100644
--- a/var/spack/repos/builtin/packages/applewmproto/package.py
+++ b/var/spack/repos/builtin/packages/applewmproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Applewmproto(AutotoolsPackage):
 
     version('1.4.2', 'ecc8a4424a893ce120f5652dba62e9e6')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/appres/package.py b/var/spack/repos/builtin/packages/appres/package.py
index 87f5c2ff96..ab798eb4c2 100644
--- a/var/spack/repos/builtin/packages/appres/package.py
+++ b/var/spack/repos/builtin/packages/appres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Appres(AutotoolsPackage):
     depends_on('libxt')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/apr-util/package.py b/var/spack/repos/builtin/packages/apr-util/package.py
index 1b68584530..0f237e8e6f 100644
--- a/var/spack/repos/builtin/packages/apr-util/package.py
+++ b/var/spack/repos/builtin/packages/apr-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/apr/package.py b/var/spack/repos/builtin/packages/apr/package.py
index f78b229229..a0e2e9f52e 100644
--- a/var/spack/repos/builtin/packages/apr/package.py
+++ b/var/spack/repos/builtin/packages/apr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/aragorn/package.py b/var/spack/repos/builtin/packages/aragorn/package.py
new file mode 100644
index 0000000000..3bd4878770
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aragorn/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aragorn(Package):
+    """ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide
+    sequences."""
+
+    homepage = "http://mbio-serv2.mbioekol.lu.se/ARAGORN"
+    url      = "http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.38.tgz"
+
+    version('1.2.38', '1df0ed600069e6f520e5cd989de1eaf0')
+
+    phases = ['build', 'install']
+
+    def build(self, spec, prefix):
+        cc = Executable(spack_cc)
+        cc('-O3', '-ffast-math', '-finline-functions',
+           '-oaragorn', 'aragorn' + format(spec.version.dotted) + '.c')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('aragorn', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/archer/package.py b/var/spack/repos/builtin/packages/archer/package.py
index 87ced1051a..fa326d13c7 100644
--- a/var/spack/repos/builtin/packages/archer/package.py
+++ b/var/spack/repos/builtin/packages/archer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/argobots/package.py b/var/spack/repos/builtin/packages/argobots/package.py
new file mode 100644
index 0000000000..3df5a2039e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/argobots/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Argobots(AutotoolsPackage):
+    """Argobots, which was developed as a part of the Argo project, is
+    a lightweight runtime system that supports integrated computation
+    and data movement with massive concurrency. It will directly
+    leverage the lowest-level constructs in the hardware and OS:
+    lightweight notification mechanisms, data movement engines, memory
+    mapping, and data placement strategies. It consists of an
+    execution model and a memory model."""
+
+    homepage = "http://www.argobots.org/"
+    url      = "https://github.com/pmodels/argobots/releases/download/v1.0b1/argobots-1.0b1.tar.gz"
+
+    version("1.0b1", "5eeab7b2c639d08bbea22db3026cdf39")
+    version("1.0a1", "9d29d57d14d718f93b505178f6ba3e08")
diff --git a/var/spack/repos/builtin/packages/argp-standalone/argp-fmtstream.h.patch b/var/spack/repos/builtin/packages/argp-standalone/argp-fmtstream.h.patch
new file mode 100644
index 0000000000..b0a518fc67
--- /dev/null
+++ b/var/spack/repos/builtin/packages/argp-standalone/argp-fmtstream.h.patch
@@ -0,0 +1,11 @@
+--- argp-fmtstream.h.orig	2003-12-11 09:37:05.000000000 +0100
++++ argp-fmtstream.h	2011-08-12 11:56:43.000000000 +0200
+@@ -192,7 +192,7 @@
+ extern int _argp_fmtstream_ensure (argp_fmtstream_t __fs, size_t __amount);
+ extern int __argp_fmtstream_ensure (argp_fmtstream_t __fs, size_t __amount);
+ 
+-#ifdef __OPTIMIZE__
++#if defined(__OPTIMIZE__) && !defined(__clang__)
+ /* Inline versions of above routines.  */
+
+ #if !_LIBC
\ No newline at end of file
diff --git a/var/spack/repos/builtin/packages/argp-standalone/package.py b/var/spack/repos/builtin/packages/argp-standalone/package.py
new file mode 100644
index 0000000000..1f82edbf87
--- /dev/null
+++ b/var/spack/repos/builtin/packages/argp-standalone/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class ArgpStandalone(AutotoolsPackage):
+    """Standalone version of the argp interface from glibc for parsing
+       unix-style arguments. """
+
+    homepage = "https://www.lysator.liu.se/~nisse/misc"
+    url      = "https://www.lysator.liu.se/~nisse/misc/argp-standalone-1.3.tar.gz"
+
+    version('1.3', '720704bac078d067111b32444e24ba69')
+
+    # Homebrew (https://github.com/Homebrew/homebrew-core) patches
+    # argp-standalone to work on Darwin; the patchfile below was taken
+    # from
+    # https://raw.githubusercontent.com/Homebrew/formula-patches/b5f0ad3/argp-standalone/patch-argp-fmtstream.h
+    patch('argp-fmtstream.h.patch', 0, 'platform=darwin', '.')
+
+    def install(self, spec, prefix):
+        make('install')
+        make('check')
+        mkdirp(self.spec.prefix.lib)
+        install('libargp.a', join_path(self.spec.prefix.lib, 'libargp.a'))
+        mkdirp(self.spec.prefix.include)
+        install('argp.h', join_path(self.spec.prefix.include, 'argp.h'))
diff --git a/var/spack/repos/builtin/packages/argtable/package.py b/var/spack/repos/builtin/packages/argtable/package.py
index f622e29837..cc280a1f7c 100644
--- a/var/spack/repos/builtin/packages/argtable/package.py
+++ b/var/spack/repos/builtin/packages/argtable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/arlecore/package.py b/var/spack/repos/builtin/packages/arlecore/package.py
index 69de30423d..e873aa8ffb 100644
--- a/var/spack/repos/builtin/packages/arlecore/package.py
+++ b/var/spack/repos/builtin/packages/arlecore/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import distutils.dir_util
 
 
 class Arlecore(Package):
@@ -37,4 +17,4 @@ class Arlecore(Package):
     depends_on('r', type=('build', 'run'))
 
     def install(self, spec, prefix):
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py
index 2037f552d8..f538b2a6ce 100644
--- a/var/spack/repos/builtin/packages/armadillo/package.py
+++ b/var/spack/repos/builtin/packages/armadillo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py
index a784baf1cc..b6b87f58fe 100644
--- a/var/spack/repos/builtin/packages/arpack-ng/package.py
+++ b/var/spack/repos/builtin/packages/arpack-ng/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -54,8 +35,13 @@ class ArpackNg(Package):
     """
 
     homepage = 'https://github.com/opencollab/arpack-ng'
-    url = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz'
+    url      = 'https://github.com/opencollab/arpack-ng/archive/3.3.0.tar.gz'
+    git      = 'https://github.com/opencollab/arpack-ng.git'
 
+    version('develop', branch='master')
+    version('3.6.3', sha256='64f3551e5a2f8497399d82af3076b6a33bf1bc95fc46bbcabe66442db366f453')
+    version('3.6.2', sha256='673c8202de996fd3127350725eb1818e534db4e79de56d5dcee8c00768db599a')
+    version('3.6.0', 'f2607c1d5f80e922d55751fbed86a8ec')
     version('3.5.0', '9762c9ae6d739a9e040f8201b1578874')
     version('3.4.0', 'ae9ca13f2143a7ea280cb0e2fd4bfae4')
     version('3.3.0', 'ed3648a23f0a868a43ef44c97a21bad5')
@@ -91,7 +77,7 @@ class ArpackNg(Package):
             libraries = ['libparpack'] + libraries
 
         return find_libraries(
-            libraries, root=self.prefix, shared=True, recurse=True
+            libraries, root=self.prefix, shared=True, recursive=True
         )
 
     @when('@3.4.0:')
diff --git a/var/spack/repos/builtin/packages/arrow/package.py b/var/spack/repos/builtin/packages/arrow/package.py
new file mode 100644
index 0000000000..7610d1fae0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/arrow/package.py
@@ -0,0 +1,64 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Arrow(CMakePackage):
+    """A cross-language development platform for in-memory data.
+
+    This package contains the C++ bindings.
+    """
+
+    homepage = "http://arrow.apache.org"
+    url      = "https://github.com/apache/arrow/archive/apache-arrow-0.9.0.tar.gz"
+
+    version('0.11.0', '0ac629a7775d86108e403eb66d9f1a3d3bdd6b3a497a86228aa4e8143364b7cc')
+    version('0.9.0', 'ebbd36c362b9e1d398ca612f6d2531ec')
+    version('0.8.0', '56436f6f61ccc68686b7e0ea30bf4d09')
+
+    depends_on('boost@1.60:')
+    depends_on('cmake@3.2.0:', type='build')
+    depends_on('flatbuffers@1.8.0 build_type=Release')  # only Release contains flatc
+    depends_on('python', when='+python')
+    depends_on('py-numpy', when='+python')
+    depends_on('rapidjson')
+    depends_on('snappy~shared')
+    depends_on('zlib+pic')
+    depends_on('zstd+pic')
+
+    variant('build_type', default='Release',
+            description='CMake build type',
+            values=('Debug', 'FastDebug', 'Release'))
+    variant('python', default=False, description='Build Python interface')
+    variant('parquet', default=False, description='Build Parquet interface')
+
+    root_cmakelists_dir = 'cpp'
+
+    def patch(self):
+        """Prevent `-isystem /usr/include` from appearing, since this confuses gcc.
+        """
+        filter_file(r'(include_directories\()SYSTEM ',
+                    r'\1',
+                    'cpp/cmake_modules/ThirdpartyToolchain.cmake')
+
+    def cmake_args(self):
+        args = [
+            "-DARROW_USE_SSE=ON",
+            "-DARROW_BUILD_SHARED=ON",
+            "-DARROW_BUILD_STATIC=OFF",
+            "-DARROW_BUILD_TESTS=OFF",
+            "-DARROW_WITH_BROTLI=OFF",
+            "-DARROW_WITH_LZ4=OFF",
+        ]
+        if self.spec.satisfies('+python'):
+            args.append("-DARROW_PYTHON:BOOL=ON")
+        if self.spec.satisfies('+parquet'):
+            args.append("-DARROW_PARQUET:BOOL=ON")
+        for dep in ('flatbuffers', 'rapidjson', 'snappy', 'zlib', 'zstd'):
+            args.append("-D{0}_HOME={1}".format(dep.upper(),
+                                                self.spec[dep].prefix))
+        args.append("-DZLIB_LIBRARIES={0}".format(self.spec['zlib'].libs))
+        return args
diff --git a/var/spack/repos/builtin/packages/ascent/package.py b/var/spack/repos/builtin/packages/ascent/package.py
index 854bf1e909..22dd639c1a 100644
--- a/var/spack/repos/builtin/packages/ascent/package.py
+++ b/var/spack/repos/builtin/packages/ascent/package.py
@@ -1,28 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -47,14 +26,11 @@ class Ascent(Package):
     simulations."""
 
     homepage = "https://github.com/Alpine-DAV/ascent"
-    url      = "https://github.com/Alpine-DAV/ascent"
+    git      = "https://github.com/Alpine-DAV/ascent.git"
 
     maintainers = ['cyrush']
 
-    version('develop',
-            git='https://github.com/Alpine-DAV/ascent.git',
-            branch='develop',
-            submodules=True)
+    version('develop', branch='develop', submodules=True)
 
     ###########################################################################
     # package variants
@@ -78,7 +54,7 @@ class Ascent(Package):
     variant("tbb", default=True, description="Build tbb support")
     variant("cuda", default=False, description="Build cuda support")
 
-    variant("adios", default=True, description="Build Adios filter support")
+    variant("adios", default=False, description="Build Adios filter support")
 
     # variants for dev-tools (docs, etc)
     variant("doc", default=False, description="Build Conduit's documentation")
@@ -88,7 +64,7 @@ class Ascent(Package):
     ###########################################################################
 
     depends_on("cmake", when="+cmake")
-    depends_on("conduit")
+    depends_on("conduit@master")
 
     #######################
     # Python
@@ -97,9 +73,7 @@ class Ascent(Package):
     # causes duplicate state issues when running compiled python modules.
     depends_on("python+shared")
     extends("python", when="+python")
-    # TODO: blas and lapack are disabled due to build
-    # issues Cyrus experienced on OSX 10.11.6
-    depends_on("py-numpy~blas~lapack", when="+python", type=('build', 'run'))
+    depends_on("py-numpy", when="+python", type=('build', 'run'))
 
     #######################
     # MPI
@@ -125,7 +99,13 @@ class Ascent(Package):
         Build and install Conduit.
         """
         with working_dir('spack-build', create=True):
-            host_cfg_fname = self.create_host_config(spec, prefix)
+            py_site_pkgs_dir = None
+            if "+python" in spec:
+                py_site_pkgs_dir = site_packages_dir
+
+            host_cfg_fname = self.create_host_config(spec,
+                                                     prefix,
+                                                     py_site_pkgs_dir)
             cmake_args = []
             # if we have a static build, we need to avoid any of
             # spack's default cmake settings related to rpaths
@@ -140,12 +120,26 @@ class Ascent(Package):
             cmake(*cmake_args)
             make()
             make("install")
-            # TODO also copy host_cfg_fname into install
+            # install copy of host config for provenance
+            install(host_cfg_fname, prefix)
 
-    def create_host_config(self, spec, prefix):
+    def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         """
         This method creates a 'host-config' file that specifies
         all of the options used to configure and build ascent.
+
+        For more details about 'host-config' files see:
+            http://ascent.readthedocs.io/en/latest/BuildingAscent.html
+
+        Note:
+          The `py_site_pkgs_dir` arg exists to allow a package that
+          subclasses this package provide a specific site packages
+          dir when calling this function. `py_site_pkgs_dir` should
+          be an absolute path or `None`.
+
+          This is necessary because the spack `site_packages_dir`
+          var will not exist in the base class. For more details
+          on this issue see: https://github.com/spack/spack/issues/6261
         """
 
         #######################
@@ -184,9 +178,9 @@ class Ascent(Package):
                 raise RuntimeError(msg)
             cmake_exe = cmake_exe.path
 
-        host_cfg_fname = "%s-%s-%s.cmake" % (socket.gethostname(),
-                                             sys_type,
-                                             spec.compiler)
+        host_cfg_fname = "%s-%s-%s-ascent.cmake" % (socket.gethostname(),
+                                                    sys_type,
+                                                    spec.compiler)
 
         cfg = open(host_cfg_fname, "w")
         cfg.write("##################################\n")
@@ -246,10 +240,10 @@ class Ascent(Package):
             cfg.write("# python from spack \n")
             cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE",
                       spec['python'].command.path))
-            # install module to standard style site packages dir
-            # so we can support spack activate
-            cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
-                                        site_packages_dir))
+            # only set dest python site packages dir if passed
+            if py_site_pkgs_dir:
+                cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
+                                            py_site_pkgs_dir))
         else:
             cfg.write(cmake_cache_entry("ENABLE_PYTHON", "OFF"))
 
@@ -260,10 +254,6 @@ class Ascent(Package):
             sphinx_build_exe = join_path(spec['py-sphinx'].prefix.bin,
                                          "sphinx-build")
             cfg.write(cmake_cache_entry("SPHINX_EXECUTABLE", sphinx_build_exe))
-
-            cfg.write("# doxygen from uberenv\n")
-            doxygen_exe = spec['doxygen'].command.path
-            cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
         else:
             cfg.write(cmake_cache_entry("ENABLE_DOCS", "OFF"))
 
@@ -280,6 +270,16 @@ class Ascent(Package):
                                         spec['mpi'].mpicxx))
             cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
                                         spec['mpi'].mpifc))
+            mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
+            if os.path.isfile(mpiexe_bin):
+                # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE
+                # vs the older versions which expect MPIEXEC
+                if self.spec["cmake"].satisfies('@3.10:'):
+                    cfg.write(cmake_cache_entry("MPIEXEC_EXECUTABLE",
+                                                mpiexe_bin))
+                else:
+                    cfg.write(cmake_cache_entry("MPIEXEC",
+                                                mpiexe_bin))
         else:
             cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF"))
 
diff --git a/var/spack/repos/builtin/packages/asciidoc/package.py b/var/spack/repos/builtin/packages/asciidoc/package.py
index 885fc02404..f186961cc1 100644
--- a/var/spack/repos/builtin/packages/asciidoc/package.py
+++ b/var/spack/repos/builtin/packages/asciidoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/aspa/package.py b/var/spack/repos/builtin/packages/aspa/package.py
index 3686ffe4ea..2081ed73e1 100644
--- a/var/spack/repos/builtin/packages/aspa/package.py
+++ b/var/spack/repos/builtin/packages/aspa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -32,12 +13,14 @@ class Aspa(MakefilePackage):
     demands upon the exascale ecosystem that need to be identified and
     quantified.
     """
-    tags = ['proxy-app']
+
     homepage = "http://www.exmatex.org/aspa.html"
-    url = "https://github.com/exmatex/ASPA/archive/master.tar.gz"
+    git      = "https://github.com/exmatex/ASPA.git"
+
+    tags = ['proxy-app']
+
+    version('master', branch='master')
 
-    version('master', git='https://github.com/exmatex/ASPA.git',
-            description='master')
     variant('mpi', default=True, description='Build with MPI Support')
 
     depends_on('lapack')
diff --git a/var/spack/repos/builtin/packages/aspcud/package.py b/var/spack/repos/builtin/packages/aspcud/package.py
new file mode 100644
index 0000000000..ca4ec49350
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aspcud/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aspcud(CMakePackage):
+    """Aspcud: Package dependency solver
+
+       Aspcud is a solver for package dependencies. A package universe
+       and a request to install, remove, or upgrade packages have to
+       be encoded in the CUDF format. Such a CUDF document can then be
+       passed to aspcud along with an optimization criteria to obtain
+       a solution to the given package problem."""
+
+    homepage = "https://potassco.org/aspcud"
+    url      = "https://github.com/potassco/aspcud/archive/v1.9.4.tar.gz"
+
+    version('1.9.4', '35e5c663a25912e4bdc94f168e827ed2')
+
+    depends_on('boost', type=('build'))
+    depends_on('cmake', type=('build'))
+    depends_on('re2c', type=('build'))
+    depends_on('clingo')
+
+    def cmake_args(self):
+        spec = self.spec
+        gringo_path = join_path(spec['clingo'].prefix.bin, 'gringo')
+        clasp_path = join_path(spec['clingo'].prefix.bin, 'clasp')
+        args = ['-DASPCUD_GRINGO_PATH={0}'.format(gringo_path),
+                '-DASPCUD_CLASP_PATH={0}'.format(clasp_path)]
+        return args
diff --git a/var/spack/repos/builtin/packages/aspect/package.py b/var/spack/repos/builtin/packages/aspect/package.py
new file mode 100644
index 0000000000..a4ab96e8cc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aspect/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Aspect(CMakePackage):
+    """Parallel, extendible finite element code to simulate convection in the
+    Earth's mantle and elsewhere."""
+
+    homepage = "https://aspect.geodynamics.org"
+    url      = "https://github.com/geodynamics/aspect/releases/download/v2.0.0/aspect-2.0.0.tar.gz"
+    git      = "https://github.com/geodynamics/aspect.git"
+
+    maintainers = ['tjhei']
+
+    version('develop', branch='master')
+    version('2.0.1', sha256='0bf5600c42afce9d39c1d285b0654ecfdeb0f30e9f3421651c95f54ca01ac165')
+    version('2.0.0', sha256='d485c07f54248e824bdfa35f3eec8971b65e8b7114552ffa2c771bc0dede8cc0')
+
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
+    variant('gui', default=False, description='Enable the deal.II parameter GUI')
+    variant('fpe', default=False, description='Enable floating point exception checks')
+
+    depends_on('dealii+p4est+trilinos+mpi')
+    depends_on('dealii-parameter-gui', when='+gui')
+
+    def cmake_args(self):
+        return [
+            '-DASPECT_USE_FP_EXCEPTIONS=%s' %
+            ('ON' if '+fpe' in self.spec else 'OFF')
+        ]
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('Aspect_DIR', self.prefix)
diff --git a/var/spack/repos/builtin/packages/aspell/darwin.patch b/var/spack/repos/builtin/packages/aspell/darwin.patch
new file mode 100644
index 0000000000..54ec257637
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aspell/darwin.patch
@@ -0,0 +1,20 @@
++++ a/interfaces/cc/aspell.h
+--- b/interfaces/cc/aspell.h
+@@ -236,7 +236,7 @@
+ 
+ /******************************** errors ********************************/
+ 
+-
++#ifndef __cplusplus
+ extern const struct AspellErrorInfo * const aerror_other;
+ extern const struct AspellErrorInfo * const aerror_operation_not_supported;
+ extern const struct AspellErrorInfo * const   aerror_cant_copy;
+@@ -322,7 +322,7 @@
+ extern const struct AspellErrorInfo * const   aerror_bad_magic;
+ extern const struct AspellErrorInfo * const aerror_expression;
+ extern const struct AspellErrorInfo * const   aerror_invalid_expression;
+-
++#endif
+ 
+ /******************************* speller *******************************/
+ 
diff --git a/var/spack/repos/builtin/packages/aspell/package.py b/var/spack/repos/builtin/packages/aspell/package.py
index c24a50ef39..5dbe7ed301 100644
--- a/var/spack/repos/builtin/packages/aspell/package.py
+++ b/var/spack/repos/builtin/packages/aspell/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from llnl.util.link_tree import LinkTree
-import spack.store
-from spack.package import ExtensionError, ExtensionConflictError
 
 
 # See also: AspellDictPackage
@@ -40,46 +18,4 @@ class Aspell(AutotoolsPackage):
 
     version('0.60.6.1', 'e66a9c9af6a60dc46134fdacf6ce97d7')
 
-    # The dictionaries install all their bits into their prefix.lib dir,
-    # we want to link them into aspell's dict-dir.
-    # These are identical to what's in spack/package.py except
-    # for using:
-    #   - extension.prefix.lib instead of extension.prefix in LinkTree()
-    #   - dest_dir instead of self.prefix in tree.(find_conflict|merge)()
-    def activate(self, extension, **kwargs):
-        extensions_layout = kwargs.get("extensions_layout",
-                                       spack.store.extensions)
-        if extensions_layout is not spack.store.extensions:
-            raise ExtensionError(
-                'aspell does not support non-global extensions')
-
-        aspell = which(self.prefix.bin.aspell)
-        dest_dir = aspell('dump', 'config', 'dict-dir', output=str).strip()
-        tree = LinkTree(extension.prefix.lib)
-
-        def ignore(filename):
-            return (filename in spack.store.layout.hidden_file_paths or
-                    kwargs.get('ignore', lambda f: False)(filename))
-
-        conflict = tree.find_conflict(dest_dir, ignore=ignore)
-        if conflict:
-            raise ExtensionConflictError(conflict)
-
-        tree.merge(dest_dir, ignore=ignore)
-
-    def deactivate(self, extension, **kwargs):
-        extensions_layout = kwargs.get("extensions_layout",
-                                       spack.store.extensions)
-        if extensions_layout is not spack.store.extensions:
-            raise ExtensionError(
-                'aspell does not support non-global extensions')
-
-        aspell = which(self.prefix.bin.aspell)
-        dest_dir = aspell('dump', 'config', 'dict-dir', output=str).strip()
-
-        def ignore(filename):
-            return (filename in spack.store.layout.hidden_file_paths or
-                    kwargs.get('ignore', lambda f: False)(filename))
-
-        tree = LinkTree(extension.prefix.lib)
-        tree.unmerge(dest_dir, ignore=ignore)
+    patch('darwin.patch', when='platform=darwin')
diff --git a/var/spack/repos/builtin/packages/aspell6-de/package.py b/var/spack/repos/builtin/packages/aspell6-de/package.py
index 5a4b1c82d8..5468829058 100644
--- a/var/spack/repos/builtin/packages/aspell6-de/package.py
+++ b/var/spack/repos/builtin/packages/aspell6-de/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,6 +10,6 @@ class Aspell6De(AspellDictPackage):
     """German (de) dictionary for aspell."""
 
     homepage = "http://aspell.net/"
-    url      = "ftp://ftp.gnu.org/gnu/aspell/dict/de/aspell6-de-20030222-1.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/aspell/dict/de/aspell6-de-20030222-1.tar.bz2"
 
     version('6-de-20030222-1', '5950c5c8a36fc93d4d7616591bace6a6')
diff --git a/var/spack/repos/builtin/packages/aspell6-en/package.py b/var/spack/repos/builtin/packages/aspell6-en/package.py
index 38d6caeabd..d49cb61188 100644
--- a/var/spack/repos/builtin/packages/aspell6-en/package.py
+++ b/var/spack/repos/builtin/packages/aspell6-en/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,6 +10,6 @@ class Aspell6En(AspellDictPackage):
     """English (en) dictionary for aspell."""
 
     homepage = "http://aspell.net/"
-    url      = "ftp://ftp.gnu.org/gnu/aspell/dict/en/aspell6-en-2017.01.22-0.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/aspell/dict/en/aspell6-en-2017.01.22-0.tar.bz2"
 
     version('2017.01.22-0', 'a6e002076574de9dc4915967032a1dab')
diff --git a/var/spack/repos/builtin/packages/aspell6-es/package.py b/var/spack/repos/builtin/packages/aspell6-es/package.py
index 84a798d41a..3e11115e9a 100644
--- a/var/spack/repos/builtin/packages/aspell6-es/package.py
+++ b/var/spack/repos/builtin/packages/aspell6-es/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,6 +10,6 @@ class Aspell6Es(AspellDictPackage):
     """Spanish (es) dictionary for aspell."""
 
     homepage = "http://aspell.net/"
-    url      = "ftp://ftp.gnu.org/gnu/aspell/dict/es/aspell6-es-1.11-2.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/aspell/dict/es/aspell6-es-1.11-2.tar.bz2"
 
     version('1.11-2', '8406336a89c64e47e96f4153d0af70c4')
diff --git a/var/spack/repos/builtin/packages/aspera-cli/package.py b/var/spack/repos/builtin/packages/aspera-cli/package.py
new file mode 100644
index 0000000000..3a903208f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/aspera-cli/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from glob import glob
+
+
+class AsperaCli(Package):
+    """The Aspera CLI client for the Fast and Secure Protocol (FASP)."""
+
+    homepage = "https://asperasoft.com"
+    url      = "https://download.asperasoft.com/download/sw/cli/3.7.7/aspera-cli-3.7.7.608.927cce8-linux-64-release.sh"
+
+    version('3.7.7', 'e92140d809e7e65112a5d1cd49c442cf',
+            url='https://download.asperasoft.com/download/sw/cli/3.7.7/aspera-cli-3.7.7.608.927cce8-linux-64-release.sh',
+            expand=False)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.cli.bin)
+
+    def install(self, spec, prefix):
+        runfile = glob(join_path(self.stage.path, 'aspera-cli*.sh'))[0]
+        # Update destination path
+        filter_file('INSTALL_DIR=~/.aspera',
+                    'INSTALL_DIR=%s' % prefix,
+                    runfile,
+                    string=True)
+        # Install
+        chmod = which('chmod')
+        chmod('+x', runfile)
+        runfile = which(runfile)
+        runfile()
diff --git a/var/spack/repos/builtin/packages/assimp/package.py b/var/spack/repos/builtin/packages/assimp/package.py
index dd9b414772..3852df5bc4 100644
--- a/var/spack/repos/builtin/packages/assimp/package.py
+++ b/var/spack/repos/builtin/packages/assimp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,25 @@ class Assimp(CMakePackage):
     import various well-known 3D model formats in a uniform manner."""
 
     homepage = "https://www.assimp.org"
-    url      = "https://github.com/assimp/assimp/archive/v3.3.1.tar.gz"
+    url      = "https://github.com/assimp/assimp/archive/v4.0.1.tar.gz"
 
     version('4.0.1', '23a6301c728a413aafbfa1cca19ba91f')
 
+    variant('shared',  default=True,
+            description='Enables the build of shared libraries')
+
     depends_on('boost')
 
     def cmake_args(self):
-        args = ['-DASSIMP_BUILD_TESTS=OFF']
+        args = [
+            '-DASSIMP_BUILD_TESTS=OFF',
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in self.spec else 'OFF'),
+        ]
         return args
+
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if name == 'cxxflags':
+            flags.append(self.compiler.cxx11_flag)
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/astra/package.py b/var/spack/repos/builtin/packages/astra/package.py
index 694a394c69..267fedddf6 100644
--- a/var/spack/repos/builtin/packages/astra/package.py
+++ b/var/spack/repos/builtin/packages/astra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/astral/package.py b/var/spack/repos/builtin/packages/astral/package.py
index 11d8b0ed23..8c9e25d1e9 100644
--- a/var/spack/repos/builtin/packages/astral/package.py
+++ b/var/spack/repos/builtin/packages/astral/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
@@ -36,6 +17,7 @@ class Astral(Package):
     version('4.10.7', '38c81020570254e3f5c75d6c3c27fc6d')
 
     depends_on('java', type=('build', 'run'))
+    depends_on('zip', type='build')
 
     phases = ['build', 'install']
 
diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py
index 62e7204168..862f6d8691 100644
--- a/var/spack/repos/builtin/packages/astyle/package.py
+++ b/var/spack/repos/builtin/packages/astyle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -32,12 +13,13 @@ class Astyle(MakefilePackage):
     """
 
     homepage = "http://astyle.sourceforge.net/"
-    # homepage is dead use Gentoo Mirror
-    # url = "http://downloads.sourceforge.net/project/astyle/astyle/astyle%202.04/astyle_2.04_linux.tar.gz"
-    url = "http://distfiles.gentoo.org/distfiles/astyle_3.0.1_linux.tar.gz"
+    url = "https://sourceforge.net/projects/astyle/files/astyle/astyle%203.0.1/astyle_3.0.1_linux.tar.gz"
+    # Gentoo alternative
+    # url = "http://distfiles.gentoo.org/distfiles/astyle_3.0.1_linux.tar.gz"
 
     maintainers = ['davydden']
 
+    version('3.1',    '7712622f62661b1d8cb1062d7fedc390')
     version('3.0.1',  'c301f09679efa2e1eb6e6b5fd33788b4')
     version('2.06',   'ff588e7fcede824591cf5b9085df109d')
     version('2.05.1', '4142d178047d7040da3e0e2f1b030a1a')
diff --git a/var/spack/repos/builtin/packages/at-spi2-atk/package.py b/var/spack/repos/builtin/packages/at-spi2-atk/package.py
new file mode 100644
index 0000000000..dc6bf63b6c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/at-spi2-atk/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class AtSpi2Atk(MesonPackage):
+    """The At-Spi2 Atk package contains a library that bridges ATK to
+       At-Spi2 D-Bus service."""
+
+    homepage = "http://www.linuxfromscratch.org/blfs/view/cvs/x/at-spi2-atk.html"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-atk/2.26/at-spi2-atk-2.26.1.tar.xz"
+    list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-atk"
+    list_depth = 1
+
+    version('2.26.2', '355c7916a69513490cb83ad34016b169')
+    version('2.26.1', 'eeec6cead3350dca48a235271c105b3e')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('at-spi2-core@2.28.0:')
+    depends_on('atk@2.28.1:')
+
+    def url_for_version(self, version):
+        """Handle gnome's version-based custom URLs."""
+        url = 'http://ftp.gnome.org/pub/gnome/sources/at-spi2-atk'
+        return url + '/%s/at-spi2-atk-%s.tar.xz' % (version.up_to(2), version)
diff --git a/var/spack/repos/builtin/packages/at-spi2-core/package.py b/var/spack/repos/builtin/packages/at-spi2-core/package.py
new file mode 100644
index 0000000000..868fae2270
--- /dev/null
+++ b/var/spack/repos/builtin/packages/at-spi2-core/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class AtSpi2Core(MesonPackage):
+    """The At-Spi2 Core package provides a Service Provider Interface for the
+       Assistive Technologies available on the GNOME platform and a library
+       against which applications can be linked."""
+
+    homepage = "http://www.linuxfromscratch.org/blfs/view/cvs/x/at-spi2-core.html"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-core/2.28/at-spi2-core-2.28.0.tar.xz"
+    list_url = "http://ftp.gnome.org/pub/gnome/sources/at-spi2-core"
+    list_depth = 1
+
+    version('2.28.0', '9c42f79636ed1c0e908b7483d789b32e')
+
+    depends_on('glib@2.56.1:')
+    depends_on('dbus@1.12.8:')
+    depends_on('libx11')
+    depends_on('libxi')
+    depends_on('libxtst', type='build')
+    depends_on('recordproto', type='build')
+    depends_on('inputproto', type='build')
+    depends_on('fixesproto', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('python', type='build')
+
+    def url_for_version(self, version):
+        """Handle gnome's version-based custom URLs."""
+        url = 'http://ftp.gnome.org/pub/gnome/sources/at-spi2-core'
+        return url + '/%s/at-spi2-core-%s.tar.xz' % (version.up_to(2), version)
+
+    def setup_environment(self, spack_env, run_env):
+        # this avoids an "import site" error in the build
+        spack_env.unset('PYTHONHOME')
diff --git a/var/spack/repos/builtin/packages/atk/package.py b/var/spack/repos/builtin/packages/atk/package.py
index 93ce88bb8a..ba6a872a69 100644
--- a/var/spack/repos/builtin/packages/atk/package.py
+++ b/var/spack/repos/builtin/packages/atk/package.py
@@ -1,47 +1,33 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Atk(AutotoolsPackage):
+class Atk(Package):
     """ATK provides the set of accessibility interfaces that are
        implemented by other toolkits and applications. Using the ATK
        interfaces, accessibility tools have full access to view and
        control running applications."""
     homepage = "https://developer.gnome.org/atk/"
-    url      = "http://ftp.gnome.org/pub/gnome/sources/atk/2.14/atk-2.14.0.tar.xz"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/atk/2.28/atk-2.28.1.tar.xz"
+    list_url = "http://ftp.gnome.org/pub/gnome/sources/atk"
+    list_depth = 1
 
+    version('2.28.1', 'dfb5e7474220afa3f4ca7e45af9f3a11')
     version('2.20.0', '5187b0972f4d3905f285540b31395e20')
     version('2.14.0', 'ecb7ca8469a5650581b1227d78051b8b')
 
+    depends_on('meson', type='build', when='@2.28.0:')
     depends_on('glib')
-    depends_on('pkg-config', type='build')
+    depends_on('gettext')
+    depends_on('pkgconfig', type='build')
     depends_on('gobject-introspection')
 
     def url_for_version(self, version):
-        """Handle atk's version-based custom URLs."""
+        """Handle gnome's version-based custom URLs."""
         url = 'http://ftp.gnome.org/pub/gnome/sources/atk'
         return url + '/%s/atk-%s.tar.xz' % (version.up_to(2), version)
 
@@ -50,3 +36,19 @@ class Atk(AutotoolsPackage):
                                self.prefix.share)
         run_env.prepend_path("XDG_DATA_DIRS",
                              self.prefix.share)
+
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            meson('..', *std_meson_args)
+            ninja('-v')
+            ninja('install')
+
+    @when('@:2.27')
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        if self.run_tests:
+            make('check')
+        make('install')
+        if self.run_tests:
+            make('installcheck')
diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py
index 7f5652bad4..0f624ae839 100644
--- a/var/spack/repos/builtin/packages/atlas/package.py
+++ b/var/spack/repos/builtin/packages/atlas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 from spack import *
@@ -37,6 +18,12 @@ class Atlas(Package):
     """
     homepage = "http://math-atlas.sourceforge.net/"
 
+    version('3.11.39', '5f3252fa980f5f060f93edd4669321e2',
+            url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.39/atlas3.11.39.tar.bz2')
+
+    version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825',
+            url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2')
+
     version('3.10.3', 'd6ce4f16c2ad301837cfb3dade2f7cef',
             url='https://sourceforge.net/projects/math-atlas/files/Stable/3.10.3/atlas3.10.3.tar.bz2')
 
@@ -50,9 +37,6 @@ class Atlas(Package):
              destination='spack-resource-lapack',
              when='@3:')
 
-    version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825',
-            url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2')
-
     variant('shared', default=True, description='Builds shared library')
 
     variant(
@@ -139,7 +123,7 @@ class Atlas(Package):
             to_find = ['liblapack'] + interfaces + ['libatlas']
             shared = False
         return find_libraries(
-            to_find, root=self.prefix, shared=shared, recurse=True
+            to_find, root=self.prefix, shared=shared, recursive=True
         )
 
     def install_test(self):
diff --git a/var/spack/repos/builtin/packages/atom-dft/package.py b/var/spack/repos/builtin/packages/atom-dft/package.py
new file mode 100644
index 0000000000..1c42382591
--- /dev/null
+++ b/var/spack/repos/builtin/packages/atom-dft/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class AtomDft(MakefilePackage):
+    """ATOM is a program for DFT calculations in atoms and pseudopotential
+       generation."""
+
+    homepage = "https://departments.icmab.es/leem/siesta/Pseudopotentials/"
+    url      = "https://departments.icmab.es/leem/siesta/Pseudopotentials/Code/atom-4.2.6.tgz"
+
+    version('4.2.6', 'c0c80cf349f951601942ed6c7cb0256b')
+
+    depends_on('libgridxc')
+    depends_on('xmlf90')
+
+    def edit(self, spec, prefix):
+        copy('arch.make.sample', 'arch.make')
+
+    @property
+    def build_targets(self):
+        return ['XMLF90_ROOT=%s' % self.spec['xmlf90'].prefix,
+                'GRIDXC_ROOT=%s' % self.spec['libgridxc'].prefix,
+                'FC=fc']
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('atm', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/atompaw/package.py b/var/spack/repos/builtin/packages/atompaw/package.py
index c86a5c5de5..430f3a4248 100644
--- a/var/spack/repos/builtin/packages/atompaw/package.py
+++ b/var/spack/repos/builtin/packages/atompaw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/atop/package.py b/var/spack/repos/builtin/packages/atop/package.py
index 6c59ee4dbe..9c8d73b693 100644
--- a/var/spack/repos/builtin/packages/atop/package.py
+++ b/var/spack/repos/builtin/packages/atop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py
index d79cde02c5..86cffa20f7 100644
--- a/var/spack/repos/builtin/packages/augustus/package.py
+++ b/var/spack/repos/builtin/packages/augustus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,12 @@ class Augustus(MakefilePackage):
        genomic sequences"""
 
     homepage = "http://bioinf.uni-greifswald.de/augustus/"
-    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.tar.gz"
+    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.1.tar.gz"
+    list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
 
-    version('3.3',   '9ebe494df78ebf6a43091cfc8551050c')
-    version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830',
-            url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz')
+    version('3.3.1', '8363ece221c799eb169f47e545efb951')
+    version('3.3',   '93691d9aafc7d3d0e1adf31ec308507f')
+    version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830')
 
     depends_on('bamtools')
     depends_on('gsl')
@@ -48,18 +30,28 @@ class Augustus(MakefilePackage):
                             'bamtools'].prefix)
             makefile.filter('INCLUDES = *',
                             'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
-            makefile.filter('LIBS = -lbamtools -lz',
-                            'LIBS = $(BAMTOOLS)/lib/bamtools'
-                            '/libbamtools.a -lz')
+            if 'bamtools@2.5:' in spec:
+                makefile.filter('LIBS = -lbamtools -lz',
+                                'LIBS = $(BAMTOOLS)/lib64/'
+                                '/libbamtools.a -lz')
+            if 'bamtools@:2.4' in spec:
+                makefile.filter('LIBS = -lbamtools -lz',
+                                'LIBS = $(BAMTOOLS)/lib/bamtools'
+                                '/libbamtools.a -lz')
         with working_dir(join_path('auxprogs', 'bam2hints')):
             makefile = FileFilter('Makefile')
             makefile.filter('# Variable definition',
                             'BAMTOOLS = %s' % self.spec['bamtools'].prefix)
             makefile.filter('INCLUDES = /usr/include/bamtools',
                             'INCLUDES = $(BAMTOOLS)/include/bamtools')
-            makefile.filter('LIBS = -lbamtools -lz',
-                            'LIBS = $(BAMTOOLS)/lib/bamtools'
-                            '/libbamtools.a -lz')
+            if 'bamtools@2.5:' in spec:
+                makefile.filter('LIBS = -lbamtools -lz',
+                                'LIBS = $(BAMTOOLS)/lib64/'
+                                '/libbamtools.a -lz')
+            if 'bamtools@:2.4' in spec:
+                makefile.filter('LIBS = -lbamtools -lz',
+                                'LIBS = $(BAMTOOLS)/lib/bamtools'
+                                '/libbamtools.a -lz')
 
     def install(self, spec, prefix):
         install_tree('bin', join_path(self.spec.prefix, 'bin'))
diff --git a/var/spack/repos/builtin/packages/autoconf/package.py b/var/spack/repos/builtin/packages/autoconf/package.py
index f178a6e264..87d24bc680 100644
--- a/var/spack/repos/builtin/packages/autoconf/package.py
+++ b/var/spack/repos/builtin/packages/autoconf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Autoconf(AutotoolsPackage):
     """Autoconf -- system configuration part of autotools"""
 
     homepage = 'https://www.gnu.org/software/autoconf/'
-    url = 'http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz'
+    url      = 'https://ftpmirror.gnu.org/autoconf/autoconf-2.69.tar.gz'
 
     version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
     version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
@@ -55,12 +36,11 @@ class Autoconf(AutotoolsPackage):
         # We have to do this after install because otherwise the install
         # target will try to rebuild the binaries (filter_file updates the
         # timestamps)
-        perl = join_path(self.spec['perl'].prefix.bin, 'perl')
 
         # Revert sbang, so Spack's sbang hook can fix it up
         filter_file('^#! /usr/bin/env perl',
-                    '#! {0} -w'.format(perl),
-                    '{0}/autom4te'.format(self.prefix.bin),
+                    '#! {0} -w'.format(self.spec['perl'].command.path),
+                    self.prefix.bin.autom4te,
                     backup=False)
 
     def _make_executable(self, name):
diff --git a/var/spack/repos/builtin/packages/autodock-vina/package.py b/var/spack/repos/builtin/packages/autodock-vina/package.py
index 255839e894..5efacf02a5 100644
--- a/var/spack/repos/builtin/packages/autodock-vina/package.py
+++ b/var/spack/repos/builtin/packages/autodock-vina/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
-from shutil import copymode
 import sys
 
 
@@ -66,7 +45,5 @@ class AutodockVina(MakefilePackage):
     def install(self, spec, prefix):
         with working_dir(self.build_directory):
             mkdirp(prefix.bin)
-            copyfile("vina", join_path(prefix.bin, "vina"))
-            copymode("vina", join_path(prefix.bin, "vina"))
-            copyfile("vina_split", join_path(prefix.bin, "vina_split"))
-            copymode("vina_split", join_path(prefix.bin, "vina_split"))
+            install('vina', prefix.bin)
+            install('vina_split', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/autofact/package.py b/var/spack/repos/builtin/packages/autofact/package.py
new file mode 100644
index 0000000000..0ad36c82dd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/autofact/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Autofact(Package):
+    """An Automatic Functional Annotation and Classification Tool"""
+
+    homepage = "http://megasun.bch.umontreal.ca/Software/AutoFACT.htm"
+    url      = "http://megasun.bch.umontreal.ca/Software/AutoFACT_v3_4.tar"
+
+    version('3_4', sha256='1465d263b19adb42f01f6e636ac40ef1c2e3dbd63461f977b89da9493fe9c6f4')
+
+    depends_on('perl', type='run')
+    depends_on('perl-bio-perl', type='run')
+    depends_on('perl-io-string', type='run')
+    depends_on('perl-lwp', type='run')
+    depends_on('blast-plus', type='run')
+
+    def patch(self):
+        with working_dir('scripts'):
+            files = glob.iglob("*.pl")
+            for file in files:
+                change = FileFilter(file)
+                change.filter('usr/bin/perl', 'usr/bin/env perl')
+
+    def install(self, spec, prefix):
+        install_tree(self.stage.source_path, prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.scripts)
+        run_env.set('PATH2AUTOFACT', self.prefix)
diff --git a/var/spack/repos/builtin/packages/autogen/package.py b/var/spack/repos/builtin/packages/autogen/package.py
index 4198ab1589..5f4c893e45 100644
--- a/var/spack/repos/builtin/packages/autogen/package.py
+++ b/var/spack/repos/builtin/packages/autogen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Autogen(AutotoolsPackage):
     synchronized."""
 
     homepage = "https://www.gnu.org/software/autogen/index.html"
-    url      = "https://ftp.gnu.org/gnu/autogen/rel5.18.12/autogen-5.18.12.tar.gz"
+    url      = "https://ftpmirror.gnu.org/autogen/rel5.18.12/autogen-5.18.12.tar.gz"
     list_url = "https://ftp.gnu.org/gnu/autogen"
     list_depth = 1
 
@@ -40,7 +21,7 @@ class Autogen(AutotoolsPackage):
 
     variant('xml', default=True, description='Enable XML support')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('guile@1.8:2.0')
     depends_on('libxml2', when='+xml')
diff --git a/var/spack/repos/builtin/packages/automaded/package.py b/var/spack/repos/builtin/packages/automaded/package.py
index 7b227afb9d..30ca8684cd 100644
--- a/var/spack/repos/builtin/packages/automaded/package.py
+++ b/var/spack/repos/builtin/packages/automaded/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/automake/package.py b/var/spack/repos/builtin/packages/automake/package.py
index 2140612b7f..94bd569614 100644
--- a/var/spack/repos/builtin/packages/automake/package.py
+++ b/var/spack/repos/builtin/packages/automake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,9 @@ class Automake(AutotoolsPackage):
     """Automake -- make file builder part of autotools"""
 
     homepage = 'http://www.gnu.org/software/automake/'
-    url      = 'http://ftp.gnu.org/gnu/automake/automake-1.15.tar.gz'
+    url      = 'https://ftpmirror.gnu.org/automake/automake-1.15.tar.gz'
 
+    version('1.16.1', '83cc2463a4080efd46a72ba2c9f6b8f5')
     version('1.15.1', '95df3f2d6eb8f81e70b8cb63a93c8853')
     version('1.15',   '716946a105ca228ab545fc37a70df3a3')
     version('1.14.1', 'd052a3e884631b9c7892f2efce542d75')
@@ -43,10 +25,14 @@ class Automake(AutotoolsPackage):
 
     def patch(self):
         # The full perl shebang might be too long
+        files_to_be_patched_fmt = 'bin/{0}.in'
+        if '@:1.15.1' in self.spec:
+            files_to_be_patched_fmt = 't/wrap/{0}.in'
+
         for file in ('aclocal', 'automake'):
             filter_file('^#!@PERL@ -w',
                         '#!/usr/bin/env perl',
-                        't/wrap/{0}.in'.format(file))
+                        files_to_be_patched_fmt.format(file))
 
     def _make_executable(self, name):
         return Executable(join_path(self.prefix.bin, name))
diff --git a/var/spack/repos/builtin/packages/axel/package.py b/var/spack/repos/builtin/packages/axel/package.py
new file mode 100644
index 0000000000..bd736b2db5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/axel/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Axel(AutotoolsPackage):
+    """Axel is a light command line download accelerator for Linux and Unix"""
+
+    homepage = "https://github.com/axel-download-accelerator/axel"
+    url      = "https://github.com/axel-download-accelerator/axel/archive/v2.16.1.tar.gz"
+
+    version('2.16.1', '3aaa7052458c66c1547bf1133609d0f2')
+
+    depends_on('m4', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('pkgconf', type='build')
+    depends_on('gettext')
+    depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/axl/package.py b/var/spack/repos/builtin/packages/axl/package.py
new file mode 100644
index 0000000000..c4118b58f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/axl/package.py
@@ -0,0 +1,56 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from spack.error import SpackError
+
+
+def async_api_validator(values):
+    if 'none' in values and len(values) != 1:
+        raise SpackError("The value 'none' is not usable"
+                         " with other async_api values.")
+    if 'ibm_bbapi' in values and 'cray_dw' in values:
+        raise SpackError("The 'ibm_bbapi' and 'cray_dw' asynchronous"
+                         " APIs are incompatible.")
+
+
+class Axl(CMakePackage):
+    """Asynchronous transfer library"""
+
+    homepage = "https://github.com/ECP-VeloC/AXL"
+    url      = "https://github.com/ECP-VeloC/AXL/archive/v0.1.0.zip"
+    git      = "https://github.com/ecp-veloc/axl.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.1.1', sha256='7ec0417447c5a3cc0b6e46ff3f646984410c77e6c2081cf0c748781384be739b')
+
+    variant('async_api', default='daemon',
+            description="Set of async transfer APIs to enable",
+            values=['cray_dw', 'ibm_bbapi', 'daemon', 'none'], multi=True,
+            validator=async_api_validator)
+
+    # not-yet implemented functionality
+    conflicts('async_api=cray_dw', when='@0.1.0')
+    conflicts('async_api=ibm_bbapi', when='@0.1.0')
+
+    depends_on('kvtree')
+
+    def cmake_args(self):
+        args = []
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DAXL_LINK_STATIC=ON")
+        args.append("-DWITH_KVTREE_PREFIX=%s" % self.spec['kvtree'].prefix)
+
+        apis = list(self.spec.variants['async_api'].value)
+        if 'daemon' in apis:
+            args.append('-DAXL_ASYNC_DAEMON=ON')
+            apis.remove('daemon')
+
+        for api in apis:
+            args.append('-DAXL_ASYNC_API={0}'.format(api))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/bamdst/package.py b/var/spack/repos/builtin/packages/bamdst/package.py
new file mode 100644
index 0000000000..5f8c2b2b04
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bamdst/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bamdst(MakefilePackage):
+    "Bamdst is a a lightweight bam file depth statistical tool."
+
+    homepage = "https://github.com/shiquan/bamdst"
+    git      = "https://github.com/shiquan/bamdst.git"
+
+    version('master', git='https://github.com/shiquan/bamdst.git')
+
+    depends_on('zlib')
+
+    parallel = False
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('CC= .*', 'CC = cc')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('bamdst', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/bamtools/package.py b/var/spack/repos/builtin/packages/bamtools/package.py
index a45cf38b80..4ad73eb78e 100644
--- a/var/spack/repos/builtin/packages/bamtools/package.py
+++ b/var/spack/repos/builtin/packages/bamtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -32,6 +13,8 @@ class Bamtools(CMakePackage):
     homepage = "https://github.com/pezmaster31/bamtools"
     url      = "https://github.com/pezmaster31/bamtools/archive/v2.4.0.tar.gz"
 
+    version('2.5.1', '98e90632058f85bd5eed6088b3ff912e')
+    version('2.5.0', 'dd4185bdba6e3adf2c24b7f93a57233d')
     version('2.4.1', '41cadf513f2744256851accac2bc7baa')
     version('2.4.0', '6139d00c1b1fe88fe15d094d8a74d8b9')
     version('2.3.0', 'd327df4ba037d6eb8beef65d7da75ebc')
diff --git a/var/spack/repos/builtin/packages/bamutil/package.py b/var/spack/repos/builtin/packages/bamutil/package.py
index d739fe1f84..73a2d322ca 100644
--- a/var/spack/repos/builtin/packages/bamutil/package.py
+++ b/var/spack/repos/builtin/packages/bamutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,8 @@ class Bamutil(MakefilePackage):
 
     version('1.0.13', '08b7d0bb1d60be104a11f0e54ddf4a79')
 
+    depends_on('zlib', type=('build', 'link'))
+
     # 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:')
diff --git a/var/spack/repos/builtin/packages/barrnap/package.py b/var/spack/repos/builtin/packages/barrnap/package.py
new file mode 100644
index 0000000000..3332b120a8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/barrnap/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Barrnap(Package):
+    """Barrnap predicts the location of ribosomal RNA genes in genomes."""
+
+    homepage = "https://github.com/tseemann/barrnap"
+    url      = "https://github.com/tseemann/barrnap/archive/0.8.tar.gz"
+
+    version('0.8', 'd02ccb800d60fa824bae946dd4fa2358')
+
+    depends_on('hmmer@3.1b:', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('db', prefix.db)
diff --git a/var/spack/repos/builtin/packages/bash-completion/package.py b/var/spack/repos/builtin/packages/bash-completion/package.py
index 2e59e6247e..668bbc237e 100644
--- a/var/spack/repos/builtin/packages/bash-completion/package.py
+++ b/var/spack/repos/builtin/packages/bash-completion/package.py
@@ -1,37 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class BashCompletion(AutotoolsPackage):
     """Programmable completion functions for bash."""
+
     homepage = "https://github.com/scop/bash-completion"
-    url = "https://github.com/scop/bash-completion/archive/2.3.tar.gz"
+    url      = "https://github.com/scop/bash-completion/archive/2.3.tar.gz"
+    git      = "https://github.com/scop/bash-completion.git"
 
+    version('develop', branch='master')
+    version('2.7', 'f72c9e2e877d188c3159956a3496a450e7279b76')
     version('2.3', '67e50f5f3c804350b43f2b664c33dde811d24292')
-    version('develop',  git='https://github.com/scop/bash-completion.git')
 
     # Build dependencies
     depends_on('automake', type='build')
@@ -41,6 +25,10 @@ class BashCompletion(AutotoolsPackage):
     # Other dependencies
     depends_on('bash@4.1:', type='run')
 
+    @run_before('install')
+    def create_install_directory(self):
+        mkdirp(join_path(self.prefix.share, 'bash-completion', 'completions'))
+
     @run_after('install')
     def show_message_to_user(self):
         prefix = self.prefix
diff --git a/var/spack/repos/builtin/packages/bash/package.py b/var/spack/repos/builtin/packages/bash/package.py
index 478edccd99..9903e1517d 100644
--- a/var/spack/repos/builtin/packages/bash/package.py
+++ b/var/spack/repos/builtin/packages/bash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,9 @@ class Bash(AutotoolsPackage):
     """The GNU Project's Bourne Again SHell."""
 
     homepage = "https://www.gnu.org/software/bash/"
-    url      = "https://ftp.gnu.org/gnu/bash/bash-4.4.tar.gz"
+    url      = "https://ftpmirror.gnu.org/bash/bash-4.4.tar.gz"
 
+    version('4.4.12', '7c112970cbdcadfc331e10eeb5f6aa41')
     version('4.4', '148888a7c95ac23705559b6f477dfe25')
     version('4.3', '81348932d5da294953e15d4814c74dd1')
 
@@ -49,3 +31,12 @@ class Bash(AutotoolsPackage):
 
     def check(self):
         make('tests')
+
+    @property
+    def install_targets(self):
+        args = ['install']
+
+        if self.spec.satisfies('@4.4:'):
+            args.append('install-headers')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/bats/package.py b/var/spack/repos/builtin/packages/bats/package.py
index 4ee05c5a1c..d7ef4088ce 100644
--- a/var/spack/repos/builtin/packages/bats/package.py
+++ b/var/spack/repos/builtin/packages/bats/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.13.0.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.13.0.patch
new file mode 100644
index 0000000000..31b4cf1a8e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.13.0.patch
@@ -0,0 +1,129 @@
+--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java.orig	2018-05-23 12:11:29.319402761 +0200
++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java	2018-05-23 12:35:21.817904301 +0200
+@@ -150,6 +150,126 @@
+       builder.put("PATH", null);
+       builder.put("LD_LIBRARY_PATH", null);
+     }
++
++      String spack_prefix = System.getenv("SPACK_PREFIX");
++      if (spack_prefix != null) {
++          builder.put("SPACK_PREFIX", spack_prefix);
++      }
++
++      String spack_env_path = System.getenv("SPACK_ENV_PATH");
++      if (spack_env_path != null) {
++          builder.put("SPACK_ENV_PATH", spack_env_path);
++      }
++
++      String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++      if (spack_debug_log_id != null) {
++          builder.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++      }
++
++      String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
++      if (spack_debug_log_dir != null) {
++          builder.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
++      }
++
++      String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC");
++      if (spack_compiler_spec != null) {
++          builder.put("SPACK_COMPILER_SPEC", spack_compiler_spec);
++      }
++
++      String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG");
++      if (spack_cc_rpath_arg != null) {
++          builder.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg);
++      }
++
++      String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG");
++      if (spack_cxx_rpath_arg != null) {
++          builder.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg);
++      }
++
++      String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG");
++      if (spack_f77_rpath_arg != null) {
++          builder.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg);
++      }
++
++      String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG");
++      if (spack_fc_rpath_arg != null) {
++          builder.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg);
++      }
++
++      String spack_short_spec = System.getenv("SPACK_SHORT_SPEC");
++      if (spack_short_spec != null) {
++          builder.put("SPACK_SHORT_SPEC", spack_short_spec);
++      }
++
++      String spack_system_dirs = System.getenv("SPACK_SYSTEM_DIRS");
++      if (spack_system_dirs != null) {
++          builder.put("SPACK_SYSTEM_DIRS", spack_system_dirs);
++      }
++
++      String spack_cc = System.getenv("SPACK_CC");
++      if (spack_cc != null) {
++          builder.put("SPACK_CC", spack_cc);
++      }
++
++      String spack_cxx = System.getenv("SPACK_CXX");
++      if (spack_cxx != null) {
++          builder.put("SPACK_CXX", spack_cxx);
++      }
++
++      String spack_f77 = System.getenv("SPACK_F77");
++      if (spack_f77 != null) {
++          builder.put("SPACK_F77", spack_f77);
++      }
++
++      String spack_fc = System.getenv("SPACK_FC");
++      if (spack_fc != null) {
++          builder.put("SPACK_FC", spack_fc);
++      }
++
++      String spack_cflags = System.getenv("SPACK_CFLAGS");
++      if (spack_cflags != null) {
++          builder.put("SPACK_CFLAGS", spack_cflags);
++      }
++
++      String spack_cxxflags = System.getenv("SPACK_CXXFLAGS");
++      if (spack_cxxflags != null) {
++          builder.put("SPACK_CXXFLAGS", spack_cxxflags);
++      }
++
++      String spack_fcflags = System.getenv("SPACK_FCFLAGS");
++      if (spack_fcflags != null) {
++          builder.put("SPACK_FCFLAGS", spack_fcflags);
++      }
++
++      String spack_fflags = System.getenv("SPACK_FFLAGS");
++      if (spack_fflags != null) {
++          builder.put("SPACK_FFLAGS", spack_fflags);
++      }
++
++      String spack_ldflags = System.getenv("SPACK_LDFLAGS");
++      if (spack_ldflags != null) {
++          builder.put("SPACK_LDFLAGS", spack_ldflags);
++      }
++
++      String spack_ldlibs = System.getenv("SPACK_LDLIBS");
++      if (spack_ldlibs != null) {
++          builder.put("SPACK_LDLIBS", spack_ldlibs);
++      }
++
++      String spack_debug = System.getenv("SPACK_DEBUG");
++      if (spack_debug != null) {
++          builder.put("SPACK_DEBUG", spack_debug);
++      }
++
++      String spack_test_command = System.getenv("SPACK_TEST_COMMAND");
++      if (spack_test_command != null) {
++          builder.put("SPACK_TEST_COMMAND", spack_test_command);
++      }
++
++      String spack_dependencies = System.getenv("SPACK_DEPENDENCIES");
++      if (spack_dependencies != null) {
++          builder.put("SPACK_DEPENDENCIES", spack_dependencies);
++      }
+   }
+ 
+   private static PathFragment determineShellExecutable(OS os, PathFragment fromOption) {
diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.17.2.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.17.2.patch
new file mode 100644
index 0000000000..89537387a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.17.2.patch
@@ -0,0 +1,131 @@
+diff --git a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
+index 72c40ac..2e73530 100755
+--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
+@@ -168,6 +168,126 @@ public class BazelRuleClassProvider {
+       env.put("PATH", null);
+     }
+ 
++    String spack_prefix = System.getenv("SPACK_PREFIX");
++    if (spack_prefix != null) {
++      env.put("SPACK_PREFIX", spack_prefix);
++    }
++
++    String spack_env_path = System.getenv("SPACK_ENV_PATH");
++    if (spack_env_path != null) {
++        env.put("SPACK_ENV_PATH", spack_env_path);
++    }
++
++    String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++    if (spack_debug_log_id != null) {
++        env.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++    }
++
++    String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
++    if (spack_debug_log_dir != null) {
++        env.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
++    }
++
++    String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC");
++    if (spack_compiler_spec != null) {
++        env.put("SPACK_COMPILER_SPEC", spack_compiler_spec);
++    }
++
++    String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG");
++    if (spack_cc_rpath_arg != null) {
++        env.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg);
++    }
++
++    String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG");
++    if (spack_cxx_rpath_arg != null) {
++        env.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg);
++    }
++
++    String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG");
++    if (spack_f77_rpath_arg != null) {
++        env.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg);
++    }
++
++    String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG");
++    if (spack_fc_rpath_arg != null) {
++        env.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg);
++    }
++
++    String spack_short_spec = System.getenv("SPACK_SHORT_SPEC");
++    if (spack_short_spec != null) {
++        env.put("SPACK_SHORT_SPEC", spack_short_spec);
++    }
++
++    String spack_system_dirs = System.getenv("SPACK_SYSTEM_DIRS");
++    if (spack_system_dirs != null) {
++        env.put("SPACK_SYSTEM_DIRS", spack_system_dirs);
++    }
++
++    String spack_cc = System.getenv("SPACK_CC");
++    if (spack_cc != null) {
++        env.put("SPACK_CC", spack_cc);
++    }
++
++    String spack_cxx = System.getenv("SPACK_CXX");
++    if (spack_cxx != null) {
++        env.put("SPACK_CXX", spack_cxx);
++    }
++
++    String spack_f77 = System.getenv("SPACK_F77");
++    if (spack_f77 != null) {
++        env.put("SPACK_F77", spack_f77);
++    }
++
++    String spack_fc = System.getenv("SPACK_FC");
++    if (spack_fc != null) {
++        env.put("SPACK_FC", spack_fc);
++    }
++
++    String spack_cflags = System.getenv("SPACK_CFLAGS");
++    if (spack_cflags != null) {
++        env.put("SPACK_CFLAGS", spack_cflags);
++    }
++
++    String spack_cxxflags = System.getenv("SPACK_CXXFLAGS");
++    if (spack_cxxflags != null) {
++        env.put("SPACK_CXXFLAGS", spack_cxxflags);
++    }
++
++    String spack_fcflags = System.getenv("SPACK_FCFLAGS");
++    if (spack_fcflags != null) {
++        env.put("SPACK_FCFLAGS", spack_fcflags);
++    }
++
++    String spack_fflags = System.getenv("SPACK_FFLAGS");
++    if (spack_fflags != null) {
++        env.put("SPACK_FFLAGS", spack_fflags);
++    }
++
++    String spack_ldflags = System.getenv("SPACK_LDFLAGS");
++    if (spack_ldflags != null) {
++        env.put("SPACK_LDFLAGS", spack_ldflags);
++    }
++
++    String spack_ldlibs = System.getenv("SPACK_LDLIBS");
++    if (spack_ldlibs != null) {
++        env.put("SPACK_LDLIBS", spack_ldlibs);
++    }
++
++    String spack_debug = System.getenv("SPACK_DEBUG");
++    if (spack_debug != null) {
++        env.put("SPACK_DEBUG", spack_debug);
++    }
++
++    String spack_test_command = System.getenv("SPACK_TEST_COMMAND");
++    if (spack_test_command != null) {
++        env.put("SPACK_TEST_COMMAND", spack_test_command);
++    }
++
++    String spack_dependencies = System.getenv("SPACK_DEPENDENCIES");
++    if (spack_dependencies != null) {
++        env.put("SPACK_DEPENDENCIES", spack_dependencies);
++    }
++
+     // Shell environment variables specified via options take precedence over the
+     // ones inherited from the fragments. In the long run, these fragments will
+     // be replaced by appropriate default rc files anyway.
diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.9.0.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.9.0.patch
new file mode 100644
index 0000000000..323748377f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/fix_env_handling-0.9.0.patch
@@ -0,0 +1,126 @@
+diff --git a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java.orig b/home/jtang/spack/var/spack/stage/bazel-0.9.0-xcsfcyrpdn3df755cwpk4sxtfwjdv4ub/spack-expanded-archive/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
+index f1a7a1f..32cd181 100755
+--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java.orig
++++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
+@@ -154,6 +154,121 @@ public class BazelConfiguration extends Fragment {
+       if (tmpdir != null) {
+         builder.put("TMPDIR", tmpdir);
+       }
++
++      String spack_prefix = System.getenv("SPACK_PREFIX");
++      if (spack_prefix != null) {
++          builder.put("SPACK_PREFIX", spack_prefix);
++      }
++
++      String spack_env_path = System.getenv("SPACK_ENV_PATH");
++      if (spack_env_path != null) {
++          builder.put("SPACK_ENV_PATH", spack_env_path);
++      }
++
++      String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++      if (spack_debug_log_id != null) {
++          builder.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++      }
++
++      String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
++      if (spack_debug_log_dir != null) {
++          builder.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
++      }
++
++      String spack_compiler_spec = System.getenv("SPACK_COMPILER_SPEC");
++      if (spack_compiler_spec != null) {
++          builder.put("SPACK_COMPILER_SPEC", spack_compiler_spec);
++      }
++
++      String spack_cc_rpath_arg = System.getenv("SPACK_CC_RPATH_ARG");
++      if (spack_cc_rpath_arg != null) {
++          builder.put("SPACK_CC_RPATH_ARG", spack_cc_rpath_arg);
++      }
++
++      String spack_cxx_rpath_arg = System.getenv("SPACK_CXX_RPATH_ARG");
++      if (spack_cxx_rpath_arg != null) {
++          builder.put("SPACK_CXX_RPATH_ARG", spack_cxx_rpath_arg);
++      }
++
++      String spack_f77_rpath_arg = System.getenv("SPACK_F77_RPATH_ARG");
++      if (spack_f77_rpath_arg != null) {
++          builder.put("SPACK_F77_RPATH_ARG", spack_f77_rpath_arg);
++      }
++
++      String spack_fc_rpath_arg = System.getenv("SPACK_FC_RPATH_ARG");
++      if (spack_fc_rpath_arg != null) {
++          builder.put("SPACK_FC_RPATH_ARG", spack_fc_rpath_arg);
++      }
++
++      String spack_short_spec = System.getenv("SPACK_SHORT_SPEC");
++      if (spack_short_spec != null) {
++          builder.put("SPACK_SHORT_SPEC", spack_short_spec);
++      }
++
++      String spack_cc = System.getenv("SPACK_CC");
++      if (spack_cc != null) {
++          builder.put("SPACK_CC", spack_cc);
++      }
++
++      String spack_cxx = System.getenv("SPACK_CXX");
++      if (spack_cxx != null) {
++          builder.put("SPACK_CXX", spack_cxx);
++      }
++
++      String spack_f77 = System.getenv("SPACK_F77");
++      if (spack_f77 != null) {
++          builder.put("SPACK_F77", spack_f77);
++      }
++
++      String spack_fc = System.getenv("SPACK_FC");
++      if (spack_fc != null) {
++          builder.put("SPACK_FC", spack_fc);
++      }
++
++      String spack_cflags = System.getenv("SPACK_CFLAGS");
++      if (spack_cflags != null) {
++          builder.put("SPACK_CFLAGS", spack_cflags);
++      }
++
++      String spack_cxxflags = System.getenv("SPACK_CXXFLAGS");
++      if (spack_cxxflags != null) {
++          builder.put("SPACK_CXXFLAGS", spack_cxxflags);
++      }
++
++      String spack_fcflags = System.getenv("SPACK_FCFLAGS");
++      if (spack_fcflags != null) {
++          builder.put("SPACK_FCFLAGS", spack_fcflags);
++      }
++
++      String spack_fflags = System.getenv("SPACK_FFLAGS");
++      if (spack_fflags != null) {
++          builder.put("SPACK_FFLAGS", spack_fflags);
++      }
++
++      String spack_ldflags = System.getenv("SPACK_LDFLAGS");
++      if (spack_ldflags != null) {
++          builder.put("SPACK_LDFLAGS", spack_ldflags);
++      }
++
++      String spack_ldlibs = System.getenv("SPACK_LDLIBS");
++      if (spack_ldlibs != null) {
++          builder.put("SPACK_LDLIBS", spack_ldlibs);
++      }
++
++      String spack_debug = System.getenv("SPACK_DEBUG");
++      if (spack_debug != null) {
++          builder.put("SPACK_DEBUG", spack_debug);
++      }
++
++      String spack_test_command = System.getenv("SPACK_TEST_COMMAND");
++      if (spack_test_command != null) {
++          builder.put("SPACK_TEST_COMMAND", spack_test_command);
++      }
++
++      String spack_dependencies = System.getenv("SPACK_DEPENDENCIES");
++      if (spack_dependencies != null) {
++          builder.put("SPACK_DEPENDENCIES", spack_dependencies);
++      }
+     }
+   }
+ 
diff --git a/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch b/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch
index 9be9f97d69..14deccf950 100644
--- a/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch
+++ b/var/spack/repos/builtin/packages/bazel/fix_env_handling.patch
@@ -1,7 +1,7 @@
 diff -pu bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java 
 --- bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java 2016-09-14 11:56:01.565756979 +0200
 +++ bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java	2016-09-14 12:04:13.292839801 +0200
-@@ -92,5 +92,115 @@ public class BazelConfiguration extends
+@@ -92,5 +92,120 @@ public class BazelConfiguration extends
      if (tmpdir != null) {
        builder.put("TMPDIR", tmpdir);
      }
@@ -16,6 +16,11 @@ diff -pu bazel-0.3.1/src/main/java/com/google/devtools/build/lib/bazel/rules/Baz
 +      builder.put("SPACK_ENV_PATH", spack_env_path);
 +    }
 +
++    String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++    if (spack_debug_log_id != null) {
++      builder.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++    }
++
 +    String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
 +    if (spack_debug_log_dir != null) {
 +      builder.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
diff --git a/var/spack/repos/builtin/packages/bazel/link.patch b/var/spack/repos/builtin/packages/bazel/link.patch
index 69d100f62c..5c8824b87d 100644
--- a/var/spack/repos/builtin/packages/bazel/link.patch
+++ b/var/spack/repos/builtin/packages/bazel/link.patch
@@ -1,6 +1,6 @@
 --- bazel-0.3.1/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkAction.java	2016-07-29 10:22:16.000000000 +0200
 +++ bazel-0.3.1/src/main/java/com/google/devtools/build/lib/rules/cpp/CppLinkAction.java	2016-10-13 15:21:35.036617890 +0200
-@@ -214,6 +214,130 @@
+@@ -214,6 +214,135 @@
                .getParentDirectory()
                .getPathString());
      }
@@ -28,6 +28,11 @@
 +      result.put("SPACK_ENV_PATH", spack_env_path);
 +    }
 +
++    String spack_debug_log_id = System.getenv("SPACK_DEBUG_LOG_ID");
++    if (spack_debug_log_id != null) {
++      result.put("SPACK_DEBUG_LOG_ID", spack_debug_log_id);
++    }
++
 +    String spack_debug_log_dir = System.getenv("SPACK_DEBUG_LOG_DIR");
 +    if (spack_debug_log_dir != null) {
 +      result.put("SPACK_DEBUG_LOG_DIR", spack_debug_log_dir);
diff --git a/var/spack/repos/builtin/packages/bazel/package.py b/var/spack/repos/builtin/packages/bazel/package.py
index ff9817be97..9f34d3d52b 100644
--- a/var/spack/repos/builtin/packages/bazel/package.py
+++ b/var/spack/repos/builtin/packages/bazel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from multiprocessing import cpu_count
 from spack.util.environment import env_flag
@@ -32,8 +13,19 @@ class Bazel(Package):
     """Bazel is Google's own build tool"""
 
     homepage = "https://www.bazel.io"
-    url = "https://github.com/bazelbuild/bazel/releases/download/0.5.0/bazel-0.5.0-dist.zip"
-
+    url = "https://github.com/bazelbuild/bazel/releases/download/0.11.1/bazel-0.11.1-dist.zip"
+
+    version('0.17.2', '9805c0593e781295126af6b8be8cc7a9')
+    version('0.16.1', 'c333d903c5275286e79316eb19dd742d')
+    version('0.15.0', 'fb6b928b62f068697bd66ad6d13aad53')
+    version('0.14.1', '841900316b3ec9b996babe1c5b0b92e1')
+    version('0.13.0', '64a5124025c1618b550faec64a9b6fa3')
+    version('0.12.0', 'b5d67564ceecfe2005a885fe2ffe0da3')
+    version('0.11.1', '80daac6b100b7f8e2b17d133150eba44')
+    version('0.11.0', 'e6caf93a805b45c33367028e575b91dd')
+    version('0.10.1', 'a7e5b9576993b752e31bd2d3259a14c5')
+    version('0.10.0', 'c2f15b34255099d25e94fce7283e5cd2')
+    version('0.9.0', '7fda74c163108f7c180bbc513bc8123b')
     version('0.4.5', '2b737be42678900470ae9e48c975ac5b2296d9ae23c007bf118350dbe7c0552b')
     version('0.4.4', '5e7c52b89071efc41277e2f0057d258f')
     version('0.3.1', '5c959467484a7fc7dd2e5e4a1e8e866b')
@@ -42,12 +34,18 @@ class Bazel(Package):
     version('0.2.2b', '75081804f073cbd194da1a07b16cba5f')
     version('0.2.2', '644bc4ea7f429d835e74f255dc1054e6')
 
-    depends_on('java@8:')
+    depends_on('java@8:', type=('build', 'link', 'run'))
     depends_on('zip')
 
-    patch('fix_env_handling.patch')
+    patch('fix_env_handling.patch', when='@:0.4.5')
+    patch('fix_env_handling-0.9.0.patch', when='@0.9.0:0.12.0')
+    patch('fix_env_handling-0.13.0.patch', when='@0.13.0:0.13.999')
+    patch('fix_env_handling-0.17.2.patch', when='@0.14.0:')
     patch('link.patch')
-    patch('cc_configure.patch')
+    patch('cc_configure.patch', when='@:0.4.5')
+    patch('unix_cc_configure.patch', when='@0.9.0')
+    patch('unix_cc_configure-0.10.0.patch', when='@0.10.0:0.14.999')
+    patch('unix_cc_configure-0.17.2.patch', when='@0.15.0:')
 
     def url_for_version(self, version):
         if version >= Version('0.4.1'):
@@ -80,8 +78,8 @@ class Bazel(Package):
 
             def __call__(self, *args, **kwargs):
                 disable = env_flag(SPACK_NO_PARALLEL_MAKE)
-                parallel = ((not disable) and
-                            kwargs.get('parallel', self.jobs > 1))
+                parallel = ((not disable) and kwargs.get('parallel',
+                                                         self.jobs > 1))
 
                 jobs = "--jobs=1"
                 if parallel:
diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.0.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.0.patch
new file mode 100644
index 0000000000..e375283fed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.10.0.patch
@@ -0,0 +1,25 @@
+diff --git a/tools/cpp/unix_cc_configure.bzl.orig b/tools/cpp/unix_cc_configure.bzl
+index f67b9b5..cc952e0 100755
+--- a/tools/cpp/unix_cc_configure.bzl.orig
++++ b/tools/cpp/unix_cc_configure.bzl
+@@ -147,9 +147,18 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, additional_flags = []):
+   else:
+     inc_dirs = result.stderr[index1 + 1:index2].strip()
+ 
+-  return [_prepare_include_path(repository_ctx, _cxx_inc_convert(p))
+-          for p in inc_dirs.split("\n")]
++  default_inc_directories = [
++    _prepare_include_path(repository_ctx, _cxx_inc_convert(p))
++      for p in inc_dirs.split("\n")
++  ]
+ 
++  env = repository_ctx.os.environ
++  if "SPACK_DEPENDENCIES" in env:
++    for dep in env["SPACK_DEPENDENCIES"].split(":"):
++      path = dep + "/include"
++      default_inc_directories.append(path)
++
++  return default_inc_directories
+ 
+ def _is_option_supported(repository_ctx, cc, option):
+   """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.17.2.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.17.2.patch
new file mode 100644
index 0000000000..d1a502a49a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure-0.17.2.patch
@@ -0,0 +1,25 @@
+diff --git a/tools/cpp/unix_cc_configure.bzl b/tools/cpp/unix_cc_configure.bzl
+index 361931b..a79129b 100755
+--- a/tools/cpp/unix_cc_configure.bzl
++++ b/tools/cpp/unix_cc_configure.bzl
+@@ -145,11 +145,19 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc, lang_flag, additional_fl
+     else:
+         inc_dirs = result.stderr[index1 + 1:index2].strip()
+ 
+-    return [
++    default_inc_directories = [
+         _prepare_include_path(repository_ctx, _cxx_inc_convert(p))
+         for p in inc_dirs.split("\n")
+     ]
+ 
++    env = repository_ctx.os.environ
++    if "SPACK_DEPENDENCIES" in env:
++        for dep in env["SPACK_DEPENDENCIES"].split(":"):
++            path = dep + "/include"
++            default_inc_directories.append(path)
++
++    return default_inc_directories
++
+ def _is_compiler_option_supported(repository_ctx, cc, option):
+     """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
+     result = repository_ctx.execute([
diff --git a/var/spack/repos/builtin/packages/bazel/unix_cc_configure.patch b/var/spack/repos/builtin/packages/bazel/unix_cc_configure.patch
new file mode 100644
index 0000000000..3f14bc2fc0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bazel/unix_cc_configure.patch
@@ -0,0 +1,32 @@
+diff --git a/spack-expanded-archive/tools/cpp/unix_cc_configure.bzl.orig b/spack-expanded-archive/tools/cpp/unix_cc_configure.bzl
+old mode 100644
+new mode 100755
+index aa46f55..ae3c689
+--- spack-expanded-archive/tools/cpp/unix_cc_configure.bzl
++++ spack-expanded-archive/tools/cpp/unix_cc_configure.bzl
+@@ -117,9 +117,23 @@ def get_escaped_cxx_inc_directories(repository_ctx, cc):
+   else:
+     inc_dirs = result.stderr[index1 + 1:index2].strip()
+ 
+-  return [escape_string(repository_ctx.path(_cxx_inc_convert(p)))
+-          for p in inc_dirs.split("\n")]
++  default_inc_directories = [
++    escape_string(repository_ctx.path(_cxx_inc_convert(p)))
++          for p in inc_dirs.split("\n")
++  ]
+ 
++  env = repository_ctx.os.environ
++  if "SPACK_DEPENDENCIES" in env:
++    for dep in env["SPACK_DEPENDENCIES"].split(":"):
++      path = dep + "/include"
++      # path = repository_ctx.os.path.join(dep, "include")
++      # if not repository_ctx.os.path.exists(path):
++      #   continue
++      default_inc_directories.append(
++        repository_ctx.path(_cxx_inc_convert(path))
++      )
++
++  return default_inc_directories
+ 
+ def _add_option_if_supported(repository_ctx, cc, option):
+   """Checks that `option` is supported by the C compiler. Doesn't %-escape the option."""
diff --git a/var/spack/repos/builtin/packages/bbcp/package.py b/var/spack/repos/builtin/packages/bbcp/package.py
index f72b4fcb12..bd597decea 100644
--- a/var/spack/repos/builtin/packages/bbcp/package.py
+++ b/var/spack/repos/builtin/packages/bbcp/package.py
@@ -1,36 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Bbcp(Package):
     """Securely and quickly copy data from source to target"""
+
     homepage = "http://www.slac.stanford.edu/~abh/bbcp/"
+    git      = "http://www.slac.stanford.edu/~abh/bbcp/bbcp.git"
 
-    version('git', git='http://www.slac.stanford.edu/~abh/bbcp/bbcp.git',
-            branch="master")
+    version('git', branch='master')
 
     depends_on('zlib')
     depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/bbmap/package.py b/var/spack/repos/builtin/packages/bbmap/package.py
index 15d7d880c3..d73b72cc2f 100644
--- a/var/spack/repos/builtin/packages/bbmap/package.py
+++ b/var/spack/repos/builtin/packages/bbmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bc/package.py b/var/spack/repos/builtin/packages/bc/package.py
new file mode 100644
index 0000000000..6f149e6fa9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bc/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bc(AutotoolsPackage):
+    """bc is an arbitrary precision numeric processing language. Syntax is
+    similar to C, but differs in many substantial areas. It supports
+    interactive execution of statements."""
+
+    homepage = "https://www.gnu.org/software/bc"
+    url      = "https://ftpmirror.gnu.org/bc/bc-1.07.tar.gz"
+
+    version('1.07', 'e91638a947beadabf4d7770bdbb3d512')
+
+    depends_on('ed', type='build')
+    depends_on('texinfo', type='build')
+
+    parallel = False
diff --git a/var/spack/repos/builtin/packages/bcftools/package.py b/var/spack/repos/builtin/packages/bcftools/package.py
index b1cccc1f21..e49c7c4bd2 100644
--- a/var/spack/repos/builtin/packages/bcftools/package.py
+++ b/var/spack/repos/builtin/packages/bcftools/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Bcftools(Package):
+class Bcftools(AutotoolsPackage):
     """BCFtools is a set of utilities that manipulate variant calls in the
        Variant Call Format (VCF) and its binary counterpart BCF. All
        commands work transparently with both VCFs and BCFs, both
@@ -34,16 +15,20 @@ class Bcftools(Package):
     homepage = "http://samtools.github.io/bcftools/"
     url      = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
 
+    version('1.9', sha256='6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8')
+    version('1.8', 'ba6c2fb7eb6dcb208f00ab8b22df475c')
+    version('1.7', 'c972db68d17af9da3a18963f4e5aeca8')
     version('1.6', 'c4dba1e8cb55db0f94b4c47724b4f9fa')
     version('1.4', '50ccf0a073bd70e99cdb3c8be830416e')
     version('1.3.1', '575001e9fca37cab0c7a7287ad4b1cdb')
     version('1.2', '8044bed8fce62f7072fc6835420f0906')
 
+    depends_on('libzip', when='@1.8:')
+
+    depends_on('htslib@1.9', when='@1.9')
+    depends_on('htslib@1.8', when='@1.8')
+    depends_on('htslib@1.7',   when='@1.7')
     depends_on('htslib@1.6',   when='@1.6')
     depends_on('htslib@1.4',   when='@1.4')
     depends_on('htslib@1.3.1', when='@1.3.1')
     depends_on('htslib@1.2', when='@1.2')
-
-    def install(self, spec, prefix):
-        make("prefix=%s" % prefix, "all")
-        make("prefix=%s" % prefix, "install")
diff --git a/var/spack/repos/builtin/packages/bcl2fastq2/package.py b/var/spack/repos/builtin/packages/bcl2fastq2/package.py
index 173bb050ff..f3eb3175ac 100644
--- a/var/spack/repos/builtin/packages/bcl2fastq2/package.py
+++ b/var/spack/repos/builtin/packages/bcl2fastq2/package.py
@@ -1,30 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
-import shutil
+import glob
 import llnl.util.tty as tty
 
 
@@ -36,8 +17,9 @@ class Bcl2fastq2(Package):
        call (BCL) files from a sequencing run into FASTQ
        files."""
 
-    homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-18.html"
+    homepage = "https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html"
 
+    version('2.20.0.422', '4dc99f1af208498b7279b66556329488')
     version('2.19.1.403', 'baba7a02767fd868e87cb36781d2be26')
     version('2.18.0.12', 'fbe06492117f65609c41be0c27e3215c')
     # 2.17.1.14 is no longer distributed.  If you have a copy of the
@@ -65,12 +47,11 @@ class Bcl2fastq2(Package):
     # v2.19.1.403 is only available via ftp.
     # who knows what the future will hold.
     def url_for_version(self, version):
+        url = "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
         if version.string == '2.19.1.403':
-            return "ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/bcl2fastq2-v2.19.1-tar.zip"
+            return url.format(version.up_to(3).dotted)
         else:
-            url = "https://support.illumina.com/content/dam/illumina-support/documents/downloads/software/bcl2fastq/bcl2fastq2-v{0}-tar.zip"
-            # - required to change the version from dots to dashes.
-            return url.format(version.dashed)
+            return url.format(version.up_to(3).dashed)
 
     # Illumina tucks the source inside a gzipped tarball inside a zip
     # file.  We let the normal Spack expansion bit unzip the zip file,
@@ -91,12 +72,12 @@ class Bcl2fastq2(Package):
                 else:
                     tty.msg("Unpacking bcl2fastq2 tarball")
                     tty.msg("cwd sez: {0}".format(os.getcwd()))
-                    tarball = 'bcl2fastq2-v{0}.tar.gz'.format(
-                        self.version.dotted)
-                    shutil.move(join_path('spack-expanded-archive', tarball),
-                                '.')
+                    tarball = glob.glob(join_path('spack-expanded-archive',
+                                        'bcl2fastq2*.tar.gz'))[0]
+                    copy(tarball, '.')
                     os.rmdir('spack-expanded-archive')
                     tar = which('tar')
+                    tarball = os.path.basename(tarball)
                     tar('-xf', tarball)
                     tty.msg("Finished unpacking bcl2fastq2 tarball")
         return wrap
diff --git a/var/spack/repos/builtin/packages/bdftopcf/package.py b/var/spack/repos/builtin/packages/bdftopcf/package.py
index a85bcf5307..7140818204 100644
--- a/var/spack/repos/builtin/packages/bdftopcf/package.py
+++ b/var/spack/repos/builtin/packages/bdftopcf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Bdftopcf(AutotoolsPackage):
 
     depends_on('libxfont')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('xproto', type='build')
     depends_on('fontsproto', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/bdw-gc/package.py b/var/spack/repos/builtin/packages/bdw-gc/package.py
index 7971dae506..4246867f22 100644
--- a/var/spack/repos/builtin/packages/bdw-gc/package.py
+++ b/var/spack/repos/builtin/packages/bdw-gc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bear/package.py b/var/spack/repos/builtin/packages/bear/package.py
index f3f46b1025..1117ef5aac 100644
--- a/var/spack/repos/builtin/packages/bear/package.py
+++ b/var/spack/repos/builtin/packages/bear/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/beast1/package.py b/var/spack/repos/builtin/packages/beast1/package.py
new file mode 100644
index 0000000000..f9c94650e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/beast1/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Beast1(Package):
+    """BEAST is a cross-platform program for Bayesian
+       analysis of molecular sequences using MCMC."""
+
+    homepage = "http://beast.community/"
+    url      = "https://github.com/beast-dev/beast-mcmc/releases/download/v1.8.4/BEASTv1.8.4.tgz"
+
+    version('1.10.0', 'bcf2f2c074319360ec8a2ebad57d2e57', 
+            url='https://github.com/beast-dev/beast-mcmc/releases/download/v1.10.0/BEAST_v1.10.0.tgz')
+    version('1.8.4', 'cb8752340c1f77a22d39ca4fe09687b0')
+
+    variant('beagle', default=True, description='Build with libbeagle support')
+
+    depends_on('java', type='run')
+    depends_on('libbeagle', type=('build', 'link', 'run'), when="+beagle")
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('BEAST1', self.prefix)
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('examples', prefix.examples)
+        install_tree('images', prefix.images)
+        install_tree('lib', prefix.lib)
+        install_tree('doc', prefix.doc)
diff --git a/var/spack/repos/builtin/packages/beast2/package.py b/var/spack/repos/builtin/packages/beast2/package.py
index 88066116a2..a5b8182e74 100644
--- a/var/spack/repos/builtin/packages/beast2/package.py
+++ b/var/spack/repos/builtin/packages/beast2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bedops/package.py b/var/spack/repos/builtin/packages/bedops/package.py
new file mode 100644
index 0000000000..9e22dbbe10
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bedops/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bedops(MakefilePackage):
+    """BEDOPS is an open-source command-line toolkit that performs highly
+    efficient and scalable Boolean and other set operations, statistical
+    calculations, archiving, conversion and other management of genomic data of
+    arbitrary scale."""
+
+    homepage = "https://bedops.readthedocs.io"
+    url      = "https://github.com/bedops/bedops/archive/v2.4.30.tar.gz"
+
+    version('2.4.35', 'b425b3e05fd4cd1024ef4dd8bf04b4e5')
+    version('2.4.34', 'fc467d96134a0efe8b134e638af87a1a')
+    version('2.4.30', '4e5d9f7b7e5432b28aef8d17a22cffab')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        make('install', "BINDIR=%s" % prefix.bin)
diff --git a/var/spack/repos/builtin/packages/bedtools2/package.py b/var/spack/repos/builtin/packages/bedtools2/package.py
index 5956491f1b..55d06175bb 100644
--- a/var/spack/repos/builtin/packages/bedtools2/package.py
+++ b/var/spack/repos/builtin/packages/bedtools2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,8 @@ class Bedtools2(Package):
     homepage = "https://github.com/arq5x/bedtools2"
     url      = "https://github.com/arq5x/bedtools2/archive/v2.26.0.tar.gz"
 
+    version('2.27.1', '8e0afcab95a824e42a6e99c5436a8438')
+    version('2.27.0', '052f22eb214ef2e7e7981b3c01167302')
     version('2.26.0', '52227e7efa6627f0f95d7d734973233d')
     version('2.25.0', '534fb4a7bf0d0c3f05be52a0160d8e3d')
     version('2.23.0', '4fa3671b3a3891eefd969ad3509222e3')
diff --git a/var/spack/repos/builtin/packages/beforelight/package.py b/var/spack/repos/builtin/packages/beforelight/package.py
index 457c547a16..fcde1adb4c 100644
--- a/var/spack/repos/builtin/packages/beforelight/package.py
+++ b/var/spack/repos/builtin/packages/beforelight/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Beforelight(AutotoolsPackage):
     depends_on('libxscrnsaver')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/benchmark/package.py b/var/spack/repos/builtin/packages/benchmark/package.py
index 8c4dc6ec1f..83abbde812 100644
--- a/var/spack/repos/builtin/packages/benchmark/package.py
+++ b/var/spack/repos/builtin/packages/benchmark/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,14 @@ class Benchmark(CMakePackage):
 
     homepage = "https://github.com/google/benchmark"
     url      = "https://github.com/google/benchmark/archive/v1.1.0.tar.gz"
-
-    version('develop', branch='master',
-            git='https://github.com/google/benchmark.git')
+    git      = "https://github.com/google/benchmark.git"
 
     # first properly installed CMake config packages in
     # 1.2.0 release: https://github.com/google/benchmark/issues/363
+
+    version('develop', branch='master')
+    version('1.4.0', 'ccfaf2cd93ae20191b94f730b945423e')
+    version('1.3.0', '19ce86516ab82d6ad3b17173cf307aac')
     version('1.2.0', '48d0b090cd7a84af2c4a28c8dc963c74')
     version('1.1.0', '66b2a23076cf70739525be0092fc3ae3')
     version('1.0.0', '1474ff826f8cd68067258db75a0835b8')
@@ -45,6 +28,14 @@ class Benchmark(CMakePackage):
             values=('Debug', 'Release', 'RelWithDebInfo',
                     'MinSizeRel', 'Coverage'))
 
+    depends_on("cmake@2.8.11:", type="build", when="@:1.1.0")
+    depends_on("cmake@2.8.12:", type="build", when="@1.2.0:")
+
+    def cmake_args(self):
+        # No need for testing for the install
+        args = ["-DBENCHMARK_ENABLE_TESTING=OFF"]
+        return args
+
     def patch(self):
         filter_file(
             r'add_cxx_compiler_flag..fstrict.aliasing.',
diff --git a/var/spack/repos/builtin/packages/berkeley-db/package.py b/var/spack/repos/builtin/packages/berkeley-db/package.py
index 3962ef3472..bd47c239af 100644
--- a/var/spack/repos/builtin/packages/berkeley-db/package.py
+++ b/var/spack/repos/builtin/packages/berkeley-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bertini/package.py b/var/spack/repos/builtin/packages/bertini/package.py
index dc3e746eae..3b9f9efd34 100644
--- a/var/spack/repos/builtin/packages/bertini/package.py
+++ b/var/spack/repos/builtin/packages/bertini/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bib2xhtml/package.py b/var/spack/repos/builtin/packages/bib2xhtml/package.py
index 3c9bab772e..0a50a18004 100644
--- a/var/spack/repos/builtin/packages/bib2xhtml/package.py
+++ b/var/spack/repos/builtin/packages/bib2xhtml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
diff --git a/var/spack/repos/builtin/packages/bigreqsproto/package.py b/var/spack/repos/builtin/packages/bigreqsproto/package.py
index e271e12777..323ea99d6c 100644
--- a/var/spack/repos/builtin/packages/bigreqsproto/package.py
+++ b/var/spack/repos/builtin/packages/bigreqsproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Bigreqsproto(AutotoolsPackage):
 
     version('1.1.2', '9b83369ac7a5eb2bf54c8f34db043a0e')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py
index c3c521bad8..59620e1cb2 100644
--- a/var/spack/repos/builtin/packages/binutils/package.py
+++ b/var/spack/repos/builtin/packages/binutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,11 +10,14 @@ class Binutils(AutotoolsPackage):
     """GNU binutils, which contain the linker, assembler, objdump and others"""
 
     homepage = "http://www.gnu.org/software/binutils/"
-    url      = "https://ftp.gnu.org/gnu/binutils/binutils-2.28.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/binutils/binutils-2.28.tar.bz2"
 
+    version('2.31.1', 'ffcc382695bf947da6135e7436b8ed52d991cf270db897190f19d6f9838564d0')
+    version('2.29.1', '9af59a2ca3488823e453bb356fe0f113')
     version('2.28', '9e8340c96626b469a603c15c9d843727')
     version('2.27', '2869c9bf3e60ee97c74ac2a6bf4e9d68')
     version('2.26', '64146a0faa3b411ba774f47d41de239f')
+    version('2.25.1', sha256='b5b14added7d78a8d1ca70b5cb75fef57ce2197264f4f5835326b0df22ac9f22')
     version('2.25', 'd9f3303f802a5b6b0bb73a335ab89d66')
     version('2.24', 'e0f71a7b2ddab0f8612336ac81d9636b')
     version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
@@ -43,29 +27,30 @@ class Binutils(AutotoolsPackage):
             description="enable plugins, needed for gold linker")
     variant('gold', default=True, description="build the gold linker")
     variant('libiberty', default=False, description='Also install libiberty.')
+    variant('nls', default=True, description='Enable Native Language Support')
 
-    patch('cr16.patch')
+    patch('cr16.patch', when='@:2.29.1')
     patch('update_symbol-2.26.patch', when='@2.26')
 
     depends_on('zlib')
+    depends_on('gettext', when='+nls')
 
-    depends_on('m4', type='build')
-    depends_on('flex', type='build')
-    depends_on('bison', type='build')
-    depends_on('gettext')
+    # Prior to 2.30, gold did not distribute the generated files and
+    # thus needs bison, even for a one-time build.
+    depends_on('m4', type='build', when='@:2.29.99 +gold')
+    depends_on('bison', type='build', when='@:2.29.99 +gold')
 
     def configure_args(self):
         spec = self.spec
 
         configure_args = [
-            '--with-system-zlib',
             '--disable-dependency-tracking',
             '--disable-werror',
-            '--enable-interwork',
             '--enable-multilib',
             '--enable-shared',
             '--enable-64-bit-bfd',
             '--enable-targets=all',
+            '--with-system-zlib',
             '--with-sysroot=/',
         ]
 
@@ -78,4 +63,15 @@ class Binutils(AutotoolsPackage):
         if '+libiberty' in spec:
             configure_args.append('--enable-install-libiberty')
 
+        if '+nls' in spec:
+            configure_args.append('--enable-nls')
+        else:
+            configure_args.append('--disable-nls')
+
+        # To avoid namespace collisions with Darwin/BSD system tools,
+        # prefix executables with "g", e.g., gar, gnm; see Homebrew
+        # https://github.com/Homebrew/homebrew-core/blob/master/Formula/binutils.rb
+        if spec.satisfies('platform=darwin'):
+            configure_args.append('--program-prefix=g')
+
         return configure_args
diff --git a/var/spack/repos/builtin/packages/bioawk/package.py b/var/spack/repos/builtin/packages/bioawk/package.py
index 386aa16953..3a5318bc70 100644
--- a/var/spack/repos/builtin/packages/bioawk/package.py
+++ b/var/spack/repos/builtin/packages/bioawk/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
-from shutil import copymode
 
 
 class Bioawk(MakefilePackage):
@@ -45,7 +24,5 @@ class Bioawk(MakefilePackage):
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
-        copyfile("bioawk", join_path(prefix.bin, "bioawk"))
-        copymode("bioawk", join_path(prefix.bin, "bioawk"))
-        copyfile("maketab", join_path(prefix.bin, "maketab"))
-        copymode("maketab", join_path(prefix.bin, "maketab"))
+        install('bioawk',  prefix.bin)
+        install('maketab', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/biopieces/package.py b/var/spack/repos/builtin/packages/biopieces/package.py
new file mode 100644
index 0000000000..c237fdf564
--- /dev/null
+++ b/var/spack/repos/builtin/packages/biopieces/package.py
@@ -0,0 +1,70 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Biopieces(Package):
+    """The Biopieces are a collection of bioinformatics tools that can be
+       pieced together in a very easy and flexible manner to perform both
+       simple and complex tasks."""
+
+    homepage = "http://maasha.github.io/biopieces/"
+    git      = "https://github.com/maasha/biopieces.git"
+
+    version('2016-04-12', commit='982f80f7c55e2cae67737d80fe35a4e784762856',
+            submodules=True)
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-module-build', type=('build', 'run'))
+    depends_on('perl-bit-vector', type=('build', 'run'))
+    depends_on('perl-svg', type=('build', 'run'))
+    depends_on('perl-term-readkey', type=('build', 'run'))
+    depends_on('perl-time-hires', type=('build', 'run'))
+    depends_on('perl-dbi', type=('build', 'run'))
+    depends_on('perl-xml-parser', type=('build', 'run'))
+    depends_on('perl-carp-clan', type=('build', 'run'))
+    depends_on('perl-class-inspector', type=('build', 'run'))
+    depends_on('perl-html-parser', type=('build', 'run'))
+    depends_on('perl-lwp', type=('build', 'run'))
+    depends_on('perl-soap-lite', type=('build', 'run'))
+    depends_on('perl-uri', type=('build', 'run'))
+    depends_on('perl-inline', type=('build', 'run'))
+    depends_on('perl-inline-c', type=('build', 'run'))
+    depends_on('perl-parse-recdescent', type=('build', 'run'))
+    depends_on('perl-version', type=('build', 'run'))
+    depends_on('perl-dbfile', type=('build', 'run'))
+    depends_on('perl-dbd-mysql', type=('build', 'run'))
+
+    depends_on('ruby@1.9:')
+    depends_on('ruby-gnuplot')
+    depends_on('ruby-narray')
+    depends_on('ruby-rubyinline')
+    depends_on('ruby-terminal-table')
+
+    depends_on('python@2.6:', type=('build', 'run'))
+    depends_on('blast-plus')
+    depends_on('muscle')
+    depends_on('mummer')
+    depends_on('blat')
+    depends_on('vmatch')
+    depends_on('bowtie')
+    depends_on('bwa')
+    depends_on('usearch')
+    depends_on('velvet')
+    depends_on('idba')
+    depends_on('ray')
+    depends_on('scan-for-matches')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        # Note: user will need to set environment variables on their own,
+        # dependent on where they will want data to be located:
+        #    BP_DATA - Contains genomic data etc.
+        #    BP_TMP - Required temporary directory
+        #    BP_LOG - Required log directory
+        run_env.prepend_path('BP_DIR', prefix)
diff --git a/var/spack/repos/builtin/packages/bismark/package.py b/var/spack/repos/builtin/packages/bismark/package.py
new file mode 100644
index 0000000000..4326c63fc6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bismark/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bismark(Package):
+    """A tool to map bisulfite converted sequence reads and determine cytosine
+    methylation states"""
+
+    homepage = "https://www.bioinformatics.babraham.ac.uk/projects/bismark"
+    url      = "https://github.com/FelixKrueger/Bismark/archive/0.19.0.tar.gz"
+
+    version('0.19.0', 'f403654aded77bf0d1dac1203867ded1')
+    version('0.18.2', '42334b7e3ed53ba246f30f1f846b4af8')
+
+    depends_on('bowtie2', type='run')
+    depends_on('perl', type='run')
+    depends_on('samtools', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('bam2nuc', prefix.bin)
+        install('bismark', prefix.bin)
+        install('bismark_genome_preparation', prefix.bin)
+        install('bismark_methylation_extractor', prefix.bin)
+        install('bismark2bedGraph', prefix.bin)
+        install('bismark2report', prefix.bin)
+        install('bismark2summary', prefix.bin)
+        install('coverage2cytosine', prefix.bin)
+        install('deduplicate_bismark', prefix.bin)
+        install('filter_non_conversion', prefix.bin)
+        install('NOMe_filtering', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/bison/package.py b/var/spack/repos/builtin/packages/bison/package.py
index 1cc2aacfaf..bd2b66d53d 100644
--- a/var/spack/repos/builtin/packages/bison/package.py
+++ b/var/spack/repos/builtin/packages/bison/package.py
@@ -1,29 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack.operating_systems.mac_os import macOS_version
+from spack.operating_systems.mac_os import macos_version
 import sys
 
 
@@ -33,16 +14,20 @@ class Bison(AutotoolsPackage):
     generalized LR (GLR) parser employing LALR(1) parser tables."""
 
     homepage = "http://www.gnu.org/software/bison/"
-    url      = "http://ftp.gnu.org/gnu/bison/bison-3.0.4.tar.gz"
+    url      = "https://ftpmirror.gnu.org/bison/bison-3.0.4.tar.gz"
 
+    version('3.0.5', '41ad57813157b61bfa47e33067a9d6f0')
     version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8')
     version('2.7',   'ded660799e76fb1667d594de1f7a0da9')
 
+    depends_on('diffutils', type='build')
     depends_on('m4', type=('build', 'run'))
+    depends_on('perl', type='build')
+    depends_on('help2man', type='build')
 
     patch('pgi.patch', when='@3.0.4')
 
-    if sys.platform == 'darwin' and macOS_version() >= Version('10.13'):
+    if sys.platform == 'darwin' and macos_version() >= Version('10.13'):
         patch('secure_snprintf.patch', level=0, when='@3.0.4')
 
     build_directory = 'spack-build'
diff --git a/var/spack/repos/builtin/packages/bitmap/package.py b/var/spack/repos/builtin/packages/bitmap/package.py
index 2ea4613a53..cc0c49aade 100644
--- a/var/spack/repos/builtin/packages/bitmap/package.py
+++ b/var/spack/repos/builtin/packages/bitmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Bitmap(AutotoolsPackage):
 
     depends_on('xbitmaps', type='build')
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/blasr-libcpp/package.py b/var/spack/repos/builtin/packages/blasr-libcpp/package.py
new file mode 100644
index 0000000000..ceb7d642ff
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blasr-libcpp/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class BlasrLibcpp(Package):
+    """Blasr_libcpp is a library used by blasr
+    and other executables such as samtoh5,
+    loadPulses for analyzing PacBio sequences."""
+
+    homepage = "https://github.com/PacificBiosciences/blasr_libcpp"
+    url      = "https://github.com/PacificBiosciences/blasr_libcpp/archive/5.3.1.tar.gz"
+
+    version('5.3.1', 'ca770042cbca508d5ff12dff0d645045')
+
+    depends_on('pbbam')
+    depends_on('hdf5+cxx@1.8.12:1.8.99')
+    # maximum version is 1.8.20 currently. There doesn't appear to be a
+    # major version 1.9 and the 1.10.1 version doesn't build correctly.
+    # https://github.com/PacificBiosciences/blasr/issues/355
+
+    depends_on('python', type='build')
+
+    phases = ['configure', 'build', 'install']
+
+    def configure(self, spec, prefix):
+        configure_args = [
+            'PBBAM_INC={0}'.format(self.spec['pbbam'].prefix.include),
+            'PBBAM_LIB={0}'.format(self.spec['pbbam'].prefix.lib),
+            'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
+            'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib)
+        ]
+        python('configure.py', *configure_args)
+
+    def build(self, spec, prefix):
+        os.environ['CPLUS_INCLUDE_PATH'] = self.stage.source_path
+        make()
+
+    def install(self, spec, prefix):
+        install_tree('alignment', prefix.alignment)
+        install_tree('hdf', prefix.hdf)
+        install_tree('pbdata', prefix.pbdata)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.prepend_path('LD_LIBRARY_PATH',
+                               self.spec.prefix.hdf)
+        spack_env.prepend_path('LD_LIBRARY_PATH',
+                               self.spec.prefix.alignment)
+        spack_env.prepend_path('LD_LIBRARY_PATH',
+                               self.spec.prefix.pbdata)
diff --git a/var/spack/repos/builtin/packages/blasr/package.py b/var/spack/repos/builtin/packages/blasr/package.py
new file mode 100644
index 0000000000..b7bbd3790f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blasr/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Blasr(Package):
+    """The PacBio long read aligner."""
+
+    homepage = "https://github.com/PacificBiosciences/blasr/wiki"
+    url      = "https://github.com/PacificBiosciences/blasr/archive/5.3.1.tar.gz"
+
+    version('5.3.1', '53c93f499aa4bc10781c87bafc33df2a') 
+
+    depends_on('ncurses')
+    depends_on('hdf5+cxx@1.8.12:1.8.99')
+    depends_on('htslib')
+    depends_on('zlib')
+    depends_on('boost')
+    depends_on('pbbam')
+    depends_on('blasr-libcpp')
+    depends_on('python', type='build')
+
+    phases = ['configure', 'build', 'install']
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix.utils)
+        spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix)
+        spack_env.prepend_path('CPATH', self.spec[
+                               'blasr-libcpp'].prefix.pbdata)
+        spack_env.prepend_path('CPATH', self.spec[
+                               'blasr-libcpp'].prefix.alignment)
+        spack_env.prepend_path('CPATH', self.spec['blasr-libcpp'].prefix.hdf)
+
+        # hdf has +mpi by default, so handle that possibility
+        if ('+mpi' in self.spec['hdf5']):
+            spack_env.set('CC', self.spec['mpi'].mpicc)
+            spack_env.set('CXX', self.spec['mpi'].mpicxx)
+
+    def configure(self, spec, prefix):
+        configure_args = [
+            'LIBPBDATA_INC={0}'.format(
+                self.spec['blasr-libcpp'].prefix),
+            'LIBPBDATA_LIB={0}'.format(
+                self.spec['blasr-libcpp'].prefix.pbdata),
+            'LIBBLASR_LIB={0}'.format(
+                self.spec['blasr-libcpp'].prefix.alignment),
+            'LIBBLASR_INC={0}'.format(
+                self.spec['blasr-libcpp'].prefix),
+            'LIBPBIHDF_INC={0}'.format(self.spec['blasr-libcpp'].prefix),
+            'LIBPBIHDF_LIB={0}'.format(self.spec['blasr-libcpp'].prefix.hdf),
+            'HDF5_INC={0}'.format(self.spec['hdf5'].prefix.include),
+            'HDF5_LIB={0}'.format(self.spec['hdf5'].prefix.lib),
+            '--shared'
+        ]
+        python('configure.py', *configure_args)
+
+    def build(self, spec, prefix):
+        os.environ['CPLUS_INCLUDE_PATH'] = join_path(
+            self.stage.source_path, 'include')
+        make()
+
+    def install(self, spec, prefix):
+        mkdir(prefix.utils)
+        mkdir(prefix.bin)
+        install('blasr', prefix.bin.blasr)
+        install('utils/loadPulses', prefix.utils)
+        install('utils/pls2fasta', prefix.utils)
+        install('utils/samFilter', prefix.utils)
+        install('utils/samtoh5', prefix.utils)
+        install('utils/samtom4', prefix.utils)
+        install('utils/sawriter', prefix.utils)
+        install('utils/sdpMatcher', prefix.utils)
+        install('utils/toAfg', prefix.utils)
diff --git a/var/spack/repos/builtin/packages/blast-plus/package.py b/var/spack/repos/builtin/packages/blast-plus/package.py
index 073eab24d1..3cc075f578 100644
--- a/var/spack/repos/builtin/packages/blast-plus/package.py
+++ b/var/spack/repos/builtin/packages/blast-plus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # This is a based largely on the Homebrew science formula:
 # https://github.com/Homebrew/homebrew-science/blob/master/blast.rb
@@ -42,6 +23,7 @@ class BlastPlus(AutotoolsPackage):
     homepage = "http://blast.ncbi.nlm.nih.gov/"
     url      = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-src.tar.gz"
 
+    version('2.7.1', sha256='10a78d3007413a6d4c983d2acbf03ef84b622b82bd9a59c6bd9fbdde9d0298ca')
     version('2.6.0',  'c8ce8055b10c4d774d995f88c7cc6225')
     version('2.2.30', 'f8e9a5eb368173142fe6867208b73715')
 
@@ -107,6 +89,8 @@ class BlastPlus(AutotoolsPackage):
     depends_on('python', when='+python')
     depends_on('perl', when='+perl')
 
+    depends_on('lmdb', when='@2.7.1:')
+
     configure_directory = 'c++'
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/blat/package.py b/var/spack/repos/builtin/packages/blat/package.py
index 60a33bbdff..8e0abb249f 100644
--- a/var/spack/repos/builtin/packages/blat/package.py
+++ b/var/spack/repos/builtin/packages/blat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/blaze/package.py b/var/spack/repos/builtin/packages/blaze/package.py
index 2f175ff7d5..ffe65b85e2 100644
--- a/var/spack/repos/builtin/packages/blaze/package.py
+++ b/var/spack/repos/builtin/packages/blaze/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -35,8 +16,10 @@ class Blaze(Package):
     """
 
     homepage = "https://bitbucket.org/blaze-lib/blaze/overview"
-    url      = "https://bitbucket.org/blaze-lib/blaze/downloads/blaze-3.1.tar.gz"
+    url      = "https://bitbucket.org/blaze-lib/blaze/downloads/blaze-3.4.tar.gz"
 
+    version('3.4', sha256='fd474ab479e81d31edf27d4a529706b418f874caa7b046c67489128c20dda66f')
+    version('3.3', sha256='138cbb7b95775c10bf56a5ab3596a32205751299b19699984b6ed55b1bf989d0')
     version('3.2', '47bd4a4f1b6292f5a6f71ed9d5287480')
     version('3.1', '2938e015f0d274e8d62ee5c4c0c1e9f3')
     version('3.0', '0c4cefb0be7b5a27ed8a377941be1ab1')
diff --git a/var/spack/repos/builtin/packages/blis/package.py b/var/spack/repos/builtin/packages/blis/package.py
new file mode 100644
index 0000000000..771797d4b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/blis/package.py
@@ -0,0 +1,117 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+# Although this looks like an Autotools package, it's not one. Refer to:
+# https://github.com/flame/blis/issues/17
+# https://github.com/flame/blis/issues/195
+# https://github.com/flame/blis/issues/197
+
+
+class Blis(Package):
+    """BLIS is a portable software framework for instantiating high-performance
+    BLAS-like dense linear algebra libraries. The framework was designed to
+    isolate essential kernels of computation that, when optimized, immediately
+    enable optimized implementations of most of its commonly used and
+    computationally intensive operations. BLIS is written in ISO C99 and
+    available under a new/modified/3-clause BSD license. While BLIS exports a
+    new BLAS-like API, it also includes a BLAS compatibility layer which gives
+    application developers access to BLIS implementations via traditional BLAS
+    routine calls. An object-based API unique to BLIS is also available."""
+
+    homepage = "https://github.com/flame/blis"
+    url      = "https://github.com/flame/blis/archive/0.4.0.tar.gz"
+    git      = "https://github.com/flame/blis.git"
+
+    version('develop', branch='master')
+    version('0.4.0', sha256='9c7efd75365a833614c01b5adfba93210f869d92e7649e0b5d9edc93fc20ea76')
+    version('0.3.2', sha256='b87e42c73a06107d647a890cbf12855925777dc7124b0c7698b90c5effa7f58f')
+    version('0.3.1', sha256='957f28d47c5cf71ffc62ce8cc1277e17e44d305b1c2fa8506b0b55617a9f28e4')
+    version('0.3.0', sha256='d34d17df7bdc2be8771fe0b7f867109fd10437ac91e2a29000a4a23164c7f0da')
+    version('0.2.2', sha256='4a7ecb56034fb20e9d1d8b16e2ef587abbc3d30cb728e70629ca7e795a7998e8')
+
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
+    variant(
+        'threads', default='none',
+        description='Multithreading support',
+        values=('pthreads', 'openmp', 'none'),
+        multi=False
+    )
+
+    variant(
+        'blas', default=True,
+        description='BLAS compatibility',
+    )
+
+    variant(
+        'cblas', default=False,
+        description='CBLAS compatibility',
+    )
+
+    variant(
+        'shared', default=True,
+        description='Build shared library',
+    )
+
+    variant(
+        'static', default=True,
+        description='Build static library',
+    )
+
+    # TODO: add cpu variants. Currently using auto.
+    # If one knl, should the default be memkind ?
+
+    # BLIS has it's own API but can be made compatible with BLAS
+    # enabling CBLAS automatically enables BLAS.
+
+    provides('blas', when="+blas")
+    provides('blas', when="+cblas")
+
+    phases = ['configure', 'build', 'install']
+
+    def configure(self, spec, prefix):
+        config_args = []
+
+        config_args.append("--enable-threading=" +
+                           spec.variants['threads'].value)
+
+        if '+cblas' in spec:
+            config_args.append("--enable-cblas")
+        else:
+            config_args.append("--disable-cblas")
+
+        if '+blas' in spec:
+            config_args.append("--enable-blas")
+        else:
+            config_args.append("--disable-blas")
+
+        if '+shared' in spec:
+            config_args.append("--enable-shared")
+        else:
+            config_args.append("--disable-shared")
+
+        if '+static' in spec:
+            config_args.append("--enable-static")
+        else:
+            config_args.append("--disable-static")
+
+        # FIXME: add cpu isa variants.
+        config_args.append("auto")
+
+        configure("--prefix=" + prefix,
+                  *config_args)
+
+    def build(self, spec, prefix):
+        make()
+
+    @run_after('build')
+    @on_package_attributes(run_tests=True)
+    def check(self):
+        make('check')
+
+    def install(self, spec, prefix):
+        make('install')
diff --git a/var/spack/repos/builtin/packages/bliss/package.py b/var/spack/repos/builtin/packages/bliss/package.py
index 6604c2dc9a..42aef78a91 100644
--- a/var/spack/repos/builtin/packages/bliss/package.py
+++ b/var/spack/repos/builtin/packages/bliss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/blitz/package.py b/var/spack/repos/builtin/packages/blitz/package.py
index 2cb9d8f5ab..cda7309b3e 100644
--- a/var/spack/repos/builtin/packages/blitz/package.py
+++ b/var/spack/repos/builtin/packages/blitz/package.py
@@ -1,36 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Blitz(AutotoolsPackage):
     """N-dimensional arrays for C++"""
     homepage = "http://github.com/blitzpp/blitz"
-    url = "https://github.com/blitzpp/blitz/tarball/1.0.0"
+    url = "https://github.com/blitzpp/blitz/archive/1.0.1.tar.gz"
 
-    version('1.0.0', '9f040b9827fe22228a892603671a77af')
+    version('1.0.1', 'fe43e2cf6c9258bc8b369264dd008971')
+    version('1.0.0', '971c43e22318bbfe8da016e6ef596234')
 
     build_targets = ['lib']
 
diff --git a/var/spack/repos/builtin/packages/bmake/package.py b/var/spack/repos/builtin/packages/bmake/package.py
new file mode 100644
index 0000000000..463a6e7134
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bmake/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bmake(Package):
+    """Portable version of NetBSD make(1)."""
+
+    homepage = "http://www.crufty.net/help/sjg/bmake.htm"
+    url      = "http://www.crufty.net/ftp/pub/sjg/bmake-20180512.tar.gz"
+
+    version('20180512', '48ba5933833a7f224d76ce482eedfec0')
+    version('20171207', '5d7f2f85f16c4a6ba34ceea68957447f')
+
+    phases = ['configure', 'build', 'install']
+
+    def patch(self):
+        # Do not pre-roff cat pages
+        filter_file('MANTARGET?', 'MANTARGET', 'mk/man.mk', string=True)
+
+    def configure(self, spec, prefix):
+        sh = which('sh')
+        sh('boot-strap', 'op=configure')
+
+    def build(self, spec, prefix):
+        sh = which('sh')
+        sh('boot-strap', 'op=build')
+
+    def install(self, spec, prefix):
+        sh = which('sh')
+        sh('boot-strap', '--prefix={0}'.format(prefix), 'op=install')
diff --git a/var/spack/repos/builtin/packages/bml/package.py b/var/spack/repos/builtin/packages/bml/package.py
index ee4b805d1b..ca00cf4a3d 100644
--- a/var/spack/repos/builtin/packages/bml/package.py
+++ b/var/spack/repos/builtin/packages/bml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,13 +13,16 @@ class Bml(CMakePackage):
 
     homepage = "http://lanl.github.io/bml/"
     url      = "https://github.com/lanl/bml/tarball/v1.2.2"
+    git      = "https://github.com/lanl/bml.git"
 
+    version('develop', branch='master')
+    version('1.3.0', '2bf8546b27a89666dab3e8f4873cd117')
+    version('1.2.3', '8133137fb56a27fade44d1588449c2ac')
     version('1.2.2', 'c86959cb0188e9d0a9a2cbad03b2782d')
     version('1.1.0', '271adecee08aee678be9eeceee06b6fb')
-    version('develop', git='https://github.com/lanl/bml', branch='master')
 
     variant('shared', default=True, description='Build shared libs')
-    variant('mpi', default=False, description='Build with MPI Support')
+    variant('mpi', default=True, description='Build with MPI Support')
 
     conflicts('+mpi', when='@:1.2.2')
 
diff --git a/var/spack/repos/builtin/packages/bohrium/cxxadd.cpp b/var/spack/repos/builtin/packages/bohrium/cxxadd.cpp
new file mode 100644
index 0000000000..94c9287807
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bohrium/cxxadd.cpp
@@ -0,0 +1,24 @@
+#include <bhxx/bhxx.hpp>
+
+int main() {
+    const size_t dim = 3;
+    bhxx::BhArray<double> a({dim});
+    bhxx::BhArray<double> b({dim});
+    bhxx::BhArray<double> c({dim});
+
+    bhxx::identity(a, 1);
+    bhxx::identity(b, 2);
+    bhxx::add(c, a, b);
+
+    bhxx::Runtime::instance().sync(c.base);
+    bhxx::Runtime::instance().flush();
+
+    for (auto it = c.data(); it < c.data() + dim; ++it) {
+        if (*it != 3) {
+            std::cout << "Failure, values not as expected." << std::endl;
+            return 1;
+        }
+    }
+    std::cout << "Success!" << std::endl;
+    return 0;
+}
diff --git a/var/spack/repos/builtin/packages/bohrium/package.py b/var/spack/repos/builtin/packages/bohrium/package.py
new file mode 100644
index 0000000000..9df2ace777
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bohrium/package.py
@@ -0,0 +1,272 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from spack.package_test import compare_output
+from spack.util.executable import Executable
+import llnl.util.tty as tty
+import os
+
+
+class Bohrium(CMakePackage, CudaPackage):
+    """Library for automatic acceleration of array operations"""
+
+    homepage = "http://bh107.org"
+    url      = "https://github.com/bh107/bohrium/archive/v0.9.0.tar.gz"
+    git      = "https://github.com/bh107/bohrium.git"
+
+    maintainers = ['mfherbst']
+
+    #
+    # Versions
+    #
+    version("develop", branch="master")
+    version('0.9.1', sha256='a8675db35ea4587ef12d5885a1aa19b59fd9c3f1366e239059de8b0f3cf51e04')
+    version('0.9.0', sha256='6f6379f1555de5a6a19138beac891a470df7df1fc9594e2b9404cf01b6e17d93')
+
+    #
+    # Variants
+    #
+    variant("cuda", default=True,
+            description="Build with CUDA code generator")
+    variant('opencl', default=True,
+            description="Build with OpenCL code generator")
+    variant('openmp', default=True,
+            description="Build with OpenMP code generator")
+
+    variant('node', default=True,
+            description="Build the node vector engine manager")
+    variant('proxy', default=False,
+            description="Build the proxy vector engine manager")
+    variant('python', default=True,
+            description="Build the numpy-like bridge "
+            "to enable use from python")
+    variant('cbridge', default=True,
+            description="Build the bridge interface towards plain C")
+
+    variant('blas', default=True,
+            description="Build with BLAS extension methods")
+    variant('lapack', default=True,
+            description="Build with LAPACK extension methods")
+    variant('opencv', default=True,
+            description="Build with OpenCV extension methods")
+
+    #
+    # Conflicts and extensions
+    #
+    conflicts('%intel')
+    conflicts('%clang@:3.5')
+    conflicts('%gcc@:4.7')
+    extends('python', when="+python")
+
+    # Bohrium needs at least one vector engine and
+    # at least one vector engine manager
+    conflicts('~node~proxy')
+    conflicts('~openmp~opencl~cuda')
+
+    #
+    # Dependencies
+    #
+    depends_on('cmake@2.8:', type="build")
+    depends_on('boost+system+serialization+filesystem+regex')
+
+    # cuda dependencies managed by CudaPackage class
+    depends_on('opencl', when="+opencl")
+
+    # NOTE The lapacke interface and hence netlib-lapack
+    #      is the strictly required lapack provider
+    #      for bohrium right now.
+    depends_on('netlib-lapack+lapacke', when="+lapack")
+    depends_on('blas', when="+blas")
+
+    # Make sure an appropriate opencv is used
+    depends_on('opencv+imgproc', when="+opencv")
+    depends_on('opencv+imgproc+cuda', when="+opencv+cuda")
+    depends_on('opencv+imgproc+openmp', when="+opencv+openmp")
+    depends_on('opencv+imgproc+openmp+cuda', when="+opencv+openmp+cuda")
+
+    depends_on('python', type="build", when="~python")
+    depends_on('python', type=("build", "link", "test"), when="+python")
+    depends_on('py-numpy', type=("build", "test", "run"), when="+python")
+    depends_on('swig', type="build", when="+python")
+    depends_on('py-cython', type="build", when="+python")
+
+    depends_on('zlib', when="+proxy")
+
+    @property
+    def config_file(self):
+        """Return the path of the Bohrium system-wide configuration file"""
+        return join_path(self.prefix.etc.bohrium, "config.ini")
+
+    #
+    # Settings and cmake cache
+    #
+    def cmake_args(self):
+        spec = self.spec
+
+        # Sanity check
+        cuda_arch = spec.variants['cuda_arch'].value
+        if "+cuda" in spec and len(cuda_arch) >= 1 and cuda_arch[0]:
+            # TODO Add cuda_arch support to Bohrium once the basic setup
+            #      via Spack works.
+            raise InstallError(
+                "Bohrium does not support setting the CUDA architecture yet."
+            )
+
+        args = [
+            # Choose a particular python version
+            "-DPYTHON_EXECUTABLE:FILEPATH=" + spec['python'].command.path,
+            #
+            # Hard-disable Jupyter, since this would override a config
+            # file in the user's home directory in some cases during
+            # the configuration stage.
+            "-DJUPYTER_FOUND=FALSE",
+            "-DJUPYTER_EXECUTABLE=FALSE",
+            #
+            # Force the configuration file to appear at a sensible place
+            "-DFORCE_CONFIG_PATH=" + os.path.dirname(self.config_file),
+            #
+            # Vector engine managers
+            "-DVEM_NODE=" + str("+node" in spec),
+            "-DVEM_PROXY=" + str("+proxy" in spec),
+            #
+            # Bridges and interfaces
+            "-DBRIDGE_BHXX=ON",
+            "-DBRIDGE_C=" + str("+cbridge" in spec or "+python" in spec),
+            "-DBRIDGE_NPBACKEND=" + str("+python" in spec),
+            "-DNO_PYTHON3=ON",  # Only build python version we provide
+        ]
+
+        #
+        # Vector engines
+        #
+        args += [
+            "-DVE_OPENCL=" + str("+opencl" in spec),
+            "-DVE_CUDA=" + str("+cuda" in spec),
+        ]
+
+        if "+openmp" in spec:
+            args += [
+                "-DVE_OPENMP=ON",
+                "-DOPENMP_FOUND=True",
+                "-DVE_OPENMP_COMPILER_CMD=" + self.compiler.cc,
+            ]
+        else:
+            args += ["-DVE_OPENMP=OFF", "-DOPENMP_FOUND=False"]
+
+        #
+        # Extension methods
+        #
+        if "+blas" in spec:
+            args += [
+                "-DEXT_BLAS=ON",
+                "-DCBLAS_FOUND=True",
+                "-DCBLAS_LIBRARIES=" + spec["blas"].libs.joined(";"),
+                "-DCBLAS_INCLUDES=" + spec["blas"].prefix.include,
+            ]
+        else:
+            args += ["-DEXT_BLAS=OFF", "-DDCBLAS_FOUND=False"]
+
+        if "+lapack" in spec:
+            args += [
+                "-DEXT_LAPACK=ON",
+                "-DLAPACKE_FOUND=True",
+                "-DLAPACKE_LIBRARIES=" + spec["lapack"].libs.joined(";"),
+                "-DLAPACKE_INCLUDE_DIR=" + spec["lapack"].prefix.include,
+            ]
+        else:
+            args += ["-DEXT_LAPACK=OFF", "-DLAPACKE_FOUND=False"]
+
+        if "+opencv" in spec:
+            args += [
+                "-DEXT_OPENCV=ON",
+                "-DOpenCV_FOUND=True",
+                "-DOpenCV_INCLUDE_DIRS=" + spec["opencv"].prefix.include,
+                "-DOpenCV_LIBS=" + spec["opencv"].libs.joined(";"),
+            ]
+        else:
+            args += ["-DEXT_OPENCV=OFF", "-DOpenCV_FOUND=False"]
+
+        # TODO Other extension methods are not ready yet,
+        #      because of missing packages in Spack
+        args += [
+            "-DEXT_CLBLAS=OFF",      # clBLAS missing
+            # Bohrium visualizer extension method
+            "-DEXT_VISUALIZER=OFF",  # freeglut missing
+        ]
+        return args
+
+    #
+    # Environment setup
+    #
+    def setup_environment(self, spack_env, run_env):
+        # Bohrium needs an extra include dir apart from
+        # the self.prefix.include dir
+        run_env.prepend_path("CPATH", self.prefix.include.bohrium)
+        run_env.set("BH_CONFIG", self.config_file)
+
+    #
+    # Quick tests
+    #
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_install(self):
+        spec = self.spec
+        test_env = {}
+
+        # Make sure the correct config is found
+        test_env["BH_CONFIG"] = self.config_file
+
+        # Remove the lib/spackenv directory from the PATH variable when
+        # executing the tests, becauses it messes with the JIT compilation
+        # inside Bohrium
+        paths = os.environ['PATH'].split(':')
+        paths = [p for p in paths if "spack/env" not in p]
+        test_env["PATH"] = ":".join(paths)
+
+        # Add the PYTHONPATH to bohrium to the PYTHONPATH environment
+        pythonpaths = [p for p in os.environ["PYTHONPATH"].split(":")]
+        pythonpaths.append(join_path(self.prefix,
+                                     spec['python'].package.site_packages_dir))
+        test_env["PYTHONPATH"] = ":".join(pythonpaths)
+
+        # Collect the stacks which should be available:
+        stacks = ["default"]
+        if "+openmp" in spec:
+            stacks.append("openmp")
+        if "+cuda" in spec:
+            stacks.append("cuda")
+        if "+opencl" in spec:
+            stacks.append("opencl")
+
+        # C++ compiler and compiler flags
+        cxx = Executable(self.compiler.cxx)
+        cxx_flags = ["-I", self.prefix.include,
+                     "-I", self.prefix.include.bohrium,
+                     "-L", self.prefix.lib, "-lbh", "-lbhxx"]
+
+        # Compile C++ test program
+        file_cxxadd = join_path(os.path.dirname(self.module.__file__),
+                                "cxxadd.cpp")
+        cxx("-o", "test_cxxadd", file_cxxadd, *cxx_flags)
+        test_cxxadd = Executable("./test_cxxadd")
+
+        # Build python test commandline
+        file_pyadd = join_path(os.path.dirname(self.module.__file__),
+                               "pyadd.py")
+        test_pyadd = Executable(spec['python'].command.path + " " + file_pyadd)
+
+        # Run tests for each available stack
+        for bh_stack in stacks:
+            tty.info("Testing with bohrium stack '" + bh_stack + "'")
+            test_env["BH_STACK"] = bh_stack
+
+            cpp_output = test_cxxadd(output=str, env=test_env)
+            compare_output(cpp_output, "Success!\n")
+
+            # Python test (if +python)
+            if "+python" in spec:
+                py_output = test_pyadd(output=str, env=test_env)
+                compare_output(py_output, "Success!\n")
diff --git a/var/spack/repos/builtin/packages/bohrium/pyadd.py b/var/spack/repos/builtin/packages/bohrium/pyadd.py
new file mode 100644
index 0000000000..fc9f6968df
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bohrium/pyadd.py
@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+import bohrium as bh
+a = bh.array([1, 2, 3])
+b = bh.array([3, 4, 5])
+c = a + b
+
+if bh.all(c == bh.array([4, 6, 8])):
+    print("Success!")
+else:
+    print("Failure, values not as expected.")
diff --git a/var/spack/repos/builtin/packages/bolt/package.py b/var/spack/repos/builtin/packages/bolt/package.py
new file mode 100644
index 0000000000..5d24e1fa15
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bolt/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bolt(CMakePackage):
+    """BOLT targets a high-performing OpenMP implementation,
+    especially specialized for fine-grain parallelism. Unlike other
+    OpenMP implementations, BOLT utilizes a lightweight threading
+    model for its underlying threading mechanism. It currently adopts
+    Argobots, a new holistic, low-level threading and tasking runtime,
+    in order to overcome shortcomings of conventional OS-level
+    threads. The current BOLT implementation is based on the OpenMP
+    runtime in LLVM, and thus it can be used with LLVM/Clang, Intel
+    OpenMP compiler, and GCC."""
+
+    homepage = "http://www.bolt-omp.org/"
+    url      = "https://github.com/pmodels/bolt/releases/download/v1.0b1/bolt-1.0b1.tar.gz"
+
+    version("1.0b1", "df76beb3a7f13ae2dcaf9ab099eea87b")
+
+    def cmake_args(self):
+        options = [
+            '-DLIBOMP_USE_ITT_NOTIFY=off',
+            '-DLIBOMP_USE_ARGOBOTS=on'
+        ]
+
+        return options
diff --git a/var/spack/repos/builtin/packages/bookleaf-cpp/package.py b/var/spack/repos/builtin/packages/bookleaf-cpp/package.py
new file mode 100644
index 0000000000..394a79fab7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bookleaf-cpp/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class BookleafCpp(CMakePackage):
+    """BookLeaf is a 2D unstructured hydrodynamics mini-app."""
+
+    homepage = "https://github.com/UK-MAC/BookLeaf_Cpp"
+    url      = "https://github.com/UK-MAC/BookLeaf_Cpp/archive/v2.0.tar.gz"
+    git      = "https://github.com/UK-MAC/BookLeaf_Cpp.git"
+
+    version('develop', branch='develop')
+
+    version('2.0.2', sha256='787ade5045415d71d9bad55fe9f93598f3a0548d13e2ff80e752cc99f62fe6d3')
+    version('2.0.1', '34a5a9e7b2b5ffc98562656a4406ba5b')
+    version('2.0',   '69819ebcbae5eaa63d1a4de2c77cac85')
+
+    variant('typhon', default=True, description='Use Typhon')
+    variant('parmetis', default=False, description='Use ParMETIS')
+    variant('silo', default=False, description='Use Silo')
+    variant('caliper', default=False, description='Use Caliper')
+
+    depends_on('caliper', when='+caliper')
+    depends_on('parmetis', when='+parmetis')
+    depends_on('silo', when='+silo')
+    depends_on('typhon', when='+typhon')
+    depends_on('mpi', when='+typhon')
+    depends_on('yaml-cpp@0.6.0:')
+
+    def cmake_args(self):
+        spec = self.spec
+        cmake_args = []
+
+        if '+typhon' in spec:
+            cmake_args.append('-DENABLE_TYPHON=ON')
+
+        if '+parmetis' in spec:
+            cmake_args.append('-DENABLE_PARMETIS=ON')
+
+        if '+silo' in spec:
+            cmake_args.append('-DENABLE_SILO=ON')
+
+        if '+caliper' in spec:
+            cmake_args.append('-DENABLE_CALIPER=ON')
+
+        return cmake_args
diff --git a/var/spack/repos/builtin/packages/boost/boost_1.67.0_pgi.patch b/var/spack/repos/builtin/packages/boost/boost_1.67.0_pgi.patch
new file mode 100644
index 0000000000..b2c7acaf6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/boost/boost_1.67.0_pgi.patch
@@ -0,0 +1,13 @@
+--- a/libs/filesystem/src/operations.cpp
++++ b/libs/filesystem/src/operations.cpp
+@@ -2056,10 +2056,6 @@
+     return ok;
+   }
+ 
+-#if defined(__PGI) && defined(__USE_FILE_OFFSET64)
+-#define dirent dirent64
+-#endif
+-
+   error_code dir_itr_first(void *& handle, void *& buffer,
+     const char* dir, string& target,
+     fs::file_status &, fs::file_status &)
diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py
index 6134456188..5b51187fea 100644
--- a/var/spack/repos/builtin/packages/boost/package.py
+++ b/var/spack/repos/builtin/packages/boost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 import os
@@ -38,18 +19,16 @@ class Boost(Package):
     """
     homepage = "http://www.boost.org"
     url      = "http://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.bz2"
+    git      = "https://github.com/boostorg/boost.git"
     list_url = "http://sourceforge.net/projects/boost/files/boost/"
     list_depth = 1
 
-    version('develop',
-            git='https://github.com/boostorg/boost.git',
-            branch='develop',
-            submodules=True)
-
-    version('1.65.1', '41d7542ce40e171f3f7982aff008ff0d',
-            url='https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2')
-    version('1.65.0', '5512d3809801b0a1b9dd58447b70915d',
-            url='https://dl.bintray.com/boostorg/release/1.65.0/source/boost_1_65_0.tar.bz2')
+    version('develop', branch='develop', submodules=True)
+    version('1.68.0', '18863a7cae4d58ae85eb63d400f774f60a383411')
+    version('1.67.0', '694ae3f4f899d1a80eb7a3b31b33be73c423c1ae')
+    version('1.66.0', 'b6b284acde2ad7ed49b44e856955d7b1ea4e9459')
+    version('1.65.1', '41d7542ce40e171f3f7982aff008ff0d')
+    version('1.65.0', '5512d3809801b0a1b9dd58447b70915d')
     # NOTE: 1.64.0 seems fine for *most* applications, but if you need
     #       +python and +mpi, there seem to be errors with out-of-date
     #       API calls from mpi/python.
@@ -91,6 +70,7 @@ class Boost(Package):
     default_install_libs = set(['atomic',
                                 'chrono',
                                 'date_time',
+                                'exception',
                                 'filesystem',
                                 'graph',
                                 'iostreams',
@@ -119,6 +99,11 @@ class Boost(Package):
         variant(lib, default=(lib not in default_noinstall_libs),
                 description="Compile with {0} library".format(lib))
 
+    variant('cxxstd',
+            default='default',
+            values=('default', '98', '11', '14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
     variant('debug', default=False,
             description='Switch to the debug version of Boost')
     variant('shared', default=True,
@@ -129,22 +114,24 @@ class Boost(Package):
             description="Build single-threaded versions of libraries")
     variant('icu', default=False,
             description="Build with Unicode and ICU suport")
-    variant('graph', default=False,
-            description="Build the Boost Graph library")
     variant('taggedlayout', default=False,
             description="Augment library names with build options")
     variant('versionedlayout', default=False,
             description="Augment library layout with versioned subdirs")
     variant('clanglibcpp', default=False,
             description='Compile with clang libc++ instead of libstdc++')
+    variant('numpy', default=False,
+            description='Build the Boost NumPy library (requires +python)')
 
     depends_on('icu4c', when='+icu')
     depends_on('python', when='+python')
     depends_on('mpi', when='+mpi')
     depends_on('bzip2', when='+iostreams')
     depends_on('zlib', when='+iostreams')
+    depends_on('py-numpy', when='+numpy', type=('build', 'run'))
 
     conflicts('+taggedlayout', when='+versionedlayout')
+    conflicts('+numpy', when='~python')
 
     # Patch fix from https://svn.boost.org/trac/boost/ticket/11856
     patch('boost_11856.patch', when='@1.60.0%gcc@4.4.7')
@@ -158,14 +145,19 @@ class Boost(Package):
     patch('xl_1_62_0_le.patch', when='@1.62.0%xl')
 
     # Patch fix from https://svn.boost.org/trac/boost/ticket/10125
-    patch('call_once_variadic.patch', when='@1.55.0:1.55.9999%gcc@5.0:5.9')
+    patch('call_once_variadic.patch', when='@1.54.0:1.55.9999%gcc@5.0:5.9')
 
     # Patch fix for PGI compiler
+    patch('boost_1.67.0_pgi.patch', when='@1.67.0%pgi')
     patch('boost_1.63.0_pgi.patch', when='@1.63.0%pgi')
     patch('boost_1.63.0_pgi_17.4_workaround.patch', when='@1.63.0%pgi@17.4')
 
     def url_for_version(self, version):
-        url = "http://downloads.sourceforge.net/project/boost/boost/{0}/boost_{1}.tar.bz2"
+        if version >= Version('1.63.0'):
+            url = "https://dl.bintray.com/boostorg/release/{0}/source/boost_{1}.tar.bz2"
+        else:
+            url = "http://downloads.sourceforge.net/project/boost/boost/{0}/boost_{1}.tar.bz2"
+
         return url.format(version.dotted, version.underscored)
 
     def determine_toolset(self, spec):
@@ -189,6 +181,10 @@ class Boost(Package):
         return 'gcc'
 
     def bjam_python_line(self, spec):
+        # avoid "ambiguous key" error
+        if spec.satisfies('@:1.58'):
+            return ''
+
         return 'using python : {0} : {1} : {2} : {3} ;\n'.format(
             spec['python'].version.up_to(2),
             spec['python'].command.path,
@@ -196,10 +192,10 @@ class Boost(Package):
             spec['python'].libs[0]
         )
 
-    def determine_bootstrap_options(self, spec, withLibs, options):
-        boostToolsetId = self.determine_toolset(spec)
-        options.append('--with-toolset=%s' % boostToolsetId)
-        options.append("--with-libraries=%s" % ','.join(withLibs))
+    def determine_bootstrap_options(self, spec, with_libs, options):
+        boost_toolset_id = self.determine_toolset(spec)
+        options.append('--with-toolset=%s' % boost_toolset_id)
+        options.append("--with-libraries=%s" % ','.join(with_libs))
 
         if '+python' in spec:
             options.append('--with-python=%s' % spec['python'].command.path)
@@ -213,7 +209,7 @@ class Boost(Package):
                 # error: duplicate initialization of intel-linux with the following parameters:  # noqa
                 # error: version = <unspecified>
                 # error: previous initialization at ./user-config.jam:1
-                f.write("using {0} : : {1} ;\n".format(boostToolsetId,
+                f.write("using {0} : : {1} ;\n".format(boost_toolset_id,
                                                        spack_cxx))
 
             if '+mpi' in spec:
@@ -235,6 +231,26 @@ class Boost(Package):
             if '+python' in spec:
                 f.write(self.bjam_python_line(spec))
 
+    def cxxstd_to_flag(self, std):
+        flag = ''
+        if self.spec.variants['cxxstd'].value == '98':
+            flag = self.compiler.cxx98_flag
+        elif self.spec.variants['cxxstd'].value == '11':
+            flag = self.compiler.cxx11_flag
+        elif self.spec.variants['cxxstd'].value == '14':
+            flag = self.compiler.cxx14_flag
+        elif self.spec.variants['cxxstd'].value == '17':
+            flag = self.compiler.cxx17_flag
+        elif self.spec.variants['cxxstd'].value == 'default':
+            # Let the compiler do what it usually does.
+            pass
+        else:
+            # The user has selected a (new?) legal value that we've
+            # forgotten to deal with here.
+            tty.die("INTERNAL ERROR: cannot accommodate unexpected variant ",
+                    "cxxstd={0}".format(spec.variants['cxxstd'].value))
+        return flag
+
     def determine_b2_options(self, spec, options):
         if '+debug' in spec:
             options.append('variant=debug')
@@ -251,16 +267,16 @@ class Boost(Package):
                 '-s', 'ZLIB_INCLUDE=%s' % spec['zlib'].prefix.include,
                 '-s', 'ZLIB_LIBPATH=%s' % spec['zlib'].prefix.lib])
 
-        linkTypes = ['static']
+        link_types = ['static']
         if '+shared' in spec:
-            linkTypes.append('shared')
+            link_types.append('shared')
 
-        threadingOpts = []
+        threading_opts = []
         if '+multithreaded' in spec:
-            threadingOpts.append('multi')
+            threading_opts.append('multi')
         if '+singlethreaded' in spec:
-            threadingOpts.append('single')
-        if not threadingOpts:
+            threading_opts.append('single')
+        if not threading_opts:
             raise RuntimeError("At least one of {singlethreaded, " +
                                "multithreaded} must be enabled")
 
@@ -269,13 +285,13 @@ class Boost(Package):
         elif '+versionedlayout' in spec:
             layout = 'versioned'
         else:
-            if len(threadingOpts) > 1:
+            if len(threading_opts) > 1:
                 raise RuntimeError("Cannot build both single and " +
                                    "multi-threaded targets with system layout")
             layout = 'system'
 
         options.extend([
-            'link=%s' % ','.join(linkTypes),
+            'link=%s' % ','.join(link_types),
             '--layout=%s' % layout
         ])
 
@@ -284,6 +300,19 @@ class Boost(Package):
                 'toolset=%s' % self.determine_toolset(spec)
             ])
 
+        # Other C++ flags.
+        cxxflags = []
+
+        # Deal with C++ standard.
+        if spec.satisfies('@1.66:'):
+            if spec.variants['cxxstd'].value != 'default':
+                options.append('cxxstd={0}'.format(
+                    spec.variants['cxxstd'].value))
+        else:  # Add to cxxflags for older Boost.
+            flag = self.cxxstd_to_flag(spec.variants['cxxstd'].value)
+            if flag:
+                cxxflags.append(flag)
+
         # clang is not officially supported for pre-compiled headers
         # and at least in clang 3.9 still fails to build
         #   http://www.boost.org/build/doc/html/bbv2/reference/precompiled_headers.html
@@ -291,11 +320,14 @@ class Boost(Package):
         if spec.satisfies('%clang'):
             options.extend(['pch=off'])
             if '+clanglibcpp' in spec:
+                cxxflags.append('-stdlib=libc++')
                 options.extend(['toolset=clang',
-                                'cxxflags="-stdlib=libc++"',
                                 'linkflags="-stdlib=libc++"'])
 
-        return threadingOpts
+        if cxxflags:
+            options.append('cxxflags="{0}"'.format(' '.join(cxxflags)))
+
+        return threading_opts
 
     def add_buildopt_symlinks(self, prefix):
         with working_dir(prefix.lib):
@@ -314,11 +346,11 @@ class Boost(Package):
             force_symlink('/usr/bin/libtool', join_path(newdir, 'libtool'))
             env['PATH'] = newdir + ':' + env['PATH']
 
-        withLibs = list()
+        with_libs = list()
         for lib in Boost.all_libs:
             if "+{0}".format(lib) in spec:
-                withLibs.append(lib)
-        if not withLibs:
+                with_libs.append(lib)
+        if not with_libs:
             # if no libraries are specified for compilation, then you dont have
             # to configure/build anything, just copy over to the prefix
             # directory.
@@ -330,25 +362,27 @@ class Boost(Package):
 
         # Remove libraries that the release version does not support
         if not spec.satisfies('@1.54.0:'):
-            withLibs.remove('log')
+            with_libs.remove('log')
         if not spec.satisfies('@1.53.0:'):
-            withLibs.remove('atomic')
+            with_libs.remove('atomic')
         if not spec.satisfies('@1.48.0:'):
-            withLibs.remove('locale')
+            with_libs.remove('locale')
         if not spec.satisfies('@1.47.0:'):
-            withLibs.remove('chrono')
+            with_libs.remove('chrono')
         if not spec.satisfies('@1.43.0:'):
-            withLibs.remove('random')
+            with_libs.remove('random')
+        if not spec.satisfies('@1.39.0:'):
+            with_libs.remove('exception')
         if '+graph' in spec and '+mpi' in spec:
-            withLibs.append('graph_parallel')
+            with_libs.append('graph_parallel')
 
         # to make Boost find the user-config.jam
-        env['BOOST_BUILD_PATH'] = './'
+        env['BOOST_BUILD_PATH'] = self.stage.source_path
 
         bootstrap = Executable('./bootstrap.sh')
 
         bootstrap_options = ['--prefix=%s' % prefix]
-        self.determine_bootstrap_options(spec, withLibs, bootstrap_options)
+        self.determine_bootstrap_options(spec, with_libs, bootstrap_options)
 
         bootstrap(*bootstrap_options)
 
@@ -360,15 +394,20 @@ class Boost(Package):
         # in 1.59 max jobs became dynamic
         if jobs > 64 and spec.satisfies('@:1.58'):
             jobs = 64
-        b2_options = ['-j', '%s' % jobs]
 
-        threadingOpts = self.determine_b2_options(spec, b2_options)
+        b2_options = [
+            '-j', '%s' % jobs,
+            '--user-config=%s' % os.path.join(
+                self.stage.source_path, 'user-config.jam')
+        ]
+
+        threading_opts = self.determine_b2_options(spec, b2_options)
 
         b2('--clean')
 
         # In theory it could be done on one call but it fails on
         # Boost.MPI if the threading options are not separated.
-        for threadingOpt in threadingOpts:
+        for threadingOpt in threading_opts:
             b2('install', 'threading=%s' % threadingOpt, *b2_options)
 
         if '+multithreaded' in spec and '~taggedlayout' in spec:
diff --git a/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py b/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py
index 7ddc65b439..d38609235c 100644
--- a/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py
+++ b/var/spack/repos/builtin/packages/boostmplcartesianproduct/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/bowtie/package.py b/var/spack/repos/builtin/packages/bowtie/package.py
index 8958352bd1..50f4c3e1cd 100644
--- a/var/spack/repos/builtin/packages/bowtie/package.py
+++ b/var/spack/repos/builtin/packages/bowtie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py
index 677020f60f..7b016710ed 100644
--- a/var/spack/repos/builtin/packages/bowtie2/package.py
+++ b/var/spack/repos/builtin/packages/bowtie2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -33,6 +14,7 @@ class Bowtie2(Package):
     homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
     url      = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
 
+    version('2.3.4.1', '8371bbb6eb02ae99c5cf633054265cb9')
     version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478')
     version('2.3.0', '3ab33f30f00f3c30fec1355b4e569ea2')
     version('2.2.5', '51fa97a862d248d7ee660efc1147c75f')
@@ -48,7 +30,7 @@ class Bowtie2(Package):
     patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)
 
     # seems to have trouble with 6's -std=gnu++14
-    conflicts('%gcc@6:')
+    conflicts('%gcc@6:', when='@:2.3.1')
 
     @run_before('install')
     def filter_sbang(self):
diff --git a/var/spack/repos/builtin/packages/boxlib/package.py b/var/spack/repos/builtin/packages/boxlib/package.py
index 833a027c29..c5f88f4896 100644
--- a/var/spack/repos/builtin/packages/boxlib/package.py
+++ b/var/spack/repos/builtin/packages/boxlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -49,7 +30,7 @@ class Boxlib(CMakePackage):
 
         options.extend([
             '-DBL_SPACEDIM=%d' % int(spec.variants['dims'].value),
-            '-DENABLE_POSITION_INDEPENDENT_CODE=ON',
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON',
             '-DENABLE_FBASELIB=ON',
             '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
             '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
diff --git a/var/spack/repos/builtin/packages/bpp-core/package.py b/var/spack/repos/builtin/packages/bpp-core/package.py
index 96a775cb60..d52e51519d 100644
--- a/var/spack/repos/builtin/packages/bpp-core/package.py
+++ b/var/spack/repos/builtin/packages/bpp-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bpp-phyl/package.py b/var/spack/repos/builtin/packages/bpp-phyl/package.py
index 3453f85a9d..9564468e3d 100644
--- a/var/spack/repos/builtin/packages/bpp-phyl/package.py
+++ b/var/spack/repos/builtin/packages/bpp-phyl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bpp-seq/package.py b/var/spack/repos/builtin/packages/bpp-seq/package.py
index bd3219523f..bd16f0828d 100644
--- a/var/spack/repos/builtin/packages/bpp-seq/package.py
+++ b/var/spack/repos/builtin/packages/bpp-seq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bpp-suite/package.py b/var/spack/repos/builtin/packages/bpp-suite/package.py
index 13fc341cfa..acf0fadf2f 100644
--- a/var/spack/repos/builtin/packages/bpp-suite/package.py
+++ b/var/spack/repos/builtin/packages/bpp-suite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bracken/package.py b/var/spack/repos/builtin/packages/bracken/package.py
new file mode 100644
index 0000000000..ed48722a59
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bracken/package.py
@@ -0,0 +1,56 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bracken(Package):
+    """Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly
+    accurate statistical method that computes the abundance of species in DNA
+    sequences from a metagenomics sample."""
+
+    homepage = "https://ccb.jhu.edu/software/bracken"
+    url      = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz"
+
+    version('1.0.0', 'bd91805655269c5f3becb8f8028bab6d')
+
+    depends_on('perl')
+    depends_on('python@2.7:')
+    depends_on('perl-exporter-tiny')
+    depends_on('perl-list-moreutils')
+    depends_on('perl-parallel-forkmanager')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('sample_data', prefix.sample_data)
+
+        filter_file(
+            r'#!/bin/env perl',
+            '#!/usr/bin/env perl',
+            'count-kmer-abundances.pl'
+        )
+
+        filter_file(
+            r'#!/usr/bin/python',
+            '#!/usr/bin/env python',
+            'est_abundance.py'
+        )
+
+        filter_file(
+            r'#!/usr/bin/python',
+            '#!/usr/bin/env python',
+            'generate_kmer_distribution.py'
+        )
+
+        files = (
+            'count-kmer-abundances.pl',
+            'est_abundance.py',
+            'generate_kmer_distribution.py',
+        )
+
+        chmod = which('chmod')
+        for name in files:
+            install(name, prefix.bin)
+            chmod('+x', join_path(self.prefix.bin, name))
diff --git a/var/spack/repos/builtin/packages/braker/package.py b/var/spack/repos/builtin/packages/braker/package.py
index 97fe9f710a..a295a4943a 100644
--- a/var/spack/repos/builtin/packages/braker/package.py
+++ b/var/spack/repos/builtin/packages/braker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,18 @@ class Braker(Package):
        that combines the advantages of GeneMark-ET and AUGUSTUS"""
 
     homepage = "http://exon.gatech.edu/braker1.html"
-    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1_v1.11.tar.gz"
+    url      = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v2.1.0.tar.gz"
+    list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
 
-    version('1.11', '297efe4cabdd239b710ac2c45d81f6a5')
+    version('2.1.0', '5f974abcceb9f96a11668fa20a6f6a56')
+    version('1.11', '297efe4cabdd239b710ac2c45d81f6a5',
+            url='http://bioinf.uni-greifswald.de/augustus/binaries/old/BRAKER1_v1.11.tar.gz')
 
     depends_on('perl', type=('build', 'run'))
-    depends_on('augustus')
+    depends_on('perl-scalar-util-numeric', type=('build', 'run'))
+    depends_on('perl-parallel-forkmanager', type=('build', 'run'))
+    depends_on('perl-file-which', type=('build', 'run'))
+    depends_on('augustus@3.2.3')
     depends_on('genemark-et')
     depends_on('bamtools')
     depends_on('samtools')
diff --git a/var/spack/repos/builtin/packages/branson/package.py b/var/spack/repos/builtin/packages/branson/package.py
index 7eedf7135e..b87e91f08a 100644
--- a/var/spack/repos/builtin/packages/branson/package.py
+++ b/var/spack/repos/builtin/packages/branson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,13 +13,14 @@ class Branson(CMakePackage):
 
     homepage = "https://github.com/lanl/branson"
     url      = "https://github.com/lanl/branson/archive/1.01.zip"
+    git      = "https://github.com/lanl/branson.git"
 
     tags = ['proxy-app']
 
-    version('develop', git='https://github.com/lanl/branson', branch='develop')
+    version('develop', branch='develop')
     version('1.01', 'cf7095a887a8dd7d417267615bd0452a')
 
-    depends_on('mpi')
+    depends_on('mpi@2:')
     depends_on('boost')
     depends_on('metis')
     depends_on('parmetis')
diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py
new file mode 100644
index 0000000000..c068094d6a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/breakdancer/package.py
@@ -0,0 +1,52 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Breakdancer(CMakePackage):
+    """BreakDancer-1.3.6, released under GPLv3, is a perl/Cpp package that
+    provides genome-wide detection of structural variants from next generation
+    paired-end sequencing reads. It includes two complementary programs.
+    BreakDancerMax predicts five types of structural variants: insertions,
+    deletions, inversions, inter- and intra-chromosomal translocations from
+    next-generation short paired-end sequencing reads using read pairs that are
+    mapped with unexpected separation distances or orientation.
+    BreakDancerMini focuses on detecting small indels (usually between 10bp and
+    100bp) using normally mapped read pairs.."""
+
+    homepage = "http://gmt.genome.wustl.edu/packages/breakdancer"
+    url      = "https://github.com/genome/breakdancer/archive/v1.4.5.tar.gz"
+
+    version('1.4.5', sha256='5d74f3a90f5c69026ebb4cf4cb9ccc51ec8dd49ac7a88595a1efabd5a73e92b6')
+    version('master', submodules='true', 
+            git='https://github.com/genome/breakdancer.git', preferred=True)
+
+    phases = ['edit', 'cmake', 'build', 'install']
+
+    depends_on('zlib')
+
+    depends_on('perl-statistics-descriptive', type='run')
+    depends_on('perl-math-cdf', type='run')
+    depends_on('perl-gd-graph', type='run')
+    depends_on('perl-gdgraph-histogram', type='run')
+    depends_on('perl-list-moreutils', type='run')
+    depends_on('perl-exporter-tiny', type='run')
+
+    # TODO: remove git submodules, and depend on boost & samtools
+
+    parallel = False
+
+    def setup_environment(self, spack_env, run_env):
+        # get the perl tools in the path
+        run_env.prepend_path('PATH', self.prefix.lib)
+
+    def edit(self, spec, prefix):
+        # perl tools end up in a silly lib subdirectory, fixing that
+        filter_file(r'set\(SUPPORT_LIBDIR lib\/breakdancer-max\$ \
+                    \{EXE_VERSION_SUFFIX\}\)',
+                    'set(SUPPORT_LIBDIR lib)',
+                    join_path(self.stage.source_path,
+                              'perl', 'CMakeLists.txt'))
diff --git a/var/spack/repos/builtin/packages/breseq/package.py b/var/spack/repos/builtin/packages/breseq/package.py
new file mode 100644
index 0000000000..6e406fba6a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/breseq/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Breseq(AutotoolsPackage):
+    """breseq is a computational pipeline for finding mutations relative to a
+    reference sequence in short-read DNA re-sequencing data for haploid
+    microbial-sized genomes."""
+
+    homepage = "http://barricklab.org/breseq"
+    url      = "https://github.com/barricklab/breseq/archive/v0.31.1.tar.gz"
+
+    version('0.31.1', 'a4e602d5481f8692833ba3d5a3cd0394')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+
+    depends_on('bedtools2', type='run')
+    depends_on('r', type='run')
diff --git a/var/spack/repos/builtin/packages/brigand/package.py b/var/spack/repos/builtin/packages/brigand/package.py
index 4c946d4f66..f92b2814b3 100644
--- a/var/spack/repos/builtin/packages/brigand/package.py
+++ b/var/spack/repos/builtin/packages/brigand/package.py
@@ -1,41 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
 class Brigand(Package):
-    """
-    Brigand Meta-programming library
-    """
+    """Brigand Meta-programming library"""
 
     homepage = "https://github.com/edouarda/brigand"
     url      = "https://github.com/edouarda/brigand/archive/1.0.0.tar.gz"
+    git      = "https://github.com/edouarda/brigand.git"
 
-    version('master', git='https://github.com/edouarda/brigand.git',
-            branch='master')
+    version('master', branch='master')
     version('1.3.0', '0bea9713b3b712229aed289e218d577b')
     version('1.2.0', '32c0f73e7e666d33ff123334f5c9c92f')
     version('1.1.0', '073b7c8e2cbda3a81bbeb1ea5b9ca0eb')
diff --git a/var/spack/repos/builtin/packages/bsseeker2/package.py b/var/spack/repos/builtin/packages/bsseeker2/package.py
index 48b2fc1e6f..f066a3e7ea 100644
--- a/var/spack/repos/builtin/packages/bsseeker2/package.py
+++ b/var/spack/repos/builtin/packages/bsseeker2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bucky/package.py b/var/spack/repos/builtin/packages/bucky/package.py
index eeac2ab2b6..98b71eb8ec 100644
--- a/var/spack/repos/builtin/packages/bucky/package.py
+++ b/var/spack/repos/builtin/packages/bucky/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bumpversion/package.py b/var/spack/repos/builtin/packages/bumpversion/package.py
new file mode 100644
index 0000000000..66dff78fc9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bumpversion/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bumpversion(PythonPackage):
+    """Version-bump your software with a single command."""
+
+    homepage = "https://pypi.python.org/pypi/bumpversion"
+    url      = "https://pypi.io/packages/source/b/bumpversion/bumpversion-0.5.0.tar.gz"
+
+    version('0.5.3', 'c66a3492eafcf5ad4b024be9fca29820')
+    version('0.5.0', '222ba619283d6408ce1bfbb0b5b542f3')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/busco/package.py b/var/spack/repos/builtin/packages/busco/package.py
index 2b50abb40a..e0d56e6d81 100644
--- a/var/spack/repos/builtin/packages/busco/package.py
+++ b/var/spack/repos/builtin/packages/busco/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,16 @@ class Busco(PythonPackage):
        Universal Single-Copy Orthologs"""
 
     homepage = "http://busco.ezlab.org/"
-    url      = "https://gitlab.com/ezlab/busco"
+    url      = "https://gitlab.com/api/v4/projects/ezlab%2Fbusco/repository/archive.tar.gz?sha=2.0.1"
+    git      = "https://gitlab.com/ezlab/busco.git"
+
+    # TODO: check the installation procedure for version 3.0.2
+    # and uncomment the following line
+    # version('3.0.2', '31d80042bb7e96422843fa43d0acbd21')
 
-    version('3.0.1', git='https://gitlab.com/ezlab/busco.git', commit='078252e00399550d7b0e8941cd4d986c8e868a83')
-    version('2.0.1', git='https://gitlab.com/ezlab/busco.git', commit='89aa1ab2527f03a87a214ca90a504ad236582a11')
+    # There is no tag for version 3.0.1
+    version('3.0.1', commit='078252e00399550d7b0e8941cd4d986c8e868a83')
+    version('2.0.1', '4dbcc8a0c18fa8f8312c103eb2fbb4e2')
 
     depends_on('python', type=('build', 'run'))
     depends_on('blast-plus')
diff --git a/var/spack/repos/builtin/packages/butter/package.py b/var/spack/repos/builtin/packages/butter/package.py
index 602f68c5b5..787a4aa759 100644
--- a/var/spack/repos/builtin/packages/butter/package.py
+++ b/var/spack/repos/builtin/packages/butter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/bwa/package.py b/var/spack/repos/builtin/packages/bwa/package.py
index 7f260fcdc9..c32dbaa72a 100644
--- a/var/spack/repos/builtin/packages/bwa/package.py
+++ b/var/spack/repos/builtin/packages/bwa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,12 +12,10 @@ 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('0.7.17', '82cba7ef695538e6a38b9d4156837381',
-            url="https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2")
-    version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554',
-            url="https://github.com/lh3/bwa/releases/download/v0.7.15/bwa-0.7.15.tar.bz2")
-    version('0.7.13', 'f094f609438511766c434178a3635ab4',
-            url="https://github.com/lh3/bwa/releases/download/v0.7.13/bwa-0.7.13.tar.bz2")
+    version('0.7.17', '82cba7ef695538e6a38b9d4156837381')
+    version('0.7.16a', 'c5115c9a5ea0406848500e4b23a7708c')
+    version('0.7.15', 'fcf470a46a1dbe2f96a1c5b87c530554')
+    version('0.7.13', 'f094f609438511766c434178a3635ab4')
     version('0.7.12', 'e24a587baaad411d5da89516ad7a261a',
             url='https://github.com/lh3/bwa/archive/0.7.12.tar.gz')
 
diff --git a/var/spack/repos/builtin/packages/bwtool/package.py b/var/spack/repos/builtin/packages/bwtool/package.py
new file mode 100644
index 0000000000..d1505bc50f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/bwtool/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Bwtool(AutotoolsPackage):
+    """bwtool is a command-line utility for bigWig files."""
+
+    homepage = "https://github.com/CRG-Barcelona/bwtool"
+    url      = "https://github.com/CRG-Barcelona/bwtool/archive/1.0.tar.gz"
+
+    version('1.0', 'cdd7a34ae457b587edfe7dc8a0bdbedd')
+
+    depends_on('libbeato')
diff --git a/var/spack/repos/builtin/packages/byobu/package.py b/var/spack/repos/builtin/packages/byobu/package.py
index 90f91db9e3..d81b641490 100644
--- a/var/spack/repos/builtin/packages/byobu/package.py
+++ b/var/spack/repos/builtin/packages/byobu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,6 +13,8 @@ class Byobu(AutotoolsPackage):
     homepage = "http://www.byobu.co"
     url      = "https://launchpad.net/byobu/trunk/5.123/+download/byobu_5.123.orig.tar.gz"
 
+    version('5.127', '4bafc7cb69ff5b0ab6998816d58cd1ef7175e5de75abc1dd7ffd6d5288a4f63b')
+    version('5.125', 'f90f15771325e8be9360f301b52182d2')
     version('5.123', '961e0072c01c78c9ce4c20d1aa1b0dc4')
 
     depends_on('tmux', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/bzip2/package.py b/var/spack/repos/builtin/packages/bzip2/package.py
index d44e97207f..2f89b73b8e 100644
--- a/var/spack/repos/builtin/packages/bzip2/package.py
+++ b/var/spack/repos/builtin/packages/bzip2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,27 +13,33 @@ class Bzip2(Package):
     compressors), whilst being around twice as fast at compression
     and six times faster at decompression."""
 
-    homepage = "http://www.bzip.org"
-    url      = "http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz"
-    list_url = "http://www.bzip.org/downloads.html"
+    # FIXME: The bzip.org domain has expired:
+    # https://lwn.net/Articles/762264/
+    # This package will need to be updated when a new home is found.
+    homepage = "https://sourceware.org/bzip2/"
+    url      = "https://fossies.org/linux/misc/bzip2-1.0.6.tar.gz"
 
     version('1.0.6', '00b516f4704d4a7cb50a1d97e6e8e15b')
 
     variant('shared', default=True, description='Enables the build of shared libraries.')
 
+    depends_on('diffutils', type='build')
+
     # override default implementation
     @property
     def libs(self):
         shared = '+shared' in self.spec
         return find_libraries(
-            'libbz2', root=self.prefix, shared=shared, recurse=True
+            'libbz2', root=self.prefix, shared=shared, recursive=True
         )
 
     def patch(self):
         # bzip2 comes with two separate Makefiles for static and dynamic builds
         # Tell both to use Spack's compiler wrapper instead of GCC
-        filter_file(r'^CC=gcc', 'CC=cc', 'Makefile')
-        filter_file(r'^CC=gcc', 'CC=cc', 'Makefile-libbz2_so')
+        filter_file(r'^CC=gcc', 'CC={0}'.format(spack_cc), 'Makefile')
+        filter_file(
+            r'^CC=gcc', 'CC={0}'.format(spack_cc), 'Makefile-libbz2_so'
+        )
 
         # The Makefiles use GCC flags that are incompatible with PGI
         if self.compiler.name == 'pgi':
diff --git a/var/spack/repos/builtin/packages/c-blosc/package.py b/var/spack/repos/builtin/packages/c-blosc/package.py
index 8bc5a76ef7..fd2ecc70cb 100644
--- a/var/spack/repos/builtin/packages/c-blosc/package.py
+++ b/var/spack/repos/builtin/packages/c-blosc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import sys
 
@@ -33,6 +14,7 @@ class CBlosc(CMakePackage):
     homepage = "http://www.blosc.org"
     url      = "https://github.com/Blosc/c-blosc/archive/v1.11.1.tar.gz"
 
+    version('1.12.1', '6fa4ecb7ef70803a190dd386bf4a2e93')
     version('1.11.1', 'e236550640afa50155f3881f2d300206')
     version('1.9.2',  'dd2d83069d74b36b8093f1c6b49defc5')
     version('1.9.1',  '7d708d3daadfacf984a87b71b1734ce2')
@@ -45,6 +27,8 @@ class CBlosc(CMakePackage):
     depends_on('cmake@2.8.10:', type='build')
     depends_on('snappy')
     depends_on('zlib')
+    depends_on('zstd')
+    depends_on('lz4')
 
     def cmake_args(self):
         args = []
@@ -54,6 +38,12 @@ class CBlosc(CMakePackage):
         else:
             args.append('-DDEACTIVATE_AVX2=ON')
 
+        if self.spec.satisfies('@1.12.0:'):
+            args.append('-DPREFER_EXTERNAL_SNAPPY=ON')
+            args.append('-DPREFER_EXTERNAL_ZLIB=ON')
+            args.append('-DPREFER_EXTERNAL_ZSTD=ON')
+            args.append('-DPREFER_EXTERNAL_LZ4=ON')
+
         return args
 
     @run_after('install')
diff --git a/var/spack/repos/builtin/packages/c-lime/package.py b/var/spack/repos/builtin/packages/c-lime/package.py
new file mode 100644
index 0000000000..916f95ffd6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/c-lime/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CLime(AutotoolsPackage):
+    """LIME (which can stand for Lattice QCD Interchange Message Encapsulation
+       or more generally, Large Internet Message Encapsulation) is a simple
+       packaging scheme for combining records containing ASCII and/or binary
+       data."""
+
+    homepage = "https://usqcd-software.github.io/c-lime/"
+    url      = "https://github.com/usqcd-software/c-lime/archive/qio2-3-9.tar.gz"
+
+    version('2-3-9', '28257e7ae75dc68c7c920e3e16db0ec9')
diff --git a/var/spack/repos/builtin/packages/cabana/package.py b/var/spack/repos/builtin/packages/cabana/package.py
new file mode 100644
index 0000000000..115bdf6a2b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cabana/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cabana(CMakePackage):
+    """The Exascale Co-Design Center for Particle Applications Toolkit
+    """
+    homepage = "https://github.com/ECP-copa/Cabana"
+    git      = "https://github.com/ECP-copa/Cabana.git"
+    url      = "https://github.com/ECP-copa/Cabana/archive/0.1.0.tar.gz"
+
+    version('develop', branch='master')
+    version('0.1.0', sha256='3280712facf6932b9d1aff375b24c932abb9f60a8addb0c0a1950afd0cb9b9cf')
+    version('0.1.0-rc0', sha256='73754d38aaa0c2a1e012be6959787108fec142294774c23f70292f59c1bdc6c5')
+
+    variant('serial', default=True, description="enable Serial backend (default)")
+    variant('openmp', default=False, description="enable OpenMP backend")
+
+    depends_on("cmake@3.9:", type='build')
+    depends_on("kokkos+serial", when="+serial")
+    depends_on("kokkos+openmp", when="+openmp")
+
+    def cmake_args(self):
+        options = [
+            '-DCabana_ENABLE_TESTING=ON',
+            '-DCabana_ENABLE_Serial=%s'  % (
+                'On' if '+serial'  in self.spec else 'Off'),
+            '-DCabana_ENABLE_OpenMP=%s'  % (
+                'On' if '+openmp'  in self.spec else 'Off')
+        ]
+
+        return options
diff --git a/var/spack/repos/builtin/packages/caffe/package.py b/var/spack/repos/builtin/packages/caffe/package.py
index 730b293adb..97e3e643cc 100644
--- a/var/spack/repos/builtin/packages/caffe/package.py
+++ b/var/spack/repos/builtin/packages/caffe/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cairo/package.py b/var/spack/repos/builtin/packages/cairo/package.py
index ec04e5ed38..b6c9deabe6 100644
--- a/var/spack/repos/builtin/packages/cairo/package.py
+++ b/var/spack/repos/builtin/packages/cairo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class Cairo(AutotoolsPackage):
     homepage = "http://cairographics.org"
     url      = "http://cairographics.org/releases/cairo-1.14.8.tar.xz"
 
+    version('1.14.12', '490025a0ba0622a853010f49fb6343f29fb70b9b')
     version('1.14.8', 'c6f7b99986f93c9df78653c3e6a3b5043f65145e')
     version('1.14.0', '53cf589b983412ea7f78feee2e1ba9cea6e3ebae')
 
@@ -45,7 +27,7 @@ class Cairo(AutotoolsPackage):
     depends_on("glib")
     depends_on("pixman")
     depends_on("freetype")
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
     depends_on("fontconfig@2.10.91:")  # Require newer version of fontconfig.
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/cairomm/package.py b/var/spack/repos/builtin/packages/cairomm/package.py
new file mode 100644
index 0000000000..323288ea5a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cairomm/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cairomm(AutotoolsPackage):
+    """Cairomm is a C++ wrapper for the cairo graphics library."""
+
+    homepage = "https://www.cairographics.org/cairomm/"
+    url      = "https://cairographics.org/releases/cairomm-1.6.4.tar.gz"
+
+    version('1.6.4', '63561c62536173a98f03005dfe55c90e')
+    version('1.6.2', 'eac5d159e4cba98e32ea174483dee24e')
+
+    depends_on('cairo')
+    depends_on('libsigcpp')
diff --git a/var/spack/repos/builtin/packages/caliper/package.py b/var/spack/repos/builtin/packages/caliper/package.py
index e3fff54e6f..5896cfb420 100644
--- a/var/spack/repos/builtin/packages/caliper/package.py
+++ b/var/spack/repos/builtin/packages/caliper/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import sys
@@ -36,13 +17,18 @@ class Caliper(CMakePackage):
     """
 
     homepage = "https://github.com/LLNL/Caliper"
-    url      = ""
+    git      = "https://github.com/LLNL/Caliper.git"
+
+    version('master')
+    version('1.7.0', tag='v1.7.0')
+    # version 1.6.0 is broken b/c it downloads the wrong gotcha version
+    version('1.6.0', tag='v1.6.0')
 
-    version('master', git='https://github.com/LLNL/Caliper.git')
+    is_linux = sys.platform.startswith('linux')
 
-    variant('mpi', default=True, 
+    variant('mpi', default=True,
             description='Enable MPI wrappers')
-    variant('dyninst', default=False, 
+    variant('dyninst', default=False,
             description='Enable symbol translation support with dyninst')
     # libunwind has some issues on Mac
     variant('callpath', default=sys.platform != 'darwin',
@@ -50,14 +36,23 @@ class Caliper(CMakePackage):
     # pthread_self() signature is incompatible with PAPI_thread_init() on Mac
     variant('papi', default=sys.platform != 'darwin',
             description='Enable PAPI service')
+    variant('libpfm', default=is_linux,
+            description='Enable libpfm (perf_events) service')
     # gotcha doesn't work on Mac
     variant('gotcha', default=sys.platform != 'darwin',
             description='Enable GOTCHA support')
+    variant('sampler', default=is_linux,
+            description='Enable sampling support on Linux')
+    variant('sosflow', default=False,
+            description='Enable SOSflow support')
 
+    depends_on('gotcha@1.0:', when='+gotcha')
     depends_on('dyninst', when='+dyninst')
     depends_on('papi', when='+papi')
+    depends_on('libpfm4', when='+libpfm')
     depends_on('mpi', when='+mpi')
-    depends_on('libunwind', when='+callpath')
+    depends_on('unwind', when='+callpath')
+    depends_on('sosflow', when='+sosflow')
 
     depends_on('cmake', type='build')
     depends_on('python', type='build')
@@ -67,17 +62,28 @@ class Caliper(CMakePackage):
 
         args = [
             '-DBUILD_TESTING=Off',
-            '-DWITH_DOCS=Off',
-            '-DWITH_TEST_APPS=Off',
+            '-DBUILD_DOCS=Off',
             '-DWITH_DYNINST=%s'  % ('On' if '+dyninst'  in spec else 'Off'),
             '-DWITH_CALLPATH=%s' % ('On' if '+callpath' in spec else 'Off'),
             '-DWITH_GOTCHA=%s'   % ('On' if '+gotcha'   in spec else 'Off'),
             '-DWITH_PAPI=%s'     % ('On' if '+papi'     in spec else 'Off'),
-            '-DWITH_MPI=%s'      % ('On' if '+mpi'      in spec else 'Off')
+            '-DWITH_LIBPFM=%s'   % ('On' if '+libpfm'   in spec else 'Off'),
+            '-DWITH_SOSFLOW=%s'  % ('On' if '+sosflow'  in spec else 'Off'),
+            '-DWITH_SAMPLER=%s'  % ('On' if '+sampler'  in spec else 'Off'),
+            '-DWITH_MPI=%s'      % ('On' if '+mpi'      in spec else 'Off'),
+            '-DWITH_MPIT=%s' % ('On' if spec.satisfies('^mpi@3:') else 'Off')
         ]
 
+        if '+gotcha' in spec:
+            args.append('-DUSE_EXTERNAL_GOTCHA=True')
         if '+papi' in spec:
-            args.append('-DPAPI_PREFIX=%s' % spec['papi'].prefix)
+            args.append('-DPAPI_PREFIX=%s'    % spec['papi'].prefix)
+        if '+libpfm' in spec:
+            args.append('-DLIBPFM_INSTALL=%s' % spec['libpfm4'].prefix)
+        if '+sosflow' in spec:
+            args.append('-DSOS_PREFIX=%s'     % spec['sosflow'].prefix)
+        if '+callpath' in spec:
+            args.append('-DLIBUNWIND_PREFIX=%s' % spec['libunwind'].prefix)
 
         if '+mpi' in spec:
             args.append('-DMPI_C_COMPILER=%s' % spec['mpi'].mpicc)
diff --git a/var/spack/repos/builtin/packages/callpath/package.py b/var/spack/repos/builtin/packages/callpath/package.py
index a9cb2bf420..479a2d0abc 100644
--- a/var/spack/repos/builtin/packages/callpath/package.py
+++ b/var/spack/repos/builtin/packages/callpath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/camellia/package.py b/var/spack/repos/builtin/packages/camellia/package.py
new file mode 100644
index 0000000000..c97a74a0d3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/camellia/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Camellia(CMakePackage):
+    """Camellia: user-friendly MPI-parallel adaptive finite element package,
+       with support for DPG and other hybrid methods, built atop Trilinos.
+    """
+
+    homepage = "https://bitbucket.org/nateroberts/Camellia"
+    git      = "https://bitbucket.org/nateroberts/camellia.git"
+
+    maintainers = ['CamelliaDPG']
+
+    version('master', branch='master')
+
+    variant('moab', default=True, description='Compile with MOAB to include support for reading standard mesh formats')
+
+    depends_on('trilinos+amesos+amesos2+belos+epetra+epetraext+exodus+ifpack+ifpack2+intrepid+intrepid2+kokkos+ml+muelu+sacado+shards+teuchos+tpetra+zoltan+mumps+superlu-dist+hdf5+zlib+pnetcdf@master,12.12.1:')
+    depends_on('moab@:4', when='+moab')
+    depends_on('hdf5@:1.8')
+    depends_on('mpi')
+
+    def cmake_args(self):
+        spec = self.spec
+        options = [
+            '-DTrilinos_PATH:PATH=%s' % spec['trilinos'].prefix,
+            '-DMPI_DIR:PATH=%s' % spec['mpi'].prefix,
+            '-DBUILD_FOR_INSTALL:BOOL=ON'
+        ]
+
+        if '+moab' in spec:
+            options.extend([
+                '-DENABLE_MOAB:BOOL=ON',
+                '-DMOAB_PATH:PATH=%s' % spec['moab'].prefix
+            ])
+        else:
+            options.append('-DENABLE_MOAB:BOOL=OFF')
+
+        return options
diff --git a/var/spack/repos/builtin/packages/candle-benchmarks/package.py b/var/spack/repos/builtin/packages/candle-benchmarks/package.py
index 7e5650c6f3..6b15e5ebec 100644
--- a/var/spack/repos/builtin/packages/candle-benchmarks/package.py
+++ b/var/spack/repos/builtin/packages/candle-benchmarks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,17 +14,23 @@ class CandleBenchmarks(Package):
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    version('1.0', '6eced30dc15374bc9f90a86d0396e470')
+    version('0.1', sha256='767f74f43ee3a5d4e0f26750f2a96b8433e25a9cd4f2d29938ac8acf263ab58d')
+    version('0.0', '6eced30dc15374bc9f90a86d0396e470')
+
+    variant('mpi', default=True, description='Build with MPI support')
 
-    depends_on('python@2.7:')
+    extends('python@2.7:')
     depends_on('py-theano +gpu', type=('build', 'run'))
     depends_on('py-keras', type=('build', 'run'))
-    depends_on('py-matplotlib +image', type=('build', 'run'))
+    depends_on('py-matplotlib +image@:2.2.3', type=('build', 'run'))
     depends_on('py-tqdm', type=('build', 'run'))
     depends_on('py-scikit-learn', type=('build', 'run'))
-    depends_on('opencv@3.2.0: +core +highgui +imgproc +jpeg +png +tiff +zlib +python -dnn')
+    depends_on('opencv@3.2.0: +core +highgui +imgproc +jpeg +png +tiff +zlib +python -dnn ~eigen ~gtk')
     depends_on('py-mdanalysis', type=('build', 'run'))
-    depends_on('py-mpi4py', type=('build', 'run'))
+    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
+    depends_on('py-h5py~mpi', when='~mpi', type=('build', 'run'))
+    depends_on('py-h5py+mpi', when='+mpi', type=('build', 'run'))
+    depends_on('py-requests', type=('build', 'run'))
 
     # see #3244, but use external for now
     # depends_on('tensorflow')
diff --git a/var/spack/repos/builtin/packages/cantera/package.py b/var/spack/repos/builtin/packages/cantera/package.py
index 03dece3af8..b710163870 100644
--- a/var/spack/repos/builtin/packages/cantera/package.py
+++ b/var/spack/repos/builtin/packages/cantera/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/canu/package.py b/var/spack/repos/builtin/packages/canu/package.py
index 0198246e72..1aec3384df 100644
--- a/var/spack/repos/builtin/packages/canu/package.py
+++ b/var/spack/repos/builtin/packages/canu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class Canu(MakefilePackage):
     homepage = "http://canu.readthedocs.io/"
     url      = "https://github.com/marbl/canu/archive/v1.5.tar.gz"
 
+    version('1.7.1', sha256='c314659c929ee05fd413274f391463a93f19b8337eabb7ee5de1ecfc061caafa')
     version('1.5', '65df275baa28ecf11b15dfd7343361e3')
 
     depends_on('gnuplot', type='run')
@@ -39,23 +21,14 @@ class Canu(MakefilePackage):
     depends_on('perl', type='run')
 
     build_directory = 'src'
+    build_targets = ['clean']
 
     def patch(self):
         # Use our perl, not whatever is in the environment
-        perl = self.spec['perl'].prefix.bin.perl
         filter_file(r'^#!/usr/bin/env perl',
-                    '#!{0}'.format(perl),
+                    '#!{0}'.format(self.spec['perl'].command.path),
                     'src/pipelines/canu.pl')
 
     def install(self, spec, prefix):
-        # replicate the Makefile logic here:
-        # https://github.com/marbl/canu/blob/master/src/Makefile#L344
-        uname = which('uname')
-        ostype = uname(output=str).strip()
-        machinetype = uname('-m', output=str).strip()
-        if machinetype == 'x86_64':
-            machinetype = 'amd64'
-        target_dir = '{0}-{1}'.format(ostype, machinetype)
-        bin = join_path(target_dir, 'bin')
-
-        install_tree(bin, prefix.bin)
+        with working_dir(self.build_directory):
+            make('all', 'TARGET_DIR={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/cap3/package.py b/var/spack/repos/builtin/packages/cap3/package.py
index 13568b40cd..e0d760ccbd 100644
--- a/var/spack/repos/builtin/packages/cap3/package.py
+++ b/var/spack/repos/builtin/packages/cap3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cares/package.py b/var/spack/repos/builtin/packages/cares/package.py
index ab3691be16..36c155a95e 100644
--- a/var/spack/repos/builtin/packages/cares/package.py
+++ b/var/spack/repos/builtin/packages/cares/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class Cares(CMakePackage):
 
     homepage = "https://c-ares.haxx.se"
     url      = "https://github.com/c-ares/c-ares/archive/cares-1_13_0.tar.gz"
+    git      = "https://github.com/c-ares/c-ares.git"
 
-    version('develop', branch='master',
-            git='https://github.com/c-ares/c-ares.git')
-
+    version('develop', branch='master')
     version('1.13.0', 'cdb21052a7eb85261da22f83c0654cfd')
 
     def url_for_version(self, version):
diff --git a/var/spack/repos/builtin/packages/cask/package.py b/var/spack/repos/builtin/packages/cask/package.py
index e1ffe284e7..ba4d29d845 100644
--- a/var/spack/repos/builtin/packages/cask/package.py
+++ b/var/spack/repos/builtin/packages/cask/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # Based on Homebrew's formula:
 # https://github.com/Homebrew/homebrew-core/blob/master/Formula/cask.rb
diff --git a/var/spack/repos/builtin/packages/casper/package.py b/var/spack/repos/builtin/packages/casper/package.py
new file mode 100644
index 0000000000..39754fe3b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/casper/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Casper(MakefilePackage):
+    """CASPER (Context-Aware Scheme for Paired-End Read) is state-of-the art
+       merging tool in terms of accuracy and robustness. Using this
+       sophisticated merging method, we could get elongated reads from the
+       forward and reverse reads."""
+
+    homepage = "http://best.snu.ac.kr/casper/index.php?name=main"
+    url      = "http://best.snu.ac.kr/casper/program/casper_v0.8.2.tar.gz"
+
+    version('0.8.2', '9e83d32ff46b876f33eb1d7b545ec9c2')
+
+    depends_on('jellyfish@2.2.3:')
+    depends_on('boost')
+
+    conflicts('%gcc@7.1.0')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/catalyst/package.py b/var/spack/repos/builtin/packages/catalyst/package.py
new file mode 100644
index 0000000000..d9be7b17dd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/catalyst/package.py
@@ -0,0 +1,152 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+import subprocess
+import llnl.util.tty as tty
+
+
+class Catalyst(CMakePackage):
+    """Catalyst is an in situ use case library, with an adaptable application
+    programming interface (API), that orchestrates the alliance between
+    simulation and analysis and/or visualization tasks."""
+
+    homepage = 'http://www.paraview.org'
+    url      = "http://www.paraview.org/files/v5.5/ParaView-v5.5.2.tar.gz"
+    _urlfmt_gz = 'http://www.paraview.org/files/v{0}/ParaView-v{1}{2}.tar.gz'
+    _urlfmt_xz = 'http://www.paraview.org/files/v{0}/ParaView-v{1}{2}.tar.xz' 
+
+    version('5.5.2', '7eb93c31a1e5deb7098c3b4275e53a4a')
+    version('5.5.1', 'a7d92a45837b67c3371006cc45163277')
+    version('5.5.0', 'a8f2f41edadffdcc89b37fdc9aa7f005')
+    version('5.4.1', '4030c70477ec5a85aa72d6fc86a30753')
+    version('5.4.0', 'b92847605bac9036414b644f33cb7163')
+    version('5.3.0', '68fbbbe733aa607ec13d1db1ab5eba71')
+    version('5.2.0', '4570d1a2a183026adb65b73c7125b8b0')
+    version('5.1.2', '44fb32fc8988fcdfbc216c9e40c3e925')
+    version('5.0.1', 'fdf206113369746e2276b95b257d2c9b')
+    version('4.4.0', 'fa1569857dd680ebb4d7ff89c2227378')
+
+    variant('python', default=False, description='Enable Python support')
+    variant('essentials', default=False, description='Enable Essentials support')
+    variant('extras', default=False, description='Enable Extras support')
+    variant('rendering', default=False, description='Enable Vtk Rendering support')
+
+    depends_on('git')
+    depends_on('mpi')
+    depends_on('python@2:2.8', when='+python', type=("build", "link", "run"))
+    depends_on('python', when='~python', type=("build"))
+    depends_on('mesa', when='+rendering')
+    depends_on("libx11", when='+rendering')
+    depends_on("libxt", when='+rendering')
+    depends_on('cmake@3.3:', type='build')
+
+    def url_for_version(self, version):
+        """Handle ParaView version-based custom URLs."""
+        if version < Version('5.1.0'):
+            return self._urlfmt_gz.format(version.up_to(2), version, '-source')
+        elif version < Version('5.6.0'):
+            return self._urlfmt_gz.format(version.up_to(2), version, '')
+        else:
+            return self._urlfmt_xz.format(version.up_to(2), version, '')
+
+    def do_stage(self, mirror_only=False):
+        """Unpacks and expands the fetched tarball.
+        Then, generate the catalyst source files."""
+        super(Catalyst, self).do_stage(mirror_only)
+
+        # extract the catalyst part
+        paraview_dir = os.path.join(self.stage.path,
+                                    'ParaView-v' + str(self.version))
+        catalyst_script = os.path.join(paraview_dir, 'Catalyst', 'catalyze.py')
+        catalyst_source_dir = os.path.abspath(self.root_cmakelists_dir)
+
+        command = ['python', catalyst_script,
+                   '-r', paraview_dir]
+
+        catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                        'Editions', 'Base')
+        command.append('-i')
+        command.append(catalyst_edition)
+        if '+python' in self.spec:
+            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                            'Editions', 'Enable-Python')
+            command.append('-i')
+            command.append(catalyst_edition)
+        if '+essentials' in self.spec:
+            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                            'Editions', 'Essentials')
+            command.append('-i')
+            command.append(catalyst_edition)
+        if '+extras' in self.spec:
+            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                            'Editions', 'Extras')
+            command.append('-i')
+            command.append(catalyst_edition)
+        if '+rendering' in self.spec:
+            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
+                                            'Editions', 'Rendering-Base')
+            command.append('-i')
+            command.append(catalyst_edition)
+
+        command.append('-o')
+        command.append(catalyst_source_dir)
+
+        if not os.path.isdir(catalyst_source_dir):
+            os.mkdir(catalyst_source_dir)
+            subprocess.check_call(command)
+            tty.msg("Generated catalyst source in %s" % self.stage.path)
+        else:
+            tty.msg("Already generated %s in %s" % (self.name,
+                                                    self.stage.path))
+
+    def setup_environment(self, spack_env, run_env):
+        if os.path.isdir(self.prefix.lib64):
+            lib_dir = self.prefix.lib64
+        else:
+            lib_dir = self.prefix.lib
+        paraview_version = 'paraview-%s' % self.spec.version.up_to(2)
+        run_env.prepend_path('LIBRARY_PATH', join_path(lib_dir,
+                             paraview_version))
+        run_env.prepend_path('LD_LIBRARY_PATH', join_path(lib_dir,
+                             paraview_version))
+
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        return os.path.join(self.stage.path, 'Catalyst-v' + str(self.version))
+
+    @property
+    def build_directory(self):
+        """Returns the directory to use when building the package
+
+        :return: directory where to build the package
+        """
+        return join_path(os.path.abspath(self.root_cmakelists_dir),
+                         'spack-build')
+
+    def cmake_args(self):
+        """Populate cmake arguments for Catalyst."""
+        cmake_args = [
+            '-DPARAVIEW_GIT_DESCRIBE=v%s' % str(self.version)
+        ]
+        return cmake_args
+
+    def cmake(self, spec, prefix):
+        """Runs ``cmake`` in the build directory through the cmake.sh script"""
+        cmake_script_path = os.path.join(
+            os.path.abspath(self.root_cmakelists_dir),
+            'cmake.sh')
+        with working_dir(self.build_directory, create=True):
+            subprocess.check_call([cmake_script_path,
+                                   os.path.abspath(self.root_cmakelists_dir)] +
+                                  self.cmake_args() + self.std_cmake_args)
diff --git a/var/spack/repos/builtin/packages/catch/package.py b/var/spack/repos/builtin/packages/catch/package.py
index 37e8d69aaf..0db27a853d 100644
--- a/var/spack/repos/builtin/packages/catch/package.py
+++ b/var/spack/repos/builtin/packages/catch/package.py
@@ -1,55 +1,66 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Catch(Package):
+class Catch(CMakePackage):
     """Catch tests"""
 
-    homepage = "https://github.com/philsquared/Catch"
-    url = "https://github.com/philsquared/Catch/archive/v1.3.0.tar.gz"
-
-    version('1.9.4', '110b9173d7f766487fed5b710836c7216a781568')
-    version('1.9.3', 'dc0cd0b344d8ccb1190ac3447efcb49c9b43d497')
-    version('1.9.2', '0580f57edd2b33ec671488dc7b6151f9e360c8c9')
-    version('1.9.1', '10784fc4c3786dfc3bd222fb3f9b048b6d68f186')
-    version('1.9.0', '62f07506d4a381d1730d494b71cff0396b9eb3d6')
-    version('1.8.2', '45a7598a8e5c47bc09fb73eec205ffe0885983dc')
-    version('1.8.1', 'd4e302f712fb7e75ce6f05b436dbaf21dca40030')
-    version('1.8.0', '26064092b5682c9c997b04015ed1565f0e198827')
-    version('1.7.2', '13018db2f0f0395456f695b0d0fbc490662e3467')
-    version('1.7.1', 'f82e11a5cdfef2d36b5687ff5970d383f9e76490')
-    version('1.7.0', 'fe39f5b3eb07a5dd0e3f84a1335ceca7de8982e6')
-    version('1.6.1', '7d46961a3131655b986123f8a1f439a04a0af623')
-    version('1.6.0', '890a3b21085d796e13c3bfaf4b6c6f1d06e4a52e')
-    version('1.5.9', '8bc32146a5a2789cd3d3ce2893772e32f412f1b1')
-    version('1.5.0', 'c87397846ea5126febd39f513b413e32f9ed552b')
-    version('1.4.0', 'c165406968fbfb46949885da571cd528c62c4d9a')
-    version('1.3.5', '31553ba6e4bd0cc61e0507d6754847e354699284')
-    version('1.3.0', 'e13694aaff72817d02af8ed27d077cd261b6e857')
+    homepage = "https://github.com/catchorg/Catch2"
+    url = "https://github.com/catchorg/Catch2/archive/v1.3.0.tar.gz"
+
+    variant('single_header', default=True,
+            description='Install a single header only.')
+
+    # - "make install" was added in 1.7.0
+    # - pkg-config package was added in 2.0.1
+    # - CMake config package was added in 2.1.2
+    conflicts('~single_header', when='@:1.6.1')
+
+    version('2.4.0', sha256='ab176de36b886a33aa745fcf34642eac853bf677bda518a88655dc750c72d756')
+    version('2.3.0', sha256='aaf6bbf81ce8522131bae2ea4d013a77b003bbb2017614f5872d5787687f8f5f')
+    # releases 2.3.0+ changed to "catch2/catch.hpp" header
+    version('2.2.1', '54e56803c84890636bd7fe6c3856b104')
+    version('2.1.0', '70b44068976d46d48f3cd8796f675691d3bc726b')
+    version('2.0.1', '5c191a031edebd0525640ed2f38cbf64bacb1803')
+    version('1.12.1', '7d89cffd9d61f4fdcbdb373b70cc92d1')
+    version('1.12.0', '8fb0a64144a2c1572dd930254c7bbdf504ecbe2d')
+    version('1.11.0', '3c03a022d8ba8dbbc931e1ce9fb28faec4890b8d')
+    version('1.10.0', 'c2033ca00b616e7e703623c68220cf5a8e12bba4')
+    version('1.9.7', '7ea41b48a23bd83f377f05a9dfde2be230cfc1b4')
+    version('1.9.6', 'e6ae3a50c6e4da64410979dcd4b2bb3f7ba1c364')
+    version('1.9.5', '7ba2bb12b5398b8b9ab7a7907f4cd345a55e179a')
+    version('1.9.4', 'b48fce35161160def587bd0d8f0e95969b20b786')
+    version('1.9.3', 'c0db82118496a2dd0637aad352f31d9356bffc28')
+    version('1.9.2', '627fd94d466c0f71ba84010adf82771ed3ce85c7')
+    version('1.9.1', '331e4a5cd32fe4c36b4bea15e5198346f18b5c3f')
+    version('1.9.0', '5bb46e99eea39224189a8a0442ec7790c635a7b0')
+    version('1.8.2', '34b8a2da76befeeaeafc393569538222605dda51')
+    version('1.8.1', 'd5f4ae9603fe27c313bc5b5b23c233bdce5c57f7')
+    version('1.8.0', '7fa6bfc50e6dbb6fd1352f41496650d56a86ac1a')
+    version('1.7.2', '45b0ab04b6da75ce56de25a81f0b0de4c7a62179')
+    version('1.7.1', '3a55985aacd5a5ff8a87c1490bbf65f0122647dc')
+    version('1.7.0', '6f9869cc066721d525bb03e8a9423b806c362140')
+    version('1.6.1', 'e88de5b611c07d5d402142d3dc20b63350fdf76c')
+    version('1.6.0', '21273cbed050b8d4785231d04812d5addf5b71b7')
+    version('1.5.9', '341bee0b642f0dc9bb6fb41243a068239468b703')
+    version('1.5.0', '2d14342c72f12b3f4b975cf6aa8594c8ad43d773')
+    version('1.4.0', '3b3b76a842508386be40d73849627bbe12fb5b7f')
+    version('1.3.5', '2cfd78bce21368355c7d3880df88716084df2186')
+    version('1.3.0', '24cd4e6518273fea20becd47a2e1edbee7ec209a')
+
+    @when('+single_header')
+    def cmake(self, spec, prefix):
+        pass
+
+    @when('+single_header')
+    def build(self, spec, prefix):
+        pass
 
+    @when('+single_header')
     def install(self, spec, prefix):
         mkdirp(prefix.include)
         install(join_path('single_include', 'catch.hpp'), prefix.include)
diff --git a/var/spack/repos/builtin/packages/cbench/package.py b/var/spack/repos/builtin/packages/cbench/package.py
index c090907af7..d7bd1a7eb7 100644
--- a/var/spack/repos/builtin/packages/cbench/package.py
+++ b/var/spack/repos/builtin/packages/cbench/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,27 +31,27 @@ class Cbench(MakefilePackage):
     conflicts('%xl')
     conflicts('%xl_r')
 
-    def edit(self, spec, prefix):
+    def setup_environment(self, build_env, run_env):
         # The location of the Cbench source tree
-        env['CBENCHOME'] = self.stage.source_path
+        build_env.set('CBENCHOME', self.stage.source_path)
 
         # The location that will contain all of your tests and their results
-        env['CBENCHTEST'] = prefix
+        build_env.set('CBENCHTEST', self.prefix)
 
         # The location of the system MPI tree
-        env['MPIHOME'] = spec['mpi'].prefix
+        build_env.set('MPIHOME', self.spec['mpi'].prefix)
 
         # Pick the compiler collection/chain you want to compile with.
         # Examples include: intel, gcc, pgi.
-        env['COMPILERCOLLECTION'] = self.compiler.name
+        build_env.set('COMPILERCOLLECTION', self.compiler.name)
 
         # Linking flags for BLAS/LAPACK and FFTW
-        env['BLASLIB']   = spec['blas'].libs.ld_flags
-        env['LAPACKLIB'] = spec['lapack'].libs.ld_flags
-        env['FFTWLIB']   = spec['fftw'].libs.ld_flags
+        build_env.set('BLASLIB', self.spec['blas'].libs.ld_flags)
+        build_env.set('LAPACKLIB', self.spec['lapack'].libs.ld_flags)
+        build_env.set('FFTWLIB', self.spec['fftw'].libs.ld_flags)
 
         # The number of make jobs (commands) to run simultaneously
-        env['JOBS'] = str(make_jobs)
+        build_env.set('JOBS', str(make_jobs))
 
     @run_before('build')
     @on_package_attributes(run_tests=True)
diff --git a/var/spack/repos/builtin/packages/cblas/package.py b/var/spack/repos/builtin/packages/cblas/package.py
index 05a3ddb43e..3a36664103 100644
--- a/var/spack/repos/builtin/packages/cblas/package.py
+++ b/var/spack/repos/builtin/packages/cblas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,10 +23,10 @@ class Cblas(Package):
     def patch(self):
         mf = FileFilter('Makefile.in')
 
-        mf.filter('^BLLIB =.*', 'BLLIB = %s/libblas.a' %
-                  self.spec['blas'].prefix.lib)
+        mf.filter('^BLLIB =.*', 'BLLIB = {0}'.format(
+                  ' '.join(self.spec['blas'].libs.libraries)))
         mf.filter('^CC =.*', 'CC = cc')
-        mf.filter('^FC =.*', 'FC = f90')
+        mf.filter('^FC =.*', 'FC = fc')
 
     def install(self, spec, prefix):
         make('all')
@@ -53,6 +34,6 @@ class Cblas(Package):
         mkdirp(prefix.include)
 
         # Rename the generated lib file to libcblas.a
-        install('./lib/cblas_LINUX.a', '%s/libcblas.a' % prefix.lib)
-        install('./include/cblas.h', '%s' % prefix.include)
-        install('./include/cblas_f77.h', '%s' % prefix.include)
+        install('lib/cblas_LINUX.a', prefix.lib.join('libcblas.a'))
+        install('include/cblas.h', prefix.include)
+        install('include/cblas_f77.h', prefix.include)
diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py
index 42f40c63ea..3d4f039371 100644
--- a/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-argonavis-gui/package.py
@@ -1,46 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# 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 GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU 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
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
+import os
 
 
 class CbtfArgonavisGui(QMakePackage):
@@ -48,21 +12,43 @@ class CbtfArgonavisGui(QMakePackage):
        performance information by loading in the Sqlite database files.
     """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
+    git      = "https://github.com/OpenSpeedShop/cbtf-argonavis-gui.git"
+
+    version('develop', branch='master')
+    version('1.3.0.0', branch='1.3.0.0')
+
+    depends_on("cmake@3.0.2:", type='build')
+
+    depends_on('qt@5.10.0:', when='@develop')
+    depends_on('qt@5.10.0', when='@1.3.0.0:9999')
 
-    version('0.8.1', branch='master',
-            git='https://github.com/OpenSpeedShop/cbtf-argonavis-gui.git')
+    depends_on("boost@1.66.0:")
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop')
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.3.0.0:9999')
+
+    # Dependencies for the openspeedshop cbtf packages.
+    depends_on("cbtf@develop", when='@develop')
+    depends_on("cbtf@1.9.1.0:9999", when='@1.3.0.0:9999')
+
+    depends_on("cbtf-krell@develop", when='@develop')
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@1.3.0.0:9999')
+
+    depends_on("cbtf-argonavis@develop", when='@develop')
+    depends_on("cbtf-argonavis@1.9.1.0:9999", when='@1.3.0.0:9999')
 
-    depends_on("cmake@3.0.2", type='build')
-    depends_on("openspeedshop+cuda gui='qt4'")
-    depends_on('qt@4.8.6:')
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("cbtf")
-    depends_on("cbtf-krell")
-    depends_on("cbtf-argonavis")
     depends_on("cuda")
-    depends_on("mrnet@5.0.1:+lwthreads")
-    depends_on("xerces-c@3.1.1:")
-    depends_on("graphviz")
+
+    depends_on("openspeedshop-utils+cuda@develop", when='@develop')
+    depends_on("openspeedshop-utils@2.3.1.3:+cuda", when='@1.3.0.0:9999')
+
+    # For Xerces-C
+    depends_on("xerces-c")
+
+    depends_on("graphviz@2.40.1:", when='@develop')
+    depends_on("graphviz@2.40.1", when='@1.3.0.0:9999')
+
     depends_on("qtgraph")
 
     parallel = False
@@ -74,7 +60,7 @@ class CbtfArgonavisGui(QMakePackage):
         spack_env.set('CBTF_KRELL_ROOT', self.spec['cbtf-krell'].prefix)
         spack_env.set('CBTF_ARGONAVIS_ROOT',
                       self.spec['cbtf-argonavis'].prefix)
-        spack_env.set('OSS_CBTF_ROOT', self.spec['openspeedshop'].prefix)
+        spack_env.set('OSS_CBTF_ROOT', self.spec['openspeedshop-utils'].prefix)
         spack_env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix)
         spack_env.set('QTGRAPHLIB_ROOT', self.spec['qtgraph'].prefix)
         spack_env.set('KRELL_ROOT_MRNET', self.spec['mrnet'].prefix)
@@ -83,14 +69,21 @@ class CbtfArgonavisGui(QMakePackage):
 
         # The implementor of qtgraph has set up the library and include
         # paths in a non-conventional way.  We reflect that here.
+        # What library suffix should be used based on library existence
+        if os.path.isdir(self.spec['qtgraph'].prefix.lib64):
+            qtgraph_lib_dir = self.spec['qtgraph'].prefix.lib64
+        else:
+            qtgraph_lib_dir = self.spec['qtgraph'].prefix.lib
+
         run_env.prepend_path(
             'LD_LIBRARY_PATH', join_path(
-                self.spec['qtgraph'].prefix.lib64,
+                qtgraph_lib_dir,
                 '{0}'.format(self.spec['qt'].version.up_to(3))))
+
         # The openspeedshop libraries are needed to actually load the
         # performance information into the GUI.
         run_env.prepend_path(
-            'LD_LIBRARY_PATH', self.spec['openspeedshop'].prefix.lib64)
+            'LD_LIBRARY_PATH', self.spec['openspeedshop-utils'].prefix.lib64)
 
     def qmake_args(self):
         options = ['-o', 'Makefile', 'openss-gui.pro']
diff --git a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
index a335754537..f56e01e46f 100644
--- a/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-argonavis/package.py
@@ -1,44 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# 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 GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU 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
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -46,22 +9,71 @@ from spack import *
 class CbtfArgonavis(CMakePackage):
     """CBTF Argo Navis project contains the CUDA collector and supporting
        libraries that was done as a result of a DOE SBIR grant.
-
     """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
+    git      = "https://github.com/OpenSpeedShop/cbtf-argonavis.git"
 
-    version('1.8', branch='master',
-            git='https://github.com/OpenSpeedShop/cbtf-argonavis.git')
+    version('develop', branch='master')
+    version('1.9.2', branch='1.9.2')
+    version('1.9.1.2', branch='1.9.1.2')
+    version('1.9.1.1', branch='1.9.1.1')
+    version('1.9.1.0', branch='1.9.1.0')
 
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+    variant('crayfe', default=False,
+            description="build only the FE tool using the runtime_dir \
+                         to point to target build.")
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
     variant('build_type', default='None', values=('None'),
             description='CMake build type')
 
     depends_on("cmake@3.0.2:", type='build')
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("papi")
-    depends_on("mrnet@5.0.1:+lwthreads")
-    depends_on("cbtf")
-    depends_on("cbtf-krell")
+
+    # To specify ^elfutils@0.170 on the command line spack
+    # apparently needs/wants this dependency explicity here
+    # even though it is referenced downstream
+    depends_on("elf", type="link")
+
+    # For boost
+    depends_on("boost@1.66.0:")
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti')
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop~cti')
+    depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti')
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999~cti')
+
+    # For CBTF
+    depends_on("cbtf@develop", when='@develop')
+    depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999')
+
+    # For CBTF with cti
+    depends_on("cbtf@develop+cti", when='@develop+cti')
+    depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti')
+
+    # For CBTF with runtime
+    depends_on("cbtf@develop+runtime", when='@develop+runtime')
+    depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime')
+
+    # For libmonitor
+    depends_on("libmonitor@2013.02.18+krellpatch")
+
+    # For PAPI
+    depends_on("papi@5.4.1:")
+
+    # For CBTF-KRELL
+    depends_on("cbtf-krell@develop", when='@develop')
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@1.9.1.0:9999')
+
+    depends_on('cbtf-krell@develop+cti', when='@develop+cti')
+    depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@1.9.1.0:9999+cti')
+
+    depends_on('cbtf-krell@develop+runtime', when='@develop+runtime')
+    depends_on('cbtf-krell@1.9.1.0:9999+runtime', when='@1.9.1.0:9999+runtime')
+
+    # For CUDA
     depends_on("cuda")
 
     parallel = False
@@ -87,6 +99,17 @@ class CbtfArgonavis(CMakePackage):
             '-DBoost_DIR=%s' % spec['boost'].prefix,
             '-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib,
             '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
+            '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
             '-DBoost_NO_SYSTEM_PATHS=ON']
 
         return cmake_args
+
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environments for a package."""
+
+        run_env.prepend_path(
+            'LD_LIBRARY_PATH',
+            self.spec['cuda'].prefix + '/extras/CUPTI/lib64')
+        spack_env.prepend_path(
+            'LD_LIBRARY_PATH',
+            self.spec['cuda'].prefix + '/extras/CUPTI/lib64')
diff --git a/var/spack/repos/builtin/packages/cbtf-krell/package.py b/var/spack/repos/builtin/packages/cbtf-krell/package.py
index 1716d83188..b30a4a6649 100644
--- a/var/spack/repos/builtin/packages/cbtf-krell/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-krell/package.py
@@ -1,46 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# 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 GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU 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
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
+import spack
+import spack.store
 
 
 class CbtfKrell(CMakePackage):
@@ -48,12 +13,15 @@ class CbtfKrell(CMakePackage):
        CBTF project.  These contributions include many performance data
        collectors and support libraries as well as some example tools
        that drive the data collection at HPC levels of scale.
-
     """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
+    git      = "https://github.com/OpenSpeedShop/cbtf-krell.git"
 
-    version('1.8', branch='master',
-            git='https://github.com/OpenSpeedShop/cbtf-krell.git')
+    version('develop', branch='master')
+    version('1.9.2', branch='1.9.2')
+    version('1.9.1.2', branch='1.9.1.2')
+    version('1.9.1.1', branch='1.9.1.1')
+    version('1.9.1.0', branch='1.9.1.0')
 
     # MPI variants
     variant('openmpi', default=False,
@@ -68,32 +36,62 @@ class CbtfKrell(CMakePackage):
             description="Build mpi experiment collector for mpich2 MPI.")
     variant('mpich', default=False,
             description="Build mpi experiment collector for mpich MPI.")
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
     variant('build_type', default='None', values=('None'),
             description='CMake build type')
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+    variant('crayfe', default=False,
+            description="build only the FE tool using the runtime_dir \
+                         to point to target build.")
 
     # Dependencies for cbtf-krell
     depends_on("cmake@3.0.2:", type='build')
 
-    # For binutils service
+    # For binutils
     depends_on("binutils")
 
-    # collectionTool
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("dyninst@9.3.2")
-    depends_on("mrnet@5.0.1:+lwthreads")
+    # For boost
+    depends_on("boost@1.66.0:")
+
+    # For Dyninst
+    depends_on("dyninst@develop", when='@develop')
+    depends_on("dyninst@10:", when='@1.9.1.0:9999')
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop', type=('build', 'link', 'run'))
 
-    depends_on("xerces-c@3.1.1:")
-    depends_on("cbtf")
+    depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999', type=('build', 'link', 'run'))
+
+    # For Xerces-C
+    depends_on("xerces-c")
+
+    # For CBTF
+    depends_on("cbtf@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999', type=('build', 'link', 'run'))
+
+    # For CBTF with cti
+    depends_on("cbtf@develop+cti", when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti', type=('build', 'link', 'run'))
+
+    # For CBTF with runtime
+    depends_on("cbtf@develop+runtime", when='@develop+runtime', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime', type=('build', 'link', 'run'))
 
     # for services and collectors
-    depends_on("libmonitor+krellpatch")
-    depends_on("libunwind")
-    depends_on("papi")
-    depends_on("llvm-openmp-ompt@towards_tr4+standalone")
+    depends_on("libmonitor@2013.02.18+krellpatch")
+
+    depends_on("libunwind", when='@develop')
+    depends_on("libunwind@1.2.1", when='@1.9.1.0:9999')
+
+    depends_on("papi@5.4.1:")
+
+    depends_on("llvm-openmp-ompt@tr6_forwards+standalone")
 
     # MPI Installations
-    # These have not worked either for build or execution, commenting out for
-    # now
     depends_on("openmpi", when='+openmpi')
     depends_on("mpich", when='+mpich')
     depends_on("mpich2", when='+mpich2')
@@ -101,36 +99,97 @@ class CbtfKrell(CMakePackage):
     depends_on("mvapich", when='+mvapich')
     depends_on("mpt", when='+mpt')
 
+    depends_on("python", when='@develop', type=('build', 'run'))
+    depends_on("python@2.7.14:2.7.15", when='@2.3.1.3:9999', type=('build', 'run'))
+
+    depends_on("gotcha")
+
     parallel = False
 
     build_directory = 'build_cbtf_krell'
 
-    def set_mpi_cmakeOptions(self, spec, cmakeOptions):
-        # Appends to cmakeOptions the options that will enable the appropriate
+    def set_rt_only_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
         # MPI implementations
 
-        MPIOptions = []
+        rt_only_options = []
+        rt_only_options.append('-DRUNTIME_ONLY=true')
+        cmake_options.extend(rt_only_options)
+
+    def set_mpi_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
+        # MPI implementations
+
+        mpi_options = []
 
         # openmpi
-        if '+openmpi' in spec:
-            MPIOptions.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
+        if spec.satisfies('+openmpi'):
+            mpi_options.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
         # mpich
-        if '+mpich' in spec:
-            MPIOptions.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
+        if spec.satisfies('+mpich'):
+            mpi_options.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
         # mpich2
-        if '+mpich2' in spec:
-            MPIOptions.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
+        if spec.satisfies('+mpich2'):
+            mpi_options.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
         # mvapich
-        if '+mvapich' in spec:
-            MPIOptions.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
+        if spec.satisfies('+mvapich'):
+            mpi_options.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
         # mvapich2
-        if '+mvapich2' in spec:
-            MPIOptions.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
+        if spec.satisfies('+mvapich2'):
+            mpi_options.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
         # mpt
-        if '+mpt' in spec:
-            MPIOptions.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
+        if spec.satisfies('+mpt'):
+            mpi_options.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
+
+        cmake_options.extend(mpi_options)
+
+    def set_cray_login_node_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
+        # the appropriate Cray login node libraries
+
+        cray_login_node_options = []
+        rt_platform = "cray"
+        # How do we get the compute node (CNL) cbtf package
+        # install directory path. spec['cbtf'].prefix is the
+        # login node path for this build, as we are building
+        # the login node components with this spack invocation. We
+        # need these paths to be the ones created in the CNL
+        # spack invocation.
+        be_cbtf = spack.store.db.query_one('cbtf arch=cray-CNL-haswell')
+        be_cbtfk = spack.store.db.query_one('cbtf-krell arch=cray-CNL-haswell')
+        be_papi = spack.store.db.query_one('papi arch=cray-CNL-haswell')
+        be_boost = spack.store.db.query_one('boost arch=cray-CNL-haswell')
+        be_mont = spack.store.db.query_one('libmonitor arch=cray-CNL-haswell')
+        be_unw = spack.store.db.query_one('libunwind arch=cray-CNL-haswell')
+        be_xer = spack.store.db.query_one('xerces-c arch=cray-CNL-haswell')
+        be_dyn = spack.store.db.query_one('dyninst arch=cray-CNL-haswell')
+        be_mrnet = spack.store.db.query_one('mrnet arch=cray-CNL-haswell')
 
-        cmakeOptions.extend(MPIOptions)
+        cray_login_node_options.append(
+            '-DCN_RUNTIME_PLATFORM=%s' % rt_platform)
+
+        # Use install directories as CMAKE args for the building
+        # of login cbtf-krell
+        cray_login_node_options.append(
+            '-DCBTF_CN_RUNTIME_DIR=%s' % be_cbtf.prefix)
+        cray_login_node_options.append(
+            '-DCBTF_KRELL_CN_RUNTIME_DIR=%s' % be_cbtfk.prefix)
+        cray_login_node_options.append(
+            '-DPAPI_CN_RUNTIME_DIR=%s' % be_papi.prefix)
+        cray_login_node_options.append(
+            '-DBOOST_CN_RUNTIME_DIR=%s' % be_boost.prefix)
+        cray_login_node_options.append(
+            '-DLIBMONITOR_CN_RUNTIME_DIR=%s' % be_mont.prefix)
+        cray_login_node_options.append(
+            '-DLIBUNWIND_CN_RUNTIME_DIR=%s' % be_unw.prefix)
+        cray_login_node_options.append(
+            '-DXERCESC_CN_RUNTIME_DIR=%s' % be_xer.prefix)
+        cray_login_node_options.append(
+            '-DDYNINST_CN_RUNTIME_DIR=%s' % be_dyn.prefix)
+        cray_login_node_options.append(
+            '-DMRNET_CN_RUNTIME_DIR=%s' % be_mrnet.prefix)
+
+        cmake_options.extend(cray_login_node_options)
 
     def cmake_args(self):
         spec = self.spec
@@ -151,9 +210,52 @@ class CbtfKrell(CMakePackage):
             '-DMRNET_DIR=%s' % spec['mrnet'].prefix,
             '-DDYNINST_DIR=%s' % spec['dyninst'].prefix,
             '-DLIBIOMP_DIR=%s' % spec['llvm-openmp-ompt'].prefix,
+            '-DGOTCHA_DIR=%s' % spec['gotcha'].prefix,
             '-DXERCESC_DIR=%s' % spec['xerces-c'].prefix]
 
+        if self.spec.satisfies('+runtime'):
+            self.set_rt_only_cmake_options(spec, cmake_args)
+
         # Add any MPI implementations coming from variant settings
-        self.set_mpi_cmakeOptions(spec, cmake_args)
+        self.set_mpi_cmake_options(spec, cmake_args)
+
+        if self.spec.satisfies('+crayfe'):
+            # We need to build target/compute node components/libraries first
+            # then pass those libraries to the cbtf-krell login node build
+            self.set_cray_login_node_cmake_options(spec, cmake_args)
 
         return cmake_args
+
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environments for a package."""
+
+        # Environment settings for cbtf-krell, bin is automatically
+        # added to the path in the module file
+        run_env.prepend_path('PATH', self.prefix.sbin)
+
+        run_env.set('XPLAT_RSH', 'ssh')
+        run_env.set('MRNET_COMM_PATH', self.prefix.sbin.cbtf_mrnet_commnode)
+
+        # Set CBTF_MPI_IMPLEMENTATON to the appropriate mpi implementation
+        # This is needed by CBTF tools to deploy the correct
+        # mpi runtimes for cbtfsummary
+        # Users may have to set the CBTF_MPI_IMPLEMENTATION variable
+        # manually if multiple mpi's are specified in the build
+
+        if self.spec.satisfies('+mpich'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mpich")
+
+        if self.spec.satisfies('+mvapich'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich")
+
+        if self.spec.satisfies('+mvapich2'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2")
+
+        if self.spec.satisfies('+mpt'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mpt")
+
+        if self.spec.satisfies('+openmpi'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "openmpi")
+
+        run_env.set('CBTF_MRNET_BACKEND_PATH',
+                    self.prefix.sbin.cbtf_libcbtf_mrnet_backend)
diff --git a/var/spack/repos/builtin/packages/cbtf-lanl/package.py b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
index 19b00e00df..460c845552 100644
--- a/var/spack/repos/builtin/packages/cbtf-lanl/package.py
+++ b/var/spack/repos/builtin/packages/cbtf-lanl/package.py
@@ -1,44 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# 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 GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU 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
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -46,20 +9,57 @@ from spack import *
 class CbtfLanl(CMakePackage):
     """CBTF LANL project contains a memory tool and data center type system
        command monitoring tool."""
+
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home/"
+    git      = "https://github.com/OpenSpeedShop/cbtf-lanl.git"
 
-    version('1.8', branch='master',
-            git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl')
+    version('develop', branch='master')
+    version('1.9.2', branch='1.9.2')
+    version('1.9.1.2', branch='1.9.1.2')
+    version('1.9.1.1', branch='1.9.1.1')
+    version('1.9.1.0', branch='1.9.1.0')
 
     variant('build_type', default='None', values=('None'),
             description='CMake build type')
 
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
+
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+
     depends_on("cmake@3.0.2:", type='build')
-    # Dependencies for cbtf-krell
-    depends_on("mrnet@5.0.1:+lwthreads")
-    depends_on("xerces-c@3.1.1:")
-    depends_on("cbtf")
-    depends_on("cbtf-krell")
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti')
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop')
+    depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti')
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999')
+
+    # For Xerces-C
+    depends_on("xerces-c")
+
+    # For CBTF
+    depends_on("cbtf@develop", when='@develop')
+    depends_on("cbtf@1.9.1.0:9999", when='@1.9.1.0:9999')
+
+    # For CBTF with cti
+    depends_on("cbtf@develop+cti", when='@develop+cti')
+    depends_on("cbtf@1.9.1.0:9999+cti", when='@1.9.1.0:9999+cti')
+
+    # For CBTF with runtime
+    depends_on("cbtf@develop+runtime", when='@develop+runtime')
+    depends_on("cbtf@1.9.1.0:9999+runtime", when='@1.9.1.0:9999+runtime')
+
+    # For CBTF-KRELL
+    depends_on("cbtf-krell@develop", when='@develop')
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@1.9.1.0:9999')
+
+    depends_on('cbtf-krell@develop+cti', when='@develop+cti')
+    depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@1.9.1.0:9999+cti')
+
+    depends_on('cbtf-krell@develop+runtime', when='@develop+runtime')
+    depends_on('cbtf-krell@1.9.1.0:9999+runtime', when='@1.9.1.0:9999+runtime')
 
     parallel = False
 
diff --git a/var/spack/repos/builtin/packages/cbtf/package.py b/var/spack/repos/builtin/packages/cbtf/package.py
index 2f0b3b275d..ba6cbd7477 100644
--- a/var/spack/repos/builtin/packages/cbtf/package.py
+++ b/var/spack/repos/builtin/packages/cbtf/package.py
@@ -1,44 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-##########################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation; either version 2 of the License, or (at your option) any later
-# version.
-#
-# 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 GNU General Public License for more
-# details.
-#
-# You should have received a copy of the GNU 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
-##########################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -51,22 +14,38 @@ class Cbtf(CMakePackage):
 
     """
     homepage = "http://sourceforge.net/p/cbtf/wiki/Home"
+    git      = "https://github.com/OpenSpeedShop/cbtf.git"
 
-    # Use when the git repository is available
-    version('1.8', branch='master',
-            git='https://github.com/OpenSpeedShop/cbtf.git')
+    version('develop', branch='master')
+    version('1.9.2', branch='1.9.2')
+    version('1.9.1.2', branch='1.9.1.2')
+    version('1.9.1.1', branch='1.9.1.1')
+    version('1.9.1.0', branch='1.9.1.0')
+
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
 
     variant('runtime', default=False,
             description="build only the runtime libraries and collectors.")
+
     variant('build_type', default='None', values=('None'),
             description='CMake build type')
 
     depends_on("cmake@3.0.2:", type='build')
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("mrnet@5.0.1:+lwthreads")
-    depends_on("xerces-c@3.1.1:")
-    # Work around for spack libxml2 package bug, take off python when fixed
-    depends_on("libxml2+python")
+
+    depends_on("boost@1.66.0:")
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti')
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop')
+    depends_on("mrnet@5.0.1-3+cti", when='@1.9.1.0:9999+cti')
+    depends_on("mrnet@5.0.1-3+lwthreads", when='@1.9.1.0:9999')
+
+    # For Xerces-C
+    depends_on("xerces-c")
+
+    # For XML2
+    depends_on("libxml2")
 
     parallel = False
 
@@ -83,7 +62,8 @@ class Cbtf(CMakePackage):
 
         compile_flags = "-O2 -g"
 
-        if '+runtime' in spec:
+        if spec.satisfies('+runtime'):
+
             # Install message tag include file for use in Intel MIC
             # cbtf-krell build
             # FIXME
diff --git a/var/spack/repos/builtin/packages/ccache/package.py b/var/spack/repos/builtin/packages/ccache/package.py
index 44b45fbea9..6446768e4f 100644
--- a/var/spack/repos/builtin/packages/ccache/package.py
+++ b/var/spack/repos/builtin/packages/ccache/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cctools/package.py b/var/spack/repos/builtin/packages/cctools/package.py
index 997a6ba6df..63cc6a83b0 100644
--- a/var/spack/repos/builtin/packages/cctools/package.py
+++ b/var/spack/repos/builtin/packages/cctools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cdbfasta/package.py b/var/spack/repos/builtin/packages/cdbfasta/package.py
index f3aafbe20a..11bccc8f9d 100644
--- a/var/spack/repos/builtin/packages/cdbfasta/package.py
+++ b/var/spack/repos/builtin/packages/cdbfasta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,11 @@ class Cdbfasta(MakefilePackage):
     """Fast indexing and retrieval of fasta records from flat file databases"""
 
     homepage = "https://github.com/gpertea/cdbfasta"
-    url      = "https://github.com/gpertea/cdbfasta"
+    git      = "https://github.com/gpertea/cdbfasta.git"
+
+    version('2017-03-16', commit='b3e481fe02dfbc767a3842bcb1b687c60376a5e8')
 
-    version('2017-03-16', git='https://github.com/gpertea/cdbfasta.git', commit='b3e481fe02dfbc767a3842bcb1b687c60376a5e8')
+    depends_on('zlib')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cdd/package.py b/var/spack/repos/builtin/packages/cdd/package.py
index cf720577ea..706ee1876d 100644
--- a/var/spack/repos/builtin/packages/cdd/package.py
+++ b/var/spack/repos/builtin/packages/cdd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/cddlib/package.py b/var/spack/repos/builtin/packages/cddlib/package.py
index 360089272e..328f76bd61 100644
--- a/var/spack/repos/builtin/packages/cddlib/package.py
+++ b/var/spack/repos/builtin/packages/cddlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/cdhit/package.py b/var/spack/repos/builtin/packages/cdhit/package.py
index 64f4940606..14857581bf 100644
--- a/var/spack/repos/builtin/packages/cdhit/package.py
+++ b/var/spack/repos/builtin/packages/cdhit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py
index ccf0769ff1..68a23730ea 100644
--- a/var/spack/repos/builtin/packages/cdo/package.py
+++ b/var/spack/repos/builtin/packages/cdo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,12 @@ class Cdo(AutotoolsPackage):
     url = 'https://code.mpimet.mpg.de/attachments/download/12760/cdo-1.7.2.tar.gz'
     list_url = 'https://code.mpimet.mpg.de/projects/cdo/files'
 
+    maintainers = ['skosukhin']
+
+    version('1.9.5', '0c60f2c94dc5c76421ecf363153a5043')
+    version('1.9.4', '377c9e5aa7d8cbcb4a6c558abb2eb053')
+    version('1.9.3', '13ae222164413dbd53532b03b072def5')
+    version('1.9.2', '38e68d34f0b5b44a52c3241be6831423')
     version('1.9.1', 'e60a89f268ba24cee5c461f2c217829e')
     version('1.9.0', '2d88561b3b4a880df0422a62e5027e40')
     version('1.8.2', '6a2e2f99b7c67ee9a512c40a8d4a7121')
@@ -133,8 +120,13 @@ class Cdo(AutotoolsPackage):
 
         config_args += self.enable_or_disable('openmp')
 
-        # Workaround for a problem in CDO
+        # Starting version 1.9.0 CDO is a C++ program but it uses the C
+        # interface of HDF5 without the parallel features. To avoid
+        # unnecessary dependencies on mpi's cxx library, we need to set the
+        # following flags. This works for OpenMPI, MPICH, MVAPICH, Intel MPI,
+        # IBM Spectrum MPI, bullx MPI, and Cray MPI.
         if self.spec.satisfies('@1.9:+hdf5^hdf5+mpi'):
-            config_args.append('CXX=' + self.spec['mpi'].mpicxx)
+            config_args.append(
+                'CPPFLAGS=-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX')
 
         return config_args
diff --git a/var/spack/repos/builtin/packages/ceed/README.md b/var/spack/repos/builtin/packages/ceed/README.md
new file mode 100644
index 0000000000..74bcae1d17
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ceed/README.md
@@ -0,0 +1,3 @@
+This is a bundle for the CEED software suite.
+
+See https://ceed.exascaleproject.org for details.
diff --git a/var/spack/repos/builtin/packages/ceed/package.py b/var/spack/repos/builtin/packages/ceed/package.py
new file mode 100644
index 0000000000..94d4d98545
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ceed/package.py
@@ -0,0 +1,92 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Ceed(Package):
+    """Ceed is a collection of benchmarks, miniapps, software libraries and
+       APIs for efficient high-order finite element and spectral element
+       discretizations for exascale applications developed in the Department of
+       Energy (DOE) and partially supported by the Exascale Computing Project
+       (ECP). This is a Spack bundle package that installs the CEED software
+       components."""
+
+    homepage = "https://ceed.exascaleproject.org"
+
+    url  = 'file://' + os.path.dirname(__file__) + '/README.md'
+    sha1 = 'b2eefd95c09ba573f663a761b84811a2d7e39788'
+
+    version('1.0.0', sha1, expand=False)
+
+    variant('cuda', default=False,
+            description='Build MAGMA; enable CUDA support in libCEED and OCCA')
+    variant('mfem', default=True, description='Build MFEM and Laghos')
+    variant('nek', default=True,
+            description='Build Nek5000, GSLIB, Nekbone, and NekCEM')
+    variant('occa', default=True,
+            description='Build OCCA; enable OCCA support in libCEED')
+    variant('petsc', default=True,
+            description='Build PETSc and HPGMG')
+    variant('pumi', default=True,
+            description='Build PUMI')
+    variant('quickbuild', default=True,
+            description='Speed-up the build by disabling variants in packages')
+    # TODO: Add 'int64' variant?
+
+    # LibCEED
+    depends_on('libceed@0.2~cuda', when='@1.0.0~cuda')
+    depends_on('libceed@0.2+cuda', when='@1.0.0+cuda')
+    depends_on('libceed@0.2+occa', when='@1.0.0+occa')
+    depends_on('libceed@0.2~occa', when='@1.0.0~occa')
+
+    # OCCA
+    depends_on('occa@v1.0.0-alpha.5~cuda', when='@1.0.0+occa~cuda')
+    depends_on('occa@v1.0.0-alpha.5+cuda', when='@1.0.0+occa+cuda')
+
+    # Nek5000, GSLIB, Nekbone, and NekCEM
+    depends_on('nek5000@17.0', when='@1.0.0+nek')
+    depends_on('gslib@1.0.2', when='@1.0.0+nek')
+    depends_on('nekbone@17.0', when='@1.0.0+nek')
+    depends_on('nekcem@0b8bedd', when='@1.0.0+nek')
+
+    # PETSc, HPGMG
+    # For a +quickbuild we disable hdf5, and superlu-dist in PETSc.
+    # Ideally, these can be turned into recommendations to Spack for
+    # concretizing the PETSc spec, if Spack ever supports recommendations.
+    depends_on('petsc@3.8.3~hdf5~superlu-dist',
+               when='@1.0.0+petsc+quickbuild')
+    depends_on('petsc@3.8.3+mpi+double~int64', when='@1.0.0+petsc~mfem')
+    # The mfem petsc examples need the petsc variants +hypre, +suite-sparse,
+    # and +mumps:
+    depends_on('petsc@3.8.3+mpi+hypre+suite-sparse+mumps+double~int64',
+               when='@1.0.0+petsc+mfem')
+    depends_on('hpgmg@a0a5510df23b+fe', when='@1.0.0+petsc')
+
+    # MAGMA
+    depends_on('magma@2.3.0', when='@1.0.0+cuda')
+
+    # PUMI
+    depends_on('pumi@2.1.0', when='@1.0.0+pumi')
+
+    # MFEM, Laghos
+    depends_on('mfem@3.3.2+mpi+examples+miniapps', when='@1.0.0+mfem~petsc')
+    depends_on('mfem@3.3.2+mpi+petsc+examples+miniapps',
+               when='@1.0.0+mfem+petsc')
+    depends_on('laghos@1.0', when='@1.0.0+mfem')
+    # The next line seems to be necessary because the concretizer somehow
+    # decides that mfem requires 'hypre+internal-superlu' even though the mfem
+    # package lists simply 'hypre' as dependency. This is only an issue because
+    # petsc explicitly requires 'hypre~internal-superlu' which for the
+    # concretizer is a conflict.
+    depends_on('hypre~internal-superlu', when='@1.0.0+mfem')
+
+    # If using gcc version <= 4.8 build suite-sparse version <= 5.1.0
+    depends_on('suite-sparse@:5.1.0', when='@1.0.0%gcc@:4.8+mfem+petsc')
+
+    # Dummy install
+    def install(self, spec, prefix):
+        install('README.md', prefix)
diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py
index 637257053e..4317303d48 100644
--- a/var/spack/repos/builtin/packages/cereal/package.py
+++ b/var/spack/repos/builtin/packages/cereal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ceres-solver/package.py b/var/spack/repos/builtin/packages/ceres-solver/package.py
new file mode 100644
index 0000000000..a30e6468cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ceres-solver/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CeresSolver(CMakePackage):
+    """Ceres Solver is an open source C++ library for modeling and solving
+    large, complicated optimization problems. It can be used to solve
+    Non-linear Least Squares problems with bounds constraints and general
+    unconstrained optimization problems. It is a mature, feature rich, and
+    performant library that has been used in production at Google since 2010.
+    """
+
+    homepage = "http://ceres-solver.org"
+    url      = "http://ceres-solver.org/ceres-solver-1.12.0.tar.gz"
+
+    version('1.12.0', '278a7b366881cc45e258da71464114d9')
+
+    depends_on('eigen@3:')
+    depends_on('lapack')
+    depends_on('glog')
+
+    def cmake_args(self):
+        args = [
+            '-DSUITESPARSE=OFF',
+            '-DCXSPARSE=OFF',
+            '-DEIGENSPARSE=ON',
+            '-DLAPACK=ON',
+            '-DBUILD_SHARED_LIBS=ON',
+            '-DSCHUR_SPECIALIZATIONS=OFF'
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/cfitsio/package.py b/var/spack/repos/builtin/packages/cfitsio/package.py
index 49d71cdcab..2fb871cce2 100644
--- a/var/spack/repos/builtin/packages/cfitsio/package.py
+++ b/var/spack/repos/builtin/packages/cfitsio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,10 @@ class Cfitsio(AutotoolsPackage):
     """
 
     homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/'
-    url      = 'http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3410.tar.gz'
+    url      = 'http://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/cfitsio3450.tar.gz'
 
+    version('3.450', 'f470849bb43561d9a9b1925eeb7f7f0d')
+    version('3.420', '26e5c0dfb85b8d00f536e706305caa13')
     version('3.410', '8a4a66fcdd816aae41768baa0b025552')
     version('3.370', 'abebd2d02ba5b0503c633581e3bfa116')
 
diff --git a/var/spack/repos/builtin/packages/cgal/package.py b/var/spack/repos/builtin/packages/cgal/package.py
index 8961ee48bc..785402b5e8 100644
--- a/var/spack/repos/builtin/packages/cgal/package.py
+++ b/var/spack/repos/builtin/packages/cgal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,12 +14,14 @@ class Cgal(CMakePackage):
     molecular biology, medical imaging, computer graphics, and robotics.
     """
     homepage = 'http://www.cgal.org/'
-    url = 'https://github.com/CGAL/cgal/archive/releases/CGAL-4.7.tar.gz'
+    url      = 'https://github.com/CGAL/cgal/releases/download/releases/CGAL-4.11/CGAL-4.11.tar.xz'
 
-    version('4.9.1', 'df6517df3320bf6c9de2e1b0361738b9')
-    version('4.9', '7b628db3e5614347f776c046b7666089')
-    version('4.7', '4826714810f3b4c65cac96b90fb03b67')
-    version('4.6.3', 'e8ee2ecc8d2b09b94a121c09257b576d')
+    version('4.12', 'b12fd24dedfa889a04abfaea565a88bd')
+    version('4.11',  '0e9566046e402f8dc514caef11155864')
+    version('4.9.1', '820ef17ffa7ed87af6cc9918a961d966')
+    version('4.9',   'ee31343dbc4bf7b5b7501ec1650e9233')
+    version('4.7',   '623d91fb2ab0a35049dc6098a0f235cc')
+    version('4.6.3', '6953897544d41ffcc63ffe58b32a688f')
 
     variant('shared', default=True,
             description='Enables the build of shared libraries')
diff --git a/var/spack/repos/builtin/packages/cgm/package.py b/var/spack/repos/builtin/packages/cgm/package.py
index 8f2fa13f9a..11de8aa7df 100644
--- a/var/spack/repos/builtin/packages/cgm/package.py
+++ b/var/spack/repos/builtin/packages/cgm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cgns/package.py b/var/spack/repos/builtin/packages/cgns/package.py
index c9d46dc8e9..e101f84c27 100644
--- a/var/spack/repos/builtin/packages/cgns/package.py
+++ b/var/spack/repos/builtin/packages/cgns/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,31 +14,53 @@ class Cgns(CMakePackage):
     homepage = "http://cgns.github.io/"
     url      = "https://github.com/CGNS/CGNS/archive/v3.3.0.tar.gz"
 
+    version('3.3.1', '65c55998270c3e125e28ec5c3742e15d')
     version('3.3.0', '64e5e8d97144c1462bee9ea6b2a81d7f')
 
     variant('hdf5', default=True, description='Enable HDF5 interface')
+    variant('fortran', default=False, description='Enable Fortran interface')
+    variant('scoping', default=True, description='Enable scoping')
+    variant('mpi', default=True, description='Enable parallel cgns')
 
-    depends_on('cmake@2.8:', type='build')
-    depends_on('hdf5', when='+hdf5')
-
-    parallel = False
+    depends_on('hdf5', when='+hdf5~mpi')
+    depends_on('hdf5+mpi', when='+hdf5+mpi')
+    depends_on('mpi', when='+mpi')
 
     def cmake_args(self):
         spec = self.spec
-        cmake_args = []
+        options = []
 
-        if self.compiler.f77 and self.compiler.fc:
-            cmake_args.append('-DCGNS_ENABLE_FORTRAN=ON')
-        else:
-            cmake_args.append('-DCGNS_ENABLE_FORTRAN=OFF')
+        options.extend([
+            '-DCGNS_ENABLE_FORTRAN:BOOL=%s' % (
+                'ON' if '+fortran' in spec else 'OFF'),
+            '-DCGNS_ENABLE_SCOPING:BOOL=%s' % (
+                'ON' if '+scoping' in spec else 'OFF'),
+            '-DCGNS_ENABLE_PARALLEL:BOOL=%s' % (
+                'ON' if '+mpi' in spec else 'OFF'),
+            '-DCGNS_ENABLE_TESTS:BOOL=OFF',
+            '-DCGNS_BUILD_CGNSTOOLS:BOOL=OFF'
+        ])
 
-        if '+hdf5' in spec:
-            cmake_args.extend([
-                '-DCGNS_ENABLE_HDF5=ON',
-                '-DHDF5_DIR=%s' % spec['hdf5'].prefix
+        if '+mpi' in spec:
+            options.extend([
+                '-DCMAKE_C_COMPILER=%s'       % spec['mpi'].mpicc,
+                '-DCMAKE_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
+                '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc
             ])
 
+        if '+hdf5' in spec:
+            options.extend([
+                '-DCGNS_ENABLE_HDF5:BOOL=ON',
+                '-DHDF5_NEED_ZLIB:BOOL=ON',
+                '-DHDF5_INCLUDE_DIR:PATH=%s' % spec['hdf5'].prefix.include,
+                '-DHDF5_LIBRARY_DIR:PATH=%s' % spec['hdf5'].prefix.lib
+            ])
+            if '+mpi' in spec:
+                options.extend([
+                    '-DHDF5_NEED_MPI:BOOL=ON',
+                    '-DHDF5_ENABLE_PARALLEL:BOOL=ON'
+                ])
         else:
-            cmake_args.append('-DCGNS_ENABLE_HDF5=OFF')
+            options.extend(['-DCGNS_ENABLE_HDF5=OFF'])
 
-        return cmake_args
+        return options
diff --git a/var/spack/repos/builtin/packages/channelflow/package.py b/var/spack/repos/builtin/packages/channelflow/package.py
new file mode 100644
index 0000000000..1a396f0600
--- /dev/null
+++ b/var/spack/repos/builtin/packages/channelflow/package.py
@@ -0,0 +1,85 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Channelflow(CMakePackage):
+    """Channelflow is a software system for numerical analysis of the
+    incompressible fluid flow in channel geometries, written in C++.
+    """
+
+    homepage = 'https://github.com/epfl-ecps/channelflow'
+    url = 'https://github.com/epfl-ecps/channelflow.git'
+
+    version(
+        'develop',
+        git='https://github.com/epfl-ecps/channelflow.git',
+        branch='master'
+    )
+
+    variant('shared', default=True, description='Build shared libs')
+    variant('mpi', default=True, description='Enable MPI parallelism')
+    variant('hdf5', default=True, description='Enable support for HDF5 I/O')
+    variant(
+        'netcdf', default='serial', values=('none', 'serial', 'parallel'),
+        multi=False, description='Level of support for NetCDF I/O'
+    )
+    variant('python', default=False, description='Build python bindings')
+
+    depends_on('eigen')
+    depends_on('fftw')
+
+    # MPI related constraints
+    depends_on('mpi', when='+mpi')
+    depends_on('fftw+mpi', when='+mpi')
+
+    # Support for different I/O formats
+    depends_on('hdf5+cxx', when='+hdf5')
+    depends_on('netcdf', when='netcdf=serial')
+    depends_on('netcdf+mpi', when='netcdf=parallel')
+
+    # Python bindings
+    depends_on('boost+python', when='+python')
+
+    conflicts('~mpi', when='netcdf=parallel', msg='Parallel NetCDF requires MPI')
+    conflicts(
+        '+mpi', when='+python',
+        msg='Building python bindings is possible only for the serial code'
+    )
+    conflicts('~mpi', when='^mpi',
+              msg='There should be no MPI in the DAG when ~mpi is active')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        on_or_off = lambda predicate: 'ON' if predicate else 'OFF'
+
+        args = [
+            '-DBUILD_SHARED_LIBS:BOOL={0}'.format(
+                on_or_off('+shared' in spec)
+            ),
+            '-DUSE_MPI:BOOL={0}'.format(on_or_off('+mpi' in spec)),
+            '-DWITH_HDF5CXX:BOOL={0}'.format(on_or_off('+hdf5' in spec)),
+            '-DWITH_PYTHON:BOOL={0}'.format(on_or_off('+python' in spec))
+        ]
+
+        netcdf_str = {
+            'none': 'OFF',
+            'serial': 'Serial',
+            'parallel': 'Parallel'
+        }
+
+        args.append('-DWITH_NETCDF:STRING={0}'.format(
+            netcdf_str[spec.variants['netcdf'].value]
+        ))
+
+        # Set an MPI compiler for parallel builds
+        if '+mpi' in spec:
+            args.append(
+                '-DCMAKE_CXX_COMPILER:PATH={0}'.format(spec['mpi'].mpicxx)
+            )
+
+        return args
diff --git a/var/spack/repos/builtin/packages/charliecloud/package.py b/var/spack/repos/builtin/packages/charliecloud/package.py
new file mode 100644
index 0000000000..c9e59fd5ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/charliecloud/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Charliecloud(MakefilePackage):
+    """Lightweight user-defined software stacks for HPC."""
+
+    homepage = "https://hpc.github.io/charliecloud"
+    url      = "https://github.com/hpc/charliecloud/archive/v0.2.4.tar.gz"
+
+    version('0.9.3', sha256='f1bf032377b8845bc9a93b8a4fad6386161e35900223c0acc61d1f3aa3a87bc7')
+    version('0.9.2', sha256='8d0e4804d412beef720a66f886a0a78bce42f3269e880ebf11f602581f8047d4')
+    version('0.9.1', sha256='8e69150a271285da71ece7a09b48251ef6593f72207c5126741d9976aa737d95')
+    version('0.9.0', sha256='7e74cb16e31fd9d502198f7509bab14d1049ec68ba90b15e277e76f805db9458')
+    version('0.2.4', 'b112de661c2c360174b42c99022c1967')
+
+    @property
+    def install_targets(self):
+        return ['install', 'PREFIX=%s' % self.prefix]
diff --git a/var/spack/repos/builtin/packages/charm/package.py b/var/spack/repos/builtin/packages/charm/package.py
deleted file mode 100644
index b5568920d9..0000000000
--- a/var/spack/repos/builtin/packages/charm/package.py
+++ /dev/null
@@ -1,182 +0,0 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 platform
-import shutil
-import sys
-from spack import *
-
-
-class Charm(Package):
-    """Charm++ is a parallel programming framework in C++ supported by
-    an adaptive runtime system, which enhances user productivity and
-    allows programs to run portably from small multicore computers
-    (your laptop) to the largest supercomputers."""
-
-    homepage = "http://charmplusplus.org"
-    url      = "http://charm.cs.illinois.edu/distrib/charm-6.7.1.tar.gz"
-
-    version("6.7.1", "a8e20cf85e9c8721158f5bbd0ade48d9")
-    version("6.7.0", "35a39a7975f1954a7db2d76736158231")
-    version("6.6.1", "9554230f741e2599deaaac4d9d93d7ab")
-    version("6.6.0", "31e95901b3f7324d52107e6ad000fcc8")
-    version("6.5.1", "034d99458474a3ab96d8bede8a691a5d")
-
-    # Support OpenMPI; see
-    # <https://charm.cs.illinois.edu/redmine/issues/1206>
-    patch("mpi.patch")
-    # Ignore compiler warnings while configuring
-    patch("strictpass.patch")
-
-    # Communication mechanisms (choose exactly one)
-    # TODO: Support Blue Gene/Q PAMI, Cray GNI, Cray shmem, CUDA
-    variant(
-        'backend',
-        default='mpi',
-        values=('mpi', 'multicore', 'net', 'netlrts', 'verbs'),
-        description='Set the backend to use'
-    )
-
-    # Other options
-    # Something is off with PAPI -- there are build errors. Maybe
-    # Charm++ expects a particular version?
-    variant("papi", default=False, description="Enable PAPI integration")
-    variant("smp", default=True,
-            description=(
-                "Enable SMP parallelism (does not work with +multicore)"))
-    variant("tcp", default=False,
-            description="Use TCP as transport mechanism (requires +net)")
-    variant("shared", default=True, description="Enable shared link support")
-
-    # Note: We could add variants for AMPI, LIBS, bigemulator, msa, Tau
-
-    depends_on('mpi', when='backend=mpi')
-    depends_on("papi", when="+papi")
-
-    def install(self, spec, prefix):
-        target = "charm++"
-
-        comm = spec.variants['backend'].value
-
-        plat = sys.platform
-        if plat.startswith("linux"):
-            plat = "linux"
-        mach = platform.machine()
-
-        # Define Charm++ version names for various (plat, mach, comm)
-        # combinations. Note that not all combinations are supported.
-        versions = {
-            ("darwin", "i386", "multicore"): "multicore-darwin-x86",
-            ("darwin", "i386", "net"): "net-darwin-x86",
-            ("darwin", "x86_64", "mpi"): "mpi-darwin-x86_64",
-            ("darwin", "x86_64", "multicore"): "multicore-darwin-x86_64",
-            ("darwin", "x86_64", "net"): "net-darwin-x86_64",
-            ("darwin", "x86_64", "netlrts"): "netlrts-darwin-x86_64",
-            ("linux", "i386", "mpi"): "mpi-linux",
-            ("linux", "i386", "multicore"): "multicore-linux32",
-            ("linux", "i386", "net"): "net-linux",
-            ("linux", "i386", "netlrts"): "netlrts-linux",
-            ("linux", "x86_64", "mpi"): "mpi-linux-x86_64",
-            ("linux", "x86_64", "multicore"): "multicore-linux64",
-            ("linux", "x86_64", "net"): "net-linux-x86_64",
-            ("linux", "x86_64", "netlrts"): "netlrts-linux-x86_64",
-            ("linux", "x86_64", "verbs"): "verbs-linux-x86_64",
-        }
-        if (plat, mach, comm) not in versions:
-            raise InstallError(
-                "The communication mechanism %s is not supported "
-                "on a %s platform with a %s CPU" %
-                (comm, plat, mach))
-        version = versions[(plat, mach, comm)]
-
-        # We assume that Spack's compiler wrappers make this work. If
-        # not, then we need to query the compiler vendor from Spack
-        # here.
-        compiler = os.path.basename(self.compiler.cc)
-
-        options = [compiler]
-        if compiler == 'icc':
-            options.append('ifort')
-
-        options.extend([
-            "--with-production",   # Note: turn this into a variant
-            "-j%d" % make_jobs,
-            "--destination=%s" % prefix])
-
-        if 'backend=mpi' in spec:
-            # in intelmpi <prefix>/include and <prefix>/lib fails so --basedir
-            # cannot be used
-            options.extend([
-                '--incdir={0}'.format(incdir)
-                for incdir in spec["mpi"].headers.directories
-            ])
-            options.extend([
-                '--libdir={0}'.format(libdir)
-                for libdir in spec["mpi"].libs.directories
-            ])
-        if "+papi" in spec:
-            options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
-        if "+smp" in spec:
-            if 'backend=multicore' in spec:
-                # This is a Charm++ limitation; it would lead to a
-                # build error
-                raise InstallError("Cannot combine +smp with +multicore")
-            options.append("smp")
-        if "+tcp" in spec:
-            if 'backend=net' not in spec:
-                # This is a Charm++ limitation; it would lead to a
-                # build error
-                raise InstallError(
-                    "The +tcp variant requires "
-                    "the backend=net communication mechanism")
-            options.append("tcp")
-        if "+shared" in spec:
-            options.append("--build-shared")
-
-        # Call "make" via the build script
-        # Note: This builds Charm++ in the "tmp" subdirectory of the
-        # install directory. Maybe we could set up a symbolic link
-        # back to the build tree to prevent this? Alternatively, we
-        # could dissect the build script; the build instructions say
-        # this wouldn't be difficult.
-        build = Executable(join_path(".", "build"))
-        build(target, version, *options)
-
-        # Charm++'s install script does not copy files, it only creates
-        # symbolic links. Fix this.
-        for dirpath, dirnames, filenames in os.walk(prefix):
-            for filename in filenames:
-                filepath = join_path(dirpath, filename)
-                if os.path.islink(filepath):
-                    tmppath = filepath + ".tmp"
-                    # Skip dangling symbolic links
-                    try:
-                        shutil.copy2(filepath, tmppath)
-                        os.remove(filepath)
-                        os.rename(tmppath, filepath)
-                    except (IOError, OSError):
-                        pass
-        shutil.rmtree(join_path(prefix, "tmp"))
diff --git a/var/spack/repos/builtin/packages/charm/mpi.patch b/var/spack/repos/builtin/packages/charmpp/mpi.patch
index e909d5f876..e909d5f876 100644
--- a/var/spack/repos/builtin/packages/charm/mpi.patch
+++ b/var/spack/repos/builtin/packages/charmpp/mpi.patch
diff --git a/var/spack/repos/builtin/packages/charmpp/package.py b/var/spack/repos/builtin/packages/charmpp/package.py
new file mode 100644
index 0000000000..d192f3e156
--- /dev/null
+++ b/var/spack/repos/builtin/packages/charmpp/package.py
@@ -0,0 +1,244 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+import os
+import platform
+import shutil
+import sys
+from spack import *
+
+
+class Charmpp(Package):
+    """Charm++ is a parallel programming framework in C++ supported by
+    an adaptive runtime system, which enhances user productivity and
+    allows programs to run portably from small multicore computers
+    (your laptop) to the largest supercomputers."""
+
+    homepage = "http://charmplusplus.org"
+    url      = "http://charm.cs.illinois.edu/distrib/charm-6.8.2.tar.gz"
+    git      = "https://github.com/UIUC-PPL/charm.git"
+
+    version("develop", branch="charm")
+    version("6.8.2", "a887a34b638a5b2f7fcf7ff3c262496d")
+    version("6.8.1", "3e95ffa760909154ef16b643c9bb8193")
+    version("6.8.0", "54df066a5aefb0bbc1a263c2383c2bba")
+    version("6.7.1", "a8e20cf85e9c8721158f5bbd0ade48d9")
+    version("6.7.0", "35a39a7975f1954a7db2d76736158231")
+    version("6.6.1", "9554230f741e2599deaaac4d9d93d7ab")
+    version("6.6.0", "31e95901b3f7324d52107e6ad000fcc8")
+    version("6.5.1", "034d99458474a3ab96d8bede8a691a5d")
+
+    # Support OpenMPI; see
+    # <https://charm.cs.illinois.edu/redmine/issues/1206>
+    # Patch is no longer needed in versions 6.8.0+
+    patch("mpi.patch", when="@:6.7.1")
+
+    # Ignore compiler warnings while configuring
+    patch("strictpass.patch", when="@:6.8.2")
+
+    # Build targets
+    # "target" is reserved, so we have to use something else.
+    variant(
+        "build-target",
+        default="LIBS",
+        # AMPI also builds charm++, LIBS also builds AMPI and charm++
+        values=("charm++", "AMPI", "LIBS"),
+        description="Specify the target to build"
+    )
+
+    # Communication mechanisms (choose exactly one)
+    variant(
+        "backend",
+        default="netlrts",
+        values=("mpi", "multicore", "netlrts", "verbs", "gni",
+                "ofi", "pami", "pamilrts"),
+        description="Set the backend to use"
+    )
+
+    # Other options
+    variant("papi", default=False, description="Enable PAPI integration")
+    variant("syncft", default=False, description="Compile with Charm++ fault tolerance support")
+    variant("smp", default=True,
+            description=(
+                "Enable SMP parallelism (does not work with +multicore)"))
+    variant("tcp", default=False,
+            description="Use TCP as transport mechanism (requires +net)")
+    variant("omp", default=False, description="Support for the integrated LLVM OpenMP runtime")
+    variant("pthreads", default=False, description="Compile with pthreads Converse threads")
+    variant("cuda", default=False, description="Enable CUDA toolkit")
+
+    variant("shared", default=True, description="Enable shared link support")
+    variant("production", default=True, description="Build charm++ with all optimizations")
+    variant("tracing", default=False, description="Enable tracing modules")
+
+    # FIXME: backend=mpi also provides mpi, but spack does not support
+    # depends_on("mpi") and provides("mpi") in the same package currently.
+    for b in ['multicore', 'netlrts', 'verbs', 'gni', 'ofi', 'pami',
+              'pamilrts']:
+        provides('mpi@2', when='@6.7.1: build-target=AMPI backend={0}'.format(b))
+        provides('mpi@2', when='@6.7.1: build-target=LIBS backend={0}'.format(b))
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('MPICC',  join_path(self.prefix.bin, 'ampicc'))
+        spack_env.set('MPICXX', join_path(self.prefix.bin, 'ampicxx'))
+        spack_env.set('MPIF77', join_path(self.prefix.bin, 'ampif77'))
+        spack_env.set('MPIF90', join_path(self.prefix.bin, 'ampif90'))
+
+    def setup_dependent_package(self, module, dependent_spec):
+        self.spec.mpicc = join_path(self.prefix.bin, 'ampicc')
+        self.spec.mpicxx = join_path(self.prefix.bin, 'ampicxx')
+        self.spec.mpifc = join_path(self.prefix.bin, 'ampif90')
+        self.spec.mpif77 = join_path(self.prefix.bin, 'ampif77')
+
+    depends_on("mpi", when="backend=mpi")
+    depends_on("papi", when="+papi")
+    depends_on("cuda", when="+cuda")
+
+    # Git versions of Charm++ require automake and autoconf
+    depends_on("automake", when="@develop")
+    depends_on("autoconf", when="@develop")
+
+    conflicts("~tracing", "+papi")
+
+    conflicts("backend=multicore", "+smp")
+
+    def install(self, spec, prefix):
+        target = spec.variants["build-target"].value
+
+        plat = sys.platform
+        if plat.startswith("linux"):
+            plat = "linux"
+        elif plat.startswith("win"):
+            plat = "win"
+        elif plat.startswith("cnl"):
+            plat = "cnl"
+        elif plat.startswith("cnk"):
+            plat = "cnk"
+
+        mach = platform.machine()
+        if mach.startswith("ppc"):
+            mach = "ppc"
+        elif mach.startswith("arm"):
+            mach = "arm"
+
+        comm = spec.variants['backend'].value
+
+        # Define Charm++ version names for various (plat, mach, comm)
+        # combinations. Note that not all combinations are supported.
+        versions = {
+            ("darwin",  "x86_64",   "mpi"):         "mpi-darwin-x86_64",
+            ("darwin",  "x86_64",   "multicore"):   "multicore-darwin-x86_64",
+            ("darwin",  "x86_64",   "netlrts"):     "netlrts-darwin-x86_64",
+            ("linux",   "i386",     "mpi"):         "mpi-linux",
+            ("linux",   "i386",     "multicore"):   "multicore-linux",
+            ("linux",   "i386",     "netlrts"):     "netlrts-linux",
+            ("linux",   "i386",     "uth"):         "uth-linux",
+            ("linux",   "x86_64",   "mpi"):         "mpi-linux-x86_64",
+            ("linux",   "x86_64",   "multicore"):   "multicore-linux-x86_64",
+            ("linux",   "x86_64",   "netlrts"):     "netlrts-linux-x86_64",
+            ("linux",   "x86_64",   "verbs"):       "verbs-linux-x86_64",
+            ("linux",   "x86_64",   "ofi"):         "ofi-linux-x86_64",
+            ("linux",   "x86_64",   "uth"):         "uth-linux-x86_64",
+            ("linux",   "ppc",      "mpi"):         "mpi-linux-ppc",
+            ("linux",   "ppc",      "multicore"):   "multicore-linux-ppc",
+            ("linux",   "ppc",      "netlrts"):     "netlrts-linux-ppc",
+            ("linux",   "ppc",      "pami"):        "pami-linux-ppc64le",
+            ("linux",   "ppc",      "verbs"):       "verbs-linux-ppc64le",
+            ("linux",   "arm",      "netlrts"):     "netlrts-linux-arm7",
+            ("linux",   "arm",      "multicore"):   "multicore-arm7",
+            ("win",     "x86_64",   "mpi"):         "mpi-win-x86_64",
+            ("win",     "x86_64",   "multicore"):   "multicore-win-x86_64",
+            ("win",     "x86_64",   "netlrts"):     "netlrts-win-x86_64",
+            ("cnl",     "x86_64",   "gni"):         "gni-crayxc",
+            ("cnl",     "x86_64",   "mpi"):         "mpi-crayxc",
+            ("cnk",     "x86_64",   "mpi"):         "mpi-bluegeneq",
+            ("cnk",     "x86_64",   "pami"):        "pami-bluegeneq",
+            ("cnk",     "x86_64",   "pamilrts"):    "pamilrts-bluegeneq",
+        }
+        if (plat, mach, comm) not in versions:
+            raise InstallError(
+                "The communication mechanism %s is not supported "
+                "on a %s platform with a %s CPU" %
+                (comm, plat, mach))
+        version = versions[(plat, mach, comm)]
+
+        # We assume that Spack's compiler wrappers make this work. If
+        # not, then we need to query the compiler vendor from Spack
+        # here.
+        options = [
+            os.path.basename(self.compiler.cc),
+            os.path.basename(self.compiler.fc),
+            "-j%d" % make_jobs,
+            "--destination=%s" % prefix,
+        ]
+
+        if 'backend=mpi' in spec:
+            # in intelmpi <prefix>/include and <prefix>/lib fails so --basedir
+            # cannot be used
+            options.extend([
+                '--incdir={0}'.format(incdir)
+                for incdir in spec["mpi"].headers.directories
+            ])
+            options.extend([
+                '--libdir={0}'.format(libdir)
+                for libdir in spec["mpi"].libs.directories
+            ])
+        if "+papi" in spec:
+            options.extend(["papi", "--basedir=%s" % spec["papi"].prefix])
+        if "+smp" in spec:
+            options.append("smp")
+        if "+tcp" in spec:
+            if 'backend=netlrts' not in spec:
+                # This is a Charm++ limitation; it would lead to a
+                # build error
+                raise InstallError(
+                    "The +tcp variant requires "
+                    "the backend=netlrts communication mechanism")
+            options.append("tcp")
+        if "+omp" in spec:
+            options.append("omp")
+        if "+pthreads" in spec:
+            options.append("pthreads")
+        if "+cuda" in spec:
+            options.append("cuda")
+
+        if "+shared" in spec:
+            options.append("--build-shared")
+        if "+production" in spec:
+            options.append("--with-production")
+        if "+tracing" in spec:
+            options.append("--enable-tracing")
+
+        # Call "make" via the build script
+        # Note: This builds Charm++ in the "tmp" subdirectory of the
+        # install directory. Maybe we could set up a symbolic link
+        # back to the build tree to prevent this? Alternatively, we
+        # could dissect the build script; the build instructions say
+        # this wouldn't be difficult.
+        build = Executable(join_path(".", "build"))
+        build(target, version, *options)
+
+        # Charm++'s install script does not copy files, it only creates
+        # symbolic links. Fix this.
+        for dirpath, dirnames, filenames in os.walk(prefix):
+            for filename in filenames:
+                filepath = join_path(dirpath, filename)
+                if os.path.islink(filepath):
+                    tmppath = filepath + ".tmp"
+                    # Skip dangling symbolic links
+                    try:
+                        copy(filepath, tmppath)
+                        os.remove(filepath)
+                        os.rename(tmppath, filepath)
+                    except (IOError, OSError):
+                        pass
+        shutil.rmtree(join_path(prefix, "tmp"))
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_build(self):
+        make('-C', join_path(self.stage.path, 'charm/tests'),
+             'test', parallel=False)
diff --git a/var/spack/repos/builtin/packages/charm/strictpass.patch b/var/spack/repos/builtin/packages/charmpp/strictpass.patch
index 44aa4fbd38..44aa4fbd38 100644
--- a/var/spack/repos/builtin/packages/charm/strictpass.patch
+++ b/var/spack/repos/builtin/packages/charmpp/strictpass.patch
diff --git a/var/spack/repos/builtin/packages/chatterbug/package.py b/var/spack/repos/builtin/packages/chatterbug/package.py
new file mode 100644
index 0000000000..abaf8e9bd9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/chatterbug/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Chatterbug(MakefilePackage):
+    """A suite of communication-intensive proxy applications that mimic
+       commonly found communication patterns in HPC codes. These codes can be
+       used as synthetic codes for benchmarking, or for trace generation using
+       Score-P / OTF2.
+    """
+    tags = ['proxy-app']
+
+    homepage = "https://chatterbug.readthedocs.io"
+    git      = "https://github.com/LLNL/chatterbug.git"
+
+    version('develop', branch='master')
+    version('1.0', tag='v1.0')
+
+    variant('scorep', default=False, description='Build with Score-P tracing')
+
+    depends_on('mpi')
+    depends_on('scorep', when='+scorep')
+
+    @property
+    def build_targets(self):
+        targets = []
+
+        targets.append('MPICXX = {0}'.format(self.spec['mpi'].mpicxx))
+
+        return targets
+
+    def build(self, spec, prefix):
+        if "+scorep" in spec:
+            make('WITH_OTF2=YES')
+        else:
+            make()
+
+    def install(self, spec, prefix):
+        if "+scorep" in spec:
+            make('WITH_OTF2=YES', 'PREFIX=' + spec.prefix, 'install')
+        else:
+            make('PREFIX=' + spec.prefix, 'install')
diff --git a/var/spack/repos/builtin/packages/check/package.py b/var/spack/repos/builtin/packages/check/package.py
index c87a982fa5..d28c428137 100644
--- a/var/spack/repos/builtin/packages/check/package.py
+++ b/var/spack/repos/builtin/packages/check/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/chlorop/package.py b/var/spack/repos/builtin/packages/chlorop/package.py
index 2bccd6d951..c6a9fd6514 100644
--- a/var/spack/repos/builtin/packages/chlorop/package.py
+++ b/var/spack/repos/builtin/packages/chlorop/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import distutils.dir_util
 import os
 
 
@@ -47,7 +27,7 @@ class Chlorop(Package):
 
     def install(self, spec, prefix):
         os.rename('chlorop', 'bin/chlorop')
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix)
 
     def setup_environment(self, spack_env, run_env):
         run_env.set('CHLOROP', self.prefix)
diff --git a/var/spack/repos/builtin/packages/chombo/package.py b/var/spack/repos/builtin/packages/chombo/package.py
index 8dd5155199..29b113b782 100644
--- a/var/spack/repos/builtin/packages/chombo/package.py
+++ b/var/spack/repos/builtin/packages/chombo/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
 import glob
 
 
@@ -34,12 +14,13 @@ class Chombo(MakefilePackage):
        logically rectangular (i.e. Cartesian) grids."""
 
     homepage = "https://commons.lbl.gov/display/chombo"
-    url      = "http://bitbucket.org/drhansj/chombo-xsdk.git"
+    git      = "http://bitbucket.org/drhansj/chombo-xsdk.git"
+
+    tags = ['ecp', 'ecp-apps']
 
     # Use whatever path Brian V. and Terry L. agreed upon, but preserve version
-    version('3.2', git='http://bitbucket.org/drhansj/chombo-xsdk.git', commit='71d856c')
-    version('develop', git='http://bitbucket.org/drhansj/chombo-xsdk.git', tag='master')
-#    version('3.2', svn='https://anag-repo.lbl.gov/svn/Chombo/release/3.2')
+    version('3.2', commit='71d856c')
+    version('develop', tag='master')
 
     variant('mpi', default=True, description='Enable MPI parallel support')
     variant('hdf5', default=True, description='Enable HDF5 support')
@@ -70,8 +51,8 @@ class Chombo(MakefilePackage):
         # Set remaining variables in Make.defs.local
         # Make.defs.local.template.patch ensures lines for USE_TIMER,
         # USE_LAPACK and lapackincflags are present
-        copyfile('./lib/mk/Make.defs.local.template',
-                 './lib/mk/Make.defs.local')
+        copy('./lib/mk/Make.defs.local.template',
+             './lib/mk/Make.defs.local')
 
         defs_file = FileFilter('./lib/mk/Make.defs.local')
 
diff --git a/var/spack/repos/builtin/packages/cistem/package.py b/var/spack/repos/builtin/packages/cistem/package.py
new file mode 100644
index 0000000000..52b7dad557
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cistem/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Cistem(AutotoolsPackage):
+    """cisTEM is user-friendly software to process cryo-EM images of
+       macromolecular complexes and obtain high-resolution 3D reconstructions
+       from them."""
+
+    homepage = "https://cistem.org/"
+    url      = "https://cistem.org/system/tdf/upload3/cistem-1.0.0-beta-source-code.tar.gz?file=1&type=cistem_details&id=37&force=0"
+
+    version('1.0.0-beta', '479f395b30ad630df3cbba9c56eb29c2')
+
+    depends_on('wx@3.0.2')
+    depends_on('fftw')
diff --git a/var/spack/repos/builtin/packages/cityhash/package.py b/var/spack/repos/builtin/packages/cityhash/package.py
index 67ee8561a3..4712e309dc 100644
--- a/var/spack/repos/builtin/packages/cityhash/package.py
+++ b/var/spack/repos/builtin/packages/cityhash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,10 @@ class Cityhash(AutotoolsPackage):
     """CityHash, a family of hash functions for strings."""
 
     homepage = "https://github.com/google/cityhash"
-    url      = "https://github.com/google/cityhash"
+    git      = "https://github.com/google/cityhash.git"
 
-    version('2013-07-31', git='https://github.com/google/cityhash.git',
-            commit='8af9b8c2b889d80c22d6bc26ba0df1afb79a30db')
-    version('master', branch='master',
-            git='https://github.com/google/cityhash.git')
+    version('master', branch='master')
+    version('2013-07-31', commit='8af9b8c2b889d80c22d6bc26ba0df1afb79a30db')
 
     def configure_args(self):
         return ['--enable-sse4.2']
diff --git a/var/spack/repos/builtin/packages/clamr/package.py b/var/spack/repos/builtin/packages/clamr/package.py
index 3608c64ca2..ce3f9b236d 100644
--- a/var/spack/repos/builtin/packages/clamr/package.py
+++ b/var/spack/repos/builtin/packages/clamr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,10 @@ class Clamr(CMakePackage):
     """
 
     homepage = "https://github.com/lanl/CLAMR"
-    url      = "https://github.com/lanl/CLAMR.git"
+    git      = "https://github.com/lanl/CLAMR.git"
     tags     = ['proxy-app']
 
-    version('master', git='https://github.com/lanl/CLAMR.git')
+    version('master')
 
     variant(
         'graphics', default='opengl',
@@ -46,6 +27,7 @@ class Clamr(CMakePackage):
         values=('single', 'mixed', 'full'),
         description='single, mixed, or full double precision values')
 
+    depends_on('cmake@3.1:')
     depends_on('mpi')
     depends_on('mpe', when='graphics=mpe')
 
diff --git a/var/spack/repos/builtin/packages/clapack/package.py b/var/spack/repos/builtin/packages/clapack/package.py
new file mode 100644
index 0000000000..70d159b336
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clapack/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Clapack(MakefilePackage):
+    """CLAPACK is a f2c'ed version of LAPACK.
+
+       The CLAPACK library was built using a Fortran to C conversion utility
+    called f2c.  The entire Fortran 77 LAPACK library is run through f2c to
+    obtain C code, and then modified to improve readability.  CLAPACK's goal
+    is to provide LAPACK for someone who does not have access to a Fortran
+    compiler."""
+
+    homepage = "http://www.netlib.org/clapack/"
+    url      = "http://www.netlib.org/clapack/clapack.tgz"
+
+    version('3.2.1', '040da31f3a7d4fbc9ac376c748d18d1f')
+
+    variant('external-blas', default=True,
+            description='Build with external BLAS (ATLAS here).')
+
+    depends_on('atlas', when='+external-blas')
+
+    def edit(self, spec, prefix):
+        copy('make.inc.example', 'make.inc')
+        if '+external-blas' in spec:
+            make_inc = FileFilter('make.inc')
+            make_inc.filter(r'^BLASLIB.*',
+                            'BLASLIB = ../../libcblaswr.a -lcblas -latlas')
+            makefile = FileFilter('Makefile')
+            makefile.filter(r'^lib.*',
+                            'lib: variants lapacklib tmglib')
+
+    def build(self, spec, prefix):
+        make('f2clib')
+        make('cblaswrap' if '+external-blas' in spec else 'blaslib')
+        make('lib')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/claw/package.py b/var/spack/repos/builtin/packages/claw/package.py
new file mode 100644
index 0000000000..d905faf2bc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/claw/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Claw(CMakePackage):
+    """CLAW Compiler targets performance portability problem in climate and
+       weather application written in Fortran. From a single source code, it
+       generates architecture specific code decorated with OpenMP or OpenACC"""
+
+    homepage = 'https://claw-project.github.io/'
+    git      = 'https://github.com/claw-project/claw-compiler.git'
+    maintainers = ['clementval']
+
+    version('1.1.0', commit='16b165a443b11b025a77cad830b1280b8c9bcf01', submodules=True)
+
+    depends_on('cmake@3.0:', type='build')
+    depends_on('java@7:')
+    depends_on('ant@1.9:')
+    depends_on('libxml2')
+    depends_on('bison')
+
+    def cmake_args(self):
+        args = []
+        spec = self.spec
+
+        args.append('-DOMNI_CONF_OPTION=--with-libxml2={0}'.
+                    format(spec['libxml2'].prefix))
+
+        args.append('-DCMAKE_Fortran_COMPILER={0}'.
+                    format(self.compiler.fc))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/cleaveland4/package.py b/var/spack/repos/builtin/packages/cleaveland4/package.py
index 910ef7cb12..c2b7fb0272 100644
--- a/var/spack/repos/builtin/packages/cleaveland4/package.py
+++ b/var/spack/repos/builtin/packages/cleaveland4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cleverleaf/package.py b/var/spack/repos/builtin/packages/cleverleaf/package.py
index 0e40d3ff4c..65e6ec5f43 100644
--- a/var/spack/repos/builtin/packages/cleverleaf/package.py
+++ b/var/spack/repos/builtin/packages/cleverleaf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,16 +12,20 @@ class Cleverleaf(CMakePackage):
        Livermore National Laboratory. The primary goal of CleverLeaf is
        to evaluate the application of AMR to the Lagrangian-Eulerian
        hydrodynamics scheme used by CloverLeaf.
-
     """
 
     homepage = "http://uk-mac.github.io/CleverLeaf/"
-    url      = "https://github.com/UK-MAC/CleverLeaf/tarball/master"
+    git      = "https://github.com/UK-MAC/CleverLeaf_ref.git"
 
-    version('develop', git='https://github.com/UK-MAC/CleverLeaf_ref.git',
-            branch='develop')
+    version('develop', branch='develop')
 
     depends_on('samrai@3.8.0:')
     depends_on('hdf5+mpi')
     depends_on('boost')
     depends_on('cmake@3.1:', type='build')
+
+    def flag_handler(self, name, flags):
+        if self.spec.satisfies('%intel') and name in ['cppflags', 'cxxflags']:
+            flags.append(self.compiler.cxx11_flag)
+
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/clfft/package.py b/var/spack/repos/builtin/packages/clfft/package.py
index d626e8964a..9851439a09 100644
--- a/var/spack/repos/builtin/packages/clfft/package.py
+++ b/var/spack/repos/builtin/packages/clfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/clhep/package.py b/var/spack/repos/builtin/packages/clhep/package.py
index f1f1d2db96..8db6263539 100644
--- a/var/spack/repos/builtin/packages/clhep/package.py
+++ b/var/spack/repos/builtin/packages/clhep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -33,22 +14,26 @@ class Clhep(CMakePackage):
     list_url = "https://proj-clhep.web.cern.ch/proj-clhep/"
     list_depth = 1
 
-    version('2.3.4.4', '8b8a33d0d19213b60d6c22ce5fc93761')
-    version('2.3.4.3', '6941279f70d69492fff1aa955f3f2562')
-    version('2.3.4.2', '1e7a9046c9ad0b347d6812f8031191da')
-    version('2.3.4.1', '5ae85571ff3d8b2c481c3f95ea89b751')
-    version('2.3.4.0', 'dd899d0791a823221927f97edf190348')
-    version('2.3.3.2', '8b9f8d7f4dccec6d058b3a078f66b6a3')
-    version('2.3.3.1', '456ef9d262ef4e776af984bfbe2f48c7')
-    version('2.3.3.0', '3637eaa6750606e589e52c9e155a382e')
-    version('2.3.2.2', '567b304b0fa017e1e9fbf199f456ebe9')
-    version('2.3.2.1', '064903cb5c23b54f520d04ca6230b901')
-    version('2.3.1.1', '16efca7641bc118c9d217cc96fe90bf5')
-    version('2.3.1.0', 'b084934fc26a4182a08c09c292e19161')
-    version('2.3.0.0', 'a00399a2ca867f2be902c22fc71d7e2e')
-    version('2.2.0.8', '5a23ed3af785ac100a25f6cb791846af')
-    version('2.2.0.5', '1584e8ce6ebf395821aed377df315c7c')
-    version('2.2.0.4', '71d2c7c2e39d86a0262e555148de01c1')
+    version('2.4.1.0', sha256='d14736eb5c3d21f86ce831dc1afcf03d423825b35c84deb6f8fd16773528c54d')
+    version('2.4.0.4', sha256='eb013841c57990befa1e977a11a552ab8328733c1c3b6cecfde86da40dc22113')
+    version('2.4.0.2', sha256='1e9891c5badb718c24933e7a5c6ee4d64fd4d5cf3a40c150ad18e864ec86b8a4')
+    version('2.4.0.1', sha256='4c7e2c6ac63e0237100e4ddcbfdc3d7e7dc6592f95bdbdcc0e43a6892b9fd6e0')
+    version('2.4.0.0', sha256='5e5cf284323898b4c807db6e684d65d379ade65fe0e93f7b10456890a6dee8cc')
+    version('2.3.4.6', sha256='3e53947036f8570c7a08bed670a862426dbca17328afcecd6c875d8487fef204')
+    version('2.3.4.5', sha256='1199d04626cb8bc1307e282b143018691077cc61fe2f286a382030262eda8764')
+    version('2.3.4.4', sha256='e54de15ffa5108a1913c4910845436345c89ddb83480cd03277a795fafabfb9d')
+    version('2.3.4.3', sha256='1019479265f956bd660c11cb439e1443d4fd1655e8d51accf8b1e703e4262dff')
+    version('2.3.4.2', sha256='6d1e15ccbe1ca6e71d541e78ca7e8c9f3d986ee0da5177a4b8cda00c619dc691')
+    version('2.3.3.2', sha256='4e69a5afb1b7ecc435395195140afc85bbbb9f4d3572f59451c3882f3015a7c1')
+    version('2.3.3.1', sha256='cd74bfae4773620dd0c7cc9c1696a08386931d7e47a3906aa632cc5cb44ed6bd')
+    version('2.3.3.0', sha256='0bcae1bed8d3aa4256e3a553a4f60484312f2121dcc83492a40f08a70881c8c0')
+    version('2.3.2.2', sha256='885481ae32c2f31c3b7f14a5e5d68bc56dc3df0c597be464d7ffa265b8a5a1af')
+    version('2.3.1.1', sha256='0e2b170df99176feb0aa4f20ea3b33463193c086682749790c5b9b79388d0ff4')
+    version('2.3.1.0', sha256='66272ae3100d3aec096b1298e1e24ec25b80e4dac28332b45ec3284023592963')
+    version('2.3.0.0', sha256='63e77f4f34baa5eaa0adb1ca2438734f2d6f5ca112d830650dd005a6109f2397')
+    version('2.2.0.8', sha256='f735e236b1f023ba7399269733b2e84eaed4de615081555b1ab3af25a1e92112')
+    version('2.2.0.5', sha256='92e8b5d32ae96154edd27d0c641ba048ad33cb69dd4f1cfb72fc578770a34818')
+    version('2.2.0.4', sha256='9bf7fcd9892313c8d1436bc4a4a285a016c4f8e81e1fc65bdf6783207ae57550')
 
     variant('cxx11', default=True, description="Compile using c++11 dialect.")
     variant('cxx14', default=False, description="Compile using c++14 dialect.")
diff --git a/var/spack/repos/builtin/packages/clingo/package.py b/var/spack/repos/builtin/packages/clingo/package.py
new file mode 100644
index 0000000000..942d502c52
--- /dev/null
+++ b/var/spack/repos/builtin/packages/clingo/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Clingo(CMakePackage):
+    """Clingo: A grounder and solver for logic programs
+
+       Clingo is part of the Potassco project for Answer Set
+       Programming (ASP). ASP offers a simple and powerful modeling
+       language to describe combinatorial problems as logic
+       programs. The clingo system then takes such a logic program and
+       computes answer sets representing solutions to the given
+       problem."""
+
+    homepage = "https://potassco.org/clingo/"
+    url      = "https://github.com/potassco/clingo/archive/v5.2.2.tar.gz"
+
+    version('5.2.2', 'd46a1567f772eebad85c6300d55d2cc3')
+
+    depends_on('doxygen', type=('build'))
+    depends_on('python')
+
+    def cmake_args(self):
+        try:
+            self.compiler.cxx14_flag
+        except UnsupportedCompilerFlag:
+            InstallError('clingo requires a C++14-compliant C++ compiler')
+
+        args = ['-DCLINGO_BUILD_WITH_PYTHON=ON',
+                '-DCLING_BUILD_PY_SHARED=ON',
+                '-DPYCLINGO_USE_INSTALL_PREFIX=ON',
+                '-DCLINGO_BUILD_WITH_LUA=OFF']
+        return args
diff --git a/var/spack/repos/builtin/packages/cloc/package.py b/var/spack/repos/builtin/packages/cloc/package.py
index a5f7f1ecf5..4b5c81b5a8 100644
--- a/var/spack/repos/builtin/packages/cloc/package.py
+++ b/var/spack/repos/builtin/packages/cloc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cloog/package.py b/var/spack/repos/builtin/packages/cloog/package.py
index b8fad45331..48322a3b22 100644
--- a/var/spack/repos/builtin/packages/cloog/package.py
+++ b/var/spack/repos/builtin/packages/cloog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cloverleaf/package.py b/var/spack/repos/builtin/packages/cloverleaf/package.py
index 1f23d5398c..27b6403b56 100644
--- a/var/spack/repos/builtin/packages/cloverleaf/package.py
+++ b/var/spack/repos/builtin/packages/cloverleaf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import glob
 
diff --git a/var/spack/repos/builtin/packages/cloverleaf3d/package.py b/var/spack/repos/builtin/packages/cloverleaf3d/package.py
index 0d00922325..4879b33473 100644
--- a/var/spack/repos/builtin/packages/cloverleaf3d/package.py
+++ b/var/spack/repos/builtin/packages/cloverleaf3d/package.py
@@ -1,27 +1,8 @@
-#############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import glob
 
diff --git a/var/spack/repos/builtin/packages/clustalo/package.py b/var/spack/repos/builtin/packages/clustalo/package.py
index 5f3911ac29..ebf6daab9a 100644
--- a/var/spack/repos/builtin/packages/clustalo/package.py
+++ b/var/spack/repos/builtin/packages/clustalo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/clustalw/package.py b/var/spack/repos/builtin/packages/clustalw/package.py
index 478fb702ce..0ebd8986c9 100644
--- a/var/spack/repos/builtin/packages/clustalw/package.py
+++ b/var/spack/repos/builtin/packages/clustalw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cmake/nag-response-files.patch b/var/spack/repos/builtin/packages/cmake/nag-response-files.patch
new file mode 100644
index 0000000000..07dc4a1aa1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cmake/nag-response-files.patch
@@ -0,0 +1,9 @@
+diff --git a/Modules/Compiler/NAG-Fortran.cmake b/Modules/Compiler/NAG-Fortran.cmake
+index 39aae1883..9973febc3 100644
+--- a/Modules/Compiler/NAG-Fortran.cmake
++++ b/Modules/Compiler/NAG-Fortran.cmake
+@@ -34,3 +34,4 @@ set(CMAKE_Fortran_FORMAT_FIXED_FLAG "-fixed")
+ set(CMAKE_Fortran_FORMAT_FREE_FLAG "-free")
+ set(CMAKE_Fortran_COMPILE_OPTIONS_PIC "-PIC")
+ set(CMAKE_Fortran_COMPILE_OPTIONS_PIE "-PIC")
++set(CMAKE_Fortran_RESPONSE_FILE_LINK_FLAG "-Wl,@")
diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py
index 150936d1cb..a43c9b7ffb 100644
--- a/var/spack/repos/builtin/packages/cmake/package.py
+++ b/var/spack/repos/builtin/packages/cmake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,20 @@ class Cmake(Package):
     list_url = 'https://cmake.org/files/'
     list_depth = 1
 
+    version('3.12.3',   'acbf13af31a741794106b76e5d22448b004a66485fc99f6d7df4d22e99da164a')
+    version('3.12.2',   '6e7c550cfa1c2e216b35903dc70d80af')
+    version('3.12.1',   '10109246a51102bfda45ff3935275fbf')
+    version('3.12.0',   'ab4aa7df9301c94cdd6f8ee4fe66458b')
+    version('3.11.4',   '72e168b3bad2f9c34dcebbad7af56ff0')
+    version('3.11.3',   '3f923154ed47128f13b08eacd207d9ee')
+    version('3.11.2',   'd2d554c05fc07cfae7846d2aa205f12a')
+    version('3.11.1',   '12a3177477e4e2c7bc514193d421dafe')
+    version('3.11.0',   'f3ebc79b5dec85b49abe75958ffa1a03')
+    version('3.10.3',   '1c38c67295ca696aeafd8c059d748b38')
+    version('3.10.2',   '732808e17fc14dc8cee50d51518c34eb')
+    version('3.10.1',   '9a726e5ec69618b172aa4b06d18c3998')
+    version('3.10.0',   'f3f8e70ca3055f3cd288f89ff233057e')
+    version('3.9.6',    '084b1c8b2efc1c1ba432dea37243c0ae')
     version('3.9.4',    '33769e001bdcd788f565bf378692e5ae')
     version('3.9.0',    '180e23b4c9b55915d271b315297f6951')
     version('3.8.2',    'b5dff61f6a7f1305271ab3f6ae261419')
@@ -78,8 +73,14 @@ class Cmake(Package):
     # https://gitlab.kitware.com/cmake/cmake/issues/16226
     patch('intel-c-gnu11.patch', when='@3.6.0:3.6.1')
 
+    # https://gitlab.kitware.com/cmake/cmake/issues/18232
+    patch('nag-response-files.patch', when='@3.7:3.12')
+
     conflicts('+qt', when='^qt@5.4.0')  # qt-5.4.0 has broken CMake modules
 
+    # https://gitlab.kitware.com/cmake/cmake/issues/18166
+    conflicts('%intel', when='@3.11.0:3.11.4')
+
     phases = ['bootstrap', 'build', 'install']
 
     def url_for_version(self, version):
diff --git a/var/spack/repos/builtin/packages/cmocka/package.py b/var/spack/repos/builtin/packages/cmocka/package.py
index 7598532476..3a09ae9100 100644
--- a/var/spack/repos/builtin/packages/cmocka/package.py
+++ b/var/spack/repos/builtin/packages/cmocka/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cmor/package.py b/var/spack/repos/builtin/packages/cmor/package.py
index 59a0330324..54aa1ae7c6 100644
--- a/var/spack/repos/builtin/packages/cmor/package.py
+++ b/var/spack/repos/builtin/packages/cmor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,7 @@ class Cmor(AutotoolsPackage):
     homepage = "http://cmor.llnl.gov"
     url = "https://github.com/PCMDI/cmor/archive/3.1.2.tar.gz"
 
+    version('3.3.0', 'cfdeeddab1aedb823e26ec38723bd67e')
     version('3.2.0', 'b48105105d4261012c19cd65e89ff7a6')
     version('3.1.2', '72f7227159c901e4bcf80d2c73a8ce77')
 
@@ -43,7 +25,7 @@ class Cmor(AutotoolsPackage):
     depends_on('uuid')
     depends_on('netcdf')
     depends_on('udunits2')
-    depends_on('hdf5@:1.8')
+    depends_on('hdf5@:1.8.19')
 
     extends('python', when='+python')
     depends_on('python@:2.8', when='+python')
diff --git a/var/spack/repos/builtin/packages/cnmem/package.py b/var/spack/repos/builtin/packages/cnmem/package.py
index 7b068e1ede..cda66b37e2 100644
--- a/var/spack/repos/builtin/packages/cnmem/package.py
+++ b/var/spack/repos/builtin/packages/cnmem/package.py
@@ -1,34 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Cnmem(CMakePackage):
     """CNMem mempool for CUDA devices"""
+
     homepage = "https://github.com/NVIDIA/cnmem"
+    git      = "https://github.com/NVIDIA/cnmem.git"
 
-    version('git', git='https://github.com/NVIDIA/cnmem.git', branch="master")
+    version('git', branch='master')
 
     depends_on('cmake@2.8.8:', type='build')
diff --git a/var/spack/repos/builtin/packages/cnpy/package.py b/var/spack/repos/builtin/packages/cnpy/package.py
index 7c868b62b4..15bd3da174 100644
--- a/var/spack/repos/builtin/packages/cnpy/package.py
+++ b/var/spack/repos/builtin/packages/cnpy/package.py
@@ -1,34 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
+import sys
+
 
 class Cnpy(CMakePackage):
     """cnpy: library to read/write .npy and .npz files in C/C++."""
 
     homepage = "https://github.com/rogersce/cnpy"
-    url      = "https://github.com/rogersce/cnpy"
+    git      = "https://github.com/rogersce/cnpy.git"
+
+    version('master', branch='master')
+
+    def cmake_args(self):
+        args = []
+        if sys.platform == 'darwin':
+            args.extend(['-DCMAKE_MACOSX_RPATH=ON'])
 
-    version('master', git='https://github.com/rogersce/cnpy.git', branch="master")
+        return args
diff --git a/var/spack/repos/builtin/packages/cns-nospec/package.py b/var/spack/repos/builtin/packages/cns-nospec/package.py
deleted file mode 100644
index f4b56d7596..0000000000
--- a/var/spack/repos/builtin/packages/cns-nospec/package.py
+++ /dev/null
@@ -1,109 +0,0 @@
-##############################################################################
-# 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/spack/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 glob
-
-
-class CnsNospec(MakefilePackage):
-    """A simple, explicit, stencil-based test code for integrating
-    the compressible Navier-Stokes equations. The code uses
-    8th order finite differences in space and a 3rd order,
-    low-storage TVD RK algorithm in time."""
-
-    homepage = "https://ccse.lbl.gov/ExaCT/index.html"
-    url      = "https://ccse.lbl.gov/ExaCT/CNS_Nospec.tgz"
-    tags     = ['proxy-app']
-
-    version('master', '14ff5be62539d829b30b17281688ee3f')
-
-    variant('mpi', default=True, description='Build with MPI support')
-    variant('debug', default=False, description='Build with debugging')
-    variant('omp', default=False, description='Build with OpenMP support')
-    variant('prof', default=False, description='Build with profiling')
-
-    depends_on('mpi', when='+mpi')
-    depends_on('gmake', type='build')
-
-    build_directory = 'MiniApps/CNS_NoSpec'
-
-    def edit(self, spec, prefix):
-        def_file = FileFilter('Tools/F_mk/GMakedefs.mak')
-        def_file.filter('tdir = t/.*', 'tdir := t/$(suf)')
-        def_file.filter('hdir = t/.*', 'hdir := t/html')
-        def_file.filter('include $(BOXLIB_HOME)/Tools/F_mk/GMakeMPI.mak', '#')
-
-        if '+mpi' in spec:
-            def_file.filter('FC.*:=.*', 'FC = {0}'.format(spec['mpi'].mpifc))
-            def_file.filter('F90.*:=.*', 'F90 = {0}'.format(spec['mpi'].mpifc))
-            def_file.filter(
-                'mpi_include_dir =.*',
-                'mpi_include_dir = {0}'.format(spec['mpi'].prefix.include))
-            def_file.filter(
-                'mpi_lib_dir =.*',
-                'mpi_lib_dir = {0}'.format(spec['mpi'].prefix.lib))
-
-        with working_dir(self.build_directory):
-            makefile = FileFilter('GNUmakefile')
-            if '+mpi' in spec:
-                makefile.filter('MPI .*', 'MPI := t')
-            if '+debug' in spec:
-                makefile.filter('NDEBUG.*', '#')
-            if '+omp' in spec:
-                makefile.filter('OMP.*', 'OMP := t')
-            if '+prof' in spec:
-                makefile.filter('PROF.*', 'PROF := t')
-
-            if self.compiler.name == 'gcc':
-                makefile.filter('COMP .*', 'COMP = gfortran')
-            if self.compiler.name == 'intel':
-                makefile.filter('COMP .*', 'COMP = Intel')
-            if self.compiler.name == 'pgi':
-                makefile.filter('COMP .*', 'COMP = PGI')
-            if self.compiler.name == 'xl':
-                makefile.filter('COMP .*', 'COMP = IBM')
-            if self.compiler.name == 'cce':
-                makefile.filter('COMP .*', 'COMP = Cray')
-
-    @property
-    def build_targets(self):
-        spec = self.spec
-        if '+mpi' in spec:
-            return ['CC = {0}'.format(spec['mpi'].mpicc),
-                    'CXX = {0}'.format(spec['mpi'].mpicxx)]
-        else:
-            return []
-
-    def build(self, spec, prefix):
-        with working_dir(self.build_directory):
-            gmake()
-
-    def install(self, spec, prefix):
-        mkdirp(prefix.bin)
-        files = glob.glob(join_path(self.build_directory, '*.exe'))
-        for f in files:
-            install(f, prefix.bin)
-        install('README.txt', prefix)
-        install('license.txt', prefix)
-        install(join_path(self.build_directory, 'README'), prefix)
diff --git a/var/spack/repos/builtin/packages/cntk/package.py b/var/spack/repos/builtin/packages/cntk/package.py
index b55c547e10..efb8cb7ca3 100644
--- a/var/spack/repos/builtin/packages/cntk/package.py
+++ b/var/spack/repos/builtin/packages/cntk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Cntk(Package):
 
     homepage = "https://www.microsoft.com/en-us/research/product/cognitive-toolkit"
     url      = "https://github.com/Microsoft/CNTK/archive/v2.0.tar.gz"
+    git      = "https://github.com/Microsoft/CNTK.git"
 
-    version('master', git='https://github.com/Microsoft/CNTK.git', branch='master')
+    version('master', branch='master')
     version('2.0', '8038780f1169ceea578e5ef4d69e4c6f')
 
     variant('opencv', default=False, description="Enable OpenCV support.")
diff --git a/var/spack/repos/builtin/packages/cntk1bitsgd/package.py b/var/spack/repos/builtin/packages/cntk1bitsgd/package.py
index 6d30792b09..c046bc34e4 100644
--- a/var/spack/repos/builtin/packages/cntk1bitsgd/package.py
+++ b/var/spack/repos/builtin/packages/cntk1bitsgd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from os import listdir
 
@@ -32,10 +13,10 @@ class Cntk1bitsgd(Package):
     the Computational Network Toolkit (CNTK)."""
 
     homepage = "https://github.com/CNTK-components/CNTK1bitSGD"
+    git      = "https://github.com/CNTK-components/CNTK1bitSGD.git"
 
-    version('master', git='https://github.com/CNTK-components/CNTK1bitSGD.git')
-    version('c8b77d', git='https://github.com/CNTK-components/CNTK1bitSGD.git',
-            commit='c8b77d6e325a4786547b27624890276c1483aed1')
+    version('master')
+    version('c8b77d', commit='c8b77d6e325a4786547b27624890276c1483aed1')
 
     def install(self, spec, prefix):
         mkdirp(prefix.include)
diff --git a/var/spack/repos/builtin/packages/codar-cheetah/package.py b/var/spack/repos/builtin/packages/codar-cheetah/package.py
index de39fb2a79..ba559342ba 100644
--- a/var/spack/repos/builtin/packages/codar-cheetah/package.py
+++ b/var/spack/repos/builtin/packages/codar-cheetah/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class CodarCheetah(Package):
@@ -32,14 +12,14 @@ class CodarCheetah(Package):
     """
 
     homepage = "https://github.com/CODARcode/cheetah"
-    url = "https://github.com/CODARcode/cheetah/archive/v0.1.tar.gz"
+    url      = "https://github.com/CODARcode/cheetah/archive/v0.1.tar.gz"
+    git      = "https://github.com/CODARcode/cheetah.git"
 
+    version('develop', branch='master')
     version('0.1', '6918021f74fa7a2f1de26c0bb31a63ef')
-    version('develop', git='https://github.com/CODARcode/cheetah.git',
-            branch='master')
 
     depends_on('python@3:', type=('build', 'run'))
     depends_on('savanna')
 
     def install(self, spec, prefix):
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/codes/codes-1.0.0.patch b/var/spack/repos/builtin/packages/codes/codes-1.0.0.patch
new file mode 100644
index 0000000000..d0fbaf7ebb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/codes/codes-1.0.0.patch
@@ -0,0 +1,16 @@
+diff --git a/configure.ac b/configure.ac
+index b3650e5..5ec28b4 100755
+--- a/configure.ac
++++ b/configure.ac
+@@ -222,9 +222,9 @@ AS_IF([test "x$enable_valgrind_clean" = "xyes"], [
+ 
+ 
+ dnl AC_CONFIG_FILES([src/iokernellang/codesparser.y])
+-if test "x$srcdir" != "x."; then
++AS_IF([test ! -d tests/conf], [
+     AC_CONFIG_LINKS([tests/conf:$srcdir/tests/conf])
+-fi
++])
+ 
+ AC_CONFIG_FILES([Makefile])
+ 
diff --git a/var/spack/repos/builtin/packages/codes/package.py b/var/spack/repos/builtin/packages/codes/package.py
new file mode 100644
index 0000000000..e3c5053e9a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/codes/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Codes(AutotoolsPackage):
+    """ CO-Design of multi-layer Exascale Storage (CODES) simulation framework
+    """
+
+    homepage = "http://www.mcs.anl.gov/projects/codes"
+    git      = "https://xgitlab.cels.anl.gov/codes/codes.git"
+
+    version('develop', branch='master')
+    version('1.0.0', tag='1.0.0')
+
+    variant('dumpi', default=False, description="Enable DUMPI support")
+
+    # Build dependencies
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('bison', type='build')
+    depends_on('flex', type='build')
+
+    depends_on('mpi')
+    depends_on('ross')
+    depends_on('sst-dumpi', when="+dumpi")
+
+    # add the local m4 directory to the search path
+    autoreconf_extra_args = ["-Im4"]
+    # Testing if srcdir is '.' in configure.ac does not work with spack
+    patch('codes-1.0.0.patch')
+
+    def configure_args(self):
+        spec = self.spec
+
+        config_args = [
+            "CC=%s" % spec['mpi'].mpicc,
+            "CXX=%s" % spec['mpi'].mpicxx,
+            "PKG_CONFIG_PATH=%s/pkgconfig" % spec['ross'].prefix.lib]
+
+        if "+dumpi" in spec:
+            config_args.extend([
+                '--with-dumpi=%s'.format(spec['sst-dumpi'].prefix)])
+
+        return config_args
diff --git a/var/spack/repos/builtin/packages/coevp/package.py b/var/spack/repos/builtin/packages/coevp/package.py
index 655f91062e..300e441fe0 100644
--- a/var/spack/repos/builtin/packages/coevp/package.py
+++ b/var/spack/repos/builtin/packages/coevp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -39,9 +20,9 @@ class Coevp(MakefilePackage):
     proxy application provides the adaptive sampling support."""
 
     homepage = 'https://github.com/exmatex/CoEVP'
+    git      = 'https://github.com/exmatex/CoEVP.git'
 
-    version('develop', git='https://github.com/exmatex/CoEVP.git',
-            branch='master')
+    version('develop', branch='master')
 
     variant('mpi', default=True, description='Build with MPI Support')
     variant('silo', default=False, description='Build with silo Support')
diff --git a/var/spack/repos/builtin/packages/cohmm/package.py b/var/spack/repos/builtin/packages/cohmm/package.py
index 70e87c70ff..a68e3a58e5 100644
--- a/var/spack/repos/builtin/packages/cohmm/package.py
+++ b/var/spack/repos/builtin/packages/cohmm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -35,13 +16,12 @@ class Cohmm(MakefilePackage):
     tags = ['proxy-app']
 
     homepage = "http://www.exmatex.org/cohmm.html"
-    url = "https://github.com/exmatex/CoHMM/archive/sad.tar.gz"
+    git      = "https://github.com/exmatex/CoHMM.git"
 
-    version('develop', git='https://github.com/exmatex/CoHMM.git',
-            branch='sad')
+    version('develop', branch='sad')
 
     variant('openmp', default=True, description='Build with OpenMP Support')
-    variant('gnuplot', default=True, description='Enable gnu plot Support')
+    variant('gnuplot', default=False, description='Enable gnu plot Support')
     depends_on('gnuplot', when='+gnuplot')
 
     def edit(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/coinhsl/package.py b/var/spack/repos/builtin/packages/coinhsl/package.py
index a97c0274d3..55c695dbc9 100644
--- a/var/spack/repos/builtin/packages/coinhsl/package.py
+++ b/var/spack/repos/builtin/packages/coinhsl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -44,4 +25,39 @@ class Coinhsl(AutotoolsPackage):
     homepage = "http://www.hsl.rl.ac.uk/ipopt/"
     url = "file://{0}/coinhsl-archive-2014.01.17.tar.gz".format(os.getcwd())
 
-    version('2014.01.17', '9eb3dd40ed034814ed8dfee75b281180c1d9d2ae')
+    # CoinHSL has a few versions that vary with respect to stability/features
+    # and licensing terms.
+
+    # Version 2015.06.23 is a full-featured "release candidate"
+    # version available via an "academic license" that can be used for
+    # personal teaching and research purposes only. For a full list of
+    # conditions, see http://www.hsl.rl.ac.uk/academic.html.
+    version('2015.06.23', sha256='3e955a2072f669b8f357ae746531b37aea921552e415dc219a5dd13577575fb3')
+
+    # Version 2014.01.17 is a full-featured "stable" version available
+    # via an "academic license" that can be used for personal teaching
+    # and research purposes only.
+    version('2014.01.17', sha256='ed49fea62692c5d2f928d4007988930da9ff9a2e944e4c559d028671d122437b')
+
+    # Version 2014.01.10 only has MA27, MA28, and MC19, and is
+    # available as a "personal license" that is free to all, and
+    # permits commercial use, but *not redistribution* (emphasis from
+    # original source).
+    version('2014.01.10', sha256='7c2be60a3913b406904c66ee83acdbd0709f229b652c4e39ee5d0876f6b2e907',
+            preferred=True)
+
+    # CoinHSL fails to build in parallel
+    parallel = False
+
+    variant('blas', default=False, description='Link to external BLAS library')
+
+    depends_on('blas', when='+blas')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        if spec.satisfies('+blas'):
+            args.append('--with-blas={0}'.format(spec['blas'].libs.ld_flags))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/colm/package.py b/var/spack/repos/builtin/packages/colm/package.py
new file mode 100644
index 0000000000..bf27dabd39
--- /dev/null
+++ b/var/spack/repos/builtin/packages/colm/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Colm(AutotoolsPackage):
+    """Colm Programming Language
+    Colm is a programming language designed for the analysis and
+    transformation of computer languages. Colm is influenced primarily
+    by TXL. It is in the family of program transformation languages.
+    """
+
+    homepage = "http://www.colm.net/open-source/colm"
+    url      = "http://www.colm.net/files/colm/colm-0.12.0.tar.gz"
+
+    version('0.12.0', '079a1ed44f71d48a349d954096c8e411')
diff --git a/var/spack/repos/builtin/packages/colordiff/package.py b/var/spack/repos/builtin/packages/colordiff/package.py
new file mode 100644
index 0000000000..cd62f2347f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/colordiff/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Colordiff(Package):
+    """Colorful diff utility."""
+
+    homepage = "https://www.colordiff.org"
+    url      = "https://www.colordiff.org/colordiff-1.0.18.tar.gz"
+
+    version('1.0.18', '07658f09a44f30a3b5c1cea9c132baed')
+
+    depends_on('perl')
+
+    def install(self, spec, prefix):
+        make("INSTALL_DIR=" + prefix.bin, "ETC_DIR=" + prefix.etc,
+             "MAN_DIR=" + prefix.man, 'install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/comd/package.py b/var/spack/repos/builtin/packages/comd/package.py
index ad7689beee..3c6d762473 100644
--- a/var/spack/repos/builtin/packages/comd/package.py
+++ b/var/spack/repos/builtin/packages/comd/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-import shutil
 
 
 class Comd(MakefilePackage):
@@ -37,18 +16,19 @@ class Comd(MakefilePackage):
     versions of CoMD will be released to incorporate the lessons learned from
     the co-design process."""
 
-    tags = ['proxy-app', 'ecp-proxy-app']
+    tags = ['proxy-app']
 
     homepage = "http://www.exmatex.org/comd.html"
     url      = "https://github.com/ECP-copa/CoMD/archive/v1.1.tar.gz"
+    git      = "https://github.com/ECP-copa/CoMD.git"
 
+    version('develop', branch='master')
     version('1.1', '5051310a8d2c93cccba63de40bcfaa78')
-    version('develop', git='https://github.com/ECP-copa/CoMD', branch='master')
 
     variant('mpi', default=True, description='Build with MPI support')
     variant('openmp', default=False, description='Build with OpenMP support')
     variant('precision', default=True, description='Toggle Precesion Options')
-    variant('graphs', default=True, description='Enable graph visuals')
+    variant('graphs', default=False, description='Enable graph visuals')
 
     depends_on('mpi', when='+mpi')
     depends_on('graphviz', when='+graphs')
@@ -57,7 +37,7 @@ class Comd(MakefilePackage):
 
     def edit(self, spec, prefix):
         with working_dir('src-mpi') or working_dir('src-openmp'):
-            shutil.copy('Makefile.vanilla', 'Makefile')
+            copy('Makefile.vanilla', 'Makefile')
 
     @property
     def build_targets(self):
diff --git a/var/spack/repos/builtin/packages/commons-lang/package.py b/var/spack/repos/builtin/packages/commons-lang/package.py
new file mode 100644
index 0000000000..dcb40f8869
--- /dev/null
+++ b/var/spack/repos/builtin/packages/commons-lang/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CommonsLang(Package):
+    """The standard Java libraries fail to provide enough methods for
+    manipulation of its core classes. Apache Commons Lang provides these
+    extra methods.
+
+    Lang provides a host of helper utilities for the java.lang API, notably
+    String manipulation methods, basic numerical methods, object reflection,
+    concurrency, creation and serialization and System properties. Additionally
+    it contains basic enhancements to java.util.Date and a series of utilities
+    dedicated to help with building methods, such as hashCode, toString and
+    equals."""
+
+    homepage = "http://commons.apache.org/proper/commons-lang/"
+    url      = "https://archive.apache.org/dist/commons/lang/binaries/commons-lang-2.6-bin.tar.gz"
+
+    version('2.6', '444075803459bffebfb5e28877861d23')
+    version('2.4', '5ff5d890e46021a2dbd77caba80f90f2')
+
+    extends('jdk')
+    depends_on('java@2:', type='run')
+
+    def install(self, spec, prefix):
+        install('commons-lang-{0}.jar'.format(self.version), prefix)
diff --git a/var/spack/repos/builtin/packages/commons-lang3/package.py b/var/spack/repos/builtin/packages/commons-lang3/package.py
new file mode 100644
index 0000000000..543b20d9f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/commons-lang3/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CommonsLang3(Package):
+    """The standard Java libraries fail to provide enough methods for
+    manipulation of its core classes. Apache Commons Lang provides these
+    extra methods.
+
+    Lang provides a host of helper utilities for the java.lang API, notably
+    String manipulation methods, basic numerical methods, object reflection,
+    concurrency, creation and serialization and System properties. Additionally
+    it contains basic enhancements to java.util.Date and a series of utilities
+    dedicated to help with building methods, such as hashCode, toString and
+    equals."""
+
+    homepage = "http://commons.apache.org/proper/commons-lang/"
+    url      = "https://archive.apache.org/dist/commons/lang/binaries/commons-lang3-3.7-bin.tar.gz"
+
+    version('3.7', 'c7577443639dc6efadc80f1cbc7fced5')
+
+    extends('jdk')
+    depends_on('java@7:', type='run')
+
+    def install(self, spec, prefix):
+        install('commons-lang3-{0}.jar'.format(self.version), prefix)
diff --git a/var/spack/repos/builtin/packages/commons-logging/package.py b/var/spack/repos/builtin/packages/commons-logging/package.py
new file mode 100644
index 0000000000..41483f8c61
--- /dev/null
+++ b/var/spack/repos/builtin/packages/commons-logging/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CommonsLogging(Package):
+    """When writing a library it is very useful to log information. However
+    there are many logging implementations out there, and a library cannot
+    impose the use of a particular one on the overall application that the
+    library is a part of.
+
+    The Logging package is an ultra-thin bridge between different logging
+    implementations. A library that uses the commons-logging API can be used
+    with any logging implementation at runtime. Commons-logging comes with
+    support for a number of popular logging implementations, and writing
+    adapters for others is a reasonably simple task."""
+
+    homepage = "http://commons.apache.org/proper/commons-logging/"
+    url      = "http://archive.apache.org/dist/commons/logging/binaries/commons-logging-1.2-bin.tar.gz"
+
+    version('1.2',   'ac043ce7ab3374eb4ed58354a6b2c3de')
+    version('1.1.3', 'b132f9a1e875677ae6b449406cff2a78')
+    version('1.1.1', 'e5de09672af9b386c30a311654d8541a')
+
+    extends('jdk')
+    depends_on('java', type='run')
+
+    def install(self, spec, prefix):
+        install('commons-logging-{0}.jar'.format(self.version), prefix)
diff --git a/var/spack/repos/builtin/packages/compiz/package.py b/var/spack/repos/builtin/packages/compiz/package.py
index 5387483879..9ce3526b89 100644
--- a/var/spack/repos/builtin/packages/compiz/package.py
+++ b/var/spack/repos/builtin/packages/compiz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/compositeproto/package.py b/var/spack/repos/builtin/packages/compositeproto/package.py
index b4a041e7a2..b160bbd5a5 100644
--- a/var/spack/repos/builtin/packages/compositeproto/package.py
+++ b/var/spack/repos/builtin/packages/compositeproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Compositeproto(AutotoolsPackage):
 
     version('0.4.2', '2dea7c339432b3363faf2d29c208e7b5')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
index 6793a391c3..d2820b92ec 100644
--- a/var/spack/repos/builtin/packages/conduit/package.py
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import socket
@@ -46,8 +27,11 @@ class Conduit(Package):
     coupling between packages in-core, serialization, and I/O tasks."""
 
     homepage = "http://software.llnl.gov/conduit"
-    url = "https://github.com/LLNL/conduit/releases/download/v0.3.0/conduit-v0.3.0-src-with-blt.tar.gz"
+    url      = "https://github.com/LLNL/conduit/releases/download/v0.3.0/conduit-v0.3.0-src-with-blt.tar.gz"
+    git      = "https://github.com/LLNL/conduit.git"
 
+    version('master', branch='master', submodules=True)
+    version('0.3.1', 'b98d1476199a46bde197220cd9cde042')
     version('0.3.0', '6396f1d1ca16594d7c66d4535d4f898e')
     # note: checksums on github automatic release source tars changed ~9/17
     version('0.2.1', 'ed7358af3463ba03f07eddd6a6e626ff')
@@ -55,11 +39,6 @@ class Conduit(Package):
 
     maintainers = ['cyrush']
 
-    version('master',
-            git='https://github.com/LLNL/conduit.git',
-            branch="master",
-            submodules=True)
-
     ###########################################################################
     # package variants
     ###########################################################################
@@ -79,6 +58,9 @@ class Conduit(Package):
 
     # variants for dev-tools (docs, etc)
     variant("doc", default=False, description="Build Conduit's documentation")
+    # doxygen support is wip, since doxygen has several dependencies
+    # we want folks to explicitly opt in to building doxygen
+    variant("doxygen", default=False, description="Build Conduit's Doxygen documentation")
 
     ###########################################################################
     # package dependencies
@@ -95,11 +77,9 @@ class Conduit(Package):
     #######################
     # we need a shared version of python b/c linking with static python lib
     # causes duplicate state issues when running compiled python modules.
-    depends_on("python+shared")
+    depends_on("python+shared", when="+python")
     extends("python", when="+python")
-    # TODO: blas and lapack are disabled due to build
-    # issues Cyrus experienced on OSX 10.11.6
-    depends_on("py-numpy~blas~lapack", when="+python", type=('build', 'run'))
+    depends_on("py-numpy", when="+python", type=('build', 'run'))
 
     #######################
     # I/O Packages
@@ -108,9 +88,10 @@ class Conduit(Package):
     # experienced on BGQ. When on, the static build tries
     # to link against shared libs.
     #
-    # we are not using hdf5's mpi or fortran features.
-    depends_on("hdf5~cxx~mpi~fortran", when="+hdf5+shared")
-    depends_on("hdf5~shared~cxx~mpi~fortran", when="+hdf5~shared")
+    # Use HDF5 1.8, for wider output compatibly
+    # variants reflect we are not using hdf5's mpi or fortran features.
+    depends_on("hdf5@1.8.19:1.8.999~cxx~mpi~fortran", when="+hdf5+shared")
+    depends_on("hdf5@1.8.19:1.8.999~shared~cxx~mpi~fortran", when="+hdf5~shared")
 
     # we are not using silo's fortran features
     depends_on("silo~fortran", when="+silo+shared")
@@ -125,7 +106,7 @@ class Conduit(Package):
     # Documentation related
     #######################
     depends_on("py-sphinx", when="+python+doc", type='build')
-    depends_on("doxygen", when="+doc")
+    depends_on("doxygen", when="+doc+doxygen")
 
     def url_for_version(self, version):
         """
@@ -136,11 +117,12 @@ class Conduit(Package):
             return "https://github.com/LLNL/conduit/archive/v0.2.0.tar.gz"
         elif v == "0.2.1":
             return "https://github.com/LLNL/conduit/archive/v0.2.1.tar.gz"
-        elif v == "0.3.0":
-            # conduit uses BLT (https://github.com/llnl/blt) as a submodule,
-            # since github does not automatically package source from
-            # submodules, conduit provides a custom src tarball
-            return "https://github.com/LLNL/conduit/releases/download/v0.3.0/conduit-v0.3.0-src-with-blt.tar.gz"
+        else:
+            # starting with v 0.3.0, conduit uses BLT
+            # (https://github.com/llnl/blt) as a submodule, since github does
+            # not automatically package source from submodules, conduit
+            # provides a custom src tarball
+            return "https://github.com/LLNL/conduit/releases/download/v{0}/conduit-v{1}-src-with-blt.tar.gz".format(v, v)
         return url
 
     def install(self, spec, prefix):
@@ -148,7 +130,13 @@ class Conduit(Package):
         Build and install Conduit.
         """
         with working_dir('spack-build', create=True):
-            host_cfg_fname = self.create_host_config(spec, prefix)
+            py_site_pkgs_dir = None
+            if "+python" in spec:
+                py_site_pkgs_dir = site_packages_dir
+
+            host_cfg_fname = self.create_host_config(spec,
+                                                     prefix,
+                                                     py_site_pkgs_dir)
             cmake_args = []
             # if we have a static build, we need to avoid any of
             # spack's default cmake settings related to rpaths
@@ -163,14 +151,26 @@ class Conduit(Package):
             cmake(*cmake_args)
             make()
             make("install")
+            # install copy of host config for provenance
+            install(host_cfg_fname, prefix)
 
-    def create_host_config(self, spec, prefix):
+    def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         """
         This method creates a 'host-config' file that specifies
         all of the options used to configure and build conduit.
 
-        For more details see about 'host-config' files see:
+        For more details about 'host-config' files see:
             http://software.llnl.gov/conduit/building.html
+
+        Note:
+          The `py_site_pkgs_dir` arg exists to allow a package that
+          subclasses this package provide a specific site packages
+          dir when calling this function. `py_site_pkgs_dir` should
+          be an absolute path or `None`.
+
+          This is necessary because the spack `site_packages_dir`
+          var will not exist in the base class. For more details
+          on this issue see: https://github.com/spack/spack/issues/6261
         """
 
         #######################
@@ -209,9 +209,9 @@ class Conduit(Package):
                 raise RuntimeError(msg)
             cmake_exe = cmake_exe.path
 
-        host_cfg_fname = "%s-%s-%s.cmake" % (socket.gethostname(),
-                                             sys_type,
-                                             spec.compiler)
+        host_cfg_fname = "%s-%s-%s-conduit.cmake" % (socket.gethostname(),
+                                                     sys_type,
+                                                     spec.compiler)
 
         cfg = open(host_cfg_fname, "w")
         cfg.write("##################################\n")
@@ -256,10 +256,10 @@ class Conduit(Package):
             cfg.write("# python from spack \n")
             cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE",
                       spec['python'].command.path))
-            # install module to standard style site packages dir
-            # so we can support spack activate
-            cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
-                                        site_packages_dir))
+            # only set dest python site packages dir if passed
+            if py_site_pkgs_dir:
+                cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
+                                            py_site_pkgs_dir))
         else:
             cfg.write(cmake_cache_entry("ENABLE_PYTHON", "OFF"))
 
@@ -270,10 +270,10 @@ class Conduit(Package):
             sphinx_build_exe = join_path(spec['py-sphinx'].prefix.bin,
                                          "sphinx-build")
             cfg.write(cmake_cache_entry("SPHINX_EXECUTABLE", sphinx_build_exe))
-
-            cfg.write("# doxygen from uberenv\n")
-            doxygen_exe = spec['doxygen'].command.path
-            cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
+            if "+doxygen" in spec:
+                cfg.write("# doxygen from uberenv\n")
+                doxygen_exe = spec['doxygen'].command.path
+                cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
         else:
             cfg.write(cmake_cache_entry("ENABLE_DOCS", "OFF"))
 
@@ -290,6 +290,16 @@ class Conduit(Package):
                                         spec['mpi'].mpicxx))
             cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
                                         spec['mpi'].mpifc))
+            mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
+            if os.path.isfile(mpiexe_bin):
+                # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE
+                # vs the older versions which expect MPIEXEC
+                if self.spec["cmake"].satisfies('@3.10:'):
+                    cfg.write(cmake_cache_entry("MPIEXEC_EXECUTABLE",
+                                                mpiexe_bin))
+                else:
+                    cfg.write(cmake_cache_entry("MPIEXEC",
+                                                mpiexe_bin))
         else:
             cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF"))
 
diff --git a/var/spack/repos/builtin/packages/constype/package.py b/var/spack/repos/builtin/packages/constype/package.py
index 731217b527..5996386854 100644
--- a/var/spack/repos/builtin/packages/constype/package.py
+++ b/var/spack/repos/builtin/packages/constype/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Constype(AutotoolsPackage):
 
     version('1.0.4', '2333b9ac9fd32e58b05afa651c4590a3')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/converge/package.py b/var/spack/repos/builtin/packages/converge/package.py
index 7a17436ed3..3d0cf54808 100644
--- a/var/spack/repos/builtin/packages/converge/package.py
+++ b/var/spack/repos/builtin/packages/converge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import glob
 import os
 
diff --git a/var/spack/repos/builtin/packages/coreutils/package.py b/var/spack/repos/builtin/packages/coreutils/package.py
index fa4298a42a..312f6f7375 100644
--- a/var/spack/repos/builtin/packages/coreutils/package.py
+++ b/var/spack/repos/builtin/packages/coreutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Coreutils(AutotoolsPackage):
        operating system.
     """
     homepage = "http://www.gnu.org/software/coreutils/"
-    url      = "http://ftp.gnu.org/gnu/coreutils/coreutils-8.26.tar.xz"
+    url      = "https://ftpmirror.gnu.org/coreutils/coreutils-8.26.tar.xz"
 
+    version('8.29', '960cfe75a42c9907c71439f8eb436303')
     version('8.26', 'd5aa2072f662d4118b9f4c63b94601a6')
     version('8.23', 'abed135279f87ad6762ce57ff6d89c41')
 
diff --git a/var/spack/repos/builtin/packages/corset/package.py b/var/spack/repos/builtin/packages/corset/package.py
index 7b5ef695cb..aa9c036090 100644
--- a/var/spack/repos/builtin/packages/corset/package.py
+++ b/var/spack/repos/builtin/packages/corset/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cosmomc/package.py b/var/spack/repos/builtin/packages/cosmomc/package.py
index c3788c53ce..e1bb2ee9bc 100644
--- a/var/spack/repos/builtin/packages/cosmomc/package.py
+++ b/var/spack/repos/builtin/packages/cosmomc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import fnmatch
diff --git a/var/spack/repos/builtin/packages/cosp2/package.py b/var/spack/repos/builtin/packages/cosp2/package.py
index 2bd69e73d3..a702a48c5f 100644
--- a/var/spack/repos/builtin/packages/cosp2/package.py
+++ b/var/spack/repos/builtin/packages/cosp2/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import shutil
 
 
 class Cosp2(MakefilePackage):
@@ -37,10 +17,9 @@ class Cosp2(MakefilePackage):
     tags = ['proxy-app']
 
     homepage = "http://www.exmatex.org/cosp2.html"
-    url = "https://github.com/exmatex/CoSP2/archive/master.tar.gz"
+    git      = "https://github.com/exmatex/CoSP2.git"
 
-    version('master', git='https://github.com/exmatex/CoSP2.git',
-            description='master')
+    version('master', branch='master')
 
     variant('double', default=True,
             description='Build with double precision.')
@@ -63,7 +42,7 @@ class Cosp2(MakefilePackage):
             if '+double' in spec:
                 filter_file('DOUBLE_PRECISION = O.*', 'DOUBLE_PRECISION = OFF',
                             'Makefile.vanilla')
-            shutil.copy('Makefile.vanilla', 'Makefile')
+            copy('Makefile.vanilla', 'Makefile')
 
     def install(self, spec, prefix):
         install_tree('bin/', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cp2k/package.py b/var/spack/repos/builtin/packages/cp2k/package.py
index 53eb29f336..e810c84eb3 100644
--- a/var/spack/repos/builtin/packages/cp2k/package.py
+++ b/var/spack/repos/builtin/packages/cp2k/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
-import shutil
 import copy
 
 from spack import *
@@ -36,33 +16,39 @@ class Cp2k(Package):
     """
     homepage = 'https://www.cp2k.org'
     url = 'https://sourceforge.net/projects/cp2k/files/cp2k-3.0.tar.bz2'
+    list_url = 'https://sourceforge.net/projects/cp2k/files/'
 
+    version('5.1', 'f25cf301aec471d7059179de4dac3ee7')
     version('4.1', 'b0534b530592de15ac89828b1541185e')
     version('3.0', 'c05bc47335f68597a310b1ed75601d35')
 
     variant('mpi', default=True, description='Enable MPI support')
+    variant('smm', default='libxsmm', values=('libxsmm', 'libsmm', 'none'),
+            description='Library for small matrix multiplications')
     variant('plumed', default=False, description='Enable PLUMED support')
 
     depends_on('python', type='build')
 
     depends_on('lapack')
     depends_on('blas')
-    depends_on('fftw')
-    depends_on('libint@:1.2', when='@3.0,4.1')
+    depends_on('fftw@3:')
+    depends_on('libint@1.1.4:1.2', when='@3.0:5.999')
+    depends_on('libxsmm', when='smm=libxsmm')
+    depends_on('libxc@2.2.2:')
 
     depends_on('mpi@2:', when='+mpi')
     depends_on('scalapack', when='+mpi')
+    depends_on('elpa@2011.12:2016.13', when='+mpi')
+    depends_on('pexsi+fortran@0.9.0:0.9.999', when='+mpi@:4.999')
+    depends_on('pexsi+fortran@0.10.0:', when='+mpi@5.0:')
     depends_on('plumed+shared+mpi', when='+plumed+mpi')
     depends_on('plumed+shared~mpi', when='+plumed~mpi')
-    depends_on('pexsi+fortran', when='+mpi')
 
     # Apparently cp2k@4.1 needs an "experimental" version of libwannier.a
     # which is only available contacting the developer directly. See INSTALL
     # in the stage of cp2k@4.1
     depends_on('wannier90', when='@3.0+mpi')
-    depends_on('elpa', when='+mpi')
 
-    # TODO : add dependency on libsmm, libxsmm
     # TODO : add dependency on CUDA
 
     parallel = False
@@ -78,24 +64,31 @@ class Cp2k(Package):
         with open(makefile, 'w') as mkf:
             # Optimization flags
             optflags = {
-                'gcc': ['-O2',
-                        '-ffast-math',
-                        '-ftree-vectorize',
-                        '-funroll-loops',
-                        '-mtune=native'],
-                'intel': ['-O2',
-                          '-pc64',
-                          '-unroll']
+                'gcc': [
+                    '-O2',
+                    '-mtune=native',
+                    '-funroll-loops',
+                    '-ffast-math',
+                    '-ftree-vectorize',
+                ], 'intel': [
+                    '-O2',
+                    '-pc64',
+                    '-unroll',
+                ]
             }
 
             dflags = ['-DNDEBUG']
 
+            libxc = spec['libxc:fortran,static']
+
             cppflags = [
                 '-D__FFTW3',
                 '-D__LIBINT',
                 '-D__LIBINT_MAX_AM=6',
                 '-D__LIBDERIV_MAX_AM1=5',
-                spec['fftw'].headers.cpp_flags
+                '-D__LIBXC',
+                spec['fftw'].headers.cpp_flags,
+                libxc.headers.cpp_flags
             ]
 
             if '^mpi@3:' in spec:
@@ -109,18 +102,15 @@ class Cp2k(Package):
             cflags = copy.deepcopy(optflags[self.spec.compiler.name])
             cxxflags = copy.deepcopy(optflags[self.spec.compiler.name])
             fcflags = copy.deepcopy(optflags[self.spec.compiler.name])
-            fcflags.extend([
-                '-ffree-form',
-                '-ffree-line-length-none',
-                spec['fftw'].headers.cpp_flags
-            ])
 
             if '%intel' in spec:
                 cflags.append('-fp-model precise')
                 cxxflags.append('-fp-model precise')
                 fcflags.extend(['-fp-model source', '-heap-arrays 64'])
+            elif '%gcc' in spec:
+                fcflags.extend(['-ffree-form', '-ffree-line-length-none'])
 
-            fftw = find_libraries('libfftw3', root=spec['fftw'].prefix.lib)
+            fftw = spec['fftw'].libs
             ldflags = [fftw.search_flags]
 
             if 'superlu-dist@4.3' in spec:
@@ -160,7 +150,7 @@ class Cp2k(Package):
                 mkf.write('CPP = # {0.compiler.cc} -P\n\n'.format(self))
                 mkf.write('AR = xiar -r\n\n')
             else:
-                mkf.write('CPP = {0.compiler.cc} -E\n\n'.format(self))
+                mkf.write('CPP = # {0.compiler.cc} -E\n\n'.format(self))
                 mkf.write('AR = ar -r\n\n')
             fc = self.compiler.fc if '~mpi' in spec else self.spec['mpi'].mpifc
             mkf.write('FC = {0}\n'.format(fc))
@@ -183,18 +173,34 @@ class Cp2k(Package):
                 cppflags.extend([
                     '-D__parallel',
                     '-D__LIBPEXSI',
-                    '-D__ELPA3',
                     '-D__SCALAPACK'
                 ])
+
+                elpa = spec['elpa']
+                if spec.satisfies('@:4.999'):
+                    if elpa.satisfies('@:2014.5.999'):
+                        cppflags.append('-D__ELPA')
+                    elif elpa.satisfies('@2014.6:2015.10.999'):
+                        cppflags.append('-D__ELPA2')
+                    else:
+                        cppflags.append('-D__ELPA3')
+                else:
+                    cppflags.append('-D__ELPA={0}{1:02d}'.format(
+                        elpa.version[0], int(elpa.version[1])))
+                    fcflags.append('-I' + join_path(
+                        elpa.prefix, 'include',
+                        'elpa-{0}'.format(str(elpa.version)), 'elpa'
+                    ))
+
                 if 'wannier90' in spec:
                     cppflags.append('-D__WANNIER90')
 
                 fcflags.extend([
                     # spec['elpa:fortran'].headers.cpp_flags
                     '-I' + join_path(
-                        spec['elpa'].prefix,
+                        elpa.prefix,
                         'include',
-                        'elpa-{0}'.format(str(spec['elpa'].version)),
+                        'elpa-{0}'.format(str(elpa.version)),
                         'modules'
                     ),
                     # spec[pexsi:fortran].headers.cpp_flags
@@ -203,7 +209,7 @@ class Cp2k(Package):
                 scalapack = spec['scalapack'].libs
                 ldflags.append(scalapack.search_flags)
                 libs.extend([
-                    join_path(spec['elpa'].prefix.lib,
+                    join_path(elpa.prefix.lib,
                               'libelpa.{0}'.format(dso_suffix)),
                     join_path(spec['pexsi'].prefix.lib, 'libpexsi.a'),
                     join_path(spec['superlu-dist'].prefix.lib,
@@ -230,9 +236,36 @@ class Cp2k(Package):
             # LAPACK / BLAS
             lapack = spec['lapack'].libs
             blas = spec['blas'].libs
-
             ldflags.append((lapack + blas).search_flags)
-            libs.extend([str(x) for x in (fftw, lapack, blas)])
+
+            ldflags.append(libxc.libs.search_flags)
+
+            libs.extend([str(x) for x in (fftw, lapack, blas, libxc.libs)])
+
+            if 'smm=libsmm' in spec:
+                lib_dir = join_path('lib', cp2k_architecture, cp2k_version)
+                mkdirp(lib_dir)
+                try:
+                    copy(env['LIBSMM_PATH'], join_path(lib_dir, 'libsmm.a'))
+                except KeyError:
+                    raise KeyError('Point environment variable LIBSMM_PATH to '
+                                   'the absolute path of the libsmm.a file')
+                except IOError:
+                    raise IOError('The file LIBSMM_PATH pointed to does not '
+                                  'exist. Note that it must be absolute path.')
+                cppflags.extend([
+                    '-D__HAS_smm_dnn',
+                    '-D__HAS_smm_vec',
+                ])
+                libs.append('-lsmm')
+            elif 'smm=libxsmm' in spec:
+                cppflags.extend([
+                    '-D__LIBXSMM',
+                    spec['libxsmm'].headers.cpp_flags,
+                ])
+                libxsmm = spec['libxsmm'].libs
+                ldflags.append(libxsmm.search_flags)
+                libs.append(str(libxsmm))
 
             dflags.extend(cppflags)
             cflags.extend(cppflags)
@@ -261,4 +294,4 @@ class Cp2k(Package):
                  'VERSION={0}'.format(cp2k_version))
             env['PWD'] = pwd_backup
         exe_dir = join_path('exe', cp2k_architecture)
-        shutil.copytree(exe_dir, self.prefix.bin)
+        install_tree(exe_dir, self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cppad/package.py b/var/spack/repos/builtin/packages/cppad/package.py
index 3b503fe1c8..aec3cc629b 100644
--- a/var/spack/repos/builtin/packages/cppad/package.py
+++ b/var/spack/repos/builtin/packages/cppad/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,10 @@ class Cppad(CMakePackage):
 
     homepage = "https://www.coin-or.org/CppAD/"
     url      = "http://www.coin-or.org/download/source/CppAD/cppad-20170114.gpl.tgz"
+    git      = "https://github.com/coin-or/CppAD.git"
 
+    version('develop', branch='master')
     version('20170114', '565a534dc813fa1289764222cd8c11ea')
-    version('develop', git='https://github.com/coin-or/CppAD.git')
 
     def cmake_args(self):
         # This package does not obey CMAKE_INSTALL_PREFIX
diff --git a/var/spack/repos/builtin/packages/cppcheck/package.py b/var/spack/repos/builtin/packages/cppcheck/package.py
index a9933920a9..ae13240537 100644
--- a/var/spack/repos/builtin/packages/cppcheck/package.py
+++ b/var/spack/repos/builtin/packages/cppcheck/package.py
@@ -1,45 +1,32 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import os
-import shutil
 
 
-class Cppcheck(Package):
+class Cppcheck(MakefilePackage):
     """A tool for static C/C++ code analysis."""
     homepage = "http://cppcheck.sourceforge.net/"
     url      = "https://downloads.sourceforge.net/project/cppcheck/cppcheck/1.78/cppcheck-1.78.tar.bz2"
 
+    version('1.81', '0c60a1d00652044ef511bdd017689938')
     version('1.78', 'f02d0ee0a4e71023703c6c5efff6cf9d')
     version('1.72', '2bd36f91ae0191ef5273bb7f6dc0d72e')
     version('1.68', 'c015195f5d61a542f350269030150708')
 
+    variant('htmlreport', default=False, description="Install cppcheck-htmlreport")
+
+    depends_on('py-pygments', when='+htmlreport', type='run')
+
+    def build(self, spec, prefix):
+        make('CFGDIR={0}'.format(prefix.cfg))
+
     def install(self, spec, prefix):
-        # cppcheck does not have a configure script
-        make("CFGDIR=%s" % os.path.join(prefix, 'cfg'))
-        # manually install the final cppcheck binary
+        # Manually install the final cppcheck binary
         mkdirp(prefix.bin)
         install('cppcheck', prefix.bin)
-        shutil.copytree('cfg', os.path.join(prefix, 'cfg'))
+        install_tree('cfg', prefix.cfg)
+        if spec.satisfies('+htmlreport'):
+            install('htmlreport/cppcheck-htmlreport', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/cppgsl/package.py b/var/spack/repos/builtin/packages/cppgsl/package.py
new file mode 100644
index 0000000000..73fdb70590
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cppgsl/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cppgsl(CMakePackage):
+    """C++ Guideline Support Library"""
+
+    homepage = "https://github.com/Microsoft/GSL"
+    url      = "https://github.com/Microsoft/GSL/archive/v2.0.0.tar.gz"
+    git      = "https://github.com/Microsoft/GSL.git"
+
+    version('develop', branch='master')
+    version('2.0.0', sha256='6cce6fb16b651e62711a4f58e484931013c33979b795d1b1f7646f640cfa9c8e')
+    version('1.0.0', sha256='9694b04cd78e5b1a769868f19fdd9eea2002de3d4c3a81a1b769209364543c36')
+
+    variant('cxxstd',
+            default='14',
+            values=('14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
+
+    depends_on('cmake@3.1.3:', type='build')
+
+    def cmake_args(self):
+        args = [
+            '-DGSL_CXX_STANDARD={0}'.format(self.spec.variants['cxxstd'].value)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/cpprestsdk/package.py b/var/spack/repos/builtin/packages/cpprestsdk/package.py
index a92b49c7a7..7b98c59b43 100644
--- a/var/spack/repos/builtin/packages/cpprestsdk/package.py
+++ b/var/spack/repos/builtin/packages/cpprestsdk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cppunit/package.py b/var/spack/repos/builtin/packages/cppunit/package.py
index ef6fa6ee24..c109076986 100644
--- a/var/spack/repos/builtin/packages/cppunit/package.py
+++ b/var/spack/repos/builtin/packages/cppunit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cppzmq/package.py b/var/spack/repos/builtin/packages/cppzmq/package.py
index 689e3924de..aa038509be 100644
--- a/var/spack/repos/builtin/packages/cppzmq/package.py
+++ b/var/spack/repos/builtin/packages/cppzmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,12 @@ class Cppzmq(CMakePackage):
 
     homepage = "http://www.zeromq.org"
     url      = "https://github.com/zeromq/cppzmq/archive/v4.2.2.tar.gz"
+    git      = "https://github.com/zeromq/cppzmq.git"
 
-    version('develop', branch='master',
-            git='https://github.com/zeromq/cppzmq.git')
-
+    version('develop', branch='master')
+    version('4.3.0', sha256='27d1f56406ba94ee779e639203218820975cf68174f92fbeae0f645df0fcada4')
     version('4.2.2', 'bd809b47296e77fe9f192bd9dafd5cc3')
 
     depends_on('cmake@3.0.0:', type='build')
-    depends_on('zeromq@4.2.2')
+    depends_on('zeromq@4.2.5', when='@4.3.0')
+    depends_on('zeromq@4.2.2', when='@4.2.2')
diff --git a/var/spack/repos/builtin/packages/cpu-features/package.py b/var/spack/repos/builtin/packages/cpu-features/package.py
new file mode 100644
index 0000000000..f54b964a20
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cpu-features/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class CpuFeatures(CMakePackage):
+    """A cross platform C99 library to get cpu features at runtime."""
+
+    homepage = "https://github.com/google/cpu_features"
+    git      = "https://github.com/google/cpu_features.git"
+
+    version('develop', branch='master')
+
+    depends_on('cmake@3.0.0:', type='build')
+
+    def cmake_args(self):
+        args = [
+            '-DBUILD_TESTING:BOOL=OFF'
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/cpuinfo/package.py b/var/spack/repos/builtin/packages/cpuinfo/package.py
new file mode 100644
index 0000000000..e3bc736415
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cpuinfo/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cpuinfo(CMakePackage):
+    """cpuinfo is a library to detect essential
+    for performance optimization information about host CPU."""
+
+    homepage = "https://github.com/Maratyszcza/cpuinfo/"
+    git      = "https://github.com/Maratyszcza/cpuinfo.git"
+
+    version('master')
diff --git a/var/spack/repos/builtin/packages/cram/package.py b/var/spack/repos/builtin/packages/cram/package.py
index 73a8584572..3f213d3118 100644
--- a/var/spack/repos/builtin/packages/cram/package.py
+++ b/var/spack/repos/builtin/packages/cram/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cryptopp/package.py b/var/spack/repos/builtin/packages/cryptopp/package.py
index c8fe6968a7..9ca8cf98d4 100644
--- a/var/spack/repos/builtin/packages/cryptopp/package.py
+++ b/var/spack/repos/builtin/packages/cryptopp/package.py
@@ -1,57 +1,35 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 glob
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Cryptopp(Package):
+class Cryptopp(MakefilePackage):
     """Crypto++ is an open-source C++ library of cryptographic schemes. The
-       library supports a number of different cryptography algorithms,
-       including authenticated encryption schemes (GCM, CCM), hash
-       functions (SHA-1, SHA2), public-key encryption (RSA, DSA), and a
-       few obsolete/historical encryption algorithms (MD5, Panama).
-
-    """
+    library supports a number of different cryptography algorithms, including
+    authenticated encryption schemes (GCM, CCM), hash functions (SHA-1, SHA2),
+    public-key encryption (RSA, DSA), and a few obsolete/historical encryption
+    algorithms (MD5, Panama)."""
 
     homepage = "http://www.cryptopp.com"
-    url      = "http://www.cryptopp.com/cryptopp563.zip"
+    url      = "http://www.cryptopp.com/cryptopp700.zip"
 
+    version('7.0.0', '8f34884b572901b6ede89bd18f1c7ef6')
+    version('6.1.0', sha256='21289d2511101a9350c87c8eb1f4982d4a266e8037b19dab79a32cc13ea108c7')
+    version('6.0.0', sha256='64ac2db96b3f1b7a23675e2be95d16c96055edffa2d5e2de6245fdb6baa92dda')
+    version('5.6.5', sha256='a75ef486fe3128008bbb201efee3dcdcffbe791120952910883b26337ec32c34')
+    version('5.6.4', sha256='be430377b05c15971d5ccb6e44b4d95470f561024ed6d701fe3da3a188c84ad7')
     version('5.6.3', '3c5b70e2ec98b7a24988734446242d07')
     version('5.6.2', '7ed022585698df48e65ce9218f6c6a67')
     version('5.6.1', '96cbeba0907562b077e26bcffb483828')
 
+    depends_on('gmake', type='build')
+
     def url_for_version(self, version):
-        url = "{0}/{1}{2}.zip"
+        url = '{0}/{1}{2}.zip'
         return url.format(self.homepage, self.name, version.joined)
 
     def install(self, spec, prefix):
-        make()
-
-        mkdirp(prefix.include)
-        for hfile in glob.glob('*.h*'):
-            install(hfile, prefix.include)
-
-        mkdirp(prefix.lib)
-        install('libcryptopp.a', prefix.lib)
+        make('install', 'PREFIX={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/cscope/package.py b/var/spack/repos/builtin/packages/cscope/package.py
index d7e7d29935..96f7ed1d67 100644
--- a/var/spack/repos/builtin/packages/cscope/package.py
+++ b/var/spack/repos/builtin/packages/cscope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,6 +18,6 @@ class Cscope(AutotoolsPackage):
 
     depends_on('flex', type='build')
     depends_on('bison', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     build_targets = ['CURSES_LIBS=-lncursesw']
diff --git a/var/spack/repos/builtin/packages/csdp/package.py b/var/spack/repos/builtin/packages/csdp/package.py
index a242f3b0c0..2735b14a41 100644
--- a/var/spack/repos/builtin/packages/csdp/package.py
+++ b/var/spack/repos/builtin/packages/csdp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ctffind/package.py b/var/spack/repos/builtin/packages/ctffind/package.py
new file mode 100644
index 0000000000..3f8fb844bd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ctffind/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ctffind(AutotoolsPackage):
+    """Fast and accurate defocus estimation from electron micrographs."""
+
+    homepage = "http://grigoriefflab.janelia.org/ctffind4"
+    url      = "http://grigoriefflab.janelia.org/sites/default/files/ctffind-4.1.8.tar.gz"
+
+    version('4.1.8', '8ae9d9abe363141a3792981b5a2fae94')
+
+    depends_on('wx')
+    depends_on('fftw@3:')
diff --git a/var/spack/repos/builtin/packages/cub/package.py b/var/spack/repos/builtin/packages/cub/package.py
index 1ca42f8e91..3db6d76eed 100644
--- a/var/spack/repos/builtin/packages/cub/package.py
+++ b/var/spack/repos/builtin/packages/cub/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cube/package.py b/var/spack/repos/builtin/packages/cube/package.py
index 4f1f643bf2..d9da5ad7e4 100644
--- a/var/spack/repos/builtin/packages/cube/package.py
+++ b/var/spack/repos/builtin/packages/cube/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,23 +15,37 @@ class Cube(AutotoolsPackage):
     """
 
     homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
-    url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.3.tar.gz"
+    url      = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubegui-4.4.2.tar.gz"
 
+    version('4.4.2', '29b6479616a524f8325f5031a883963bf965fb92569de33271a020f08650ec7b')
+    version('4.4',   '0620bae3ac357d0486ce7f5f97e448eeb2494c9a31865b679380ee08c6750e70')
     version('4.3.5', 'e5dce986e3c6381ea3a5fcb66c553adc')
     version('4.3.4', '50f73060f55311cb12c5b3cb354d59fa')
     version('4.3.3', '07e109248ed8ffc7bdcce614264a2909')
-
     version('4.2.3', '8f95b9531f5a8f8134f279c2767c9b20')
 
-    variant('gui', default=False, description='Build CUBE GUI')
+    variant('gui', default=True, description='Build Cube GUI')
+
+    patch('qt-version.patch', when='@4.3.0:4.3.999 +gui')
+
+    depends_on('cubelib', when='@4.4:')
 
+    depends_on('pkgconfig', type='build')
+    depends_on('dbus')
     depends_on('zlib')
 
-    depends_on('qt@5:', when='@4.3.0:4.3.999 +gui')
+    depends_on('qt@5:', when='@4.3.0: +gui')
     depends_on('qt@4.8:', when='@4.2.0:4.2.999 +gui')
 
+    conflicts('~gui', when='@4.4:')
+
     def url_for_version(self, version):
-        return 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cube-{1}.tar.gz'.format(version.up_to(2), version)
+        if version >= Version('4.4'):
+            url = 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cubegui-{1}.tar.gz'
+        else:
+            url = 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cube-{1}.tar.gz'
+
+        return url.format(version.up_to(2), version)
 
     def configure_args(self):
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/cube/qt-version.patch b/var/spack/repos/builtin/packages/cube/qt-version.patch
new file mode 100644
index 0000000000..33f36e76d2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cube/qt-version.patch
@@ -0,0 +1,24 @@
+diff -ruw cube-4.3.5.orig/build-backend/configure cube-4.3.5/build-backend/configure
+--- cube-4.3.5.orig/build-backend/configure	2017-05-23 13:15:46.121704000 +0200
++++ cube-4.3.5/build-backend/configure	2018-02-14 15:07:27.313842086 +0100
+@@ -5589,7 +5589,7 @@
+ else
+   echo "$as_me:$LINENO: Running $QMAKE --version:" >&5
+   $QMAKE --version >&5 2>&1
+-  qmake_version_sed='/^.*Qt.version.\([0-9]\.[0-9]\.[0-9]\).in.*$/!d;s//\1/'
++  qmake_version_sed='/^.*Qt.version.\([0-9]\.[0-9]\+\.[0-9]\+\).in.*$/!d;s//\1/'
+   at_cv_QT_VERSION=`$QMAKE --version 2>&1 | sed "$qmake_version_sed"`
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $at_cv_QT_VERSION" >&5
+diff -ruw cube-4.3.5.orig/build-frontend/configure cube-4.3.5/build-frontend/configure
+--- cube-4.3.5.orig/build-frontend/configure	2017-05-23 13:16:00.499773000 +0200
++++ cube-4.3.5/build-frontend/configure	2018-02-14 15:07:46.349487111 +0100
+@@ -19757,7 +19757,7 @@
+ else
+   echo "$as_me:$LINENO: Running $QMAKE --version:" >&5
+   $QMAKE --version >&5 2>&1
+-  qmake_version_sed='/^.*Qt.version.\([0-9]\.[0-9]\.[0-9]\).in.*$/!d;s//\1/'
++  qmake_version_sed='/^.*Qt.version.\([0-9]\.[0-9]\+\.[0-9]\+\).in.*$/!d;s//\1/'
+   at_cv_QT_VERSION=`$QMAKE --version 2>&1 | sed "$qmake_version_sed"`
+ fi
+ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $at_cv_QT_VERSION" >&5
diff --git a/var/spack/repos/builtin/packages/cubelib/package.py b/var/spack/repos/builtin/packages/cubelib/package.py
new file mode 100644
index 0000000000..8ccd9f1bcd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cubelib/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cubelib(AutotoolsPackage):
+    """Component of CubeBundle: General purpose C++ library and tools """
+
+    homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
+    url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubelib-4.4.tar.gz"
+
+    version('4.4.2', '843335c7d238493f1b4cb8e07555ccfe99a3fa521bf162e9d8eaa6733aa1f949')
+    version('4.4',   'c903f3c44d3228ebefd00c831966988e')
+
+    depends_on('zlib')
+
+    def url_for_version(self, version):
+        url = 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cubelib-{1}.tar.gz'
+
+        return url.format(version.up_to(2), version)
+
+    def configure_args(self):
+        configure_args = ['--enable-shared']
+
+        return configure_args
+
+    def install(self, spec, prefix):
+        make('install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/cubew/package.py b/var/spack/repos/builtin/packages/cubew/package.py
new file mode 100644
index 0000000000..79c8464c62
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cubew/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Cubew(AutotoolsPackage):
+    """Component of CubeBundle: High performance C Writer library """
+
+    homepage = "http://www.scalasca.org/software/cube-4.x/download.html"
+    url = "http://apps.fz-juelich.de/scalasca/releases/cube/4.4/dist/cubew-4.4.tar.gz"
+
+    version('4.4.1', 'c09e3f5a3533ebedee2cc7dfaacd7bac4680c14c3fa540669466583a23f04b67')
+    version('4.4',   'e9beb140719c2ad3d971e1efb99e0916')
+
+    depends_on('zlib')
+
+    def url_for_version(self, version):
+        url = 'http://apps.fz-juelich.de/scalasca/releases/cube/{0}/dist/cubew-{1}.tar.gz'
+
+        return url.format(version.up_to(2), version)
+
+    def configure_args(self):
+        configure_args = ['--enable-shared']
+
+        return configure_args
+
+    def install(self, spec, prefix):
+        make('install', parallel=True)
diff --git a/var/spack/repos/builtin/packages/cuda-memtest/package.py b/var/spack/repos/builtin/packages/cuda-memtest/package.py
index d7a4e2a04a..53a7204950 100644
--- a/var/spack/repos/builtin/packages/cuda-memtest/package.py
+++ b/var/spack/repos/builtin/packages/cuda-memtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,10 +16,11 @@ class CudaMemtest(CMakePackage):
     """
 
     homepage = "https://github.com/ComputationalRadiationPhysics/cuda_memtest"
-    url      = "https://github.com/ComputationalRadiationPhysics/cuda_memtest.git"
+    git      = "https://github.com/ComputationalRadiationPhysics/cuda_memtest.git"
+
+    maintainers = ['ax3l']
 
-    version('master', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/cuda_memtest.git')
+    version('master', branch='dev')
 
     depends_on('cmake@2.8.5:', type='build')
     # depends_on('nvml', when='+nvml')
diff --git a/var/spack/repos/builtin/packages/cuda/package.py b/var/spack/repos/builtin/packages/cuda/package.py
index e54501d8fe..b807ddd966 100644
--- a/var/spack/repos/builtin/packages/cuda/package.py
+++ b/var/spack/repos/builtin/packages/cuda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -33,11 +14,16 @@ class Cuda(Package):
 
     Note: This package does not currently install the drivers necessary
     to run CUDA. These will need to be installed manually. See:
-    http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-linux for
-    details."""
+    https://docs.nvidia.com/cuda/ for details."""
 
-    homepage = "http://www.nvidia.com/object/cuda_home_new.html"
+    homepage = "https://developer.nvidia.com/cuda-zone"
 
+    version('10.0.130', sha256='92351f0e4346694d0fcb4ea1539856c9eb82060c25654463bfd8574ec35ee39a', expand=False,
+            url="https://developer.nvidia.com/compute/cuda/10.0/Prod/local_installers/cuda_10.0.130_410.48_linux")
+    version('9.2.88', 'dd6e33e10d32a29914b7700c7b3d1ca0', expand=False,
+            url="https://developer.nvidia.com/compute/cuda/9.2/Prod/local_installers/cuda_9.2.88_396.26_linux")
+    version('9.1.85', '67a5c3933109507df6b68f80650b4b4a', expand=False,
+            url="https://developer.nvidia.com/compute/cuda/9.1/Prod/local_installers/cuda_9.1.85_387.26_linux")
     version('9.0.176', '7a00187b2ce5c5e350e68882f42dd507', expand=False,
             url="https://developer.nvidia.com/compute/cuda/9.0/Prod/local_installers/cuda_9.0.176_384.81_linux-run")
     version('8.0.61', '33e1bd980e91af4e55f3ef835c103f9b', expand=False,
@@ -50,7 +36,7 @@ class Cuda(Package):
             url="http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run")
 
     def install(self, spec, prefix):
-        runfile = glob(join_path(self.stage.path, 'cuda*run'))[0]
+        runfile = glob(join_path(self.stage.path, 'cuda*_linux*'))[0]
         chmod = which('chmod')
         chmod('+x', runfile)
         runfile = which(runfile)
@@ -59,6 +45,7 @@ class Cuda(Package):
         # compilers.  For example, on CentOS 6, you must use GCC 4.4.7 or
         # older. See:
         # http://docs.nvidia.com/cuda/cuda-installation-guide-linux/#system-requirements
+        # https://gist.github.com/ax3l/9489132
         # for details.
 
         runfile(
diff --git a/var/spack/repos/builtin/packages/cudnn/package.py b/var/spack/repos/builtin/packages/cudnn/package.py
index 53af7f9635..2524749ca2 100644
--- a/var/spack/repos/builtin/packages/cudnn/package.py
+++ b/var/spack/repos/builtin/packages/cudnn/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Cudnn(Package):
@@ -32,6 +12,8 @@ class Cudnn(Package):
 
     homepage = "https://developer.nvidia.com/cudnn"
 
+    version('7.3', '72666d3532850752612706601258a0b2',
+            url='https://developer.nvidia.com/compute/machine-learning/cudnn/secure/v7.3.0/prod/9.0_2018920/cudnn-9.0-linux-x64-v7.3.0.29.tgz')
     version('6.0', 'a08ca487f88774e39eb6b0ef6507451d',
             url='http://developer.download.nvidia.com/compute/redist/cudnn/v6.0/cudnn-8.0-linux-x64-v6.0.tgz')
     version('5.1', '406f4ac7f7ee8aa9e41304c143461a69',
@@ -40,4 +22,4 @@ class Cudnn(Package):
     depends_on('cuda@8:')
 
     def install(self, spec, prefix):
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/cufflinks/package.py b/var/spack/repos/builtin/packages/cufflinks/package.py
index 97197258dd..a0c039ff1f 100644
--- a/var/spack/repos/builtin/packages/cufflinks/package.py
+++ b/var/spack/repos/builtin/packages/cufflinks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/cups/package.py b/var/spack/repos/builtin/packages/cups/package.py
index b674bd637a..f9f60f70e0 100644
--- a/var/spack/repos/builtin/packages/cups/package.py
+++ b/var/spack/repos/builtin/packages/cups/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/curl/package.py b/var/spack/repos/builtin/packages/curl/package.py
index c12e50b71c..5dabe83f80 100644
--- a/var/spack/repos/builtin/packages/curl/package.py
+++ b/var/spack/repos/builtin/packages/curl/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
 class Curl(AutotoolsPackage):
@@ -31,8 +13,10 @@ class Curl(AutotoolsPackage):
 
     homepage = "http://curl.haxx.se"
     # URL must remain http:// so Spack can bootstrap curl
-    url      = "http://curl.haxx.se/download/curl-7.54.0.tar.bz2"
+    url      = "http://curl.haxx.se/download/curl-7.60.0.tar.bz2"
 
+    version('7.60.0', 'bd2aabf78ded6a9aec8a54532fd6b5d7')
+    version('7.59.0', 'a2192804f7c2636a09320416afcf888e')
     version('7.56.0', 'e0caf257103e0c77cee5be7e9ac66ca4')
     version('7.54.0', '89bb7ba87384dfbf4f1a3f953da42458')
     version('7.53.1', 'fb1f03a142236840c1a77c035fa4c542')
@@ -48,15 +32,37 @@ class Curl(AutotoolsPackage):
     version('7.43.0', '11bddbb452a8b766b932f859aaeeed39')
     version('7.42.1', '296945012ce647b94083ed427c1877a8')
 
-    depends_on('openssl')
+    variant('nghttp2',    default=False, description='build nghttp2 library (requires C++11)')
+    variant('libssh2',    default=False, description='enable libssh2 support')
+    variant('libssh',     default=False, description='enable libssh support')  # , when='7.58:')
+    variant('darwinssl',  default=sys.platform == 'darwin', description="use Apple's SSL/TLS implementation")
+
+    conflicts('+libssh', when='@:7.57.99')
+    # on OSX and --with-ssh the configure steps fails with
+    # one or more libs available at link-time are not available run-time
+    # unless the libssh are installed externally (e.g. via homebrew), even
+    # though spack isn't supposed to know about such a libssh installation.
+    # C.f. https://github.com/spack/spack/issues/7777
+    conflicts('platform=darwin', when='+libssh2')
+    conflicts('platform=darwin', when='+libssh')
+    conflicts('platform=linux', when='+darwinssl')
+
+    depends_on('openssl', when='~darwinssl')
     depends_on('zlib')
-    depends_on('nghttp2')
+    depends_on('nghttp2', when='+nghttp2')
+    depends_on('libssh2', when='+libssh2')
+    depends_on('libssh', when='+libssh')
 
     def configure_args(self):
         spec = self.spec
 
-        return [
-            '--with-zlib={0}'.format(spec['zlib'].prefix),
-            '--with-ssl={0}'.format(spec['openssl'].prefix),
-            '--with-http2={0}'.format(spec['nghttp2'].prefix),
-        ]
+        args = ['--with-zlib={0}'.format(spec['zlib'].prefix)]
+        if spec.satisfies('+darwinssl'):
+            args.append('--with-darwinssl')
+        else:
+            args.append('--with-ssl={0}'.format(spec['openssl'].prefix))
+
+        args += self.with_or_without('nghttp2')
+        args += self.with_or_without('libssh2')
+        args += self.with_or_without('libssh')
+        return args
diff --git a/var/spack/repos/builtin/packages/cvs/package.py b/var/spack/repos/builtin/packages/cvs/package.py
index 58943886bf..be5c0baeda 100644
--- a/var/spack/repos/builtin/packages/cvs/package.py
+++ b/var/spack/repos/builtin/packages/cvs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -29,7 +10,7 @@ from spack import *
 class Cvs(AutotoolsPackage):
     """CVS a very traditional source control system"""
     homepage = "http://www.nongnu.org/cvs/"
-    url      = "https://ftp.gnu.org/non-gnu/cvs/source/feature/1.12.13/cvs-1.12.13.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/non-gnu/cvs/source/feature/1.12.13/cvs-1.12.13.tar.bz2"
 
     version('1.12.13', '93a8dacc6ff0e723a130835713235863f1f5ada9')
 
diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py
index 799b577398..f567637a78 100644
--- a/var/spack/repos/builtin/packages/czmq/package.py
+++ b/var/spack/repos/builtin/packages/czmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,13 +11,15 @@ class Czmq(AutotoolsPackage):
     homepage = "http://czmq.zeromq.org"
     url      = "https://github.com/zeromq/czmq/archive/v4.0.2.tar.gz"
 
+    version('4.1.1', 'a2ab03cddd14399c6ba75b030a256211')
     version('4.0.2', 'a65317a3fb8238cf70e3e992e381f9cc')
     version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1')
 
     depends_on('libtool', type='build')
     depends_on('automake', type='build')
     depends_on('autoconf', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on("libuuid")
     depends_on('zeromq')
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/dakota/package.py b/var/spack/repos/builtin/packages/dakota/package.py
index b90fb5641a..09b34fc1b2 100644
--- a/var/spack/repos/builtin/packages/dakota/package.py
+++ b/var/spack/repos/builtin/packages/dakota/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/daligner/package.py b/var/spack/repos/builtin/packages/daligner/package.py
index 91322b5b3a..fd7fe30dd8 100644
--- a/var/spack/repos/builtin/packages/daligner/package.py
+++ b/var/spack/repos/builtin/packages/daligner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/damageproto/package.py b/var/spack/repos/builtin/packages/damageproto/package.py
index 06d8815bb4..d439814375 100644
--- a/var/spack/repos/builtin/packages/damageproto/package.py
+++ b/var/spack/repos/builtin/packages/damageproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Damageproto(AutotoolsPackage):
 
     version('1.2.1', 'bf8c47b7f48625230cff155180f8ddce')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/damaris/package.py b/var/spack/repos/builtin/packages/damaris/package.py
new file mode 100644
index 0000000000..8bc0f7497f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/damaris/package.py
@@ -0,0 +1,64 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Damaris(CMakePackage):
+    """Damaris is a middleware for I/O and in situ analytics
+    targeting large-scale, MPI-based HPC simulations."""
+
+    homepage = "https://project.inria.fr/damaris/"
+    url = "https://gitlab.inria.fr/Damaris/damaris"
+
+    version('master', git='https://gitlab.inria.fr/Damaris/damaris.git')
+    version('1.3.1',  git='https://gitlab.inria.fr/Damaris/damaris.git', tag='v1.3.1', preferred=True)
+
+    variant('fortran',  default=True,  description='Enables Fortran support')
+    variant('hdf5',     default=False, description='Enables the HDF5 storage plugin')
+    variant('static',   default=False, description='Builds a static version of the library')
+    variant('catalyst', default=False, description='Enables the Catalyst visualization plugin')
+    variant('visit',    default=False, description='Enables the VisIt visualization plugin')
+
+    depends_on('mpi')
+    depends_on('cmake@3.12.0:', type=('build'))
+    depends_on('boost +thread+log+filesystem+date_time @1.67:')
+    depends_on('xsd')
+    depends_on('xerces-c')
+    depends_on('hdf5@1.8.20:', when='+hdf5')
+    depends_on('catalyst+python', when='+catalyst')
+    depends_on('visit+mpi', when='+visit')
+
+    def cmake_args(self):
+
+        args = []
+        if(not self.spec.variants['static'].value):
+            args.extend(['-DBUILD_SHARED_LIBS=ON'])
+
+        args.extend(['-DCMAKE_CXX_COMPILER=%s' % self.spec['mpi'].mpicxx])
+        args.extend(['-DCMAKE_C_COMPILER=%s' % self.spec['mpi'].mpicc])
+        args.extend(['-DBOOST_ROOT=%s' % self.spec['boost'].prefix])
+        args.extend(['-DXercesC_ROOT=%s' % self.spec['xerces-c'].prefix])
+        args.extend(['-DXSD_ROOT=%s' % self.spec['xsd'].prefix])
+
+        if (self.spec.variants['fortran'].value):
+            args.extend(['-DCMAKE_Fortran_COMPILER=%s'
+                         % self.spec['mpi'].mpifc])
+            args.extend(['-DENABLE_FORTRAN:BOOL=ON'])
+
+        if (self.spec.variants['hdf5'].value):
+            args.extend(['-DENABLE_HDF5:BOOL=ON'])
+            args.extend(['-DHDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix])
+
+        if (self.spec.variants['catalyst'].value):
+            args.extend(['-DENABLE_CATALYST:BOOL=ON'])
+            args.extend(['-DParaView_ROOT:PATH=%s'
+                         % self.spec['catalyst'].prefix])
+
+        if (self.spec.variants['visit'].value):
+            args.extend(['-DENABLE_VISIT:BOOL=ON'])
+            args.extend(['-DVisIt_ROOT:PATH=%s' % self.spec['visit'].prefix])
+        return args
diff --git a/var/spack/repos/builtin/packages/damselfly/package.py b/var/spack/repos/builtin/packages/damselfly/package.py
index c98ad5ca7b..6e7ecaf3de 100644
--- a/var/spack/repos/builtin/packages/damselfly/package.py
+++ b/var/spack/repos/builtin/packages/damselfly/package.py
@@ -1,36 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Damselfly(CMakePackage):
     """Damselfly is a model-based parallel network simulator."""
     homepage = "https://github.com/llnl/damselfly"
-    url      = "https://github.com/llnl/damselfly"
+    url      = "https://github.com/LLNL/damselfly/archive/v1.0.tar.gz"
 
-    version('1.0', '05cf7e2d8ece4408c0f2abb7ab63fd74c0d62895',
-            git='https://github.com/llnl/damselfly.git', tag='v1.0')
+    version('1.0', sha256='560e1b800c9036766396a1033c00914bd8d181b911e87140c3ac8879baf6545a')
 
     depends_on('cmake@2.6:', type='build')
diff --git a/var/spack/repos/builtin/packages/darshan-runtime/package.py b/var/spack/repos/builtin/packages/darshan-runtime/package.py
index 7be03f19c1..5aff9a0a1b 100644
--- a/var/spack/repos/builtin/packages/darshan-runtime/package.py
+++ b/var/spack/repos/builtin/packages/darshan-runtime/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -36,6 +17,7 @@ class DarshanRuntime(Package):
     homepage = "http://www.mcs.anl.gov/research/projects/darshan/"
     url = "http://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
 
+    version('3.1.6', 'ce5b8f1e69d602edd4753b57258b57c1')
     version('3.1.0', '439d717323e6265b2612ed127886ae52')
     version('3.0.0', '732577fe94238936268d74d7d74ebd08')
 
diff --git a/var/spack/repos/builtin/packages/darshan-util/package.py b/var/spack/repos/builtin/packages/darshan-util/package.py
index 35d3ddb97a..af2d56be81 100644
--- a/var/spack/repos/builtin/packages/darshan-util/package.py
+++ b/var/spack/repos/builtin/packages/darshan-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,13 @@ class DarshanUtil(Package):
     homepage = "http://www.mcs.anl.gov/research/projects/darshan/"
     url = "http://ftp.mcs.anl.gov/pub/darshan/releases/darshan-3.1.0.tar.gz"
 
+    version('3.1.6', 'ce5b8f1e69d602edd4753b57258b57c1')
     version('3.1.0', '439d717323e6265b2612ed127886ae52')
     version('3.0.0', '732577fe94238936268d74d7d74ebd08')
 
+    variant('bzip2', default=False, description="Enable bzip2 compression")
     depends_on('zlib')
+    depends_on('bzip2', when="+bzip2", type=("build", "link", "run"))
 
     def install(self, spec, prefix):
 
diff --git a/var/spack/repos/builtin/packages/dash/package.py b/var/spack/repos/builtin/packages/dash/package.py
index 9c79be238e..06adb572d0 100644
--- a/var/spack/repos/builtin/packages/dash/package.py
+++ b/var/spack/repos/builtin/packages/dash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/datamash/package.py b/var/spack/repos/builtin/packages/datamash/package.py
index b72a1c21bb..ce80da9add 100644
--- a/var/spack/repos/builtin/packages/datamash/package.py
+++ b/var/spack/repos/builtin/packages/datamash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Datamash(AutotoolsPackage):
     """
 
     homepage = "https://www.gnu.org/software/datamash/"
-    url      = "http://ftp.gnu.org/gnu/datamash/datamash-1.0.5.tar.gz"
+    url      = "https://ftpmirror.gnu.org/datamash/datamash-1.0.5.tar.gz"
 
+    version('1.3',   '47d382090e367ddb4967d640aba77b66')
     version('1.1.0', '79a6affca08107a095e97e4237fc8775')
     version('1.0.7', '9f317bab07454032ba9c068e7f17b04b')
     version('1.0.6', 'ff26fdef0f343cb695cf1853e14a1a5b')
diff --git a/var/spack/repos/builtin/packages/dataspaces/package.py b/var/spack/repos/builtin/packages/dataspaces/package.py
index 37121c2b47..552d0a0219 100644
--- a/var/spack/repos/builtin/packages/dataspaces/package.py
+++ b/var/spack/repos/builtin/packages/dataspaces/package.py
@@ -1,28 +1,11 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the LICENSE file for our notice and the LGPL.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 ##############################################################################
+# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
+
 
 from spack import *
 import six
@@ -41,9 +24,9 @@ class Dataspaces(AutotoolsPackage):
 
     homepage = "http://www.dataspaces.org"
     url      = "http://personal.cac.rutgers.edu/TASSL/projects/data/downloads/dataspaces-1.6.2.tar.gz"
+    git      = "https://github.com/melrom/dataspaces.git"
 
-    version('develop', git='https://github.com/melrom/dataspaces.git',
-            branch='master')
+    version('develop', branch='master')
     version('1.6.2', '73caa4920b6f2c0c6d6cb87640ff04be')
 
     variant('dimes',
@@ -70,7 +53,7 @@ class Dataspaces(AutotoolsPackage):
     depends_on('libtool', type='build')
     depends_on('mpi', when='+mpi')
 
-    def autoreconf(spec, prefix, self):
+    def autoreconf(self, spec, prefix):
         bash = which('bash')
         bash('./autogen.sh')
 
diff --git a/var/spack/repos/builtin/packages/davix/package.py b/var/spack/repos/builtin/packages/davix/package.py
new file mode 100644
index 0000000000..3338cad733
--- /dev/null
+++ b/var/spack/repos/builtin/packages/davix/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Davix(CMakePackage):
+    """High-performance file management over WebDAV/HTTP."""
+
+    homepage = "https://dmc.web.cern.ch/projects/davix"
+    url      = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.7/davix-0.6.7.tar.gz"
+    list_url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/"
+    list_depth = 1
+
+    version('0.6.8', 'e1820f4cc3fc44858ae97197a3922cce2a1130ff553b080ba19e06eb8383ddf7',
+            url='http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.8/davix-0.6.8.tar.gz')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('libxml2')
+    depends_on('libuuid')
+    depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/dbcsr/package.py b/var/spack/repos/builtin/packages/dbcsr/package.py
new file mode 100644
index 0000000000..af1ba5f749
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dbcsr/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Dbcsr(CMakePackage):
+    """Distributed Block Compressed Sparse Row matrix library."""
+
+    homepage = "https://github.com/cp2k/dbcsr"
+    url      = "https://github.com/cp2k/dbcsr/archive/v1.0.0-rc.0.tar.gz"
+
+    version('develop', git='https://github.com/cp2k/dbcsr.git', branch='develop')
+
+    variant('mpi',    default=True,  description='Compile with MPI')
+    variant('openmp', default=False, description='Build with OpenMP support')
+
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('mpi', when='+mpi')
+    depends_on('py-fypp')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DUSE_MPI=%s' % ('ON' if '+mpi' in spec else 'OFF'),
+            '-DUSE_OPENMP=%s' % (
+                'ON' if '+openmp' in spec else 'OFF'),
+            '-DWITH_C_API=ON',
+            '-DLAPACK_FOUND=true',
+            '-DLAPACK_LIBRARIES=%s' % spec['lapack'].libs.joined(';'),
+            '-DBLAS_FOUND=true',
+            '-DBLAS_LIBRARIES=%s' % spec['blas'].libs.joined(';'),
+            '-DWITH_EXAMPLES=OFF',
+            '-DBUILD_SHARED_LIBS=ON'
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/dbus/package.py b/var/spack/repos/builtin/packages/dbus/package.py
index 4d55665a4e..2b70ecab40 100644
--- a/var/spack/repos/builtin/packages/dbus/package.py
+++ b/var/spack/repos/builtin/packages/dbus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,6 +19,7 @@ class Dbus(Package):
     homepage = "http://dbus.freedesktop.org/"
     url      = "http://dbus.freedesktop.org/releases/dbus/dbus-1.8.8.tar.gz"
 
+    version('1.12.8', '2764bf150e5aa8005b7bc0d6c388756a')
     version('1.11.2', '957a07f066f3730d2bb3ea0932f0081b')
     version('1.9.0', 'ec6895a4d5c0637b01f0d0e7689e2b36')
     version('1.8.8', 'b9f4a18ee3faa1e07c04aa1d83239c43')
@@ -45,6 +27,7 @@ class Dbus(Package):
     version('1.8.4', '4717cb8ab5b80978fcadf2b4f2f72e1b')
     version('1.8.2', 'd6f709bbec0a022a1847c7caec9d6068')
 
+    depends_on('pkgconfig', type='build')
     depends_on('expat')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py b/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py
new file mode 100644
index 0000000000..86f4527197
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dealii-parameter-gui/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class DealiiParameterGui(CMakePackage):
+    """A qt based graphical user interface for editing deal.II .prm parameter
+    files."""
+
+    homepage = "https://github.com/dealii/parameter_gui"
+    git      = "https://github.com/dealii/parameter_gui.git"
+
+    version('develop', branch='master')
+
+    depends_on('qt')
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('PARAMETER_GUI_DIR', self.prefix)
diff --git a/var/spack/repos/builtin/packages/dealii/boost_1.65.1_singleton.patch b/var/spack/repos/builtin/packages/dealii/boost_1.65.1_singleton.patch
new file mode 100644
index 0000000000..fffd85aa1a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dealii/boost_1.65.1_singleton.patch
@@ -0,0 +1,43 @@
+diff --git a/boost/serialization/singleton.hpp b/boost/serialization/singleton.hpp
+index b50afed..e891d55 100644
+--- a/boost/serialization/singleton.hpp
++++ b/boost/serialization/singleton.hpp
+@@ -91,7 +91,7 @@ class BOOST_SYMBOL_VISIBLE singleton_module :
+     public boost::noncopyable
+ {
+ private:
+-    BOOST_SERIALIZATION_DECL BOOST_DLLEXPORT static bool & get_lock() BOOST_USED;
++    BOOST_DLLEXPORT static bool & get_lock() BOOST_USED;
+ public:
+     BOOST_DLLEXPORT static void lock(){
+         get_lock() = true;
+@@ -115,7 +115,7 @@ private:
+         // use a wrapper so that types T with protected constructors
+         // can be used
+         class singleton_wrapper : public T {};
+-        static singleton_wrapper t;
++        static singleton_wrapper* t = new singleton_wrapper;
+         // refer to instance, causing it to be instantiated (and
+         // initialized at startup on working compilers)
+         BOOST_ASSERT(! is_destroyed());
+@@ -125,7 +125,9 @@ private:
+         // our usage/implementation of "locking" and introduce uncertainty into
+         // the sequence of object initializaition.
+         use(& m_instance);
+-        return static_cast<T &>(t);
++        if (!t)
++            t = new singleton_wrapper;
++        return static_cast<T &>(*t);
+     }
+     static bool & get_is_destroyed(){
+         static bool is_destroyed;
+@@ -147,6 +149,9 @@ public:
+         get_is_destroyed() = false;
+     }
+     BOOST_DLLEXPORT ~singleton() {
++        if (!get_is_destroyed()) {
++            delete &(get_instance());
++        }
+         get_is_destroyed() = true;
+     }
+ };
diff --git a/var/spack/repos/builtin/packages/dealii/boost_1.68.0.patch b/var/spack/repos/builtin/packages/dealii/boost_1.68.0.patch
new file mode 100644
index 0000000000..e5b5e86f5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dealii/boost_1.68.0.patch
@@ -0,0 +1,135 @@
+diff --git a/boost/archive/impl/archive_serializer_map.ipp b/boost/archive/impl/archive_serializer_map.ipp
+index 7f163ec..8dabf0d 100644
+--- a/boost/archive/impl/archive_serializer_map.ipp
++++ b/boost/archive/impl/archive_serializer_map.ipp
+@@ -47,10 +47,6 @@ archive_serializer_map<Archive>::insert(const basic_serializer * bs){
+ template<class Archive>
+ BOOST_ARCHIVE_OR_WARCHIVE_DECL void
+ archive_serializer_map<Archive>::erase(const basic_serializer * bs){
+-    BOOST_ASSERT(! boost::serialization::singleton<
+-            extra_detail::map<Archive>
+-        >::is_destroyed()
+-    );
+     if(boost::serialization::singleton<
+         extra_detail::map<Archive>
+     >::is_destroyed())
+diff --git a/boost/serialization/singleton.hpp b/boost/serialization/singleton.hpp
+index 3437f38..3eac8eb 100644
+--- a/boost/serialization/singleton.hpp
++++ b/boost/serialization/singleton.hpp
+@@ -108,6 +108,29 @@ public:
+     }
+ };
+ 
++namespace detail {
++// This is the class actually instantiated and hence the real singleton.
++// So there will only be one instance of this class. This does not hold
++// for singleton<T> as a class derived from singleton<T> could be
++// instantiated multiple times.
++template<class T>
++class singleton_wrapper : public T
++{
++public:
++    singleton_wrapper(){
++        BOOST_ASSERT(!get_is_destroyed());
++    }
++    ~singleton_wrapper(){
++        get_is_destroyed() = true;
++    }
++    static bool & get_is_destroyed(){
++        // Prefer a static function member to avoid LNK1179. Note: Never reset!
++        static bool is_destroyed = false;
++        return is_destroyed;
++    }
++};
++} // detail
++
+ template <class T>
+ class singleton : public singleton_module
+ {
+@@ -116,14 +139,11 @@ private:
+     // include this to provoke instantiation at pre-execution time
+     static void use(T const *) {}
+     static T & get_instance() {
+-        // use a wrapper so that types T with protected constructors
+-        // can be used
+-        class singleton_wrapper : public T {};
+-        static singleton_wrapper t;
++        BOOST_ASSERT(!is_destroyed());
+ 
+-        // refer to instance, causing it to be instantiated (and
+-        // initialized at startup on working compilers)
+-        BOOST_ASSERT(! is_destroyed());
++        // use a wrapper so that types T with protected constructors can be used
++        // Using a static function member avoids LNK1179
++        static detail::singleton_wrapper< T > t;
+ 
+         // note that the following is absolutely essential.
+         // commenting out this statement will cause compilers to fail to
+@@ -134,10 +154,11 @@ private:
+ 
+         return static_cast<T &>(t);
+     }
+-    static bool & get_is_destroyed(){
+-        static bool is_destroyed;
+-        return is_destroyed;
+-    }
++
++protected:
++    // Do not allow instantiation of a singleton<T>. But we want to allow
++    // `class T: public singleton<T>` so we can't delete this ctor
++    BOOST_DLLEXPORT singleton(){}
+ 
+ public:
+     BOOST_DLLEXPORT static T & get_mutable_instance(){
+@@ -148,13 +169,7 @@ public:
+         return get_instance();
+     }
+     BOOST_DLLEXPORT static bool is_destroyed(){
+-        return get_is_destroyed();
+-    }
+-    BOOST_DLLEXPORT singleton(){
+-        get_is_destroyed() = false;
+-    }
+-    BOOST_DLLEXPORT ~singleton() {
+-        get_is_destroyed() = true;
++        return detail::singleton_wrapper< T >::get_is_destroyed();
+     }
+ };
+ 
+diff --git a/libs/serialization/src/extended_type_info.cpp b/libs/serialization/src/extended_type_info.cpp
+index 364fe56..13a60c3 100644
+--- a/libs/serialization/src/extended_type_info.cpp
++++ b/libs/serialization/src/extended_type_info.cpp
+@@ -125,7 +125,6 @@ BOOST_SERIALIZATION_DECL void
+ extended_type_info::key_unregister() const{
+     if(NULL == get_key())
+         return;
+-    BOOST_ASSERT(! singleton<detail::ktmap>::is_destroyed());
+     if(! singleton<detail::ktmap>::is_destroyed()){
+         detail::ktmap & x = singleton<detail::ktmap>::get_mutable_instance();
+         detail::ktmap::iterator start = x.lower_bound(this);
+diff --git a/libs/serialization/src/extended_type_info_typeid.cpp b/libs/serialization/src/extended_type_info_typeid.cpp
+index 7413d2e..af188ef 100644
+--- a/libs/serialization/src/extended_type_info_typeid.cpp
++++ b/libs/serialization/src/extended_type_info_typeid.cpp
+@@ -95,7 +95,6 @@ BOOST_SERIALIZATION_DECL void
+ extended_type_info_typeid_0::type_unregister()
+ {
+     if(NULL != m_ti){
+-        BOOST_ASSERT(! singleton<tkmap>::is_destroyed());
+         if(! singleton<tkmap>::is_destroyed()){
+             tkmap & x = singleton<tkmap>::get_mutable_instance();
+ 
+diff --git a/libs/serialization/src/void_cast.cpp b/libs/serialization/src/void_cast.cpp
+index 4051303..9009993 100644
+--- a/libs/serialization/src/void_cast.cpp
++++ b/libs/serialization/src/void_cast.cpp
+@@ -276,7 +276,6 @@ void_caster::recursive_register(bool includes_virtual_base) const {
+ 
+ BOOST_SERIALIZATION_DECL void
+ void_caster::recursive_unregister() const {
+-    BOOST_ASSERT(! void_caster_registry::is_destroyed());
+     if(void_caster_registry::is_destroyed())
+         return;
+ 
diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py
index 8f3e5d80ea..55cd7cbd00 100644
--- a/var/spack/repos/builtin/packages/dealii/package.py
+++ b/var/spack/repos/builtin/packages/dealii/package.py
@@ -1,36 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import os
 
 
-class Dealii(CMakePackage):
+class Dealii(CMakePackage, CudaPackage):
     """C++ software library providing well-documented tools to build finite
     element codes for a broad variety of PDEs."""
+
     homepage = "https://www.dealii.org"
-    url = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz"
+    url      = "https://github.com/dealii/dealii/releases/download/v8.4.1/dealii-8.4.1.tar.gz"
+    git      = "https://github.com/dealii/dealii.git"
 
     maintainers = ['davydden', 'jppelteret']
 
@@ -38,30 +20,34 @@ class Dealii(CMakePackage):
     # only add for immediate deps.
     transitive_rpaths = False
 
-    version('8.5.1', '39b9ebd6ab083d63cfc9044319aaa2ee')
-    version('8.5.0', 'ef999cc310b007559a6343bf5b1759bc')
-    version('8.4.2', '84c6bd3f250d3e0681b645d24cb987a7')
-    version('8.4.1', 'efbaf16f9ad59cfccad62302f36c3c1d')
-    version('8.4.0', 'ac5dbf676096ff61e092ce98c80c2b00')
-    version('8.3.0', 'fc6cdcb16309ef4bea338a4f014de6fa')
-    version('8.2.1', '71c728dbec14f371297cd405776ccf08')
-    version('8.1.0', 'aa8fadc2ce5eb674f44f997461bf668d')
-    version('develop', git='https://github.com/dealii/dealii.git', branch='master')
+    version('develop', branch='master')
+    version('9.0.1', sha256='df2f0d666f2224be07e3741c0e8e02132fd67ea4579cd16a2429f7416146ee64')
+    version('9.0.0', sha256='c918dc5c1a31d62f6eea7b524dcc81c6d00b3c378d4ed6965a708ab548944f08')
+    version('8.5.1', sha256='d33e812c21a51f7e5e3d3e6af86aec343155650b611d61c1891fbc3cabce09ae')
+    version('8.5.0', sha256='e6913ff6f184d16bc2598c1ba31f879535b72b6dff043e15aef048043ff1d779')
+    version('8.4.2', sha256='ec7c00fadc9d298d1a0d16c08fb26818868410a9622c59ba624096872f3058e4')
+    version('8.4.1', sha256='00a0e92d069cdafd216816f1aff460f7dbd48744b0d9e0da193287ebf7d6b3ad')
+    version('8.4.0', sha256='36a20e097a03f17b557e11aad1400af8c6252d25f7feca40b611d5fc16d71990')
+    version('8.3.0', sha256='4ddf72632eb501e1c814e299f32fc04fd680d6fda9daff58be4209e400e41779')
+    version('8.2.1', sha256='d75674e45fe63cd9fa294460fe45228904d51a68f744dbb99cd7b60720f3b2a0')
+    version('8.1.0', sha256='d666bbda2a17b41b80221d7029468246f2658051b8c00d9c5907cd6434c4df99')
 
     variant('mpi',      default=True,  description='Compile with MPI')
-    variant('assimp',   default=False,
+    variant('assimp',   default=True,
             description='Compile with Assimp')
     variant('arpack',   default=True,
             description='Compile with Arpack and PArpack (only with MPI)')
-    variant('adol-c',   default=False,
+    variant('adol-c',   default=True,
             description='Compile with Adol-c')
     variant('doc',      default=False,
             description='Compile with documentation')
+    variant('gmsh',     default=True,  description='Compile with GMSH')
     variant('gsl',      default=True,  description='Compile with GSL')
     variant('hdf5',     default=True,
             description='Compile with HDF5 (only with MPI)')
     variant('metis',    default=True,  description='Compile with Metis')
-    variant('nanoflann', default=False, description='Compile with Nanoflann')
+    variant('muparser', default=True,  description='Compile with muParser')
+    variant('nanoflann', default=True, description='Compile with Nanoflann')
     variant('netcdf',   default=True,
             description='Compile with Netcdf (only with MPI)')
     variant('oce',      default=True,  description='Compile with OCE')
@@ -69,13 +55,15 @@ class Dealii(CMakePackage):
             description='Compile with P4est (only with MPI)')
     variant('petsc',    default=True,
             description='Compile with Petsc (only with MPI)')
-    variant('sundials', default=False,
+    variant('scalapack', default=True,
+            description='Compile with ScaLAPACK (only with MPI)')
+    variant('sundials', default=True,
             description='Compile with Sundials')
     variant('slepc',    default=True,
             description='Compile with Slepc (only with Petsc and MPI)')
     variant('trilinos', default=True,
             description='Compile with Trilinos (only with MPI)')
-    variant('python',   default=True,
+    variant('python',   default=False,
             description='Compile with Python bindings')
     variant('int64',    default=False,
             description='Compile with 64 bit indices support')
@@ -84,83 +72,115 @@ class Dealii(CMakePackage):
     variant('build_type', default='DebugRelease',
             description='The build type to build',
             values=('Debug', 'Release', 'DebugRelease'))
-    variant('cuda', default=False,
-            description='Build with CUDA')
 
     # required dependencies, light version
-    depends_on("blas")
-    # Boost 1.58 is blacklisted, see
+    depends_on('blas')
+    # Boost 1.58 is blacklisted, require at least 1.59, see
     # https://github.com/dealii/dealii/issues/1591
-    # Require at least 1.59
-    # +python won't affect @:8.4.2
-    # FIXME: once concretizer can unite unconditional and
-    # conditional dependencies, simplify to:
-    # depends_on("boost@1.59.0+thread+system+serialization+iostreams")
-    # depends_on("boost+mpi", when='+mpi')
-    # depends_on("boost+python", when='+python')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams",
-               when='@:8.4.2~mpi')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams+mpi",
-               when='@:8.4.2+mpi')
-    # since @8.5.0: (and @develop) python bindings are introduced:
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams",
-               when='@8.5.0:~mpi~python')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams+mpi",
-               when='@8.5.0:+mpi~python')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams+python",
-               when='@8.5.0:~mpi+python')
-    depends_on("boost@1.59.0:1.63,1.66:+thread+system+serialization+iostreams+mpi+python",
-               when='@8.5.0:+mpi+python')
+    # There are issues with 1.65.1 and 1.65.0:
+    # https://github.com/dealii/dealii/issues/5262
+    # we take the patch from https://github.com/boostorg/serialization/pull/79
+    # more precisely its variation https://github.com/dealii/dealii/pull/5572#issuecomment-349742019
+    # 1.68.0 has issues with serialization https://github.com/dealii/dealii/issues/7074
+    # adopt https://github.com/boostorg/serialization/pull/105 as a fix
+    depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams',
+               patches=[patch('boost_1.65.1_singleton.patch',
+                              level=1,
+                              when='@1.65.1'),
+                        patch('boost_1.68.0.patch',
+                              level=1,
+                              when='@1.68.0'),
+                       ],
+               when='~python')
+    depends_on('boost@1.59.0:1.63,1.65.1,1.67.0:+thread+system+serialization+iostreams+python',
+               patches=[patch('boost_1.65.1_singleton.patch',
+                              level=1,
+                              when='@1.65.1'),
+                        patch('boost_1.68.0.patch',
+                              level=1,
+                              when='@1.68.0'),
+                       ],
+               when='+python')
     # bzip2 is not needed since 9.0
-    depends_on("bzip2", when='@:8.99')
-    depends_on("lapack")
-    depends_on("muparser")
-    depends_on("suite-sparse")
-    depends_on("tbb")
-    depends_on("zlib")
+    depends_on('bzip2', when='@:8.99')
+    depends_on('lapack')
+    depends_on('suite-sparse')
+    depends_on('tbb')
+    depends_on('zlib')
 
     # optional dependencies
-    depends_on("mpi",              when="+mpi")
-    depends_on("adol-c@2.6.4:",    when='@9.0:+adol-c')
-    depends_on("arpack-ng+mpi",    when='+arpack+mpi')
-    depends_on("assimp",           when='@9.0:+assimp')
-    depends_on("doxygen+graphviz", when='+doc')
-    depends_on("graphviz",         when='+doc')
-    depends_on("gsl",              when='@8.5.0:+gsl')
-    depends_on("hdf5+mpi",         when='+hdf5+mpi')
-    depends_on("cuda@8:",          when='+cuda')
-    depends_on("cmake@3.9:",       when='+cuda')
+    depends_on('mpi',              when='+mpi')
+    depends_on('adol-c@2.6.4:',    when='@9.0:+adol-c')
+    depends_on('arpack-ng+mpi',    when='+arpack+mpi')
+    depends_on('assimp',           when='@9.0:+assimp')
+    depends_on('doxygen+graphviz', when='+doc')
+    depends_on('graphviz',         when='+doc')
+    depends_on('gmsh+tetgen+netgen+oce', when='@9.0:+gmsh', type=('build', 'run'))
+    depends_on('gsl',              when='@8.5.0:+gsl')
+    depends_on('hdf5+mpi+hl',      when='+hdf5+mpi')
+    depends_on('cuda@8:',          when='+cuda')
+    depends_on('cmake@3.9:',       when='+cuda')
+    # older version of deal.II do not build with Cmake 3.10, see
+    # https://github.com/dealii/dealii/issues/5510
+    depends_on('cmake@:3.9.99',    when='@:8.99')
     # FIXME: concretizer bug. The two lines mimic what comes from PETSc
     # but we should not need it
-    depends_on("metis@5:+int64+real64",   when='+metis+int64')
-    depends_on("metis@5:~int64+real64",   when='+metis~int64')
-    depends_on("nanoflann",        when="@9.0:+nanoflann")
-    depends_on("netcdf+mpi",       when="+netcdf+mpi")
-    depends_on("netcdf-cxx",       when='+netcdf+mpi')
-    depends_on("oce",              when='+oce')
-    depends_on("p4est",            when='+p4est+mpi')
-    depends_on("petsc+mpi~int64",  when='+petsc+mpi~int64')
-    depends_on("petsc+mpi+int64",  when='+petsc+mpi+int64')
-    depends_on("petsc@:3.6.4",     when='@:8.4.1+petsc+mpi')
+    depends_on('metis@5:+int64+real64',   when='+metis+int64')
+    depends_on('metis@5:~int64+real64',   when='+metis~int64')
+    depends_on('muparser', when='+muparser')
+    depends_on('nanoflann',        when='@9.0:+nanoflann')
+    depends_on('netcdf+mpi',       when='+netcdf+mpi')
+    depends_on('netcdf-cxx',       when='+netcdf+mpi')
+    depends_on('oce',              when='+oce')
+    depends_on('p4est',            when='+p4est+mpi')
+    depends_on('petsc+mpi~int64',  when='+petsc+mpi~int64')
+    depends_on('petsc+mpi+int64',  when='+petsc+mpi+int64')
+    depends_on('petsc@:3.6.4',     when='@:8.4.1+petsc+mpi')
     depends_on('python',           when='@8.5.0:+python')
-    depends_on("slepc",            when='+slepc+petsc+mpi')
-    depends_on("slepc@:3.6.3",     when='@:8.4.1+slepc+petsc+mpi')
-    depends_on("slepc~arpack",     when='+slepc+petsc+mpi+int64')
-    depends_on("sundials~pthread", when='@9.0:+sundials')
-    depends_on("trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos",       when='+trilinos+mpi~int64')
-    depends_on("trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos~hypre", when="+trilinos+mpi+int64")
+    depends_on('scalapack',        when='@9.0:+scalapack')
+    depends_on('slepc',            when='+slepc+petsc+mpi')
+    depends_on('slepc@:3.6.3',     when='@:8.4.1+slepc+petsc+mpi')
+    depends_on('slepc~arpack',     when='+slepc+petsc+mpi+int64')
+    depends_on('sundials~pthread', when='@9.0:+sundials')
+    # do not require +rol to make concretization of xsdk possible
+    depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos',       when='+trilinos+mpi~int64~cuda')
+    depends_on('trilinos+amesos+aztec+epetra+ifpack+ml+muelu+sacado+teuchos~hypre', when='+trilinos+mpi+int64~cuda')
+    # FIXME: temporary disable Tpetra when using CUDA due to
+    # namespace "Kokkos::Impl" has no member "cuda_abort"
+    depends_on('trilinos@master+amesos+aztec+epetra+ifpack+ml+muelu+rol+sacado+teuchos~amesos2~ifpack2~intrepid2~kokkos~tpetra~zoltan2',       when='+trilinos+mpi~int64+cuda')
+    depends_on('trilinos@master+amesos+aztec+epetra+ifpack+ml+muelu+rol+sacado+teuchos~hypre~amesos2~ifpack2~intrepid2~kokkos~tpetra~zoltan2', when='+trilinos+mpi+int64+cuda')
 
     # check that the combination of variants makes sense
-    conflicts('+assimp', when='@:8.5.1')
-    conflicts('+nanoflann', when='@:8.5.1')
-    conflicts('+sundials', when='@:8.5.1')
-    conflicts('+adol-c', when='@:8.5.1')
-    conflicts('+gsl',    when='@:8.4.2')
-    conflicts('+python', when='@:8.4.2')
-    conflicts('+cuda', when='%gcc@6:')
-    for p in ['+arpack', '+hdf5', '+netcdf', '+p4est', '+petsc',
-              '+slepc', '+trilinos']:
-        conflicts(p, when='~mpi')
+    # 64-bit BLAS:
+    for p in ['openblas', 'intel-mkl', 'intel-parallel-studio+mkl']:
+        conflicts('^{0}+ilp64'.format(p), when='@:8.5.1',
+                  msg='64bit BLAS is only supported from 9.0.0')
+
+    # interfaces added in 9.0.0:
+    for p in ['assimp', 'gmsh', 'nanoflann', 'scalapack', 'sundials',
+              'adol-c']:
+        conflicts('+{0}'.format(p), when='@:8.5.1',
+                  msg='The interface to {0} is supported from version 9.0.0 '
+                      'onwards. Please explicitly disable this variant '
+                      'via ~{0}'.format(p))
+
+    conflicts('+slepc', when='~petsc',
+              msg='It is not possible to enable slepc interfaces '
+                  'without petsc.')
+
+    # interfaces added in 8.5.0:
+    for p in ['gsl', 'python']:
+        conflicts('+{0}'.format(p), when='@:8.4.2',
+                  msg='The interface to {0} is supported from version 8.5.0 '
+                      'onwards. Please explicitly disable this variant '
+                      'via ~{0}'.format(p))
+
+    # MPI requirements:
+    for p in ['arpack', 'hdf5', 'netcdf', 'p4est', 'petsc', 'scalapack',
+              'slepc', 'trilinos']:
+        conflicts('+{0}'.format(p), when='~mpi',
+                  msg='To enable {0} it is necessary to build deal.II with '
+                      'MPI support enabled.'.format(p))
 
     def cmake_args(self):
         spec = self.spec
@@ -182,13 +202,17 @@ class Dealii(CMakePackage):
             '-DLAPACK_INCLUDE_DIRS=%s;%s' % (
                 spec['lapack'].prefix.include, spec['blas'].prefix.include),
             '-DLAPACK_LIBRARIES=%s' % lapack_blas.joined(';'),
-            '-DMUPARSER_DIR=%s' % spec['muparser'].prefix,
             '-DUMFPACK_DIR=%s' % spec['suite-sparse'].prefix,
             '-DTBB_DIR=%s' % spec['tbb'].prefix,
             '-DZLIB_DIR=%s' % spec['zlib'].prefix,
             '-DDEAL_II_ALLOW_BUNDLED=OFF'
         ])
 
+        if (spec.satisfies('^openblas+ilp64') or
+            spec.satisfies('^intel-mkl+ilp64') or
+            spec.satisfies('^intel-parallel-studio+mkl+ilp64')):
+            options.append('-DLAPACK_WITH_64BIT_BLAS_INDICES=ON')
+
         if spec.satisfies('@:8.99'):
             options.extend([
                 # Cmake may still pick up system's bzip2, fix this:
@@ -215,6 +239,15 @@ class Dealii(CMakePackage):
                 '-DDEAL_II_COMPONENT_PYTHON_BINDINGS=%s' %
                 ('ON' if '+python' in spec else 'OFF')
             ])
+            if '+python' in spec:
+                python_exe = spec['python'].command.path
+                python_library = spec['python'].libs[0]
+                python_include = spec['python'].headers.directories[0]
+                options.extend([
+                    '-DPYTHON_EXECUTABLE=%s' % python_exe,
+                    '-DPYTHON_INCLUDE_DIR=%s' % python_include,
+                    '-DPYTHON_LIBRARY=%s' % python_library
+                ])
 
         # Set directory structure:
         if spec.satisfies('@:8.2.1'):
@@ -227,12 +260,25 @@ class Dealii(CMakePackage):
             ])
 
         # CUDA
-        # FIXME  -DDEAL_II_CUDA_FLAGS="-arch=sm_60"
         if '+cuda' in spec:
-            options.extend([
-                '-DDEAL_II_WITH_CUDA=ON',
-                '-DDEAL_II_WITH_CXX14=OFF'
-            ])
+            options.append(
+                '-DDEAL_II_WITH_CUDA=ON'
+            )
+            if not spec.satisfies('^cuda@9:'):
+                options.append('-DDEAL_II_WITH_CXX14=OFF')
+            cuda_arch = spec.variants['cuda_arch'].value
+            if cuda_arch is not None and cuda_arch[0] is not '':
+                if len(cuda_arch) > 1:
+                    raise InstallError(
+                        'deal.II only supports compilation for a single GPU!'
+                    )
+                flags = '-arch=sm_{0}'.format(cuda_arch[0])
+                # FIXME: there are some compiler errors in dealii
+                # with: flags = ' '.join(self.cuda_flags(cuda_arch))
+                # Stick with -arch=sm_xy for now.
+                options.append(
+                    '-DDEAL_II_CUDA_FLAGS={0}'.format(flags)
+                )
         else:
             options.extend([
                 '-DDEAL_II_WITH_CUDA=OFF',
@@ -255,8 +301,8 @@ class Dealii(CMakePackage):
         # variables:
         for library in (
                 'gsl', 'hdf5', 'p4est', 'petsc', 'slepc', 'trilinos', 'metis',
-                'sundials', 'nanoflann'):
-            if library in spec:
+                'sundials', 'nanoflann', 'assimp', 'gmsh', 'muparser'):
+            if ('+' + library) in spec:
                 options.extend([
                     '-D%s_DIR=%s' % (library.upper(), spec[library].prefix),
                     '-DDEAL_II_WITH_%s:BOOL=ON' % library.upper()
@@ -295,36 +341,12 @@ class Dealii(CMakePackage):
                 '-DDEAL_II_WITH_ARPACK=OFF'
             ])
 
-        # Assimp
-        if '+assimp' in spec:
-            options.extend([
-                '-DDEAL_II_WITH_ASSIMP=ON',
-                '-DASSIMP_DIR=%s' % spec['assimp'].prefix
-            ])
-        else:
-            options.extend([
-                '-DDEAL_II_WITH_ASSIMP=OFF'
-            ])
-
         # since Netcdf is spread among two, need to do it by hand:
         if '+netcdf' in spec and '+mpi' in spec:
-            # take care of lib64 vs lib installed lib locations:
-            if os.path.isdir(spec['netcdf-cxx'].prefix.lib):
-                netcdfcxx_lib_dir = spec['netcdf-cxx'].prefix.lib
-            else:
-                netcdfcxx_lib_dir = spec['netcdf-cxx'].prefix.lib64
-            if os.path.isdir(spec['netcdf'].prefix.lib):
-                netcdf_lib_dir = spec['netcdf'].prefix.lib
-            else:
-                netcdf_lib_dir = spec['netcdf'].prefix.lib64
-
+            netcdf = spec['netcdf-cxx'].libs + spec['netcdf'].libs
             options.extend([
                 '-DNETCDF_FOUND=true',
-                '-DNETCDF_LIBRARIES=%s;%s' % (
-                    join_path(netcdfcxx_lib_dir,
-                              'libnetcdf_c++.%s' % dso_suffix),
-                    join_path(netcdf_lib_dir,
-                              'libnetcdf.%s' % dso_suffix)),
+                '-DNETCDF_LIBRARIES=%s' % netcdf.joined(';'),
                 '-DNETCDF_INCLUDE_DIRS=%s;%s' % (
                     spec['netcdf-cxx'].prefix.include,
                     spec['netcdf'].prefix.include),
@@ -334,6 +356,20 @@ class Dealii(CMakePackage):
                 '-DDEAL_II_WITH_NETCDF=OFF'
             ])
 
+        if '+scalapack' in spec:
+            scalapack = spec['scalapack'].libs
+            options.extend([
+                '-DSCALAPACK_FOUND=true',
+                '-DSCALAPACK_INCLUDE_DIRS=%s' % (
+                    spec['scalapack'].prefix.include),
+                '-DSCALAPACK_LIBRARIES=%s' % scalapack.joined(';'),
+                '-DDEAL_II_WITH_SCALAPACK=ON'
+            ])
+        else:
+            options.extend([
+                '-DDEAL_II_WITH_SCALAPACK=OFF'
+            ])
+
         # Open Cascade
         if '+oce' in spec:
             options.extend([
diff --git a/var/spack/repos/builtin/packages/deconseq-standalone/package.py b/var/spack/repos/builtin/packages/deconseq-standalone/package.py
new file mode 100644
index 0000000000..ab6d2c3099
--- /dev/null
+++ b/var/spack/repos/builtin/packages/deconseq-standalone/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class DeconseqStandalone(Package):
+    """The DeconSeq tool can be used to automatically detect and efficiently
+    remove sequence contaminations from genomic and metagenomic datasets."""
+
+    homepage = "http://deconseq.sourceforge.net"
+    url      = "https://sourceforge.net/projects/deconseq/files/standalone/deconseq-standalone-0.4.3.tar.gz"
+
+    version('0.4.3', 'cb3fddb90e584d89fd9c2b6b8f2e20a2')
+
+    depends_on('perl@5:')
+
+    def install(self, spec, prefix):
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl', 'deconseq.pl')
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl', 'splitFasta.pl')
+
+        mkdirp(prefix.bin)
+        install('bwa64', prefix.bin)
+        install('bwaMAC', prefix.bin)
+        install('deconseq.pl', prefix.bin)
+        install('splitFasta.pl', prefix.bin)
+        install('DeconSeqConfig.pm', prefix)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(prefix.bin, 'bwa64'))
+        chmod('+x', join_path(prefix.bin, 'bwaMAC'))
+        chmod('+x', join_path(prefix.bin, 'deconseq.pl'))
+        chmod('+x', join_path(prefix.bin, 'splitFasta.pl'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PERL5LIB', prefix)
diff --git a/var/spack/repos/builtin/packages/dejagnu/package.py b/var/spack/repos/builtin/packages/dejagnu/package.py
index 7b083d00b4..f659f3174b 100644
--- a/var/spack/repos/builtin/packages/dejagnu/package.py
+++ b/var/spack/repos/builtin/packages/dejagnu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,7 @@ class Dejagnu(AutotoolsPackage):
     is to provide a single front end for all tests."""
 
     homepage = "https://www.gnu.org/software/dejagnu/"
-    url      = "http://mirror.team-cymru.org/gnu/dejagnu/dejagnu-1.6.tar.gz"
+    url      = "https://ftpmirror.gnu.org/dejagnu/dejagnu-1.6.tar.gz"
 
     version('1.6',   '1fdc2eb0d592c4f89d82d24dfdf02f0b')
     version('1.4.4', '053f18fd5d00873de365413cab17a666')
diff --git a/var/spack/repos/builtin/packages/delly2/package.py b/var/spack/repos/builtin/packages/delly2/package.py
index e922d2c566..d7dffea4a7 100644
--- a/var/spack/repos/builtin/packages/delly2/package.py
+++ b/var/spack/repos/builtin/packages/delly2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class Delly2(MakefilePackage):
        short-read massively parallel sequencing data.."""
 
     homepage = "https://github.com/dellytools/delly"
-    url      = "https://github.com/dellytools/delly"
+    git      = "https://github.com/dellytools/delly.git"
 
-    version('2017-08-03', commit='e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc',
-            git='https://github.com/dellytools/delly.git')
+    version('2017-08-03', commit='e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc')
 
     depends_on('htslib')
     depends_on('boost')
diff --git a/var/spack/repos/builtin/packages/denovogear/package.py b/var/spack/repos/builtin/packages/denovogear/package.py
new file mode 100644
index 0000000000..cd7cd87813
--- /dev/null
+++ b/var/spack/repos/builtin/packages/denovogear/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Denovogear(CMakePackage):
+    """DeNovoGear is a software package to detect de novo mutations using
+    next-generation sequencing data. It supports the analysis of many
+    differential experimental designs and uses advanced statistical models
+    to reduce the false positve rate."""
+
+    homepage = "https://github.com/denovogear/denovogear"
+    url      = "https://github.com/denovogear/denovogear/archive/v1.1.1.tar.gz"
+
+    version('1.1.1', 'da30e46851c3a774653e57f98fe62e5f')
+    version('1.1.0', '7d441d56462efb7ff5d3a6f6bddfd8b9')
+
+    depends_on('cmake@3.1:', type=('build'))
+    depends_on('boost@1.47:1.60', type=('build'))
+    depends_on('htslib@1.2:', type=('build'))
+    depends_on('eigen', type=('build'))
diff --git a/var/spack/repos/builtin/packages/dftfe/package.py b/var/spack/repos/builtin/packages/dftfe/package.py
new file mode 100644
index 0000000000..bac67b1fbe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dftfe/package.py
@@ -0,0 +1,65 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack import *
+
+
+class Dftfe(CMakePackage):
+    """Real-space DFT calculations using Finite Elements"""
+
+    homepage = "https://sites.google.com/umich.edu/dftfe/"
+    url      = "https://github.com/dftfeDevelopers/dftfe/archive/0.5.1.tar.gz"
+
+    maintainers = ['rmsds']
+
+    version('0.6.0', sha256='66b633a3aae2f557f241ee45b2faa41aa179e4a0bdf39c4ae2e679a2970845a1')
+    version('0.5.2', sha256='9dc4fa9f16b00be6fb1890d8af4a1cd3e4a2f06a2539df999671a09f3d26ec64')
+    version('0.5.1', sha256='e47272d3783cf675dcd8bc31da07765695164110bfebbbab29f5815531f148c1')
+    version('0.5.0', sha256='9aadb9a9b059f98f88c7756b417423dc67d02f1cdd2ed7472ba395fcfafc6dcb')
+
+    variant('scalapack', default=True, description='Use ScaLAPACK, strongly recommended for problem sizes >5000 electrons')
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
+
+    depends_on('mpi')
+    depends_on('dealii+p4est+petsc+slepc+int64+scalapack+mpi')
+    depends_on('dealii+p4est+petsc+slepc+int64+scalapack+mpi@9.0.0:', when='@0.5.1:')
+    depends_on('scalapack', when='+scalapack')
+    depends_on('alglib')
+    depends_on('libxc')
+    depends_on('spglib')
+    depends_on('libxml2')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DCMAKE_C_COMPILER={0}'.format(spec['mpi'].mpicc),
+            '-DCMAKE_CXX_COMPILER={0}'.format(spec['mpi'].mpicxx),
+            '-DALGLIB_DIR={0}'.format(spec['alglib'].prefix),
+            '-DLIBXC_DIR={0}'.format(spec['libxc'].prefix),
+            '-DXML_LIB_DIR={0}/lib'.format(spec['libxml2'].prefix),
+            '-DXML_INCLUDE_DIR={0}/include'.format(spec['libxml2'].prefix),
+            '-DSPGLIB_DIR={0}'.format(spec['spglib'].prefix),
+        ]
+
+        if spec.satisfies('^intel-mkl'):
+            args.append('-DWITH_INTEL_MKL=ON')
+        else:
+            args.append('-DWITH_INTEL_MKL=OFF')
+
+        if spec.satisfies('%gcc'):
+            args.append('-DCMAKE_C_FLAGS=-fpermissive')
+            args.append('-DCMAKE_CXX_FLAGS=-fpermissive')
+
+        return args
+
+    @when('@:0.5.2')
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        mkdirp(prefix.lib64)
+        install(join_path(self.build_directory, 'main'),
+                join_path(prefix.bin, 'dftfe'))
+        install(join_path(self.build_directory, 'libdftfe.so'),
+                prefix.lib64)
diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py
index 59abc88b15..b0459d5faa 100644
--- a/var/spack/repos/builtin/packages/dia/package.py
+++ b/var/spack/repos/builtin/packages/dia/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,9 @@ class Dia(Package):
     version('0.97.3',    '0e744a0f6a6c4cb6a089e4d955392c3c')
 
     depends_on('intltool', type='build')
-    depends_on('gtkplus@2.6.0:+X')
+    depends_on('gettext', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('gtkplus@2.6.0:')
     depends_on('libxslt')
     depends_on('python')
     depends_on('swig')
diff --git a/var/spack/repos/builtin/packages/dialign-tx/package.py b/var/spack/repos/builtin/packages/dialign-tx/package.py
index 009793216f..a5daf8f088 100644
--- a/var/spack/repos/builtin/packages/dialign-tx/package.py
+++ b/var/spack/repos/builtin/packages/dialign-tx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/diamond/package.py b/var/spack/repos/builtin/packages/diamond/package.py
new file mode 100644
index 0000000000..bf51e174ea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/diamond/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Diamond(CMakePackage):
+    """DIAMOND is a sequence aligner for protein and translated DNA searches,
+    designed for high performance analysis of big sequence data."""
+
+    homepage = "https://ab.inf.uni-tuebingen.de/software/diamond"
+    url      = "https://github.com/bbuchfink/diamond/archive/v0.9.14.tar.gz"
+
+    version('0.9.21', '6f3c53520f3dad37dfa3183d61f21dd5')
+    version('0.9.20', 'd73f4955909d16456d83b30d9c294b2b')
+    version('0.9.19', '8565d2d3bfe407ee778eeabe7c6a7fde')
+    version('0.9.14', 'b9e1d0bc57f07afa05dbfbb53c31aae2')
+    version('0.8.38', 'd4719c8a7947ba9f743446ac95cfe644')
+    version('0.8.26', '0d86305ab25cc9b3bb3564188d30fff2')
+
+    depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/diffsplice/package.py b/var/spack/repos/builtin/packages/diffsplice/package.py
new file mode 100644
index 0000000000..fa6c4f2907
--- /dev/null
+++ b/var/spack/repos/builtin/packages/diffsplice/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Diffsplice(MakefilePackage):
+    """A novel tool for discovering and quantitating alternative splicing
+    variants present in an RNA-seq dataset, without relying on annotated
+    transcriptome or pre-determined splice pattern."""
+
+    homepage = "http://www.netlab.uky.edu/p/bioinfo/DiffSplice"
+    url      = "http://protocols.netlab.uky.edu/~yin/download/diffsplice/diffsplice_0.1.1.tgz"
+
+    version('0.1.2beta', 'a1df6e0b50968f2c229d5d7f97327336')
+    version('0.1.1',     'be90e6c072402d5aae0b4e2cbb8c10ac')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('diffsplice', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/diffutils/package.py b/var/spack/repos/builtin/packages/diffutils/package.py
new file mode 100644
index 0000000000..b37ca50e15
--- /dev/null
+++ b/var/spack/repos/builtin/packages/diffutils/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Diffutils(AutotoolsPackage):
+    """GNU Diffutils is a package of several programs related to finding
+    differences between files."""
+
+    homepage = "https://www.gnu.org/software/diffutils/"
+    url      = "https://ftp.gnu.org/gnu/diffutils/diffutils-3.6.tar.xz"
+
+    version('3.6', sha256='d621e8bdd4b573918c8145f7ae61817d1be9deb4c8d2328a65cea8e11d783bd6')
+
+    build_directory = 'spack-build'
diff --git a/var/spack/repos/builtin/packages/direnv/package.py b/var/spack/repos/builtin/packages/direnv/package.py
index 83ec1db935..82272e472d 100644
--- a/var/spack/repos/builtin/packages/direnv/package.py
+++ b/var/spack/repos/builtin/packages/direnv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/discovar/package.py b/var/spack/repos/builtin/packages/discovar/package.py
index e0521d3e95..48e3509a17 100644
--- a/var/spack/repos/builtin/packages/discovar/package.py
+++ b/var/spack/repos/builtin/packages/discovar/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/discovardenovo/package.py b/var/spack/repos/builtin/packages/discovardenovo/package.py
new file mode 100644
index 0000000000..e3c86e314e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/discovardenovo/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Discovardenovo(AutotoolsPackage):
+    """DISCOVAR de novo is a large (and small) de novo genome assembler.
+       It quickly generates highly accurate and complete assemblies using the
+       same single library data as used by DISCOVAR. It currently doesn't
+       support variant calling, for that, please use DISCOVAR instead."""
+
+    homepage = "https://software.broadinstitute.org/software/discovar/blog/"
+    url      = "ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/discovardenovo-52488.tar.gz"
+
+    version('52488', '2b08c77b1b998d85be8048e5efb10358')
+
+    # lots of compiler errors with GCC7, works with 4.8.5
+    # and devs claim it works with 4.7 so I'm assuming 4.7-4.8'll work
+    conflicts('%gcc@5:')
+    conflicts('%gcc@:4.7.0')
+
+    depends_on('samtools')
+    depends_on('jemalloc')
diff --git a/var/spack/repos/builtin/packages/dislin/package.py b/var/spack/repos/builtin/packages/dislin/package.py
new file mode 100644
index 0000000000..ebf82b6394
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dislin/package.py
@@ -0,0 +1,57 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Dislin(Package):
+    """DISLIN is a high level and easy to use graphics library for displaying
+       data as curves,  bar graphs,  pie charts,  3D-colour plots,  surfaces,
+       contours and maps."""
+
+    homepage = "http://www.mps.mpg.de/dislin"
+    url      = "ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.tar.gz"
+
+    version('11.1.linux.i586_64', '34218c257efedaf706f058bdf111ce9d')
+    version('11.0.linux.i586_64', '6fb099b54f41db009cafc702eebb5bc6')
+
+    depends_on('motif')
+    depends_on('mesa')
+
+    @property
+    def libs(self):
+        query_parameters = self.spec.last_query.extra_parameters
+        query2libraries = {
+            tuple(): ['libdislin'],
+            ('d',): ['libdislin_d'],
+            ('c', ): ['libdislnc'],
+            ('cd',): ['libdislnc_d'],
+            ('cxx',): ['libdiscpp'],
+            ('java',): ['libdisjava']
+        }
+
+        key = tuple(query_parameters)
+        libraries = query2libraries[key]
+
+        return find_libraries(
+            libraries, root=self.prefix, shared=True, recursive=True
+        )
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('DISLIN', self.prefix)
+        run_env.set('DISLIN', self.prefix)
+        run_env.prepend_path('PATH', self.prefix)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.prefix)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.spec['motif'].prefix.lib)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.spec['mesa'].prefix.lib)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        run_env.prepend_path('LD_LIBRARY_PATH', self.prefix)
+
+    def install(self, spec, prefix):
+        install = Executable('./INSTALL')
+        install()
+        with working_dir('examples'):
+            install('dislin_d.h', prefix)
diff --git a/var/spack/repos/builtin/packages/diy/package.py b/var/spack/repos/builtin/packages/diy/package.py
new file mode 100644
index 0000000000..c05419682c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/diy/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Diy(CMakePackage):
+    """Data-parallel out-of-core library"""
+
+    homepage = "https://github.com/diatomic/diy"
+    url      = "https://github.com/diatomic/diy/archive/3.5.0.tar.gz"
+    git      = "https://github.com/diatomic/diy.git"
+
+    version('3.5.0', sha256='b3b5490441d521b6e9b33471c782948194bf95c7c3df3eb97bc5cf4530b91576')
+    version('master', branch='master')
+
+    def cmake_args(self):
+        args = ['-Dbuild_examples=off', '-Dbuild_tests=off']
+        return args
diff --git a/var/spack/repos/builtin/packages/dlpack/package.py b/var/spack/repos/builtin/packages/dlpack/package.py
index 69dd99b5a0..80db27a27b 100644
--- a/var/spack/repos/builtin/packages/dlpack/package.py
+++ b/var/spack/repos/builtin/packages/dlpack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Dlpack(Package):
     in deep learning systems."""
 
     homepage = "https://github.com/sjtuhpcc/dlpack"
+    git      = "https://github.com/dmlc/dlpack.git"
 
-    version('master', git='https://github.com/dmlc/dlpack.git', branch='master')
+    version('master', branch='master')
 
     def install(self, spec, prefix):
         install_tree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/dmd/package.py b/var/spack/repos/builtin/packages/dmd/package.py
new file mode 100644
index 0000000000..a84d65987b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dmd/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Dmd(MakefilePackage):
+    """DMD is the reference compiler for the D programming language."""
+
+    homepage = "https://github.com/dlang/dmd"
+    url      = "https://github.com/dlang/dmd/archive/v2.081.1.tar.gz"
+
+    version('2.081.1', sha256='14f3aafe1c93c86646aaeb3ed7361a5fc5a24374cf25c8848c81942bfd9fae1a')
+
+    depends_on('openssl')
+    depends_on('curl')
+
+    # https://wiki.dlang.org/Building_under_Posix
+    resource(name='druntime',
+             url='https://github.com/dlang/druntime/archive/v2.081.1.tar.gz',
+             md5='49c8ba48fcb1e53d553a52d8ed7f9164',
+             placement='druntime')
+    resource(name='phobos',
+             url='https://github.com/dlang/phobos/archive/v2.081.1.tar.gz',
+             md5='ccf4787275b490eb2ddfc6713f9e9882',
+             placement='phobos')
+    resource(name='tools',
+             url='https://github.com/dlang/tools/archive/v2.081.1.tar.gz',
+             md5='a3bc7ed3d60b39712ef011bf19b3d427',
+             placement='tools')
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.linux.bin64)
+        run_env.prepend_path('LIBRARY_PATH', self.prefix.linux.lib64)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.prefix.linux.lib64)
+
+    def edit(self, spec, prefix):
+        # Move contents to dmd/
+        mkdir = which('mkdir')
+        mkdir('dmd')
+        mv = which('mv')
+        dmd_files = [f for f in os.listdir('.')
+                     if not f.startswith(('dmd',
+                                          'druntime',
+                                          'phobos',
+                                          'tools',
+                                          'spack-build'))]
+        for f in dmd_files:
+            mv(f, 'dmd')
+        # Edit
+        dmd_mak = FileFilter('dmd/posix.mak')
+        dmd_mak.filter('$(PWD)/../install', prefix, string=True)
+        dr_mak = FileFilter('druntime/posix.mak')
+        dr_mak.filter('INSTALL_DIR=.*', 'INSTALL_DIR={0}'.format(prefix))
+        pb_mak = FileFilter('phobos/posix.mak')
+        pb_mak.filter('INSTALL_DIR = .*', 'INSTALL_DIR = {0}'.format(prefix))
+        tl_mak = FileFilter('tools/posix.mak')
+        tl_mak.filter('INSTALL_DIR = .*', 'INSTALL_DIR = {0}'.format(prefix))
+
+    def build(self, spec, prefix):
+        with working_dir('dmd'):
+            make('-f', 'posix.mak', 'AUTO_BOOTSTRAP=1')
+        with working_dir('phobos'):
+            make('-f', 'posix.mak')
+
+    def install(self, spec, prefix):
+        with working_dir('dmd'):
+            make('-f', 'posix.mak', 'install', 'AUTO_BOOTSTRAP=1')
+        with working_dir('phobos'):
+            make('-f', 'posix.mak', 'install')
+        with working_dir('tools'):
+            make('-f', 'posix.mak', 'install')
+        with working_dir('druntime'):
+            make('-f', 'posix.mak', 'install')
diff --git a/var/spack/repos/builtin/packages/dmlc-core/package.py b/var/spack/repos/builtin/packages/dmlc-core/package.py
index f463acb836..93da95f932 100644
--- a/var/spack/repos/builtin/packages/dmlc-core/package.py
+++ b/var/spack/repos/builtin/packages/dmlc-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,10 @@ class DmlcCore(CMakePackage):
     distributed machine learning libraries."""
 
     homepage = "https://github.com/dmlc/dmlc-core"
-    url      = "https://github.com/dmlc/dmlc-core.git"
+    git      = "https://github.com/dmlc/dmlc-core.git"
 
-    version('master', git='https://github.com/dmlc/dmlc-core.git')
-    version('20170508', git='https://github.com/dmlc/dmlc-core.git',
-    commit='a6c5701219e635fea808d264aefc5b03c3aec314')
+    version('master')
+    version('20170508', commit='a6c5701219e635fea808d264aefc5b03c3aec314')
 
     variant('openmp', default=False, description='Enable OpenMP support')
 
diff --git a/var/spack/repos/builtin/packages/dmtcp/package.py b/var/spack/repos/builtin/packages/dmtcp/package.py
new file mode 100644
index 0000000000..41665ef3f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dmtcp/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Dmtcp(AutotoolsPackage):
+    """DMTCP (Distributed MultiThreaded Checkpointing) transparently
+    checkpoints a single-host or distributed computation in user-space --
+    with no modifications to user code or to the O/S."""
+
+    homepage = "http://dmtcp.sourceforge.net/"
+    url      = "https://sourceforge.net/projects/dmtcp/files/2.5.2/dmtcp-2.5.2.tar.gz/download"
+
+    version('2.5.2', sha256='0e3e5e15bd401b7b6937f2b678cd7d6a252eab0a143d5740b89cc3bebb4282be')
diff --git a/var/spack/repos/builtin/packages/dmxproto/package.py b/var/spack/repos/builtin/packages/dmxproto/package.py
index b668dc9b58..ee1eb91be6 100644
--- a/var/spack/repos/builtin/packages/dmxproto/package.py
+++ b/var/spack/repos/builtin/packages/dmxproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Dmxproto(AutotoolsPackage):
 
     version('2.3.1', '7c52af95aac192e8de31bd9a588ce121')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/docbook-xml/package.py b/var/spack/repos/builtin/packages/docbook-xml/package.py
index c91473a669..62f87a6ae1 100644
--- a/var/spack/repos/builtin/packages/docbook-xml/package.py
+++ b/var/spack/repos/builtin/packages/docbook-xml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/docbook-xsl/package.py b/var/spack/repos/builtin/packages/docbook-xsl/package.py
index 1f3d774b82..1cd1c3ae3d 100644
--- a/var/spack/repos/builtin/packages/docbook-xsl/package.py
+++ b/var/spack/repos/builtin/packages/docbook-xsl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/dos2unix/package.py b/var/spack/repos/builtin/packages/dos2unix/package.py
index 2457f9b9e6..c73f53614f 100644
--- a/var/spack/repos/builtin/packages/dos2unix/package.py
+++ b/var/spack/repos/builtin/packages/dos2unix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py
new file mode 100644
index 0000000000..8b1f1ad9b6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from os import symlink
+from spack import *
+
+
+class DotnetCoreSdk(Package):
+    """The .NET Core SDK is a powerful development environment to write
+    applications for all types of infrastructure."""
+
+    homepage = "https://www.microsoft.com/net/"
+    url      = "https://github.com/dotnet/core/"
+
+    version('2.1.300',
+            url='https://download.microsoft.com/download/8/8/5/88544F33-836A'
+                '-49A5-8B67-451C24709A8F/dotnet-sdk-2.1.300-linux-x64.tar.gz',
+            sha224='80a6bfb1db5862804e90f819c1adeebe3d624eae0d6147e5d6694333'
+                'f0458afd7d34ce73623964752971495a310ff7fcc266030ce5aef82d5de'
+                '7293d94d13770')
+
+    variant('telemetry', default=False,
+            description='allow collection of telemetry data')
+
+    def setup_environment(self, spack_env, run_env):
+        if '-telemetry' in self.spec:
+            spack_env.set('DOTNET_CLI_TELEMETRY_OPTOUT', 1)
+
+    def install(self, spec, prefix):
+        mkdirp('bin')
+        symlink('../dotnet', 'bin/dotnet')
+        install_tree(".", prefix)
diff --git a/var/spack/repos/builtin/packages/double-conversion/package.py b/var/spack/repos/builtin/packages/double-conversion/package.py
index e4f4803a24..ca132f8b03 100644
--- a/var/spack/repos/builtin/packages/double-conversion/package.py
+++ b/var/spack/repos/builtin/packages/double-conversion/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/doxygen/package.py b/var/spack/repos/builtin/packages/doxygen/package.py
index 61cfdf8a89..3fa767f50d 100644
--- a/var/spack/repos/builtin/packages/doxygen/package.py
+++ b/var/spack/repos/builtin/packages/doxygen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Doxygen(CMakePackage):
     homepage = "http://www.stack.nl/~dimitri/doxygen/"
     url      = "http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.10.src.tar.gz"
 
+    version('1.8.14', '41d8821133e8d8104280030553e2b42b')
     version('1.8.12', '08e0f7850c4d22cb5188da226b209a96')
     version('1.8.11', 'f4697a444feaed739cfa2f0644abc19b')
     version('1.8.10', '79767ccd986f12a0f949015efb5f058f')
@@ -49,3 +31,8 @@ class Doxygen(CMakePackage):
 
     # optional dependencies
     depends_on("graphviz", when="+graphviz", type='run')
+
+    # Support C++14's std::shared_ptr. For details about this patch, see
+    # https://github.com/Sleepyowl/doxygen/commit/6c380ba91ae41c6d5c409a5163119318932ae2a3?diff=unified
+    # Also - https://github.com/doxygen/doxygen/pull/6588
+    patch('shared_ptr.patch', when='@1.8.14')
diff --git a/var/spack/repos/builtin/packages/doxygen/shared_ptr.patch b/var/spack/repos/builtin/packages/doxygen/shared_ptr.patch
new file mode 100644
index 0000000000..87581b5152
--- /dev/null
+++ b/var/spack/repos/builtin/packages/doxygen/shared_ptr.patch
@@ -0,0 +1,26 @@
+diff --git a/src/doxygen.cpp b/src/doxygen.cpp
+index 00826d6..a474129 100644
+--- a/src/doxygen.cpp
++++ b/src/doxygen.cpp
+@@ -342,6 +342,7 @@ static STLInfo g_stlinfo[] =
+   { "auto_ptr",             0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // deprecated
+   { "smart_ptr",            0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // C++11
+   { "unique_ptr",           0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // C++11
++  { "shared_ptr",           0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // C++14
+   { "weak_ptr",             0,                              0,                     "T",           "ptr",         0,            0,             FALSE,              FALSE }, // C++11
+   { "ios_base",             0,                              0,                     0,             0,             0,            0,             FALSE,              FALSE }, // C++11
+   { "error_code",           0,                              0,                     0,             0,             0,            0,             FALSE,              FALSE }, // C++11
+@@ -515,7 +516,7 @@ static void addSTLClasses(EntryNav *rootNav)
+     {
+       addSTLMember(classEntryNav,info->templType2,info->templName2);
+     }
+-    if (fullName=="std::auto_ptr" || fullName=="std::smart_ptr" ||
++    if (fullName=="std::auto_ptr" || fullName=="std::smart_ptr" || fullName=="std::shared_ptr" ||
+         fullName=="std::unique_ptr" || fullName=="std::weak_ptr")
+     {
+       Entry *memEntry = new Entry;
+@@ -11770,4 +11771,3 @@ void generateOutput()
+   delete Doxygen::symbolStorage;
+   g_successfulRun=TRUE;
+ }
+-
diff --git a/var/spack/repos/builtin/packages/dri2proto/package.py b/var/spack/repos/builtin/packages/dri2proto/package.py
index 00c4cc812d..86ee95a00f 100644
--- a/var/spack/repos/builtin/packages/dri2proto/package.py
+++ b/var/spack/repos/builtin/packages/dri2proto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Dri2proto(AutotoolsPackage):
 
     version('2.8', '19ea18f63d8ae8053c9fa84b60365b77')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/dri3proto/package.py b/var/spack/repos/builtin/packages/dri3proto/package.py
index 5f4604789d..6568e10f71 100644
--- a/var/spack/repos/builtin/packages/dri3proto/package.py
+++ b/var/spack/repos/builtin/packages/dri3proto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Dri3proto(AutotoolsPackage):
 
     version('1.0', '25e84a49a076862277ee12aebd49ff5f')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/dsdp/malloc.patch b/var/spack/repos/builtin/packages/dsdp/malloc.patch
new file mode 100644
index 0000000000..54b92628be
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dsdp/malloc.patch
@@ -0,0 +1,16 @@
+malloc.h does not exist on macOS. The same functionality is
+already provided by stdlib.h, so there's no need for it.
+Patch stolen from:
+https://github.com/sjackman/homebrew-science-deprecated/blob/master/dsdp.rb
+
+diff --git a/src/sys/dsdploginfo.c b/src/sys/dsdploginfo.c
+index 9313549..cee4f93 100644
+--- a/src/sys/dsdploginfo.c
++++ b/src/sys/dsdploginfo.c
+@@ -6,7 +6,6 @@
+ #include <stdarg.h>
+ #include <sys/types.h>
+ #include <stdlib.h>
+-#include <malloc.h>
+ #include "dsdpsys.h"
+ #include "dsdpbasictypes.h"
diff --git a/var/spack/repos/builtin/packages/dsdp/package.py b/var/spack/repos/builtin/packages/dsdp/package.py
new file mode 100644
index 0000000000..d10325c664
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dsdp/package.py
@@ -0,0 +1,52 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Dsdp(MakefilePackage):
+    """The DSDP software is a free open source implementation of an
+    interior-point method for semidefinite programming. It provides primal and
+    dual solutions, exploits low-rank structure and sparsity in the data, and
+    has relatively low memory requirements for an interior-point method. It
+    allows feasible and infeasible starting points and provides approximate
+    certificates of infeasibility when no feasible solution exists."""
+
+    homepage = "http://www.mcs.anl.gov/hs/software/DSDP/"
+    url      = "http://www.mcs.anl.gov/hs/software/DSDP/DSDP5.8.tar.gz"
+
+    version('5.8', '37c15a3c6c3f13e31262f65ac4364b5e')
+
+    depends_on('blas')
+    depends_on('lapack')
+
+    patch('malloc.patch')
+
+    build_targets = ['dsdpapi']
+
+    def edit(self, spec, prefix):
+        make_include = FileFilter('make.include')
+
+        # STEP 1: Set DSDPROOT.
+        make_include.filter('^#DSDPROOT.*=.*',
+                            'DSDPROOT = {0}'.format(os.getcwd()))
+
+        # STEP 2: Set the name of the C compiler.
+        make_include.filter('^CC.*=.*', 'CC = {0}'.format(spack_cc))
+
+        # STEP 5:
+        # Location of BLAS AND LAPACK libraries.
+        # Also include the math library and other libraries needed to
+        # link the BLAS to the C files that call them.
+        lapackblas = spec['lapack'].libs + spec['blas'].libs
+        make_include.filter('^LAPACKBLAS.*=.*',
+                            'LAPACKBLAS = {0}'.format(
+                                lapackblas.link_flags + ' -lm'))
+
+    def install(self, spec, prefix):
+        # Manual installation
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/dsrc/package.py b/var/spack/repos/builtin/packages/dsrc/package.py
new file mode 100644
index 0000000000..9846bc2b34
--- /dev/null
+++ b/var/spack/repos/builtin/packages/dsrc/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Dsrc(MakefilePackage):
+    """DNA Sequence Reads Compression is an application designed for
+    compression of data files containing reads from DNA sequencing in
+    FASTQ format."""
+
+    homepage = "http://sun.aei.polsl.pl/dsrc"
+    url      = "https://github.com/refresh-bio/DSRC/archive/v2.0.2.tar.gz"
+
+    version('2.0.2', '0a75deb6db948f9179df0756c259b870')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
+        install_tree('examples', prefix.examples)
diff --git a/var/spack/repos/builtin/packages/dtcmp/package.py b/var/spack/repos/builtin/packages/dtcmp/package.py
index c64fa540fa..2b93cf1ce2 100644
--- a/var/spack/repos/builtin/packages/dtcmp/package.py
+++ b/var/spack/repos/builtin/packages/dtcmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/dyninst/package.py b/var/spack/repos/builtin/packages/dyninst/package.py
index 8a18b99940..9d9ab52669 100644
--- a/var/spack/repos/builtin/packages/dyninst/package.py
+++ b/var/spack/repos/builtin/packages/dyninst/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,29 +11,38 @@ class Dyninst(Package):
     are executing without recompiling, re-linking, or re-executing."""
 
     homepage = "https://paradyn.org"
-    url = "https://github.com/dyninst/dyninst/archive/v9.2.0.tar.gz"
-    list_url = "http://www.dyninst.org/downloads/dyninst-8.x"
+    git      = "https://github.com/dyninst/dyninst.git"
 
-    version('9.3.2', 'a2bf03b6d1d424853e80d39b13e9c229')
-    version('9.3.0', 'edde7847dc673ca69bd59412af572450')
-    version('9.2.0', 'ad023f85e8e57837ed9de073b59d6bab',
-            url="https://github.com/dyninst/dyninst/archive/v9.2.0.tar.gz")
-    version('9.1.0', '5c64b77521457199db44bec82e4988ac',
-            url="http://www.paradyn.org/release9.1.0/DyninstAPI-9.1.0.tgz")
-    version('8.2.1', 'abf60b7faabe7a2e4b54395757be39c7',
-            url="http://www.paradyn.org/release8.2/DyninstAPI-8.2.1.tgz")
-    version('8.1.2', 'bf03b33375afa66fe0efa46ce3f4b17a',
-            url="http://www.paradyn.org/release8.1.2/DyninstAPI-8.1.2.tgz")
-    version('8.1.1', 'd1a04e995b7aa70960cd1d1fac8bd6ac',
-            url="http://www.paradyn.org/release8.1/DyninstAPI-8.1.1.tgz")
+    version('develop', branch='master')
+    version('10.0.0', tag='v10.0.0')
+    version('9.3.2', tag='v9.3.2')
+    version('9.3.0', tag='v9.3.0')
+    version('9.2.0', tag='v9.2.0')
+    version('9.1.0', tag='v9.1.0')
+    version('8.2.1', tag='v8.2.1')
+    version('8.1.2', tag='v8.1.2')
+    version('8.1.1', tag='v8.1.1')
 
     variant('stat_dysect', default=False,
             description="patch for STAT's DySectAPI")
 
+    # Dyninst depends on libelf and libdwarf prior to @9.3.0
+    # Dyninst depends on elfutils and libdwarf from @9.3.0 to but
+    # not including @develop
+    # Dyninst depends on elfutils and elfutils libdw from @develop forward
+    # elf@0 is an abstaction for libelf
+    # elf@1 is an abstaction for elfutils
     depends_on("elf@0", type='link', when='@:9.2.99')
+    # The sorting algorithm puts numbered releases as newer than alphabetic
+    # releases, but spack has special logic in place to ensure that
+    # develop is considered newer than all other releases.
+    # So, develop is included in the elf@1 line below.
     depends_on("elf@1", type='link', when='@9.3.0:')
-    depends_on("libdwarf")
+    depends_on("libdwarf", when='@:9')
     depends_on("boost@1.42:")
+    depends_on('libiberty+pic')
+    depends_on("tbb@2018.6:", when='@develop')
+    depends_on("tbb@2018.6:", when='@10:')
     depends_on('cmake', type='build')
 
     patch('stat_dysect.patch', when='+stat_dysect')
@@ -67,7 +57,8 @@ class Dyninst(Package):
             return
 
         libelf = spec['elf'].prefix
-        libdwarf = spec['libdwarf'].prefix
+        if spec.satisfies('@:9'):
+            libdwarf = spec['libdwarf'].prefix
 
         with working_dir('spack-build', create=True):
             args = ['..',
@@ -77,10 +68,21 @@ class Dyninst(Package):
                     '-DLIBELF_INCLUDE_DIR=%s'   % join_path(
                         libelf.include, 'libelf'),
                     '-DLIBELF_LIBRARIES=%s'     % join_path(
-                        libelf.lib, 'libelf.so'),
-                    '-DLIBDWARF_INCLUDE_DIR=%s' % libdwarf.include,
-                    '-DLIBDWARF_LIBRARIES=%s'   % join_path(
-                        libdwarf.lib, 'libdwarf.so')]
+                        libelf.lib, "libelf." + dso_suffix)]
+            if spec.satisfies('@:9'):
+                args.append('-DLIBDWARF_INCLUDE_DIR=%s' % libdwarf.include)
+                args.append('-DLIBDWARF_LIBRARIES=%s'   % join_path(
+                    libdwarf.lib, "libdwarf." + dso_suffix))
+            # For @develop + use elfutils libdw, libelf is an abstraction
+            # we are really using elfutils here
+            if spec.satisfies('@develop') or spec.satisfies('@10:'):
+                tbb = spec['tbb'].prefix
+                args.append('-DTBB_INCLUDE_DIRS=%s' % tbb.include)
+                args.append('-DTBB_LIBRARIES=%s'    % join_path(
+                    tbb.lib, "libtbb." + dso_suffix))
+                args.append('-DLIBDWARF_INCLUDE_DIR=%s' % libelf.include)
+                args.append('-DLIBDWARF_LIBRARIES=%s'   % join_path(
+                    libelf.lib, "libdw." + dso_suffix))
             if spec.satisfies('arch=linux-redhat7-ppc64le'):
                 args.append('-Darch_ppc64_little_endian=1')
             args += std_cmake_args
diff --git a/var/spack/repos/builtin/packages/ea-utils/package.py b/var/spack/repos/builtin/packages/ea-utils/package.py
index 181248a401..acbdd641ef 100644
--- a/var/spack/repos/builtin/packages/ea-utils/package.py
+++ b/var/spack/repos/builtin/packages/ea-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/easybuild/package.py b/var/spack/repos/builtin/packages/easybuild/package.py
index 4fa7eb99fb..333e308bb8 100644
--- a/var/spack/repos/builtin/packages/easybuild/package.py
+++ b/var/spack/repos/builtin/packages/easybuild/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ebms/package.py b/var/spack/repos/builtin/packages/ebms/package.py
index 252be1bd3d..3bef478c94 100644
--- a/var/spack/repos/builtin/packages/ebms/package.py
+++ b/var/spack/repos/builtin/packages/ebms/package.py
@@ -1,27 +1,8 @@
-#############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -37,13 +18,13 @@ class Ebms(MakefilePackage):
     """
 
     homepage = "https://github.com/ANL-CESAR/EBMS"
-    url = "https://github.com/ANL-CESAR/EBMS/archive/master.tar.gz"
+    git      = "https://github.com/ANL-CESAR/EBMS.git"
 
-    version('develop', git='https://github.com/ANL-CESAR/EBMS.git')
+    version('develop')
 
     variant('mpi', default=True, description='Build with MPI support')
 
-    depends_on('mpi', when='+mpi')
+    depends_on('mpi@2:', when='+mpi')
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/eccodes/cmake_install_rpath.patch b/var/spack/repos/builtin/packages/eccodes/cmake_install_rpath.patch
new file mode 100644
index 0000000000..7e2b250883
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eccodes/cmake_install_rpath.patch
@@ -0,0 +1,11 @@
+--- a/cmake/ecbuild_append_to_rpath.cmake
++++ b/cmake/ecbuild_append_to_rpath.cmake
+@@ -31,7 +31,7 @@ function( _path_append var path )
+ 	else()
+ 		list( FIND ${var} ${path} _found )
+ 		if( _found EQUAL "-1" )
+-			set( ${var} "${${var}}:${path}" PARENT_SCOPE )
++			set( ${var} "${${var}};${path}" PARENT_SCOPE )
+ 		endif()
+ 	endif()
+ endfunction()
diff --git a/var/spack/repos/builtin/packages/eccodes/enable_only_jasper.patch b/var/spack/repos/builtin/packages/eccodes/enable_only_jasper.patch
index 9f7dc22ac5..ad09c75199 100644
--- a/var/spack/repos/builtin/packages/eccodes/enable_only_jasper.patch
+++ b/var/spack/repos/builtin/packages/eccodes/enable_only_jasper.patch
@@ -1,17 +1,25 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index bf4d78b..ea2f3e9 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -162,8 +162,6 @@ if( ENABLE_JPG )
-     set(CMAKE_PREFIX_PATH ${_CMAKE_PREFIX_PATH})    # Restore CMAKE_PREFIX_PATH
-     set(CMAKE_WARN_DEPRECATED ON)  # Remove suppression
+@@ -151,18 +151,7 @@ set( HAVE_LIBOPENJPEG 0 )
  
--    find_package( OpenJPEG )
+ if( ENABLE_JPG )
+ 
+-    # Note: This is a deprecated feature but we need it to find Jasper at ECMWF.
+-    #       ecbuild_add_extra_search_paths modifies CMAKE_PREFIX_PATH
+-    #       which can affect future package discovery if not undone by the caller.
+-    #       The current CMAKE_PREFIX_PATH is backed up as _CMAKE_PREFIX_PATH
+-    #
+-    set(CMAKE_WARN_DEPRECATED OFF) # Suppress deprecation message
+-    ecbuild_add_extra_search_paths( jasper )
+     find_package( Jasper )
+-    set(CMAKE_PREFIX_PATH ${_CMAKE_PREFIX_PATH})    # Restore CMAKE_PREFIX_PATH
+-    set(CMAKE_WARN_DEPRECATED ON)  # Remove suppression
 -
+-    find_package( OpenJPEG )
+ 
      if( JASPER_FOUND )
          list( APPEND ECCODES_TPLS Jasper )
-         set( HAVE_JPEG 1 )
-@@ -172,12 +170,6 @@ if( ENABLE_JPG )
+@@ -172,12 +161,6 @@ if( ENABLE_JPG )
          string(REGEX REPLACE "^([0-9]+)\\.[0-9]+\\.[0-9]+.*" "\\1" JASPER_VERSION_MAJOR "${JASPER_VERSION_STRING}")
      endif()
  
diff --git a/var/spack/repos/builtin/packages/eccodes/enable_only_openjpeg.patch b/var/spack/repos/builtin/packages/eccodes/enable_only_openjpeg.patch
index 7bf8b7b59f..29a6dff454 100644
--- a/var/spack/repos/builtin/packages/eccodes/enable_only_openjpeg.patch
+++ b/var/spack/repos/builtin/packages/eccodes/enable_only_openjpeg.patch
@@ -1,5 +1,3 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index bf4d78b..3ae50ba 100644
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
 @@ -151,27 +151,8 @@ set( HAVE_LIBOPENJPEG 0 )
diff --git a/var/spack/repos/builtin/packages/eccodes/package.py b/var/spack/repos/builtin/packages/eccodes/package.py
index 3843ce2ddc..55303d4ed2 100644
--- a/var/spack/repos/builtin/packages/eccodes/package.py
+++ b/var/spack/repos/builtin/packages/eccodes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
@@ -30,9 +11,11 @@ class Eccodes(CMakePackage):
     """ecCodes is a package developed by ECMWF for processing meteorological
     data in GRIB (1/2), BUFR (3/4) and GTS header formats."""
 
-    homepage = "https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home"
-    url      = "https://software.ecmwf.int/wiki/download/attachments/45757960/eccodes-2.2.0-Source.tar.gz?api=v2"
-    list_url = "https://software.ecmwf.int/wiki/display/ECC/Releases"
+    homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home'
+    url = 'https://software.ecmwf.int/wiki/download/attachments/45757960/eccodes-2.2.0-Source.tar.gz?api=v2'
+    list_url = 'https://software.ecmwf.int/wiki/display/ECC/Releases'
+
+    maintainers = ['skosukhin']
 
     version('2.5.0', '5a7e92c58418d855082fa573efd352aa')
     version('2.2.0', 'b27e6f0a3eea5b92dac37372e4c45a62')
@@ -53,17 +36,28 @@ class Eccodes(CMakePackage):
             description='Enable memory based access to definitions/samples')
     variant('python', default=False,
             description='Enable the Python interface')
-    variant('fortran', default=True, description='Enable the Fortran support')
+    variant('fortran', default=False, description='Enable the Fortran support')
+    variant('examples', default=True,
+            description='Build the examples (part of the full test suite)')
+    variant('test', default=True, description='Enable the tests')
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo', 'Production'))
 
+    # The building script tries to find an optional package valgrind when
+    # tests are enabled but the testing scripts don't use it.
+    # depends_on('valgrind', type='test', when='+test')
+
     depends_on('netcdf', when='+netcdf')
-    depends_on('openjpeg', when='jp2k=openjpeg')
+    depends_on('openjpeg@1.5.0:1.5.999,2.1.0:2.1.999', when='jp2k=openjpeg')
     depends_on('jasper', when='jp2k=jasper')
     depends_on('libpng', when='+png')
     depends_on('libaec', when='+aec')
-    depends_on('python@:2', when='+python')
+    # Can be built with Python2 or Python3.
+    depends_on('python', when='+memfs', type='build')
+    # The interface works only for Python2.
+    depends_on('python@2.6:2.999', when='+python',
+               type=('build', 'link', 'run'))
     depends_on('py-numpy', when='+python', type=('build', 'run'))
     extends('python', when='+python')
 
@@ -74,21 +68,62 @@ class Eccodes(CMakePackage):
     patch('enable_only_openjpeg.patch', when='jp2k=openjpeg')
     patch('enable_only_jasper.patch', when='jp2k=jasper')
 
+    # CMAKE_INSTALL_RPATH must be a semicolon-separated list.
+    patch('cmake_install_rpath.patch')
+
+    @run_before('cmake')
+    def check_fortran(self):
+        if '+fortran' in self.spec and self.compiler.fc is None:
+            raise InstallError(
+                'Fortran interface requires a Fortran compiler!')
+
     def cmake_args(self):
-        variants = ['+netcdf', '+png', '+aec', '+pthreads',
-                    '+openmp', '+memfs', '+python', '+fortran']
-        options = ['NETCDF', 'PNG', 'AEC', 'ECCODES_THREADS',
-                   'ECCODES_OMP_THREADS', 'MEMFS', 'PYTHON', 'FORTRAN']
+        var_opt_list = [('+pthreads', 'ECCODES_THREADS'),
+                        ('+openmp', 'ECCODES_OMP_THREADS'),
+                        ('+memfs', 'MEMFS'),
+                        ('+python', 'PYTHON'),
+                        ('+fortran', 'FORTRAN'),
+                        ('+examples', 'EXAMPLES'),
+                        ('+test', 'TESTS'),
+                        ('+test', 'EXTRA_TESTS')]
 
-        args = map(lambda var, opt:
-                   "-DENABLE_%s=%s" %
-                   (opt, 'ON' if var in self.spec else 'OFF'),
-                   variants,
-                   options)
+        args = ['-DENABLE_%s=%s' % (opt, 'ON' if var in self.spec else 'OFF')
+                for var, opt in var_opt_list]
+
+        if '+netcdf' in self.spec:
+            args.extend(['-DENABLE_NETCDF=ON',
+                         # Prevent overriding by environment variable
+                         # HDF5_ROOT.
+                         '-DHDF5_ROOT=' + self.spec['hdf5'].prefix,
+                         # Prevent possible overriding by environment variables
+                         # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH.
+                         '-DNETCDF_PATH=' + self.spec['netcdf'].prefix])
+        else:
+            args.append('-DENABLE_NETCDF=OFF')
 
         if self.spec.variants['jp2k'].value == 'none':
             args.append('-DENABLE_JPG=OFF')
         else:
             args.append('-DENABLE_JPG=ON')
 
+        if self.spec.variants['jp2k'].value == 'openjpeg':
+            args.append('-DOPENJPEG_PATH=' + self.spec['openjpeg'].prefix)
+
+        if '+png' in self.spec:
+            args.extend(['-DENABLE_PNG=ON',
+                         '-DZLIB_ROOT=' + self.spec['zlib'].prefix])
+        else:
+            args.append('-DENABLE_PNG=OFF')
+
+        if '+aec' in self.spec:
+            args.extend(['-DENABLE_AEC=ON',
+                         # Prevent overriding by environment variables
+                         # AEC_DIR and AEC_PATH.
+                         '-DAEC_DIR=' + self.spec['libaec'].prefix])
+        else:
+            args.append('-DENABLE_AEC=OFF')
+
+        if '^python' in self.spec:
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH=' + python.path)
+
         return args
diff --git a/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py
new file mode 100644
index 0000000000..52937c57d0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eclipse-gcj-parser/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class EclipseGcjParser(Package):
+    """GCJ requires the Eclipse Java parser, but does not ship with it.
+    This builds that parser into an executable binary, thereby
+    making GCJ work."""
+
+    homepage = "https://github.com/spack/spack/issues/8165"
+    url = "ftp://sourceware.org/pub/java/ecj-4.8.jar"
+    # Official download found at (see ecj-4.8M4.jar and ecjsrc-4.8M4.jar)
+    # http://download.eclipse.org/eclipse/downloads/drops4/S-4.8M4-201712062000/
+
+    maintainers = ['citibeth']
+
+    version('4.8', 'd7cd6a27c8801e66cbaa964a039ecfdb', expand=False)
+
+    phases = ('build', 'install')
+
+    @property
+    def gcj(self):
+        """Obtain Executable for the gcj included with this GCC,
+        even in the face of GCC binaries with version numbers
+        included in their names."""
+
+        dir, gcc = os.path.split(str(self.compiler.cc))
+        if 'gcc' not in gcc:
+            raise ValueError(
+                'Package {0} requires GCC to build'.format(self.name))
+
+        return Executable(join_path(dir, gcc.replace('gcc', 'gcj')))
+
+    def build(self, spec, prefix):
+        self.gcj(
+            '-o', 'ecj1',
+            '--main=org.eclipse.jdt.internal.compiler.batch.GCCMain',
+            'ecj-4.8.jar')
+
+    def install(self, spec, prefix):
+        mkdirp(spec.prefix.bin)
+        install('ecj1', spec.prefix.bin)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py b/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py
index ee1a881aff..bd2117cd99 100644
--- a/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py
+++ b/var/spack/repos/builtin/packages/ecp-proxy-apps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
 from spack import *
@@ -33,27 +14,56 @@ class EcpProxyApps(Package):
        installs the ECP proxy application suite.
     """
 
-    homepage = "https://exascaleproject.github.io/proxy-apps"
+    tags = ['proxy-app', 'ecp-proxy-app']
+    maintainers = ['bhatele']
 
+    homepage = "https://exascaleproject.github.io/proxy-apps"
     # Dummy url
     url = 'https://github.com/exascaleproject/proxy-apps/archive/v1.0.tar.gz'
 
-    tags = ['proxy-app', 'ecp-proxy-app']
+    version('2.0', sha256='5f3cb3a772224e738c1dab42fb34d40f6b313af51ab1c575fb334e573e41e09a')
+    version('1.1', '15825c318acd3726fd8e72803b1c1090')
+    version('1.0', '8b3f00f05e6cde88d8d913da4293ee62')
+
+    variant('candle', default=False,
+            description='Also build CANDLE Benchmarks')
+
+    # Added with release 2.0
+    depends_on('ember@1.0.0', when='@2.0:')
+    depends_on('miniqmc@0.4.0', when='@2.0:')
+    depends_on('minivite@1.0', when='@2.0:')
+    depends_on('picsarlite@0.1', when='@2.0:')
+    depends_on('thornado-mini@1.0', when='@2.0:')
+
+    depends_on('amg@1.1', when='@2.0:')
+    depends_on('candle-benchmarks@0.1', when='+candle @2.0:')
+    depends_on('laghos@1.1', when='@2.0:')
+    depends_on('macsio@1.1', when='@2.0:')
+    depends_on('miniamr@1.4.1', when='@2.0:')
+    depends_on('sw4lite@1.1', when='@2.0:')
+    depends_on('xsbench@18', when='@2.0:')
+
+    # Added with release 1.1
+    depends_on('examinimd@1.0', when='@1.1:')
+
+    depends_on('nekbone@17.0', when='@1.0:')
+    depends_on('swfft@1.0', when='@1.0:')
+
+    # Dependencies for versions 1.0:1.1
+    depends_on('amg@1.0', when='@1.0:1.1')
+    depends_on('candle-benchmarks@0.0', when='+candle @1.0:1.1')
+    depends_on('laghos@1.0', when='@1.0:1.1')
+    depends_on('macsio@1.0', when='@1.0:1.1')
+    depends_on('miniamr@1.4.0', when='@1.0:1.1')
+    depends_on('sw4lite@1.0', when='@1.0:1.1')
+    depends_on('xsbench@14', when='@1.0:1.1')
 
-    version('1.0', '5a26b184f506afeb7d221f15c0e8f153')
+    # Removed after release 1.1
+    depends_on('minife@2.1.0', when='@1.0:1.1')
+    depends_on('minitri@1.0', when='@1.0:1.1')
 
-    depends_on('amg@1.0', when='@1.0')
-    depends_on('candle-benchmarks@1.0', when='@1.0')
+    # Removed after release 1.0
     depends_on('comd@1.1', when='@1.0')
-    depends_on('laghos@1.0', when='@1.0')
-    depends_on('macsio@1.0', when='@1.0')
-    depends_on('miniamr@1.4.0', when='@1.0')
-    depends_on('minife@2.1.0', when='@1.0')
-    depends_on('minitri@1.0', when='@1.0')
-    depends_on('nekbone@17.0', when='@1.0')
-    depends_on('sw4lite@1.0', when='@1.0')
-    depends_on('swfft@1.0', when='@1.0')
-    depends_on('xsbench@14', when='@1.0')
 
     # Dummy install for now,  will be removed when metapackage is available
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/ed/package.py b/var/spack/repos/builtin/packages/ed/package.py
new file mode 100644
index 0000000000..c9b8b872b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ed/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ed(AutotoolsPackage):
+    """GNU ed is a line-oriented text editor. It is used to create,
+       display, modify and otherwise manipulate text files, both
+       interactively and via shell scripts."""
+
+    homepage = "https://www.gnu.org/software/ed"
+    url      = "https://ftpmirror.gnu.org/ed/ed-1.4.tar.gz"
+
+    version('1.4', 'da0ddc0e0b0bec2da4b13b0d0d1bce2b')
+
+    parallel = False
diff --git a/var/spack/repos/builtin/packages/editres/package.py b/var/spack/repos/builtin/packages/editres/package.py
index 1bba68d305..9501f00637 100644
--- a/var/spack/repos/builtin/packages/editres/package.py
+++ b/var/spack/repos/builtin/packages/editres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Editres(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxmu')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/eigen/find-ptscotch.patch b/var/spack/repos/builtin/packages/eigen/find-ptscotch.patch
new file mode 100644
index 0000000000..4f6e286b72
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eigen/find-ptscotch.patch
@@ -0,0 +1,27 @@
+Version 3.3.4 contained a bug that prevented it from finding scotch~mpi.
+
+diff --git a/tmp/FindPTSCOTCH.cmake b/cmake/FindPTSCOTCH.cmake
+index 1396d05..23451b1 100644
+--- a/tmp/FindPTSCOTCH.cmake
++++ b/cmake/FindPTSCOTCH.cmake
+@@ -167,11 +167,11 @@ endif()
+
+ # If found, add path to cmake variable
+ # ------------------------------------
++unset(PTSCOTCH_INCLUDE_DIRS)
+ foreach(ptscotch_hdr ${PTSCOTCH_hdrs_to_find})
+   if (PTSCOTCH_${ptscotch_hdr}_DIRS)
+     list(APPEND PTSCOTCH_INCLUDE_DIRS "${PTSCOTCH_${ptscotch_hdr}_DIRS}")
+   else ()
+-    set(PTSCOTCH_INCLUDE_DIRS "PTSCOTCH_INCLUDE_DIRS-NOTFOUND")
+     if (NOT PTSCOTCH_FIND_QUIETLY)
+       message(STATUS "Looking for ptscotch -- ${ptscotch_hdr} not found")
+     endif()
+@@ -255,7 +255,6 @@ foreach(ptscotch_lib ${PTSCOTCH_libs_to_find})
+     list(APPEND PTSCOTCH_LIBRARIES "${PTSCOTCH_${ptscotch_lib}_LIBRARY}")
+     list(APPEND PTSCOTCH_LIBRARY_DIRS "${${ptscotch_lib}_lib_path}")
+   else ()
+-    list(APPEND PTSCOTCH_LIBRARIES "${PTSCOTCH_${ptscotch_lib}_LIBRARY}")
+     if (NOT PTSCOTCH_FIND_QUIETLY)
+       message(STATUS "Looking for ptscotch -- lib ${ptscotch_lib} not found")
+     endif()
diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py
index 9e7d8c392e..6e5582d233 100644
--- a/var/spack/repos/builtin/packages/eigen/package.py
+++ b/var/spack/repos/builtin/packages/eigen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,10 @@ class Eigen(CMakePackage):
     """
 
     homepage = 'http://eigen.tuxfamily.org/'
-    url      = 'https://bitbucket.org/eigen/eigen/get/3.3.3.tar.bz2'
+    url      = 'https://bitbucket.org/eigen/eigen/get/3.3.4.tar.bz2'
 
+    version('3.3.5', 'e83549a79d1b721da0f8899ab34edf95')
+    version('3.3.4', 'a7aab9f758249b86c93221ad417fbe18')
     version('3.3.3', 'b2ddade41040d9cf73b39b4b51e8775b')
     version('3.3.1', 'edb6799ef413b0868aace20d2403864c')
     version('3.2.10', 'a85bb68c82988648c3d53ba9768d7dcbcfe105f8')
@@ -58,3 +41,5 @@ class Eigen(CMakePackage):
     depends_on('suite-sparse', when='+suitesparse')
     depends_on('mpfr@2.3.0:', when='+mpfr')
     depends_on('gmp', when='+mpfr')
+
+    patch('find-ptscotch.patch', when='@3.3.4')
diff --git a/var/spack/repos/builtin/packages/elasticsearch/package.py b/var/spack/repos/builtin/packages/elasticsearch/package.py
new file mode 100644
index 0000000000..3492774c35
--- /dev/null
+++ b/var/spack/repos/builtin/packages/elasticsearch/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Elasticsearch(Package):
+    """Elasticsearch is a search engine based on Lucene. It provides a
+    distributed, multitenant-capable full-text search engine with an HTTP web
+    interface and schema-free JSON documents.
+    """
+
+    homepage = "https://www.elastic.co/"
+    url      = "https://artifacts.elastic.co/downloads/elasticsearch/elasticsearch-6.2.4.tar.gz"
+
+    version('6.4.0', '5c23c99a52600b250a6871bf6a744e8b')
+    version('6.2.4', '692d01956fe7aee2d08ac0fbf7b7a19e')
+
+    depends_on('jdk', type='run')
+
+    def install(self, spec, prefix):
+        dirs = [
+            'bin',
+            'config',
+            'lib',
+            'modules',
+            'plugins']
+
+        for d in dirs:
+            install_tree(d, join_path(prefix, d))
diff --git a/var/spack/repos/builtin/packages/elemental/package.py b/var/spack/repos/builtin/packages/elemental/package.py
index 14e376628c..43a34fcc40 100644
--- a/var/spack/repos/builtin/packages/elemental/package.py
+++ b/var/spack/repos/builtin/packages/elemental/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 from spack.spec import UnsupportedCompilerError
@@ -32,9 +13,10 @@ class Elemental(CMakePackage):
        and optimization library."""
 
     homepage = "http://libelemental.org"
-    url      = "https://github.com/elemental/Elemental/archive/v0.87.6.tar.gz"
+    url      = "https://github.com/elemental/Elemental/archive/v0.87.7.tar.gz"
+    git      = "https://github.com/elemental/Elemental.git"
 
-    version('develop', git='https://github.com/elemental/Elemental.git', branch='master')
+    version('develop', branch='master')
     version('0.87.7', '6c1e7442021c59a36049e37ea69b8075')
     version('0.87.6', '9fd29783d45b0a0e27c0df85f548abe9')
 
@@ -66,8 +48,8 @@ class Elemental(CMakePackage):
     variant('build_type', default='Release',
             description='The build type to build',
             values=('Debug', 'Release'))
-    variant('blas', default='openblas', values=('openblas', 'mkl'),
-            description='Enable the use of OpenBlas/MKL')
+    variant('blas', default='openblas', values=('openblas', 'mkl', 'accelerate', 'essl'),
+            description='Enable the use of OpenBlas/MKL/Accelerate/ESSL')
     variant('mpfr', default=False,
             description='Support GNU MPFR\'s'
             'arbitrary-precision floating-point arithmetic')
@@ -75,6 +57,7 @@ class Elemental(CMakePackage):
     # Note that #1712 forces us to enumerate the different blas variants
     depends_on('blas', when='~openmp_blas ~int64_blas')
     # Hack to forward variant to openblas package
+    depends_on('openblas', when='blas=openblas ~openmp_blas ~int64_blas')
     # Allow Elemental to build internally when using 8-byte ints
     depends_on('openblas threads=openmp', when='blas=openblas +openmp_blas ~int64_blas')
 
@@ -82,8 +65,15 @@ class Elemental(CMakePackage):
     depends_on('intel-mkl threads=openmp', when='blas=mkl +openmp_blas ~int64_blas')
     depends_on('intel-mkl@2017.1 +openmp +ilp64', when='blas=mkl +openmp_blas +int64_blas')
 
+    depends_on('veclibfort', when='blas=accelerate')
+
+    depends_on('essl ~cuda', when='blas=essl ~openmp_blas ~int64_blas')
+    depends_on('essl threads=openmp', when='blas=essl +openmp_blas ~int64_blas')
+
     # Note that this forces us to use OpenBLAS until #1712 is fixed
     depends_on('lapack', when='blas=openblas ~openmp_blas')
+    depends_on('netlib-lapack +external-blas', when='blas=essl')
+
     depends_on('metis')
     depends_on('metis +int64', when='+int64')
     depends_on('mpi')
@@ -102,7 +92,7 @@ class Elemental(CMakePackage):
     def libs(self):
         shared = True if '+shared' in self.spec else False
         return find_libraries(
-            'libEl', root=self.prefix, shared=shared, recurse=True
+            'libEl', root=self.prefix, shared=shared, recursive=True
         )
 
     def cmake_args(self):
@@ -134,14 +124,23 @@ class Elemental(CMakePackage):
             ifort = env['SPACK_F77']
             intel_bin = os.path.dirname(ifort)
             intel_root = os.path.dirname(intel_bin)
-            libfortran = LibraryList('{0}/lib/intel64/libifcoremt.{1}'
-                                     .format(intel_root, dso_suffix))
+            libfortran = find_libraries('libifcoremt',
+                                        root=intel_root, recursive=True)
         elif self.spec.satisfies('%gcc'):
             # see <stage_folder>/debian/rules as an example:
             mpif77 = Executable(spec['mpi'].mpif77)
             libfortran = LibraryList(mpif77('--print-file-name',
                                             'libgfortran.%s' % dso_suffix,
-                                            output=str))
+                                            output=str).strip())
+        elif self.spec.satisfies('%xl') or self.spec.satisfies('%xl_r'):
+            xl_fort = env['SPACK_F77']
+            xl_bin = os.path.dirname(xl_fort)
+            xl_root = os.path.dirname(xl_bin)
+            libfortran = find_libraries('libxlf90_r',
+                                        root=xl_root, recursive=True)
+        else:
+            libfortran = None
+
         if libfortran:
             args.append('-DGFORTRAN_LIB=%s' % libfortran.libraries[0])
 
diff --git a/var/spack/repos/builtin/packages/elfutils/package.py b/var/spack/repos/builtin/packages/elfutils/package.py
index 2db5d71d3a..1234f5007a 100644
--- a/var/spack/repos/builtin/packages/elfutils/package.py
+++ b/var/spack/repos/builtin/packages/elfutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,19 +20,58 @@ class Elfutils(AutotoolsPackage):
     list_url = "https://sourceware.org/elfutils/ftp"
     list_depth = 1
 
+    version('0.173', '35decb1ebfb90d565e4c411bee4185cc')
     version('0.170', '03599aee98c9b726c7a732a2dd0245d5')
     version('0.168', '52adfa40758d0d39e5d5c57689bf38d6')
-    version('0.163', '77ce87f259987d2e54e4d87b86cbee41', preferred=True)
+    version('0.163', '77ce87f259987d2e54e4d87b86cbee41')
+
+    # Libraries for reading compressed DWARF sections.
+    variant('bzip2', default=False,
+            description='Support bzip2 compressed sections.')
+    variant('xz', default=False,
+            description='Support xz compressed sections.')
+
+    # Native language support from libintl.
+    variant('nls', default=True,
+            description='Enable Native Language Support.')
 
-    depends_on('flex', type='build')
-    depends_on('bison', type='build')
-    depends_on('gettext')
+    depends_on('bzip2', type='link', when='+bzip2')
+    depends_on('xz',    type='link', when='+xz')
+    depends_on('zlib',  type='link')
+    depends_on('gettext', when='+nls')
+
+    conflicts('%gcc@7.2.0:', when='@0.163')
 
     provides('elf@1')
 
+    # Elfutils uses nested functions in C code, which is implemented
+    # in gcc, but not in clang. C code compiled with gcc is
+    # binary-compatible with clang, so it should be possible to build
+    # elfutils with gcc, and then link it to clang-built libraries.
+    conflicts('%clang')
+
     def configure_args(self):
-        # configure doesn't use LIBS correctly
-        gettext_lib = self.spec['gettext'].prefix.lib,
-        return [
-            'LDFLAGS=-Wl,--no-as-needed -L%s -lintl' % gettext_lib,
-            '--enable-maintainer-mode']
+        spec = self.spec
+        args = []
+
+        if '+bzip2' in spec:
+            args.append('--with-bzlib=%s' % spec['bzip2'].prefix)
+        else:
+            args.append('--without-bzlib')
+
+        if '+xz' in spec:
+            args.append('--with-lzma=%s' % spec['xz'].prefix)
+        else:
+            args.append('--without-lzma')
+
+        # zlib is required
+        args.append('--with-zlib=%s' % spec['zlib'].prefix)
+
+        if '+nls' in spec:
+            # configure doesn't use LIBS correctly
+            args.append('LDFLAGS=-Wl,--no-as-needed -L%s -lintl' %
+                        spec['gettext'].prefix.lib)
+        else:
+            args.append('--disable-nls')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py
index 6abebb4174..fad0153014 100644
--- a/var/spack/repos/builtin/packages/elk/package.py
+++ b/var/spack/repos/builtin/packages/elk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/elpa/package.py b/var/spack/repos/builtin/packages/elpa/package.py
index 3761f26cc0..13c31a26b3 100644
--- a/var/spack/repos/builtin/packages/elpa/package.py
+++ b/var/spack/repos/builtin/packages/elpa/package.py
@@ -1,27 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -32,12 +12,17 @@ class Elpa(AutotoolsPackage):
     homepage = 'http://elpa.mpcdf.mpg.de/'
     url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
 
+    version('2018.05.001.rc1', 'ccd77bd8036988ee624f43c04992bcdd')
+    version('2017.11.001', '4a437be40cc966efb07aaab84c20cd6e', preferred=True)
+    version('2017.05.003', '7c8e5e58cafab212badaf4216695700f')
+    version('2017.05.002', 'd0abc1ac1f493f93bf5e30ec8ab155dc')
     version('2016.11.001.pre', '5656fd066cf0dcd071dbcaf20a639b37')
-    version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376', preferred=True)
+    version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376')
     version('2016.05.003', '88a9f3f3bfb63e16509dd1be089dcf2c')
     version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6')
 
     variant('openmp', default=False, description='Activates OpenMP support')
+    variant('optflags', default=True, description='Build with optimization flags')
 
     depends_on('mpi')
     depends_on('blas')
@@ -53,18 +38,14 @@ class Elpa(AutotoolsPackage):
     # override default implementation which returns static lib
     @property
     def libs(self):
-
         libname = 'libelpa_openmp' if '+openmp' in self.spec else 'libelpa'
-
         return find_libraries(
-            libname, root=self.prefix, shared=True, recurse=True
+            libname, root=self.prefix, shared=True, recursive=True
         )
 
     build_directory = 'spack-build'
 
     def setup_environment(self, spack_env, run_env):
-        # TODO: set optimum flags for platform+compiler combo, see
-        # https://github.com/hfp/xconfigure/tree/master/elpa
         spec = self.spec
 
         spack_env.set('CC', spec['mpi'].mpicc)
@@ -76,7 +57,20 @@ class Elpa(AutotoolsPackage):
         spack_env.set('SCALAPACK_LDFLAGS', spec['scalapack'].libs.joined())
 
     def configure_args(self):
+        # TODO: set optimum flags for platform+compiler combo, see
+        # https://github.com/hfp/xconfigure/tree/master/elpa
+        # also see:
+        # https://src.fedoraproject.org/cgit/rpms/elpa.git/
+        # https://packages.qa.debian.org/e/elpa.html
         options = []
+        # without -march=native there is configure error for 2017.05.02
+        # Could not compile test program, try with --disable-sse, or
+        # adjust the C compiler or CFLAGS
+        if '+optflags' in self.spec:
+            options.extend([
+                'FCFLAGS=-O2 -march=native -ffree-line-length-none',
+                'CFLAGS=-O2 -march=native'
+            ])
         if '+openmp' in self.spec:
-            options.append("--enable-openmp")
+            options.append('--enable-openmp')
         return options
diff --git a/var/spack/repos/builtin/packages/emacs/package.py b/var/spack/repos/builtin/packages/emacs/package.py
index 4b0d7a9689..1599782d50 100644
--- a/var/spack/repos/builtin/packages/emacs/package.py
+++ b/var/spack/repos/builtin/packages/emacs/package.py
@@ -1,36 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
+import sys
+
 
 class Emacs(AutotoolsPackage):
     """The Emacs programmable text editor."""
 
     homepage = "https://www.gnu.org/software/emacs"
-    url      = "http://ftp.gnu.org/gnu/emacs/emacs-24.5.tar.gz"
+    url      = "https://ftpmirror.gnu.org/emacs/emacs-24.5.tar.gz"
 
+    version('26.1', '544d2ab5eb142e9ca69adb023d17bf4b')
     version('25.3', '74ddd373dc52ac05ca7a8c63b1ddbf58')
     version('25.2', '0a36d1cdbba6024d4dbbac027f87995f')
     version('25.1', '95c12e6a9afdf0dcbdd7d2efa26ca42c')
@@ -43,10 +27,12 @@ class Emacs(AutotoolsPackage):
         values=('gtk', 'athena'),
         description="Select an X toolkit (gtk, athena)"
     )
+    variant('tls', default=False, description="Build Emacs with gnutls")
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('ncurses')
+    depends_on('pcre')
     depends_on('zlib')
     depends_on('libtiff', when='+X')
     depends_on('libpng', when='+X')
@@ -54,7 +40,8 @@ class Emacs(AutotoolsPackage):
     depends_on('giflib', when='+X')
     depends_on('libx11', when='+X')
     depends_on('libxaw', when='+X toolkit=athena')
-    depends_on('gtkplus+X', when='+X toolkit=gtk')
+    depends_on('gtkplus', when='+X toolkit=gtk')
+    depends_on('gnutls', when='+tls')
 
     def configure_args(self):
         spec = self.spec
@@ -68,4 +55,14 @@ class Emacs(AutotoolsPackage):
         else:
             args = ['--without-x']
 
+        # On OS X/macOS, do not build "nextstep/Emacs.app", because
+        # doing so throws an error at build-time
+        if sys.platform == 'darwin':
+            args.append('--without-ns')
+
+        if '+tls' in spec:
+            args.append('--with-gnutls')
+        else:
+            args.append('--without-gnutls')
+
         return args
diff --git a/var/spack/repos/builtin/packages/ember/package.py b/var/spack/repos/builtin/packages/ember/package.py
new file mode 100644
index 0000000000..261dc27ba7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ember/package.py
@@ -0,0 +1,87 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ember(MakefilePackage):
+    """
+    Ember Communication Pattern Library
+    The Ember suite provides communication patterns in a simplified setting
+    (simplified by the removal of application calculations, control flow,
+    etc.).
+    """
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "http://sst-simulator.org/SSTPages/SSTElementEmber/"
+    git      = "https://github.com/sstsimulator/ember.git"
+    url      = "https://github.com/sstsimulator/ember/archive/v1.0.0.tar.gz"
+
+    version('1.0.0', sha256='5b2a6b8055b46ab3ea2c7baabaf4d280d837bb7c21eba0c9f59e092c6fc1c4a6')
+
+    depends_on('mpi')
+
+    # TODO: shmem variant disabled due to lack of shmem spackage
+    def edit(self, spec, prefix):
+        file = open('Makefile', 'w')
+
+        file.write('CC = mpicc\n')
+        file.write('CFLAGS = -O3 -std=c99\n')
+        file.write('OSHMEM_CC=cc\n')
+        file.write('OSHMEM_C_FLAGS=-O3 -g\n')
+
+        file.write('export CC CFLAGS OSHMEM_CC OSHMEM_C_FLAGS\n')
+
+        file.write('all:\n')
+        file.write('\t@$(MAKE) -C mpi/halo3d -f Makefile\n')
+        file.write('\t@$(MAKE) -C mpi/halo3d-26 -f Makefile\n')
+        file.write('\t@$(MAKE) -C mpi/incast -f Makefile\n')
+        file.write('\t@$(MAKE) -C mpi/pingpong -f Makefile\n')
+        file.write('\t@$(MAKE) -C mpi/sweep3d -f Makefile\n')
+        # file.write('\t@$(MAKE) -C shmem/hotspotinc -f Makefile\n')
+        # file.write('\t@$(MAKE) -C shmem/randominc -f Makefile\n')
+
+        file.write('.PHONY: clean\n')
+        file.write('clean:\n')
+        file.write('\t@$(MAKE) -C mpi/halo3d -f Makefile clean\n')
+        file.write('\t@$(MAKE) -C mpi/halo3d-26 -f Makefile clean\n')
+        file.write('\t@$(MAKE) -C mpi/incast -f Makefile clean\n')
+        file.write('\t@$(MAKE) -C mpi/pingpong -f Makefile clean\n')
+        file.write('\t@$(MAKE) -C mpi/sweep3d -f Makefile clean\n')
+        # file.write('\t@$(MAKE) -C shmem/hotspotinc -f Makefile clean\n')
+        # file.write('\t@$(MAKE) -C shmem/randominc -f Makefile clean\n')
+
+        file.close()
+
+    @property
+    def build_targets(self):
+        targets = []
+        cc = self.spec['mpi'].mpicc
+        cflags = '-O3 -std=c99'
+        oshmem_cc = 'cc'
+        oshmem_c_flags = '-O3 -g'
+
+        targets.append('CC = {0}'.format(cc))
+        targets.append('CFLAGS = {0}'.format(cflags))
+        targets.append('OSHMEM_CC = {0}'.format(oshmem_cc))
+        targets.append('OSHMEM_C_FLAGS = {0}'.format(oshmem_c_flags))
+
+        return targets
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.docs)
+        install('README.md', prefix.docs)
+        install('README.MPI.halo3d', prefix.docs)
+        install('README.MPI.halo3d-26', prefix.docs)
+        install('README.MPI.incast', prefix.docs)
+        install('README.MPI.sweep3d', prefix.docs)
+
+        mkdirp(prefix.bin)
+        install('mpi/halo3d/halo3d', prefix.bin)
+        install('mpi/halo3d-26/halo3d-26', prefix.bin)
+        install('mpi/incast/incast', prefix.bin)
+        install('mpi/pingpong/pingpong', prefix.bin)
+        install('mpi/sweep3d/sweep3d', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/emboss/package.py b/var/spack/repos/builtin/packages/emboss/package.py
index fe3f18a0dc..bc36c8938b 100644
--- a/var/spack/repos/builtin/packages/emboss/package.py
+++ b/var/spack/repos/builtin/packages/emboss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,3 +19,8 @@ class Emboss(AutotoolsPackage):
     depends_on('libxpm')
     depends_on('libgd')
     depends_on('postgresql')
+
+    @run_after('configure')
+    def skip_update_checks(self):
+        # Delete $(bindir)/embossupdate to skip update checks
+        filter_file('$(bindir)/embossupdate', '', 'Makefile', string=True)
diff --git a/var/spack/repos/builtin/packages/encodings/package.py b/var/spack/repos/builtin/packages/encodings/package.py
index f356b052fc..0ea51bf7da 100644
--- a/var/spack/repos/builtin/packages/encodings/package.py
+++ b/var/spack/repos/builtin/packages/encodings/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Encodings(Package):
     depends_on('font-util')
 
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/energyplus/package.py b/var/spack/repos/builtin/packages/energyplus/package.py
new file mode 100644
index 0000000000..48cc19cf41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/energyplus/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os
+
+
+class Energyplus(Package):
+    """EnergyPlus is a whole building energy simulation program that engineers,
+       architects, and researchers use to model both energy consumption for
+       heating, cooling, ventilation, lighting and plug and process loads
+       and water use in buildings"""
+
+    homepage = "https://energyplus.net"
+
+    # versions require explicit URLs as they contain hashes
+    version('8.9.0', sha256='13a5192b25815eb37b3ffd019ce3b99fd9f854935f8cc4362814f41c56e9ca98',
+            url="https://github.com/NREL/EnergyPlus/releases/download/v8.9.0-WithIDDFixes/EnergyPlus-8.9.0-eba93e8e1b-Linux-x86_64.tar.gz")
+
+    def install(self, spec, prefix):
+        # binary distribution, we just unpack to lib/energyplus
+        # and then symlink the appropriate targets
+
+        # there is only one folder with a semi-predictable name so we glob it
+        install_tree(glob.glob('EnergyPlus*')[0],
+                     join_path(prefix.lib, 'energyplus'))
+
+        mkdirp(prefix.bin)
+        os.symlink(join_path(prefix.lib, 'energyplus/energyplus'),
+                   join_path(prefix.bin, 'energyplus'))
+        os.symlink(join_path(prefix.lib, 'energyplus/EPMacro'),
+                   join_path(prefix.bin, 'EPMacro'))
+        os.symlink(join_path(prefix.lib, 'energyplus/ExpandObjects'),
+                   join_path(prefix.bin, 'ExpandObjects'))
diff --git a/var/spack/repos/builtin/packages/environment-modules/package.py b/var/spack/repos/builtin/packages/environment-modules/package.py
index ed84cea0a9..60307d3865 100644
--- a/var/spack/repos/builtin/packages/environment-modules/package.py
+++ b/var/spack/repos/builtin/packages/environment-modules/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/eospac/flang.patch b/var/spack/repos/builtin/packages/eospac/flang.patch
new file mode 100644
index 0000000000..dcde70ff50
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eospac/flang.patch
@@ -0,0 +1,62 @@
+--- a/Source/config/Makefile.-linux-gnu.detect
++++ b/Source/config/Makefile.-linux-gnu.detect
+@@ -19,7 +19,7 @@
+ # Compiler suite configurations based upon F90                 ###
+ ##################################################################
+ # Default: use the first F90 compiler found from F90_List
+-F90_List = gfortran pgfortran pgf90 lf95 f90 ifort g95 ftn pathf90
++F90_List = gfortran pgfortran pgf90 lf95 f90 ifort g95 ftn pathf90 flang
+ F90_Found_List = $(foreach compiler,$(F90_List),$(call pathsearch,$(compiler)))
+ F90 = $(firstword $(F90_Found_List))
+ F90_Key = $(strip $(firstword $(foreach compiler,$(F90_List),$(call match_r1,$(compiler),$(F90)))))
+
+--- a/Source/config/Makefile.-linux-gnu.hashes
++++ b/Source/config/Makefile.-linux-gnu.hashes
+@@ -32,6 +32,7 @@
+ $(call set,_CC,g95,        gcc                       )   # G95
+ $(call set,_CC,gfortran,   gcc                       )   # gfortran
+ $(call set,_CC,ftn,        cc        gcc             )   # Cray Computing Environment (cce)
++$(call set,_CC,flang,      clang                     )   # flang/clang
+
+ $(call set,_CXX,pgfortran, pgCC      g++             )   # PGI
+ $(call set,_CXX,pgf90,     pgCC      g++             )   # PGI
+@@ -42,6 +43,7 @@
+ $(call set,_CXX,g95,       g++                       )   # G95
+ $(call set,_CXX,gfortran,  g++                       )   # gfortran
+ $(call set,_CXX,ftn,       CC        g++             )   # Cray Computing Environment (cce)
++$(call set,_CC,flang,      clang++                   )   # flang/clang++
+
+ $(call set,_F77,pgfortran, pgfortran pgf77     pgf90 )   # PGI
+ $(call set,_F77,pgf90,     pgfortran pgf77     pgf90 )   # PGI
+@@ -52,6 +54,7 @@
+ $(call set,_F77,g95,       $(F90)                    )   # G95
+ $(call set,_F77,gfortran,  $(F90)                    )   # gfortran
+ $(call set,_F77,ftn,       $(F90)                    )   # Cray Computing Environment (cce)
++$(call set,_CC,flang,      flang                     )   # flang
+
+ ##################################################################
+ ### Define CC, CXX and  F77 according to $(F90_Key).           ###
+@@ -94,6 +97,7 @@
+ $(call set,_COMP_FLAGS,gfortran,     -I"$(INCDIR)" -Wno-c-binding-type)   # gfortran
+ $(call set,_COMP_FLAGS,ppu-gfortran, -I"$(INCDIR)"                    )   # ppu-gfortran
+ $(call set,_COMP_FLAGS,ftn,          -e m -I"$(INCDIR)" -hfp0         )   # Cray Computing Environment (cce)
++$(call set,_COMP_FLAGS,flang,        -I"$(INCDIR)"                    )   # flang
+
+ # define define_module_subdir script options
+ $(call set,_DEFINE_MODULE_SUBDIR_FLAGS,f90,)           # Absoft f90
+@@ -105,6 +109,7 @@
+ $(call set,_DEFINE_MODULE_SUBDIR_FLAGS,g95,)           # G95
+ $(call set,_DEFINE_MODULE_SUBDIR_FLAGS,gfortran,)      # gfortran
+ $(call set,_DEFINE_MODULE_SUBDIR_FLAGS,ftn,)           # Cray Computing Environment (cce)
++$(call set,_DEFINE_MODULE_SUBDIR_FLAGS,flang,)         # flang
+
+ # define define_module_subdir script patterns
+ $(call set,_DEFINE_MODULE_SUBDIR_PATTS,f90,absoft)           # Absoft f90
+@@ -116,6 +121,7 @@
+ $(call set,_DEFINE_MODULE_SUBDIR_PATTS,g95,$(F90_Key))       # G95
+ $(call set,_DEFINE_MODULE_SUBDIR_PATTS,gfortran,gcc)         # gfortran
+ $(call set,_DEFINE_MODULE_SUBDIR_PATTS,ftn,cce)              # Cray Computing Environment (cce)
++$(call set,_DEFINE_MODULE_SUBDIR_PATTS,flang,clang)          # flang/clang
+
+ # define optional modules for cross-compiling
+ X_Compile_Module_List = craype-haswell craype-mic-knl
diff --git a/var/spack/repos/builtin/packages/eospac/package.py b/var/spack/repos/builtin/packages/eospac/package.py
new file mode 100644
index 0000000000..54000d6b5f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/eospac/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Eospac(Package):
+    """A collection of C routines that can be used to access the Sesame data
+       library.
+    """
+
+    homepage = "https://laws.lanl.gov/projects/data/eos.html"
+    list_url = "https://laws.lanl.gov/projects/data/eos/eospacReleases.php"
+
+    version('6.4.0beta.2', '9b6e48090647221d5ffe7ec5f9ea4c71',
+            url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.2_69196eadbc77506561eef711f19d2f03b4ab0ffa.tgz")
+    version('6.4.0beta.1', 'e4e4beabf946f0b8953532832002afc2',
+            url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz")
+    version('6.3.1', '549fda008c4169a69b02ec2a9de1e434', preferred=True,
+            url="https://laws.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.3.1_r20161202150449.tgz")
+
+    # This patch allows the use of spack's compile wrapper 'flang'
+    patch('flang.patch', when='@:6.4.0beta.2%clang')
+
+    def install(self, spec, prefix):
+        with working_dir('Source'):
+            make('install',
+                 'CC={0}'.format(spack_cc),
+                 'CXX={0}'.format(spack_cxx),
+                 'F77={0}'.format(spack_f77),
+                 'F90={0}'.format(spack_fc),
+                 'prefix={0}'.format(prefix),
+                 'INSTALLED_LIBRARY_DIR={0}'.format(prefix.lib),
+                 'INSTALLED_INCLUDE_DIR={0}'.format(prefix.include),
+                 'INSTALLED_EXAMPLE_DIR={0}'.format(prefix.example),
+                 'INSTALLED_BIN_DIR={0}'.format(prefix.bin))
diff --git a/var/spack/repos/builtin/packages/er/package.py b/var/spack/repos/builtin/packages/er/package.py
new file mode 100644
index 0000000000..0638b792fb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/er/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Er(CMakePackage):
+    """Encoding and redundancy on a file set"""
+
+    homepage = "https://github.com/ECP-VeloC/er"
+    url      = "https://github.com/ECP-VeloC/er/archive/v0.0.2.zip"
+    git      = "https://github.com/ecp-veloc/er.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.0.3', sha256='9aa08f9fe70e42f0da27a5d90d4643b520d61f24742303bf016322823b3c4d26')
+
+    depends_on('mpi')
+    depends_on('kvtree')
+    depends_on('redset')
+    depends_on('shuffile')
+
+    def cmake_args(self):
+        args = []
+        args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DER_LINK_STATIC=ON")
+        args.append("-DWITH_KVTREE_PREFIX=%s" % self.spec['kvtree'].prefix)
+        args.append("-DWITH_REDSET_PREFIX=%s" % self.spec['redset'].prefix)
+        args.append("-DWITH_SHUFFILE_PREFIX=%s" % self.spec['shuffile'].prefix)
+        return args
diff --git a/var/spack/repos/builtin/packages/es/package.py b/var/spack/repos/builtin/packages/es/package.py
index 6a73488e8f..8b918919bb 100644
--- a/var/spack/repos/builtin/packages/es/package.py
+++ b/var/spack/repos/builtin/packages/es/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/esmf/darwin_dylib_install_name.patch b/var/spack/repos/builtin/packages/esmf/darwin_dylib_install_name.patch
new file mode 100644
index 0000000000..0f363b378c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/esmf/darwin_dylib_install_name.patch
@@ -0,0 +1,18 @@
+--- a/build/common.mk	2017-11-25 17:16:31.000000000 +1100
++++ b/build/common.mk	2017-11-25 17:26:20.000000000 +1100
+@@ -3415,11 +3415,11 @@
+ 		    mkdir tmp_$$NEXTLIB ;\
+ 		    cd tmp_$$NEXTLIB  ;\
+ 	                $(ESMF_AREXTRACT) ../$$NEXTLIB.a ;\
+-                    echo $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -o $(ESMF_LDIR)/$$NEXTLIB.$(ESMF_SL_SUFFIX) *.o $(ESMF_SL_LIBLIBS) ;\
+-		    $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -o $(ESMF_LDIR)/$$NEXTLIB.$(ESMF_SL_SUFFIX) *.o $(ESMF_SL_LIBLIBS) ;\
++		    echo $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -Wl,-install_name -Wl,@rpath/$$NEXTLIB.$(ESMF_SL_SUFFIX) -o $(ESMF_LDIR)/$$NEXTLIB.$(ESMF_SL_SUFFIX) *.o $(ESMF_SL_LIBLIBS) ;\
++		    $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -Wl,-install_name -Wl,@rpath/$$NEXTLIB.$(ESMF_SL_SUFFIX) -o $(ESMF_LDIR)/$$NEXTLIB.$(ESMF_SL_SUFFIX) *.o $(ESMF_SL_LIBLIBS) ;\
+ 		    echo Converting $$NEXTLIB.a to $$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) ;\
+-                    echo $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -o $(ESMF_LDIR)/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) *.o $(ESMF_CXXLINKOPTS) $(ESMF_CXXLINKPATHS) $(ESMF_CXXLINKRPATHS) $(ESMF_CXXLINKLIBS) ;\
+-		    $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -o $(ESMF_LDIR)/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) *.o $(ESMF_CXXLINKOPTS) $(ESMF_CXXLINKPATHS) $(ESMF_CXXLINKRPATHS) $(ESMF_CXXLINKLIBS) ;\
++		    echo $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -Wl,-install_name -Wl,@rpath/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) -o $(ESMF_LDIR)/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) *.o $(ESMF_CXXLINKOPTS) $(ESMF_CXXLINKPATHS) $(ESMF_CXXLINKRPATHS) $(ESMF_CXXLINKLIBS) ;\
++		    $(ESMF_SL_LIBLINKER) $(ESMF_SL_LIBOPTS) -Wl,-install_name -Wl,@rpath/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) -o $(ESMF_LDIR)/$$NEXTLIB\_fullylinked.$(ESMF_SL_SUFFIX) *.o $(ESMF_CXXLINKOPTS) $(ESMF_CXXLINKPATHS) $(ESMF_CXXLINKRPATHS) $(ESMF_CXXLINKLIBS) ;\
+ 		    cd .. ;\
+ 		    $(ESMF_RM) -r tmp_$$NEXTLIB ;\
+ 		fi ;\
diff --git a/var/spack/repos/builtin/packages/esmf/package.py b/var/spack/repos/builtin/packages/esmf/package.py
index 394e316751..107aaffaa2 100644
--- a/var/spack/repos/builtin/packages/esmf/package.py
+++ b/var/spack/repos/builtin/packages/esmf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -59,7 +40,7 @@ class Esmf(MakefilePackage):
     depends_on('xerces-c@3.1.0:', when='+xerces')
 
     # Testing dependencies
-    # depends_on('perl', type='test')  # TODO: Add a test deptype
+    depends_on('perl', type='test')
 
     # Make esmf build with newer gcc versions
     # https://sourceforge.net/p/esmf/esmf/ci/3706bf758012daebadef83d6575c477aeff9c89b/
@@ -69,6 +50,10 @@ class Esmf(MakefilePackage):
     # https://sourceforge.net/p/esmf/esmf/ci/34de0ccf556ba75d35c9687dae5d9f666a1b2a18/
     patch('mvapich2.patch', when='@:7.0.99')
 
+    # Allow different directories for creation and
+    # installation of dynamic libraries on OSX:
+    patch('darwin_dylib_install_name.patch', when='platform=darwin')
+
     # Make script from mvapich2.patch executable
     @run_before('build')
     @when('@:7.0.99')
@@ -104,7 +89,7 @@ class Esmf(MakefilePackage):
         # bin/binO/Linux.gfortran.64.default.default
         os.environ['ESMF_INSTALL_BINDIR'] = 'bin'
         os.environ['ESMF_INSTALL_LIBDIR'] = 'lib'
-        os.environ['ESMF_INSTALL_MODDIR'] = 'mod'
+        os.environ['ESMF_INSTALL_MODDIR'] = 'include'
 
         ############
         # Compiler #
@@ -149,11 +134,17 @@ class Esmf(MakefilePackage):
         # ESMF_COMM must be set to indicate which MPI implementation
         # is used to build the ESMF library.
         if '+mpi' in spec:
-            if '^mvapich2' in spec:
+            if 'platform=cray' in self.spec:
+                os.environ['ESMF_COMM'] = 'mpi'
+            elif '^mvapich2' in spec:
                 os.environ['ESMF_COMM'] = 'mvapich2'
             elif '^mpich' in spec:
-                # FIXME: mpich or mpich2?
+                # esmf@7.0.1 does not include configs for mpich3,
+                # so we start with the configs for mpich2:
                 os.environ['ESMF_COMM'] = 'mpich2'
+                # The mpich 3 series split apart the Fortran and C bindings,
+                # so we link the Fortran libraries when building C programs:
+                os.environ['ESMF_CXXLINKLIBS'] = '-lmpifort'
             elif '^openmpi' in spec:
                 os.environ['ESMF_COMM'] = 'openmpi'
             elif '^intel-parallel-studio+mpi' in spec:
diff --git a/var/spack/repos/builtin/packages/essl/package.py b/var/spack/repos/builtin/packages/essl/package.py
new file mode 100644
index 0000000000..565b0ec6e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/essl/package.py
@@ -0,0 +1,65 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Essl(Package):
+    """IBM's Engineering and Scientific Subroutine Library (ESSL)."""
+
+    homepage = "https://www.ibm.com/systems/power/software/essl/"
+
+    variant('ilp64', default=False, description='64 bit integers')
+    variant(
+        'threads', default='openmp',
+        description='Multithreading support',
+        values=('openmp', 'none'),
+        multi=False
+    )
+    variant('cuda', default=False, description='CUDA acceleration')
+
+    provides('blas')
+
+    conflicts('+cuda', when='+ilp64',
+              msg='ESSL+cuda+ilp64 cannot combine CUDA acceleration'
+              ' 64 bit integers')
+
+    conflicts('+cuda', when='threads=none',
+              msg='ESSL+cuda threads=none cannot combine CUDA acceleration'
+              ' without multithreading support')
+
+    @property
+    def blas_libs(self):
+        spec = self.spec
+        prefix = self.prefix
+
+        if '+ilp64' in spec:
+            essl_lib = ['libessl6464']
+        else:
+            essl_lib = ['libessl']
+
+        if spec.satisfies('threads=openmp'):
+            # ESSL SMP support requires XL or Clang OpenMP library
+            if '%xl' in spec or '%xl_r' in spec or '%clang' in spec:
+                if '+ilp64' in spec:
+                    essl_lib = ['libesslsmp6464']
+                else:
+                    if '+cuda' in spec:
+                        essl_lib = ['libesslsmpcuda']
+                    else:
+                        essl_lib = ['libesslsmp']
+
+        essl_root = prefix.lib64
+        essl_libs = find_libraries(
+            essl_lib,
+            root=essl_root,
+            shared=True
+        )
+
+        return essl_libs
+
+    def install(self, spec, prefix):
+        raise InstallError('IBM ESSL is not installable;'
+                           ' it is vendor supplied')
diff --git a/var/spack/repos/builtin/packages/ethminer/package.py b/var/spack/repos/builtin/packages/ethminer/package.py
new file mode 100644
index 0000000000..0689d6faed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ethminer/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ethminer(CMakePackage):
+    """The ethminer is an Ethereum GPU mining worker."""
+
+    homepage = "https://github.com/ethereum-mining/ethminer"
+    url = "https://github.com/ethereum-mining/ethminer/archive/v0.12.0.tar.gz"
+
+    version('0.12.0', '1c7e3df8476a146702a4050ad984ae5a')
+
+    variant('opencl', default=True, description='Enable OpenCL mining.')
+    variant('cuda', default=False, description='Enable CUDA mining.')
+    variant('stratum', default=True,
+            description='Build with Stratum protocol support.')
+
+    depends_on('python')
+    depends_on('boost')
+    depends_on('json-c')
+    depends_on('curl')
+    depends_on('zlib')
+    depends_on('cuda', when='+cuda')
+    depends_on('mesa', when='+opencl')
+
+    def cmake_args(self):
+        spec = self.spec
+        return [
+            '-DETHASHCL=%s' % ('YES' if '+opencl' in spec else 'NO'),
+            '-DETHASHCUDA=%s' % ('YES' if '+cuda' in spec else 'NO'),
+            '-DETHSTRATUM=%s' % ('YES' if '+stratum' in spec else 'NO')]
diff --git a/var/spack/repos/builtin/packages/etsf-io/package.py b/var/spack/repos/builtin/packages/etsf-io/package.py
index dc0dac415f..cade69c89c 100644
--- a/var/spack/repos/builtin/packages/etsf-io/package.py
+++ b/var/spack/repos/builtin/packages/etsf-io/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/everytrace-example/package.py b/var/spack/repos/builtin/packages/everytrace-example/package.py
index cedcd684fc..1eff5f6451 100644
--- a/var/spack/repos/builtin/packages/everytrace-example/package.py
+++ b/var/spack/repos/builtin/packages/everytrace-example/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class EverytraceExample(CMakePackage):
     """Get stack trace EVERY time a program exits."""
 
     homepage = "https://github.com/citibeth/everytrace-example"
-    version('develop',
-            git='https://github.com/citibeth/everytrace-example.git',
-            branch='develop')
+    git      = "https://github.com/citibeth/everytrace-example.git"
+
+    version('develop', branch='develop')
 
     depends_on('everytrace+mpi+fortran')
 
diff --git a/var/spack/repos/builtin/packages/everytrace/package.py b/var/spack/repos/builtin/packages/everytrace/package.py
index 96813672ad..8aaf928add 100644
--- a/var/spack/repos/builtin/packages/everytrace/package.py
+++ b/var/spack/repos/builtin/packages/everytrace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,15 +10,18 @@ class Everytrace(CMakePackage):
     """Get stack trace EVERY time a program exits."""
 
     homepage = "https://github.com/citibeth/everytrace"
-    url = "https://github.com/citibeth/everytrace/tarball/0.2.0"
+    url      = "https://github.com/citibeth/everytrace/archive/0.2.2.tar.gz"
+    git      = "https://github.com/citibeth/everytrace.git"
+
+    maintainers = ['citibeth']
 
-    version('0.2.0', '2af0e5b6255064d5191accebaa70d222')
-    version('develop',
-            git='https://github.com/citibeth/everytrace.git', branch='develop')
+    version('develop', branch='develop')
+    version('0.2.2', 'dd60b8bf68cbf3dc2be305a040f2fe3e')
 
     variant('mpi', default=True, description='Enables MPI parallelism')
     variant('fortran', default=True,
             description='Enable use with Fortran programs')
+    variant('cxx', default=True, description='Enable C++ Exception-based features')
 
     depends_on('mpi', when='+mpi')
 
@@ -45,7 +29,8 @@ class Everytrace(CMakePackage):
         spec = self.spec
         return [
             '-DUSE_MPI=%s' % ('YES' if '+mpi' in spec else 'NO'),
-            '-DUSE_FORTRAN=%s' % ('YES' if '+fortran' in spec else 'NO')]
+            '-DUSE_FORTRAN=%s' % ('YES' if '+fortran' in spec else 'NO'),
+            '-DUSE_CXX=%s' % ('YES' if '+cxx' in spec else 'NO')]
 
     def setup_environment(self, spack_env, run_env):
         run_env.prepend_path('PATH', join_path(self.prefix, 'bin'))
diff --git a/var/spack/repos/builtin/packages/evieext/package.py b/var/spack/repos/builtin/packages/evieext/package.py
index a88764516e..e857c0d5d5 100644
--- a/var/spack/repos/builtin/packages/evieext/package.py
+++ b/var/spack/repos/builtin/packages/evieext/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Evieext(AutotoolsPackage):
 
     version('1.1.1', '018a7d24d0c7926d594246320bcb6a86')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/exabayes/package.py b/var/spack/repos/builtin/packages/exabayes/package.py
index 1529261397..2e951f6d75 100644
--- a/var/spack/repos/builtin/packages/exabayes/package.py
+++ b/var/spack/repos/builtin/packages/exabayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/examinimd/package.py b/var/spack/repos/builtin/packages/examinimd/package.py
new file mode 100644
index 0000000000..ffb31a8ff8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/examinimd/package.py
@@ -0,0 +1,67 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Examinimd(MakefilePackage):
+    """ExaMiniMD is a proxy application and research vehicle for particle codes,
+    in particular Molecular Dynamics (MD). Compared to previous MD proxy apps
+    (MiniMD, COMD), its design is significantly more modular in order to allow
+    independent investigation of different aspects. To achieve that the main
+    components such as force calculation, communication, neighbor list
+    construction and binning are derived classes whose main functionality is
+    accessed via virtual functions. This allows a developer to write a new
+    derived class and drop it into the code without touching much of the
+    rest of the application."""
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "https://github.com/ECP-copa/ExaMiniMD"
+    url      = "https://github.com/ECP-copa/ExaMiniMD/archive/1.0.zip"
+    git      = "https://github.com/ECP-copa/ExaMiniMD.git"
+
+    version('develop', branch='master')
+    version('1.0', '5db7679a4b9296c0cc3b2ff3a7e8f38f')
+
+    variant('mpi', default=True, description='Build with MPI support')
+    variant('openmp', default=False, description='Build with OpenMP support')
+    variant('pthreads', default=False, description='Build with POSIX Threads support')
+    # TODO: Set up cuda variant when test machine available
+
+    conflicts('+openmp', when='+pthreads')
+
+    depends_on('kokkos')
+    depends_on('mpi', when='+mpi')
+
+    @property
+    def build_targets(self):
+        targets = []
+        # Append Kokkos
+        targets.append('KOKKOS_PATH={0}'.format(self.spec['kokkos'].prefix))
+        # Set kokkos device
+        if 'openmp' in self.spec:
+            targets.append('KOKKOS_DEVICES=OpenMP')
+        elif 'pthreads' in self.spec:
+            targets.append('KOKKOS_DEVICES=Pthread')
+        else:
+            targets.append('KOKKOS_DEVICES=Serial')
+        # Set MPI as needed
+        if '+mpi' in self.spec:
+            targets.append('MPI=1')
+            targets.append('CXX = {0}'.format(self.spec['mpi'].mpicxx))
+        else:
+            targets.append('MPI=0')
+            targets.append('CXX = {0}'.format('spack_cxx'))
+        return targets
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('src/ExaMiniMD', prefix.bin)
+        install_tree('input', prefix.input)
+        mkdirp(prefix.docs)
+        install('README.md', prefix.docs)
+        install('LICENSE', prefix.docs)
diff --git a/var/spack/repos/builtin/packages/exampm/package.py b/var/spack/repos/builtin/packages/exampm/package.py
index eba2fbc442..8ea259daae 100644
--- a/var/spack/repos/builtin/packages/exampm/package.py
+++ b/var/spack/repos/builtin/packages/exampm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,8 @@ class Exampm(CMakePackage):
     """Exascale Material Point Method (MPM) Mini-App"""
 
     homepage = "https://github.com/ECP-copa/ExaMPM"
-    url      = "https://github.com/ECP-copa/ExaMPM"
+    git      = "https://github.com/ECP-copa/ExaMPM.git"
 
-    version('develop', git='https://github.com/ECP-copa/ExaMPM',
-            branch='master')
+    version('develop', branch='master')
 
     tags = ['proxy-app']
diff --git a/var/spack/repos/builtin/packages/exasp2/package.py b/var/spack/repos/builtin/packages/exasp2/package.py
index aac5419893..511ff984a7 100644
--- a/var/spack/repos/builtin/packages/exasp2/package.py
+++ b/var/spack/repos/builtin/packages/exasp2/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import glob
 
 
 class Exasp2(MakefilePackage):
@@ -42,9 +24,11 @@ class Exasp2(MakefilePackage):
     tags = ['proxy-app']
 
     homepage = "https://github.com/ECP-copa/ExaSP2"
+    url      = "https://github.com/ECP-copa/ExaSP2/tarball/v1.0"
+    git      = "https://github.com/ECP-copa/ExaSP2.git"
 
-    version('develop', git='https://github.com/ECP-copa/ExaSP2',
-            branch='master')
+    version('develop', branch='master')
+    version('1.0', 'dba545995acc73f2bd1101bcb377bff5')
 
     variant('mpi', default=True, description='Build With MPI Support')
 
@@ -78,17 +62,15 @@ class Exasp2(MakefilePackage):
         math_includes += " -I" + spec['blas'].prefix.include
         targets.append('SPACKBLASINCLUDES=' + math_includes)
         # And BML
-        bmlLibDirs = spec['bml'].libs.directories[0]
-        targets.append('BML_PATH=' + bmlLibDirs)
+        bml_lib_dirs = spec['bml'].libs.directories[0]
+        targets.append('BML_PATH=' + bml_lib_dirs)
         targets.append('--file=Makefile.vanilla')
         return targets
 
     def install(self, spec, prefix):
         mkdir(prefix.bin)
         mkdir(prefix.doc)
-        if '+mpi' in self.spec:
-            install('bin/ExaSP2-parallel', prefix.bin)
-        else:
-            install('bin/ExaSP2-serial', prefix.bin)
+        for files in glob.glob('bin/ExaSP2-*'):
+            install(files, prefix.bin)
         install('LICENSE.md', prefix.doc)
         install('README.md', prefix.doc)
diff --git a/var/spack/repos/builtin/packages/exmcutils/package.py b/var/spack/repos/builtin/packages/exmcutils/package.py
index 02010deaf3..33b1827f00 100644
--- a/var/spack/repos/builtin/packages/exmcutils/package.py
+++ b/var/spack/repos/builtin/packages/exmcutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,8 +11,8 @@ class Exmcutils(AutotoolsPackage):
     """ExM C-Utils: Generic C utility library for ADLB/X and Swift/T"""
 
     homepage = 'http://swift-lang.org/Swift-T'
-    url      = 'http://swift-lang.github.io/swift-t-downloads/exmcutils-0.5.3.tar.gz'
+    url      = 'http://swift-lang.github.io/swift-t-downloads/spack/exmcutils-0.0.0.tar.gz'
 
-    version('0.5.3', '0e3ed6cc2991c684cd8f08db45c99a39')
+    version('0.5.6', 'b12a8dc163e3369492ec7c1403fe86e4')
 
     # This package has no dependencies.
diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py
index d74137533c..669929abce 100644
--- a/var/spack/repos/builtin/packages/exodusii/package.py
+++ b/var/spack/repos/builtin/packages/exodusii/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 # TODO: Add support for a C++11 enabled installation that filters out the
@@ -35,13 +16,12 @@ class Exodusii(CMakePackage):
        data transfer between codes.  An Exodus II data file is a random
        access, machine independent, binary file that is written and read
        via C, C++, or Fortran API routines.
-
     """
 
     homepage = "https://github.com/gsjaardema/seacas"
-    url      = "https://github.com/gsjaardema/seacas/archive/master.zip"
+    git      = "https://github.com/gsjaardema/seacas.git"
 
-    version('2016-08-09', git='https://github.com/gsjaardema/seacas.git', commit='2ffeb1b')
+    version('2016-08-09', commit='2ffeb1b')
 
     variant('mpi', default=True, description='Enables MPI parallelism.')
 
diff --git a/var/spack/repos/builtin/packages/exonerate/package.py b/var/spack/repos/builtin/packages/exonerate/package.py
index 2dae693b72..27b1c557c3 100644
--- a/var/spack/repos/builtin/packages/exonerate/package.py
+++ b/var/spack/repos/builtin/packages/exonerate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class Exonerate(Package):
 
     version('2.4.0', '126fbade003b80b663a1d530c56f1904')
 
-    depends_on('pkg-config', type="build")
+    depends_on('pkgconfig', type="build")
     depends_on('glib')
 
     parallel = False
diff --git a/var/spack/repos/builtin/packages/expat/package.py b/var/spack/repos/builtin/packages/expat/package.py
index a4ca544e57..2068401160 100644
--- a/var/spack/repos/builtin/packages/expat/package.py
+++ b/var/spack/repos/builtin/packages/expat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -29,8 +10,8 @@ import sys
 class Expat(AutotoolsPackage):
     """Expat is an XML parser library written in C."""
 
-    homepage = "http://expat.sourceforge.net/"
-    url      = "https://sourceforge.net/projects/expat/files/expat/2.2.2/expat-2.2.2.tar.bz2"
+    homepage = "https://libexpat.github.io/"
+    url      = "https://github.com/libexpat/libexpat/releases/download/R_2_2_2/expat-2.2.2.tar.bz2"
 
     # Version 2.2.2 introduced a requirement for a high quality
     # entropy source.  "Older" linux systems (aka CentOS 7) do not
@@ -44,9 +25,14 @@ class Expat(AutotoolsPackage):
             description="Use libbsd (for high quality randomness)")
     depends_on('libbsd', when="@2.2.1:+libbsd")
 
+    version('2.2.5', '789e297f547980fc9ecc036f9a070d49')
     version('2.2.2', '1ede9a41223c78528b8c5d23e69a2667')
     version('2.2.0', '2f47841c829facb346eb6e3fab5212e2')
 
+    def url_for_version(self, version):
+        url = 'https://github.com/libexpat/libexpat/releases/download/R_{0}/expat-{1}.tar.bz2'
+        return url.format(version.underscored, version.dotted)
+
     def configure_args(self):
         spec = self.spec
         args = []
diff --git a/var/spack/repos/builtin/packages/expect/package.py b/var/spack/repos/builtin/packages/expect/package.py
index 786539d025..8e17b3d5d9 100644
--- a/var/spack/repos/builtin/packages/expect/package.py
+++ b/var/spack/repos/builtin/packages/expect/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/express/package.py b/var/spack/repos/builtin/packages/express/package.py
new file mode 100644
index 0000000000..cfb262d313
--- /dev/null
+++ b/var/spack/repos/builtin/packages/express/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+import glob
+
+
+class Express(CMakePackage):
+    """eXpress is a streaming tool for quantifying the abundances of a set of
+       target sequences from sampled subsequences."""
+
+    homepage = "http://bio.math.berkeley.edu/eXpress/"
+    git      = "https://github.com/adarob/eXpress.git"
+
+    version('2015-11-29', commit='f845cab2c7f2d9247b35143e4aa05869cfb10e79')
+
+    depends_on('boost')
+    depends_on('bamtools')
+    depends_on('zlib')
+
+    conflicts('%gcc@6.0.0:', when='@2015-11-29')
+
+    def patch(self):
+        with working_dir('src'):
+            files = glob.iglob('*.*')
+            for file in files:
+                if os.path.isfile(file):
+                    edit = FileFilter(file)
+                    edit.filter('#include <api', '#include <%s' % self.spec[
+                                'bamtools'].prefix.include.bamtools.api)
+            edit = FileFilter('CMakeLists.txt')
+            edit.filter('\${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/'
+                        'libbamtools.a', '%s' % self.spec['bamtools'].libs)
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.prepend_path('CPATH', self.spec[
+                               'bamtools'].prefix.include.bamtools)
diff --git a/var/spack/repos/builtin/packages/extrae/package.py b/var/spack/repos/builtin/packages/extrae/package.py
index a13963655b..c79573424d 100644
--- a/var/spack/repos/builtin/packages/extrae/package.py
+++ b/var/spack/repos/builtin/packages/extrae/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 # typical working line with extrae 3.0.1
diff --git a/var/spack/repos/builtin/packages/exuberant-ctags/package.py b/var/spack/repos/builtin/packages/exuberant-ctags/package.py
index 4a4f56e270..f77678b397 100644
--- a/var/spack/repos/builtin/packages/exuberant-ctags/package.py
+++ b/var/spack/repos/builtin/packages/exuberant-ctags/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/f90cache/package.py b/var/spack/repos/builtin/packages/f90cache/package.py
index ff18433912..02f37540e8 100644
--- a/var/spack/repos/builtin/packages/f90cache/package.py
+++ b/var/spack/repos/builtin/packages/f90cache/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/fabtests/package.py b/var/spack/repos/builtin/packages/fabtests/package.py
new file mode 100644
index 0000000000..77d11e68a7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fabtests/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fabtests(AutotoolsPackage):
+    """Fabtests provides a set of examples that uses libfabric"""
+
+    homepage = "http://libfabric.org"
+    url      = "https://github.com/ofiwg/fabtests/releases/download/v1.5.3/fabtests-1.5.3.tar.gz"
+
+    version('1.6.0', '0441aa0aeda391b1bf1eb71250a4afbc')
+    version('1.5.3', 'f60cb95843ebf62e4eaa128e08ccdc7d')
+
+    depends_on('libfabric')
diff --git a/var/spack/repos/builtin/packages/falcon/package.py b/var/spack/repos/builtin/packages/falcon/package.py
index d2ca55d443..85d130a1d2 100644
--- a/var/spack/repos/builtin/packages/falcon/package.py
+++ b/var/spack/repos/builtin/packages/falcon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -36,11 +17,9 @@ class Falcon(PythonPackage):
     front-end written in Python for convenience."""
 
     homepage = "https://github.com/PacificBiosciences/FALCON"
-    url      = "https://github.com/PacificBiosciences/FALCON.git"
+    git      = "https://github.com/PacificBiosciences/FALCON.git"
 
-    version('2017-05-30',
-            git='https://github.com/PacificBiosciences/FALCON.git',
-            commit='86cec6157291679095ea6080b0cde6561eccc041')
+    version('2017-05-30', commit='86cec6157291679095ea6080b0cde6561eccc041')
 
     depends_on('py-setuptools', type='run')
     depends_on('py-pypeflow', type='run')
diff --git a/var/spack/repos/builtin/packages/farmhash/CMakeLists.txt b/var/spack/repos/builtin/packages/farmhash/CMakeLists.txt
deleted file mode 100644
index 0286f29ad0..0000000000
--- a/var/spack/repos/builtin/packages/farmhash/CMakeLists.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-cmake_minimum_required(VERSION 2.8.3)
-
-project(farmhash)
-
-set(FARMHASH_SRCS
-    "src/farmhash.h"
-    "src/farmhash.cc"
-)
-
-set(FARMHASH_INCLUDES
-    "src/farmhash.h"
-)
-
-include_directories("${CMAKE_CURRENT_SOURCE_DIR}")
-
-add_library(farmhash ${FARMHASH_SRCS})
-add_definitions(-DFARMHASH_NO_BUILTIN_EXPECT)
-
-install(TARGETS farmhash
-  LIBRARY DESTINATION lib COMPONENT RuntimeLibraries
-  ARCHIVE DESTINATION lib COMPONENT Development)
-
-foreach(FARMHASH_INCLUDE ${FARMHASH_INCLUDES})
-  install(FILES ${FARMHASH_INCLUDE} DESTINATION include COMPONENT Development)
-endforeach()
diff --git a/var/spack/repos/builtin/packages/farmhash/package.py b/var/spack/repos/builtin/packages/farmhash/package.py
deleted file mode 100644
index 071a43c1a2..0000000000
--- a/var/spack/repos/builtin/packages/farmhash/package.py
+++ /dev/null
@@ -1,42 +0,0 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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.path
-from shutil import copyfile
-
-
-class Farmhash(CMakePackage):
-    """
-    FarmHash provides hash functions for strings and other data.
-    """
-
-    homepage = "https://github.com/google/farmhash"
-
-    version('92e897', git='https://github.com/google/farmhash.git', 
-            commit='92e897b282426729f4724d91a637596c7e2fe28f')
-
-    def patch(self):
-        copyfile(join_path(os.path.dirname(__file__), "CMakeLists.txt"),
-                 "CMakeLists.txt")
diff --git a/var/spack/repos/builtin/packages/fast-global-file-status/package.py b/var/spack/repos/builtin/packages/fast-global-file-status/package.py
new file mode 100644
index 0000000000..79b35b54ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fast-global-file-status/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class FastGlobalFileStatus(AutotoolsPackage):
+    """provides a scalable mechanism to retrieve such information of a file,
+       including its degree of distribution or replication and consistency."""
+
+    homepage = "https://github.com/LLNL/FastGlobalFileStatus"
+    url = 'https://github.com/LLNL/FastGlobalFileStatus/files/2271592/fastglobalfilestatus-1.1.tar.gz'
+
+    version('1.1', 'c3d764c47a60310823947c489cd0f2df')
+
+    depends_on('mrnet')
+    depends_on('mount-point-attributes')
+    depends_on('mpi')
+
+    def configure_args(self):
+        spec = self.spec
+        args = [
+            "--with-mpa=%s"   % spec['mount-point-attributes'].prefix,
+            "--with-mrnet=%s"       % spec['mrnet'].prefix
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/fasta/package.py b/var/spack/repos/builtin/packages/fasta/package.py
new file mode 100644
index 0000000000..6a70762320
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fasta/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fasta(MakefilePackage):
+    """The FASTA programs find regions of local or global similarity
+    between Protein or DNA sequences, either by searching Protein or
+    DNA databases, or by identifying local duplications within a
+    sequence. Other programs provide information on the statistical
+    significance of an alignment. Like BLAST, FASTA can be used to
+    infer functional and evolutionary relationships between sequences
+    as well as help identify members of gene families.
+    """
+
+    homepage = "https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml"
+    url      = "https://github.com/wrpearson/fasta36/archive/fasta-v36.3.8g.tar.gz"
+
+    version('36.3.8g', sha256='fa5318b6f8d6a3cfdef0d29de530eb005bfd3ca05835faa6ad63663f8dce7b2e')
+
+    depends_on('zlib')
+
+    # The src tree includes a plethora of variant Makefiles and the
+    # builder is expected to choose one that's appropriate.  This'll
+    # do for a first cut.  I can't test anything else....
+    @property
+    def makefile_name(self):
+        if self.spec.satisfies('platform=darwin'):
+            name = 'Makefile.os_x86_64'
+        elif (self.spec.satisfies('platform=linux') and
+              self.spec.satisfies('target=x86_64')):
+            name = 'Makefile.linux64_sse2'
+        else:
+            tty.die('''Unsupported platform/target, must be
+Darwin (assumes 64-bit)
+Linux x86_64
+''')
+        return name
+
+    @property
+    def makefile_path(self):
+        return join_path(self.stage.source_path, 'make', self.makefile_name)
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter(self.makefile_path)
+        makefile.filter('XDIR = .*', 'XDIR = {0}'.format(prefix.bin))
+
+    def build(self, spec, prefix):
+        with working_dir('src'):
+            make('-f', self.makefile_path)
+
+    def install(self, spec, prefix):
+        with working_dir('src'):
+            mkdir(prefix.bin)
+            make('-f', self.makefile_path, 'install')
diff --git a/var/spack/repos/builtin/packages/fastjar/package.py b/var/spack/repos/builtin/packages/fastjar/package.py
index 19af359e81..15c98729aa 100644
--- a/var/spack/repos/builtin/packages/fastjar/package.py
+++ b/var/spack/repos/builtin/packages/fastjar/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastmath/package.py b/var/spack/repos/builtin/packages/fastmath/package.py
index c91289afaa..35e245e1fd 100644
--- a/var/spack/repos/builtin/packages/fastmath/package.py
+++ b/var/spack/repos/builtin/packages/fastmath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastme/package.py b/var/spack/repos/builtin/packages/fastme/package.py
index a64cd3163c..2aae0380f7 100644
--- a/var/spack/repos/builtin/packages/fastme/package.py
+++ b/var/spack/repos/builtin/packages/fastme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastphase/package.py b/var/spack/repos/builtin/packages/fastphase/package.py
index 857e13b3bd..80faa0d504 100644
--- a/var/spack/repos/builtin/packages/fastphase/package.py
+++ b/var/spack/repos/builtin/packages/fastphase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastq-screen/package.py b/var/spack/repos/builtin/packages/fastq-screen/package.py
index 81289a5cb1..c798fdb5a8 100644
--- a/var/spack/repos/builtin/packages/fastq-screen/package.py
+++ b/var/spack/repos/builtin/packages/fastq-screen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fastqc/package.py b/var/spack/repos/builtin/packages/fastqc/package.py
index 9d20805907..bcebd2b4cf 100644
--- a/var/spack/repos/builtin/packages/fastqc/package.py
+++ b/var/spack/repos/builtin/packages/fastqc/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree, mkpath
-from distutils.file_util import copy_file
 
 
 class Fastqc(Package):
@@ -33,6 +12,7 @@ class Fastqc(Package):
     homepage = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"
     url = "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip"
 
+    version('0.11.7', '8fead05fa62c5e723f0d2157a9b5fcd4')
     version('0.11.5', '3524f101c0ab0bae77c7595983170a76')
     version('0.11.4', '104ff2e0e9aebf5bee1f6b068a059b0d')
 
@@ -42,15 +22,15 @@ class Fastqc(Package):
     patch('fastqc.patch', level=0)
 
     def install(self, spec, prefix):
-        mkpath(self.prefix.bin)
-        mkpath(self.prefix.lib)
-        copy_file('fastqc', self.prefix.bin)
+        mkdir(prefix.bin)
+        mkdir(prefix.lib)
+        install('fastqc', prefix.bin)
         for j in ['cisd-jhdf5.jar', 'jbzip2-0.9.jar', 'sam-1.103.jar']:
-            copy_file(j, self.prefix.lib)
+            install(j, prefix.lib)
         for d in ['Configuration', 'net', 'org', 'Templates', 'uk']:
-            copy_tree(d, join_path(self.prefix.lib, d))
+            install_tree(d, join_path(prefix.lib, d))
         chmod = which('chmod')
-        chmod('+x', join_path(self.prefix.bin, 'fastqc'))
+        chmod('+x', prefix.bin.fastqc)
 
     # In theory the 'run' dependency on 'jdk' above should take
     # care of this for me. In practice, it does not.
@@ -58,5 +38,4 @@ class Fastqc(Package):
         """Add <prefix> to the path; the package has a script at the
            top level.
         """
-        run_env.prepend_path('PATH', join_path(self.spec['java'].prefix,
-                             'bin'))
+        run_env.prepend_path('PATH', self.spec['java'].prefix.bin)
diff --git a/var/spack/repos/builtin/packages/fastqvalidator/package.py b/var/spack/repos/builtin/packages/fastqvalidator/package.py
index d91ea6d0ba..38ccafa069 100644
--- a/var/spack/repos/builtin/packages/fastqvalidator/package.py
+++ b/var/spack/repos/builtin/packages/fastqvalidator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class Fastqvalidator(MakefilePackage):
     """The fastQValidator validates the format of fastq files."""
 
     homepage = "http://genome.sph.umich.edu/wiki/FastQValidator"
-    url      = "https://github.com/statgen/fastQValidator/archive/v0.1.1a.tar.gz"
+    git      = "https://github.com/statgen/fastQValidator.git"
 
-    version('2017-01-10', commit='6d619a34749e9d33c34ef0d3e0e87324ca77f320',
-            git='https://github.com/statgen/fastQValidator.git')
+    version('2017-01-10', commit='6d619a34749e9d33c34ef0d3e0e87324ca77f320')
 
     resource(
         name='libStatGen',
diff --git a/var/spack/repos/builtin/packages/fasttree/package.py b/var/spack/repos/builtin/packages/fasttree/package.py
new file mode 100644
index 0000000000..813b5eb0d6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fasttree/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fasttree(Package):
+    """FastTree infers approximately-maximum-likelihood phylogenetic
+       trees from alignments of nucleotide or protein sequences.
+       FastTree can handle alignments with up to a million of sequences
+       in a reasonable amount of time and memory."""
+
+    homepage = "http://www.microbesonline.org/fasttree"
+    url      = "http://www.microbesonline.org/fasttree/FastTree-2.1.10.c"
+
+    version('2.1.10', '1c2c6425a638ec0c61ef064cda687987', expand=False, url='http://www.microbesonline.org/fasttree/FastTree-2.1.10.c')
+
+    phases = ['build', 'install']
+
+    def build(self, spec, prefix):
+        cc = Executable(spack_cc)
+        cc('-O3', self.compiler.openmp_flag,
+           '-DOPENMP', '-finline-functions', '-funroll-loops', '-Wall',
+           '-oFastTreeMP', 'FastTree-' + format(spec.version.dotted) + '.c',
+           '-lm')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('FastTreeMP', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/fastx-toolkit/package.py b/var/spack/repos/builtin/packages/fastx-toolkit/package.py
index db9a1e1d6e..c1e74163d0 100644
--- a/var/spack/repos/builtin/packages/fastx-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/fastx-toolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fenics/package.py b/var/spack/repos/builtin/packages/fenics/package.py
index d95c826c34..f9707895fc 100644
--- a/var/spack/repos/builtin/packages/fenics/package.py
+++ b/var/spack/repos/builtin/packages/fenics/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -77,7 +58,7 @@ class Fenics(CMakePackage):
     depends_on('boost+filesystem+program_options+system+iostreams+timer+regex+chrono')
 
     depends_on('mpi', when='+mpi')
-    depends_on('hdf5', when='+hdf5')
+    depends_on('hdf5+hl', when='+hdf5')
     depends_on('parmetis@4.0.2:^metis+real64', when='+parmetis')
     depends_on('scotch~metis', when='+scotch~mpi')
     depends_on('scotch+mpi~metis', when='+scotch+mpi')
diff --git a/var/spack/repos/builtin/packages/fermi/package.py b/var/spack/repos/builtin/packages/fermi/package.py
new file mode 100644
index 0000000000..2c4693107d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fermi/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fermi(MakefilePackage):
+    """A WGS de novo assembler based on the FMD-index for large genomes."""
+
+    homepage = "https://github.com/lh3/fermi"
+    url      = "https://github.com/downloads/lh3/fermi/fermi-1.1.tar.bz2"
+
+    version('1.1', 'd5f006315652b6f18070b31474ca5ebb')
+
+    depends_on('zlib')
+    depends_on('perl', type='run')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('fermi', prefix.bin)
+        install('run-fermi.pl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/fermikit/package.py b/var/spack/repos/builtin/packages/fermikit/package.py
new file mode 100644
index 0000000000..0f44174fda
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fermikit/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fermikit(MakefilePackage):
+    """De novo assembly based variant calling pipeline for Illumina short
+    reads"""
+
+    homepage = "https://github.com/lh3/fermikit"
+    git      = "https://github.com/lh3/fermikit.git"
+
+    version('2017-11-7', commit='bf9c7112221577ba110665bddca8f1987250bdc7',
+            submodules=True)
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        install_tree('fermi.kit', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/fermisciencetools/package.py b/var/spack/repos/builtin/packages/fermisciencetools/package.py
new file mode 100644
index 0000000000..b2e67e7c27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fermisciencetools/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fermisciencetools(Package):
+    """The Fermi Science Tools consists of the basic tools necessary to
+    analyze Fermi data.
+
+    This is the binary version for Linux x86_64 with libc-2.17."""
+
+    homepage = "https://fermi.gsfc.nasa.gov/ssc/data/analysis/software/"
+    url      = "https://fermi.gsfc.nasa.gov/ssc/data/analysis/software/v11r5p3/ScienceTools-v11r5p3-fssc-20180124-x86_64-unknown-linux-gnu-libc2.17.tar.gz"
+
+    # Now we are using the binary distribution. The source distribution is also
+    # available, but there might be some logical errors in the configure codes,
+    # which leads to failing in building it from source. Hopefully someone else
+    # can figure it out and we can use the source distribution instead.
+    version('11r5p3', 'cf050ddddfe9251b6ebe8d3fd7de3c3f')
+
+    def install(self, spec, prefix):
+        install_tree('x86_64-unknown-linux-gnu-libc2.17', prefix)
diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py
index 33a6cfcb92..7ecffc3429 100644
--- a/var/spack/repos/builtin/packages/ferret/package.py
+++ b/var/spack/repos/builtin/packages/ferret/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
diff --git a/var/spack/repos/builtin/packages/ffmpeg/package.py b/var/spack/repos/builtin/packages/ffmpeg/package.py
index 1a7e3b253b..e5f8aab78f 100644
--- a/var/spack/repos/builtin/packages/ffmpeg/package.py
+++ b/var/spack/repos/builtin/packages/ffmpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fftw/package.py b/var/spack/repos/builtin/packages/fftw/package.py
index e2fc311166..d3d8795fee 100644
--- a/var/spack/repos/builtin/packages/fftw/package.py
+++ b/var/spack/repos/builtin/packages/fftw/package.py
@@ -1,29 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
+import llnl.util.lang
+
 
 class Fftw(AutotoolsPackage):
     """FFTW is a C subroutine library for computing the discrete Fourier
@@ -37,6 +20,8 @@ class Fftw(AutotoolsPackage):
     url      = "http://www.fftw.org/fftw-3.3.4.tar.gz"
     list_url = "http://www.fftw.org/download.html"
 
+    version('3.3.8', '8aac833c943d8e90d51b697b27d4384d')
+    version('3.3.7', '0d5915d7d39b3253c1cc05030d79ac47')
     version('3.3.6-pl2', '927e481edbb32575397eb3d62535a856')
     version('3.3.5', '6cc08a3b9c7ee06fdd5b9eb02e06f569')
     version('3.3.4', '2edab8c06b24feeb3b82bbb3ebf3e7b3')
@@ -65,15 +50,62 @@ class Fftw(AutotoolsPackage):
         'pfft_patches', default=False,
         description='Add extra transpose functions for PFFT compatibility')
 
+    variant(
+        'simd',
+        default='sse2,avx,avx2',
+        values=(
+            'sse', 'sse2', 'avx', 'avx2', 'avx512',  # Intel
+            'avx-128-fma', 'kcvi',  # Intel
+            'altivec', 'vsx',  # IBM
+            'neon',  # ARM
+            'generic-simd128', 'generic-simd256'  # Generic
+        ),
+        description='Optimizations that are enabled in this build',
+        multi=True
+    )
+    variant('fma', default=False, description='Activate support for fma')
+
     depends_on('mpi', when='+mpi')
     depends_on('automake', type='build', when='+pfft_patches')
     depends_on('autoconf', type='build', when='+pfft_patches')
     depends_on('libtool', type='build', when='+pfft_patches')
+    # https://github.com/FFTW/fftw3/commit/902d0982522cdf6f0acd60f01f59203824e8e6f3
+    conflicts('%gcc@8:8.9999', when="@3.3.7")
+
+    provides('fftw-api@2', when='@2.1.5')
+    provides('fftw-api@3', when='@3:')
 
     @property
     def libs(self):
-        result = find_libraries(['libfftw3'], root=self.prefix, recurse=True)
-        return result
+
+        # Reduce repetitions of entries
+        query_parameters = list(llnl.util.lang.dedupe(
+            self.spec.last_query.extra_parameters
+        ))
+
+        # List of all the suffixes associated with float precisions
+        precisions = [
+            ('float', 'f'),
+            ('double', ''),
+            ('long_double', 'l'),
+            ('quad', 'q')
+        ]
+
+        # Retrieve the correct suffixes, or use double as a default
+        suffixes = [v for k, v in precisions if k in query_parameters] or ['']
+
+        # Construct the list of libraries that needs to be found
+        libraries = []
+        for sfx in suffixes:
+            if 'mpi' in query_parameters and '+mpi' in self.spec:
+                libraries.append('libfftw3' + sfx + '_mpi')
+
+            if 'openmp' in query_parameters and '+openmp' in self.spec:
+                libraries.append('libfftw3' + sfx + '_omp')
+
+            libraries.append('libfftw3' + sfx)
+
+        return find_libraries(libraries, root=self.prefix, recursive=True)
 
     def autoreconf(self, spec, prefix):
         if '+pfft_patches' in spec:
@@ -108,12 +140,11 @@ class Fftw(AutotoolsPackage):
             options.append('--enable-mpi')
 
         # SIMD support
-        # TODO: add support for more architectures
-        float_options = []
-        double_options = []
-        if 'x86_64' in spec.architecture and spec.satisfies('@3:'):
-            float_options.append('--enable-sse2')
-            double_options.append('--enable-sse2')
+        float_options, double_options = [], []
+        if spec.satisfies('@3:', strict=True):
+            for opts in (float_options, double_options):
+                opts += self.enable_or_disable('simd')
+                opts += self.enable_or_disable('fma')
 
         configure = Executable('../configure')
 
diff --git a/var/spack/repos/builtin/packages/figtree/package.py b/var/spack/repos/builtin/packages/figtree/package.py
new file mode 100644
index 0000000000..bb4cd8258a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/figtree/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Figtree(Package):
+    """FigTree is designed as a graphical viewer of phylogenetic trees and
+       as a program for producing publication-ready figures. As with most of
+       my programs, it was written for my own needs so may not be as polished
+       and feature-complete as a commercial program. In particular it is
+       designed to display summarized and annotated trees produced by BEAST."""
+
+    homepage = "https://github.com/rambaut/figtree"
+    url      = "https://github.com/rambaut/figtree/releases/download/v1.4.3/FigTree_v1.4.3.tgz"
+
+    version('1.4.3', sha256='f497d4dd3a6d220f6b62495b6f47a12ade50d87dbd8d6089f168e94d202f937b')
+
+    depends_on('java', type='run')
+
+    def patch(self):
+        # we have to change up the executable to point to the right program
+        filter_file('lib/figtree.jar',
+                    join_path(self.spec.prefix.lib, 'figtree.jar'),
+                    'bin/figtree', string=True)
+
+        # also set proper executable flags
+        os.chmod('bin/figtree', 0o775)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('bin', prefix.bin)
+
+        mkdirp(prefix.lib)
+        install_tree('lib', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/fimpute/package.py b/var/spack/repos/builtin/packages/fimpute/package.py
index 177ba05640..10e93d2a54 100644
--- a/var/spack/repos/builtin/packages/fimpute/package.py
+++ b/var/spack/repos/builtin/packages/fimpute/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/findutils/package.py b/var/spack/repos/builtin/packages/findutils/package.py
index 3abd8e2728..2f301d42ee 100644
--- a/var/spack/repos/builtin/packages/findutils/package.py
+++ b/var/spack/repos/builtin/packages/findutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,7 @@ class Findutils(AutotoolsPackage):
        utilities of the GNU operating system."""
 
     homepage = "https://www.gnu.org/software/findutils/"
-    url      = "http://ftpmirror.gnu.org/findutils/findutils-4.6.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/findutils/findutils-4.6.0.tar.gz"
 
     version('4.6.0',  '9936aa8009438ce185bea2694a997fc1')
     version('4.4.2',  '351cc4adb07d54877fa15f75fb77d39f')
@@ -51,3 +32,32 @@ class Findutils(AutotoolsPackage):
     version('4.2.15', 'a881b15aa7170aea045bf35cc92d48e7')
     version('4.1.20', 'e90ce7222daadeb8616b8db461e17cbc')
     version('4.1',    '3ea8fe58ef5386da75f6c707713aa059')
+
+    depends_on('autoconf', type='build', when='@4.6.0')
+    depends_on('automake', type='build', when='@4.6.0')
+    depends_on('libtool', type='build', when='@4.6.0')
+    depends_on('m4', type='build', when='@4.6.0')
+    depends_on('texinfo', type='build', when='@4.6.0')
+
+    # findutils does not build with newer versions of glibc
+    patch('https://src.fedoraproject.org/rpms/findutils/raw/97ba2d7a18d1f9ae761b6ff0b4f1c4d33d7a8efc/f/findutils-4.6.0-gnulib-fflush.patch', sha256='84b916c0bf8c51b7e7b28417692f0ad3e7030d1f3c248ba77c42ede5c1c5d11e', when='@4.6.0')
+    patch('https://src.fedoraproject.org/rpms/findutils/raw/97ba2d7a18d1f9ae761b6ff0b4f1c4d33d7a8efc/f/findutils-4.6.0-gnulib-makedev.patch', sha256='bd9e4e5cc280f9753ae14956c4e4aa17fe7a210f55dd6c84aa60b12d106d47a2', when='@4.6.0')
+
+    build_directory = 'spack-build'
+
+    @property
+    def force_autoreconf(self):
+        # Run autoreconf due to build system patch (gnulib-makedev)
+        return self.spec.satisfies('@4.6.0')
+
+    @when('@4.6.0')
+    def patch(self):
+        # We have to patch out gettext support, otherwise autoreconf tries to
+        # call autopoint, which depends on find, which is part of findutils.
+        filter_file('^AM_GNU_GETTEXT.*',
+                    '',
+                    'configure.ac')
+
+        filter_file(r'^SUBDIRS = (.*) po (.*)',
+                    r'SUBDIRS = \1 \2',
+                    'Makefile.am')
diff --git a/var/spack/repos/builtin/packages/fio/package.py b/var/spack/repos/builtin/packages/fio/package.py
index 1119961ad0..59372e0a0c 100644
--- a/var/spack/repos/builtin/packages/fio/package.py
+++ b/var/spack/repos/builtin/packages/fio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fish/package.py b/var/spack/repos/builtin/packages/fish/package.py
index 922aca5eb8..0f7c0eb2e9 100644
--- a/var/spack/repos/builtin/packages/fish/package.py
+++ b/var/spack/repos/builtin/packages/fish/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,12 @@ class Fish(AutotoolsPackage):
     the rest of the family.
     """
 
-    homepage = "http://fishshell.com/"
-    url      = "http://fishshell.com/files/2.2.0/fish-2.2.0.tar.gz"
-    list_url = "http://fishshell.com/"
+    homepage = "https://fishshell.com/"
+    url      = "https://github.com/fish-shell/fish-shell/releases/download/2.7.1/fish-2.7.1.tar.gz"
+    list_url = "https://fishshell.com/"
 
     depends_on('ncurses')
 
+    version('2.7.1', 'e42bb19c7586356905a58578190be792df960fa81de35effb1ca5a5a981f0c5a')
+    version('2.7.0', '3a76b7cae92f9f88863c35c832d2427fb66082f98e92a02203dc900b8fa87bcb')
     version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a')
diff --git a/var/spack/repos/builtin/packages/fixesproto/package.py b/var/spack/repos/builtin/packages/fixesproto/package.py
index b98437b9ff..ed062c1a08 100644
--- a/var/spack/repos/builtin/packages/fixesproto/package.py
+++ b/var/spack/repos/builtin/packages/fixesproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Fixesproto(AutotoolsPackage):
 
     version('5.0', '1b3115574cadd4cbea1f197faa7c1de4')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/flac/package.py b/var/spack/repos/builtin/packages/flac/package.py
index 2b95a5a6f2..5c41641855 100644
--- a/var/spack/repos/builtin/packages/flac/package.py
+++ b/var/spack/repos/builtin/packages/flac/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/flang/package.py b/var/spack/repos/builtin/packages/flang/package.py
index fb84e9841d..b058febe86 100644
--- a/var/spack/repos/builtin/packages/flang/package.py
+++ b/var/spack/repos/builtin/packages/flang/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
@@ -29,22 +10,23 @@ import os
 
 class Flang(CMakePackage):
     """Flang is a Fortran compiler targeting LLVM."""
+
     homepage = "https://github.com/flang-compiler/flang"
-    url      = "https://github.com/flang-compiler/flang/flecsi/tarball/v1.0"
 
-    version('develop', git='https://github.com/flang-compiler/flang', branch='master')
+    url      = "https://github.com/flang-compiler/flang/archive/flang_20180612.tar.gz"
+    git      = "https://github.com/flang-compiler/flang.git"
 
-    depends_on(
-            "llvm+clang@4.0.1,5.0.0",
-        patches=[
-            patch('https://github.com/llvm-mirror/clang/pull/33.diff',
-                      sha256='e46d7ab305e5e95c51f4656d9b52058143cd85d859b312b3c80e93a02d54b4a5',
-                      when='@4.0.1', level=1, working_dir='tools/clang'),
-            patch('https://github.com/llvm-mirror/clang/pull/35.diff',
-                      sha256='7f39555783993f78b75c380ca5ef167c1d8b88cc75c6542f6c94e0b6acfb7c5d',
-                      when='@5.0.0', level=1, working_dir='tools/clang')
-        ]
-    )
+    version('develop', branch='master')
+    version('20180612', '62284e26214eaaff261a922c67f6878c')
+
+    depends_on('llvm@flang-develop', when='@develop')
+    depends_on('llvm@flang-20180612', when='@20180612 target=x86_64')
+
+    # LLVM version specific to OpenPOWER.
+    depends_on('llvm@flang-ppc64le-20180612', when='@20180612 target=ppc64le')
+
+    depends_on('pgmath@develop', when='@develop')
+    depends_on('pgmath@20180612', when='@20180612')
 
     def cmake_args(self):
         options = [
@@ -72,11 +54,20 @@ class Flang(CMakePackage):
         with open(flang, 'w') as out:
             out.write('#!/bin/bash\n')
             out.write(
-                '{0} -I{1} -L{2} {3}{4} -B{5} "$@"\n'.format(
-                    os.path.join(self.spec['llvm'].prefix.bin, 'flang'),
+                '{0} -I{1} -L{2} -L{3} {4}{5} {6}{7} -B{8} "$@"\n'.format(
+                    self.spec['llvm'].prefix.bin.flang,
                     self.prefix.include, self.prefix.lib,
+                    self.spec['pgmath'].prefix.lib,
                     self.compiler.fc_rpath_arg, self.prefix.lib,
-                    self.spec.prefix.bin))
+                    self.compiler.fc_rpath_arg,
+                    self.spec['pgmath'].prefix.lib, self.spec.prefix.bin))
             out.close()
         chmod = which('chmod')
         chmod('+x', flang)
+
+    def setup_environment(self, spack_env, run_env):
+        # to find llvm's libc++.so
+        spack_env.set('LD_LIBRARY_PATH', self.spec['llvm'].prefix.lib)
+        run_env.set('FC', join_path(self.spec.prefix.bin, 'flang'))
+        run_env.set('F77', join_path(self.spec.prefix.bin, 'flang'))
+        run_env.set('F90', join_path(self.spec.prefix.bin, 'flang'))
diff --git a/var/spack/repos/builtin/packages/flann/linux-gcc-cmakev3.11-plus.patch b/var/spack/repos/builtin/packages/flann/linux-gcc-cmakev3.11-plus.patch
new file mode 100644
index 0000000000..d8a7dbd0d2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flann/linux-gcc-cmakev3.11-plus.patch
@@ -0,0 +1,24 @@
+--- a/src/cpp/CMakeLists.txt
++++ b/src/cpp/CMakeLists.txt
+@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB)
+ endif()
+ 
+ if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC)
+-    add_library(flann_cpp SHARED "")
++    add_library(flann_cpp SHARED "empty.cpp")
+     set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX)
+     target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive)
+ 
+@@ -83,7 +83,7 @@ if (BUILD_C_BINDINGS)
+     set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC)
+ 
+     if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC)
+-        add_library(flann SHARED "")
++        add_library(flann SHARED "empty.cpp")
+         set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX)
+         target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive)
+     else()
+--- /dev/null
++++ b/src/cpp/empty.cpp
+@@ -0,0 +1 @@
++/* empty */
diff --git a/var/spack/repos/builtin/packages/flann/package.py b/var/spack/repos/builtin/packages/flann/package.py
index 1ed996bd51..7aee67b66c 100644
--- a/var/spack/repos/builtin/packages/flann/package.py
+++ b/var/spack/repos/builtin/packages/flann/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -92,6 +73,12 @@ class Flann(CMakePackage):
     # Example uses hdf5.
     depends_on("hdf5", when="+examples")
 
+    depends_on('hdf5', type='test')
+    depends_on('gtest', type='test')
+
+    # See: https://github.com/mariusmuja/flann/issues/369
+    patch('linux-gcc-cmakev3.11-plus.patch', when='%gcc^cmake@3.11:')
+
     def patch(self):
         # Fix up the python setup.py call inside the install(CODE
         filter_file("setup.py install",
@@ -109,10 +96,6 @@ class Flann(CMakePackage):
                     "# install( FILES",
                     "src/python/CMakeLists.txt", string=True)
 
-    # TODO: revisit after https://github.com/spack/spack/issues/1279
-    # depends_on('hdf5', type='test')
-    # depends_on('gtest', type='test')
-
     def cmake_args(self):
         spec = self.spec
         args = []
diff --git a/var/spack/repos/builtin/packages/flash/package.py b/var/spack/repos/builtin/packages/flash/package.py
index 6c918feb1a..4b464bfb11 100644
--- a/var/spack/repos/builtin/packages/flash/package.py
+++ b/var/spack/repos/builtin/packages/flash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/flatbuffers/package.py b/var/spack/repos/builtin/packages/flatbuffers/package.py
new file mode 100644
index 0000000000..0f90221c06
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flatbuffers/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Flatbuffers(CMakePackage):
+    """Memory Efficient Serialization Library
+    """
+
+    homepage = "http://google.github.io/flatbuffers/"
+    url      = "https://github.com/google/flatbuffers/archive/v1.9.0.tar.gz"
+
+    version('1.9.0', '8be7513bf960034f6873326d09521a4b')
+    version('1.8.0', '276cab8303c4189cbe3b8a70e0515d65')
diff --git a/var/spack/repos/builtin/packages/flecsale/package.py b/var/spack/repos/builtin/packages/flecsale/package.py
index 1160ea642e..803624acd0 100644
--- a/var/spack/repos/builtin/packages/flecsale/package.py
+++ b/var/spack/repos/builtin/packages/flecsale/package.py
@@ -1,37 +1,19 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
 class Flecsale(CMakePackage):
     """Flecsale is an ALE code based on FleCSI"""
+
     homepage = "https://github.com/laristra/flecsale"
-    url      = "https://github.com/laristra/flecsale/tarball/v1.0"
+    git      = "https://github.com/laristra/flecsale.git"
 
-    version('develop', git='https://github.com/laristra/flecsale', branch='master', submodules=True)
+    version('develop', branch='master', submodules=True)
 
     variant('mpi', default=True,
             description='Build on top of mpi conduit for mpi inoperability')
diff --git a/var/spack/repos/builtin/packages/flecsi/package.py b/var/spack/repos/builtin/packages/flecsi/package.py
index 049b28d15d..ac10a63e49 100644
--- a/var/spack/repos/builtin/packages/flecsi/package.py
+++ b/var/spack/repos/builtin/packages/flecsi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -37,9 +18,9 @@ class Flecsi(CMakePackage):
        interfaces,and dependency closures.
     """
     homepage = "http://flecsi.lanl.gov/"
-    url      = "https://github.com/laristra/flecsi/tarball/v1.0"
+    git      = "https://github.com/laristra/flecsi.git"
 
-    version('develop', git='https://github.com/laristra/flecsi', branch='master', submodules=True)
+    version('develop', branch='master', submodules=True)
 
     variant('mpi', default=True,
             description='Build on top of mpi conduit for mpi inoperability')
@@ -47,6 +28,7 @@ class Flecsi(CMakePackage):
     depends_on("cmake@3.1:", type='build')
     depends_on("legion+shared", when='~mpi')
     depends_on("legion+shared+mpi", when='+mpi')
+    depends_on("parmetis")
 
     def cmake_args(self):
         options = ['-DENABLE_UNIT_TESTS=ON']
diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py
index 8d5ffe11c3..2bbef402a6 100644
--- a/var/spack/repos/builtin/packages/flex/package.py
+++ b/var/spack/repos/builtin/packages/flex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -33,7 +14,10 @@ class Flex(AutotoolsPackage):
     url = "https://github.com/westes/flex/releases/download/v2.6.1/flex-2.6.1.tar.gz"
 
     version('2.6.4', '2882e3179748cc9f9c23ec593d6adc8d')
-    version('2.6.3', 'a5f65570cd9107ec8a8ec88f17b31bb1')
+    # 2.6.4 fails to compile with gcc@7.2:
+    # see https://github.com/spack/spack/issues/8152 and
+    # https://github.com/spack/spack/issues/6942
+    version('2.6.3', 'a5f65570cd9107ec8a8ec88f17b31bb1', preferred=True)
     # Avoid flex '2.6.2' (major bug)
     # See issue #2554; https://github.com/westes/flex/issues/113
     version('2.6.1', '05bcd8fb629e0ae130311e8a6106fa82')
@@ -53,6 +37,10 @@ class Flex(AutotoolsPackage):
     depends_on('automake', type='build', when='@:2.6.0')
     depends_on('libtool',  type='build', when='@:2.6.0')
 
+    # Build issue for v2.6.4 when gcc@7.2.0: is used
+    # See issue #219; https://github.com/westes/flex/issues/219
+    conflicts('%gcc@7.2.0:', when='@2.6.4')
+
     def url_for_version(self, version):
         url = "https://github.com/westes/flex"
         if version >= Version('2.6.1'):
diff --git a/var/spack/repos/builtin/packages/flint/package.py b/var/spack/repos/builtin/packages/flint/package.py
index 630a57c9bd..193f071013 100644
--- a/var/spack/repos/builtin/packages/flint/package.py
+++ b/var/spack/repos/builtin/packages/flint/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,11 @@ class Flint(Package):
 
     homepage = "http://www.flintlib.org"
     url      = "http://mirrors.mit.edu/sage/spkg/upstream/flint/flint-2.5.2.tar.gz"
+    git      = "https://github.com/wbhart/flint2.git"
 
+    version('develop', branch='trunk')
     version('2.5.2', 'cda885309362150196aed66a5e0f0383')
     version('2.4.5', '6504b9deabeafb9313e57153a1730b33')
-    version('develop', git='https://github.com/wbhart/flint2.git')
 
     # Overlap in functionality between gmp and mpir
     # All other dependencies must also be built with
diff --git a/var/spack/repos/builtin/packages/flit/package.py b/var/spack/repos/builtin/packages/flit/package.py
new file mode 100644
index 0000000000..44ab5cbbcf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flit/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Flit(MakefilePackage):
+    """Floating-point Litmus Tests (FLiT) is a C++ test infrastructure for
+    detecting variability in floating-point code caused by variations in
+    compiler code generation, hardware and execution environments."""
+
+    homepage = "https://pruners.github.io/flit"
+    url      = "https://github.com/PRUNERS/FLiT"
+    url      = "https://github.com/PRUNERS/FLiT/archive/v2.0-alpha.1.tar.gz"
+
+    version('2.0-alpha.1', '62cf7784bcdc15b962c813b11e478159')
+    # FIXME: fix install and build to handle the old version, which is not
+    #        installable
+    # version('1.0.0',       '27763c89b044c5e3cfe62dd319a36a2b')
+    conflicts("@:1.999", msg="Only can build version 2.0 and up")
+
+    # Add dependencies
+    depends_on('python@3:', type='run')
+    depends_on('py-numpy', type='run')
+    depends_on('py-matplotlib tk=False', type='run')
+    depends_on('py-toml', type='run')
+
+    @property
+    def install_targets(self):
+        return ['install', 'PREFIX=%s' % self.prefix]
diff --git a/var/spack/repos/builtin/packages/fltk/package.py b/var/spack/repos/builtin/packages/fltk/package.py
index 62fe84bb44..7f240b37eb 100644
--- a/var/spack/repos/builtin/packages/fltk/package.py
+++ b/var/spack/repos/builtin/packages/fltk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,6 +23,8 @@ class Fltk(Package):
 
     version('1.3.3', '9ccdb0d19dc104b87179bd9fd10822e3')
 
+    depends_on('libx11')
+
     patch('font.patch', when='@1.3.3')
 
     variant('shared', default=True,
diff --git a/var/spack/repos/builtin/packages/flux-core/package.py b/var/spack/repos/builtin/packages/flux-core/package.py
new file mode 100644
index 0000000000..4dea197de2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flux-core/package.py
@@ -0,0 +1,120 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class FluxCore(AutotoolsPackage):
+    """ A next-generation resource manager (pre-alpha) """
+
+    homepage = "https://github.com/flux-framework/flux-core"
+    url      = "https://github.com/flux-framework/flux-core/releases/download/v0.8.0/flux-core-0.8.0.tar.gz"
+    git      = "https://github.com/flux-framework/flux-core.git"
+
+    version('master',  branch='master')
+    version('0.10.0', 'a84a1ed53a69c805c253bc940540cbf667a059b2008fd2a6a9bb890a985ead08e88dcbba68c01567f887357306fbfded41b93cc33edfa7809955ba5ba5870284')
+    version('0.9.0',  '70eaec1005aa49e8d8cf397570789cebedfb5d917efe963390d456ee4c473eefb15b0c81ea83f60a1fd057fe7be356bbafdebcae64b499844d194c48f6aefa05')
+    version('0.8.0',  'b0fec05acedc530bcdf75b2477ac22f39d2adddc7af8ff76496208a5e1e8185b1b4a18677871d95c3cfbf34b05f391953651200917fe029931f4e2beb79d70df')
+
+    # Avoid the infinite symlink issue
+    # This workaround is documented in PR #3543
+    build_directory = 'spack-build'
+
+    variant('docs', default=False, description='Build flux manpages')
+    variant('cuda', default=False, description='Build dependencies with support for CUDA')
+
+    depends_on("zeromq@4.0.4:")
+    depends_on("czmq")
+    depends_on("czmq@2.2:3.99", when="@0.1:0.6.99")
+    depends_on("czmq@3.0.1:", when="@0.7:,master")
+    depends_on("hwloc@1.11.1:1.99")
+    depends_on("hwloc +cuda", when='+cuda')
+    depends_on("lua", type=('build', 'run', 'link'))
+    depends_on("lua@5.1:5.1.99", when="@0.1.0:0.9.0")
+    depends_on("lua@5.1:5.2.99", when="@0.10.0:,master")
+    depends_on("lua-luaposix")
+    depends_on("munge")
+    depends_on("libuuid")
+    depends_on("python", type=('build', 'run'))
+    depends_on("python@2.7:2.99", when="@0.1.0:0.10.0")
+    depends_on("python@2.7:", when="@0.11.0:,master")
+    depends_on("py-cffi", type=('build', 'run'))
+    depends_on("py-six", type=('build', 'run'), when="@0.11.0:,master")
+    depends_on("jansson")
+    depends_on("yaml-cpp")
+    depends_on("lz4", when="@0.11.0:,master")
+
+    # versions up to 0.8.0 uses pylint to check Flux's python binding
+    # later versions provide a configure flag and disable the check by default
+    depends_on("py-pylint", when='@:0.8.0', type='build')
+
+    depends_on("asciidoc", type='build', when="+docs")
+
+    # Need autotools when building on master:
+    depends_on("autoconf", type='build', when='@master')
+    depends_on("automake", type='build', when='@master')
+    depends_on("libtool", type='build', when='@master')
+
+    def setup(self):
+        pass
+
+    @when('@master')
+    def setup(self):
+        with working_dir(self.stage.source_path):
+            # Allow git-describe to get last tag so flux-version works:
+            git = which('git')
+            git('fetch', '--unshallow')
+            git("config", "remote.origin.fetch",
+                "+refs/heads/*:refs/remotes/origin/*")
+            git('fetch', 'origin')
+
+    def autoreconf(self, spec, prefix):
+        self.setup()
+        if not os.path.exists('configure'):
+            # Bootstrap with autotools
+            bash = which('bash')
+            bash('./autogen.sh')
+
+    @property
+    def lua_version(self):
+        return self.spec['lua'].version.up_to(2)
+
+    @property
+    def lua_share_dir(self):
+        return os.path.join('share', 'lua', str(self.lua_version))
+
+    @property
+    def lua_lib_dir(self):
+        return os.path.join('lib', 'lua', str(self.lua_version))
+
+    def setup_environment(self, spack_env, run_env):
+        #  Ensure ./fluxometer.lua can be found during flux's make check
+        spack_env.append_path('LUA_PATH', './?.lua', separator=';')
+
+        run_env.prepend_path(
+            'LUA_PATH',
+            os.path.join(self.spec.prefix, self.lua_share_dir, '?.lua'),
+            separator=';')
+        run_env.prepend_path(
+            'LUA_CPATH',
+            os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'),
+            separator=';')
+        run_env.prepend_path(
+            'PYTHONPATH',
+            os.path.join(
+                self.spec.prefix.lib,
+                "python{0}".format(self.spec['python'].version.up_to(2)),
+                "site-packages"),
+        )
+        run_env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules)
+        run_env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd)
+        run_env.prepend_path('FLUX_RC_PATH', self.prefix.etc.flux)
+
+    def configure_args(self):
+        args = ['--enable-pylint=no']
+        if '+docs' not in self.spec:
+            args.append('--disable-docs')
+        return args
diff --git a/var/spack/repos/builtin/packages/flux-sched/package.py b/var/spack/repos/builtin/packages/flux-sched/package.py
new file mode 100644
index 0000000000..d3c424f716
--- /dev/null
+++ b/var/spack/repos/builtin/packages/flux-sched/package.py
@@ -0,0 +1,91 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class FluxSched(AutotoolsPackage):
+    """ A scheduler for flux-core (pre-alpha) """
+
+    homepage = "https://github.com/flux-framework/flux-sched"
+    url      = "https://github.com/flux-framework/flux-sched/releases/download/v0.5.0/flux-sched-0.5.0.tar.gz"
+    git      = "https://github.com/flux-framework/flux-sched.git"
+
+    version('master', branch='master')
+    version('0.6.0', '8aad185949038c7fb6b277e6a8282947917084ebbec5c5bf0ee3a81a0dcdbe41ba18b1df837c669ae7b48ca5f1e492a5172bffa6b9feb4dda1c6a7a85abed4e8')
+    version('0.5.0', 'a9835c9c478aa41123a4e12672500052228aaf1ea770f74cb0901dbf4a049bd7d329e99d8d3484e39cfed1f911705030b2775dcfede39bc8bea59c6afe2549b1')
+    version('0.4.0', '82732641ac4594ffe9b94ca442a99e92bf5f91bc14745af92203a887a40610dd44edda3ae07f9b6c8d63799b2968d87c8da28f1488edef1310d0d12be9bd6319')
+
+    variant('cuda', default=False, description='Build dependencies with support for CUDA')
+
+    depends_on("boost+graph", when='@0.5.0:,master')
+    depends_on("py-pyyaml", when="@0.7.0:,master")
+    depends_on("libxml2@2.9.1:", when="@0.6.0,master")
+
+    depends_on("flux-core", type=('build', 'link', 'run'))
+    depends_on("flux-core+cuda", when='+cuda')
+    depends_on("flux-core@0.8.0", when='@0.4.0')
+    depends_on("flux-core@0.9.0", when='@0.5.0')
+    depends_on("flux-core@0.10.0", when='@0.6.0')
+    depends_on("flux-core@master", when='@master')
+
+    # Need autotools when building on master:
+    depends_on("autoconf", type='build', when='@master')
+    depends_on("automake", type='build', when='@master')
+    depends_on("libtool", type='build', when='@master')
+
+    def setup(self):
+        pass
+
+    @when('@master')
+    def setup(self):
+        with working_dir(self.stage.source_path):
+            # Allow git-describe to get last tag so flux-version works:
+            git = which('git')
+            git('fetch', '--unshallow')
+            git("config", "remote.origin.fetch",
+                "+refs/heads/*:refs/remotes/origin/*")
+            git('fetch', 'origin')
+
+    def autoreconf(self, spec, prefix):
+        self.setup()
+        if not os.path.exists('configure'):
+            # Bootstrap with autotools
+            bash = which('bash')
+            bash('./autogen.sh')
+
+    def configure_args(self):
+        # flux-sched's ax_boost is sometimes weird about non-system locations
+        # explicitly setting the path guarantees success
+        return ['--with-boost={0}'.format(self.spec['boost'].prefix)]
+
+    @property
+    def lua_version(self):
+        return self.spec['lua'].version.up_to(2)
+
+    @property
+    def lua_share_dir(self):
+        return os.path.join('share', 'lua', str(self.lua_version))
+
+    @property
+    def lua_lib_dir(self):
+        return os.path.join('lib', 'lua', str(self.lua_version))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path(
+            'LUA_PATH',
+            os.path.join(self.spec.prefix, self.lua_share_dir, '?.lua'),
+            separator=';')
+        run_env.prepend_path(
+            'LUA_CPATH',
+            os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'),
+            separator=';')
+
+        run_env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules)
+        run_env.prepend_path('FLUX_MODULE_PATH',
+                             self.prefix.lib.flux.modules.sched)
+        run_env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd)
+        run_env.prepend_path('FLUX_RC_EXTRA', self.prefix.etc.flux)
diff --git a/var/spack/repos/builtin/packages/flux/package.py b/var/spack/repos/builtin/packages/flux/package.py
deleted file mode 100644
index 6bca4c541c..0000000000
--- a/var/spack/repos/builtin/packages/flux/package.py
+++ /dev/null
@@ -1,80 +0,0 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 Flux(AutotoolsPackage):
-    """ A next-generation resource manager (pre-alpha) """
-
-    homepage = "https://github.com/flux-framework/flux-core"
-    url      = "https://github.com/flux-framework/flux-core/releases/download/v0.8.0/flux-core-0.8.0.tar.gz"
-
-    version('0.8.0', md5='9ee12974a8b2ab9a30533f69826f3bec')
-    version('master', branch='master',
-            git='https://github.com/flux-framework/flux-core')
-
-    variant('docs', default=True, description='Build flux manpages')
-
-    depends_on("zeromq@4.0.4:")
-    depends_on("czmq@2.2:")
-    depends_on("hwloc")
-    depends_on("lua@5.1:5.1.99")
-    depends_on("lua-luaposix")
-    depends_on("munge")
-    depends_on("libuuid")
-    depends_on("python")
-    depends_on("py-cffi", type=('build', 'run'))
-    depends_on("jansson")
-
-    depends_on("asciidoc", type='build', when="+docs")
-
-    # Need autotools when building on master:
-    depends_on("autoconf", type='build', when='@master')
-    depends_on("automake", type='build', when='@master')
-    depends_on("libtool", type='build', when='@master')
-
-    def setup():
-        pass
-
-    @when('@master')
-    def setup(self):
-        # Allow git-describe to get last tag so flux-version works:
-        git = which('git')
-        git('pull', '--depth=50', '--tags')
-
-    def autoreconf(self, spec, prefix):
-        self.setup()
-        if os.path.exists('autogen.sh'):
-            # Bootstrap with autotools
-            bash = which('bash')
-            bash('./autogen.sh')
-
-    def setup_environment(self, spack_env, run_env):
-        #  Ensure ./fluxometer.lua can be found during flux's make check
-        spack_env.append_path('LUA_PATH', './?.lua', separator=';')
-
-    def configure_args(self):
-        return ['--disable-docs'] if '+docs' not in self.spec else []
diff --git a/var/spack/repos/builtin/packages/fluxbox/package.py b/var/spack/repos/builtin/packages/fluxbox/package.py
new file mode 100644
index 0000000000..9d4600fe1c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fluxbox/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+
+
+class Fluxbox(AutotoolsPackage):
+    """Fluxbox is a windowmanager for X that was based on the Blackbox 0.61.1 code.
+
+    It is very light on resources and easy to handle but yet full of features
+    to make an easy, and extremely fast, desktop experience.
+    """
+
+    homepage = "http://fluxbox.org/"
+    url      = "http://sourceforge.net/projects/fluxbox/files/fluxbox/1.3.7/fluxbox-1.3.7.tar.gz"
+
+    version('1.3.7', 'd99d7710f9daf793e0246dae5304b595')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('freetype')
+    depends_on('libxrender')
+    depends_on('libxext')
+    depends_on('expat')
+    depends_on('libx11')
diff --git a/var/spack/repos/builtin/packages/fmt/package.py b/var/spack/repos/builtin/packages/fmt/package.py
index 78b4bfd664..e969fc29ee 100644
--- a/var/spack/repos/builtin/packages/fmt/package.py
+++ b/var/spack/repos/builtin/packages/fmt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,17 +12,33 @@ class Fmt(CMakePackage):
     to C++ IOStreams."""
 
     homepage = "http://fmtlib.net/latest/index.html"
-    url      = "https://github.com/fmtlib/fmt/releases/download/4.0.0/fmt-4.0.0.zip"
+    url      = "https://github.com/fmtlib/fmt/releases/download/5.2.1/fmt-5.2.1.zip"
+
+    version('5.2.1', sha256='43894ab8fe561fc9e523a8024efc23018431fa86b95d45b06dbe6ddb29ffb6cd')
+    version('5.2.0', sha256='c016db7f825bce487a7929e1edb747b9902a2935057af6512cad3df3a080a027')
+    version('5.1.0', sha256='77ef9fea638dc846e484409fbc1ea710bb9bcea042e7b35b8805041bf7655ad5')
+    version('5.0.0', sha256='8dd58daf13e7e8adca99f8725ef3ae598f9c97efda7d6d8d4c49db5047879097')
+    version('4.1.0', sha256='9d49bf02ceb9d0eec51144b203b63b77e69d3798bb402fb82e7d0bdb06c79eeb')
+    version('4.0.0', sha256='10a9f184d4d66f135093a08396d3b0a0ebe8d97b79f8b3ddb8559f75fe4fcbc3')
+    version('3.0.2', sha256='51407b62a202b29d1a9c0eb5ecd4095d30031aea65407c42c25cb10cb5c59ad4')
+    version('3.0.1', sha256='4c9af0dc919a8ae7022b44e1a03c435e42d65c866f44667d8d920d342b098550')
+    version('3.0.0', sha256='1b050b66fa31b74f1d75a14f15e99e728ab79572f176a53b2f8ad7c201c30ceb')
+
+    depends_on('cmake@3.1.0:', type='build')
 
-    version('4.0.0', '605b5abee11b83195191234f4f414cf1')
-    version('3.0.2', 'b190a7b8f2a5e522ee70cf339a53d3b2')
-    version('3.0.1', '14505463b838befe1513b09cae112715')
-    version('3.0.0', 'c099561e70fa194bb03b3fd5de2d3fd0')
+    # Supported compilers are detailed here:
+    # http://fmtlib.net/latest/index.html#portability
+    conflicts('%gcc@:4.3.999', when='@5:')
+    conflicts('%llvm@:2.8.999', when='@5:')
 
-    depends_on('cmake@2.8.12:', type='build')
+    variant('pic', default=True, description='Enable generation of position-independent code')
 
     def cmake_args(self):
-        return [
-            '-DCMAKE_C_FLAGS={0}'.format(self.compiler.pic_flag),
-            '-DCMAKE_CXX_FLAGS={0}'.format(self.compiler.pic_flag),
-        ]
+        spec = self.spec
+        args = []
+        if '+pic' in spec:
+            args.append([
+                '-DCMAKE_C_FLAGS={0}'.format(self.compiler.pic_flag),
+                '-DCMAKE_CXX_FLAGS={0}'.format(self.compiler.pic_flag)
+            ])
+        return args
diff --git a/var/spack/repos/builtin/packages/foam-extend/package.py b/var/spack/repos/builtin/packages/foam-extend/package.py
index c6861da8d3..e36fec1efb 100644
--- a/var/spack/repos/builtin/packages/foam-extend/package.py
+++ b/var/spack/repos/builtin/packages/foam-extend/package.py
@@ -1,29 +1,8 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
-#
-# License
-# -------
-# 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
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Legal Notice
 # ------------
 # OPENFOAM is a trademark owned by OpenCFD Ltd
@@ -54,14 +33,15 @@
 ##############################################################################
 import glob
 import re
-import shutil
 import os
 
 from spack import *
+from spack.util.environment import EnvironmentModifications
 from spack.pkg.builtin.openfoam_com import OpenfoamArch
 from spack.pkg.builtin.openfoam_com import add_extra_files
 from spack.pkg.builtin.openfoam_com import write_environ
 from spack.pkg.builtin.openfoam_com import rewrite_environ_files
+import llnl.util.tty as tty
 
 
 class FoamExtend(Package):
@@ -74,10 +54,10 @@ class FoamExtend(Package):
 
     homepage = "http://www.extend-project.de/"
 
-    version('4.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-4.0')
-    version('3.2', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.2')
-    version('3.1', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.1')
-    version('3.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.0')
+    version('4.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-4.0.git')
+    version('3.2', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.2.git')
+    version('3.1', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.1.git')
+    version('3.0', git='http://git.code.sf.net/p/foam-extend/foam-extend-3.0.git')
 
     # variant('int64', default=False,
     #         description='Compile with 64-bit label')
@@ -140,14 +120,77 @@ class FoamExtend(Package):
     #
 
     def setup_environment(self, spack_env, run_env):
-        run_env.set('FOAM_INST_DIR', os.path.dirname(self.projectdir)),
-        run_env.set('FOAM_PROJECT_DIR', self.projectdir)
-        run_env.set('WM_PROJECT_DIR', self.projectdir)
-        for d in ['wmake', self.archbin]:  # bin already added automatically
-            run_env.prepend_path('PATH', join_path(self.projectdir, d))
+        """Add environment variables to the generated module file.
+        These environment variables come from running:
+
+        .. code-block:: console
+
+           $ . $WM_PROJECT_DIR/etc/bashrc
+        """
+
+        # NOTE: Spack runs setup_environment twice.
+        # 1) pre-build to set up the build environment
+        # 2) post-install to determine runtime environment variables
+        # The etc/bashrc is only available (with corrrect content)
+        # post-installation.
+
+        bashrc = join_path(self.projectdir, 'etc', 'bashrc')
+        minimal = True
+        if os.path.isfile(bashrc):
+            # post-install: source the installed bashrc
+            try:
+                mods = EnvironmentModifications.from_sourcing_file(
+                    bashrc,
+                    clean=True,  # Remove duplicate entries
+                    blacklist=[  # Blacklist these
+                        # Inadvertent changes
+                        # -------------------
+                        'PS1',            # Leave unaffected
+                        'MANPATH',        # Leave unaffected
+
+                        # Unneeded bits
+                        # -------------
+                        'FOAM_INST_DIR',  # Possibly incorrect
+                        'FOAM_(APP|ETC|SRC|SOLVERS|UTILITIES)',
+                        'FOAM_TEST_.*_DIR',
+                        'WM_NCOMPPROCS',
+                        # 'FOAM_TUTORIALS',  # can be useful
+
+                        # Lots of third-party cruft
+                        # -------------------------
+                        '[A-Z].*_(BIN|LIB|INCLUDE)_DIR',
+                        '[A-Z].*_SYSTEM',
+                        'WM_THIRD_PARTY_.*',
+                        '(BISON|FLEX|CMAKE|ZLIB)_DIR',
+                        '(METIS|PARMETIS|PARMGRIDGEN|SCOTCH)_DIR',
+
+                        # User-specific
+                        # -------------
+                        'FOAM_RUN',
+                        '(FOAM|WM)_.*USER_.*',
+                    ],
+                    whitelist=[  # Whitelist these
+                        'MPI_ARCH_PATH',  # Can be needed for compilation
+                        'PYTHON_BIN_DIR',
+                    ])
+
+                run_env.extend(mods)
+                minimal = False
+                tty.info('foam-extend env: {0}'.format(bashrc))
+            except Exception:
+                minimal = True
+
+        if minimal:
+            # pre-build or minimal environment
+            tty.info('foam-extend minimal env {0}'.format(self.prefix))
+            run_env.set('FOAM_INST_DIR', os.path.dirname(self.projectdir)),
+            run_env.set('FOAM_PROJECT_DIR', self.projectdir)
+            run_env.set('WM_PROJECT_DIR', self.projectdir)
+            for d in ['wmake', self.archbin]:  # bin added automatically
+                run_env.prepend_path('PATH', join_path(self.projectdir, d))
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        """Provide location of the OpenFOAM project.
+        """Location of the OpenFOAM project.
         This is identical to the WM_PROJECT_DIR value, but we avoid that
         variable since it would mask the normal OpenFOAM cleanup of
         previous versions.
@@ -317,7 +360,6 @@ class FoamExtend(Package):
 
     def install(self, spec, prefix):
         """Install under the projectdir"""
-        opts = str(self.foam_arch)
 
         # Fairly ugly since intermediate targets are scattered inside sources
         appdir = 'applications'
@@ -354,19 +396,22 @@ class FoamExtend(Package):
             subitem = join_path(appdir, 'Allwmake')
             install(subitem, join_path(self.projectdir, subitem))
 
-            ignored = [opts]  # Ignore intermediate targets
+            foam_arch_str = str(self.foam_arch)
+            # Ignore intermediate targets
+            ignore = lambda p: os.path.basename(p) == foam_arch_str
+
             for d in ['src', 'tutorials']:
                 install_tree(
                     d,
                     join_path(self.projectdir, d),
-                    ignore=shutil.ignore_patterns(*ignored),
+                    ignore=ignore,
                     symlinks=True)
 
             for d in ['solvers', 'utilities']:
                 install_tree(
                     join_path(appdir, d),
                     join_path(self.projectdir, appdir, d),
-                    ignore=shutil.ignore_patterns(*ignored),
+                    ignore=ignore,
                     symlinks=True)
 
         etc_dir = join_path(self.projectdir, 'etc')
diff --git a/var/spack/repos/builtin/packages/folly/package.py b/var/spack/repos/builtin/packages/folly/package.py
index 9dca4bd6cf..0a2d1f36a4 100644
--- a/var/spack/repos/builtin/packages/folly/package.py
+++ b/var/spack/repos/builtin/packages/folly/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -50,7 +31,7 @@ class Folly(AutotoolsPackage):
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
     depends_on('libtool', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     # TODO: folly requires gcc 4.9+ and a version of boost compiled with
     # TODO: C++14 support (but there's no neat way to check that these
diff --git a/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py
index 8efdebb802..bf1817238f 100644
--- a/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontAdobe100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py
index 0b73bd1b9a..6e1f8402ca 100644
--- a/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontAdobe75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-adobe-utopia-100dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-utopia-100dpi/package.py
index 7a61e04de5..fe4f5eb862 100644
--- a/var/spack/repos/builtin/packages/font-adobe-utopia-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-utopia-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontAdobeUtopia100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-adobe-utopia-75dpi/package.py b/var/spack/repos/builtin/packages/font-adobe-utopia-75dpi/package.py
index dddd546cad..9fa00f29a3 100644
--- a/var/spack/repos/builtin/packages/font-adobe-utopia-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-utopia-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontAdobeUtopia75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-adobe-utopia-type1/package.py b/var/spack/repos/builtin/packages/font-adobe-utopia-type1/package.py
index 0d03c12822..c5e832cb29 100644
--- a/var/spack/repos/builtin/packages/font-adobe-utopia-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-adobe-utopia-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class FontAdobeUtopiaType1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-alias/package.py b/var/spack/repos/builtin/packages/font-alias/package.py
index 15a14bf2cb..2819678e71 100644
--- a/var/spack/repos/builtin/packages/font-alias/package.py
+++ b/var/spack/repos/builtin/packages/font-alias/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,7 +16,7 @@ class FontAlias(Package):
 
     depends_on('font-util')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-arabic-misc/package.py b/var/spack/repos/builtin/packages/font-arabic-misc/package.py
index 20ca7a2df0..910ff1af57 100644
--- a/var/spack/repos/builtin/packages/font-arabic-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-arabic-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontArabicMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-100dpi/package.py b/var/spack/repos/builtin/packages/font-bh-100dpi/package.py
index 3472783671..48ca9aa37a 100644
--- a/var/spack/repos/builtin/packages/font-bh-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBh100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-75dpi/package.py b/var/spack/repos/builtin/packages/font-bh-75dpi/package.py
index bb5268208c..0af3c8e1d1 100644
--- a/var/spack/repos/builtin/packages/font-bh-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBh75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-100dpi/package.py b/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-100dpi/package.py
index 6fe18e703b..7b001c32e3 100644
--- a/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBhLucidatypewriter100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-75dpi/package.py b/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-75dpi/package.py
index f44596b882..ce0677144f 100644
--- a/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-lucidatypewriter-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBhLucidatypewriter75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-ttf/package.py b/var/spack/repos/builtin/packages/font-bh-ttf/package.py
index 83ad928c8b..ae662cd40c 100644
--- a/var/spack/repos/builtin/packages/font-bh-ttf/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-ttf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBhTtf(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bh-type1/package.py b/var/spack/repos/builtin/packages/font-bh-type1/package.py
index 594efb0460..d75bb953f3 100644
--- a/var/spack/repos/builtin/packages/font-bh-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-bh-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBhType1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bitstream-100dpi/package.py b/var/spack/repos/builtin/packages/font-bitstream-100dpi/package.py
index a5722733da..286a2dec5b 100644
--- a/var/spack/repos/builtin/packages/font-bitstream-100dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bitstream-100dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBitstream100dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bitstream-75dpi/package.py b/var/spack/repos/builtin/packages/font-bitstream-75dpi/package.py
index 8dcf9dfe2c..028121c2a9 100644
--- a/var/spack/repos/builtin/packages/font-bitstream-75dpi/package.py
+++ b/var/spack/repos/builtin/packages/font-bitstream-75dpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBitstream75dpi(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bitstream-speedo/package.py b/var/spack/repos/builtin/packages/font-bitstream-speedo/package.py
index e2ae5fea3c..ca3b5a2e48 100644
--- a/var/spack/repos/builtin/packages/font-bitstream-speedo/package.py
+++ b/var/spack/repos/builtin/packages/font-bitstream-speedo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBitstreamSpeedo(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-bitstream-type1/package.py b/var/spack/repos/builtin/packages/font-bitstream-type1/package.py
index c6699b7521..efb427de3a 100644
--- a/var/spack/repos/builtin/packages/font-bitstream-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-bitstream-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontBitstreamType1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-cronyx-cyrillic/package.py b/var/spack/repos/builtin/packages/font-cronyx-cyrillic/package.py
index 829f28ee1e..0ac07e9669 100644
--- a/var/spack/repos/builtin/packages/font-cronyx-cyrillic/package.py
+++ b/var/spack/repos/builtin/packages/font-cronyx-cyrillic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontCronyxCyrillic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-cursor-misc/package.py b/var/spack/repos/builtin/packages/font-cursor-misc/package.py
index 34479c7fc6..321bd01b13 100644
--- a/var/spack/repos/builtin/packages/font-cursor-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-cursor-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontCursorMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-daewoo-misc/package.py b/var/spack/repos/builtin/packages/font-daewoo-misc/package.py
index 9c346c3b8b..737d3dfac9 100644
--- a/var/spack/repos/builtin/packages/font-daewoo-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-daewoo-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontDaewooMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-dec-misc/package.py b/var/spack/repos/builtin/packages/font-dec-misc/package.py
index 22c52a95da..e4cc9cbab8 100644
--- a/var/spack/repos/builtin/packages/font-dec-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-dec-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontDecMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-ibm-type1/package.py b/var/spack/repos/builtin/packages/font-ibm-type1/package.py
index a8d06ef092..213be77570 100644
--- a/var/spack/repos/builtin/packages/font-ibm-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-ibm-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontIbmType1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-isas-misc/package.py b/var/spack/repos/builtin/packages/font-isas-misc/package.py
index 86353f22ce..d51f7daf62 100644
--- a/var/spack/repos/builtin/packages/font-isas-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-isas-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontIsasMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-jis-misc/package.py b/var/spack/repos/builtin/packages/font-jis-misc/package.py
index 18723cc129..5165a97c8a 100644
--- a/var/spack/repos/builtin/packages/font-jis-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-jis-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontJisMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-micro-misc/package.py b/var/spack/repos/builtin/packages/font-micro-misc/package.py
index 664cc158a7..4212aac2b6 100644
--- a/var/spack/repos/builtin/packages/font-micro-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-micro-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMicroMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-misc-cyrillic/package.py b/var/spack/repos/builtin/packages/font-misc-cyrillic/package.py
index 52d2e0ca33..24085afdee 100644
--- a/var/spack/repos/builtin/packages/font-misc-cyrillic/package.py
+++ b/var/spack/repos/builtin/packages/font-misc-cyrillic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMiscCyrillic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-misc-ethiopic/package.py b/var/spack/repos/builtin/packages/font-misc-ethiopic/package.py
index ed10f2ecad..5fcc5a50d1 100644
--- a/var/spack/repos/builtin/packages/font-misc-ethiopic/package.py
+++ b/var/spack/repos/builtin/packages/font-misc-ethiopic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMiscEthiopic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-misc-meltho/package.py b/var/spack/repos/builtin/packages/font-misc-meltho/package.py
index beef19e00a..29be9bfebd 100644
--- a/var/spack/repos/builtin/packages/font-misc-meltho/package.py
+++ b/var/spack/repos/builtin/packages/font-misc-meltho/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMiscMeltho(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-misc-misc/package.py b/var/spack/repos/builtin/packages/font-misc-misc/package.py
index b818cd6a84..d29384eaa5 100644
--- a/var/spack/repos/builtin/packages/font-misc-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-misc-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMiscMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-mutt-misc/package.py b/var/spack/repos/builtin/packages/font-mutt-misc/package.py
index 0f303923b0..376f6d3f22 100644
--- a/var/spack/repos/builtin/packages/font-mutt-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-mutt-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontMuttMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-schumacher-misc/package.py b/var/spack/repos/builtin/packages/font-schumacher-misc/package.py
index 66e8002877..fefe1e1c61 100644
--- a/var/spack/repos/builtin/packages/font-schumacher-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-schumacher-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontSchumacherMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-screen-cyrillic/package.py b/var/spack/repos/builtin/packages/font-screen-cyrillic/package.py
index 71c2230d1f..0eec73060d 100644
--- a/var/spack/repos/builtin/packages/font-screen-cyrillic/package.py
+++ b/var/spack/repos/builtin/packages/font-screen-cyrillic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontScreenCyrillic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-sony-misc/package.py b/var/spack/repos/builtin/packages/font-sony-misc/package.py
index ccea5883ac..912957ab12 100644
--- a/var/spack/repos/builtin/packages/font-sony-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-sony-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontSonyMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-sun-misc/package.py b/var/spack/repos/builtin/packages/font-sun-misc/package.py
index 26e0c935ed..8555fdb428 100644
--- a/var/spack/repos/builtin/packages/font-sun-misc/package.py
+++ b/var/spack/repos/builtin/packages/font-sun-misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class FontSunMisc(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-util/package.py b/var/spack/repos/builtin/packages/font-util/package.py
index 4f55412457..7a5e163482 100644
--- a/var/spack/repos/builtin/packages/font-util/package.py
+++ b/var/spack/repos/builtin/packages/font-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,5 +14,5 @@ class FontUtil(AutotoolsPackage):
 
     version('1.3.1', 'd153a9af216e4498fa171faea2c82514')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/font-winitzki-cyrillic/package.py b/var/spack/repos/builtin/packages/font-winitzki-cyrillic/package.py
index dade47b7d2..e15236a20f 100644
--- a/var/spack/repos/builtin/packages/font-winitzki-cyrillic/package.py
+++ b/var/spack/repos/builtin/packages/font-winitzki-cyrillic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontWinitzkiCyrillic(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('bdftopcf', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/font-xfree86-type1/package.py b/var/spack/repos/builtin/packages/font-xfree86-type1/package.py
index 2a4dfea233..5cb5de7eb8 100644
--- a/var/spack/repos/builtin/packages/font-xfree86-type1/package.py
+++ b/var/spack/repos/builtin/packages/font-xfree86-type1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class FontXfree86Type1(Package):
     depends_on('fontconfig', type='build')
     depends_on('mkfontdir', type='build')
     depends_on('mkfontscale', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/fontcacheproto/package.py b/var/spack/repos/builtin/packages/fontcacheproto/package.py
index 94e952de52..77c8e4a38a 100644
--- a/var/spack/repos/builtin/packages/fontcacheproto/package.py
+++ b/var/spack/repos/builtin/packages/fontcacheproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fontconfig/package.py b/var/spack/repos/builtin/packages/fontconfig/package.py
index 8cfd5c0d54..0ef1a3ebc9 100644
--- a/var/spack/repos/builtin/packages/fontconfig/package.py
+++ b/var/spack/repos/builtin/packages/fontconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class Fontconfig(AutotoolsPackage):
     depends_on('freetype')
     depends_on('gperf', type='build', when='@2.12.2:')
     depends_on('libxml2')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('font-util')
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/fontsproto/package.py b/var/spack/repos/builtin/packages/fontsproto/package.py
index c243f9de97..22ea479567 100644
--- a/var/spack/repos/builtin/packages/fontsproto/package.py
+++ b/var/spack/repos/builtin/packages/fontsproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,5 +14,5 @@ class Fontsproto(AutotoolsPackage):
 
     version('2.1.3', '0415f0360e33f3202af67c6c46782251')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/fonttosfnt/package.py b/var/spack/repos/builtin/packages/fonttosfnt/package.py
index 145e619c54..02928b26b8 100644
--- a/var/spack/repos/builtin/packages/fonttosfnt/package.py
+++ b/var/spack/repos/builtin/packages/fonttosfnt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Fonttosfnt(AutotoolsPackage):
     depends_on('libfontenc')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/fp16/package.py b/var/spack/repos/builtin/packages/fp16/package.py
new file mode 100644
index 0000000000..e20b215ce1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fp16/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fp16(Package):
+    """FP16 is a header-only library for
+    conversion to/from half-precision floating point formats"""
+
+    homepage = "https://github.com/Maratyszcza/FP16/"
+    git      = "https://github.com/Maratyszcza/FP16.git"
+
+    version('master')
+
+    def install(self, spec, prefix):
+        install_tree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/fpc/package.py b/var/spack/repos/builtin/packages/fpc/package.py
index 905aae3314..ec0fca7b68 100644
--- a/var/spack/repos/builtin/packages/fpc/package.py
+++ b/var/spack/repos/builtin/packages/fpc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fr-hit/binning.patch b/var/spack/repos/builtin/packages/fr-hit/binning.patch
new file mode 100644
index 0000000000..4ee81d5d83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fr-hit/binning.patch
@@ -0,0 +1,7 @@
+--- a/binning-1.1.1/binning.py	2018-01-30 10:46:27.302198293 -0600
++++ b/binning-1.1.1/binning.py	2018-01-30 10:50:58.482866704 -0600
+@@ -1,3 +1,4 @@
++#!/usr/bin/env python
+ ######################################################
+ #      Taxonamy binning using FR-HIT output          #
+ ######################################################
diff --git a/var/spack/repos/builtin/packages/fr-hit/package.py b/var/spack/repos/builtin/packages/fr-hit/package.py
new file mode 100644
index 0000000000..a6dc337882
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fr-hit/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class FrHit(Package):
+    """An efficient algorithm for fragment recruitment for next generation
+    sequences against microbial reference genomes."""
+
+    homepage = "http://weizhong-lab.ucsd.edu/frhit"
+    url      = "http://weizhong-lab.ucsd.edu/frhit/fr-hit-v0.7.1-2013-02-20.tar.gz"
+
+    version('0.7.1-2013-02-20', '3e8ea41ba09ab0c13e9973fe6f493f96')
+
+    depends_on('perl')
+    depends_on('python@2.7:')
+
+    # The patch adds the python interpreter to the beginning of the script
+    # allowing it to be run directly without passing the entire path to the
+    # script to python.
+    patch('binning.patch')
+
+    def install(self, spec, prefix):
+        make()
+
+        filter_file(
+            r'#!/bin/env perl',
+            '#!/usr/bin/env perl',
+            'frhit2pairend.pl'
+        )
+        filter_file(
+            r'#!/bin/env perl',
+            '#!/usr/bin/env perl',
+            'psl2sam.pl'
+        )
+
+        mkdirp(prefix.bin)
+        install('fr-hit', prefix.bin)
+        install('frhit2pairend.pl', prefix.bin)
+        install('psl2sam.pl', prefix.bin)
+        install('binning-1.1.1/bacteria_gitax.pkl', prefix.bin)
+        install('binning-1.1.1/binning.py', prefix.bin)
+        install('binning-1.1.1/tax.pkl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/freebayes/package.py b/var/spack/repos/builtin/packages/freebayes/package.py
index bd5c2b06a3..a50362d453 100644
--- a/var/spack/repos/builtin/packages/freebayes/package.py
+++ b/var/spack/repos/builtin/packages/freebayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Freebayes(MakefilePackage):
        genotyping."""
 
     homepage = "https://github.com/ekg/freebayes"
+    git      = "https://github.com/ekg/freebayes.git"
 
-    version('1.1.0', git='https://github.com/ekg/freebayes.git',
-            commit='39e5e4bcb801556141f2da36aba1df5c5c60701f',
+    version('1.1.0', commit='39e5e4bcb801556141f2da36aba1df5c5c60701f',
             submodules=True)
 
     depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/freeglut/package.py b/var/spack/repos/builtin/packages/freeglut/package.py
new file mode 100644
index 0000000000..6327a20839
--- /dev/null
+++ b/var/spack/repos/builtin/packages/freeglut/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Freeglut(CMakePackage):
+    """FreeGLUT is a free-software/open-source alternative to the OpenGL
+       Utility Toolkit (GLUT) library"""
+
+    homepage = "http://freeglut.sourceforge.net/"
+    url      = "http://prdownloads.sourceforge.net/freeglut/freeglut-3.0.0.tar.gz"
+
+    version('3.0.0', '90c3ca4dd9d51cf32276bc5344ec9754')
+
+    depends_on('gl')
+    depends_on('glu')
+    depends_on('libx11')
+    depends_on('libxrandr')
+    depends_on('libxi')
+    depends_on('xrandr')
+    depends_on('inputproto')
diff --git a/var/spack/repos/builtin/packages/freetype/package.py b/var/spack/repos/builtin/packages/freetype/package.py
index 1ad65a9750..acecc649ad 100644
--- a/var/spack/repos/builtin/packages/freetype/package.py
+++ b/var/spack/repos/builtin/packages/freetype/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,13 +15,21 @@ class Freetype(AutotoolsPackage):
     homepage = "https://www.freetype.org/index.html"
     url      = "http://download.savannah.gnu.org/releases/freetype/freetype-2.7.1.tar.gz"
 
+    version('2.9.1', 'ec391504e55498adceb30baceebd147a6e963f636eb617424bcfc47a169898ce')
     version('2.7.1', '78701bee8d249578d83bb9a2f3aa3616')
     version('2.7',   '337139e5c7c5bd645fe130608e0fa8b5')
     version('2.5.3', 'cafe9f210e45360279c730d27bf071e9')
 
     depends_on('libpng')
     depends_on('bzip2')
-    depends_on('pkg-config@0.24:', type='build')
+    depends_on('pkgconfig', type='build')
 
     def configure_args(self):
-        return ['--with-harfbuzz=no']
+        args = ['--with-harfbuzz=no']
+        if self.spec.satisfies('@2.9.1:'):
+            args.append('--enable-freetype-config')
+        return args
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.prepend_path('CPATH', self.prefix.include.freetype2)
+        run_env.prepend_path('CPATH', self.prefix.include.freetype2)
diff --git a/var/spack/repos/builtin/packages/fseq/package.py b/var/spack/repos/builtin/packages/fseq/package.py
index 037aa4f648..5397c64d1f 100644
--- a/var/spack/repos/builtin/packages/fseq/package.py
+++ b/var/spack/repos/builtin/packages/fseq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/fsl/package.py b/var/spack/repos/builtin/packages/fsl/package.py
index 2191be1ce3..a0675ae6cf 100644
--- a/var/spack/repos/builtin/packages/fsl/package.py
+++ b/var/spack/repos/builtin/packages/fsl/package.py
@@ -1,31 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack.environment import EnvironmentModifications
+from spack.util.environment import EnvironmentModifications
 import os
-import distutils.dir_util
 
 
 class Fsl(Package):
@@ -68,7 +48,7 @@ class Fsl(Package):
         build = Executable('./build')
         build()
 
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix)
 
     def setup_environment(self, spack_env, run_env):
         if not self.stage.source_path:
diff --git a/var/spack/repos/builtin/packages/fslsfonts/package.py b/var/spack/repos/builtin/packages/fslsfonts/package.py
index ce5b04f0ee..1f540a5509 100644
--- a/var/spack/repos/builtin/packages/fslsfonts/package.py
+++ b/var/spack/repos/builtin/packages/fslsfonts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Fslsfonts(AutotoolsPackage):
     depends_on('libfs')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/fstobdf/package.py b/var/spack/repos/builtin/packages/fstobdf/package.py
index dd51473d41..1605edddc3 100644
--- a/var/spack/repos/builtin/packages/fstobdf/package.py
+++ b/var/spack/repos/builtin/packages/fstobdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Fstobdf(AutotoolsPackage):
     depends_on('libfs')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/ftgl/package.py b/var/spack/repos/builtin/packages/ftgl/package.py
new file mode 100644
index 0000000000..030fa441ac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ftgl/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import sys
+import os
+
+
+class Ftgl(AutotoolsPackage):
+    """Library to use arbitrary fonts in OpenGL applications."""
+
+    homepage = "http://ftgl.sourceforge.net/docs/html/"
+    url      = "https://sourceforge.net/projects/ftgl/files/FTGL%20Source/2.1.2/ftgl-2.1.2.tar.gz/download"
+    list_url = "https://sourceforge.net/projects/ftgl/files/FTGL%20Source/"
+    list_depth = 1
+
+    version('2.1.2', 'f81c0a7128192ba11e036186f9a968f2')
+
+    # There is an unnecessary qualifier around, which makes modern GCC sad
+    patch('remove-extra-qualifier.diff')
+
+    # Ftgl does not come with a configure script
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('gl')
+    depends_on('glu')
+    depends_on('freetype@2.0.9:')
+
+    # Currently, "make install" will fail if the docs weren't built
+    #
+    # FIXME: Can someone with autotools experience fix the build system
+    #        so that it doesn't fail when that happens?
+    #
+    depends_on('doxygen', type='build')
+
+    @property
+    @when('@2.1.2')
+    def configure_directory(self):
+        subdir = 'unix'
+        if sys.platform == 'darwin':
+            subdir = 'mac'
+        return os.path.join(self.stage.source_path, subdir)
diff --git a/var/spack/repos/builtin/packages/ftgl/remove-extra-qualifier.diff b/var/spack/repos/builtin/packages/ftgl/remove-extra-qualifier.diff
new file mode 100644
index 0000000000..cff9a3836e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ftgl/remove-extra-qualifier.diff
@@ -0,0 +1,11 @@
+--- FTGL/include/FTTextureGlyph.h   2018-07-26 08:30:55.144488976 +0000
++++ FTGL/include/FTTextureGlyph.h   2018-07-26 08:29:42.072489186 +0000
+@@ -52,7 +52,7 @@
+          * Reset the currently active texture to zero to get into a known state before
+          * drawing a string. This is to get round possible threading issues.
+          */
+-        static void FTTextureGlyph::ResetActiveTexture(){ activeTextureID = 0;}
++        static void ResetActiveTexture(){ activeTextureID = 0;}
+         
+     private:
+         /**
diff --git a/var/spack/repos/builtin/packages/funhpc/package.py b/var/spack/repos/builtin/packages/funhpc/package.py
index 26863ae4f4..8082be7b24 100644
--- a/var/spack/repos/builtin/packages/funhpc/package.py
+++ b/var/spack/repos/builtin/packages/funhpc/package.py
@@ -1,36 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
 class Funhpc(CMakePackage):
     """FunHPC: Functional HPC Programming"""
+
     homepage = "https://github.com/eschnett/FunHPC.cxx"
-    url = "https://github.com/eschnett/FunHPC.cxx/archive/version/0.1.0.tar.gz"
+    url      = "https://github.com/eschnett/FunHPC.cxx/archive/version/0.1.0.tar.gz"
+    git      = "https://github.com/eschnett/FunHPC.cxx.git"
 
+    version('develop', branch='master')
     version('1.3.0', '71a1e57c4d882cdf001f29122edf7fc6')
     version('1.2.0', 'ba2bbeea3091e999b6b85eaeb1b67a83')
     version('1.1.1', '7b9ef638b02fffe35b75517e8eeff580')
@@ -38,8 +22,6 @@ class Funhpc(CMakePackage):
     version('1.0.0', 'f34e71ccd5548b42672e692c913ba5ee')
     version('0.1.1', 'f0248710f2de88ed2a595ad40d99997c')
     version('0.1.0', '00f7dabc08ed1ab77858785ce0809f50')
-    version('develop',
-            git='https://github.com/eschnett/FunHPC.cxx', branch='master')
 
     variant('pic', default=True,
             description="Produce position-independent code")
diff --git a/var/spack/repos/builtin/packages/fyba/gcc-6.patch b/var/spack/repos/builtin/packages/fyba/gcc-6.patch
new file mode 100644
index 0000000000..33551d6546
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fyba/gcc-6.patch
@@ -0,0 +1,18 @@
+diff -Nuar a/src/FYBA/FYLU.cpp b/src/FYBA/FYLU.cpp
+--- a/src/FYBA/FYLU.cpp	2014-09-22 00:36:49.000000000 -0500
++++ b/src/FYBA/FYLU.cpp	2018-05-24 15:35:43.584181379 -0500
+@@ -4,12 +4,12 @@
+ /*  Innhold: Rutiner for utvalg                                             */

+ /* ======================================================================== */

+ 

+-#include "stdafx.h"

+-

+ #include <ctype.h>

+ #include <math.h>

+ #include <locale>

+ 

++#include "stdafx.h"

++

+ using namespace std;

+ 

+ #define U_PARA_LEN    128     /* Max lengde av parameterstreng */

diff --git a/var/spack/repos/builtin/packages/fyba/package.py b/var/spack/repos/builtin/packages/fyba/package.py
new file mode 100644
index 0000000000..e0cfc046cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fyba/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Fyba(AutotoolsPackage):
+    """OpenFYBA is the source code release of the FYBA library, distributed
+    by the National Mapping Authority of Norway (Statens kartverk) to read
+    and write files in the National geodata standard format SOSI."""
+
+    homepage = "https://github.com/kartverket/fyba"
+    url      = "https://github.com/kartverket/fyba/archive/4.1.1.tar.gz"
+
+    version('4.1.1', 'ab687582efdef26593796271529a10cb')
+
+    # configure: error: cannot find install-sh or install.sh
+    force_autoreconf = True
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    # error: macro "min" passed 3 arguments, but takes just 2
+    # https://github.com/kartverket/fyba/issues/21
+    patch('gcc-6.patch')
+
+    # fatal error: 'sys/vfs.h' file not found
+    # https://github.com/kartverket/fyba/issues/12
+    patch('vfs-mount-darwin.patch', when='platform=darwin')
diff --git a/var/spack/repos/builtin/packages/fyba/vfs-mount-darwin.patch b/var/spack/repos/builtin/packages/fyba/vfs-mount-darwin.patch
new file mode 100644
index 0000000000..134db87a1c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/fyba/vfs-mount-darwin.patch
@@ -0,0 +1,48 @@
+diff -Naur a/configure.ac b/configure.ac
+--- a/configure.ac	2014-09-22 00:36:49.000000000 -0500
++++ b/configure.ac	2018-05-19 12:37:15.000000000 -0500
+@@ -18,7 +18,7 @@
+ # Checks for libraries.
+ 
+ # Checks for header files.
+-AC_CHECK_HEADERS([fcntl.h float.h inttypes.h limits.h locale.h memory.h stdint.h stdlib.h string.h sys/ioctl.h sys/statvfs.h sys/time.h sys/vfs.h termios.h unistd.h])
++AC_CHECK_HEADERS([fcntl.h float.h inttypes.h limits.h locale.h memory.h stdint.h stdlib.h string.h sys/ioctl.h sys/statvfs.h sys/time.h sys/mount.h termios.h unistd.h])
+ 
+ # Checks for typedefs, structures, and compiler characteristics.
+ AC_HEADER_STDBOOL
+diff -Naur a/src/UT/DISKINFO.cpp b/src/UT/DISKINFO.cpp
+--- a/src/UT/DISKINFO.cpp	2014-09-22 00:36:49.000000000 -0500
++++ b/src/UT/DISKINFO.cpp	2018-05-19 12:38:08.000000000 -0500
+@@ -17,7 +17,7 @@
+ #     include <sys/statvfs.h>

+ #  else

+ #     include <sys/stat.h>

+-#     include <sys/vfs.h>

++#     include <sys/mount.h>

+ #  endif

+ 

+ #  include <sys/types.h>

+diff -Naur a/src/UT/INQSIZE.cpp b/src/UT/INQSIZE.cpp
+--- a/src/UT/INQSIZE.cpp	2014-09-22 00:36:49.000000000 -0500
++++ b/src/UT/INQSIZE.cpp	2018-05-19 12:37:45.000000000 -0500
+@@ -16,7 +16,7 @@
+ #  include<stdio.h>

+ #  include<sys/time.h>

+ #  include<sys/types.h>

+-#  include<sys/vfs.h>

++#  include<sys/mount.h>

+ #  include<fcntl.h>

+ #  include<sys/stat.h>

+ #  include<errno.h>

+diff -Naur a/src/UT/INQTID.cpp b/src/UT/INQTID.cpp
+--- a/src/UT/INQTID.cpp	2014-09-22 00:36:49.000000000 -0500
++++ b/src/UT/INQTID.cpp	2018-05-19 12:37:57.000000000 -0500
+@@ -15,7 +15,7 @@
+ #  include<stdio.h>

+ #  include<sys/time.h>

+ #  include<sys/types.h>

+-#  include<sys/vfs.h>

++#  include<sys/mount.h>

+ #  include<fcntl.h>

+ #  include<sys/stat.h>

+ #  include<errno.h>

diff --git a/var/spack/repos/builtin/packages/gapbs/package.py b/var/spack/repos/builtin/packages/gapbs/package.py
new file mode 100644
index 0000000000..f62cbb790f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gapbs/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gapbs(MakefilePackage):
+    """The GAP Benchmark Suite is intended to help graph processing research by
+    standardizing evaluations. Fewer differences between graph processing
+    evaluations will make it easier to compare different research efforts and
+    quantify improvements. The benchmark not only specifies graph kernels,
+    input graphs, and evaluation methodologies, but it also provides an
+    optimized baseline implementation (this repo). These baseline
+    implementations are representative of state-of-the-art performance, and
+    thus new contributions should outperform them to demonstrate an
+    improvement."""
+
+    homepage = "http://gap.cs.berkeley.edu/benchmark.html"
+    url      = "https://github.com/sbeamer/gapbs/archive/v1.0.tar.gz"
+
+    version('1.0', 'ac2efa793f44e58553449f42b9779f3ff2d47634')
+
+    variant('serial', default=False, description='Version with no parallelism')
+
+    def build(self, spec, prefix):
+        cxx_flags = ['-O3', self.compiler.cxx11_flag]
+
+        if '-serial' in spec:
+            cxx_flags.append(self.compiler.openmp_flag)
+
+        make('CXX_FLAGS=' + ' '.join(cxx_flags))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        for app in ["bc", "bfs", "cc", "converter", "pr", "sssp", "tc"]:
+            install(app, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/gapcloser/package.py b/var/spack/repos/builtin/packages/gapcloser/package.py
index b59b46af00..d4ff137816 100644
--- a/var/spack/repos/builtin/packages/gapcloser/package.py
+++ b/var/spack/repos/builtin/packages/gapcloser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gapfiller/package.py b/var/spack/repos/builtin/packages/gapfiller/package.py
index 43e6eeaac0..883874007b 100644
--- a/var/spack/repos/builtin/packages/gapfiller/package.py
+++ b/var/spack/repos/builtin/packages/gapfiller/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
+import glob
 
 
 class Gapfiller(Package):
@@ -44,9 +26,20 @@ class Gapfiller(Package):
         return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
                 os.getcwd(), version.dashed)
 
-    depends_on('perl', type=('build', 'run'))
+    depends_on('perl+threads', type=('build', 'run'))
+
+    def patch(self):
+        with working_dir('.'):
+            files = glob.iglob("*.pl")
+            for file in files:
+                change = FileFilter(file)
+                change.filter('usr/bin/perl', 'usr/bin/env perl')
+                change.filter('require "getopts.pl";', 'use Getopt::Std;')
+                change.filter('&Getopts', 'getopts')
+                change.filter('\r', '')
+                set_executable(file)
 
     def install(self, spec, prefix):
-        install_tree('bowtie', prefix.bowtie)
-        install_tree('bwa', prefix.bwa)
-        install('GapFiller.pl', prefix)
+        install_tree('bowtie', prefix.bin.bowtie)
+        install_tree('bwa', prefix.bin.bwa)
+        install('GapFiller.pl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/gasnet/package.py b/var/spack/repos/builtin/packages/gasnet/package.py
index 6b8a498671..7681af2d21 100644
--- a/var/spack/repos/builtin/packages/gasnet/package.py
+++ b/var/spack/repos/builtin/packages/gasnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,8 +14,9 @@ class Gasnet(AutotoolsPackage):
        Cray Chapel, and Titanium.
     """
     homepage = "http://gasnet.lbl.gov"
-    url      = "http://gasnet.lbl.gov/GASNet-1.24.0.tar.gz"
+    url      = "http://gasnet.lbl.gov/download/GASNet-1.24.0.tar.gz"
 
+    version('1.32.0', sha256='42e4774b3bbc7c142f77c41b6ce86b594f579073f46c31f47f424c7e31ee1511')
     version('1.30.0', '2ddb1d8397d62acfd389095ca8da72f6')
     version('1.28.2', '6ca0463dc2430570e40646c4d1e97b36')
     version('1.28.0', 'b44446d951d3d8954aa1570e3556ba61')
diff --git a/var/spack/repos/builtin/packages/gatk/gatk.sh b/var/spack/repos/builtin/packages/gatk/gatk.sh
new file mode 100755
index 0000000000..2bd68247a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gatk/gatk.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+# convenience wrapper for the gatk jar file
+java -jar GenomeAnalysisTK.jar "$@"
+
diff --git a/var/spack/repos/builtin/packages/gatk/package.py b/var/spack/repos/builtin/packages/gatk/package.py
new file mode 100644
index 0000000000..32bb771530
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gatk/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os.path
+import re
+
+
+class Gatk(Package):
+    """Genome Analysis Toolkit
+       Variant Discovery in High-Throughput Sequencing Data
+    """
+    homepage = "https://software.broadinstitute.org/gatk/"
+    url      = "https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip"
+
+    version('4.0.8.1', sha256='6d47463dfd8c16ffae82fd29e4e73503e5b7cd0fcc6fea2ed50ee3760dd9acd9',
+            url='https://github.com/broadinstitute/gatk/archive/4.0.8.1.tar.gz')
+    version('4.0.4.0', '083d655883fb251e837eb2458141fc2b',
+            url="https://github.com/broadinstitute/gatk/releases/download/4.0.4.0/gatk-4.0.4.0.zip")
+    version('3.8-0', '0581308d2a25f10d11d3dfd0d6e4d28e', extension='tar.gz',
+            url="https://software.broadinstitute.org/gatk/download/auth?package=GATK")
+
+    depends_on('java@8:', type='run')
+    depends_on('python@2.6:2.8,3.6:', type='run', when='@4.0:')
+    depends_on('r@3.2:', type='run', when='@4.0:')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        # Install all executable non-script files to prefix bin
+        files = [x for x in glob.glob("*")
+                 if not re.match("^.*\.sh$", x) and is_exe(x)]
+        for f in files:
+            install(f, prefix.bin)
+
+        # Skip helper script settings
+        if spec.satisfies('@:4.0'):
+            return
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "gatk.sh")
+        script = join_path(prefix.bin, "gatk")
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = join_path(self.spec['java'].prefix, 'bin', 'java')
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('GenomeAnalysisTK.jar', join_path(prefix.bin,
+                    'GenomeAnalysisTK.jar'),
+                    script, **kwargs)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('GATK',
+                             join_path(self.prefix, 'bin',
+                                                    'GenomeAnalysisTK.jar'))
diff --git a/var/spack/repos/builtin/packages/gaussian/package.py b/var/spack/repos/builtin/packages/gaussian/package.py
index ef8c599b94..a9088d11e6 100644
--- a/var/spack/repos/builtin/packages/gaussian/package.py
+++ b/var/spack/repos/builtin/packages/gaussian/package.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
-import shutil
 
 
 class Gaussian(Package):
@@ -36,7 +16,7 @@ class Gaussian(Package):
     version('09', '7d4c95b535e68e48af183920df427e4e')
 
     def install(self, spec, prefix):
-        shutil.copytree(os.getcwd(), prefix.bin)
+        install_tree('.', prefix.bin)
         patch_install_files = ['flc',
                                'linda8.2/opteron-linux/bin/flc',
                                'linda8.2/opteron-linux/bin/LindaLauncher',
diff --git a/var/spack/repos/builtin/packages/gawk/package.py b/var/spack/repos/builtin/packages/gawk/package.py
index 8f9f205ff6..61e08f3158 100644
--- a/var/spack/repos/builtin/packages/gawk/package.py
+++ b/var/spack/repos/builtin/packages/gawk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Gawk(AutotoolsPackage):
     """
 
     homepage = "https://www.gnu.org/software/gawk/"
-    url      = "http://ftp.gnu.org/gnu/gawk/gawk-4.1.4.tar.xz"
+    url      = "https://ftpmirror.gnu.org/gawk/gawk-4.1.4.tar.xz"
 
     version('4.1.4', '4e7dbc81163e60fd4f0b52496e7542c9')
 
diff --git a/var/spack/repos/builtin/packages/gblocks/package.py b/var/spack/repos/builtin/packages/gblocks/package.py
index 7e6401bc6d..38fc44b86a 100644
--- a/var/spack/repos/builtin/packages/gblocks/package.py
+++ b/var/spack/repos/builtin/packages/gblocks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gcc/darwin/headers-10.13-fix.patch b/var/spack/repos/builtin/packages/gcc/darwin/headers-10.13-fix.patch
new file mode 100644
index 0000000000..3dbfde0255
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/darwin/headers-10.13-fix.patch
@@ -0,0 +1,127 @@
+diff -pur fixincludes/fixincl.x gcc-5.5.0/fixincludes/fixincl.x
+--- a/fixincludes/fixincl.x	2017-01-30 17:08:42.000000000 +0100
++++ b/fixincludes/fixincl.x	2017-12-21 14:34:35.000000000 +0100
+@@ -1,12 +1,12 @@
+ /*  -*- buffer-read-only: t -*- vi: set ro:
+- * 
++ *
+  * DO NOT EDIT THIS FILE   (fixincl.x)
+- * 
+- * It has been AutoGen-ed  January  5, 2017 at 06:05:06 PM by AutoGen 5.16.2
++ *
++ * It has been AutoGen-ed  December 21, 2017 at 02:34:35 PM by AutoGen 5.18.7
+  * From the definitions    inclhack.def
+  * and the template file   fixincl
+  */
+-/* DO NOT SVN-MERGE THIS FILE, EITHER Thu Jan  5 18:05:06 CET 2017
++/* DO NOT SVN-MERGE THIS FILE, EITHER Thu Dec 21 14:34:35 CET 2017
+  *
+  * You must regenerate it.  Use the ./genfixes script.
+  *
+@@ -15,7 +15,7 @@
+  * certain ANSI-incompatible system header files which are fixed to work
+  * correctly with ANSI C and placed in a directory that GNU C will search.
+  *
+- * This file contains 240 fixup descriptions.
++ * This file contains 241 fixup descriptions.
+  *
+  * See README for more information.
+  *
+@@ -2579,6 +2579,43 @@ extern \"C\" {\n\
+ 
+ /* * * * * * * * * * * * * * * * * * * * * * * * * *
+  *
++ *  Description of Darwin_Osavailability fix
++ */
++tSCC zDarwin_OsavailabilityName[] =
++     "darwin_osavailability";
++
++/*
++ *  File name selection pattern
++ */
++tSCC zDarwin_OsavailabilityList[] =
++  "os/availability.h\0";
++/*
++ *  Machine/OS name selection pattern
++ */
++tSCC* apzDarwin_OsavailabilityMachs[] = {
++        "*-*-darwin*",
++        (const char*)NULL };
++
++/*
++ *  content selection pattern - do fix if pattern found
++ */
++tSCC zDarwin_OsavailabilitySelect0[] =
++       "#define[ \t]+__(API_[A-Z_]*)\\(\\.\\.\\.\\)";
++
++#define    DARWIN_OSAVAILABILITY_TEST_CT  1
++static tTestDesc aDarwin_OsavailabilityTests[] = {
++  { TT_EGREP,    zDarwin_OsavailabilitySelect0, (regex_t*)NULL }, };
++
++/*
++ *  Fix Command Arguments for Darwin_Osavailability
++ */
++static const char* apzDarwin_OsavailabilityPatch[] = {
++    "format",
++    "#define %1(...)",
++    (char*)NULL };
++
++/* * * * * * * * * * * * * * * * * * * * * * * * * *
++ *
+  *  Description of Darwin_9_Long_Double_Funcs_2 fix
+  */
+ tSCC zDarwin_9_Long_Double_Funcs_2Name[] =
+@@ -9818,9 +9855,9 @@ static const char* apzX11_SprintfPatch[]
+  *
+  *  List of all fixes
+  */
+-#define REGEX_COUNT          276
++#define REGEX_COUNT          277
+ #define MACH_LIST_SIZE_LIMIT 187
+-#define FIX_COUNT            240
++#define FIX_COUNT            241
+ 
+ /*
+  *  Enumerate the fixes
+@@ -9885,6 +9922,7 @@ typedef enum {
+     CTRL_QUOTES_DEF_FIXIDX,
+     CTRL_QUOTES_USE_FIXIDX,
+     CXX_UNREADY_FIXIDX,
++    DARWIN_OSAVAILABILITY_FIXIDX,
+     DARWIN_9_LONG_DOUBLE_FUNCS_2_FIXIDX,
+     DARWIN_EXTERNC_FIXIDX,
+     DARWIN_GCC4_BREAKAGE_FIXIDX,
+@@ -10364,6 +10402,11 @@ tFixDesc fixDescList[ FIX_COUNT ] = {
+      CXX_UNREADY_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,
+      aCxx_UnreadyTests,   apzCxx_UnreadyPatch, 0 },
+ 
++  {  zDarwin_OsavailabilityName,    zDarwin_OsavailabilityList,
++     apzDarwin_OsavailabilityMachs,
++     DARWIN_OSAVAILABILITY_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,
++     aDarwin_OsavailabilityTests,   apzDarwin_OsavailabilityPatch, 0 },
++
+   {  zDarwin_9_Long_Double_Funcs_2Name,    zDarwin_9_Long_Double_Funcs_2List,
+      apzDarwin_9_Long_Double_Funcs_2Machs,
+      DARWIN_9_LONG_DOUBLE_FUNCS_2_TEST_CT, FD_MACH_ONLY | FD_SUBROUTINE,
+diff -pur fixincludes/inclhack.def gcc-5.5.0/fixincludes/inclhack.def
+--- a/fixincludes/inclhack.def	2017-01-30 17:08:42.000000000 +0100
++++ b/fixincludes/inclhack.def	2017-12-21 14:34:28.000000000 +0100
+@@ -1337,6 +1337,18 @@ fix = {
+     test_text = "extern void* malloc( size_t );";
+ };
+ 
++fix = {
++    hackname  = darwin_osavailability;
++    mach      = "*-*-darwin*";
++    files     = os/availability.h;
++    select    = "#define[ \t]+__(API_[A-Z_]*)\\(\\.\\.\\.\\)";
++    c_fix     = format;
++    c_fix_arg = "#define %1(...)";
++
++    test_text = "#define __API_AVAILABLE(...)\n"
++		"#define API_AVAILABLE(...)\n";
++};
++
+ /*
+  *  For the AAB_darwin7_9_long_double_funcs fix to be useful,
+  *  you have to not use "" includes.
diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py
index df7060e742..a029a9e0c5 100644
--- a/var/spack/repos/builtin/packages/gcc/package.py
+++ b/var/spack/repos/builtin/packages/gcc/package.py
@@ -1,34 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack.operating_systems.mac_os import macOS_version
+from spack.operating_systems.mac_os import macos_version
 from llnl.util import tty
 
 import glob
 import os
-import shutil
 import sys
 
 
@@ -37,10 +17,13 @@ class Gcc(AutotoolsPackage):
     Fortran, Ada, and Go, as well as libraries for these languages."""
 
     homepage = 'https://gcc.gnu.org'
-    url      = 'http://ftp.gnu.org/gnu/gcc/gcc-7.1.0/gcc-7.1.0.tar.bz2'
+    url      = 'https://ftpmirror.gnu.org/gcc/gcc-7.1.0/gcc-7.1.0.tar.bz2'
     list_url = 'http://ftp.gnu.org/gnu/gcc/'
     list_depth = 1
 
+    version('8.2.0', '64898a165f67e136d802a92e7633bf1b06c85266027e52127ea025bf5fc2291b5e858288aac0bdba246e6cdf7c6ec88bc8e0e7f3f6f1985f4297710cafde56ed')
+    version('8.1.0', '65f7c65818dc540b3437605026d329fc')
+    version('7.3.0', 'be2da21680f27624f3a87055c4ba5af2')
     version('7.2.0', 'ff370482573133a7fcdd96cd2f552292')
     version('7.1.0', '6bf56a2bca9dac9dbbf8e8d1036964a8')
     version('6.4.0', '11ba51a0cfb8471927f387c8895fe232')
@@ -62,12 +45,17 @@ class Gcc(AutotoolsPackage):
     version('4.6.4', 'b407a3d1480c11667f293bfb1f17d1a4')
     version('4.5.4', '27e459c2566b8209ab064570e1b378f7')
 
-    # Builds all default languages by default.
-    # Ada, Go, Jit, and Objective-C++ are not default languages.
+    # We specifically do not add 'all' variant here because:
+    # (i) Ada, Go, Jit, and Objective-C++ are not default languages.
     # In that respect, the name 'all' is rather misleading.
+    # (ii) Languages other than c,c++,fortran are prone to configure bug in GCC
+    # For example, 'java' appears to ignore custom location of zlib
+    # (iii) meaning of 'all' changes with GCC version, i.e. 'java' is not part
+    # of gcc7. Correctly specifying conflicts() and depends_on() in such a
+    # case is a PITA.
     variant('languages',
-            default='all',
-            values=('all', 'ada', 'brig', 'c', 'c++', 'fortran',
+            default='c,c++,fortran',
+            values=('ada', 'brig', 'c', 'c++', 'fortran',
                     'go', 'java', 'jit', 'lto', 'objc', 'obj-c++'),
             multi=True,
             description='Compilers and runtime libraries to build')
@@ -83,27 +71,32 @@ class Gcc(AutotoolsPackage):
 
     # https://gcc.gnu.org/install/prerequisites.html
     depends_on('gmp@4.3.2:')
-    depends_on('mpfr@2.4.2:')
+    # GCC 7.3 does not compile with newer releases on some platforms, see
+    #   https://github.com/spack/spack/issues/6902#issuecomment-433030376
+    depends_on('mpfr@2.4.2:3.1.6')
     depends_on('mpc@0.8.1:', when='@4.5:')
-    depends_on('isl@0.14', when='@5:5.9')
-    depends_on('isl@0.15:', when='@6:')
+    # Already released GCC versions do not support any newer version of ISL
+    #   GCC 5.4 https://github.com/spack/spack/issues/6902#issuecomment-433072097
+    #   GCC 7.3 https://github.com/spack/spack/issues/6902#issuecomment-433030376
+    #   GCC 9+  https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86724
+    depends_on('isl@0.15', when='@5:5.9')
+    depends_on('isl@0.15:0.18', when='@6:8.9')
+    depends_on('isl@0.15:0.20', when='@9:')
     depends_on('zlib', when='@6:')
     depends_on('gnat', when='languages=ada')
     depends_on('binutils~libiberty', when='+binutils')
     depends_on('zip', type='build', when='languages=java')
-    depends_on('zip', type='build', when='@:6 languages=all')
 
     # TODO: integrate these libraries.
     # depends_on('ppl')
     # depends_on('cloog')
 
-    # TODO: Add a 'test' deptype
-    # https://github.com/spack/spack/issues/1279
-    # depends_on('dejagnu@1.4.4', type='test')
-    # depends_on('expect', type='test')
-    # depends_on('tcl', type='test')
-    # depends_on('autogen@5.5.4:', type='test')
-    # depends_on('guile@1.4.1:', type='test')
+    # https://gcc.gnu.org/install/test.html
+    depends_on('dejagnu@1.4.4', type='test')
+    depends_on('expect', type='test')
+    depends_on('tcl', type='test')
+    depends_on('autogen@5.5.4:', type='test')
+    depends_on('guile@1.4.1:', type='test')
 
     # See https://golang.org/doc/install/gccgo#Releases
     provides('golang',        when='languages=go @4.6:')
@@ -152,16 +145,30 @@ class Gcc(AutotoolsPackage):
     if sys.platform == 'darwin':
         # Fix parallel build on APFS filesystem
         # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81797
-        if macOS_version() >= Version('10.13'):
-            patch('darwin/apfs.patch', when='@7.2.0')
+        if macos_version() >= Version('10.13'):
+            patch('darwin/apfs.patch', when='@5.5.0,6.1:6.4,7.1:7.3')
+            # from homebrew via macports
+            # https://trac.macports.org/ticket/56502#no1
+            # see also: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=83531
+            patch('darwin/headers-10.13-fix.patch', when='@5.5.0')
         patch('darwin/gcc-7.1.0-headerpad.patch', when='@5:')
-        patch('darwin/gcc-6.1.0-jit.patch', when='@5:')
+        patch('darwin/gcc-6.1.0-jit.patch', when='@5:7')
         patch('darwin/gcc-4.9.patch1', when='@4.9.0:4.9.3')
         patch('darwin/gcc-4.9.patch2', when='@4.9.0:4.9.3')
 
     patch('piclibs.patch', when='+piclibs')
     patch('gcc-backport.patch', when='@4.7:4.9.2,5:5.3')
 
+    # Older versions do not compile with newer versions of glibc
+    # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81712
+    patch('ucontext_t.patch', when='@4.9,5.1:5.4,6.1:6.4,7.1')
+    patch('ucontext_t-java.patch', when='@4.9,5.1:5.4,6.1:6.4 languages=java')
+    # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81066
+    patch('stack_t-4.9.patch', when='@4.9')
+    patch('stack_t.patch', when='@5.1:5.4,6.1:6.4,7.1')
+    # https://bugs.busybox.net/show_bug.cgi?id=10061
+    patch('signal.patch', when='@4.9,5.1:5.4')
+
     build_directory = 'spack-build'
 
     def url_for_version(self, version):
@@ -187,7 +194,7 @@ class Gcc(AutotoolsPackage):
                 new_dispatch_dir = join_path(prefix, 'include', 'dispatch')
                 mkdirp(new_dispatch_dir)
                 new_header = join_path(new_dispatch_dir, 'object.h')
-                shutil.copyfile('/usr/include/dispatch/object.h', new_header)
+                install('/usr/include/dispatch/object.h', new_header)
                 filter_file(r'typedef void \(\^dispatch_block_t\)\(void\)',
                             'typedef void* dispatch_block_t',
                             new_header)
@@ -290,3 +297,10 @@ class Gcc(AutotoolsPackage):
                     out.write('-rpath {0}:{1} '.format(
                               self.prefix.lib, self.prefix.lib64))
         set_install_permissions(specs_file)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('CC', join_path(self.spec.prefix.bin, 'gcc'))
+        run_env.set('CXX', join_path(self.spec.prefix.bin, 'g++'))
+        run_env.set('FC', join_path(self.spec.prefix.bin, 'gfortran'))
+        run_env.set('F77', join_path(self.spec.prefix.bin, 'gfortran'))
+        run_env.set('F90', join_path(self.spec.prefix.bin, 'gfortran'))
diff --git a/var/spack/repos/builtin/packages/gcc/signal.patch b/var/spack/repos/builtin/packages/gcc/signal.patch
new file mode 100644
index 0000000000..21bf9e030f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/signal.patch
@@ -0,0 +1,28 @@
+From 6c709b6262e8b6441b1e94526d6d65d4ce7a7dec Mon Sep 17 00:00:00 2001
+From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Thu, 7 Sep 2017 07:18:57 +0000
+Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>
+
+        * asan/asan_linux.cc: Include <signal.h>
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251830 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libsanitizer/asan/asan_linux.cc | 1 +
+ 2 files changed, 5 insertions(+)
+
+diff --git a/libsanitizer/asan/asan_linux.cc b/libsanitizer/asan/asan_linux.cc
+index c504168..59087b9 100644
+--- a/libsanitizer/asan/asan_linux.cc
++++ b/libsanitizer/asan/asan_linux.cc
+@@ -29,6 +29,7 @@
+ #include <dlfcn.h>
+ #include <fcntl.h>
+ #include <pthread.h>
++#include <signal.h>
+ #include <stdio.h>
+ #include <unistd.h>
+ #include <unwind.h>
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gcc/stack_t-4.9.patch b/var/spack/repos/builtin/packages/gcc/stack_t-4.9.patch
new file mode 100644
index 0000000000..b894557c8c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/stack_t-4.9.patch
@@ -0,0 +1,80 @@
+From 833e00c01e96f61e24cd7ec97b93fad212dc914b Mon Sep 17 00:00:00 2001
+From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Thu, 7 Sep 2017 07:17:17 +0000
+Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>
+
+        Backported from mainline
+        2017-07-14  Jakub Jelinek  <jakub@redhat.com>
+
+        PR sanitizer/81066
+        * sanitizer_common/sanitizer_linux.h: Cherry-pick upstream r307969.
+        * sanitizer_common/sanitizer_linux.cc: Likewise.
+        * sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc: Likewise.
+        * tsan/tsan_platform_linux.cc: Likewise.
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251829 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libsanitizer/sanitizer_common/sanitizer_linux.cc              |  3 +--
+ libsanitizer/sanitizer_common/sanitizer_linux.h               |  4 +---
+ .../sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc  |  2 +-
+ libsanitizer/tsan/tsan_platform_linux.cc                      |  2 +-
+ 5 files changed, 15 insertions(+), 7 deletions(-)
+
+diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.cc b/libsanitizer/sanitizer_common/sanitizer_linux.cc
+index 9feb307..821b26d 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_linux.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_linux.cc
+@@ -514,8 +514,7 @@ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5) {
+ }
+ #endif
+ 
+-uptr internal_sigaltstack(const struct sigaltstack *ss,
+-                         struct sigaltstack *oss) {
++uptr internal_sigaltstack(const void *ss, void *oss) {
+   return internal_syscall(__NR_sigaltstack, (uptr)ss, (uptr)oss);
+ }
+ 
+diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.h b/libsanitizer/sanitizer_common/sanitizer_linux.h
+index 086834c..3a6f4cd 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_linux.h
++++ b/libsanitizer/sanitizer_common/sanitizer_linux.h
+@@ -27,8 +26,7 @@ struct linux_dirent;
+ // Syscall wrappers.
+ uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);
+ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5);
+-uptr internal_sigaltstack(const struct sigaltstack* ss,
+-                          struct sigaltstack* oss);
++uptr internal_sigaltstack(const void* ss, void* oss);
+ uptr internal_sigaction(int signum, const __sanitizer_kernel_sigaction_t *act,
+     __sanitizer_kernel_sigaction_t *oldact);
+ uptr internal_sigprocmask(int how, __sanitizer_kernel_sigset_t *set,
+diff --git a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
+index 5881202..c54894d 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
+@@ -234,7 +234,7 @@ static int TracerThread(void* argument) {
+ 
+   // Alternate stack for signal handling.
+   InternalScopedBuffer<char> handler_stack_memory(kHandlerStackSize);
+-  struct sigaltstack handler_stack;
++  stack_t handler_stack;
+   internal_memset(&handler_stack, 0, sizeof(handler_stack));
+   handler_stack.ss_sp = handler_stack_memory.data();
+   handler_stack.ss_size = kHandlerStackSize;
+diff --git a/libsanitizer/tsan/tsan_platform_linux.cc b/libsanitizer/tsan/tsan_platform_linux.cc
+index 3259131..b8e9078 100644
+--- a/libsanitizer/tsan/tsan_platform_linux.cc
++++ b/libsanitizer/tsan/tsan_platform_linux.cc
+@@ -377,7 +377,7 @@ bool IsGlobalVar(uptr addr) {
+ int ExtractResolvFDs(void *state, int *fds, int nfd) {
+ #if SANITIZER_LINUX
+   int cnt = 0;
+-  __res_state *statp = (__res_state*)state;
++  struct __res_state *statp = (struct __res_state*)state;
+   for (int i = 0; i < MAXNS && cnt < nfd; i++) {
+     if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)
+       fds[cnt++] = statp->_u._ext.nssocks[i];
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gcc/stack_t.patch b/var/spack/repos/builtin/packages/gcc/stack_t.patch
new file mode 100644
index 0000000000..48a5a47ade
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/stack_t.patch
@@ -0,0 +1,88 @@
+From 833e00c01e96f61e24cd7ec97b93fad212dc914b Mon Sep 17 00:00:00 2001
+From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Thu, 7 Sep 2017 07:17:17 +0000
+Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>
+
+        Backported from mainline
+        2017-07-14  Jakub Jelinek  <jakub@redhat.com>
+
+        PR sanitizer/81066
+        * sanitizer_common/sanitizer_linux.h: Cherry-pick upstream r307969.
+        * sanitizer_common/sanitizer_linux.cc: Likewise.
+        * sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc: Likewise.
+        * tsan/tsan_platform_linux.cc: Likewise.
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251829 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libsanitizer/sanitizer_common/sanitizer_linux.cc              |  3 +--
+ libsanitizer/sanitizer_common/sanitizer_linux.h               |  4 +---
+ .../sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc  |  2 +-
+ libsanitizer/tsan/tsan_platform_linux.cc                      |  2 +-
+ 5 files changed, 15 insertions(+), 7 deletions(-)
+
+diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.cc b/libsanitizer/sanitizer_common/sanitizer_linux.cc
+index 9feb307..821b26d 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_linux.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_linux.cc
+@@ -514,8 +514,7 @@ uptr internal_prctl(int option, uptr arg2, uptr arg3, uptr arg4, uptr arg5) {
+ }
+ #endif
+ 
+-uptr internal_sigaltstack(const struct sigaltstack *ss,
+-                         struct sigaltstack *oss) {
++uptr internal_sigaltstack(const void *ss, void *oss) {
+   return internal_syscall(SYSCALL(sigaltstack), (uptr)ss, (uptr)oss);
+ }
+ 
+diff --git a/libsanitizer/sanitizer_common/sanitizer_linux.h b/libsanitizer/sanitizer_common/sanitizer_linux.h
+index 086834c..3a6f4cd 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_linux.h
++++ b/libsanitizer/sanitizer_common/sanitizer_linux.h
+@@ -18,7 +18,6 @@
+ #include "sanitizer_platform_limits_posix.h"
+ 
+ struct link_map;  // Opaque type returned by dlopen().
+-struct sigaltstack;
+ 
+ namespace __sanitizer {
+ // Dirent structure for getdents(). Note that this structure is different from
+@@ -27,8 +26,7 @@ struct linux_dirent;
+ 
+ // Syscall wrappers.
+ uptr internal_getdents(fd_t fd, struct linux_dirent *dirp, unsigned int count);
+-uptr internal_sigaltstack(const struct sigaltstack* ss,
+-                          struct sigaltstack* oss);
++uptr internal_sigaltstack(const void* ss, void* oss);
+ uptr internal_sigprocmask(int how, __sanitizer_sigset_t *set,
+     __sanitizer_sigset_t *oldset);
+ void internal_sigfillset(__sanitizer_sigset_t *set);
+diff --git a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
+index 5881202..c54894d 100644
+--- a/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
++++ b/libsanitizer/sanitizer_common/sanitizer_stoptheworld_linux_libcdep.cc
+@@ -234,7 +234,7 @@ static int TracerThread(void* argument) {
+ 
+   // Alternate stack for signal handling.
+   InternalScopedBuffer<char> handler_stack_memory(kHandlerStackSize);
+-  struct sigaltstack handler_stack;
++  stack_t handler_stack;
+   internal_memset(&handler_stack, 0, sizeof(handler_stack));
+   handler_stack.ss_sp = handler_stack_memory.data();
+   handler_stack.ss_size = kHandlerStackSize;
+diff --git a/libsanitizer/tsan/tsan_platform_linux.cc b/libsanitizer/tsan/tsan_platform_linux.cc
+index 3259131..b8e9078 100644
+--- a/libsanitizer/tsan/tsan_platform_linux.cc
++++ b/libsanitizer/tsan/tsan_platform_linux.cc
+@@ -377,7 +377,7 @@ bool IsGlobalVar(uptr addr) {
+ int ExtractResolvFDs(void *state, int *fds, int nfd) {
+ #if SANITIZER_LINUX
+   int cnt = 0;
+-  __res_state *statp = (__res_state*)state;
++  struct __res_state *statp = (struct __res_state*)state;
+   for (int i = 0; i < MAXNS && cnt < nfd; i++) {
+     if (statp->_u._ext.nsaddrs[i] && statp->_u._ext.nssocks[i] != -1)
+       fds[cnt++] = statp->_u._ext.nssocks[i];
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gcc/ucontext_t-java.patch b/var/spack/repos/builtin/packages/gcc/ucontext_t-java.patch
new file mode 100644
index 0000000000..a43e0b5aa2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/ucontext_t-java.patch
@@ -0,0 +1,60 @@
+From 9b9287cde20ea57578cf07efb2a96ed4cc0da36f Mon Sep 17 00:00:00 2001
+From: doko <doko@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Thu, 7 Sep 2017 07:22:07 +0000
+Subject: [PATCH] 2017-09-07  Matthias Klose  <doko@ubuntu.com>
+
+        * include/x86_64-signal.h (HANDLE_DIVIDE_OVERFLOW): Replace
+        'struct ucontext' with ucontext_t.
+        * include/i386-signal.h (HANDLE_DIVIDE_OVERFLOW): Likewise.
+        * include/s390-signal.h (HANDLE_DIVIDE_OVERFLOW): Likewise.
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@251832 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libjava/include/i386-signal.h   | 2 +-
+ libjava/include/s390-signal.h   | 2 +-
+ libjava/include/x86_64-signal.h | 2 +-
+ 4 files changed, 10 insertions(+), 3 deletions(-)
+
+diff --git a/libjava/include/i386-signal.h b/libjava/include/i386-signal.h
+index c2409b0..ef77e7e 100644
+--- a/libjava/include/i386-signal.h
++++ b/libjava/include/i386-signal.h
+@@ -29,7 +29,7 @@ static void _Jv_##_name (int, siginfo_t *,			\
+ #define HANDLE_DIVIDE_OVERFLOW						\
+ do									\
+ {									\
+-  struct ucontext *_uc = (struct ucontext *)_p;				\
++  ucontext_t *_uc = (ucontext_t *)_p;					\
+   gregset_t &_gregs = _uc->uc_mcontext.gregs;				\
+   unsigned char *_eip = (unsigned char *)_gregs[REG_EIP];		\
+ 									\
+diff --git a/libjava/include/s390-signal.h b/libjava/include/s390-signal.h
+index 4ca4c10..9261b52 100644
+--- a/libjava/include/s390-signal.h
++++ b/libjava/include/s390-signal.h
+@@ -51,7 +51,7 @@ do									\
+   struct                                                                \
+   {                                                                     \
+     unsigned long int uc_flags;                                         \
+-    struct ucontext *uc_link;                                           \
++    ucontext_t *uc_link;                                                \
+     stack_t uc_stack;                                                   \
+     mcontext_t uc_mcontext;                                             \
+     unsigned long sigmask[2];                                           \
+diff --git a/libjava/include/x86_64-signal.h b/libjava/include/x86_64-signal.h
+index 12383b5..e36c5a3 100644
+--- a/libjava/include/x86_64-signal.h
++++ b/libjava/include/x86_64-signal.h
+@@ -28,7 +28,7 @@ static void _Jv_##_name (int, siginfo_t *,			\
+ #define HANDLE_DIVIDE_OVERFLOW						\
+ do									\
+ {									\
+-  struct ucontext *_uc = (struct ucontext *)_p;				\
++  ucontext_t *_uc = (ucontext_t *)_p;					\
+   gregset_t &_gregs = _uc->uc_mcontext.gregs;				\
+   unsigned char *_rip = (unsigned char *)_gregs[REG_RIP];		\
+ 									\
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gcc/ucontext_t.patch b/var/spack/repos/builtin/packages/gcc/ucontext_t.patch
new file mode 100644
index 0000000000..a4f04b4715
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcc/ucontext_t.patch
@@ -0,0 +1,189 @@
+From ecf0d1a107133c715763940c2b197aa814710e1b Mon Sep 17 00:00:00 2001
+From: jsm28 <jsm28@138bc75d-0d04-0410-961f-82ee72b054a4>
+Date: Tue, 4 Jul 2017 10:25:10 +0000
+Subject: [PATCH] Use ucontext_t not struct ucontext in linux-unwind.h files.
+
+Current glibc no longer gives the ucontext_t type the tag struct
+ucontext, to conform with POSIX namespace rules.  This requires
+various linux-unwind.h files in libgcc, that were previously using
+struct ucontext, to be fixed to use ucontext_t instead.  This is
+similar to the removal of the struct siginfo tag from siginfo_t some
+years ago.
+
+This patch changes those files to use ucontext_t instead.  As the
+standard name that should be unconditionally safe, so this is not
+restricted to architectures supported by glibc, or conditioned on the
+glibc version.
+
+Tested compilation together with current glibc with glibc's
+build-many-glibcs.py.
+
+	* config/aarch64/linux-unwind.h (aarch64_fallback_frame_state),
+	config/alpha/linux-unwind.h (alpha_fallback_frame_state),
+	config/bfin/linux-unwind.h (bfin_fallback_frame_state),
+	config/i386/linux-unwind.h (x86_64_fallback_frame_state,
+	x86_fallback_frame_state), config/m68k/linux-unwind.h (struct
+	uw_ucontext), config/nios2/linux-unwind.h (struct nios2_ucontext),
+	config/pa/linux-unwind.h (pa32_fallback_frame_state),
+	config/sh/linux-unwind.h (sh_fallback_frame_state),
+	config/tilepro/linux-unwind.h (tile_fallback_frame_state),
+	config/xtensa/linux-unwind.h (xtensa_fallback_frame_state): Use
+	ucontext_t instead of struct ucontext.
+
+
+git-svn-id: svn+ssh://gcc.gnu.org/svn/gcc/branches/gcc-5-branch@249958 138bc75d-0d04-0410-961f-82ee72b054a4
+---
+ libgcc/config/aarch64/linux-unwind.h |  2 +-
+ libgcc/config/alpha/linux-unwind.h   |  2 +-
+ libgcc/config/bfin/linux-unwind.h    |  2 +-
+ libgcc/config/i386/linux-unwind.h    |  4 ++--
+ libgcc/config/m68k/linux-unwind.h    |  2 +-
+ libgcc/config/nios2/linux-unwind.h   |  2 +-
+ libgcc/config/pa/linux-unwind.h      |  2 +-
+ libgcc/config/sh/linux-unwind.h      |  2 +-
+ libgcc/config/tilepro/linux-unwind.h |  2 +-
+ libgcc/config/xtensa/linux-unwind.h  |  2 +-
+ 11 files changed, 25 insertions(+), 11 deletions(-)
+
+diff --git a/libgcc/config/aarch64/linux-unwind.h b/libgcc/config/aarch64/linux-unwind.h
+index 86d17b1..909f68f 100644
+--- a/libgcc/config/aarch64/linux-unwind.h
++++ b/libgcc/config/aarch64/linux-unwind.h
+@@ -52,7 +52,7 @@ aarch64_fallback_frame_state (struct _Unwind_Context *context,
+   struct rt_sigframe
+   {
+     siginfo_t info;
+-    struct ucontext uc;
++    ucontext_t uc;
+   };
+ 
+   struct rt_sigframe *rt_;
+diff --git a/libgcc/config/alpha/linux-unwind.h b/libgcc/config/alpha/linux-unwind.h
+index d65474f..9a226b1 100644
+--- a/libgcc/config/alpha/linux-unwind.h
++++ b/libgcc/config/alpha/linux-unwind.h
+@@ -51,7 +51,7 @@ alpha_fallback_frame_state (struct _Unwind_Context *context,
+     {
+       struct rt_sigframe {
+ 	siginfo_t info;
+-	struct ucontext uc;
++	ucontext_t uc;
+       } *rt_ = context->cfa;
+       sc = &rt_->uc.uc_mcontext;
+     }
+diff --git a/libgcc/config/bfin/linux-unwind.h b/libgcc/config/bfin/linux-unwind.h
+index 0c270e4..7fa95d2 100644
+--- a/libgcc/config/bfin/linux-unwind.h
++++ b/libgcc/config/bfin/linux-unwind.h
+@@ -52,7 +52,7 @@ bfin_fallback_frame_state (struct _Unwind_Context *context,
+ 	void *puc;
+ 	char retcode[8];
+ 	siginfo_t info;
+-	struct ucontext uc;
++	ucontext_t uc;
+       } *rt_ = context->cfa;
+ 
+       /* The void * cast is necessary to avoid an aliasing warning.
+diff --git a/libgcc/config/i386/linux-unwind.h b/libgcc/config/i386/linux-unwind.h
+index e54bf73..d35fc45 100644
+--- a/libgcc/config/i386/linux-unwind.h
++++ b/libgcc/config/i386/linux-unwind.h
+@@ -58,7 +58,7 @@ x86_64_fallback_frame_state (struct _Unwind_Context *context,
+   if (*(unsigned char *)(pc+0) == 0x48
+       && *(unsigned long long *)(pc+1) == RT_SIGRETURN_SYSCALL)
+     {
+-      struct ucontext *uc_ = context->cfa;
++      ucontext_t *uc_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+          because it does not alias anything.  */
+@@ -138,7 +138,7 @@ x86_fallback_frame_state (struct _Unwind_Context *context,
+ 	siginfo_t *pinfo;
+ 	void *puc;
+ 	siginfo_t info;
+-	struct ucontext uc;
++	ucontext_t uc;
+       } *rt_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+diff --git a/libgcc/config/m68k/linux-unwind.h b/libgcc/config/m68k/linux-unwind.h
+index fb79a4d..b2f5ea4 100644
+--- a/libgcc/config/m68k/linux-unwind.h
++++ b/libgcc/config/m68k/linux-unwind.h
+@@ -33,7 +33,7 @@ see the files COPYING3 and COPYING.RUNTIME respectively.  If not, see
+ /* <sys/ucontext.h> is unfortunately broken right now.  */
+ struct uw_ucontext {
+ 	unsigned long	  uc_flags;
+-	struct ucontext  *uc_link;
++	ucontext_t	 *uc_link;
+ 	stack_t		  uc_stack;
+ 	mcontext_t	  uc_mcontext;
+ 	unsigned long	  uc_filler[80];
+diff --git a/libgcc/config/nios2/linux-unwind.h b/libgcc/config/nios2/linux-unwind.h
+index dff1c20..1d88afe 100644
+--- a/libgcc/config/nios2/linux-unwind.h
++++ b/libgcc/config/nios2/linux-unwind.h
+@@ -38,7 +38,7 @@ struct nios2_mcontext {
+ 
+ struct nios2_ucontext {
+   unsigned long uc_flags;
+-  struct ucontext *uc_link;
++  ucontext_t *uc_link;
+   stack_t uc_stack;
+   struct nios2_mcontext uc_mcontext;
+   sigset_t uc_sigmask;	/* mask last for extensibility */
+diff --git a/libgcc/config/pa/linux-unwind.h b/libgcc/config/pa/linux-unwind.h
+index 0149468..9157535 100644
+--- a/libgcc/config/pa/linux-unwind.h
++++ b/libgcc/config/pa/linux-unwind.h
+@@ -80,7 +80,7 @@ pa32_fallback_frame_state (struct _Unwind_Context *context,
+   struct sigcontext *sc;
+   struct rt_sigframe {
+     siginfo_t info;
+-    struct ucontext uc;
++    ucontext_t uc;
+   } *frame;
+ 
+   /* rt_sigreturn trampoline:
+diff --git a/libgcc/config/sh/linux-unwind.h b/libgcc/config/sh/linux-unwind.h
+index e63091f..67033f0 100644
+--- a/libgcc/config/sh/linux-unwind.h
++++ b/libgcc/config/sh/linux-unwind.h
+@@ -180,7 +180,7 @@ sh_fallback_frame_state (struct _Unwind_Context *context,
+     {
+       struct rt_sigframe {
+ 	siginfo_t info;
+-	struct ucontext uc;
++	ucontext_t uc;
+       } *rt_ = context->cfa;
+       /* The void * cast is necessary to avoid an aliasing warning.
+          The aliasing warning is correct, but should not be a problem
+diff --git a/libgcc/config/tilepro/linux-unwind.h b/libgcc/config/tilepro/linux-unwind.h
+index fd83ba7..e3c9ef0 100644
+--- a/libgcc/config/tilepro/linux-unwind.h
++++ b/libgcc/config/tilepro/linux-unwind.h
+@@ -61,7 +61,7 @@ tile_fallback_frame_state (struct _Unwind_Context *context,
+   struct rt_sigframe {
+     unsigned char save_area[C_ABI_SAVE_AREA_SIZE];
+     siginfo_t info;
+-    struct ucontext uc;
++    ucontext_t uc;
+   } *rt_;
+ 
+   /* Return if this is not a signal handler.  */
+diff --git a/libgcc/config/xtensa/linux-unwind.h b/libgcc/config/xtensa/linux-unwind.h
+index 9a67b5d..98b7ea6 100644
+--- a/libgcc/config/xtensa/linux-unwind.h
++++ b/libgcc/config/xtensa/linux-unwind.h
+@@ -67,7 +67,7 @@ xtensa_fallback_frame_state (struct _Unwind_Context *context,
+ 
+   struct rt_sigframe {
+     siginfo_t info;
+-    struct ucontext uc;
++    ucontext_t uc;
+   } *rt_;
+ 
+   /* movi a2, __NR_rt_sigreturn; syscall */
+-- 
+2.9.3
+
diff --git a/var/spack/repos/builtin/packages/gccmakedep/package.py b/var/spack/repos/builtin/packages/gccmakedep/package.py
index a8ece20f43..ae0bade1fd 100644
--- a/var/spack/repos/builtin/packages/gccmakedep/package.py
+++ b/var/spack/repos/builtin/packages/gccmakedep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,4 +14,4 @@ class Gccmakedep(AutotoolsPackage):
 
     version('1.0.3', '127ddb6131eb4a56fdf6644a63ade788')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/gccxml/gcc-5.patch b/var/spack/repos/builtin/packages/gccxml/gcc-5.patch
new file mode 100644
index 0000000000..4348d10184
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gccxml/gcc-5.patch
@@ -0,0 +1,57 @@
+--- a/GCC/gcc/toplev.c
++++ b/GCC/gcc/toplev.c
+@@ -537,7 +537,7 @@ read_integral_parameter (const char *p, const char *pname, const int  defval)
+    for floor_log2 and exact_log2; see toplev.h.  That construct, however,
+    conflicts with the ISO C++ One Definition Rule.   */
+
+-#if GCC_VERSION < 3004 || !defined (__cplusplus)
++#if GCC_VERSION < 3004
+
+ /* Given X, an unsigned number, return the largest int Y such that 2**Y <= X.
+    If X is 0, return -1.  */
+@@ -589,7 +589,7 @@ exact_log2 (unsigned HOST_WIDE_INT x)
+ #endif
+ }
+
+-#endif /*  GCC_VERSION < 3004 || !defined (__cplusplus)  */
++#endif /*  GCC_VERSION < 3004 */
+
+ /* Handler for fatal signals, such as SIGSEGV.  These are transformed
+    into ICE messages, which is much more user friendly.  In case the
+diff --git a/GCC/gcc/toplev.h b/GCC/gcc/toplev.h
+index c935f7e..1edd5e5 100644
+--- a/GCC/gcc/toplev.h
++++ b/GCC/gcc/toplev.h
+@@ -151,6 +151,7 @@ extern void decode_d_option     (const char *);
+ /* Return true iff flags are set as if -ffast-math.  */
+ extern bool fast_math_flags_set_p  (void);
+
++#if GCC_VERSION < 3004
+ /* Return log2, or -1 if not exact.  */
+ extern int exact_log2                  (unsigned HOST_WIDE_INT);
+
+@@ -158,7 +159,7 @@ extern int exact_log2                  (unsigned HOST_WIDE_INT);
+ extern int floor_log2                  (unsigned HOST_WIDE_INT);
+
+ /* Inline versions of the above for speed.  */
+-#if GCC_VERSION >= 3004
++#else /* GCC_VERSION >= 3004 */
+ # if HOST_BITS_PER_WIDE_INT == HOST_BITS_PER_LONG
+ #  define CLZ_HWI __builtin_clzl
+ #  define CTZ_HWI __builtin_ctzl
+@@ -170,13 +171,13 @@ extern int floor_log2                  (unsigned HOST_WIDE_INT);
+ #  define CTZ_HWI __builtin_ctz
+ # endif
+
+-extern inline int
++static inline int
+ floor_log2 (unsigned HOST_WIDE_INT x)
+ {
+   return x ? HOST_BITS_PER_WIDE_INT - 1 - (int) CLZ_HWI (x) : -1;
+ }
+
+-extern inline int
++static inline int
+ exact_log2 (unsigned HOST_WIDE_INT x)
+ {
+   return x == (x & -x) && x ? (int) CTZ_HWI (x) : -1;
diff --git a/var/spack/repos/builtin/packages/gccxml/package.py b/var/spack/repos/builtin/packages/gccxml/package.py
index d7f75f8631..99ebf75a5f 100644
--- a/var/spack/repos/builtin/packages/gccxml/package.py
+++ b/var/spack/repos/builtin/packages/gccxml/package.py
@@ -1,24 +1,8 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -27,10 +11,12 @@ class Gccxml(CMakePackage):
     the GCC C++ compiler."""
 
     homepage = "http://gccxml.github.io"
-    url      = "https://github.com/gccxml/gccxml/archive/v0.6.x.tar.gz"
+    git      = "https://github.com/gccxml/gccxml.git"
 
-    version('develop', git='https://github.com/gccxml/gccxml.git', branch='master')
-    version('latest', git='https://github.com/gccxml/gccxml.git',
-            commit='3afa8ba5be6866e603dcabe80aff79856b558e24', preferred=True)
+    version('develop', branch='master')
+    version('latest', commit='3afa8ba5be6866e603dcabe80aff79856b558e24',
+            preferred=True)
 
     patch('darwin-gcc.patch', when='%gcc platform=darwin')
+    # taken from https://github.com/gccxml/gccxml/issues/11#issuecomment-140334118
+    patch('gcc-5.patch', when='%gcc@5:')
diff --git a/var/spack/repos/builtin/packages/gconf/package.py b/var/spack/repos/builtin/packages/gconf/package.py
index 395ec2ff44..abafae9c36 100644
--- a/var/spack/repos/builtin/packages/gconf/package.py
+++ b/var/spack/repos/builtin/packages/gconf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gcta/package.py b/var/spack/repos/builtin/packages/gcta/package.py
new file mode 100644
index 0000000000..8ff01ebe05
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gcta/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gcta(Package):
+
+    """GCTA (Genome-wide Complex Trait Analysis) was originally designed to
+    estimate the proportion of phenotypic variance explained by all genome-wide
+    SNPs for complex traits (the GREML method), and has subsequently extended
+    for many other analyses to better understand the genetic architecture of
+    complex traits. GCTA currently supports the following analyses."""
+
+    homepage = "http://cnsgenomics.com/software/gcta/#Overview"
+    url      = "http://cnsgenomics.com/software/gcta/gcta_1.91.2beta.zip"
+
+    version('1.91.2beta_mac', 'ce0882ad35dd9474ffe40911da369274700af1ecb9916c0a355b7bad14850234')
+    version('1.91.2beta', '192efb767be1c7ca9c2dac5d2c2317a97c7a9db1f801168d19ad2a51b98d9b10', preferred=True)
+
+    conflicts('@1.91.2beta', when='platform=darwin')
+    conflicts('@1.91.2beta_mac', when='platform=linux')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('gcta64', join_path(prefix.bin, 'gcta64'))
+        set_executable(join_path(prefix.bin, 'gcta64'))
diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py
index 044013c88d..2ca0df636f 100644
--- a/var/spack/repos/builtin/packages/gdal/package.py
+++ b/var/spack/repos/builtin/packages/gdal/package.py
@@ -1,94 +1,453 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
-class Gdal(Package):
-    """GDAL is a translator library for raster and vector geospatial
-    data formats that is released under an X/MIT style Open Source
-    license by the Open Source Geospatial Foundation. As a library,
-    it presents a single raster abstract data model and vector
-    abstract data model to the calling application for all supported
-    formats. It also comes with a variety of useful command line
-    utilities for data translation and processing.
+class Gdal(AutotoolsPackage):
+    """GDAL (Geospatial Data Abstraction Library) is a translator library for
+    raster and vector geospatial data formats that is released under an X/MIT
+    style Open Source license by the Open Source Geospatial Foundation. As a
+    library, it presents a single raster abstract data model and vector
+    abstract data model to the calling application for all supported formats.
+    It also comes with a variety of useful command line utilities for data
+    translation and processing.
     """
 
     homepage   = "http://www.gdal.org/"
-    url        = "http://download.osgeo.org/gdal/2.1.2/gdal-2.1.2.tar.xz"
+    url        = "http://download.osgeo.org/gdal/2.3.1/gdal-2.3.1.tar.xz"
     list_url   = "http://download.osgeo.org/gdal/"
     list_depth = 1
 
-    version('2.1.2', 'ae85b78888514c75e813d658cac9478e')
-    version('2.0.2', '940208e737c87d31a90eaae43d0efd65')
-
-    extends('python')
-
-    variant('hdf5', default=False, description='Enable HDF5 support')
-    variant('hdf', default=False, description='Enable HDF4 support')
-    variant('openjpeg', default=False, description='Enable JPEG2000 support')
-    variant('geos', default=False, description='Enable GEOS support')
-    variant('kea', default=False, description='Enable KEA support')
-    variant('netcdf', default=False, description='Enable netcdf support')
-
-    depends_on('swig')
-    depends_on("hdf5", when='+hdf5')
-    depends_on("hdf", when='+hdf')
-    depends_on("openjpeg", when='+openjpeg')
-    depends_on("geos", when='+geos')
-    depends_on("kealib", when='+kea')
-    depends_on("netcdf", when='+netcdf')
-    depends_on("libtiff")
-    depends_on("libpng")
-    depends_on("zlib")
-    depends_on("proj")
-    depends_on("py-numpy", type=('build', 'run'))
-
-    parallel = False
-
-    def install(self, spec, prefix):
-        args = []
-        args.append("--prefix=%s" % prefix)
-        args.append("--with-liblzma=yes")
-        args.append("--with-zlib=%s" % spec['zlib'].prefix)
-        args.append("--with-python=%s" % spec['python'].command.path)
-        args.append("--without-libtool")
+    maintainers = ['adamjstewart']
+
+    import_modules = [
+        'osgeo', 'osgeo.gdal', 'osgeo.ogr', 'osgeo.osr',
+        'osgeo.gdal_array', 'osgeo.gdalconst'
+    ]
+
+    version('2.3.1',  sha256='9c4625c45a3ee7e49a604ef221778983dd9fd8104922a87f20b99d9bedb7725a')
+    version('2.3.0',  sha256='6f75e49aa30de140525ccb58688667efe3a2d770576feb7fbc91023b7f552aa2')
+    version('2.1.2',  sha256='b597f36bd29a2b4368998ddd32b28c8cdf3c8192237a81b99af83cc17d7fa374')
+    version('2.0.2',  sha256='90f838853cc1c07e55893483faa7e923e4b4b1659c6bc9df3538366030a7e622')
+    version('1.11.5', sha256='d4fdc3e987b9926545f0a514b4328cd733f2208442f8d03bde630fe1f7eff042')
+
+    variant('libtool',   default=True,  description='Use libtool to build the library')
+    variant('libz',      default=True,  description='Include libz support')
+    variant('libiconv',  default=False, description='Include libiconv support')
+    variant('liblzma',   default=True,  description='Include liblzma support')
+    variant('zstd',      default=False, description='Include zstd support')
+    variant('pg',        default=False, description='Include PostgreSQL support')
+    variant('cfitsio',   default=False, description='Include FITS support')
+    variant('png',       default=False, description='Include PNG support')
+    variant('jpeg',      default=True,  description='Include JPEG support')
+    variant('gif',       default=False, description='Include GIF support')
+    variant('sosi',      default=False, description='Include SOSI support')
+    variant('hdf4',      default=False, description='Include HDF4 support')
+    variant('hdf5',      default=False, description='Include HDF5 support')
+    variant('kea',       default=False, description='Include kealib')
+    variant('netcdf',    default=False, description='Include netCDF support')
+    variant('jasper',    default=False, description='Include JPEG-2000 support via JasPer library')
+    variant('openjpeg',  default=False, description='Include JPEG-2000 support via OpenJPEG 2.x library')
+    variant('xerces',    default=False, description='Use Xerces-C++ parser')
+    variant('expat',     default=False, description='Use Expat XML parser')
+    variant('odbc',      default=False, description='Include ODBC support')
+    variant('curl',      default=False, description='Include curl')
+    variant('xml2',      default=False, description='Include libxml2')
+    variant('sqlite3',   default=False, description='Use SQLite 3 library')
+    variant('pcre',      default=False, description='Include libpcre support')
+    variant('geos',      default=False, description='Include GEOS support')
+    variant('qhull',     default=False, description='Include QHull support')
+    variant('opencl',    default=False, description='Include OpenCL (GPU) support')
+    variant('poppler',   default=False, description='Include poppler (for PDF) support')
+    variant('proj',      default=True,  description='Compile with PROJ.x')
+    variant('perl',      default=False, description='Enable perl bindings')
+    variant('python',    default=False, description='Enable python bindings')
+    variant('java',      default=False, description='Include Java support')
+    variant('mdb',       default=False, description='Include MDB driver')
+    variant('armadillo', default=False, description='Include Armadillo support for faster TPS transform computation')
+    variant('cryptopp',  default=False, description='Include cryptopp support')
+    variant('crypto',    default=False, description='Include crypto (from openssl) support')
+
+    # FIXME: Allow packages to extend multiple packages
+    # See https://github.com/spack/spack/issues/987
+    # extends('perl', when='+perl')
+    extends('python', when='+python')
+
+    # GDAL depends on GNUmake on Unix platforms.
+    # https://trac.osgeo.org/gdal/wiki/BuildingOnUnix
+    depends_on('gmake', type='build')
+    depends_on('pkgconfig', type='build')
+
+    # Required dependencies
+    depends_on('libtiff@3.6.0:')  # 3.9.0+ needed to pass testsuite
+    depends_on('libgeotiff@1.2.1:')
+    depends_on('json-c', when='@2.3:')
+    depends_on('json-c@0.12.1', when='@:2.2.99')
+
+    # Optional dependencies
+    depends_on('libtool', type='build', when='+libtool')
+    depends_on('zlib', when='+libz')
+    depends_on('libiconv', when='+libiconv')
+    depends_on('xz', when='+liblzma')
+    depends_on('zstd', when='+zstd @2.3:')
+    depends_on('postgresql', when='+pg')
+    depends_on('cfitsio', when='+cfitsio')
+    depends_on('libpng', when='+png')
+    depends_on('jpeg', when='+jpeg')
+    depends_on('giflib', when='+gif')
+    depends_on('fyba', when='+sosi')
+    depends_on('hdf', when='+hdf4')
+    depends_on('hdf5', when='+hdf5')
+    depends_on('kealib', when='+kea @2:')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('jasper@1.900.1', patches='uuid.patch', when='+jasper')
+    depends_on('openjpeg', when='+openjpeg')
+    depends_on('xerces-c', when='+xerces')
+    depends_on('expat', when='+expat')
+    depends_on('unixodbc', when='+odbc')
+    depends_on('curl@7.10.8:', when='+curl')
+    depends_on('libxml2', when='+xml2')
+    depends_on('sqlite@3:', when='+sqlite3')
+    depends_on('pcre', when='+pcre')
+    depends_on('geos', when='+geos')
+    depends_on('qhull', when='+qhull @2.1:')
+    depends_on('opencl', when='+opencl')
+    depends_on('poppler', when='+poppler')
+    depends_on('poppler@:0.63', when='@:2.3.0 +poppler')
+    depends_on('proj', when='+proj @2.3:')
+    depends_on('perl', type=('build', 'run'), when='+perl')
+    depends_on('python', type=('build', 'link', 'run'), when='+python')
+    # swig/python/setup.py
+    depends_on('py-setuptools', type='build', when='+python')
+    depends_on('py-numpy@1.0.0:', type=('build', 'run'), when='+python')
+    depends_on('java', type=('build', 'link', 'run'), when='+java')
+    depends_on('jackcess@1.2.0:1.2.999', type='run', when='+mdb')
+    depends_on('armadillo', when='+armadillo')
+    depends_on('cryptopp', when='+cryptopp @2.1:')
+    depends_on('openssl', when='+crypto @2.3:')
+
+    # https://trac.osgeo.org/gdal/wiki/SupportedCompilers
+    msg = 'GDAL requires C++11 support'
+    conflicts('%gcc@:4.8.0', msg=msg)
+    conflicts('%clang@:3.2', msg=msg)
+    conflicts('%intel@:12',  msg=msg)
+    conflicts('%xl@:13.0',   msg=msg)
+    conflicts('%xl_r@:13.0', msg=msg)
+
+    conflicts('+mdb', when='~java', msg='MDB driver requires Java')
+
+    def setup_environment(self, spack_env, run_env):
+        # Needed to install Python bindings to GDAL installation
+        # prefix instead of Python installation prefix.
+        # See swig/python/GNUmakefile for more details.
+        spack_env.set('PREFIX', self.prefix)
+        spack_env.set('DESTDIR', '/')
+
+    # https://trac.osgeo.org/gdal/wiki/BuildHints
+    def configure_args(self):
+        spec = self.spec
+
+        # Required dependencies
+        args = [
+            # https://trac.osgeo.org/gdal/wiki/TIFF
+            '--with-libtiff={0}'.format(spec['libtiff'].prefix),
+            '--with-geotiff={0}'.format(spec['libgeotiff'].prefix),
+            '--with-libjson-c={0}'.format(spec['json-c'].prefix),
+        ]
+
+        if spec.satisfies('@2.3:'):
+            if '+zstd' in spec:
+                args.append('--with-zstd={0}'.format(spec['zstd'].prefix))
+            else:
+                args.append('--with-zstd=no')
+
+            if '+proj' in spec:
+                args.append('--with-proj={0}'.format(spec['proj'].prefix))
+                if spec.satisfies('^proj@5.0:5.999'):
+                    args.append('--with-proj5-api=yes')
+                else:
+                    args.append('--with-proj5-api=no')
+            else:
+                args.append('--with-proj=no')
+
+            if '+crypto' in spec:
+                args.append('--with-crypto={0}'.format(spec['openssl'].prefix))
+            else:
+                args.append('--with-crypto=no')
+
+        if spec.satisfies('@2.1:'):
+            if '+qhull' in spec:
+                args.append('--with-qhull=yes')
+            else:
+                args.append('--with-qhull=no')
+
+            if '+cryptopp' in spec:
+                args.append('--with-cryptopp={0}'.format(
+                    spec['cryptopp'].prefix))
+            else:
+                args.append('--with-cryptopp=no')
+
+        if spec.satisfies('@2:'):
+            if '+kea' in spec:
+                args.append('--with-kea={0}'.format(
+                    join_path(spec['kealib'].prefix.bin, 'kea-config')))
+            else:
+                args.append('--with-kea=no')
+
+        # Optional dependencies
+        if '+libtool' in spec:
+            args.append('--with-libtool=yes')
+        else:
+            args.append('--with-libtool=no')
+
+        if '+libz' in spec:
+            args.append('--with-libz={0}'.format(spec['zlib'].prefix))
+        else:
+            args.append('--with-libz=no')
+
+        if '+libiconv' in spec:
+            args.append('--with-libiconv-prefix={0}'.format(
+                spec['libiconv'].prefix))
+        else:
+            args.append('--with-libiconv-prefix=no')
+
+        if '+liblzma' in spec:
+            args.append('--with-liblzma=yes')
+        else:
+            args.append('--with-liblzma=no')
+
+        if '+pg' in spec:
+            args.append('--with-pg={0}'.format(
+                spec['postgresql'].prefix.bin.pg_config))
+        else:
+            args.append('--with-pg=no')
+
+        if '+cfitsio' in spec:
+            args.append('--with-cfitsio={0}'.format(spec['cfitsio'].prefix))
+        else:
+            args.append('--with-cfitsio=no')
+
+        if '+png' in spec:
+            args.append('--with-png={0}'.format(spec['libpng'].prefix))
+        else:
+            args.append('--with-png=no')
+
+        if '+jpeg' in spec:
+            args.append('--with-jpeg={0}'.format(spec['jpeg'].prefix))
+        else:
+            args.append('--with-jpeg=no')
+
+        if '+gif' in spec:
+            args.append('--with-gif={0}'.format(spec['giflib'].prefix))
+        else:
+            args.append('--with-gif=no')
+
+        # https://trac.osgeo.org/gdal/wiki/SOSI
+        if '+sosi' in spec:
+            args.append('--with-sosi={0}'.format(spec['fyba'].prefix))
+        else:
+            args.append('--with-sosi=no')
+
+        # https://trac.osgeo.org/gdal/wiki/HDF
+        if '+hdf4' in spec:
+            args.append('--with-hdf4={0}'.format(spec['hdf'].prefix))
+        else:
+            args.append('--with-hdf4=no')
 
-        if '+geos' in spec:
-            args.append('--with-geos=yes')
-        if '+hdf' in spec:
-            args.append('--with-hdf4=%s' % spec['hdf'].prefix)
         if '+hdf5' in spec:
-            args.append('--with-hdf5=%s' % spec['hdf5'].prefix)
-        if '+openjpeg' in spec:
-            args.append('--with-openjpeg=%s' % spec['openjpeg'].prefix)
-        if '+kea' in spec:
-            args.append('--with-kea=yes')
+            args.append('--with-hdf5={0}'.format(spec['hdf5'].prefix))
+        else:
+            args.append('--with-hdf5=no')
+
+        # https://trac.osgeo.org/gdal/wiki/NetCDF
         if '+netcdf' in spec:
-            args.append('--with-netcdf=%s' % spec['netcdf'].prefix)
+            args.append('--with-netcdf={0}'.format(spec['netcdf'].prefix))
+        else:
+            args.append('--with-netcdf=no')
+
+        # https://trac.osgeo.org/gdal/wiki/JasPer
+        if '+jasper' in spec:
+            args.append('--with-jasper={0}'.format(spec['jasper'].prefix))
+        else:
+            args.append('--with-jasper=no')
+
+        if '+openjpeg' in spec:
+            args.append('--with-openjpeg=yes')
+        else:
+            args.append('--with-openjpeg=no')
+
+        if '+xerces' in spec:
+            args.append('--with-xerces={0}'.format(spec['xerces-c'].prefix))
+        else:
+            args.append('--with-xerces=no')
+
+        if '+expat' in spec:
+            args.append('--with-expat={0}'.format(spec['expat'].prefix))
+        else:
+            args.append('--with-expat=no')
+
+        if '+odbc' in spec:
+            args.append('--with-odbc={0}'.format(spec['unixodbc'].prefix))
+        else:
+            args.append('--with-odbc=no')
+
+        # https://trac.osgeo.org/gdal/wiki/LibCurl
+        if '+curl' in spec:
+            args.append('--with-curl={0}'.format(
+                join_path(spec['curl'].prefix.bin, 'curl-config')))
+        else:
+            args.append('--with-curl=no')
+
+        if '+xml2' in spec:
+            args.append('--with-xml2={0}'.format(
+                join_path(spec['libxml2'].prefix.bin, 'xml2-config')))
+        else:
+            args.append('--with-xml2=no')
+
+        # https://trac.osgeo.org/gdal/wiki/SQLite
+        if '+sqlite3' in spec:
+            args.append('--with-sqlite3={0}'.format(spec['sqlite'].prefix))
+        else:
+            args.append('--with-sqlite3=no')
+
+        if '+pcre' in spec:
+            args.append('--with-pcre={0}'.format(spec['pcre'].prefix))
+        else:
+            args.append('--with-pcre=no')
+
+        if '+geos' in spec:
+            args.append('--with-geos={0}'.format(
+                join_path(spec['geos'].prefix.bin, 'geos-config')))
+        else:
+            args.append('--with-geos=no')
+
+        if '+opencl' in spec:
+            args.append('--with-opencl={0}'.format(spec['opencl'].prefix))
+        else:
+            args.append('--with-opencl=no')
+
+        if '+poppler' in spec:
+            args.append('--with-poppler={0}'.format(spec['poppler'].prefix))
+        else:
+            args.append('--with-poppler=no')
+
+        if '+perl' in spec:
+            args.append('--with-perl=yes')
+        else:
+            args.append('--with-perl=no')
+
+        if '+python' in spec:
+            args.append('--with-python={0}'.format(
+                spec['python'].command.path))
+        else:
+            args.append('--with-python=no')
+
+        # https://trac.osgeo.org/gdal/wiki/GdalOgrInJava
+        if '+java' in spec:
+            args.extend([
+                '--with-java={0}'.format(spec['java'].home),
+                '--with-jvm-lib={0}'.format(
+                    spec['java'].libs.directories[0]),
+                '--with-jvm-lib-add-rpath'
+            ])
+        else:
+            args.append('--with-java=no')
+
+        # https://trac.osgeo.org/gdal/wiki/mdbtools
+        # http://www.gdal.org/drv_mdb.html
+        if '+mdb' in spec:
+            args.append('--with-mdb=yes')
+        else:
+            args.append('--with-mdb=no')
+
+        if '+armadillo' in spec:
+            args.append('--with-armadillo={0}'.format(
+                spec['armadillo'].prefix))
+        else:
+            args.append('--with-armadillo=no')
+
+        # TODO: add packages for these dependencies
+        args.extend([
+            # https://trac.osgeo.org/gdal/wiki/GRASS
+            '--with-grass=no',
+            '--with-libgrass=no',
+            '--with-pcraster=no',
+            '--with-dds=no',
+            '--with-gta=no',
+            '--with-pcidsk=no',
+            '--with-ogdi=no',
+            '--with-fme=no',
+            # https://trac.osgeo.org/gdal/wiki/FileGDB
+            '--with-fgdb=no',
+            # https://trac.osgeo.org/gdal/wiki/ECW
+            '--with-ecw=no',
+            # https://trac.osgeo.org/gdal/wiki/JP2KAK
+            '--with-kakadu=no',
+            # https://trac.osgeo.org/gdal/wiki/MrSID
+            '--with-mrsid=no',
+            '--with-jp2mrsid=no',
+            '--with-mrsid_lidar=no',
+            # https://trac.osgeo.org/gdal/wiki/MSG
+            '--with-msg=no',
+            '--with-bsb=no',
+            # https://trac.osgeo.org/gdal/wiki/Oracle
+            '--with-oci=no',
+            '--with-grib=no',
+            '--with-mysql=no',
+            # https://trac.osgeo.org/gdal/wiki/Ingres
+            '--with-ingres=no',
+            # https://trac.osgeo.org/gdal/wiki/LibKML
+            '--with-libkml=no',
+            '--with-dods-root=no',
+            '--with-spatialite=no',
+            '--with-idb=no',
+            # https://trac.osgeo.org/gdal/wiki/ArcSDE
+            '--with-sde=no',
+            # https://trac.osgeo.org/gdal/wiki/Epsilon
+            '--with-epsilon=no',
+            '--with-webp=no',
+            '--with-freexl=no',
+            '--with-pam=no',
+            '--with-podofo=no',
+            '--with-php=no',
+            '--with-rasdaman=no',
+        ])
+
+        # TODO: add packages for these dependencies (only for 2.3 and newer)
+        if spec.satisfies('@2.3:'):
+            args.extend([
+                '--with-jp2lura=no',
+                '--with-rasterlite2=no',
+                # https://trac.osgeo.org/gdal/wiki/DxfDwg
+                '--with-teigha=no',
+                '--with-sfcgal=no',
+                '--with-mrf=no',
+            ])
+
+        # TODO: add packages for these dependencies (only for 2.1 and newer)
+        if spec.satisfies('@2.1:'):
+            args.extend([
+                '--with-mongocxx=no',
+                '--with-gnm=no',
+                '--with-pdfium=no',
+            ])
+
+        return args
 
-        configure(*args)
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def import_module_test(self):
+        if '+python' in self.spec:
+            with working_dir('spack-test', create=True):
+                for module in self.import_modules:
+                    python('-c', 'import {0}'.format(module))
 
-        make()
-        make("install")
+    @run_after('install')
+    def darwin_fix(self):
+        # The shared library is not installed correctly on Darwin; fix this
+        if sys.platform == 'darwin':
+            fix_darwin_install_name(self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/gdal/uuid.patch b/var/spack/repos/builtin/packages/gdal/uuid.patch
new file mode 100644
index 0000000000..3990dad0cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gdal/uuid.patch
@@ -0,0 +1,234 @@
+diff -Naur jasper-1.900.1/src/libjasper/jp2/jp2_cod.c jasper-1.900.1.uuid/src/libjasper/jp2/jp2_cod.c
+--- jasper-1.900.1/src/libjasper/jp2/jp2_cod.c	2007-01-19 15:43:05.000000000 -0600
++++ jasper-1.900.1.uuid/src/libjasper/jp2/jp2_cod.c	2007-03-06 07:49:58.000000000 -0600
+@@ -5,6 +5,11 @@
+  * All rights reserved.
+  */
+ 
++/*
++ * Modified by Andrey Kiselev <dron@ak4719.spb.edu> to properly handle UUID
++ * box.
++ */
++
+ /* __START_OF_JASPER_LICENSE__
+  * 
+  * JasPer License Version 2.0
+@@ -127,6 +132,9 @@
+ static int jp2_pclr_getdata(jp2_box_t *box, jas_stream_t *in);
+ static int jp2_pclr_putdata(jp2_box_t *box, jas_stream_t *out);
+ static void jp2_pclr_dumpdata(jp2_box_t *box, FILE *out);
++static void jp2_uuid_destroy(jp2_box_t *box);
++static int jp2_uuid_getdata(jp2_box_t *box, jas_stream_t *in);
++static int jp2_uuid_putdata(jp2_box_t *box, jas_stream_t *out);
+ 
+ /******************************************************************************\
+ * Local data.
+@@ -164,7 +172,7 @@
+ 	{JP2_BOX_XML, "XML", 0,
+ 	  {0, 0, 0, 0, 0}},
+ 	{JP2_BOX_UUID, "UUID", 0,
+-	  {0, 0, 0, 0, 0}},
++	  {0, jp2_uuid_destroy, jp2_uuid_getdata, jp2_uuid_putdata, 0}},
+ 	{JP2_BOX_UINF, "UINF", JP2_BOX_SUPER,
+ 	  {0, 0, 0, 0, 0}},
+ 	{JP2_BOX_ULST, "ULST", 0,
+@@ -271,7 +279,7 @@
+ 	} else {
+ 		box->datalen = box->len - JP2_BOX_HDRLEN(false);
+ 	}
+-	if (box->len != 0 && box->len < 8) {
++	if (box->len != 0 && box->len < JP2_BOX_HDRLEN(false)) {
+ 		goto error;
+ 	}
+ 
+@@ -876,6 +884,56 @@
+ 	}
+ }
+ 
++static void jp2_uuid_destroy(jp2_box_t *box)
++{
++	jp2_uuid_t *uuid = &box->data.uuid;
++	if (uuid->data)
++	{
++	    jas_free(uuid->data);
++	    uuid->data = NULL;
++	}
++}
++
++static int jp2_uuid_getdata(jp2_box_t *box, jas_stream_t *in)
++{
++	jp2_uuid_t *uuid = &box->data.uuid;
++	int i;
++	
++	for (i = 0; i < 16; i++)
++	{
++	    if (jp2_getuint8(in, &uuid->uuid[i]))
++		return -1;
++	}
++	
++	uuid->datalen = box->datalen - 16;
++	uuid->data = jas_malloc(uuid->datalen * sizeof(uint_fast8_t));
++	for (i = 0; i < uuid->datalen; i++)
++	{
++	    if (jp2_getuint8(in, &uuid->data[i]))
++		return -1;
++	}
++	return 0;
++}
++
++static int jp2_uuid_putdata(jp2_box_t *box, jas_stream_t *out)
++{
++	jp2_uuid_t *uuid = &box->data.uuid;
++	int i;
++	
++	for (i = 0; i < 16; i++)
++	{
++	    if (jp2_putuint8(out, uuid->uuid[i]))
++		return -1;
++	}
++	
++	for (i = 0; i < uuid->datalen; i++)
++	{
++	    if (jp2_putuint8(out, uuid->data[i]))
++		return -1;
++	}
++	return 0;
++}
++
+ static int jp2_getint(jas_stream_t *in, int s, int n, int_fast32_t *val)
+ {
+ 	int c;
+diff -Naur jasper-1.900.1/src/libjasper/jp2/jp2_cod.h jasper-1.900.1.uuid/src/libjasper/jp2/jp2_cod.h
+--- jasper-1.900.1/src/libjasper/jp2/jp2_cod.h	2007-01-19 15:43:05.000000000 -0600
++++ jasper-1.900.1.uuid/src/libjasper/jp2/jp2_cod.h	2007-03-06 07:49:58.000000000 -0600
+@@ -5,6 +5,11 @@
+  * All rights reserved.
+  */
+ 
++/*
++ * Modified by Andrey Kiselev <dron@ak4719.spb.edu> to properly handle UUID
++ * box.
++ */
++
+ /* __START_OF_JASPER_LICENSE__
+  * 
+  * JasPer License Version 2.0
+@@ -229,6 +234,12 @@
+ 	jp2_cmapent_t *ents;
+ } jp2_cmap_t;
+ 
++typedef struct {
++	uint_fast32_t datalen;
++	uint_fast8_t uuid[16];
++	uint_fast8_t *data;
++} jp2_uuid_t;
++
+ #define	JP2_CMAP_DIRECT		0
+ #define	JP2_CMAP_PALETTE	1
+ 
+@@ -257,6 +268,7 @@
+ 		jp2_pclr_t pclr;
+ 		jp2_cdef_t cdef;
+ 		jp2_cmap_t cmap;
++		jp2_uuid_t uuid;
+ 	} data;
+ 
+ } jp2_box_t;
+diff -Naur jasper-1.900.1/src/libjasper/jp2/jp2_enc.c jasper-1.900.1.uuid/src/libjasper/jp2/jp2_enc.c
+--- jasper-1.900.1/src/libjasper/jp2/jp2_enc.c	2007-01-19 15:43:05.000000000 -0600
++++ jasper-1.900.1.uuid/src/libjasper/jp2/jp2_enc.c	2007-03-06 07:49:58.000000000 -0600
+@@ -5,6 +5,11 @@
+  * All rights reserved.
+  */
+ 
++/*
++ * Modified by Andrey Kiselev <dron@ak4719.spb.edu> to properly handle UUID
++ * box.
++ */
++
+ /* __START_OF_JASPER_LICENSE__
+  * 
+  * JasPer License Version 2.0
+@@ -86,7 +91,7 @@
+ * Functions.
+ \******************************************************************************/
+ 
+-int jp2_encode(jas_image_t *image, jas_stream_t *out, char *optstr)
++int jp2_write_header(jas_image_t *image, jas_stream_t *out)
+ {
+ 	jp2_box_t *box;
+ 	jp2_ftyp_t *ftyp;
+@@ -97,8 +102,6 @@
+ 	long len;
+ 	uint_fast16_t cmptno;
+ 	jp2_colr_t *colr;
+-	char buf[4096];
+-	uint_fast32_t overhead;
+ 	jp2_cdefchan_t *cdefchanent;
+ 	jp2_cdef_t *cdef;
+ 	int i;
+@@ -326,6 +329,26 @@
+ 	jas_stream_close(tmpstream);
+ 	tmpstream = 0;
+ 
++	return 0;
++	abort();
++
++error:
++
++	if (box) {
++		jp2_box_destroy(box);
++	}
++	if (tmpstream) {
++		jas_stream_close(tmpstream);
++	}
++	return -1;
++}
++
++int jp2_write_codestream(jas_image_t *image, jas_stream_t *out, char *optstr)
++{
++	jp2_box_t *box;
++	char buf[4096];
++	uint_fast32_t overhead;
++
+ 	/*
+ 	 * Output the contiguous code stream box.
+ 	 */
+@@ -358,12 +381,34 @@
+ 	if (box) {
+ 		jp2_box_destroy(box);
+ 	}
+-	if (tmpstream) {
+-		jas_stream_close(tmpstream);
+-	}
+ 	return -1;
+ }
+ 
++int jp2_encode(jas_image_t *image, jas_stream_t *out, char *optstr)
++{
++	if (jp2_write_header(image, out) < 0)
++		return -1;
++	if (jp2_write_codestream(image, out, optstr) < 0)
++		return -1;
++
++	return 0;
++}
++
++int jp2_encode_uuid(jas_image_t *image, jas_stream_t *out,
++		    char *optstr, jp2_box_t *uuid)
++{
++	if (jp2_write_header(image, out) < 0)
++		return -1;
++	if (uuid) {
++		if (jp2_box_put(uuid, out))
++			return -1;
++	}
++	if (jp2_write_codestream(image, out, optstr) < 0)
++		return -1;
++
++	return 0;
++}
++
+ static uint_fast32_t jp2_gettypeasoc(int colorspace, int ctype)
+ {
+ 	int type;
diff --git a/var/spack/repos/builtin/packages/gdb/package.py b/var/spack/repos/builtin/packages/gdb/package.py
index dedefe5191..5d6b265961 100644
--- a/var/spack/repos/builtin/packages/gdb/package.py
+++ b/var/spack/repos/builtin/packages/gdb/package.py
@@ -1,39 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Gdb(Package):
+class Gdb(AutotoolsPackage):
     """GDB, the GNU Project debugger, allows you to see what is going on
     'inside' another program while it executes -- or what another
     program was doing at the moment it crashed.
     """
 
     homepage = "https://www.gnu.org/software/gdb"
-    url = "http://ftp.gnu.org/gnu/gdb/gdb-7.10.tar.gz"
+    url      = "https://ftpmirror.gnu.org/gdb/gdb-7.10.tar.gz"
 
+    version('8.2', '0783c6d86775c5aff06cccc8a3d7cad8')
+    version('8.1', '0c85ecbb43569ec43b1c9230622e84ab')
+    version('8.0.1', 'bb45869f8126a84ea2ba13a8c0e7c90e')
+    version('8.0', '9bb49d134916e73b2c01d01bf20363df')
     version('7.12.1', '06c8f40521ed65fe36ebc2be29b56942')
     version('7.11', 'f585059252836a981ea5db9a5f8ce97f')
     version('7.10.1', 'b93a2721393e5fa226375b42d567d90b')
@@ -43,17 +28,19 @@ class Gdb(Package):
     version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc')
 
     variant('python', default=True, description='Compile with Python support')
+    variant('xz', default=True, description='Compile with lzma support')
 
     # Required dependency
     depends_on('texinfo', type='build')
 
-    # Optional dependency
+    # Optional dependencies
     depends_on('python', when='+python')
-
-    def install(self, spec, prefix):
-        options = ['--prefix=%s' % prefix]
-        if '+python' in spec:
-            options.extend(['--with-python'])
-        configure(*options)
-        make()
-        make("install")
+    depends_on('xz', when='+xz')
+
+    def configure_args(self):
+        args = []
+        if '+python' in self.spec:
+            args.append('--with-python')
+            args.append('LDFLAGS={0}'.format(
+                self.spec['python'].libs.ld_flags))
+        return args
diff --git a/var/spack/repos/builtin/packages/gdbm/package.py b/var/spack/repos/builtin/packages/gdbm/package.py
index 1e4a4831b7..d041c283bf 100644
--- a/var/spack/repos/builtin/packages/gdbm/package.py
+++ b/var/spack/repos/builtin/packages/gdbm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
@@ -33,8 +14,9 @@ class Gdbm(AutotoolsPackage):
     manipulate a hashed database."""
 
     homepage = "http://www.gnu.org.ua/software/gdbm/gdbm.html"
-    url      = "http://ftp.gnu.org/gnu/gdbm/gdbm-1.13.tar.gz"
+    url      = "https://ftpmirror.gnu.org/gdbm/gdbm-1.13.tar.gz"
 
+    version('1.14.1', 'c2ddcb3897efa0f57484af2bd4f4f848')
     version('1.13',  '8929dcda2a8de3fd2367bdbf66769376')
     version('1.12',  '9ce96ff4c99e74295ea19040931c8fb9')
     version('1.11',  '72c832680cf0999caedbe5b265c8c1bd')
@@ -45,9 +27,12 @@ class Gdbm(AutotoolsPackage):
     depends_on("readline")
 
     def configure_args(self):
-        config_args = [
-            '--enable-libgdbm-compat',
-            'CC=%s' % spack_cc
-        ]
 
-        return config_args
+        # GDBM uses some non-standard GNU extensions,
+        # enabled with -D_GNU_SOURCE.  See:
+        #   https://patchwork.ozlabs.org/patch/771300/
+        #   https://stackoverflow.com/questions/5582211
+        #   https://www.gnu.org/software/automake/manual/html_node/Flag-Variables-Ordering.html
+        return [
+            '--enable-libgdbm-compat',
+            'CPPFLAGS=-D_GNU_SOURCE']
diff --git a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
index 63d24d64c4..9aaa91b2dd 100644
--- a/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
+++ b/var/spack/repos/builtin/packages/gdk-pixbuf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class GdkPixbuf(AutotoolsPackage):
 
     version('2.31.2', '6be6bbc4f356d4b79ab4226860ab8523')
 
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
     depends_on("gettext")
     depends_on("glib")
     depends_on("jpeg")
diff --git a/var/spack/repos/builtin/packages/gdl/package.py b/var/spack/repos/builtin/packages/gdl/package.py
new file mode 100644
index 0000000000..ac49f17236
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gdl/package.py
@@ -0,0 +1,110 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gdl(CMakePackage):
+    """A free and open-source IDL/PV-WAVE compiler.
+
+    GNU Data Language (GDL) is a free/libre/open source incremental compiler
+    compatible with IDL and to some extent with PV-WAVE.
+    """
+
+    homepage = "https://github.com/gnudatalanguage/gdl"
+    url      = "https://github.com/gnudatalanguage/gdl/archive/v0.9.8.tar.gz"
+
+    version('0.9.8', '447b0362e1df5ea8af814a969e89d3ec')
+
+    variant(
+            'graphicsmagick',
+            default=False,
+            description='Enable GraphicsMagick'
+           )
+    variant('hdf4', default=False, description='Enable HDF4')
+    variant('hdf5', default=True, description='Enable HDF5')
+    variant('openmp', default=True, description='Enable OpenMP')
+    variant('proj', default=True, description='Enable LIBPROJ4')
+    variant('python', default=False, description='Enable Python')
+    variant('wx', default=False, description='Enable WxWidgets')
+    variant('x11', default=False, description='Enable X11')
+
+    extends('python', when='+python')
+
+    depends_on('graphicsmagick', when='+graphicsmagick')
+    depends_on('hdf', when='+hdf4')
+    depends_on('hdf5', when='+hdf5')
+    depends_on('libx11', when='+x11')
+    depends_on('plplot+wx', when='+wx@:5.11')
+    depends_on('plplot+wx+wxold', when='+wx@5.12:')
+    depends_on('plplot~wx', when='~wx')
+    depends_on('proj', when='+proj')
+    depends_on('py-numpy', type=('build', 'run'), when='+python')
+    depends_on('python@2.7:2.8', type=('build', 'run'), when='+python')
+    depends_on('wx', when='+wx')
+
+    depends_on('eigen')
+    depends_on('fftw')
+    depends_on('gsl')
+    depends_on('jpeg')
+    depends_on('libice')
+    depends_on('libsm')
+    depends_on('libxinerama')
+    depends_on('libxxf86vm')
+    depends_on('netcdf')
+    depends_on('pslib')
+    depends_on('readline')
+
+    def cmake_args(self):
+        args = []
+
+        # GraphicsMagick covers the same features as ImageMagick and
+        # only version 6 of ImageMagick is supported (version 7 is packaged)
+        args += ['-DMAGICK=OFF']
+
+        if '+graphicsmagick' in self.spec:
+            args += ['-DGRAPHICSMAGICK=ON']
+        else:
+            args += ['-DGRAPHICSMAGICK=OFF']
+
+        if '+hdf4' in self.spec:
+            args += ['-DHDF=ON']
+        else:
+            args += ['-DHDF=OFF']
+
+        if '+hdf5' in self.spec:
+            args += ['-DHDF5=ON']
+        else:
+            args += ['-DHDF5=OFF']
+
+        if '+openmp' in self.spec:
+            args += ['-DOPENMP=ON']
+        else:
+            args += ['-DOPENMP=OFF']
+
+        if '+proj' in self.spec:
+            args += [
+                '-DLIBPROJ4=ON',
+                '-DLIBPROJ4DIR={0}'.format(self.spec['proj'].prefix)
+            ]
+        else:
+            args += ['-DLIBPROJ4=OFF']
+
+        if '+python' in self.spec:
+            args += ['-DPYTHON=ON']
+        else:
+            args += ['-DPYTHON=OFF']
+
+        if '+wx' in self.spec:
+            args += ['-DWXWIDGETS=ON']
+        else:
+            args += ['-DWXWIDGETS=OFF']
+
+        if '+x11' in self.spec:
+            args += ['-DX11=ON']
+        else:
+            args += ['-DX11=OFF']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/geant4/package.py b/var/spack/repos/builtin/packages/geant4/package.py
index 2b935673c4..0685de3cd9 100644
--- a/var/spack/repos/builtin/packages/geant4/package.py
+++ b/var/spack/repos/builtin/packages/geant4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import platform
@@ -36,22 +17,50 @@ class Geant4(CMakePackage):
     homepage = "http://geant4.cern.ch/"
     url = "http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz"
 
+    version('10.04', 'b84beeb756821d0c61f7c6c93a2b83de')
+    version('10.03.p03', 'ccae9fd18e3908be78784dc207f2d73b')
+    version('10.02.p03', '2b887e66f0d41174016160707662a77b')
     version('10.02.p02', '6aae1d0fc743b0edc358c5c8fbe48657')
     version('10.02.p01', 'b81f7082a15f6a34b720b6f15c6289cfe4ddbbbdcef0dc52719f71fac95f7f1c')
     version('10.01.p03', '4fb4175cc0dabcd517443fbdccd97439')
 
-    variant('qt', default=True, description='Enable Qt support')
+    variant('qt', default=False, description='Enable Qt support')
+    variant('vecgeom', default=False, description='Enable vecgeom support')
+    variant('cxx11', default=True, description='Enable CXX11 support')
+    variant('cxx14', default=False, description='Enable CXX14 support')
+    variant('opengl', default=False, description='Optional OpenGL support')
+    variant('x11', default=False, description='Optional X11 support')
+    variant('motif', default=False, description='Optional motif support')
+    variant('threads', default=True, description='Build with multithreading')
 
     depends_on('cmake@3.5:', type='build')
 
-    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p02")
-    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p01")
-    depends_on("clhep@2.2.0.4~cxx11+cxx14", when="@10.01.p03")
+    conflicts('+cxx14', when='+cxx11')
+    conflicts('+cxx11', when='+cxx14')
+
+    # C++11 support
+    depends_on("clhep@2.4.0.0+cxx11~cxx14", when="@10.04+cxx11~cxx14")
+    depends_on("clhep@2.3.4.3+cxx11~cxx14", when="@10.03.p03+cxx11~cxx14")
+    depends_on("clhep@2.3.1.1+cxx11~cxx14", when="@10.02.p01+cxx11~cxx14")
+    depends_on("clhep@2.3.1.1+cxx11~cxx14", when="@10.02.p01+cxx11~cxx14")
+    depends_on("clhep@2.2.0.4+cxx11~cxx14", when="@10.01.p03+cxx11~cxx14")
+
+    # C++14 support
+    depends_on("clhep@2.4.0.0+cxx11~cxx14", when="@10.04~cxx11+cxx14")
+    depends_on("clhep@2.3.4.3+cxx11~cxx14", when="@10.03.p03~cxx11+cxx14")
+    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p02~cxx11+cxx14")
+    depends_on("clhep@2.3.1.1~cxx11+cxx14", when="@10.02.p01~cxx11+cxx14")
+    depends_on("clhep@2.2.0.4~cxx11+cxx14", when="@10.01.p03~cxx11+cxx14")
+
     depends_on("expat")
     depends_on("zlib")
-    depends_on("vecgeom")
     depends_on("xerces-c")
-    depends_on("qt@4.8:", when="+qt")
+    depends_on("mesa", when='+opengl')
+    depends_on("libx11", when='+x11')
+    depends_on("libxmu", when='+x11')
+    depends_on("motif", when='+motif')
+    depends_on("vecgeom", when="+vecgeom")
+    depends_on("qt@4.8:4.999", when="+qt")
 
     def cmake_args(self):
         spec = self.spec
@@ -62,32 +71,38 @@ class Geant4(CMakePackage):
             '-DGEANT4_USE_G3TOG4=ON',
             '-DGEANT4_INSTALL_DATA=ON',
             '-DGEANT4_BUILD_TLS_MODEL=global-dynamic',
-            '-DGEANT4_BUILD_MULTITHREADED=ON',
-            '-DGEANT4_USE_USOLIDS=ON',
             '-DGEANT4_USE_SYSTEM_EXPAT=ON',
             '-DGEANT4_USE_SYSTEM_ZLIB=ON',
             '-DXERCESC_ROOT_DIR:STRING=%s' %
-            spec['xerces-c'].prefix,
-            '-DUSolids_DIR=%s' %
-            join_path(spec['vecgeom'].prefix, 'lib/CMake/USolids')]
+            spec['xerces-c'].prefix, ]
 
         arch = platform.system().lower()
         if arch is not 'darwin':
-            options.append('-DGEANT4_USE_OPENGL_X11=ON')
-            options.append('-DGEANT4_USE_XM=ON')
-            options.append('-DGEANT4_USE_RAYTRACER_X11=ON')
+            if "+x11" in spec and "+opengl" in spec:
+                options.append('-DGEANT4_USE_OPENGL_X11=ON')
+            if "+motif" in spec and "+opengl" in spec:
+                options.append('-DGEANT4_USE_XM=ON')
+            if "+x11" in spec:
+                options.append('-DGEANT4_USE_RAYTRACER_X11=ON')
 
         if '+cxx11' in spec:
             options.append('-DGEANT4_BUILD_CXXSTD=c++11')
-        if '+cxx14' or '+cxx1y' in spec:
+        if '+cxx14' in spec:
             options.append('-DGEANT4_BUILD_CXXSTD=c++14')
 
         if '+qt' in spec:
             options.append('-DGEANT4_USE_QT=ON')
             options.append(
                 '-DQT_QMAKE_EXECUTABLE=%s' %
-                spec['qt'].prefix + '/bin/qmake'
-            )
+                spec['qt'].prefix.bin.qmake)
+
+        if '+vecgeom' in spec:
+            options.append('-DGEANT4_USE_USOLIDS=ON')
+            options.append('-DUSolids_DIR=%s' % spec[
+                'vecgeom'].prefix.lib.CMake.USolids)
+
+        on_or_off = lambda opt: 'ON' if '+' + opt in spec else 'OFF'
+        options.append('-DGEANT4_BUILD_MULTITHREADED=' + on_or_off('threads'))
 
         return options
 
diff --git a/var/spack/repos/builtin/packages/gearshifft/package.py b/var/spack/repos/builtin/packages/gearshifft/package.py
index 8b6f5c8a31..7b71f2e2ee 100644
--- a/var/spack/repos/builtin/packages/gearshifft/package.py
+++ b/var/spack/repos/builtin/packages/gearshifft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,14 +10,16 @@ class Gearshifft(CMakePackage):
     """Benchmark Suite for Heterogenuous FFT Implementations"""
 
     homepage = "https://github.com/mpicbg-scicomp/gearshifft"
-    url      = "https://github.com/mpicbg-scicomp/gearshifft/archive/v0.2.0.tar.gz"
+    url      = "https://github.com/mpicbg-scicomp/gearshifft/archive/v0.2.1-lw.tar.gz"
+
+    maintainers = ['ax3l']
 
     version('0.2.1-lw', 'c3208b767b24255b488a83e5d9e517ea')
 
     variant('cufft', default=True,
             description='Compile gearshifft_cufft')
-    # variant('clfft', default=True,
-    #         description='Compile gearshifft_clfft')
+    variant('clfft', default=True,
+            description='Compile gearshifft_clfft')
     variant('fftw', default=True,
             description='Compile gearshifft_fftw')
     variant('openmp', default=True,
@@ -48,8 +31,8 @@ class Gearshifft(CMakePackage):
     depends_on('cmake@2.8.0:', type='build')
     depends_on('boost@1.56.0:')
     depends_on('cuda@8.0:', when='+cufft')
-    # depends_on('opencl@1.2:', when='+clfft')
-    # depends_on('clfft@2.12.0:', when='+clfft')
+    depends_on('opencl@1.2:', when='+clfft')
+    depends_on('clfft@2.12.0:', when='+clfft')
     depends_on('fftw@3.3.4:~mpi~openmp', when='+fftw~openmp')
     depends_on('fftw@3.3.4:~mpi+openmp', when='+fftw+openmp')
 
@@ -62,13 +45,13 @@ class Gearshifft(CMakePackage):
             '-DGEARSHIFFT_CLFFT:BOOL=OFF'
         ]
         args.extend([
-            '-DGEARSHIFFT_FFTW:BOOL={0}'.format((
-                'ON' if '+fftw' in spec else 'OFF')),
-            '-DGEARSHIFFT_FFTW_OPENMP:BOOL={0}'.format((
-                'ON' if '+openmp' in spec else 'OFF')),
-            '-DGEARSHIFFT_CUFFT:BOOL={0}'.format((
-                'ON' if '+cufft' in spec else 'OFF'))
-            # '-DGEARSHIFFT_CLFFT:BOOL={0}'.format((
-            #     'ON' if '+clfft' in spec else 'OFF'))
+            '-DGEARSHIFFT_FFTW:BOOL={0}'.format(
+                'ON' if '+fftw' in spec else 'OFF'),
+            '-DGEARSHIFFT_FFTW_OPENMP:BOOL={0}'.format(
+                'ON' if '+openmp' in spec else 'OFF'),
+            '-DGEARSHIFFT_CUFFT:BOOL={0}'.format(
+                'ON' if '+cufft' in spec else 'OFF'),
+            '-DGEARSHIFFT_CLFFT:BOOL={0}'.format(
+                'ON' if '+clfft' in spec else 'OFF')
         ])
         return args
diff --git a/var/spack/repos/builtin/packages/gemmlowp/package.py b/var/spack/repos/builtin/packages/gemmlowp/package.py
index 7cd3047716..d293a9b254 100644
--- a/var/spack/repos/builtin/packages/gemmlowp/package.py
+++ b/var/spack/repos/builtin/packages/gemmlowp/package.py
@@ -1,27 +1,8 @@
-#############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,9 @@ class Gemmlowp(Package):
     """Google low-precision matrix multiplication library"""
 
     homepage = "https://github.com/google/gemmlowp"
-    version('a6f29d9ac', git='https://github.com/google/gemmlowp.git',
-            commit='a6f29d8ac48d63293f845f2253eccbf86bc28321')
+    git      = "https://github.com/google/gemmlowp.git"
+
+    version('a6f29d9ac', commit='a6f29d8ac48d63293f845f2253eccbf86bc28321')
 
     def install(self, spec, prefix):
         header_directories = ('eight_bit_int_gemm', 'fixedpoint',
diff --git a/var/spack/repos/builtin/packages/genemark-et/package.py b/var/spack/repos/builtin/packages/genemark-et/package.py
index faf5acce6a..d38a84522a 100644
--- a/var/spack/repos/builtin/packages/genemark-et/package.py
+++ b/var/spack/repos/builtin/packages/genemark-et/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import glob
diff --git a/var/spack/repos/builtin/packages/genomefinisher/genomefinisher.sh b/var/spack/repos/builtin/packages/genomefinisher/genomefinisher.sh
new file mode 100644
index 0000000000..b44c048751
--- /dev/null
+++ b/var/spack/repos/builtin/packages/genomefinisher/genomefinisher.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the GenomeFinisher jar file
+java $JAVA_ARGS $JAVA_OPTS -jar GenomeFinisher.jar "$@"
diff --git a/var/spack/repos/builtin/packages/genomefinisher/package.py b/var/spack/repos/builtin/packages/genomefinisher/package.py
new file mode 100644
index 0000000000..d9030c2a19
--- /dev/null
+++ b/var/spack/repos/builtin/packages/genomefinisher/package.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Genomefinisher(Package):
+    """GFinisher is an application tools for refinement and finalization of
+    prokaryotic genomes assemblies using the bias of GC Skew to identify
+    assembly errors and organizes the contigs/scaffolds with genomes
+    references."""
+
+    homepage = "http://gfinisher.sourceforge.net"
+    url      = "https://sourceforge.net/projects/gfinisher/files/GenomeFinisher_1.4.zip"
+
+    version('1.4', 'bd9bbca656fe15ecbe615c4732714bc7')
+
+    depends_on('java@8:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'GenomeFinisher.jar'
+        install(jar_file, prefix.bin)
+        install_tree('lib', prefix.lib)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "genomefinisher.sh")
+        script = prefix.bin.genomefinisher
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the jar file
+        # jar file.
+        java = spec['jdk'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file(jar_file, join_path(prefix.bin, jar_file),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/genometools/package.py b/var/spack/repos/builtin/packages/genometools/package.py
index 00f359e6d2..5d88fa0416 100644
--- a/var/spack/repos/builtin/packages/genometools/package.py
+++ b/var/spack/repos/builtin/packages/genometools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-#############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,3 +24,6 @@ class Genometools(MakefilePackage):
 
     def install(self, spec, prefix):
         make('install', 'prefix=%s' % prefix)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('CPATH', self.prefix.include.genometools)
diff --git a/var/spack/repos/builtin/packages/geopm/package.py b/var/spack/repos/builtin/packages/geopm/package.py
new file mode 100644
index 0000000000..37047ab1b0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/geopm/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Geopm(AutotoolsPackage):
+    """GEOPM is an extensible power management framework targeting HPC.
+    The GEOPM package provides libgeopm, libgeopmpolicy and applications
+    geopmctl and geopmpolicy, as well as tools for postprocessing.
+    GEOPM is designed to be extended for new control algorithms and new
+    hardware power management features via its plugin infrastructure.
+
+    Note: GEOPM interfaces with hardware using Model Specific Registers (MSRs).
+    For propper usage make sure MSRs are made available directly or via the
+    msr-safe kernel module by your administrator."""
+
+    homepage = "https://geopm.github.io"
+    url      = "https://github.com/geopm/geopm/releases/download/v0.4.0/geopm-0.4.0.tar.gz"
+    git      = "https://github.com/geopm/geopm.git"
+
+    # Add additional proper versions and checksums here. "spack checksum geopm"
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('0.5.0', '61b454bc74d4606fe84818aef16c1be4')
+    version('0.4.0', 'd4cc8fffe521296dab379857d7e2064d')
+    version('0.3.0', '568fd37234396fff134f8d57b60f2b83')
+
+    # Variants reflecting most ./configure --help options
+    variant('debug', default=False, description='Enable debug.')
+    variant('coverage', default=False, description='Enable test coverage support, enables debug by default.')
+    variant('overhead', default=False, description='Enable GEOPM to calculate and display time spent in GEOPM API calls.')
+    variant('procfs', default=True, description='Enable procfs (disable for OSes not using procfs).')
+    variant('mpi', default=True, description='Enable MPI dependent components.')
+    variant('fortran', default=True, description='Build fortran interface.')
+    variant('doc', default=True, description='Create man pages with ruby-ronn.')
+    variant('openmp', default=True, description='Build with OpenMP.')
+    variant('ompt', default=False, description='Use OpenMP Tools Interface.')
+    variant('hwloc', default=True, description='Build with hwloc.')
+    variant('gnu-ld', default=False, description='Assume C compiler uses gnu-ld.')
+
+    # Added dependencies.
+    depends_on('m4', type='build')
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('libtool', type='build')
+    depends_on('ruby-ronn', type='build', when='+doc')
+    depends_on('doxygen', type='build', when='+doc')
+    depends_on('numactl')
+    depends_on('mpi', when='+mpi')
+    # TODO: check if hwloc@specific-version still required with future openmpi
+    depends_on('hwloc@1.11.9', when='+hwloc')
+    depends_on('json-c')
+    depends_on('py-pandas', type='run')
+    depends_on('py-numpy', type='run')
+    depends_on('py-natsort', type='run')
+    depends_on('py-matplotlib', type='run')
+
+    parallel = False
+
+    def configure_args(self):
+        args = []
+        args.extend(self.enable_or_disable('debug'))
+        args.extend(self.enable_or_disable('coverage'))
+        args.extend(self.enable_or_disable('overhead'))
+        args.extend(self.enable_or_disable('procfs'))
+        args.extend(self.enable_or_disable('mpi'))
+        args.extend(self.enable_or_disable('fortran'))
+        args.extend(self.enable_or_disable('doc'))
+        args.extend(self.enable_or_disable('openmp'))
+        args.extend(self.enable_or_disable('ompt'))
+        args.extend(self.with_or_without('hwloc', activation_value='prefix'))
+        args.extend(self.with_or_without('gnu-ld'))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/geos/package.py b/var/spack/repos/builtin/packages/geos/package.py
index f74e03ff57..3bd4a8f7e4 100644
--- a/var/spack/repos/builtin/packages/geos/package.py
+++ b/var/spack/repos/builtin/packages/geos/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Geos(Package):
+class Geos(AutotoolsPackage):
     """GEOS (Geometry Engine - Open Source) is a C++ port of the Java
        Topology Suite (JTS). As such, it aims to contain the complete
        functionality of JTS in C++. This includes all the OpenGIS
@@ -33,12 +14,14 @@ class Geos(Package):
        operators, as well as specific JTS enhanced topology functions."""
 
     homepage = "http://trac.osgeo.org/geos/"
-    url      = "http://download.osgeo.org/geos/geos-3.4.2.tar.bz2"
+    url      = "http://download.osgeo.org/geos/geos-3.6.2.tar.bz2"
 
-    # Verison 3.5.0 supports Autotools and CMake
+    version('3.6.2', 'a32142343c93d3bf151f73db3baa651f')
+    version('3.6.1', 'c97e338b3bc81f9848656e9d693ca6cc')
+    version('3.6.0', '55de5fdf075c608d2d7b9348179ee649')
+    version('3.5.1', '2e3e1ccbd42fee9ec427106b65e43dc0')
     version('3.5.0', '136842690be7f504fba46b3c539438dd')
-
-    # Versions through 3.4.2 have CMake, but only Autotools is supported
+    version('3.4.3', '77f2c2cca1e9f49bc1bece9037ac7a7a')
     version('3.4.2', 'fc5df2d926eb7e67f988a43a92683bae')
     version('3.4.1', '4c930dec44c45c49cd71f3e0931ded7e')
     version('3.4.0', 'e41318fc76b5dc764a69d43ac6b18488')
@@ -50,21 +33,39 @@ class Geos(Package):
     version('3.3.4', '1bb9f14d57ef06ffa41cb1d67acb55a1')
     version('3.3.3', '8454e653d7ecca475153cc88fd1daa26')
 
-#    # Python3 is not supported.
-#    variant('python', default=False, description='Enable Python support')
+    # Ruby bindings are fully supported
+    variant('ruby',   default=False, description='Enable Ruby support')
 
-#    extends('python', when='+python')
-#    depends_on('python', when='+python')
-#    depends_on('swig', when='+python')
+    # Since version 3.0, the Python bindings are unsupported
+    variant('python', default=False, description='Enable Python support')
 
-    def install(self, spec, prefix):
-        args = ["--prefix=%s" % prefix]
-#        if '+python' in spec:
-#            os.environ['PYTHON'] = spec['python'].command.path
-#            os.environ['SWIG'] = spec['swig'].command.path
-#
-#            args.append("--enable-python")
+    extends('ruby', when='+ruby')
+
+    # Python 3 is supposedly supported, but I couldn't get it to work
+    # https://trac.osgeo.org/geos/ticket/774
+    extends('python@:2', when='+python')
+
+    depends_on('swig', type='build', when='+ruby')
+    depends_on('swig', type='build', when='+python')
+
+    # `make check` fails with:
+    # FAIL: geos_unit
+
+    # I wasn't able to get the ruby bindings working.
+    # It resulted in "Undefined symbols for architecture x86_64".
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        if '+ruby' in spec:
+            args.append('--enable-ruby')
+        else:
+            args.append('--disable-ruby')
+
+        if '+python' in spec:
+            args.append('--enable-python')
+        else:
+            args.append('--disable-python')
 
-        configure(*args)
-        make()
-        make("install")
+        return args
diff --git a/var/spack/repos/builtin/packages/gettext/package.py b/var/spack/repos/builtin/packages/gettext/package.py
index f25f3e7889..7676bb8cfb 100644
--- a/var/spack/repos/builtin/packages/gettext/package.py
+++ b/var/spack/repos/builtin/packages/gettext/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Gettext(AutotoolsPackage):
     """GNU internationalization (i18n) and localization (l10n) library."""
 
     homepage = "https://www.gnu.org/software/gettext/"
-    url      = "http://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz"
+    url      = "https://ftpmirror.gnu.org/gettext/gettext-0.19.7.tar.xz"
 
     version('0.19.8.1', 'df3f5690eaa30fd228537b00cb7b7590')
     version('0.19.7',   'f81e50556da41b44c1d59ac93474dca5')
@@ -84,8 +65,10 @@ class Gettext(AutotoolsPackage):
             config_args.append('--disable-curses')
 
         if '+libxml2' in spec:
-            config_args.append('--with-libxml2-prefix={0}'.format(
+            config_args.append('CPPFLAGS=-I{0}/include'.format(
                 spec['libxml2'].prefix))
+            config_args.append('LDFLAGS=-L{0} -Wl,-rpath,{0}'.format(
+                spec['libxml2'].libs.directories[0]))
         else:
             config_args.append('--with-included-libxml')
 
diff --git a/var/spack/repos/builtin/packages/gflags/package.py b/var/spack/repos/builtin/packages/gflags/package.py
index 05a168d6fa..4984af3406 100644
--- a/var/spack/repos/builtin/packages/gflags/package.py
+++ b/var/spack/repos/builtin/packages/gflags/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ghost/package.py b/var/spack/repos/builtin/packages/ghost/package.py
new file mode 100644
index 0000000000..246f990133
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ghost/package.py
@@ -0,0 +1,65 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Ghost(CMakePackage, CudaPackage):
+    """GHOST: a General, Hybrid and Optimized Sparse Toolkit.
+       This library provides highly optimized building blocks for implementing
+       sparse iterative eigenvalue and linear solvers multi- and manycore
+       clusters and on heterogenous CPU/GPU machines. For an iterative solver
+       library using these kernels, see the phist package.
+    """
+
+    homepage = "https://www.bitbucket.org/essex/ghost/"
+    git      = "https://bitbucket.org/essex/ghost/ghost.git"
+
+    version('develop', branch='devel')
+
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    variant('mpi', default=True,
+            description='enable/disable MPI')
+    variant('scotch', default=False,
+            description='enable/disable matrix reordering with PT-SCOTCH')
+    variant('zoltan', default=False,
+            description='enable/disable matrix reordering with Zoltan')
+
+    # ###################### Dependencies ##########################
+
+    # Everything should be compiled position independent (-fpic)
+    depends_on('cmake@3.5:')
+    depends_on('hwloc')
+    depends_on('blas')
+    depends_on('mpi', when='+mpi')
+    depends_on('scotch', when='+scotch')
+    depends_on('zoltan', when='+zoltan')
+
+    def cmake_args(self):
+        spec = self.spec
+        # note: we require the cblas_include_dir property from the blas
+        # provider, this is implemented at least for intel-mkl and
+        # netlib-lapack
+        args = ['-DGHOST_ENABLE_MPI:BOOL=%s'
+                % ('ON' if '+mpi' in spec else 'OFF'),
+                '-DGHOST_USE_CUDA:BOOL=%s'
+                % ('ON' if '+cuda' in spec else 'OFF'),
+                '-DGHOST_USE_SCOTCH:BOOL=%s'
+                % ('ON' if '+scotch' in spec else 'OFF'),
+                '-DGHOST_USE_ZOLTAN:BOOL=%s'
+                % ('ON' if '+zoltan' in spec else 'OFF'),
+                '-DBUILD_SHARED_LIBS:BOOL=%s'
+                % ('ON' if '+shared' in spec else 'OFF'),
+                '-DCBLAS_INCLUDE_DIR:STRING=%s'
+                % format(spec['blas'].headers.directories[0]),
+                '-DBLAS_LIBRARIES=%s'
+                % spec['blas:c'].libs.joined(';')
+                ]
+        return args
+
+    def check(self):
+        make('test')
diff --git a/var/spack/repos/builtin/packages/ghostscript-fonts/package.py b/var/spack/repos/builtin/packages/ghostscript-fonts/package.py
index 9dc7e8cead..198108fd4e 100644
--- a/var/spack/repos/builtin/packages/ghostscript-fonts/package.py
+++ b/var/spack/repos/builtin/packages/ghostscript-fonts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/ghostscript/package.py b/var/spack/repos/builtin/packages/ghostscript/package.py
index 991f77199e..d5d478bf90 100644
--- a/var/spack/repos/builtin/packages/ghostscript/package.py
+++ b/var/spack/repos/builtin/packages/ghostscript/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import shutil
 
@@ -35,7 +16,7 @@ class Ghostscript(AutotoolsPackage):
     version('9.21', '5f213281761d2750fcf27476c404d17f')
     version('9.18', '33a47567d7a591c00a253caddd12a88a')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('freetype@2.4.2:')
     depends_on('jpeg')
@@ -43,6 +24,7 @@ class Ghostscript(AutotoolsPackage):
     depends_on('libpng')
     depends_on('libtiff')
     depends_on('zlib')
+    depends_on('libxext')
 
     def url_for_version(self, version):
         baseurl = "https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs{0}/ghostscript-{1}.tar.gz"
diff --git a/var/spack/repos/builtin/packages/giflib/bsd-head.patch b/var/spack/repos/builtin/packages/giflib/bsd-head.patch
new file mode 100644
index 0000000000..3831f2ca57
--- /dev/null
+++ b/var/spack/repos/builtin/packages/giflib/bsd-head.patch
@@ -0,0 +1,19 @@
+The BSD version of head does not accept the --bytes option,
+nor does it accept negative integers. Use dd instead for
+BSD support.
+
+--- a/tests/makefile	2014-05-16 05:46:53.000000000 -0500
++++ b/tests/makefile	2018-03-18 18:29:47.000000000 -0500
+@@ -103,10 +103,10 @@
+ 
+ giffix-rebuild:
+ 	@echo "Rebuilding giffix test."
+-	@head --bytes=-20 <$(PICS)/treescap.gif | $(UTILS)/giffix 2>/dev/null | $(UTILS)/gifbuild -d >giffixed.ico
++	@dd if=$(PICS)/treescap.gif bs=1 count=387 | $(UTILS)/giffix 2>/dev/null | $(UTILS)/gifbuild -d >giffixed.ico
+ giffix-regress:
+ 	@echo "giffix: Testing giffix behavior"
+-	@head --bytes=-20 <$(PICS)/treescap.gif | $(UTILS)/giffix 2>/dev/null | $(UTILS)/gifbuild -d | diff -u giffixed.ico -
++	@dd if=$(PICS)/treescap.gif bs=1 count=387 | $(UTILS)/giffix 2>/dev/null | $(UTILS)/gifbuild -d | diff -u giffixed.ico -
+ 
+ gifinto-regress:
+ 	@echo "gifinto: Checking behavior on short files."
diff --git a/var/spack/repos/builtin/packages/giflib/package.py b/var/spack/repos/builtin/packages/giflib/package.py
index 3ab0d8453f..a951143a12 100644
--- a/var/spack/repos/builtin/packages/giflib/package.py
+++ b/var/spack/repos/builtin/packages/giflib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,3 +14,8 @@ class Giflib(AutotoolsPackage):
     url      = "https://downloads.sourceforge.net/project/giflib/giflib-5.1.4.tar.bz2"
 
     version('5.1.4', '2c171ced93c0e83bb09e6ccad8e3ba2b')
+
+    patch('bsd-head.patch')
+
+    def check(self):
+        make('check', parallel=False)
diff --git a/var/spack/repos/builtin/packages/git-imerge/package.py b/var/spack/repos/builtin/packages/git-imerge/package.py
new file mode 100644
index 0000000000..524a8b28ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/git-imerge/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class GitImerge(MakefilePackage):
+    """git-imerge: Incremental merge & rebase for git
+
+       Perform a merge between two branches incrementally. If
+       conflicts are encountered, figure out exactly which pairs of
+       commits conflict, and present the user with one pairwise
+       conflict at a time for resolution.
+
+       git-imerge has two primary design goals:
+
+       * Reduce the pain of resolving merge conflicts to its
+         unavoidable minimum, by finding and presenting the smallest
+         possible conflicts: those between the changes introduced by
+         one commit from each branch.
+
+       * Allow a merge to be saved, tested, interrupted, published,
+         and collaborated on while it is in progress."""
+
+    homepage = "https://github.com/mhagger/git-imerge"
+    url      = "https://github.com/mhagger/git-imerge/archive/v1.1.0.tar.gz"
+
+    version('1.1.0', '94a44dcbe5e764d75770a24517572a76')
+    version('1.0.0', 'e5e69a22610828cc33bf2cbd31685438')
+
+    depends_on('python@2.6:')
+    depends_on('py-argparse', when='^python@2.6')
+    depends_on('git')
+
+    # Package copies a Python script and bash-completion files, so
+    # there's no need to "build" anything.
+    def build(self, spec, prefix):
+        pass
+
+    def install(self, spec, prefix):
+        make('DESTDIR={0}'.format(prefix), 'PREFIX=', 'install')
diff --git a/var/spack/repos/builtin/packages/git-lfs/package.py b/var/spack/repos/builtin/packages/git-lfs/package.py
index 7e557dd0a8..902540a603 100644
--- a/var/spack/repos/builtin/packages/git-lfs/package.py
+++ b/var/spack/repos/builtin/packages/git-lfs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,13 +14,13 @@ class GitLfs(Package):
        Git LFS server."""
 
     homepage = "https://git-lfs.github.com"
-    git_url  = "https://github.com/github/git-lfs.git"
+    git      = "https://github.com/github/git-lfs.git"
 
-    version('2.3.0', git=git_url, tag='v2.3.0')
-    version('2.2.1', git=git_url, tag='v2.2.1')
-    version('2.0.2', git=git_url, tag='v2.0.2')
-    version('1.4.1', git=git_url, tag='v1.4.1')
-    version('1.3.1', git=git_url, tag='v1.3.1')
+    version('2.3.0', tag='v2.3.0')
+    version('2.2.1', tag='v2.2.1')
+    version('2.0.2', tag='v2.0.2')
+    version('1.4.1', tag='v1.4.1')
+    version('1.3.1', tag='v1.3.1')
 
     # TODO: Add tests by following the instructions at this location:
     # https://github.com/github/git-lfs/blob/master/CONTRIBUTING.md#building
diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py
index 293f85974f..ba0e717fac 100644
--- a/var/spack/repos/builtin/packages/git/package.py
+++ b/var/spack/repos/builtin/packages/git/package.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import sys
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Git(AutotoolsPackage):
@@ -34,117 +14,146 @@ class Git(AutotoolsPackage):
     """
 
     homepage = "http://git-scm.com"
-    url      = "https://github.com/git/git/archive/v2.12.0.tar.gz"
+    url      = "https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.12.0.tar.gz"
 
     # In order to add new versions here, add a new list entry with:
     # * version: {version}
-    # * md5: the md5sum of the v{version}.tar.gz
-    # * md5_manpages: the md5sum of the corresponding manpage from
+    # * sha256: the sha256sum of the git-{version}.tar.gz
+    # * sha256_manpages: the sha256sum of the corresponding manpage from
     #       https://www.kernel.org/pub/software/scm/git/git-manpages-{version}.tar.xz
+    # You can find the source here: https://mirrors.edge.kernel.org/pub/software/scm/git/sha256sums.asc
 
     releases = [
         {
+            'version': '2.19.1',
+            'sha256': 'ec4dc96456612c65bf6d944cee9ac640145ec7245376832b781cb03e97cbb796',
+            'sha256_manpages': 'bd27f58dc90a661e3080b97365eb7322bfa185de95634fc59d98311925a7d894'
+        },
+        {
+            'version': '2.18.0',
+            'sha256': '94faf2c0b02a7920b0b46f4961d8e9cad08e81418614102898a55f980fa3e7e4',
+            'sha256_manpages': '6cf38ab3ad43ccdcd6a73ffdcf2a016d56ab6b4b240a574b0bb96f520a04ff55'
+        },
+        {
+            'version': '2.17.1',
+            'sha256': 'ec6452f0c8d5c1f3bcceabd7070b8a8a5eea11d4e2a04955c139b5065fd7d09a',
+            'sha256_manpages': '9732053c1a618d2576c1751d0249e43702f632a571f84511331882beb360677d'
+        },
+        {
+            'version': '2.17.0',
+            'sha256': '7a0cff35dbb14b77dca6924c33ac9fe510b9de35d5267172490af548ec5ee1b8',
+            'sha256_manpages': '41b58c68e90e4c95265c75955ddd5b68f6491f4d57b2f17c6d68e60bbb07ba6a'
+        },
+        {
+            'version': '2.15.1',
+            'sha256': '85fca8781a83c96ba6db384cc1aa6a5ee1e344746bafac1cbe1f0fe6d1109c84',
+            'sha256_manpages': '472454c494c9a7f50ad38060c3eec372f617de654b20f3eb3be59fc17a683fa1',
+        },
+        {
             'version': '2.14.1',
-            'md5': 'e965a37b3d277f2e7e78f5b04de28e2a',
-            'md5_manpages': 'da2e75ea3972b9e93fb47023e3bf1401',
+            'sha256': '01925349b9683940e53a621ee48dd9d9ac3f9e59c079806b58321c2cf85a4464',
+            'sha256_manpages': '8c5810ce65d44cd333327d3a115c5b462712a2f81225d142e07bd889ad8dc0e0',
         },
         {
             'version': '2.13.0',
-            'md5': 'd0f14da0ef1d22f1ce7f7876fadcb39f',
-            'md5_manpages': 'fda8d6d5314eb5a47e315405830f9970',
+            'sha256': '9f2fa8040ebafc0c2caae4a9e2cb385c6f16c0525bcb0fbd84938bc796372e80',
+            'sha256_manpages': 'e764721796cad175a4cf9a4afe7fb4c4fc57582f6f9a6e214239498e0835355b',
         },
         {
             'version': '2.12.2',
-            'md5': 'f1a50c09ce8b5dd197f3c6c6d5ea8e75',
-            'md5_manpages': '9358777e9a67e57427b03884c82311bd',
+            'sha256': 'd9c6d787a24670d7e5100db2367c250ad9756ef8084fb153a46b82f1d186f8d8',
+            'sha256_manpages': '6e7ed503f1190734e57c9427df356b42020f125fa36ab0478777960a682adf50',
         },
         {
             'version': '2.12.1',
-            'md5': 'a05c614c80ecd41e50699f1562e1130c',
-            'md5_manpages': '8dfba0c9f51c6c23fb135d136c061c78',
+            'sha256': '65d62d10caf317fc1daf2ca9975bdb09dbff874c92d24f9529d29a7784486b43',
+            'sha256_manpages': '35e46b8acd529ea671d94035232b1795919be8f3c3a363ea9698f1fd08d7d061',
         },
         {
             'version': '2.12.0',
-            'md5': '11a440ce0ed02098adf554c797facfd3',
-            'md5_manpages': '4d11e05068231e37d7e42935e9cc43a1',
+            'sha256': '882f298daf582a07c597737eb4bbafb82c6208fe0e73c047defc12169c221a92',
+            'sha256_manpages': '1f7733a44c59f9ae8dd321d68a033499a76c82046025cc2a6792299178138d65',
         },
         {
             'version': '2.11.1',
-            'md5': '2cf960f19e56f27248816809ae896794',
-            'md5_manpages': 'ade1e458a34a89d03dda9a6de85976bd',
+            'sha256': 'a1cdd7c820f92c44abb5003b36dc8cb7201ba38e8744802399f59c97285ca043',
+            'sha256_manpages': 'ee567e7b0f95333816793714bb31c54e288cf8041f77a0092b85e62c9c2974f9',
         },
         {
             'version': '2.11.0',
-            'md5': 'c63fb83b86431af96f8e9722ebb3ca01',
-            'md5_manpages': '72718851626e5b2267877cc2194a1ac9',
+            'sha256': 'd3be9961c799562565f158ce5b836e2b90f38502d3992a115dfb653d7825fd7e',
+            'sha256_manpages': '437a0128acd707edce24e1a310ab2f09f9a09ee42de58a8e7641362012dcfe22',
         },
         {
             'version': '2.9.3',
-            'md5': 'b0edfc0f3cb046aec7ed68a4b7282a75',
-            'md5_manpages': '337165a3b2bbe4814c73075cb6854ca2',
+            'sha256': 'a252b6636b12d5ba57732c8469701544c26c2b1689933bd1b425e603cbb247c0',
+            'sha256_manpages': '8ea1a55b048fafbf0c0c6fcbca4b5b0f5e9917893221fc7345c09051d65832ce',
         },
         {
             'version': '2.9.2',
-            'md5': '3ff8a9b30fd5c99a02e6d6585ab543fc',
-            'md5_manpages': 'c4f415b4fc94cf75a1deb651ba769594',
+            'sha256': '3cb09a3917c2d8150fc1708f3019cf99a8f0feee6cd61bba3797e3b2a85be9dc',
+            'sha256_manpages': 'ac5c600153d1e4a1c6494e250cd27ca288e7667ad8d4ea2f2386f60ba1b78eec',
         },
         {
             'version': '2.9.1',
-            'md5': 'a5d806743a992300b45f734d1667ddd2',
-            'md5_manpages': '2aa797ff70c704a563c910e04c0f620a',
+            'sha256': 'c2230873bf77f93736473e6a06501bf93eed807d011107de6983dc015424b097',
+            'sha256_manpages': '324f5f173f2bd50b0102b66e474b81146ccc078d621efeb86d7f75e3c1de33e6',
         },
         {
             'version': '2.9.0',
-            'md5': 'bf33a13c2adc05bc9d654c415332bc65',
-            'md5_manpages': 'c840c968062251b768ba9852fd29054c',
+            'sha256': 'bff7560f5602fcd8e37669e0f65ef08c6edc996e4f324e4ed6bb8a84765e30bd',
+            'sha256_manpages': '35ba69a8560529aa837e395a6d6c8d42f4d29b40a3c1cc6e3dc69bb1faadb332',
         },
         {
             'version': '2.8.4',
-            'md5': '86afb10254c3803894c9863fb5896bb6',
-            'md5_manpages': '8340e772d60ccd04a5da88fa9c976dad',
+            'sha256': '626e319f8a24fc0866167ea5f6bf3e2f38f69d6cb2e59e150f13709ca3ebf301',
+            'sha256_manpages': '953a8eadaf4ae96dbad2c3ec12384c677416843917ef83d94b98367ffd55afc0',
         },
         {
             'version': '2.8.3',
-            'md5': '0e19f31f96f9364fd247b8dc737dacfd',
-            'md5_manpages': '553827e1b6c422ecc485499c1a1ae28d',
+            'sha256': '2dad50c758339d6f5235309db620e51249e0000ff34aa2f2acbcb84c2123ed09',
+            'sha256_manpages': '2dad50c758339d6f5235309db620e51249e0000ff34aa2f2acbcb84c2123ed09',
         },
         {
             'version': '2.8.2',
-            'md5': '3d55550880af98f6e35c7f1d7c5aecfe',
-            'md5_manpages': '33330463af27eb1238cbc2b4ca100b3a',
+            'sha256': 'a029c37ee2e0bb1efea5c4af827ff5afdb3356ec42fc19c1d40216d99e97e148',
+            'sha256_manpages': '82d322211aade626d1eb3bcf3b76730bfdd2fcc9c189950fb0a8bdd69c383e2f',
         },
         {
             'version': '2.8.1',
-            'md5': '1308448d95afa41a4135903f22262fc8',
-            'md5_manpages': '87bc202c6f6ae32c1c46c2dda3134ed1',
+            'sha256': 'cfc66324179b9ed62ee02833f29d39935f4ab66874125a3ab9d5bb9055c0cb67',
+            'sha256_manpages': 'df46de0c172049f935cc3736361b263c5ff289b77077c73053e63ae83fcf43f4',
         },
         {
             'version': '2.8.0',
-            'md5': 'eca687e46e9750121638f258cff8317b',
-            'md5_manpages': 'd67a7db0f363e8c3b2960cd84ad0373f',
+            'sha256': '2c6eee5506237e0886df9973fd7938a1b2611ec93d07f64ed3447493ebac90d1',
+            'sha256_manpages': '2c48902a69df3bec3b8b8f0350a65fd1b662d2f436f0e64d475ecd1c780767b6',
         },
         {
             'version': '2.7.3',
-            'md5': 'fa1c008b56618c355a32ba4a678305f6',
-            'md5_manpages': '97a525cca7fe38ff6bd7aaa4f0438896',
+            'sha256': '30d067499b61caddedaf1a407b4947244f14d10842d100f7c7c6ea1c288280cd',
+            'sha256_manpages': '84b487c9071857ab0f15f11c4a102a583d59b524831cda0dc0954bd3ab73920b',
         },
         {
             'version': '2.7.1',
-            'md5': 'bf0706b433a8dedd27a63a72f9a66060',
-            'md5_manpages': '19881ca231f73dec91fb456d74943950',
+            'sha256': 'b4ab42798b7fb038eaefabb0c32ce9dbde2919103e5e2a35adc35dd46258a66f',
+            'sha256_manpages': '0313cf4d283336088883d8416692fb6c547512233e11dbf06e5b925b7e762d61',
         },
     ]
 
     for release in releases:
-        version(release['version'], release['md5'])
+        version(release['version'], sha256=release['sha256'])
         resource(
             name='git-manpages',
-            url="https://www.kernel.org/pub/software/scm/git/git-manpages-{0}.tar.xz".format(
+            url="https://www.kernel.org/pub/software/scm/git/git-manpages-{0}.tar.gz".format(
                 release['version']),
-            md5=release['md5_manpages'],
+            sha256=release['sha256_manpages'],
             placement='git-manpages',
             when='@{0}'.format(release['version']))
 
+    variant('tcltk', default=False,
+            description='Gitk: provide Tcl/Tk in the run environment')
+
     depends_on('curl')
     depends_on('expat')
     depends_on('gettext')
@@ -159,19 +168,36 @@ class Git(AutotoolsPackage):
     depends_on('automake', type='build')
     depends_on('libtool',  type='build')
     depends_on('m4',       type='build')
+    depends_on('tk',       type=('build', 'link'), when='+tcltk')
+
+    # See the comment in setup_environment re EXTLIBS.
+    def patch(self):
+        filter_file(r'^EXTLIBS =$',
+                    '#EXTLIBS =',
+                    'Makefile')
 
     def setup_environment(self, spack_env, run_env):
-        # This is done to avoid failures when git is an external package.
+        # We use EXTLIBS rather than LDFLAGS so that git's Makefile
+        # inserts the information into the proper place in the link commands
+        # (alongside the # other libraries/paths that configure discovers).
+        # LDFLAGS is inserted *before* libgit.a, which requires libintl.
+        # EXTFLAGS is inserted *after* libgit.a.
+        # This depends on the patch method above, which keeps the Makefile
+        # from stepping on the value that we pass in via the environment.
+        #
+        # The test avoids failures when git is an external package.
         # In that case the node in the DAG gets truncated and git DOES NOT
         # have a gettext dependency.
         if 'gettext' in self.spec:
-            spack_env.append_flags('LDFLAGS', '-L{0} -lintl'.format(
+            spack_env.append_flags('EXTLIBS', '-L{0} -lintl'.format(
                 self.spec['gettext'].prefix.lib))
+            spack_env.append_flags('CFLAGS', '-I{0}'.format(
+                self.spec['gettext'].prefix.include))
 
     def configure_args(self):
         spec = self.spec
 
-        return [
+        configure_args = [
             '--with-curl={0}'.format(spec['curl'].prefix),
             '--with-expat={0}'.format(spec['expat'].prefix),
             '--with-iconv={0}'.format(spec['libiconv'].prefix),
@@ -181,15 +207,26 @@ class Git(AutotoolsPackage):
             '--with-zlib={0}'.format(spec['zlib'].prefix),
         ]
 
+        if '+tcltk' in self.spec:
+            configure_args.append('--with-tcltk={0}'.format(
+                self.spec['tk'].prefix.bin.wish))
+        else:
+            configure_args.append('--without-tcltk')
+
+        return configure_args
+
     @run_after('configure')
     def filter_rt(self):
         if sys.platform == 'darwin':
             # Don't link with -lrt; the system has no (and needs no) librt
             filter_file(r' -lrt$', '', 'Makefile')
 
+    def check(self):
+        make('test')
+
     @run_after('install')
     def install_completions(self):
-        copy_tree('contrib/completion', self.prefix.share)
+        install_tree('contrib/completion', self.prefix.share)
 
     @run_after('install')
     def install_manpages(self):
diff --git a/var/spack/repos/builtin/packages/gl2ps/package.py b/var/spack/repos/builtin/packages/gl2ps/package.py
index fbe38d4bc9..16e4453bfd 100644
--- a/var/spack/repos/builtin/packages/gl2ps/package.py
+++ b/var/spack/repos/builtin/packages/gl2ps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/glew/package.py b/var/spack/repos/builtin/packages/glew/package.py
index 4ba7eb5894..58c5ef686e 100644
--- a/var/spack/repos/builtin/packages/glew/package.py
+++ b/var/spack/repos/builtin/packages/glew/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,7 @@ class Glew(Package):
     version('2.0.0',  '2a2cd7c98f13854d2fcddae0d2b20411')
 
     depends_on("cmake", type='build')
+    depends_on("gl")
 
     def install(self, spec, prefix):
         options = []
diff --git a/var/spack/repos/builtin/packages/glfmultiples/package.py b/var/spack/repos/builtin/packages/glfmultiples/package.py
new file mode 100644
index 0000000000..deb5789e24
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glfmultiples/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Glfmultiples(MakefilePackage):
+    """glfMultiples is a GLF-based variant caller for next-generation
+       sequencing data. It takes a set of GLF format genotype likelihood
+       files as input and generates a VCF-format set of variant calls
+       as output. """
+
+    homepage = "https://genome.sph.umich.edu/wiki/GlfMultiples"
+    url      = "http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-06-16.tar.gz"
+
+    version('2010-06-16', '64bf6bb7c76543f4c8fabce015a3cb11')
+
+    depends_on('zlib')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('CXX=.*', 'CXX = ' + env['CXX'])
+        makefile.filter('CFLAGS=.*',
+                        'CFLAGS=-O2 -I./libsrc -I./pdf ' +
+                        '-D_FILE_OFFSET_BITS=64 -D__USE_LONG_INT')
+
+    def install(self, spec, prefix):
+        make('INSTALLDIR=%s' % prefix, 'install')
diff --git a/var/spack/repos/builtin/packages/glib/old-kernels.patch b/var/spack/repos/builtin/packages/glib/old-kernels.patch
new file mode 100644
index 0000000000..4061410320
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glib/old-kernels.patch
@@ -0,0 +1,16 @@
+--- a/gio/gfile.c     2018-06-11 15:28:30.527667202 -0500
++++ b/gio/gfile.c     2018-03-12 11:23:37.000000000 -0500
+@@ -3014,11 +3014,11 @@
+ 
+   /* Try a 1MiB buffer for improved throughput. If that fails, use the default
+    * pipe size. See: https://bugzilla.gnome.org/791457 */
+-  buffer_size = fcntl (buffer[1], F_SETPIPE_SZ, 1024 * 1024);
++  buffer_size = -1;
+   if (buffer_size <= 0)
+     {
+       int errsv;
+-      buffer_size = fcntl (buffer[1], F_GETPIPE_SZ);
++      buffer_size = 65536;
+       errsv = errno;
+ 
+       if (buffer_size <= 0)
diff --git a/var/spack/repos/builtin/packages/glib/package.py b/var/spack/repos/builtin/packages/glib/package.py
index 5997987fa6..ab554165a1 100644
--- a/var/spack/repos/builtin/packages/glib/package.py
+++ b/var/spack/repos/builtin/packages/glib/package.py
@@ -1,39 +1,30 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
+import os.path
+
 
 class Glib(AutotoolsPackage):
-    """The GLib package contains a low-level libraries useful for
-       providing data structure handling for C, portability wrappers
-       and interfaces for such runtime functionality as an event loop,
-       threads, dynamic loading and an object system."""
+    """GLib provides the core application building blocks for
+    libraries and applications written in C.
+
+    The GLib package contains a low-level libraries useful for
+    providing data structure handling for C, portability wrappers
+    and interfaces for such runtime functionality as an event loop,
+    threads, dynamic loading and an object system.
+    """
 
     homepage = "https://developer.gnome.org/glib/"
     url      = "https://ftp.gnome.org/pub/gnome/sources/glib/2.53/glib-2.53.1.tar.xz"
 
+    version('2.56.2', 'd64abd16813501c956c4e123ae79f47f1b58de573df9fdd3b0795f1e2c1aa789')
+    version('2.56.1', '40ef3f44f2c651c7a31aedee44259809b6f03d3d20be44545cd7d177221c0b8d')
+    version('2.56.0', 'f2b59392f2fb514bbe7791dda0c36da5')
+    version('2.55.1', '9cbb6b3c7e75ba75575588497c7707b6')
     version('2.53.1', '3362ef4da713f834ea26904caf3a75f5')
     version('2.49.7', '397ead3fcf325cb921d54e2c9e7dfd7a')
     version('2.49.4', 'e2c87c03017b0cd02c4c73274b92b148')
@@ -41,12 +32,20 @@ class Glib(AutotoolsPackage):
     version('2.42.1', '89c4119e50e767d3532158605ee9121a')
 
     variant('libmount', default=False, description='Build with libmount support')
+    variant(
+        'tracing',
+        default='',
+        values=('dtrace', 'systemtap'),
+        multi=True,
+        description='Enable tracing support'
+    )
 
-    depends_on('pkg-config@0.16:+internal_glib', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('libffi')
     depends_on('zlib')
     depends_on('gettext')
     depends_on('perl', type=('build', 'run'))
+    depends_on('python', type=('build', 'run'), when='@2.53.4:')
     depends_on('pcre+utf', when='@2.48:')
     depends_on('util-linux', when='+libmount')
 
@@ -55,6 +54,10 @@ class Glib(AutotoolsPackage):
     # Clang doesn't seem to acknowledge the pragma lines to disable the -Werror
     # around a legitimate usage.
     patch('no-Werror=format-security.patch')
+    # Patch to prevent compiler errors in kernels older than 2.6.35
+    patch('old-kernels.patch', when='@2.56.0:2.56.1 os=rhel6')
+    patch('old-kernels.patch', when='@2.56.0:2.56.1 os=centos6')
+    patch('old-kernels.patch', when='@2.56.0:2.56.1 os=scientific6')
 
     def url_for_version(self, version):
         """Handle glib's version-based custom URLs."""
@@ -62,20 +65,69 @@ class Glib(AutotoolsPackage):
         return url + '/%s/glib-%s.tar.xz' % (version.up_to(2), version)
 
     def configure_args(self):
-        spec = self.spec
         args = []
+        args.extend(self.enable_or_disable('libmount'))
+        if self.spec.satisfies('@2.53.4:'):
+            args.append('--with-python={0}'.format(
+                os.path.basename(self.spec['python'].command.path))
+            )
+        args.extend(self.enable_or_disable('tracing'))
+        return args
 
-        if '+libmount' in spec:
-            args.append('--enable-libmount')
-        else:
-            args.append('--disable-libmount')
+    @property
+    def dtrace_copy_path(self):
+        return join_path(self.stage.source_path, 'dtrace-copy')
 
-        return args
+    @run_before('configure')
+    def fix_python_path(self):
+        if not self.spec.satisfies('@2.53.4:'):
+            return
+
+        files = ['gobject/glib-genmarshal.in', 'gobject/glib-mkenums.in']
+
+        filter_file('^#!/usr/bin/env @PYTHON@',
+                    '#!/usr/bin/env python',
+                    *files)
+
+    @run_before('configure')
+    def fix_dtrace_usr_bin_path(self):
+        if 'tracing=dtrace' not in self.spec:
+            return
 
-    @run_before('install')
+        # dtrace may cause glib build to fail because it uses
+        # '/usr/bin/python' in the shebang. To work around that
+        # we copy the original script into a temporary folder, and
+        # change the shebang to '/usr/bin/env python'
+        dtrace = which('dtrace').path
+        dtrace_copy = join_path(self.dtrace_copy_path, 'dtrace')
+
+        with working_dir(self.dtrace_copy_path, create=True):
+            copy(dtrace, dtrace_copy)
+            filter_file(
+                '^#!/usr/bin/python',
+                '#!/usr/bin/env python',
+                dtrace_copy
+            )
+
+        # To have our own copy of dtrace in PATH, we need to
+        # prepend to PATH the temporary folder where it resides
+        env['PATH'] = ':'.join(
+            [self.dtrace_copy_path] + env['PATH'].split(':')
+        )
+
+    @run_after('install')
     def filter_sbang(self):
-        # Filter sbang before install so Spack's sbang hook can fix it up
-        perl = join_path(self.spec['perl'].prefix.bin, 'perl')
-        files = ['gobject/glib-mkenums']
+        # Revert sbang, so Spack's sbang hook can fix it up (we have to do
+        # this after install because otherwise the install target will try
+        # to rebuild files as filter_file updates the timestamps)
+        if self.spec.satisfies('@2.53.4:'):
+            pattern = '^#!/usr/bin/env python'
+            repl = '#!{0}'.format(self.spec['python'].command.path)
+            files = ['glib-genmarshal', 'glib-mkenums']
+        else:
+            pattern = '^#! /usr/bin/perl'
+            repl = '#!{0}'.format(self.spec['perl'].command.path)
+            files = ['glib-mkenums']
 
-        filter_file('^#! /usr/bin/perl', '#!{0}'.format(perl), *files)
+        files = [join_path(self.prefix.bin, file) for file in files]
+        filter_file(pattern, repl, *files, backup=False)
diff --git a/var/spack/repos/builtin/packages/glibmm/guint16_cast.patch b/var/spack/repos/builtin/packages/glibmm/guint16_cast.patch
new file mode 100644
index 0000000000..325eb4d21f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glibmm/guint16_cast.patch
@@ -0,0 +1,36 @@
+diff --git a/glib/glibmm/class.cc b/glib/glibmm/class.cc
+index dc1c4a8..fc640ae 100644
+--- a/glib/glibmm/class.cc
++++ b/glib/glibmm/class.cc
+@@ -37,13 +37,13 @@ void Class::register_derived_type(GType base_type)
+ 
+   const GTypeInfo derived_info =
+   {
+-    base_query.class_size,
++    (guint16) base_query.class_size,
+     0, // base_init
+     0, // base_finalize
+     class_init_func_,
+     0, // class_finalize
+     0, // class_data
+-    base_query.instance_size,
++    (guint16) base_query.instance_size,
+     0, // n_preallocs
+     0, // instance_init
+     0, // value_table
+@@ -75,13 +75,13 @@ GType Class::clone_custom_type(const char* custom_type_name) const
+ 
+     const GTypeInfo derived_info =
+     {
+-      base_query.class_size,
++      (guint16) base_query.class_size,
+       0, // base_init
+       0, // base_finalize
+       &Class::custom_class_init_function,
+       0, // class_finalize
+       this, // class_data
+-      base_query.instance_size,
++      (guint16) base_query.instance_size,
+       0, // n_preallocs
+       0, // instance_init
+       0, // value_table
diff --git a/var/spack/repos/builtin/packages/glibmm/package.py b/var/spack/repos/builtin/packages/glibmm/package.py
new file mode 100644
index 0000000000..5fcf28ed83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glibmm/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Glibmm(AutotoolsPackage):
+    """Glibmm is a C++ wrapper for the glib library."""
+
+    homepage = "https://developer.gnome.org/glib/"
+    url      = "https://ftp.gnome.org/pub/GNOME/sources/glibmm/2.19/glibmm-2.19.3.tar.gz"
+
+    version('2.19.3', 'b50180bb93f501172a2ac4c54e83e88a')
+    version('2.16.0', '24390d2da1734205f1e572f24d4942f0')
+    version('2.4.8', 'fa8b2889cd845752446c6ce15a94bb32')
+
+    depends_on('libsigcpp')
+    depends_on('glib')
+
+    patch('guint16_cast.patch', when='@2.19.3')
+
+    def url_for_version(self, version):
+        """Handle glibmm's version-based custom URLs."""
+        url = "https://ftp.acc.umu.se/pub/GNOME/sources/glibmm"
+        ext = '.tar.gz' if version < Version('2.28.2') else '.tar.xz'
+        return url + "/%s/glibmm-%s%s" % (version.up_to(2), version, ext)
diff --git a/var/spack/repos/builtin/packages/glimmer/package.py b/var/spack/repos/builtin/packages/glimmer/package.py
new file mode 100644
index 0000000000..b93aefc08f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glimmer/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Glimmer(MakefilePackage):
+    """Glimmer is a system for finding genes in microbial DNA, especially the
+    genomes of bacteria, archaea, and viruses."""
+
+    homepage = "https://ccb.jhu.edu/software/glimmer"
+
+    version('3.02b', '344d012ae12596de905866fe9eb7f16c')
+
+    build_directory = 'src'
+
+    def url_for_version(self, version):
+        url = "https://ccb.jhu.edu/software/glimmer/glimmer{0}.tar.gz"
+        return url.format(version.joined)
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/glm/package.py b/var/spack/repos/builtin/packages/glm/package.py
index d2bf9da282..c628872feb 100644
--- a/var/spack/repos/builtin/packages/glm/package.py
+++ b/var/spack/repos/builtin/packages/glm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/global/package.py b/var/spack/repos/builtin/packages/global/package.py
index 040b7d6e71..66be9777c1 100644
--- a/var/spack/repos/builtin/packages/global/package.py
+++ b/var/spack/repos/builtin/packages/global/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/globalarrays/ibm-xl.patch b/var/spack/repos/builtin/packages/globalarrays/ibm-xl.patch
deleted file mode 100644
index 644e3a559a..0000000000
--- a/var/spack/repos/builtin/packages/globalarrays/ibm-xl.patch
+++ /dev/null
@@ -1,250 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 2022280..dac3b7f 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -174,6 +174,15 @@ option (F2C_HIDDEN_STRING_LENGTH_AFTER_ARGS "Set F77 macros" ON)
- if (ENABLE_FORTRAN)
-   include( FortranCInterface )
-   FortranCInterface_HEADER(${CMAKE_SOURCE_DIR}/f2c_cmake.h MACRO_NAMESPACE F77_FUNC_)
-+  add_custom_command(
-+    OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.fh
-+    COMMAND ${CMAKE_COMMAND} -D INPUT:PATH="${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.h" -D OUTPUT:PATH="${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.fh" -P ${PROJECT_SOURCE_DIR}/tools/f2c_cmake_fh_from_h.cmake DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.h
-+    DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.h
-+  )
-+  add_custom_target(
-+    GenerateF2c_cmakeFH ALL
-+    DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/f2c_cmake.fh
-+  )
- else()
-   CONFIGURE_FILE( ${CMAKE_SOURCE_DIR}/cmake/f2c_dummy.h.in
-                 ${CMAKE_SOURCE_DIR}/f2c_cmake.h )
-@@ -336,6 +345,15 @@ if (ENABLE_FORTRAN)
-      set (F77_IARGC IARGC)
-      set (F77_FLUSH flush)
-      set (HAVE_F77_FLUSH 1)
-+  elseif (CMAKE_Fortran_COMPILER MATCHES "xlf.*")
-+     message(STATUS "Using IBM XL Fortran compiler settings")
-+     set (F90_MODULE )
-+     set (F77_GETARG GETARG)
-+     set (F77_GETARG_ARGS "i,s")
-+     set (F77_GETARG_DECLS "intrinsic GETARG")
-+     set (F77_IARGC IARGC)
-+     set (F77_FLUSH flush_)
-+     set (HAVE_F77_FLUSH 1)
-   endif()
- else()
- # need to set these variable even if only compiling C/C++
-diff --git a/cmake/config.h.in b/cmake/config.h.in
-index 3ce6a32..9ad868f 100644
---- a/cmake/config.h.in
-+++ b/cmake/config.h.in
-@@ -58,11 +58,11 @@
- 
- #cmakedefine01 F2C_HIDDEN_STRING_LENGTH_AFTER_ARGS
- 
--/*#define F77_FUNC(name,NAME) F77_FUNC_GLOBAL(name,NAME)*/
--/*#define F77_FUNC_(name,NAME) F77_FUNC_GLOBAL_(name,NAME)*/
-+#define F77_FUNC(name,NAME) F77_FUNC_GLOBAL(name,NAME)
-+#define F77_FUNC_(name,NAME) F77_FUNC_GLOBAL_(name,NAME)
- 
--#define F77_FUNC(name,NAME) name ## _
--#define F77_FUNC_(name,NAME) name ## _
-+/* #define F77_FUNC(name,NAME) name ## _ */
-+/* #define F77_FUNC_(name,NAME) name ## _ */
- 
- #define FXX_MODULE ${F90_MODULE}
- #define F77_GETARG ${F77_GETARG}
-diff --git a/tools/config_fh_from_h.cmake b/tools/config_fh_from_h.cmake
-index acdf776..fb10422 100644
---- a/tools/config_fh_from_h.cmake
-+++ b/tools/config_fh_from_h.cmake
-@@ -7,6 +7,13 @@ if (INPUT)
-     foreach (l in ${in0})
-       # Only retain lines that start with "#"
-       set(found "")
-+      string(REGEX MATCH "^#include" found "${l}")
-+      if (found)
-+        # don't include f2c_cmake.h
-+        set(out "#include \"f2c_cmake.fh\"\n")
-+       continue ()
-+      endif ()
-+      set(found "") 
-       string(REGEX MATCH "^#" found "${l}")
-       if (found)
-         set(out "${out}${l}\n")
-diff --git a/tools/f2c_cmake_fh_from_h.cmake b/tools/f2c_cmake_fh_from_h.cmake
-new file mode 100644
-index 0000000..acdf776
---- /dev/null
-+++ b/tools/f2c_cmake_fh_from_h.cmake
-@@ -0,0 +1,21 @@
-+if (INPUT)
-+  if (OUTPUT)
-+    file(READ "${INPUT}" in0)
-+# replace carriage returns with a semi-colon
-+    string (REGEX REPLACE "\n" ";" in0 "${in0}")
-+    set(out "")
-+    foreach (l in ${in0})
-+      # Only retain lines that start with "#"
-+      set(found "")
-+      string(REGEX MATCH "^#" found "${l}")
-+      if (found)
-+        set(out "${out}${l}\n")
-+      endif ()  
-+    endforeach ()
-+    file(WRITE "${OUTPUT}" "${out}")
-+  else (OUTPUT)
-+    message(ERROR "OUTPUT variable must be set")
-+  endif (OUTPUT)
-+else (INPUT)
-+  message(ERROR "INPUT variable must be set")
-+endif (INPUT)
-diff --git a/global/src/cnames.h b/global/src/cnames.h
-index efdec60..cadfd0a 100644
---- a/global/src/cnames.h
-+++ b/global/src/cnames.h
-@@ -2268,6 +2268,7 @@
- #define nga_iupdate_ghosts_ F77_FUNC_(nga_iupdate_ghosts,NGA_IUPDATE_GHOSTS)
- #define nga_supdate_ghosts_ F77_FUNC_(nga_supdate_ghosts,NGA_SUPDATE_GHOSTS)
- #define nga_zupdate_ghosts_ F77_FUNC_(nga_zupdate_ghosts,NGA_ZUPDATE_GHOSTS)
-+#define nga_update_ghosts_nb_ F77_FUNC_(nga_update_ghosts_nb, NGA_UPDATE_GHOSTS_NB)
- #define ga_update6_ghosts_  F77_FUNC_(ga_update6_ghosts, GA_UPDATE6_GHOSTS)
- #define ga_cupdate6_ghosts_ F77_FUNC_(ga_cupdate6_ghosts,GA_CUPDATE6_GHOSTS)
- #define ga_dupdate6_ghosts_ F77_FUNC_(ga_dupdate6_ghosts,GA_DUPDATE6_GHOSTS)
-diff --git a/global/testing/perform.F b/global/testing/perform.F
-index b18146d..e1b9641 100644
---- a/global/testing/perform.F
-+++ b/global/testing/perform.F
-@@ -110,7 +110,7 @@ c
-      &        ilo,ihi,jlo,jhi
-         write(6,*)'bytes  loop         get                    put',
-      &           '                 accumulate'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -145,7 +145,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, count, tg, 1d-6*bytes/tg,
-      &               tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-diff --git a/global/testing/mir_perf1.F b/global/testing/mir_perf1.F
-index 074e838..3548552 100644
---- a/global/testing/mir_perf1.F
-+++ b/global/testing/mir_perf1.F
-@@ -133,7 +133,7 @@ c
-      &           '           accumulate'
-         write(6,*)' bytes    dim     sec      MB/s     sec      MB/s',
-      &           '     sec      MB/s'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -174,7 +174,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, chunk(loop), tg, 
-      &          1d-6*bytes/tg,tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-@@ -388,7 +388,7 @@ c
-      &           '           accumulate'
-         write(6,*)' bytes    dim     sec      MB/s     sec      MB/s',
-      &           '     sec      MB/s'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -427,7 +427,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, chunk(loop), tg, 
-      &          1d-6*bytes/tg,tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-diff --git a/global/testing/mir_perf2.F b/global/testing/mir_perf2.F
-index fb50398..3b3bed6 100644
---- a/global/testing/mir_perf2.F
-+++ b/global/testing/mir_perf2.F
-@@ -124,7 +124,7 @@ c
-      &           '           accumulate'
-         write(6,*)' bytes    dim     sec      MB/s     sec      MB/s',
-      &           '     sec      MB/s'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -163,7 +163,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, chunk(loop), tg, 
-      &          1d-6*bytes/tg,tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-@@ -377,7 +377,7 @@ c
-      &           '           accumulate'
-         write(6,*)' bytes    dim     sec      MB/s     sec      MB/s',
-      &           '     sec      MB/s'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -416,7 +416,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, chunk(loop), tg, 
-      &          1d-6*bytes/tg,tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-diff --git a/global/testing/perfmod.F b/global/testing/perfmod.F
-index ec3fe37..7770be7 100644
---- a/global/testing/perfmod.F
-+++ b/global/testing/perfmod.F
-@@ -119,7 +119,7 @@ c
- 
-         write(6,*)'bytes  loop         get                    put',
-      &           '                 accumulate'
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
-       call ga_sync()
- c
-@@ -157,7 +157,7 @@ c
-         if (me .eq. 0) then
-           write(6,77)bytes, count, tg, 1d-6*bytes/tg,
-      &               tp, 1d-6*bytes/tp, ta, 1d-6*bytes/ta
--          call flush(6)
-+          call F77_FLUSH(6)
-         endif
-       enddo
- c
-diff --git a/global/testing/sprsmatmult.F b/global/testing/sprsmatmult.F
-index 3fdeb3f..3682c3b 100644
---- a/global/testing/sprsmatmult.F
-+++ b/global/testing/sprsmatmult.F
-@@ -108,7 +108,7 @@ c
-         print *,'Comparing distributed multiply with serial multiply'
-         print *
- #endif
--        call flush(6)
-+        call F77_FLUSH(6)
-       endif
- c
- c***  Initialize the MA package
diff --git a/var/spack/repos/builtin/packages/globalarrays/package.py b/var/spack/repos/builtin/packages/globalarrays/package.py
index 2473be5620..a3074bccbf 100644
--- a/var/spack/repos/builtin/packages/globalarrays/package.py
+++ b/var/spack/repos/builtin/packages/globalarrays/package.py
@@ -1,66 +1,63 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at IBM.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Serban Maerean, serban@ibm.com, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Globalarrays(CMakePackage):
-    """The Global Arrays (GA) toolkit provides a shared memory style
-    programming environment in the context of distributed array data
-    structures.
-    """
+class Globalarrays(AutotoolsPackage):
+    """Global Arrays (GA) is a Partitioned Global Address Space (PGAS)
+    programming model. It provides primitives for one-sided communication
+    (Get, Put, Accumulate) and Atomic Operations (read increment).
+    It supports blocking and non-blocking primtives, and supports location
+    consistency."""
 
     homepage = "http://hpc.pnl.gov/globalarrays/"
-    url = "https://github.com/GlobalArrays/ga"
-
-    version('master', git='https://github.com/GlobalArrays/ga', branch='master')
+    url = "https://github.com/GlobalArrays/ga/releases/download/v5.7/ga-5.7.tar.gz"
+
+    version('5.7',   'bb9a441a6b4fbb8b52b58c2d3f4cd07f')
+    version('5.6.5', '90da628dc72048deeda3f0cd095cb5b3')
+    version('5.6.4', '051901b316c9766b8ba54306bff7f6b3')
+    version('5.6.3', 'df3cf6cc8288d9f202b7fd0ea82f5491')
+    version('5.6.2', '901e4612203bac45059be524fc1abfb7')
+    version('5.6.1', '674c0ea9bf413840b1ff1e669de73fca')
+    version('5.6',   '49d7e997daed094eeb9565423879ba36')
+
+    variant('int64', default=False, description='Compile with 64 bit indices support')
+    variant('blas', default=False, description='Enable BLAS')
+    variant('lapack', default=False, description='Enable LAPACK')
+    variant('scalapack', default=False, description='Enable SCALAPACK')
+    variant('armci', values=('mpi-ts', 'mpi-pr', 'mpi3', 'openib', 'ofi'), 
+        default='mpi-ts', description='ARMCI runtime')
 
-    variant('i8', default=False, description='Build with 8 byte integers')
-
-    depends_on('blas')
-    depends_on('lapack')
     depends_on('mpi')
+    depends_on('blas', when='+blas')
+    depends_on('lapack', when='+lapack')
+    depends_on('scalapack', when='+scalapack')
+
+    conflicts('+lapack', when='~blas')
+    conflicts('+scalapack', when='~blas')
+    conflicts('+scalapack', when='~lapack')
 
-    patch('ibm-xl.patch', when='%xl')
-    patch('ibm-xl.patch', when='%xl_r')
+    def configure_args(self):
+        args = ['--with-mpi']
 
-    def cmake_args(self):
-        options = []
+        if '+blas' in self.spec:
+            if '+int64' in self.spec:
+                args.append('--with-blas8')
+            else:
+                args.append('--with-blas')
 
-        options.extend([
-            '-DENABLE_FORTRAN=ON',
-            '-DENABLE_BLAS=ON',
-        ])
+        if '+lapack' in self.spec:
+            args.append('--with-lapack')
 
-        if self.compiler.name == 'xl' or self.compiler.name == 'xl_r':
-            # use F77 compiler if IBM XL
-            options.extend([
-                '-DCMAKE_Fortran_COMPILER=%s' % self.compiler.f77,
-                '-DCMAKE_Fortran_FLAGS=-qzerosize'
-            ])
+        if '+scalapack' in self.spec:
+            if '+int64' in self.spec:
+                args.append('--with-scalapack8')
+            else:
+                args.append('--with-scalapack')
 
-        if "+i8" in self.spec:
-            options.extend(['-DENABLE_I8=ON'])
+        args.append('--with-' + self.spec.variants['armci'].value)
 
-        return options
+        return args
diff --git a/var/spack/repos/builtin/packages/globus-toolkit/package.py b/var/spack/repos/builtin/packages/globus-toolkit/package.py
index 05944b2dd5..537bcb3a3b 100644
--- a/var/spack/repos/builtin/packages/globus-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/globus-toolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,9 @@ class GlobusToolkit(AutotoolsPackage):
        grids"""
 
     homepage = "http://toolkit.globus.org"
-    url      = "http://toolkit.globus.org/ftppub/gt6/installers/src/globus_toolkit-6.0.1470089956.tar.gz"
+    url      = "http://toolkit.globus.org/ftppub/gt6/installers/src/globus_toolkit-6.0.1506371041.tar.gz"
+
+    version('6.0.1506371041', 'e17146f68e03b3482aaea3874d4087a5')
+    version('6.0.1493989444', '9e9298b61d045e65732e12c9727ceaa8')
 
-    version('6.0.1470089956', 'b77fe3cc5a5844df995688b0e630d077')
+    depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/glog/package.py b/var/spack/repos/builtin/packages/glog/package.py
index cc62b1250e..78c59c3b14 100644
--- a/var/spack/repos/builtin/packages/glog/package.py
+++ b/var/spack/repos/builtin/packages/glog/package.py
@@ -1,40 +1,35 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Glog(CMakePackage):
+class Glog(Package):
     """C++ implementation of the Google logging module."""
 
     homepage = "https://github.com/google/glog"
-    url      = "https://github.com/google/glog/archive/v0.3.4.tar.gz"
+    url      = "https://github.com/google/glog/archive/v0.3.5.tar.gz"
 
+    version('0.3.5', '5df6d78b81e51b90ac0ecd7ed932b0d4')
     version('0.3.4', 'df92e05c9d02504fb96674bc776a41cb')
     version('0.3.3', 'c1f86af27bd9c73186730aa957607ed0')
 
     depends_on('gflags')
+    depends_on('cmake', when="@0.3.5:")
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make('install')
+
+    @when('@0.3.5:')
+    def install(self, spec, prefix):
+        cmake_args = ['-DBUILD_SHARED_LIBS=TRUE']
+        cmake_args.extend(std_cmake_args)
 
-    def cmake_args(self):
-        return ['-DBUILD_SHARED_LIBS=TRUE']
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/gloo/package.py b/var/spack/repos/builtin/packages/gloo/package.py
new file mode 100644
index 0000000000..3fdfa1c295
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gloo/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gloo(CMakePackage):
+    """Gloo is a collective communications library."""
+
+    homepage = "https://github.com/facebookincubator/gloo"
+    git      = "https://github.com/facebookincubator/gloo.git"
+
+    version('master')
diff --git a/var/spack/repos/builtin/packages/glpk/package.py b/var/spack/repos/builtin/packages/glpk/package.py
index 7693ba7b9a..eab6df6d1f 100644
--- a/var/spack/repos/builtin/packages/glpk/package.py
+++ b/var/spack/repos/builtin/packages/glpk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,10 @@ class Glpk(AutotoolsPackage):
     """
 
     homepage = "https://www.gnu.org/software/glpk"
-    url = "http://ftp.gnu.org/gnu/glpk/glpk-4.57.tar.gz"
+    url      = "https://ftpmirror.gnu.org/glpk/glpk-4.65.tar.gz"
 
-    version('4.61', '3ce3e224a8b6e75a1a0b378445830f21')    
+    version('4.65', '470a984a8b1c0e027bdb6d5859063fe8')
+    version('4.61', '3ce3e224a8b6e75a1a0b378445830f21')
     version('4.57', '237531a54f73155842f8defe51aedb0f')
 
     variant(
diff --git a/var/spack/repos/builtin/packages/glproto/package.py b/var/spack/repos/builtin/packages/glproto/package.py
index eaaabc884b..78dc23b645 100644
--- a/var/spack/repos/builtin/packages/glproto/package.py
+++ b/var/spack/repos/builtin/packages/glproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Glproto(AutotoolsPackage):
 
     version('1.4.17', 'd69554c1b51a83f2c6976a640819911b')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/glvis/package.py b/var/spack/repos/builtin/packages/glvis/package.py
new file mode 100644
index 0000000000..dca29403ea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/glvis/package.py
@@ -0,0 +1,125 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Glvis(MakefilePackage):
+    """GLVis: an OpenGL tool for visualization of FEM meshes and functions"""
+
+    homepage = "http://glvis.org"
+    git      = "https://github.com/glvis/glvis.git"
+
+    maintainers = ['goxberry', 'v-dobrev', 'tzanio']
+
+    # glvis (like mfem) is downloaded from a URL shortener at request
+    # of upstream author Tzanio Kolev <tzanio@llnl.gov>.  See here:
+    # https://github.com/mfem/mfem/issues/53
+    #
+    # The following procedure should be used to verify security when a
+    # new version is added:
+    #
+    # 1. Verify that no checksums on old versions have changed.
+    #
+    # 2. Verify that the shortened URL for the new version is listed at:
+    #    http://glvis.org/download/
+    #
+    # 3. Use http://getlinkinfo.com or similar to verify that the
+    #    underling download link for the latest version comes has the
+    #    prefix: http://glvis.github.io/releases
+    #
+    # If this quick verification procedure fails, additional discussion
+    # will be required to verify the new version.
+
+    version('develop', branch='master')
+
+    version('3.4',
+            '289fbd2e09d4456e5fee6162bdc3e0b4c8c8d54625f3547ad2a69fef319279e7',
+            url='https://bit.ly/glvis-3-4',
+            extension='.tar.gz')
+
+    version('3.3',
+            'e24d7c5cb53f208b691c872fe82ea898242cfdc0fd68dd0579c739e070dcd800',
+            url='http://goo.gl/C0Oadw',
+            extension='.tar.gz')
+
+    version('3.2',
+            'c82cb110396e63b6436a770c55eb6d578441eaeaf3f9cc20436c242392e44e80',
+            url='http://goo.gl/hzupg1',
+            extension='.tar.gz')
+
+    version('3.1',
+            '793e984ddfbf825dcd13dfe1ca00eccd686cd40ad30c8789ba80ee175a1b488c',
+            url='http://goo.gl/gQZuu9',
+            extension='tar.gz')
+
+    variant('screenshots',
+            default='png',
+            values=('xwd', 'png', 'tiff'),
+            description='Backend used for screenshots')
+    variant('fonts', default=True,
+            description='Use antialiased fonts via freetype & fontconfig')
+
+    depends_on('mfem@develop', when='@develop')
+    depends_on('mfem@3.4.0', when='@3.4')
+    depends_on('mfem@3.3', when='@3.3')
+    depends_on('mfem@3.2', when='@3.2')
+    depends_on('mfem@3.1', when='@3.1')
+
+    depends_on('gl')
+    depends_on('glu')
+    depends_on('libx11')
+
+    depends_on('libpng', when='screenshots=png')
+    depends_on('libtiff', when='screenshots=tiff')
+    depends_on('freetype', when='+fonts')
+    depends_on('fontconfig', when='+fonts')
+
+    def edit(self, spec, prefix):
+
+        def yes_no(s):
+            return 'YES' if self.spec.satisfies(s) else 'NO'
+
+        mfem = spec['mfem']
+        config_mk = mfem.package.config_mk
+
+        gl_libs = spec['glu'].libs + spec['gl'].libs + spec['libx11'].libs
+        args = ['CC={0}'.format(env['CC']),
+                'PREFIX={0}'.format(prefix.bin),
+                'MFEM_DIR={0}'.format(mfem.prefix),
+                'CONFIG_MK={0}'.format(config_mk),
+                'GL_OPTS=-I{0} -I{1} -I{2}'.format(
+                    spec['libx11'].prefix.include,
+                    spec['gl'].prefix.include,
+                    spec['glu'].prefix.include),
+                'GL_LIBS={0}'.format(gl_libs.ld_flags)]
+
+        if 'screenshots=png' in spec:
+            args += [
+                'USE_LIBPNG=YES', 'USE_LIBTIFF=NO',
+                'PNG_OPTS=-DGLVIS_USE_LIBPNG -I{0}'.format(
+                    spec['libpng'].prefix.include),
+                'PNG_LIBS={0}'.format(spec['libpng'].libs.ld_flags)]
+        elif 'screenshots=tiff' in spec:
+            args += [
+                'USE_LIBPNG=NO', 'USE_LIBTIFF=YES',
+                'TIFF_OPTS=-DGLVIS_USE_LIBTIFF -I{0}'.format(
+                    spec['libtiff'].prefix.include),
+                'TIFF_LIBS={0}'.format(spec['libtiff'].libs.ld_flags)]
+        else:
+            args += ['USE_LIBPNG=NO', 'USE_LIBTIFF=NO']
+
+        args.append('USE_FREETYPE={0}'.format(yes_no('+fonts')))
+        if '+fonts' in spec:
+            args += [
+                'FT_OPTS=-DGLVIS_USE_FREETYPE -I{0} -I{1}'.format(
+                    spec['freetype'].prefix.include.freetype2,
+                    spec['fontconfig'].prefix.include),
+                'FT_LIBS={0} {1}'.format(
+                    spec['freetype'].libs.ld_flags,
+                    spec['fontconfig'].libs.ld_flags)]
+
+        self.build_targets = args
+        self.install_targets += args
diff --git a/var/spack/repos/builtin/packages/gmake/package.py b/var/spack/repos/builtin/packages/gmake/package.py
index 29042eaad6..c40b476568 100644
--- a/var/spack/repos/builtin/packages/gmake/package.py
+++ b/var/spack/repos/builtin/packages/gmake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,17 +11,22 @@ class Gmake(AutotoolsPackage):
     other non-source files of a program from the program's source files."""
 
     homepage = "https://www.gnu.org/software/make/"
-    url      = "https://ftp.gnu.org/gnu/make/make-4.2.1.tar.gz"
+    url      = "https://ftpmirror.gnu.org/make/make-4.2.1.tar.gz"
 
     version('4.2.1', '7d0dcb6c474b258aab4d54098f2cf5a7')
     version('4.0',   'b5e558f981326d9ca1bfdb841640721a')
 
     variant('guile', default=False, description='Support GNU Guile for embedded scripting')
+    variant('nls', default=True, description='Enable Native Language Support')
 
+    depends_on('gettext', when='+nls')
     depends_on('guile', when='+guile')
 
     build_directory = 'spack-build'
 
+    patch('https://src.fedoraproject.org/rpms/make/raw/519a7c5bcbead22e6ea2d2c2341d981ef9e25c0d/f/make-4.2.1-glob-fix-2.patch', level=1, sha256='fe5b60d091c33f169740df8cb718bf4259f84528b42435194ffe0dd5b79cd125', when='@4.2.1')
+    patch('https://src.fedoraproject.org/rpms/make/raw/519a7c5bcbead22e6ea2d2c2341d981ef9e25c0d/f/make-4.2.1-glob-fix-3.patch', level=1, sha256='ca60bd9c1a1b35bc0dc58b6a4a19d5c2651f7a94a4b22b2c5ea001a1ca7a8a7f', when='@:4.2.1')
+
     def configure_args(self):
         args = []
 
@@ -49,6 +35,11 @@ class Gmake(AutotoolsPackage):
         else:
             args.append('--without-guile')
 
+        if '+nls' in self.spec:
+            args.append('--enable-nls')
+        else:
+            args.append('--disable-nls')
+
         return args
 
     @run_after('install')
diff --git a/var/spack/repos/builtin/packages/gmap-gsnap/package.py b/var/spack/repos/builtin/packages/gmap-gsnap/package.py
index 7db09fb72d..bfa53525f2 100644
--- a/var/spack/repos/builtin/packages/gmap-gsnap/package.py
+++ b/var/spack/repos/builtin/packages/gmap-gsnap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,4 +14,42 @@ class GmapGsnap(AutotoolsPackage):
     homepage = "http://research-pub.gene.com/gmap/"
     url      = "http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-06-16.tar.gz"
 
+    version('2018-07-04', sha256='a9f8c1f0810df65b2a089dc10be79611026f4c95e4681dba98fea3d55d598d24')
+    version('2018-03-25', 'f08e65c1e4d9574a3eb7f15f8ca6af16')
+    version('2018-02-12', '13152aedeef9ac66be915fc6bf6464f2')
     version('2017-06-16', 'fcc91b8bdd4bf12ae3124de0c00db0c0')
+    version('2014-12-28', '1ab07819c9e5b5b8970716165ccaa7da')
+
+    depends_on('zlib')
+    depends_on('bzip2')
+
+    variant(
+        'simd',
+        description='CPU support.',
+        values=('avx2', 'sse42', 'avx512', 'sse2'),
+        multi=True,
+        default='sse2'
+    )
+
+    def configure(self, spec, prefix):
+        configure = Executable('../configure')
+
+        for simd in spec.variants['simd'].value:
+            with working_dir(simd, create=True):
+                configure('--with-simd-level={0}'.format(simd),
+                          '--prefix={0}'.format(prefix))
+
+    def build(self, spec, prefix):
+        for simd in spec.variants['simd'].value:
+            with working_dir(simd):
+                make()
+
+    def check(self):
+        for simd in self.spec.variants['simd'].value:
+            with working_dir(simd):
+                make('check')
+
+    def install(self, spec, prefix):
+        for simd in spec.variants['simd'].value:
+            with working_dir(simd):
+                make('install')
diff --git a/var/spack/repos/builtin/packages/gmime/package.py b/var/spack/repos/builtin/packages/gmime/package.py
index d5d0e44d60..888732ee48 100644
--- a/var/spack/repos/builtin/packages/gmime/package.py
+++ b/var/spack/repos/builtin/packages/gmime/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gmodel/package.py b/var/spack/repos/builtin/packages/gmodel/package.py
new file mode 100644
index 0000000000..65ab123158
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gmodel/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gmodel(CMakePackage):
+    """Gmsh model generation library
+
+      Gmodel is a C++11 library that implements a minimal CAD kernel based
+      on the .geo format used by the Gmsh mesh generation code, and is
+      designed to make it easier for users to quickly construct CAD models
+      for Gmsh.
+    """
+    homepage = "https://github.com/ibaned/gmodel"
+    url      = "https://github.com/ibaned/gmodel/archive/v2.1.0.tar.gz"
+
+    version('2.1.0', '80df0c6dc413a9ffa0f0e7b65118b05b643ba3e1bfcac28fb91d2d3ad017fda0')
diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py
index 0367a35200..c49be8f485 100644
--- a/var/spack/repos/builtin/packages/gmp/package.py
+++ b/var/spack/repos/builtin/packages/gmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,13 +11,16 @@ class Gmp(AutotoolsPackage):
     on signed integers, rational numbers, and floating-point numbers."""
 
     homepage = "https://gmplib.org"
-    url      = "https://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/gmp/gmp-6.1.2.tar.bz2"
 
     version('6.1.2',  '8ddbb26dc3bd4e2302984debba1406a5')
     version('6.1.1',  '4c175f86e11eb32d8bf9872ca3a8e11d')
     version('6.1.0',  '86ee6e54ebfc4a90b643a65e402c4048')
     version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470')
     version('6.0.0',  '6ef5869ae735db9995619135bd856b84')
+    version('5.1.3', 'a082867cbca5e898371a97bb27b31fea')
+    # Old version needed for a binary package in ghc-bootstrap
+    version('4.3.2',  'dd60683d7057917e34630b4a787932e8')
 
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py
index 94794ed8a5..c56c2d415a 100644
--- a/var/spack/repos/builtin/packages/gmsh/package.py
+++ b/var/spack/repos/builtin/packages/gmsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,25 +19,24 @@ class Gmsh(CMakePackage):
     homepage = 'http://gmsh.info'
     url = 'http://gmsh.info/src/gmsh-2.11.0-source.tgz'
 
+    version('4.0.0', sha256='fb0c8afa37425c6f4315ab3b3124e9e102fcf270a35198423a4002796f04155f')
+    version('3.0.6',  '9700bcc440d7a6b16a49cbfcdcdc31db33efe60e1f5113774316b6fa4186987b')
     version('3.0.1',  '830b5400d9f1aeca79c3745c5c9fdaa2900cdb2fa319b664a5d26f7e615c749f')
     version('2.16.0', 'e829eaf32ea02350a385202cc749341f2a3217c464719384b18f653edd028eea')
     version('2.15.0', '992a4b580454105f719f5bc05441d3d392ab0b4b80d4ea07b61ca3bdc974070a')
     version('2.12.0', '7fbd2ec8071e79725266e72744d21e902d4fe6fa9e7c52340ad5f4be5c159d09')
-    version('2.11.0', 'f15b6e7ac9ca649c9a74440e1259d0db')
-
-    variant('shared',      default=True,
-            description='Enables the build of shared libraries')
-    variant('mpi',         default=True,
-            description='Builds MPI support for parser and solver')
-    variant('fltk',        default=False,
-            description='Enables the build of the FLTK GUI')
+    version('develop', branch='master', git='https://gitlab.onelab.info/gmsh/gmsh.git')
+
+    variant('shared',      default=True,  description='Enables the build of shared libraries')
+    variant('mpi',         default=True,  description='Builds MPI support for parser and solver')
+    variant('fltk',        default=False, description='Enables the build of the FLTK GUI')
     variant('hdf5',        default=False, description='Enables HDF5 support')
-    variant('compression', default=True,
-            description='Enables IO compression through zlib')
+    variant('compression', default=True,  description='Enables IO compression through zlib')
+    variant('netgen',      default=False, description='Build with Netgen')
     variant('oce',         default=False, description='Build with OCE')
     variant('petsc',       default=False, description='Build with PETSc')
-    variant('slepc',       default=False,
-            description='Build with SLEPc (only when PETSc is enabled)')
+    variant('slepc',       default=False, description='Build with SLEPc (only when PETSc is enabled)')
+    variant('tetgen',      default=False, description='Build with Tetgen')
 
     depends_on('blas')
     depends_on('lapack')
@@ -66,12 +46,16 @@ class Gmsh(CMakePackage):
     # Assumes OpenGL with GLU is already provided by the system:
     depends_on('fltk', when='+fltk')
     depends_on('hdf5', when='+hdf5')
+    depends_on('netgen', when='+netgen')
     depends_on('oce',  when='+oce')
     depends_on('petsc+mpi', when='+petsc+mpi')
     depends_on('petsc', when='+petsc~mpi')
     depends_on('slepc', when='+slepc+petsc')
+    depends_on('tetgen', when='+tetgen')
     depends_on('zlib',  when='+compression')
 
+    conflicts('+slepc', when='~petsc')
+
     def cmake_args(self):
         spec = self.spec
         prefix = self.prefix
@@ -102,21 +86,33 @@ class Gmsh(CMakePackage):
 
         if '+oce' in spec:
             env['CASROOT'] = self.spec['oce'].prefix
-            options.extend(['-DENABLE_OCC=ON'])
+            options.append('-DENABLE_OCC=ON')
         else:
-            options.extend(['-DENABLE_OCC=OFF'])
+            options.append('-DENABLE_OCC=OFF')
 
         if '+petsc' in spec:
             env['PETSC_DIR'] = self.spec['petsc'].prefix
-            options.extend(['-DENABLE_PETSC=ON'])
+            options.append('-DENABLE_PETSC=ON')
+        else:
+            options.append('-DENABLE_PETSC=OFF')
+
+        if '+tetgen' in spec:
+            env['TETGEN_DIR'] = self.spec['tetgen'].prefix
+            options.append('-DENABLE_TETGEN=ON')
+        else:
+            options.append('-DENABLE_TETGEN=OFF')
+
+        if '+netgen' in spec:
+            env['NETGEN_DIR'] = self.spec['netgen'].prefix
+            options.append('-DENABLE_NETGEN=ON')
         else:
-            options.extend(['-DENABLE_PETSC=OFF'])
+            options.append('-DENABLE_NETGEN=OFF')
 
         if '+slepc' in spec:
             env['SLEPC_DIR'] = self.spec['slepc'].prefix
-            options.extend(['-DENABLE_SLEPC=ON'])
+            options.append('-DENABLE_SLEPC=ON')
         else:
-            options.extend(['-DENABLE_SLEPC=OFF'])
+            options.append('-DENABLE_SLEPC=OFF')
 
         if '+shared' in spec:
             # Builds dynamic executable and installs shared library
diff --git a/var/spack/repos/builtin/packages/gnat/package.py b/var/spack/repos/builtin/packages/gnat/package.py
index 843d81d9e4..1c3ef8d5d2 100644
--- a/var/spack/repos/builtin/packages/gnat/package.py
+++ b/var/spack/repos/builtin/packages/gnat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gnu-prolog/package.py
index 819e57498a..b96e026e87 100644
--- a/var/spack/repos/builtin/packages/gnu-prolog/package.py
+++ b/var/spack/repos/builtin/packages/gnu-prolog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/gnupg/package.py b/var/spack/repos/builtin/packages/gnupg/package.py
index 756f8404bc..d1d3efd014 100644
--- a/var/spack/repos/builtin/packages/gnupg/package.py
+++ b/var/spack/repos/builtin/packages/gnupg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Gnupg(AutotoolsPackage):
        standard as defined by RFC4880 """
 
     homepage = "https://gnupg.org/index.html"
-    url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.1.21.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/gnupg/gnupg-2.2.3.tar.bz2"
 
+    version('2.2.3', '6911c0127e4231ce52d60f26029dba68')
     version('2.1.21', '685ebf4c3a7134ba0209c96b18b2f064')
 
     depends_on('libgcrypt')
diff --git a/var/spack/repos/builtin/packages/gnuplot/package.py b/var/spack/repos/builtin/packages/gnuplot/package.py
index 1af9cbfb08..374d6cd234 100644
--- a/var/spack/repos/builtin/packages/gnuplot/package.py
+++ b/var/spack/repos/builtin/packages/gnuplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -45,6 +26,8 @@ class Gnuplot(AutotoolsPackage):
     # dependency of readline. Fix it with a small patch
     patch('term_include.patch')
 
+    version('5.2.5', '039db2cce62ddcfd31a6696fe576f4224b3bc3f919e66191dfe2cdb058475caa')
+    version('5.2.2', '60aedd08998160593199459dea8467fe')
     version('5.2.0', '0bd8f9af84c0ad2fa9de16772c366416')
     version('5.0.7', '8eaafddb0b12795f82ed6dd2a6ebbe80')
     version('5.0.6', '8ec46520a86a61163a701b00404faf1a')
@@ -66,7 +49,7 @@ class Gnuplot(AutotoolsPackage):
 
     # required dependencies
     depends_on('readline')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('libxpm')
     depends_on('libiconv')
 
diff --git a/var/spack/repos/builtin/packages/gnutls/package.py b/var/spack/repos/builtin/packages/gnutls/package.py
index 7f41eb3204..9f81cfda9a 100644
--- a/var/spack/repos/builtin/packages/gnutls/package.py
+++ b/var/spack/repos/builtin/packages/gnutls/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -49,7 +30,7 @@ class Gnutls(AutotoolsPackage):
     depends_on('zlib', when='+zlib')
     depends_on('gettext')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     build_directory = 'spack-build'
 
diff --git a/var/spack/repos/builtin/packages/go-bootstrap/package.py b/var/spack/repos/builtin/packages/go-bootstrap/package.py
index 0228aa74d9..b1f94fc594 100644
--- a/var/spack/repos/builtin/packages/go-bootstrap/package.py
+++ b/var/spack/repos/builtin/packages/go-bootstrap/package.py
@@ -1,30 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 glob
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 # THIS PACKAGE SHOULD NOT EXIST
@@ -36,8 +14,8 @@ from spack import *
 
 class GoBootstrap(Package):
     """Old C-bootstrapped go to bootstrap real go"""
+
     homepage = "https://golang.org"
-    url = "https://go.googlesource.com/go"
 
     extendable = True
 
@@ -46,12 +24,14 @@ class GoBootstrap(Package):
     # See: https://golang.org/doc/install/source#go14 and
     # https://github.com/golang/go/issues/17545 and
     # https://github.com/golang/go/issues/16352
+    version('1.4-bootstrap-20171003', 'dbf727a4b0e365bf88d97cbfde590016',
+            url='https://dl.google.com/go/go1.4-bootstrap-20171003.tar.gz')
     version('1.4-bootstrap-20170531', 'd2cc61cb9f829b3510ee39c0c5568014',
             url='https://storage.googleapis.com/golang/go1.4-bootstrap-20170531.tar.gz')
     version('1.4-bootstrap-20161024', '76e42c8152e8560ded880a6d1d1f53cb',
             url='https://storage.googleapis.com/golang/go1.4-bootstrap-20161024.tar.gz')
 
-    provides('golang@:1.4-bootstrap-20170531')
+    provides('golang@:1.4-bootstrap-20171003')
 
     depends_on('git', type=('build', 'link', 'run'))
 
@@ -73,15 +53,7 @@ class GoBootstrap(Package):
         with working_dir('src'):
             bash('{0}.bash'.format('all' if self.run_tests else 'make'))
 
-        try:
-            os.makedirs(prefix)
-        except OSError:
-            pass
-        for f in glob.glob('*'):
-            if os.path.isdir(f):
-                shutil.copytree(f, os.path.join(prefix, f))
-            else:
-                shutil.copy2(f, os.path.join(prefix, f))
+        install_tree('.', prefix)
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.set('GOROOT_BOOTSTRAP', self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/go/package.py b/var/spack/repos/builtin/packages/go/package.py
index b112ebe7d8..5fcdc57a5d 100644
--- a/var/spack/repos/builtin/packages/go/package.py
+++ b/var/spack/repos/builtin/packages/go/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
-import shutil
-import glob
 import llnl.util.tty as tty
 from spack import *
 
@@ -52,19 +31,25 @@ from spack import *
 class Go(Package):
     """The golang compiler and build environment"""
     homepage = "https://golang.org"
-    url = 'https://storage.googleapis.com/golang/go1.7.4.src.tar.gz'
+    url = 'https://dl.google.com/go/go1.10.1.src.tar.gz'
 
     extendable = True
 
-    version('1.9.2', '44105c865a1a810464df79233a05a568')
-    version('1.9.1', '27bce1ffb05f4f6bd90d90081e5d4169')
-    version('1.9',   'da2d44ea384076efec43ee1f8b7d45d2')
-    version('1.8.3', '64e9380e07bba907e26a00cf5fcbe77e')
-    version('1.8.1', '409dd21e7347dd1ea9efe64a700073cc')
-    version('1.8',   '7743960c968760437b6e39093cfe6f67')
-    version('1.7.5', '506de2d870409e9003e1440bcfeb3a65')
-    version('1.7.4', '49c1076428a5d3b5ad7ac65233fcca2f')
-    version('1.6.4', 'b023240be707b34059d2c114d3465c92')
+    version('1.11.1', '558f8c169ae215e25b81421596e8de7572bd3ba824b79add22fba6e284db1117')
+    version('1.11',   'afc1e12f5fe49a471e3aae7d906c73e9d5b1fdd36d52d72652dde8f6250152fb')
+    version('1.10.3', '567b1cc66c9704d1c019c50bef946272e911ec6baf244310f87f4e678be155f2')
+    version('1.10.2', '6264609c6b9cd8ed8e02ca84605d727ce1898d74efa79841660b2e3e985a98bd')
+    version('1.10.1', '589449ff6c3ccbff1d391d4e7ab5bb5d5643a5a41a04c99315e55c16bbf73ddc')
+    version('1.9.5',  'f1c2bb7f32bbd8fa7a19cc1608e0d06582df32ff5f0340967d83fb0017c49fbc')
+    version('1.9.2',  '44105c865a1a810464df79233a05a568')
+    version('1.9.1',  '27bce1ffb05f4f6bd90d90081e5d4169')
+    version('1.9',    'da2d44ea384076efec43ee1f8b7d45d2')
+    version('1.8.3',  '64e9380e07bba907e26a00cf5fcbe77e')
+    version('1.8.1',  '409dd21e7347dd1ea9efe64a700073cc')
+    version('1.8',    '7743960c968760437b6e39093cfe6f67')
+    version('1.7.5',  '506de2d870409e9003e1440bcfeb3a65')
+    version('1.7.4',  '49c1076428a5d3b5ad7ac65233fcca2f')
+    version('1.6.4',  'b023240be707b34059d2c114d3465c92')
 
     provides('golang')
 
@@ -97,15 +82,7 @@ class Go(Package):
         with working_dir('src'):
             bash('{0}.bash'.format('all' if self.run_tests else 'make'))
 
-        try:
-            os.makedirs(prefix)
-        except OSError:
-            pass
-        for f in glob.glob('*'):
-            if os.path.isdir(f):
-                shutil.copytree(f, os.path.join(prefix, f))
-            else:
-                shutil.copy2(f, os.path.join(prefix, f))
+        install_tree('.', prefix)
 
     def setup_environment(self, spack_env, run_env):
         spack_env.set('GOROOT_FINAL', self.spec.prefix)
@@ -119,10 +96,9 @@ class Go(Package):
 
         In most cases, extensions will only need to set GOPATH and use go::
 
-        env = os.environ
         env['GOPATH'] = self.source_path + ':' + env['GOPATH']
         go('get', '<package>', env=env)
-        shutil.copytree('bin', os.path.join(prefix, '/bin'))
+        install_tree('bin', prefix.bin)
         """
         #  Add a go command/compiler for extensions
         module.go = self.spec['go'].command
diff --git a/var/spack/repos/builtin/packages/gobject-introspection/package.py b/var/spack/repos/builtin/packages/gobject-introspection/package.py
index ec71e3cddd..7466458cd7 100644
--- a/var/spack/repos/builtin/packages/gobject-introspection/package.py
+++ b/var/spack/repos/builtin/packages/gobject-introspection/package.py
@@ -1,29 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack import spack_root
+from spack.paths import spack_root
 
 
 class GobjectIntrospection(Package):
@@ -44,7 +25,7 @@ class GobjectIntrospection(Package):
     depends_on("cairo")
     depends_on("bison", type="build")
     depends_on("flex", type="build")
-    depends_on("pkg-config@0.9.0:", type="build")
+    depends_on("pkgconfig", type="build")
 
     # GobjectIntrospection does not build with sed from darwin:
     depends_on('sed', when='platform=darwin', type='build')
diff --git a/var/spack/repos/builtin/packages/googletest/package.py b/var/spack/repos/builtin/packages/googletest/package.py
index 5eab658bac..95bdff7473 100644
--- a/var/spack/repos/builtin/packages/googletest/package.py
+++ b/var/spack/repos/builtin/packages/googletest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,6 +18,11 @@ class Googletest(CMakePackage):
     variant('gmock', default=False, description='Build with gmock')
     conflicts('+gmock', when='@:1.7.0')
 
+    variant('pthreads', default=True,
+            description='Build multithreaded version with pthreads')
+    variant('shared', default=True,
+            description='Build shared libraries (DLLs)')
+
     def cmake_args(self):
         spec = self.spec
         if '@1.8.0:' in spec:
@@ -49,6 +35,11 @@ class Googletest(CMakePackage):
         else:
             # Old style (contains only GTest)
             options = []
+
+        options.append('-Dgtest_disable_pthreads={0}'.format(
+            'ON' if '+pthreads' in spec else 'OFF'))
+        options.append('-DBUILD_SHARED_LIBS={0}'.format(
+            'ON' if '+shared' in spec else 'OFF'))
         return options
 
     @when('@:1.7.0')
@@ -61,5 +52,9 @@ class Googletest(CMakePackage):
                          prefix.include)
 
             mkdirp(prefix.lib)
-            install('libgtest.a', prefix.lib)
-            install('libgtest_main.a', prefix.lib)
+            if '+shared' in spec:
+                install('libgtest.{0}'.format(dso_suffix), prefix.lib)
+                install('libgtest_main.{0}'.format(dso_suffix), prefix.lib)
+            else:
+                install('libgtest.a', prefix.lib)
+                install('libgtest_main.a', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/gotcha/package.py b/var/spack/repos/builtin/packages/gotcha/package.py
new file mode 100644
index 0000000000..e1677a4711
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gotcha/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gotcha(CMakePackage):
+    """C software library for shared library function wrapping,
+    enables tools to intercept calls into shared libraries"""
+
+    homepage = "http://github.com/LLNL/gotcha"
+    git      = "https://github.com/LLNL/gotcha.git"
+
+    version('develop', branch='develop')
+    version('master', branch='master')
+    version('1.0.2', tag='1.0.2')
+    version('0.0.2', tag='0.0.2')
+
+    variant('test', default=False, description='Build tests for Gotcha')
+
+    def configure_args(self):
+        spec = self.spec
+        return [
+            '-DGOTCHA_ENABLE_TESTS=%s' % ('ON' if '+test' in spec else 'OFF')
+        ]
diff --git a/var/spack/repos/builtin/packages/gource/package.py b/var/spack/repos/builtin/packages/gource/package.py
index 3d9ddd1ff6..3d9fe00c80 100644
--- a/var/spack/repos/builtin/packages/gource/package.py
+++ b/var/spack/repos/builtin/packages/gource/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class Gource(AutotoolsPackage):
     depends_on('autoconf',   type='build')
     depends_on('libtool',    type='build')
     depends_on('glm',        type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('freetype@2.0:')
     depends_on('pcre')
diff --git a/var/spack/repos/builtin/packages/gperf/package.py b/var/spack/repos/builtin/packages/gperf/package.py
index e51f86fb4b..d3c5863c6b 100644
--- a/var/spack/repos/builtin/packages/gperf/package.py
+++ b/var/spack/repos/builtin/packages/gperf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class Gperf(AutotoolsPackage):
     single string comparison only."""
 
     homepage = "https://www.gnu.org/software/gperf/"
-    url      = "http://ftp.gnu.org/pub/gnu/gperf/gperf-3.0.4.tar.gz"
+    url      = "https://ftpmirror.gnu.org/gperf/gperf-3.0.4.tar.gz"
 
     version('3.0.4', 'c1f1db32fb6598d6a93e6e88796a8632')
 
diff --git a/var/spack/repos/builtin/packages/gperftools/package.py b/var/spack/repos/builtin/packages/gperftools/package.py
index c5653f696c..df26272a71 100644
--- a/var/spack/repos/builtin/packages/gperftools/package.py
+++ b/var/spack/repos/builtin/packages/gperftools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,12 +12,11 @@ class Gperftools(AutotoolsPackage):
        heap-profiler, and cpu-profiler.
 
     """
-    homepage = "https://code.google.com/p/gperftools"
-    url      = "https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz"
+    homepage = "https://github.com/gperftools/gperftools"
+    url      = "https://github.com/gperftools/gperftools/releases/download/gperftools-2.7/gperftools-2.7.tar.gz"
 
-    version('2.4', '2171cea3bbe053036fb5d5d25176a160',
-            url="https://github.com/gperftools/gperftools/releases/download/gperftools-2.4/gperftools-2.4.tar.gz")
-    version('2.3', 'f54dd119f0e46ac1f13264f8d97adf90',
-            url="https://googledrive.com/host/0B6NtGsLhIcf7MWxMMF9JdTN3UVk/gperftools-2.3.tar.gz")
+    version('2.7', '1ee8c8699a0eff6b6a203e59b43330536b22bbcbe6448f54c7091e5efb0763c9')
+    version('2.4', '982a37226eb42f40714e26b8076815d5ea677a422fb52ff8bfca3704d9c30a2d')
+    version('2.3', '093452ad45d639093c144b4ec732a3417e8ee1f3744f2b0f8d45c996223385ce')
 
-    depends_on("libunwind")
+    depends_on("unwind")
diff --git a/var/spack/repos/builtin/packages/gplates/package.py b/var/spack/repos/builtin/packages/gplates/package.py
new file mode 100644
index 0000000000..6d54c80822
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gplates/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gplates(CMakePackage):
+    """GPlates is desktop software for the interactive visualisation of
+    plate-tectonics. GPlates offers a novel combination of interactive
+    plate-tectonic reconstructions, geographic information system (GIS)
+    functionality and raster data visualisation. GPlates enables both the
+    visualisation and the manipulation of plate-tectonic reconstructions
+    and associated data through geological time."""
+
+    homepage = 'https://www.gplates.org'
+    url      = 'https://sourceforge.net/projects/gplates/files/gplates/2.0/gplates-2.0.0-unixsrc.tar.bz2/download'
+
+    version('2.0.0', '9e95874b35a01f4c9bff5845a1621ad5')
+
+    depends_on('cmake@2.6.2:', type='build')
+    # Qt 5 does not support (at least) the Q_WS_* constants.
+    depends_on('qt+opengl@4.4.0:4.99')
+    depends_on('qwt@6.0.1:')
+    depends_on('mesa-glu')
+    depends_on('glew')
+    # GDAL's OGRSFDriverRegistrar is not compatible anymore starting with 2.0.
+    depends_on('gdal@1.3.2:1.99')
+    depends_on('cgal@3.5:')
+    depends_on('proj@4.6.0:')
+    # Boost's Python library has a different name starting with 1.67.
+    # There were changes to Boost's optional in 1.61 that make the build fail.
+    depends_on('boost+python@1.34:1.60')
+    depends_on('python@2:2.99')
+
+    # Officially, GPlates only supports GCC 4. Moreover, it requires
+    # QtXmlPatterns, which Qt 4 only builds with GCC 4.
+    conflicts('%gcc@5:')
+
+    # When built in parallel, headers are not generated before they are used
+    # (specifically, ViewportWindowUi.h).
+    parallel = False
+
+    def url_for_version(self, version):
+        url = 'https://sourceforge.net/projects/gplates/files/gplates/{0}/gplates-{1}-unixsrc.tar.bz2/download'
+        return url.format(version.up_to(2), version)
+
+    def patch(self):
+        # GPlates overrides FindPythonLibs and finds the static library, which
+        # can not be used easily. Fall back to CMake's version, which finds
+        # the shared library instead.
+        force_remove('cmake/modules/FindPythonLibs.cmake')
+
+        # GPlates only installs its binary for the Release configuration.
+        filter_file('CONFIGURATIONS release',
+                    'CONFIGURATIONS Debug Release RelWithDebInfo MinSizeRel',
+                    'src/CMakeLists.txt')
diff --git a/var/spack/repos/builtin/packages/grackle/package.py b/var/spack/repos/builtin/packages/grackle/package.py
index 06689a3c4c..6163f72bbc 100644
--- a/var/spack/repos/builtin/packages/grackle/package.py
+++ b/var/spack/repos/builtin/packages/grackle/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os.path
-import shutil
 import inspect
 
 from spack import *
@@ -35,12 +15,16 @@ class Grackle(Package):
     generalized and trimmed down version of the chemistry network of the Enzo
     simulation code
     """
-    homepage = 'http://grackle.readthedocs.io/en/grackle-2.2/'
-    url = 'https://bitbucket.org/grackle/grackle/get/grackle-2.0.1.tar.bz2'
+    homepage = 'http://grackle.readthedocs.io/en/grackle-3.1/'
+    url = 'https://bitbucket.org/grackle/grackle/get/grackle-3.1.tar.bz2'
 
+    version('3.1', 'cee7799dc505010e2e875950561bbbe1')
+    version('3.0', 'dc85e664da7e70b65b3ef7164477a959')
     version('2.2', 'ec49ed1db5a42db21f478285150c2ba3')
     version('2.0.1', 'a9624ad13a60c592c1a0a4ea8e1ae86d')
 
+    variant('float', default=False, description='Build with float')
+
     depends_on('libtool', when='@2.2')
 
     depends_on('mpi')
@@ -74,7 +58,7 @@ class Grackle(Package):
             'clib',
             'Make.mach.{0}'.format(grackle_architecture)
         )
-        shutil.copy(template, makefile)
+        copy(template, makefile)
         for key, value in substitutions.items():
             filter_file(key, value, makefile)
 
@@ -83,6 +67,8 @@ class Grackle(Package):
             make('clean')
             make('machine-{0}'.format(grackle_architecture))
             make('opt-high')
+            if spec.satisfies("+float"):
+                make('precision-32')
             make('show-config')
             make()
             mkdirp(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/gradle/package.py b/var/spack/repos/builtin/packages/gradle/package.py
index 1d4112132a..54f288e500 100644
--- a/var/spack/repos/builtin/packages/gradle/package.py
+++ b/var/spack/repos/builtin/packages/gradle/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Gradle(Package):
@@ -37,6 +17,7 @@ class Gradle(Package):
     homepage = "https://gradle.org"
     url      = "https://services.gradle.org/distributions/gradle-3.4-all.zip"
 
+    version('4.8.1', 'bf87b4c64bb6a43861f1964fb8a7f3bc')
     version('3.4',    '5ae23dbd730dea22eb79cd97a072f06a')
     version('3.3',    '355f61e9c5d092d49577765ab3712dc0')
     version('3.2.1',  'd44dba900ff364103e1f45c0f4b27bbe')
@@ -80,4 +61,4 @@ class Gradle(Package):
     depends_on('java')
 
     def install(self, spec, prefix):
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/grandr/package.py b/var/spack/repos/builtin/packages/grandr/package.py
index 14da4896f4..233b97b9b9 100644
--- a/var/spack/repos/builtin/packages/grandr/package.py
+++ b/var/spack/repos/builtin/packages/grandr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/graph500/package.py b/var/spack/repos/builtin/packages/graph500/package.py
new file mode 100644
index 0000000000..c689cba2ad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/graph500/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Graph500(MakefilePackage):
+    """Graph500 reference implementations."""
+
+    homepage = "https://graph500.org"
+    url      = "https://github.com/graph500/graph500/archive/graph500-3.0.0.tar.gz"
+
+    version('3.0.0', 'a2ebb4783b21e2d86387a217776395e3')
+
+    depends_on('mpi@2.0:')
+
+    build_directory = 'src'
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter(join_path(self.build_directory, 'Makefile'))
+        makefile.filter(r'^MPICC\s*=.*', 'MPICC={0}'.format(spec['mpi'].mpicc))
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            mkdir(prefix.bin)
+            install('graph500_reference_bfs', prefix.bin)
+            install('graph500_reference_bfs_sssp', prefix.bin)
+            install('graph500_custom_bfs', prefix.bin)
+            install('graph500_custom_bfs_sssp', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/graphicsmagick/package.py b/var/spack/repos/builtin/packages/graphicsmagick/package.py
new file mode 100644
index 0000000000..295ba9034b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/graphicsmagick/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Graphicsmagick(AutotoolsPackage):
+    """GraphicsMagick is the swiss army knife of image processing.
+
+    Provides a robust and efficient collection of tools and libraries which
+    support reading, writing, and manipulating an image in over 88 major
+    formats including important formats like DPX, GIF, JPEG, JPEG-2000, PNG,
+    PDF, PNM, and TIFF.
+    """
+
+    homepage = "http://www.graphicsmagick.org/"
+    url      = "https://sourceforge.net/projects/graphicsmagick/files/graphicsmagick/1.3.29/GraphicsMagick-1.3.29.tar.xz/download"
+
+    version('1.3.29', 'ddde0dd239592db50c5378472355c03c')
+
+    depends_on('bzip2')
+    depends_on('ghostscript')
+    depends_on('ghostscript-fonts')
+    depends_on('graphviz')
+    depends_on('jasper')
+    depends_on('jpeg')
+    depends_on('lcms')
+    depends_on('libice')
+    depends_on('libpng')
+    depends_on('libsm')
+    depends_on('libtiff')
+    depends_on('libtool')
+    depends_on('libxml2')
+    depends_on('xz')
+    depends_on('zlib')
+
+    def configure_args(self):
+        args = ['--enable-shared']
+        return args
diff --git a/var/spack/repos/builtin/packages/graphlib/package.py b/var/spack/repos/builtin/packages/graphlib/package.py
index 0fa82267d8..d5b50acfe1 100644
--- a/var/spack/repos/builtin/packages/graphlib/package.py
+++ b/var/spack/repos/builtin/packages/graphlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/graphmap/package.py b/var/spack/repos/builtin/packages/graphmap/package.py
index 0e4a676588..25af904306 100644
--- a/var/spack/repos/builtin/packages/graphmap/package.py
+++ b/var/spack/repos/builtin/packages/graphmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Graphmap(MakefilePackage):
     """A highly sensitive and accurate mapper for long, error-prone reads"""
 
     homepage = "https://github.com/isovic/graphmap"
-    url      = "https://github.com/isovic/graphmap/archive/v0.3.0.tar.gz"
+    git      = "https://github.com/isovic/graphmap.git"
 
-    version('0.3.0', git='https://github.com/isovic/graphmap.git', commit='eb8c75d68b03be95464318afa69b645a59f8f6b7')
+    version('0.3.0', commit='eb8c75d68b03be95464318afa69b645a59f8f6b7')
 
     def edit(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/graphviz/package.py b/var/spack/repos/builtin/packages/graphviz/package.py
index 0ec35f09e8..efb32328fa 100644
--- a/var/spack/repos/builtin/packages/graphviz/package.py
+++ b/var/spack/repos/builtin/packages/graphviz/package.py
@@ -1,38 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import os
 import sys
-import shutil
 
 
 class Graphviz(AutotoolsPackage):
     """Graph Visualization Software"""
+
     homepage = 'http://www.graphviz.org'
-    url      = 'http://www.graphviz.org/pub/graphviz/stable/SOURCES/graphviz-2.38.0.tar.gz'
+    git      = 'https://gitlab.com/graphviz/graphviz.git'
 
-    version('2.38.0', '5b6a829b2ac94efcd5fa3c223ed6d3ae')
+    # This commit hash is tag='stable_release_2.40.1'
+    version('2.40.1', commit='67cd2e5121379a38e0801cc05cce5033f8a2a609')
 
     # We try to leave language bindings enabled if they don't cause
     # build issues or add dependencies.
@@ -78,9 +61,16 @@ class Graphviz(AutotoolsPackage):
             description='Build with pango+cairo support (more output formats)')
     variant('libgd', default=False,
             description='Build with libgd support (more output formats)')
-
     variant('gts', default=False,
             description='Build with GNU Triangulated Surface Library')
+    variant('expat', default=False,
+            description='Build with Expat support (enables HTML-like labels)')
+    variant('ghostscript', default=False,
+            description='Build with Ghostscript support')
+    variant('qt', default=False,
+            description='Build with Qt support')
+    variant('gtkplus', default=False,
+            description='Build with GTK+ support')
 
     parallel = False
 
@@ -96,28 +86,51 @@ class Graphviz(AutotoolsPackage):
         '+python', '+r', '+ruby', '+tcl')
 
     for b in tested_bindings + untested_bindings:
-        depends_on('swig', when=b)
+        depends_on('swig', type='build', when=b)
 
+    depends_on('java', when='+java')
+    depends_on('python@2:2.8', when='+python')
+
+    # +pangocairo
     depends_on('cairo', when='+pangocairo')
     depends_on('pango', when='+pangocairo')
+    depends_on('freetype', when='+pangocairo')
+    depends_on('glib', when='+pangocairo')
+    depends_on('fontconfig', when='+pangocairo')
+    depends_on('libpng', when='+pangocairo')
+    depends_on('zlib', when='+pangocairo')
+    # +libgd
     depends_on('libgd', when='+libgd')
+    depends_on('fontconfig', when='+libgd')
+    depends_on('freetype', when='+libgd')
+    # +gts
     depends_on('gts', when='+gts')
-    depends_on('ghostscript')
-    depends_on('freetype')
-    depends_on('expat')
-    depends_on('libtool')
-    depends_on('pkg-config', type='build')
-
-    depends_on('java', when='+java')
-    depends_on('python@2:2.8', when='+python')
-
-    def patch(self):
-        # Fix a few variable names, gs after 9.18 renamed them
-        # See http://lists.linuxfromscratch.org/pipermail/blfs-book/2015-October/056960.html
-        if self.spec.satisfies('^ghostscript@9.18:'):
-            kwargs = {'ignore_absent': False, 'backup': True, 'string': True}
-            filter_file(' e_', ' gs_error_', 'plugin/gs/gvloadimage_gs.c',
-                        **kwargs)
+    # +expat
+    depends_on('expat', when='+expat')
+    # +ghostscript
+    depends_on('ghostscript', when='+ghostscript')
+    # +qt
+    depends_on('qt', when='+qt')
+    # +gtkplus
+    depends_on('gtkplus', when='+gtkplus')
+
+    # Build dependencies
+    depends_on('pkgconfig', type='build')
+    # The following are needed when building from git
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('bison', type='build')
+    depends_on('flex', type='build')
+    depends_on('libtool', type='build')
+
+    def autoreconf(self, spec, prefix):
+        # We need to generate 'configure' when checking out sources from git
+        # If configure exists nothing needs to be done
+        if os.path.exists(self.configure_abs_path):
+            return
+        # Else bootstrap (disabling auto-configure with NOCONFIG)
+        bash = which('bash')
+        bash('./autogen.sh', 'NOCONFIG')
 
     def configure_args(self):
         spec = self.spec
@@ -150,11 +163,17 @@ class Graphviz(AutotoolsPackage):
         else:
             options.append('--enable-swig=no')
 
-        for var in ('+pangocairo', '+libgd', '+gts'):
+        for var in ('+pangocairo', '+libgd', '+gts', '+expat', '+ghostscript',
+                    '+qt', '+gtkplus'):
+            feature = var[1:]
+            if feature == 'gtkplus':
+                # In spack terms, 'gtk+' is 'gtkplus' while
+                # the relative configure option is 'gtk'
+                feature = 'gtk'
             if var in spec:
-                options.append('--with-{0}'.format(var[1:]))
+                options.append('--with-{0}'.format(feature))
             else:
-                options.append('--without-{0}'.format(var[1:]))
+                options.append('--without-{0}'.format(feature))
 
         # On OSX fix the compiler error:
         # In file included from tkStubLib.c:15:
@@ -163,7 +182,4 @@ class Graphviz(AutotoolsPackage):
         if sys.platform == 'darwin':
             options.append('CFLAGS=-I/opt/X11/include')
 
-        # A hack to patch config.guess in the libltdl sub directory
-        shutil.copyfile('./config/config.guess', 'libltdl/config/config.guess')
-
         return options
diff --git a/var/spack/repos/builtin/packages/grass/package.py b/var/spack/repos/builtin/packages/grass/package.py
new file mode 100644
index 0000000000..a703c09327
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grass/package.py
@@ -0,0 +1,185 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Grass(AutotoolsPackage):
+    """GRASS GIS (Geographic Resources Analysis Support System), is a free
+       and open source Geographic Information System (GIS) software suite
+       used for geospatial data management and analysis, image processing,
+       graphics and maps production, spatial modeling, and visualization."""
+
+    homepage = "http://grass.osgeo.org"
+    url      = "https://grass.osgeo.org/grass74/source/grass-7.4.1.tar.gz"
+
+    version('7.4.1',    'bf7add62cbeb05a3ed5ad832344ba524')
+
+    variant('cxx',       default=True,  description='Add c++ functionality')
+    variant('tiff',      default=True,  description='Add TIFF functionality')
+    variant('png',       default=True,  description='Add PNG functionality')
+    variant('postgres',  default=False, description='Add PostgreSQL functionality')
+    variant('mysql',     default=False, description='Add MySQL functionality')
+    variant('sqlite',    default=True,  description='Add SQLite functionality')
+    variant('opengl',    default=True,  description='Add OpenGL functionality')
+    variant('fftw',      default=True,  description='Add FFTW functionality')
+    variant('blas',      default=False, description='Add BLAS functionality')
+    variant('lapack',    default=False, description='Add LAPACK functionality')
+    variant('cairo',     default=True,  description='Add Cairo functionality')
+    variant('freetype',  default=True,  description='Add FreeType functionality')
+    variant('readline',  default=False, description='Add Readline functionality')
+    variant('regex',     default=True,  description='Add regex functionality')
+    variant('pthread',   default=False, description='Add POSIX threads functionality')
+    variant('openmp',    default=False, description='Add OpenMP functionality')
+    variant('opencl',    default=False, description='Add OpenCL functionality')
+    variant('bzlib',     default=False, description='Add BZIP2 functionality')
+    variant('netcdf',    default=False, description='Enable NetCDF support')
+    variant('geos',      default=False, description='Geometry Engine for v.buffer')
+
+    # required components
+    depends_on('gmake@3.8.1:', type='build')
+    depends_on('zlib')
+    depends_on('flex', type='build')
+    depends_on('bison', type='build')
+    depends_on('proj')
+    depends_on('gdal')
+    depends_on('python@2.7:2.9', type=('build', 'run'))
+    depends_on('libx11')
+
+    # optional pieces
+    depends_on('libtiff', when='+tiff')
+    depends_on('libpng', when='+png')
+    depends_on('postgresql', when='+postgres')
+    depends_on('mariadb', when='+mysql')
+    depends_on('sqlite', when='+sqlite')
+    depends_on('gl', when='+opengl')
+    depends_on('fftw', when='+fftw')
+    depends_on('blas', when='+blas')
+    depends_on('lapack', when='+lapack')
+    depends_on('cairo', when='+cairo')
+    depends_on('freetype', when='+freetype')
+    depends_on('readline', when='+readline')
+    depends_on('opencl', when='+opencl')
+    depends_on('bzip2', when='+bzlib')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('geos', when='+geos')
+
+    def configure_args(self):
+        spec = self.spec
+
+        args = [
+            '--without-odbc',
+            '--without-nls',
+            '--without-opendwg',
+            '--with-x',
+            '--with-gdal={0}/bin/gdal-config'.format(
+                spec['gdal'].prefix),
+            '--with-proj-share={0}/share/proj'.format(
+                spec['proj'].prefix),
+        ]
+
+        if '+cxx' in spec:
+            args.append('--with-cxx')
+        else:
+            args.append('--without-cxx')
+
+        if '+tiff' in spec:
+            args.append('--with-tiff')
+        else:
+            args.append('--without-tiff')
+
+        if '+png' in spec:
+            args.append('--with-png')
+        else:
+            args.append('--without-png')
+
+        if '+postgres' in spec:
+            args.append('--with-postgres')
+        else:
+            args.append('--without-postgres')
+
+        if '+mysql' in spec:
+            args.append('--with-mysql')
+        else:
+            args.append('--without-mysql')
+
+        if '+sqlite' in spec:
+            args.append('--with-sqlite')
+        else:
+            args.append('--without-sqlite')
+
+        if '+opengl' in spec:
+            args.append('--with-opengl')
+        else:
+            args.append('--without-opengl')
+
+        if '+fftw' in spec:
+            args.append('--with-fftw')
+        else:
+            args.append('--without-fftw')
+
+        if '+blas' in spec:
+            args.append('--with-blas')
+        else:
+            args.append('--without-blas')
+
+        if '+lapack' in spec:
+            args.append('--with-lapack')
+        else:
+            args.append('--without-lapack')
+
+        if '+cairo' in spec:
+            args.append('--with-cairo')
+        else:
+            args.append('--without-cairo')
+
+        if '+freetype' in spec:
+            args.append('--with-freetype')
+        else:
+            args.append('--without-freetype')
+
+        if '+readline' in spec:
+            args.append('--with-readline')
+        else:
+            args.append('--without-readline')
+
+        if '+regex' in spec:
+            args.append('--with-regex')
+        else:
+            args.append('--without-regex')
+
+        if '+pthread' in spec:
+            args.append('--with-pthread')
+        else:
+            args.append('--without-pthread')
+
+        if '+openmp' in spec:
+            args.append('--with-openmp')
+        else:
+            args.append('--without-openmp')
+
+        if '+opencl' in spec:
+            args.append('--with-opencl')
+        else:
+            args.append('--without-opencl')
+
+        if '+bzlib' in spec:
+            args.append('--with-bzlib')
+        else:
+            args.append('--without-bzlib')
+
+        if '+netcdf' in spec:
+            args.append('--with-netcdf={0}/bin/nc-config'.format(
+                spec['netcdf'].prefix))
+        else:
+            args.append('--without-netcdf')
+
+        if '+geos' in spec:
+            args.append('--with-geos={0}/bin/geos-config'.format(
+                spec['geos'].prefix))
+        else:
+            args.append('--without-geos')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/grib-api/cmake_install_rpath.patch b/var/spack/repos/builtin/packages/grib-api/cmake_install_rpath.patch
new file mode 100644
index 0000000000..7e2b250883
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/cmake_install_rpath.patch
@@ -0,0 +1,11 @@
+--- a/cmake/ecbuild_append_to_rpath.cmake
++++ b/cmake/ecbuild_append_to_rpath.cmake
+@@ -31,7 +31,7 @@ function( _path_append var path )
+ 	else()
+ 		list( FIND ${var} ${path} _found )
+ 		if( _found EQUAL "-1" )
+-			set( ${var} "${${var}}:${path}" PARENT_SCOPE )
++			set( ${var} "${${var}};${path}" PARENT_SCOPE )
+ 		endif()
+ 	endif()
+ endfunction()
diff --git a/var/spack/repos/builtin/packages/grib-api/disable_numpy.patch b/var/spack/repos/builtin/packages/grib-api/disable_numpy.patch
new file mode 100644
index 0000000000..c056388da8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/disable_numpy.patch
@@ -0,0 +1,12 @@
+--- a/python/CMakeLists.txt
++++ b/python/CMakeLists.txt
+@@ -6,7 +6,8 @@ if( HAVE_PYTHON )
+     #endif()
+ 
+     # check for Numpy
+-    find_package( NumPy )
++    # find_package( NumPy )
++    set(NUMPY_FOUND FALSE)
+ 
+     ###############################################################################
+     # swig python interface
diff --git a/var/spack/repos/builtin/packages/grib-api/enable_only_jasper.patch b/var/spack/repos/builtin/packages/grib-api/enable_only_jasper.patch
new file mode 100644
index 0000000000..06e9790f59
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/enable_only_jasper.patch
@@ -0,0 +1,34 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -106,18 +106,7 @@ set( HAVE_LIBOPENJPEG 0 )
+ 
+ if( ENABLE_JPG )
+ 
+-    # Note: This is a deprecated feature but we need it to find Jasper at ECMWF.
+-    #       ecbuild_add_extra_search_paths modifies CMAKE_PREFIX_PATH
+-    #       which can affect future package discovery if not undone by the caller.
+-    #       The current CMAKE_PREFIX_PATH is backed up as _CMAKE_PREFIX_PATH
+-    #
+-    set(CMAKE_WARN_DEPRECATED OFF) # Suppress deprecation message
+-    ecbuild_add_extra_search_paths( jasper )
+     find_package( Jasper )
+-    set(CMAKE_PREFIX_PATH ${_CMAKE_PREFIX_PATH})    # Restore CMAKE_PREFIX_PATH
+-    set(CMAKE_WARN_DEPRECATED ON)  # Remove suppression
+-
+-    find_package( OpenJPEG )
+ 
+     if( JASPER_FOUND )
+         list( APPEND GRIB_API_TPLS Jasper )
+@@ -125,12 +114,6 @@ if( ENABLE_JPG )
+         set( HAVE_LIBJASPER 1 )
+     endif()
+ 
+-    if( OPENJPEG_FOUND )
+-        list( APPEND GRIB_API_TPLS OpenJPEG )
+-        set( HAVE_JPEG 1 )
+-        set( HAVE_LIBOPENJPEG 1 )
+-    endif()
+-
+ endif()
+ 
+ 
diff --git a/var/spack/repos/builtin/packages/grib-api/enable_only_openjpeg.patch b/var/spack/repos/builtin/packages/grib-api/enable_only_openjpeg.patch
new file mode 100644
index 0000000000..a440477029
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grib-api/enable_only_openjpeg.patch
@@ -0,0 +1,28 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -106,25 +106,8 @@ set( HAVE_LIBOPENJPEG 0 )
+ 
+ if( ENABLE_JPG )
+ 
+-    # Note: This is a deprecated feature but we need it to find Jasper at ECMWF.
+-    #       ecbuild_add_extra_search_paths modifies CMAKE_PREFIX_PATH
+-    #       which can affect future package discovery if not undone by the caller.
+-    #       The current CMAKE_PREFIX_PATH is backed up as _CMAKE_PREFIX_PATH
+-    #
+-    set(CMAKE_WARN_DEPRECATED OFF) # Suppress deprecation message
+-    ecbuild_add_extra_search_paths( jasper )
+-    find_package( Jasper )
+-    set(CMAKE_PREFIX_PATH ${_CMAKE_PREFIX_PATH})    # Restore CMAKE_PREFIX_PATH
+-    set(CMAKE_WARN_DEPRECATED ON)  # Remove suppression
+-
+     find_package( OpenJPEG )
+ 
+-    if( JASPER_FOUND )
+-        list( APPEND GRIB_API_TPLS Jasper )
+-        set( HAVE_JPEG 1 )
+-        set( HAVE_LIBJASPER 1 )
+-    endif()
+-
+     if( OPENJPEG_FOUND )
+         list( APPEND GRIB_API_TPLS OpenJPEG )
+         set( HAVE_JPEG 1 )
diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py
index 5da851c1ba..dd782a97d1 100644
--- a/var/spack/repos/builtin/packages/grib-api/package.py
+++ b/var/spack/repos/builtin/packages/grib-api/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,51 +11,122 @@ class GribApi(CMakePackage):
        C, FORTRAN and Python programs developed for encoding and decoding WMO
        FM-92 GRIB edition 1 and edition 2 messages."""
 
-    homepage = "https://software.ecmwf.int/wiki/display/GRIB/Home"
-    url      = "https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz"
+    homepage = 'https://software.ecmwf.int/wiki/display/GRIB/Home'
+    url = 'https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz?api=v2'
+    list_url = 'https://software.ecmwf.int/wiki/display/GRIB/Releases'
+
+    maintainers = ['skosukhin']
 
+    version('1.24.0', 'dcc549069cdeeaa1959732c36ab3136f')
     version('1.21.0', 'eb64c5eb72e6e90841237cba9d644016')
     version('1.17.0', 'bca7114d2c3100501a08190a146818d2')
     version('1.16.0', '8c7fdee03344e4379d400ae20976a460')
 
-    variant('netcdf', default=False, description='Enable netcdf encoding/decoding using netcdf library')
-    variant('jpeg', default=True, description='Enable jpeg 2000 for grib 2 decoding/encoding')
-    variant('png', default=False, description='Enable png for decoding/encoding')
+    variant('netcdf', default=False,
+            description='Enable netcdf encoding/decoding using netcdf library')
+    variant('jp2k', default='openjpeg', values=('openjpeg', 'jasper', 'none'),
+            description='Specify JPEG2000 decoding/encoding backend')
+    variant('png', default=False,
+            description='Enable png for decoding/encoding')
+    variant('aec', default=False,
+            description='Enable Adaptive Entropy Coding for decoding/encoding')
+    variant('pthreads', default=False,
+            description='Enable POSIX threads')
+    variant('openmp', default=False,
+            description='Enable OpenMP threads')
+    variant('python', default=False,
+            description='Enable the Python interface')
+    variant('numpy', default=False,
+            description='Enable numpy support in the Python interface')
+    variant('fortran', default=False, description='Enable the Fortran support')
+    variant('examples', default=True,
+            description='Build the examples (part of the full test suite)')
+    variant('test', default=True, description='Enable the tests')
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo', 'Production'))
 
-    depends_on('libpng', when='+png')
+    # The building script tries to find an optional package valgrind when
+    # tests are enabled but the testing scripts don't use it.
+    # depends_on('valgrind', type='test', when='+test')
+
     depends_on('netcdf', when='+netcdf')
-    depends_on('jasper', when='+jpeg')
-    depends_on('cmake@2.8.11:', type='build')
+    depends_on('openjpeg@1.5.0:1.5.999', when='jp2k=openjpeg')
+    depends_on('jasper', when='jp2k=jasper')
+    depends_on('libpng', when='+png')
+    depends_on('libaec', when='+aec')
+    depends_on('python@2.5:2.999', when='+python',
+               type=('build', 'link', 'run'))
+    depends_on('py-numpy', when='+python+numpy', type=('build', 'run'))
+    extends('python', when='+python')
 
-    def cmake_args(self):
-        spec = self.spec
-        args = ['-DBUILD_SHARED_LIBS=BOTH']
+    conflicts('+openmp', when='+pthreads',
+              msg='Cannot enable both POSIX threads and OMP')
+    conflicts('+numpy', when='~python',
+              msg='Numpy variant is valid only when the Python interface is '
+                  'enabled')
+
+    # The following enforces linking against the specified JPEG2000 backend.
+    patch('enable_only_openjpeg.patch', when='jp2k=openjpeg')
+    patch('enable_only_jasper.patch', when='jp2k=jasper')
+
+    # Disable NumPy even if it's available.
+    patch('disable_numpy.patch', when='+python~numpy')
 
-        # We will add python support later.
-        args.append('-DENABLE_PYTHON=OFF')
+    # CMAKE_INSTALL_RPATH must be a semicolon-separated list.
+    patch('cmake_install_rpath.patch')
 
-        # Disable FORTRAN interface if we don't have it.
-        if (self.compiler.f77 is None) or (self.compiler.fc is None):
-            args.append('-DENABLE_FORTRAN=OFF')
+    @run_before('cmake')
+    def check_fortran(self):
+        if '+fortran' in self.spec and self.compiler.fc is None:
+            raise InstallError(
+                'Fortran interface requires a Fortran compiler!')
 
-        if '+netcdf' in spec:
-            args.append('-DENABLE_NETCDF=ON')
-            args.append('-DNETCDF_PATH=%s' % spec['netcdf'].prefix)
+    def cmake_args(self):
+        var_opt_list = [('+pthreads', 'GRIB_THREADS'),
+                        ('+openmp', 'GRIB_OMP_THREADS'),
+                        ('+python', 'PYTHON'),
+                        ('+fortran', 'FORTRAN'),
+                        ('+examples', 'EXAMPLES'),
+                        ('+test', 'TESTS')]
+
+        args = ['-DENABLE_%s=%s' % (opt, 'ON' if var in self.spec else 'OFF')
+                for var, opt in var_opt_list]
+
+        if '+netcdf' in self.spec:
+            args.extend(['-DENABLE_NETCDF=ON',
+                         # Prevent overriding by environment variable
+                         # HDF5_ROOT.
+                         '-DHDF5_ROOT=' + self.spec['hdf5'].prefix,
+                         # Prevent possible overriding by environment variables
+                         # NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH.
+                         '-DNETCDF_PATH=' + self.spec['netcdf'].prefix])
         else:
             args.append('-DENABLE_NETCDF=OFF')
 
-        if '+jpeg' in spec:
-            args.append('-DENABLE_JPG=ON')
-            args.append('-DJASPER_PATH=%s' % spec['jasper'].prefix)
-        else:
+        if self.spec.variants['jp2k'].value == 'none':
             args.append('-DENABLE_JPG=OFF')
+        else:
+            args.append('-DENABLE_JPG=ON')
+
+        if self.spec.variants['jp2k'].value == 'openjpeg':
+            args.append('-DOPENJPEG_PATH=' + self.spec['openjpeg'].prefix)
 
-        if '+png' in spec:
-            args.append('-DENABLE_PNG=ON')
+        if '+png' in self.spec:
+            args.extend(['-DENABLE_PNG=ON',
+                         '-DZLIB_ROOT=' + self.spec['zlib'].prefix])
         else:
             args.append('-DENABLE_PNG=OFF')
 
+        if '+aec' in self.spec:
+            args.extend(['-DENABLE_AEC=ON',
+                         # Prevent overriding by environment variables
+                         # AEC_DIR and AEC_PATH.
+                         '-DAEC_DIR=' + self.spec['libaec'].prefix])
+        else:
+            args.append('-DENABLE_AEC=OFF')
+
+        if '^python' in self.spec:
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH=' + python.path)
+
         return args
diff --git a/var/spack/repos/builtin/packages/grnboost/package.py b/var/spack/repos/builtin/packages/grnboost/package.py
new file mode 100644
index 0000000000..e2e8fcaae0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/grnboost/package.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Grnboost(Package):
+    """GRNBoost is a library built on top of Apache Spark that implements a
+    scalable strategy for gene regulatory network (GRN) inference.
+
+    See https://github.com/aertslab/GRNBoost/blob/master/docs/user_guide.md
+    for the user guide. The location of xgboost4j-<version>.jar and
+    GRNBoost.jar are set to $XGBOOST_JAR and $GRNBOOST_JAR. Path to
+    xgboost4j-<version>.jar is also added to CLASSPATH."""
+
+    homepage = "https://github.com/aertslab/GRNBoost"
+
+    version('2017-10-9', git='https://github.com/aertslab/GRNBoost.git',
+            commit='26c836b3dcbb85852d3c6f4b8340e8655434da02')
+
+    depends_on('sbt', type='build')
+    depends_on('java', type=('build', 'run'))
+    depends_on('xgboost+jvm-packages', type='run')
+    depends_on('spark+hadoop', type='run')
+
+    def setup_environment(self, spack_env, run_env):
+        grnboost_jar = join_path(self.prefix, 'target',
+                                 'scala-2.11', 'GRNBoost.jar')
+        xgboost_version = self.spec['xgboost'].version.string
+        xgboost_jar = join_path(self.spec['xgboost'].prefix,
+                                'xgboost4j-' + xgboost_version + '.jar')
+        run_env.set('GRNBOOST_JAR', grnboost_jar)
+        run_env.set('JAVA_HOME', self.spec['java'].prefix)
+        run_env.set('CLASSPATH', xgboost_jar)
+        run_env.set('XGBOOST_JAR', xgboost_jar)
+
+    def install(self, spec, prefix):
+        sbt = which('sbt')
+        sbt('assembly')
+        install_tree('target', prefix.target)
diff --git a/var/spack/repos/builtin/packages/groff/package.py b/var/spack/repos/builtin/packages/groff/package.py
index bc10c102be..d8854c71c6 100644
--- a/var/spack/repos/builtin/packages/groff/package.py
+++ b/var/spack/repos/builtin/packages/groff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Groff(AutotoolsPackage):
     ASCII/UTF8 for display at the terminal."""
 
     homepage = "https://www.gnu.org/software/groff/"
-    url      = "http://ftp.gnu.org/gnu/groff/groff-1.22.3.tar.gz"
+    url      = "https://ftpmirror.gnu.org/groff/groff-1.22.3.tar.gz"
 
     # TODO: add html variant, spack doesn't have netpbm and its too
     # complicated for me to find out at this point in time.
diff --git a/var/spack/repos/builtin/packages/gromacs/package.py b/var/spack/repos/builtin/packages/gromacs/package.py
index 22f0527439..f51aa9d7d7 100644
--- a/var/spack/repos/builtin/packages/gromacs/package.py
+++ b/var/spack/repos/builtin/packages/gromacs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,13 +20,19 @@ class Gromacs(CMakePackage):
     """
 
     homepage = 'http://www.gromacs.org'
-    url = 'http://ftp.gromacs.org/gromacs/gromacs-5.1.2.tar.gz'
+    url      = 'http://ftp.gromacs.org/gromacs/gromacs-5.1.2.tar.gz'
+    git      = 'https://github.com/gromacs/gromacs.git'
 
+    version('develop', branch='master')
+    version('2018.2', '7087462bb08393aec4ce3192fa4cd8df')
+    version('2018.1', '7ee393fa3c6b7ae351d47eae2adf980e')
+    version('2018',   '6467ffb1575b8271548a13abfba6374c')
+    version('2016.5', 'f41807e5b2911ccb547a3fd11f105d47')
     version('2016.4', '19c8b5c85f3ec62df79d2249a3c272f8')
     version('2016.3', 'e9e3a41bd123b52fbcc6b32d09f8202b')
-    version('5.1.4', 'ba2e34d59b3982603b4935d650c08040')
-    version('5.1.2', '614d0be372f1a6f1f36382b7a6fcab98')
-    version('develop', git='https://github.com/gromacs/gromacs', branch='master')
+    version('5.1.5',  '831fe741bcd9f1612155dffc919885f2')
+    version('5.1.4',  'ba2e34d59b3982603b4935d650c08040')
+    version('5.1.2',  '614d0be372f1a6f1f36382b7a6fcab98')
 
     variant('mpi', default=True, description='Activate MPI support')
     variant('shared', default=True,
@@ -64,7 +51,8 @@ class Gromacs(CMakePackage):
     depends_on('plumed+mpi', when='+plumed+mpi')
     depends_on('plumed~mpi', when='+plumed~mpi')
     depends_on('fftw')
-    depends_on('cmake@2.8.8:', type='build')
+    depends_on('cmake@2.8.8:3.9.99', type='build')
+    depends_on('cmake@3.4.3:3.9.99', type='build', when='@2018:')
     depends_on('cuda', when='+cuda')
 
     def patch(self):
diff --git a/var/spack/repos/builtin/packages/gsl/package.py b/var/spack/repos/builtin/packages/gsl/package.py
index 27be6b0d35..691c02b7e9 100644
--- a/var/spack/repos/builtin/packages/gsl/package.py
+++ b/var/spack/repos/builtin/packages/gsl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,8 +15,9 @@ class Gsl(AutotoolsPackage):
     over 1000 functions in total with an extensive test suite."""
 
     homepage = "http://www.gnu.org/software/gsl"
-    url      = "http://mirror.switch.ch/ftp/mirror/gnu/gsl/gsl-2.3.tar.gz"
+    url      = "https://ftpmirror.gnu.org/gsl/gsl-2.3.tar.gz"
 
+    version('2.5', sha256='0460ad7c2542caaddc6729762952d345374784100223995eb14d614861f2258d')
     version('2.4',   'dba736f15404807834dc1c7b93e83b92')
     version('2.3',   '905fcbbb97bc552d1037e34d200931a0')
     version('2.2.1', '3d90650b7cfe0a6f4b29c2d7b0f86458')
diff --git a/var/spack/repos/builtin/packages/gslib/package.py b/var/spack/repos/builtin/packages/gslib/package.py
new file mode 100644
index 0000000000..f11ed17a56
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gslib/package.py
@@ -0,0 +1,70 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gslib(Package):
+    """Highly scalable Gather-scatter code with AMG and XXT solvers"""
+
+    homepage = "https://github.com/gslib/gslib"
+    git      = "https://github.com/gslib/gslib.git"
+
+    version('1.0.2', tag='v1.0.2')
+    version('1.0.1', tag='v1.0.1')
+    version('1.0.0', tag='v1.0.0')
+
+    variant('mpi', default=True, description='Build with MPI')
+    variant('mpiio', default=True, description='Build with MPI I/O')
+    variant('blas', default=False, description='Build with BLAS')
+
+    depends_on('mpi', when="+mpi")
+    depends_on('mpi', when="+mpiio")
+    depends_on('blas', when="+blas")
+
+    conflicts('~mpi', when='+mpiio')
+
+    def install(self, spec, prefix):
+        src_dir = 'src'
+        lib_dir = 'lib'
+        libname = 'libgs.a'
+
+        if self.version == Version('1.0.1'):
+            makefile = 'Makefile'
+        else:
+            makefile = 'src/Makefile'
+
+        cc  = self.compiler.cc
+
+        if '+mpiio' not in spec:
+            filter_file(r'MPIIO.*?=.*1', 'MPIIO = 0', makefile)
+
+        if '+mpi' in spec:
+            cc  = spec['mpi'].mpicc
+        else:
+            filter_file(r'MPI.*?=.*1', 'MPI = 0', makefile)
+            filter_file(r'MPIIO.*?=.*1', 'MPIIO = 0', makefile)
+
+        make_cmd = "CC=" + cc
+
+        if '+blas' in spec:
+            filter_file(r'BLAS.*?=.*0', 'BLAS = 1', makefile)
+            blas = spec['blas'].libs
+            ld_flags = blas.ld_flags
+            filter_file(r'\$\(LDFLAGS\)', ld_flags, makefile)
+
+        if self.version == Version('1.0.1'):
+            make(make_cmd)
+            make('install')
+            install_tree(lib_dir, prefix.lib)
+        elif self.version == Version('1.0.0'):
+            with working_dir(src_dir):
+                make(make_cmd)
+                mkdir(prefix.lib)
+                install(libname, prefix.lib)
+
+        # Should only install the headers (this will be fixed in gslib on
+        # future releases).
+        install_tree(src_dir, prefix.include)
diff --git a/var/spack/repos/builtin/packages/gtkmm/package.py b/var/spack/repos/builtin/packages/gtkmm/package.py
new file mode 100644
index 0000000000..911d1e7ebf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gtkmm/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Gtkmm(AutotoolsPackage):
+    """Gtkmm is the official C++ interface for the popular GUI library GTK+."""
+
+    homepage = "https://www.gtkmm.org/en/"
+    url      = "https://ftp.acc.umu.se/pub/GNOME/sources/gtkmm/2.16/gtkmm-2.16.0.tar.gz"
+
+    version('2.19.7', '2afc018e5b15cde293cd2d21db9b6a55')
+    version('2.19.6', 'fb140e82e583620defe0d70bfe7eefd7')
+    version('2.19.4', '60006a23306487938dfe0e4b17e3fa46')
+    version('2.19.2', 'dc208575a24e8d5265af2fd59c08f3d8')
+    version('2.17.11', '2326ff83439aac83721ed4694acf14e5')
+    version('2.17.1', '19358644e5e620ad738658be2cb6d739')
+    version('2.16.0', 'de178c2a6f23eda0b6a8bfb0219e2e1c')
+    version('2.4.11', 'a339958bc4ab7f74201b312bd3562d46')
+
+    depends_on('glibmm')
+    depends_on('atk')
+    depends_on('gtkplus')
+    depends_on('pangomm')
+    depends_on('cairomm')
+
+    def url_for_version(self, version):
+        """Handle glib's version-based custom URLs."""
+        url = "https://ftp.acc.umu.se/pub/GNOME/sources/gtkmm"
+        ext = '.tar.gz' if version < Version('3.1.0') else '.tar.xz'
+        return url + "/%s/gtkmm-%s%s" % (version.up_to(2), version, ext)
diff --git a/var/spack/repos/builtin/packages/gtkorvo-atl/package.py b/var/spack/repos/builtin/packages/gtkorvo-atl/package.py
index 72bcf12c1d..1dad459cb3 100644
--- a/var/spack/repos/builtin/packages/gtkorvo-atl/package.py
+++ b/var/spack/repos/builtin/packages/gtkorvo-atl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,14 +12,25 @@ class GtkorvoAtl(CMakePackage):
     """
 
     homepage = "https://github.com/GTkorvo/atl"
-    url = "https://github.com/GTkorvo/atl/archive/v2.1.tar.gz"
+    url      = "https://github.com/GTkorvo/atl/archive/v2.1.tar.gz"
+    git      = "https://github.com/GTkorvo/atl.git"
 
-    version('develop', git='https://github.com/GTkorvo/atl.git',
-            branch='master')
+    version('develop', branch='master')
+    version('2.2', 'f0e3581e4b4c6943bf4b203685630564')
     version('2.1', 'b2324ff041bccba127330a0e1b241978')
 
     depends_on('gtkorvo-cercs-env')
 
     def cmake_args(self):
-        args = ["-DENABLE_TESTING=0", "-DENABLE_BUILD_STATIC=STATIC"]
+        args = []
+        if self.spec.satisfies('@2.2:'):
+            args.append("-DBUILD_SHARED_LIBS=OFF")
+        else:
+            args.append("-DENABLE_BUILD_STATIC=STATIC")
+
+        if self.run_tests:
+            args.append('-DENABLE_TESTING=1')
+        else:
+            args.append('-DENABLE_TESTING=0')
+
         return args
diff --git a/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py b/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py
index 2fcfc21467..a042dd154b 100644
--- a/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py
+++ b/var/spack/repos/builtin/packages/gtkorvo-cercs-env/package.py
@@ -1,39 +1,19 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class GtkorvoCercsEnv(CMakePackage):
-    """A utility library used by some GTkorvo packages.
-    """
+    """A utility library used by some GTkorvo packages."""
 
     homepage = "https://github.com/GTkorvo/cercs_env"
-    url = "https://github.com/GTkorvo/cercs_env/archive/v1.0.tar.gz"
+    url      = "https://github.com/GTkorvo/cercs_env/archive/v1.0.tar.gz"
+    git      = "https://github.com/GTkorvo/cercs_env.git"
 
-    version('develop', git='https://github.com/GTkorvo/cercs_env.git',
-            branch='master')
+    version('develop', branch='master')
     version('1.0', '08f0532d0c2f7bc9b53dfa7a1c40ea4d')
 
     def cmake_args(self):
diff --git a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py
index af2c433ed6..6af9ebc9ab 100644
--- a/var/spack/repos/builtin/packages/gtkorvo-dill/package.py
+++ b/var/spack/repos/builtin/packages/gtkorvo-dill/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,23 @@ class GtkorvoDill(CMakePackage):
     """
 
     homepage = "https://github.com/GTkorvo/dill"
-    url = "https://github.com/GTkorvo/dill/archive/v2.1.tar.gz"
+    url      = "https://github.com/GTkorvo/dill/archive/v2.1.tar.gz"
+    git      = "https://github.com/GTkorvo/dill.git"
 
-    version('develop', git='https://github.com/GTkorvo/dill.git',
-            branch='master')
+    version('develop', branch='master')
+    version('2.4', '6836673b24f395eaae044b8bb976511d')
     version('2.1', '14c835e79b66c9acd2beee01d56e6200')
 
     def cmake_args(self):
-        args = ["-DENABLE_TESTING=0", "-DBUILD_SHARED_STATIC=STATIC"]
+        args = []
+        if self.spec.satisfies('@2.4:'):
+            args.append("-DBUILD_SHARED_LIBS=OFF")
+        else:
+            args.append("-DENABLE_BUILD_STATIC=STATIC")
+
+        if self.run_tests:
+            args.append('-DENABLE_TESTING=1')
+        else:
+            args.append('-DENABLE_TESTING=0')
+
         return args
diff --git a/var/spack/repos/builtin/packages/gtkorvo-enet/package.py b/var/spack/repos/builtin/packages/gtkorvo-enet/package.py
index 2130085b93..5c9148d471 100644
--- a/var/spack/repos/builtin/packages/gtkorvo-enet/package.py
+++ b/var/spack/repos/builtin/packages/gtkorvo-enet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,4 +16,5 @@ class GtkorvoEnet(AutotoolsPackage):
     homepage = "http://www.github.com/GTkorvo/enet"
     url = "https://github.com/GTkorvo/enet/archive/v1.3.13.tar.gz"
 
+    version('1.3.14', '05272cac1a8cb0500995eeca310e7fac')
     version('1.3.13', '3490f924a4d421e4832e45850e6ec142')
diff --git a/var/spack/repos/builtin/packages/gtkplus/package.py b/var/spack/repos/builtin/packages/gtkplus/package.py
index 033c325eb6..d7ce1c57d6 100644
--- a/var/spack/repos/builtin/packages/gtkplus/package.py
+++ b/var/spack/repos/builtin/packages/gtkplus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,24 +11,32 @@ class Gtkplus(AutotoolsPackage):
        interfaces for applications."""
     homepage = "http://www.gtk.org"
     url = "http://ftp.gnome.org/pub/gnome/sources/gtk+/2.24/gtk+-2.24.31.tar.xz"
-
+    version('3.20.10', 'e81da1af1c5c1fee87ba439770e17272fa5c06e64572939814da406859e56b70')
+    version('2.24.32', 'b6c8a93ddda5eabe3bfee1eb39636c9a03d2a56c7b62828b359bf197943c582e')
     version('2.24.31', '68c1922732c7efc08df4656a5366dcc3afdc8791513400dac276009b40954658')
     version('2.24.25', '38af1020cb8ff3d10dda2c8807f11e92af9d2fa4045de61c62eedb7fbc7ea5b3')
 
-    variant('X', default=False, description="Enable an X toolkit")
+    depends_on('pkgconfig', type='build')
 
-    depends_on('pkg-config', type='build')
-
-    depends_on("atk")
-    depends_on("gdk-pixbuf")
-    depends_on("glib")
-    depends_on("pango")
-    depends_on("pango~X", when='~X')
-    depends_on("pango+X", when='+X')
-    depends_on('gobject-introspection', when='+X')
+    depends_on('atk')
+    depends_on('gdk-pixbuf')
+    depends_on('glib')
     depends_on('shared-mime-info')
-
-    patch('no-demos.patch')
+    # Hardcode X11 support (former +X variant),
+    # see #6940 for rationale:
+    depends_on('pango+X')
+    depends_on('gobject-introspection')
+    depends_on('libepoxy', when='@3:')
+    depends_on('libxi', when='@3:')
+    depends_on('inputproto', when='@3:')
+    depends_on('fixesproto', when='@3:')
+    depends_on('at-spi2-atk', when='@3:')
+
+    patch('no-demos.patch', when='@2:2.99')
+
+    def url_for_version(self, version):
+        url = 'http://ftp.gnome.org/pub/gnome/sources/gtk+'
+        return url + '/%s/gtk+-%s.tar.xz' % (version.up_to(2), version)
 
     def patch(self):
         # remove disable deprecated flag.
diff --git a/var/spack/repos/builtin/packages/gts/package.py b/var/spack/repos/builtin/packages/gts/package.py
index b340df34f2..d19c539f7e 100644
--- a/var/spack/repos/builtin/packages/gts/package.py
+++ b/var/spack/repos/builtin/packages/gts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/guidance/package.py b/var/spack/repos/builtin/packages/guidance/package.py
index 6cb4e0cfc6..4246b2b49e 100644
--- a/var/spack/repos/builtin/packages/guidance/package.py
+++ b/var/spack/repos/builtin/packages/guidance/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/guile/package.py b/var/spack/repos/builtin/packages/guile/package.py
index 81b61510be..1861f7da5a 100644
--- a/var/spack/repos/builtin/packages/guile/package.py
+++ b/var/spack/repos/builtin/packages/guile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,13 +11,14 @@ class Guile(AutotoolsPackage):
     the official extension language for the GNU operating system."""
 
     homepage = "https://www.gnu.org/software/guile/"
-    url      = "https://ftp.gnu.org/gnu/guile/guile-2.2.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/guile/guile-2.2.0.tar.gz"
 
     version('2.2.0',  '0d5de8075b965f9ee5ea04399b60a3f9')
     version('2.0.14', '333b6eec83e779935a45c818f712484e')
     version('2.0.11', 'e532c68c6f17822561e3001136635ddd')
 
     variant('readline', default=True, description='Use the readline library')
+    variant('threads', default=True, description='Use the thread interface')
 
     depends_on('gmp@4.2:')
     depends_on('gettext')
@@ -45,10 +27,12 @@ class Guile(AutotoolsPackage):
     depends_on('bdw-gc@7.0:')
     depends_on('libffi')
     depends_on('readline', when='+readline')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     build_directory = 'spack-build'
 
+    conflicts('+threads', when='%intel')
+
     def configure_args(self):
         spec = self.spec
 
@@ -57,8 +41,9 @@ class Guile(AutotoolsPackage):
                 spec['libunistring'].prefix),
             '--with-libltdl-prefix={0}'.format(spec['libtool'].prefix),
             '--with-libgmp-prefix={0}'.format(spec['gmp'].prefix),
-            '--with-libintl-prefix={0}'.format(spec['gettext'].prefix)
+            '--with-libintl-prefix={0}'.format(spec['gettext'].prefix),
         ]
+        config_args += self.with_or_without('threads')
 
         if '+readline' in spec:
             config_args.append('--with-libreadline-prefix={0}'.format(
diff --git a/var/spack/repos/builtin/packages/gurobi/package.py b/var/spack/repos/builtin/packages/gurobi/package.py
new file mode 100644
index 0000000000..3c9747aef4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/gurobi/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Gurobi(Package):
+    """The Gurobi Optimizer was designed from the ground up to be the fastest,
+    most powerful solver available for your LP, QP, QCP, and MIP (MILP, MIQP,
+    and MIQCP) problems.
+
+    Note: Gurobi is licensed software. You will need to create an account on
+    the Gurobi homepage and download Gurobi Optimizer yourself. Spack will
+    search your current directory for the download file. Alternatively, add
+    this file to a mirror so that Spack can find it. For instructions on how to
+    set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html
+
+    Please set the path to licence file with the following command (for bash)
+    export GRB_LICENSE_FILE=/path/to/gurobi/license/. See section 4 in
+    $GUROBI_HOME/docs/quickstart_linux.pdf for more details."""
+
+    homepage = "http://www.gurobi.com/index"
+
+    version('7.5.2', '01f6dbb8d165838cca1664a1a14e4a85')
+
+    # Licensing
+    license_required = True
+    license_vars     = ['GRB_LICENSE_FILE']
+    license_url      = 'http://www.gurobi.com/downloads/download-center'
+
+    def url_for_version(self, version):
+        return "file://{0}/gurobi{1}_linux64.tar.gz".format(os.getcwd(), version)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('GUROBI_HOME', self.prefix)
+
+    def install(self, spec, prefix):
+        install_tree('linux64', prefix)
diff --git a/var/spack/repos/builtin/packages/h5hut/package.py b/var/spack/repos/builtin/packages/h5hut/package.py
index ed9ede92d6..9b34183bff 100644
--- a/var/spack/repos/builtin/packages/h5hut/package.py
+++ b/var/spack/repos/builtin/packages/h5hut/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/h5part/package.py b/var/spack/repos/builtin/packages/h5part/package.py
index f105a26831..957e9dcf89 100644
--- a/var/spack/repos/builtin/packages/h5part/package.py
+++ b/var/spack/repos/builtin/packages/h5part/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/h5utils/package.py b/var/spack/repos/builtin/packages/h5utils/package.py
index 202eb0e232..946a494cbb 100644
--- a/var/spack/repos/builtin/packages/h5utils/package.py
+++ b/var/spack/repos/builtin/packages/h5utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/h5z-zfp/package.py b/var/spack/repos/builtin/packages/h5z-zfp/package.py
index dff0126f01..943c874e4b 100644
--- a/var/spack/repos/builtin/packages/h5z-zfp/package.py
+++ b/var/spack/repos/builtin/packages/h5z-zfp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,14 +11,16 @@ class H5zZfp(MakefilePackage):
        HDF5 library using ZFP compression."""
 
     homepage = "http://h5z-zfp.readthedocs.io/en/latest"
-    url      = "https://github.com/LLNL/H5Z-ZFP"
+    git      = "https://github.com/LLNL/H5Z-ZFP.git"
 
-    version('develop', git='https://github.com/LLNL/H5Z-ZFP.git', tag='master')
-    version('0.7.0', git='https://github.com/LLNL/H5Z-ZFP.git', commit='58ac811')
+    version('develop', tag='master')
+    version('0.8.0', commit='af165c4')
+    version('0.7.0', commit='58ac811')
 
     variant('fortran', default=True, description='Enable Fortran support')
 
-    depends_on('hdf5')
+    depends_on('hdf5+fortran', when='+fortran')
+    depends_on('hdf5',         when='~fortran')
     depends_on('zfp bsws=8')
 
     @property
diff --git a/var/spack/repos/builtin/packages/hacckernels/package.py b/var/spack/repos/builtin/packages/hacckernels/package.py
index db48910165..d93dc42e7d 100644
--- a/var/spack/repos/builtin/packages/hacckernels/package.py
+++ b/var/spack/repos/builtin/packages/hacckernels/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,12 +14,11 @@ class Hacckernels(CMakePackage):
     cores and beyond."""
 
     homepage = "https://xgitlab.cels.anl.gov/hacc/HACCKernels"
-    url      = "https://xgitlab.cels.anl.gov/hacc/HACCKernels.git"
+    git      = "https://xgitlab.cels.anl.gov/hacc/HACCKernels.git"
 
     tags = ['proxy-app']
 
-    version('develop', git='https://xgitlab.cels.anl.gov/hacc/HACCKernels.git',
-            branch='master')
+    version('develop', branch='master')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/hadoop/package.py b/var/spack/repos/builtin/packages/hadoop/package.py
index 66deb7c5d2..e581deb868 100644
--- a/var/spack/repos/builtin/packages/hadoop/package.py
+++ b/var/spack/repos/builtin/packages/hadoop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,10 @@ class Hadoop(Package):
     """
 
     homepage = "http://hadoop.apache.org/"
-    url      = "http://mirrors.ocf.berkeley.edu/apache/hadoop/common/hadoop-2.6.4/hadoop-2.6.4.tar.gz"
+    url      = "http://mirrors.ocf.berkeley.edu/apache/hadoop/common/hadoop-3.1.1/hadoop-3.1.1.tar.gz"
 
-    version('2.6.4', '37019f13d7dcd819727be158440b9442')
+    version('3.1.1', '0b6ab06b59ae75f433de387783f19011')
+    version('2.9.0', 'b443ead81aa2bd5086f99e62e66a8f64')
 
     depends_on('java', type='run')
 
diff --git a/var/spack/repos/builtin/packages/halc/package.py b/var/spack/repos/builtin/packages/halc/package.py
new file mode 100644
index 0000000000..7d2e76be75
--- /dev/null
+++ b/var/spack/repos/builtin/packages/halc/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Halc(MakefilePackage):
+    """HALC is software that makes error correction for long reads with
+     high throughput."""
+
+    homepage = "https://github.com/lanl001/halc"
+    url      = "https://github.com/lanl001/halc/archive/v1.1.tar.gz"
+
+    version('1.1', '4b289b366f6a5400ca481993aa68dd9c')
+
+    depends_on('blasr', type='run')
+    depends_on('lordec', type='run')
+    depends_on('dos2unix', type='build')
+    depends_on('python', type='run')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install('runHALC.py', prefix.bin)
+        dos2unix = which('dos2unix')
+        dos2unix(join_path(self.prefix.bin, 'runHALC.py'))
diff --git a/var/spack/repos/builtin/packages/hapcut2/package.py b/var/spack/repos/builtin/packages/hapcut2/package.py
index 612a1c25ba..60596b4185 100644
--- a/var/spack/repos/builtin/packages/hapcut2/package.py
+++ b/var/spack/repos/builtin/packages/hapcut2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,10 @@ class Hapcut2(MakefilePackage):
        and accuracy."""
 
     homepage = "https://github.com/vibansal/HapCUT2"
-    url      = "https://github.com/vibansal/HapCUT2"
+    git      = "https://github.com/vibansal/HapCUT2.git"
 
-    version('2017-07-10', git='https://github.com/vibansal/HapCUT2.git',
-            commit='2966b94c2c2f97813b757d4999b7a6471df1160e', submodules=True)
+    version('2017-07-10', commit='2966b94c2c2f97813b757d4999b7a6471df1160e',
+            submodules=True)
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/hapdip/package.py b/var/spack/repos/builtin/packages/hapdip/package.py
new file mode 100644
index 0000000000..92673b2b34
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hapdip/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hapdip(Package):
+    """The CHM1-NA12878 benchmark for single-sample SNP/INDEL calling from
+    WGS Illumina data."""
+
+    homepage = "https://github.com/lh3/hapdip"
+    git      = "https://github.com/lh3/hapdip.git"
+
+    version('2018.02.20', commit='7c12f684471999a543fdacce972c9c86349758a3')
+
+    depends_on('k8', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/haploview/package.py b/var/spack/repos/builtin/packages/haploview/package.py
index 9d1b4b3e0f..dd6acefad7 100644
--- a/var/spack/repos/builtin/packages/haploview/package.py
+++ b/var/spack/repos/builtin/packages/haploview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin/packages/harfbuzz/package.py b/var/spack/repos/builtin/packages/harfbuzz/package.py
index 492a4694a8..5a6ded2e77 100644
--- a/var/spack/repos/builtin/packages/harfbuzz/package.py
+++ b/var/spack/repos/builtin/packages/harfbuzz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class Harfbuzz(AutotoolsPackage):
     version('1.4.6', '21a78b81cd20cbffdb04b59ac7edfb410e42141869f637ae1d6778e74928d293')
     version('0.9.37', 'bfe733250e34629a188d82e3b971bc1e')
 
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
     depends_on("glib")
     depends_on("icu4c")
     depends_on("freetype")
diff --git a/var/spack/repos/builtin/packages/harminv/package.py b/var/spack/repos/builtin/packages/harminv/package.py
index d92405e8c7..f3aaf33bdd 100644
--- a/var/spack/repos/builtin/packages/harminv/package.py
+++ b/var/spack/repos/builtin/packages/harminv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hdf/package.py b/var/spack/repos/builtin/packages/hdf/package.py
index 0aefe3aa8c..3f5be4b95f 100644
--- a/var/spack/repos/builtin/packages/hdf/package.py
+++ b/var/spack/repos/builtin/packages/hdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hdf5-blosc/package.py b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
index 704f508cb3..c79ed76c1b 100644
--- a/var/spack/repos/builtin/packages/hdf5-blosc/package.py
+++ b/var/spack/repos/builtin/packages/hdf5-blosc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import shutil
 import sys
@@ -34,13 +15,13 @@ def _install_shlib(name, src, dst):
     if sys.platform == "darwin":
         shlib0 = name + ".0.dylib"
         shlib = name + ".dylib"
-        shutil.copyfile(join_path(src, shlib0), join_path(dst, shlib0))
+        install(join_path(src, shlib0), join_path(dst, shlib0))
         os.symlink(shlib0, join_path(dst, shlib))
     else:
         shlib000 = name + ".so.0.0.0"
         shlib0 = name + ".so.0"
         shlib = name + ".dylib"
-        shutil.copyfile(join_path(src, shlib000), join_path(dst, shlib000))
+        install(join_path(src, shlib000), join_path(dst, shlib000))
         os.symlink(shlib000, join_path(dst, shlib0))
         os.symlink(shlib0, join_path(dst, shlib))
 
@@ -48,10 +29,9 @@ def _install_shlib(name, src, dst):
 class Hdf5Blosc(Package):
     """Blosc filter for HDF5"""
     homepage = "https://github.com/Blosc/hdf5-blosc"
-    url      = "https://github.com/Blosc/hdf5-blosc"
+    git      = "https://github.com/Blosc/hdf5-blosc.git"
 
-    version('master', git='https://github.com/Blosc/hdf5-blosc',
-            branch='master')
+    version('master', branch='master')
 
     depends_on("c-blosc")
     depends_on("hdf5")
diff --git a/var/spack/repos/builtin/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch b/var/spack/repos/builtin/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch
new file mode 100644
index 0000000000..8bf5c142e9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch
@@ -0,0 +1,16 @@
+diff --git a/fortran/src/H5f90global.F90 b/fortran/src/H5f90global.F90
+index dd2b171..629418a 100644
+--- a/fortran/src/H5f90global.F90
++++ b/fortran/src/H5f90global.F90
+@@ -142,10 +142,7 @@ MODULE H5GLOBAL
+
+   INTEGER(HID_T), DIMENSION(PREDEF_TYPES_LEN) :: predef_types
+   EQUIVALENCE (predef_types(1), H5T_NATIVE_INTEGER_KIND(1))
+-  EQUIVALENCE (predef_types(2), H5T_NATIVE_INTEGER_KIND(2))
+-  EQUIVALENCE (predef_types(3), H5T_NATIVE_INTEGER_KIND(3))
+-  EQUIVALENCE (predef_types(4), H5T_NATIVE_INTEGER_KIND(4))
+-  EQUIVALENCE (predef_types(5), H5T_NATIVE_INTEGER_KIND(5))
++  ! EQUIVALENCE predef_types(2:5) are unnecessary and violate the standard
+   EQUIVALENCE (predef_types(6), H5T_NATIVE_INTEGER)
+   EQUIVALENCE (predef_types(7), H5T_NATIVE_REAL)
+   EQUIVALENCE (predef_types(8), H5T_NATIVE_DOUBLE)
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 5a15b33d98..00fd80dc54 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -1,31 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 *
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import shutil
 import sys
 
+from spack import *
+
 
 class Hdf5(AutotoolsPackage):
     """HDF5 is a data model, library, and file format for storing and managing
@@ -38,6 +20,9 @@ class Hdf5(AutotoolsPackage):
     list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
     list_depth = 3
 
+    version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2')
+    version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
+    version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3')
     version('1.10.1', '43a2f9466702fb1db31df98ae6677f15')
     version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295')
     version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
@@ -49,6 +34,7 @@ class Hdf5(AutotoolsPackage):
     version('1.8.14', 'a482686e733514a51cde12d6fe5c5d95')
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
     version('1.8.12', 'd804802feb99b87fc668a90e6fa34411')
+    version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157')
 
     variant('debug', default=False,
             description='Builds a debug version of the library')
@@ -90,6 +76,30 @@ class Hdf5(AutotoolsPackage):
     #    described in #2 we allow for such combination.
     # conflicts('+mpi+cxx')
 
+    # There are known build failures with intel@18.0.1. This issue is
+    # discussed and patch is provided at
+    # https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
+    patch('h5f90global-mult-obj-same-equivalence-same-common-block.patch',
+          when='@1.10.1%intel@18')
+
+    # Turn line comments into block comments to conform with pre-C99 language
+    # standards. Versions of hdf5 after 1.8.10 don't require this patch,
+    # either because they conform to pre-C99 or neglect to ask for pre-C99
+    # language standards from their compiler. The hdf5 build system adds
+    # the -ansi cflag (run 'man gcc' for info on -ansi) for some versions
+    # of some compilers (see hdf5-1.8.10/config/gnu-flags). The hdf5 build
+    # system does not provide an option to disable -ansi, but since the
+    # pre-C99 code is restricted to just five lines of line comments in
+    # three src files, this patch accomplishes the simple task of patching the
+    # three src files and leaves the hdf5 build system alone.
+    patch('pre-c99-comments.patch', when='@1.8.10')
+
+    # There are build errors with GCC 8, see
+    # https://forum.hdfgroup.org/t/1-10-2-h5detect-compile-error-gcc-8-1-0-on-centos-7-2-solved/4441
+    patch('https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch', sha256='57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523', when='@1.10.2%gcc@8:')
+
+    filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin')
+
     def url_for_version(self, version):
         url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
         return url.format(version.up_to(2), version)
@@ -154,7 +164,7 @@ class Hdf5(AutotoolsPackage):
         libraries = query2libraries[key]
 
         return find_libraries(
-            libraries, root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
 
     @run_before('configure')
@@ -268,8 +278,8 @@ HDF5 version {version} {version}
             else:
                 cc = Executable(self.compiler.cc)
             cc(*(['-c', "check.c"] + spec['hdf5'].headers.cpp_flags.split()))
-            cc(*(['-o', "check", "check.o"] +
-                 spec['hdf5'].libs.ld_flags.split()))
+            cc(*(['-o', "check",
+                  "check.o"] + spec['hdf5'].libs.ld_flags.split()))
             try:
                 check = Executable('./check')
                 output = check(output=str)
diff --git a/var/spack/repos/builtin/packages/hdf5/pre-c99-comments.patch b/var/spack/repos/builtin/packages/hdf5/pre-c99-comments.patch
new file mode 100644
index 0000000000..97743e8fa5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hdf5/pre-c99-comments.patch
@@ -0,0 +1,43 @@
+diff --git a/test/th5s.c b/test/th5s.c
+index 462bc36..8e18fad 100644
+--- a/test/th5s.c
++++ b/test/th5s.c
+@@ -730,8 +730,8 @@ test_h5s_zero_dim(void)
+         ret = H5Pset_chunk(plist_id, SPACE1_RANK, chunk_dims);
+         CHECK(ret, FAIL, "H5Pset_chunk");
+ 
+-        // ret = H5Pset_alloc_time(plist_id, alloc_time);
+-        // CHECK(ret, FAIL, "H5Pset_alloc_time");
++        /* ret = H5Pset_alloc_time(plist_id, alloc_time); */
++        /* CHECK(ret, FAIL, "H5Pset_alloc_time"); */
+ 
+         dset1 = H5Dcreate2(fid1, BASICDATASET1, H5T_NATIVE_INT, sid_chunk, H5P_DEFAULT, plist_id, H5P_DEFAULT);
+         CHECK(dset1, FAIL, "H5Dcreate2");
+diff --git a/tools/h5dump/h5dump_ddl.c b/tools/h5dump/h5dump_ddl.c
+index ee6de5e..3ed6045 100644
+--- a/tools/h5dump/h5dump_ddl.c
++++ b/tools/h5dump/h5dump_ddl.c
+@@ -1341,8 +1341,8 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe
+     string_dataformat.do_escape = display_escape;
+     outputformat = &string_dataformat;
+ 
+-    //attr_name = attr + j + 1;
+-	// need to replace escape characters
++    /* attr_name = attr + j + 1; */
++	/* need to replace escape characters */
+ 	attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/");
+ 
+ 
+diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
+index 9ce3524..3b4e5e7 100644
+--- a/tools/lib/h5tools_str.c
++++ b/tools/lib/h5tools_str.c
+@@ -632,7 +632,7 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info,
+         h5tools_str_append(str, "%s", OPT(info->line_indent, ""));
+     }
+ 
+-//    ctx->need_prefix = 0;
++/*    ctx->need_prefix = 0; */
+ }
+ 
+ /*-------------------------------------------------------------------------
diff --git a/var/spack/repos/builtin/packages/help2man/package.py b/var/spack/repos/builtin/packages/help2man/package.py
index cc86affeaa..39ad9037f0 100644
--- a/var/spack/repos/builtin/packages/help2man/package.py
+++ b/var/spack/repos/builtin/packages/help2man/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Help2man(AutotoolsPackage):
     output of other commands."""
 
     homepage = "https://www.gnu.org/software/help2man/"
-    url      = "http://gnu.askapache.com/help2man/help2man-1.47.4.tar.xz"
+    url      = "https://ftpmirror.gnu.org/help2man/help2man-1.47.4.tar.xz"
 
     version('1.47.4', '544aca496a7d89de3e5d99e56a2f03d3')
 
     depends_on('gettext', type='build')
+    depends_on('perl', type='build')
diff --git a/var/spack/repos/builtin/packages/henson/package.py b/var/spack/repos/builtin/packages/henson/package.py
new file mode 100644
index 0000000000..b41fb080fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/henson/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Henson(CMakePackage):
+    """Cooperative multitasking for in situ processing."""
+
+    homepage = "https://github.com/henson-insitu/henson"
+    url      = "https://github.com/henson-insitu/henson"
+    git      = "https://github.com/henson-insitu/henson.git"
+
+    version('develop', branch='master')
+
+    depends_on('mpi')
+
+    variant('python', default=False, description='Build Python bindings')
+    extends('python', when='+python')
+    variant('mpi-wrappers', default=False, description='Build MPI wrappers (PMPI)')
+
+    conflicts('^openmpi', when='+mpi-wrappers')
+
+    def cmake_args(self):
+        args = []
+        if '+python' in self.spec:
+            args += ['-Dpython=on']
+        else:
+            args += ['-Dpython=off']
+
+        if '+mpi-wrappers' in self.spec:
+            args += ['-Dmpi-wrappers=on']
+        else:
+            args += ['-Dmpi-wrappers=off']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/hepmc/package.py b/var/spack/repos/builtin/packages/hepmc/package.py
index b5470225b5..16b4c707f5 100644
--- a/var/spack/repos/builtin/packages/hepmc/package.py
+++ b/var/spack/repos/builtin/packages/hepmc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -33,7 +14,8 @@ class Hepmc(CMakePackage):
     homepage = "http://hepmc.web.cern.ch/hepmc/"
     url      = "http://hepmc.web.cern.ch/hepmc/releases/hepmc2.06.09.tgz"
 
-    version('2.06.09', 'c47627ced4255b40e731b8666848b087')
+    version('3.0.0',   '2212a5e8d693fbf726c28b43ebc6377a')
+    version('2.06.09', '52518437a64f6b4284e9acc2ecad6212')
     version('2.06.08', 'a2e889114cafc4f60742029d69abd907')
     version('2.06.07', '11d7035dccb0650b331f51520c6172e7')
     version('2.06.06', '102e5503537a3ecd6ea6f466aa5bc4ae')
@@ -46,3 +28,10 @@ class Hepmc(CMakePackage):
             '-Dmomentum:STRING=GEV',
             '-Dlength:STRING=MM',
         ]
+
+    def url_for_version(self, version):
+        if version <= Version("2.06.08"):
+            url = "http://lcgapp.cern.ch/project/simu/HepMC/download/HepMC-{0}.tar.gz"
+        else:
+            url = "http://hepmc.web.cern.ch/hepmc/releases/hepmc{0}.tgz"
+        return url.format(version)
diff --git a/var/spack/repos/builtin/packages/heppdt/package.py b/var/spack/repos/builtin/packages/heppdt/package.py
index 613d8d9f8e..5933317c50 100644
--- a/var/spack/repos/builtin/packages/heppdt/package.py
+++ b/var/spack/repos/builtin/packages/heppdt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/hic-pro/package.py b/var/spack/repos/builtin/packages/hic-pro/package.py
new file mode 100644
index 0000000000..6cb89d8839
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hic-pro/package.py
@@ -0,0 +1,61 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class HicPro(MakefilePackage):
+    """HiC-Pro is a package designed to process Hi-C data,
+    from raw fastq files (paired-end Illumina data)
+    to the normalized contact maps"""
+
+    homepage = "https://github.com/nservant/HiC-Pro"
+    url      = "https://github.com/nservant/HiC-Pro/archive/v2.10.0.tar.gz"
+
+    version('2.10.0', '6ae2213dcc984b722d1a1f65fcbb21a2')
+
+    depends_on('bowtie2')
+    depends_on('samtools')
+    depends_on('python+ucs4@2.7:2.8')
+    depends_on('r')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-pysam', type=('build', 'run'))
+    depends_on('py-bx-python', type=('build', 'run'))
+    depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+
+    def edit(self, spec, prefix):
+        config = FileFilter('config-install.txt')
+        config.filter('PREFIX =.*', 'PREFIX = {0}'.format(prefix))
+        config.filter('BOWTIE2 PATH =.*',
+                      'BOWTIE2_PATH = {0}'.format(spec['bowtie2'].prefix))
+        config.filter('SAMTOOLS_PATH =.*',
+                      'SAMTOOLS_PATH = {0}'.format(spec['samtools'].prefix))
+        config.filter('R_PATH =.*',
+                      'R_RPTH ={0}'.format(spec['r'].prefix))
+        config.filter('PYTHON_PATH =.*',
+                      'PYTHON_RPTH ={0}'.format(spec['python'].prefix))
+
+    def build(self, spec, preifx):
+        make('-f', './scripts/install/Makefile',
+             'CONFIG_SYS=./config-install.txt')
+        make('mapbuilder')
+        make('readstrimming')
+        make('iced')
+
+    def install(self, spec, prefix):
+        # Patch INSTALLPATH in config-system.txt
+        config = FileFilter('config-system.txt')
+        config.filter('/HiC-Pro_%s' % self.version, '')
+        # Install
+        install('config-hicpro.txt', prefix)
+        install('config-install.txt', prefix)
+        install('config-system.txt', prefix)
+        install_tree('bin', prefix.bin)
+        install_tree('annotation', prefix.annotation)
+        install_tree('doc', prefix.doc)
+        install_tree('scripts', prefix.scripts)
+        install_tree('test-op', join_path(prefix, 'test-op'))
diff --git a/var/spack/repos/builtin/packages/highfive/package.py b/var/spack/repos/builtin/packages/highfive/package.py
index ad97e716e0..cbd57f98fc 100644
--- a/var/spack/repos/builtin/packages/highfive/package.py
+++ b/var/spack/repos/builtin/packages/highfive/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,6 +13,7 @@ class Highfive(CMakePackage):
     homepage = "https://github.com/BlueBrain/HighFive"
     url      = "https://github.com/BlueBrain/HighFive/archive/v1.2.tar.gz"
 
+    version('1.5', '5e631c91d2ea7f3677e99d6bb6db8167')
     version('1.2', '030728d53519c7e13b5a522d34240301')
     version('1.1', '986f0bd18c5264709688a536c02d2b2a')
     version('1.0', 'e44e548560ea92afdb244c223b7655b6')
diff --git a/var/spack/repos/builtin/packages/highwayhash/package.py b/var/spack/repos/builtin/packages/highwayhash/package.py
index 3a12736aae..240faadf13 100644
--- a/var/spack/repos/builtin/packages/highwayhash/package.py
+++ b/var/spack/repos/builtin/packages/highwayhash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 import os
@@ -34,9 +15,9 @@ class Highwayhash(MakefilePackage):
     """
 
     homepage = "https://github.com/google/highwayhash"
+    git      = "https://github.com/google/highwayhash.git"
 
-    version('dfcb97', git='https://github.com/google/highwayhash.git',
-            commit='dfcb97ca4fe9277bf9dc1802dd979b071896453b')
+    version('dfcb97', commit='dfcb97ca4fe9277bf9dc1802dd979b071896453b')
 
     build_targets = ['all', 'libhighwayhash.a']
 
diff --git a/var/spack/repos/builtin/packages/hiop/package.py b/var/spack/repos/builtin/packages/hiop/package.py
new file mode 100644
index 0000000000..cc2b07a822
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hiop/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hiop(CMakePackage):
+    """HiOp is an optimization solver for solving certain mathematical
+    optimization problems expressed as nonlinear programming problems.
+    HiOp is a lightweight HPC solver that leverages application's existing
+    data parallelism to parallelize the optimization iterations by using
+    specialized linear algebra kernels."""
+
+    homepage = "https://github.com/LLNL/hiop"
+    git      = "https://github.com/LLNL/hiop.git"
+
+    version('0.1', tag='v0.1')
+
+    variant('mpi', default=True,
+            description='Enable/Disable MPI')
+
+    variant('deepchecking', default=True,
+            description='Ultra safety checks - \
+            used for increased robustness and self-diagnostics')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('lapack')
+    depends_on('blas')
+
+    flag_handler = build_system_flags
+
+    def cmake_args(self):
+        args = []
+        spec = self.spec
+
+        if '+mpi' in spec:
+            args.append("-DWITH_MPI=ON")
+        else:
+            args.append("-DWITH_MPI=OFF")
+
+        if '+deepchecking' in spec:
+            args.append("-DDEEP_CHECKING=ON")
+        else:
+            args.append("-DDEEP_CHECKING=OFF")
+
+        lapack_blas_libs = (
+            spec['lapack'].libs + spec['blas'].libs).joined(';')
+        args.extend([
+            '-DLAPACK_FOUND=TRUE',
+            '-DLAPACK_LIBRARIES={0}'.format(lapack_blas_libs)
+        ])
+
+        return args
diff --git a/var/spack/repos/builtin/packages/hisat2/package.py b/var/spack/repos/builtin/packages/hisat2/package.py
index 1b945c61c8..34fbf6e910 100644
--- a/var/spack/repos/builtin/packages/hisat2/package.py
+++ b/var/spack/repos/builtin/packages/hisat2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os.path
diff --git a/var/spack/repos/builtin/packages/hisea/package.py b/var/spack/repos/builtin/packages/hisea/package.py
new file mode 100644
index 0000000000..f2d215242b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hisea/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Hisea(MakefilePackage):
+    """HISEA is an efficient all-vs-all long read aligner for SMRT sequencing
+       data. Its algorithm is designed to produce highest alignment sensitivity
+       among others."""
+
+    homepage = "https://doi.org/10.1186/s12859-017-1953-9"
+    url      = "https://github.com/lucian-ilie/HISEA"
+
+    version('2017.12.26', '54211bdc33b7ce52a8f1e76845935eb8',
+            url='https://github.com/lucian-ilie/HISEA/tarball/39e01e98caa0f2101da806ca59306296effe789c')
+
+    depends_on('boost')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('hisea', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/hmmer/package.py b/var/spack/repos/builtin/packages/hmmer/package.py
index 2681282b7d..2b9b045a00 100644
--- a/var/spack/repos/builtin/packages/hmmer/package.py
+++ b/var/spack/repos/builtin/packages/hmmer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Hmmer(Package):
     probabilistic models called profile hidden Markov models (profile HMMs).
     """
     homepage = 'http://www.hmmer.org'
-    url      = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz'
+    url      = 'http://eddylab.org/software/hmmer/hmmer-3.2.1.tar.gz'
 
+    version('3.2.1', '4e0ad5ed45462d4e36807d21e6d82b69')
     version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
     version('3.0',   '4cf685f3bc524ba5b5cdaaa070a83588')
     version('2.4i',  'dab234c87e026ac1de942450750acd20')
@@ -45,14 +27,6 @@ class Hmmer(Package):
     depends_on('mpi', when='+mpi')
     depends_on('gsl', when='+gsl')
 
-    def url_for_version(self, version):
-        base_url = 'http://eddylab.org/software'
-
-        if version >= Version('3.0'):
-            return '{0}/hmmer3/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
-        else:
-            return '{0}/hmmer/{1}/hmmer-{1}.tar.gz'.format(base_url, version)
-
     def install(self, spec, prefix):
         configure_args = [
             '--prefix={0}'.format(prefix)
diff --git a/var/spack/repos/builtin/packages/homer/package.py b/var/spack/repos/builtin/packages/homer/package.py
new file mode 100644
index 0000000000..14293169dc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/homer/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from os import symlink
+
+
+class Homer(Package):
+    """Software for motif discovery and next generation sequencing analysis"""
+
+    homepage = "http://homer.ucsd.edu/homer"
+    url      = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.zip"
+
+    version('4.9.1', sha256='ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('r-biocgenerics', type='run')
+    depends_on('r-biocparallel', type='run')
+    depends_on('r-edger', type='run')
+    depends_on('r-deseq2', type='run')
+
+    variant('data', default=False,
+            description='Download genome data packages')
+
+    def install(self, spec, prefix):
+        # initialize homer directories
+        basedir = join_path(prefix.lib, 'homer')
+        mkdirp(basedir)
+
+        install_tree('.', basedir)
+
+        # symlink bin so it is included in the PATH
+        symlink(join_path(basedir, 'bin'), prefix.bin)
+
+        # override homer base directory in configure script
+        filter_file('my $homeDir = $1;',
+                    'my $homeDir = \"{0}\";'.format(basedir),
+                    'configureHomer.pl', string=True)
+
+        # compile/prepare binaries and perl scripts with the correct paths
+        perl = which('perl')
+        perl('configureHomer.pl', '-local')
+
+        # download extra data if requested
+        if '+data' in spec:
+            perl('configureHomer.pl', '-install', '-all')
diff --git a/var/spack/repos/builtin/packages/hoomd-blue/package.py b/var/spack/repos/builtin/packages/hoomd-blue/package.py
index 547a15ae6b..4120e03410 100644
--- a/var/spack/repos/builtin/packages/hoomd-blue/package.py
+++ b/var/spack/repos/builtin/packages/hoomd-blue/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -37,20 +18,17 @@ class HoomdBlue(CMakePackage):
     and perform in situ analysis."""
 
     homepage = "http://glotzerlab.engin.umich.edu/hoomd-blue/"
-    git      = "https://bitbucket.org/glotzer/hoomd-blue"
-
-    # TODO: There is a bug in Spack that requires a url to be defined
-    # even if it isn't used. This URL can hopefully be removed someday.
-    url      = "https://bitbucket.org/glotzer/hoomd-blue/get/v2.1.6.tar.bz2"
+    git      = "https://bitbucket.org/glotzer/hoomd-blue.git"
 
-    version('develop', git=git, submodules=True)
+    version('develop', submodules=True)
 
     # Bitbucket has tarballs for each release, but they cannot be built.
     # The tarball doesn't come with the git submodules, nor does it come
     # with a .git directory, causing the build to fail. As a workaround,
     # clone a specific tag from Bitbucket instead of using the tarballs.
     # https://bitbucket.org/glotzer/hoomd-blue/issues/238
-    version('2.1.6', git=git, tag='v2.1.6', submodules=True)
+    version('2.2.2', tag='v2.2.2', submodules=True)
+    version('2.1.6', tag='v2.1.6', submodules=True)
 
     variant('mpi',  default=True,  description='Compile with MPI enabled')
     variant('cuda', default=True,  description='Compile with CUDA Toolkit')
@@ -61,26 +39,32 @@ class HoomdBlue(CMakePackage):
     # https://gcc.gnu.org/projects/cxx-status.html
     conflicts('%gcc@:4.6')
 
-    # HOOMD-blue uses hexadecimal floats, which are not technically part of
-    # the C++11 standard. GCC 6.0+ produces an error when this happens.
+    # HOOMD-blue 2.1.6 uses hexadecimal floats, which are not technically
+    # part of the C++11 standard. GCC 6.0+ produces an error when this happens.
     # https://bitbucket.org/glotzer/hoomd-blue/issues/239
     # https://bugzilla.redhat.com/show_bug.cgi?id=1321986
-    conflicts('%gcc@6.0:')
+    conflicts('%gcc@6.0:', when='@2.1.6')
+
+    # HOOMD-blue GCC 7+ is not yet supported
+    conflicts('%gcc@7.0:')
 
     extends('python')
     depends_on('python@2.7:')
     depends_on('py-numpy@1.7:', type=('build', 'run'))
-    depends_on('cmake@2.8.0:', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('cmake@2.8.0:3.9.6', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('mpi', when='+mpi')
     depends_on('cuda@7.0:', when='+cuda')
     depends_on('doxygen@1.8.5:', when='+doc', type='build')
 
     def cmake_args(self):
         spec = self.spec
+        install_dir = spec['python'].package.site_packages_dir
+        install_path = os.path.join(spec.prefix, install_dir)
 
         cmake_args = [
             '-DPYTHON_EXECUTABLE={0}'.format(spec['python'].command.path),
+            '-DCMAKE_INSTALL_PREFIX={0}'.format(install_path)
         ]
 
         # MPI support
diff --git a/var/spack/repos/builtin/packages/hpccg/package.py b/var/spack/repos/builtin/packages/hpccg/package.py
index 97fddc4f12..1a6256fe7c 100644
--- a/var/spack/repos/builtin/packages/hpccg/package.py
+++ b/var/spack/repos/builtin/packages/hpccg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py b/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
index 73ee39539f..1c7c7c4622 100644
--- a/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
+++ b/var/spack/repos/builtin/packages/hpctoolkit-externals/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,10 @@ class HpctoolkitExternals(Package):
     HpctoolkitExternals package provides all these prerequisites."""
 
     homepage = "http://hpctoolkit.org"
-    url = "https://github.com/HPCToolkit/hpctoolkit-externals"
+    git      = "https://github.com/HPCToolkit/hpctoolkit-externals.git"
 
-    version('2017.06', git=url, tag='release-2017.06')
-    version('master', git=url)
+    version('master')
+    version('2017.06', tag='release-2017.06')
 
     parallel = False
 
diff --git a/var/spack/repos/builtin/packages/hpctoolkit/package.py b/var/spack/repos/builtin/packages/hpctoolkit/package.py
index 14be6af8ef..0f4d188d4f 100644
--- a/var/spack/repos/builtin/packages/hpctoolkit/package.py
+++ b/var/spack/repos/builtin/packages/hpctoolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,10 @@ class Hpctoolkit(Package):
     and attributes them to the full calling context in which they occur."""
 
     homepage = "http://hpctoolkit.org"
-    url = "https://github.com/HPCToolkit/hpctoolkit"
+    git      = "https://github.com/HPCToolkit/hpctoolkit.git"
 
-    version('2017.06', git=url, tag='release-2017.06')
-    version('master', git=url)
+    version('master')
+    version('2017.06', tag='release-2017.06')
 
     variant('mpi', default=True, description='Enable MPI supoort')
     variant('papi', default=True, description='Enable PAPI counter support')
diff --git a/var/spack/repos/builtin/packages/hpgmg/package.py b/var/spack/repos/builtin/packages/hpgmg/package.py
index db9b0ce225..e4a533a024 100644
--- a/var/spack/repos/builtin/packages/hpgmg/package.py
+++ b/var/spack/repos/builtin/packages/hpgmg/package.py
@@ -1,53 +1,38 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Hpgmg(Package):
-    """HPGMG implements full multigrid (FMG) algorithms using
-    finite-volume and finite-element methods.
-    Different algorithmic variants adjust the arithmetic intensity
-    and architectural properties that are tested. These FMG methods
-    converge up to discretization error in one F-cycle,
-    thus may be considered direct solvers. An F-cycle visits
-    the finest level a total of two times,
-    the first coarsening (8x smaller) 4 times,
-    the second coarsening 6 times, etc."""
+    """HPGMG implements full multigrid (FMG) algorithms using finite-volume and
+       finite-element methods.  Different algorithmic variants adjust the
+       arithmetic intensity and architectural properties that are tested. These
+       FMG methods converge up to discretization error in one F-cycle, thus may
+       be considered direct solvers. An F-cycle visits the finest level a total
+       of two times, the first coarsening (8x smaller) 4 times, the second
+       coarsening 6 times, etc.
+    """
 
     homepage = "https://bitbucket.org/hpgmg/hpgmg"
-    url      = "https://bitbucket.org/hpgmg/hpgmg/get/master.tar.gz"
-    tags     = ['proxy-app']
+    url      = "https://hpgmg.org/static/hpgmg-0.tar.gz"
+    git      = "https://bitbucket.org/hpgmg/hpgmg.git"
 
-    version('master', '4a2b139e1764c84ed7fe06334d3f8d8a')
+    tags = ['proxy-app']
+
+    version('develop', branch='master')
+    version('a0a5510df23b', 'b9c50f25e541428d4735fb07344d1d0ed9fc821bdde918d8e0defa78c0d9b4f9')
+    version('0.3',          '12a65da216fec91daea78594ae4b5a069c8f1a700f1ba21eed9f45a79a68c793')
 
     variant(
-        'fe', default=True, description='Build finite element solver')
+        'fe', default=False, description='Build finite element solver')
     variant(
         'fv', default='mpi', values=('serial', 'mpi', 'none'),
         description='Build finite volume solver with or without MPI support')
     variant('cuda', default=False, description='Build with CUDA')
+    variant('debug', default=False, description='Build in debug mode')
 
     depends_on('petsc', when='+fe')
     depends_on('mpi', when='+fe')
@@ -59,7 +44,7 @@ class Hpgmg(Package):
 
     def configure_args(self):
         args = []
-        if '+fe' in self.spec:
+        if '+fe' in self.spec and not ('@0.3' in self.spec):
             args.append('--fe')
 
         if 'fv=serial' in self.spec:
@@ -68,10 +53,24 @@ class Hpgmg(Package):
         if 'mpi' in self.spec:
             args.append('--CC={0}'.format(self.spec['mpi'].mpicc))
 
+        cflags = []
         if 'fv=none' in self.spec:
             args.append('--no-fv')
         else:
-            args.append('--CFLAGS=' + self.compiler.openmp_flag)
+            # Apple's Clang doesn't support OpenMP
+            if not (self.spec.satisfies('%clang') and self.compiler.is_apple):
+                cflags.append(self.compiler.openmp_flag)
+
+        if '+debug' in self.spec:
+            cflags.append('-g')
+        elif any(map(self.spec.satisfies, ['%gcc', '%clang', '%intel'])):
+            cflags += ['-O3', '-march=native']
+
+        args.append('--CFLAGS=' + ' '.join(cflags))
+
+        # Explicitly specify the build directory to ensure that
+        # PETSC_ARCH is not used from the environment.
+        args.append('--arch=build')
 
         return args
 
@@ -79,7 +78,7 @@ class Hpgmg(Package):
         configure(*self.configure_args())
 
     def build(self, spec, prefix):
-        make()
+        make('-C', 'build')
 
     def install(self, spec, prefix):
         install_tree('build/bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/hpl/package.py b/var/spack/repos/builtin/packages/hpl/package.py
index 0c484fc1f7..94fc2d5fb9 100644
--- a/var/spack/repos/builtin/packages/hpl/package.py
+++ b/var/spack/repos/builtin/packages/hpl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import platform
diff --git a/var/spack/repos/builtin/packages/hpx/package.py b/var/spack/repos/builtin/packages/hpx/package.py
index 2c5e0c1402..9f4b3c6113 100644
--- a/var/spack/repos/builtin/packages/hpx/package.py
+++ b/var/spack/repos/builtin/packages/hpx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py
index dfc112fb24..d292f2c360 100644
--- a/var/spack/repos/builtin/packages/hpx5/package.py
+++ b/var/spack/repos/builtin/packages/hpx5/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -76,7 +57,7 @@ class Hpx5(AutotoolsPackage):
     depends_on("mpi", when='+photon')
     depends_on("opencl", when='+opencl')
     # depends_on("papi")
-    depends_on("pkg-config", type='build')
+    depends_on("pkgconfig", type='build')
 
     configure_directory = "hpx"
     build_directory = "spack-build"
diff --git a/var/spack/repos/builtin/packages/hsakmt/package.py b/var/spack/repos/builtin/packages/hsakmt/package.py
index 5574486066..d599dc13f5 100644
--- a/var/spack/repos/builtin/packages/hsakmt/package.py
+++ b/var/spack/repos/builtin/packages/hsakmt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hstr/package.py b/var/spack/repos/builtin/packages/hstr/package.py
index e019e9c3af..e8ab7fadb6 100644
--- a/var/spack/repos/builtin/packages/hstr/package.py
+++ b/var/spack/repos/builtin/packages/hstr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/htop/package.py b/var/spack/repos/builtin/packages/htop/package.py
index 168c03302d..f6ae2c04b2 100644
--- a/var/spack/repos/builtin/packages/htop/package.py
+++ b/var/spack/repos/builtin/packages/htop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class Htop(AutotoolsPackage):
     list_url = "https://hisham.hm/htop/releases"
     list_depth = 1
 
+    version('2.2.0', '0d816b6beed31edc75babcfbf863ffa8')
     version('2.0.2', '7d354d904bad591a931ad57e99fea84a')
 
     depends_on('ncurses')
diff --git a/var/spack/repos/builtin/packages/htslib/package.py b/var/spack/repos/builtin/packages/htslib/package.py
index 000c68e245..c223ffc359 100644
--- a/var/spack/repos/builtin/packages/htslib/package.py
+++ b/var/spack/repos/builtin/packages/htslib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,9 @@ class Htslib(AutotoolsPackage):
 
     homepage = "https://github.com/samtools/htslib"
 
+    version('1.9', '2ac92c9c3eef9986345ac69a05dd4d24')
+    version('1.8', '54e9b3a04251fa59b1878f6b546b5c79')
+    version('1.7', 'd3cc7e080a9a8c4161d8f62b56d3b98d')
     version('1.6', 'd6fd14e208aca7e08cbe9072233d0af9')
     version('1.4', '2a22ff382654c033c40e4ec3ea880050')
     version('1.3.1', '16d78f90b72f29971b042e8da8be6843')
diff --git a/var/spack/repos/builtin/packages/httpie/package.py b/var/spack/repos/builtin/packages/httpie/package.py
index 2ec4c6eaad..8ac07a61e9 100644
--- a/var/spack/repos/builtin/packages/httpie/package.py
+++ b/var/spack/repos/builtin/packages/httpie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hub/package.py b/var/spack/repos/builtin/packages/hub/package.py
index ff38385242..3595ac6c2e 100644
--- a/var/spack/repos/builtin/packages/hub/package.py
+++ b/var/spack/repos/builtin/packages/hub/package.py
@@ -1,37 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
 
 class Hub(Package):
     """The github git wrapper"""
+
     homepage = "https://github.com/github/hub"
-    url = "https://github.com/github/hub/archive/v2.2.3.tar.gz"
+    url      = "https://github.com/github/hub/archive/v2.2.3.tar.gz"
+    git      = "https://github.com/github/hub.git"
 
-    version('head', git='https://github.com/github/hub')
+    version('head', branch='master')
     version('2.2.3', '6675992ddd16d186eac7ba4484d57f5b')
     version('2.2.2', '7edc8f5b5d3c7c392ee191dd999596fc')
     version('2.2.1', '889a31ee9d10ae9cb333480d8dbe881f')
diff --git a/var/spack/repos/builtin/packages/hunspell/package.py b/var/spack/repos/builtin/packages/hunspell/package.py
index 2fef3d369e..ed400f3a4d 100644
--- a/var/spack/repos/builtin/packages/hunspell/package.py
+++ b/var/spack/repos/builtin/packages/hunspell/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py
index 7961d930db..3214496a0e 100644
--- a/var/spack/repos/builtin/packages/hwloc/package.py
+++ b/var/spack/repos/builtin/packages/hwloc/package.py
@@ -1,49 +1,38 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import sys
 
 
 class Hwloc(AutotoolsPackage):
-    """The Portable Hardware Locality (hwloc) software package
-       provides a portable abstraction (across OS, versions,
-       architectures, ...) of the hierarchical topology of modern
-       architectures, including NUMA memory nodes, sockets, shared
-       caches, cores and simultaneous multithreading. It also gathers
-       various system attributes such as cache and memory information
-       as well as the locality of I/O devices such as network
-       interfaces, InfiniBand HCAs or GPUs. It primarily aims at
-       helping applications with gathering information about modern
-       computing hardware so as to exploit it accordingly and
-       efficiently."""
+    """The Hardware Locality (hwloc) software project.
+
+    The Portable Hardware Locality (hwloc) software package
+    provides a portable abstraction (across OS, versions,
+    architectures, ...) of the hierarchical topology of modern
+    architectures, including NUMA memory nodes, sockets, shared
+    caches, cores and simultaneous multithreading. It also gathers
+    various system attributes such as cache and memory information
+    as well as the locality of I/O devices such as network
+    interfaces, InfiniBand HCAs or GPUs. It primarily aims at
+    helping applications with gathering information about modern
+    computing hardware so as to exploit it accordingly and
+    efficiently.
+    """
+
     homepage = "http://www.open-mpi.org/projects/hwloc/"
-    url      = "http://www.open-mpi.org/software/hwloc/v1.9/downloads/hwloc-1.9.tar.gz"
+    url      = "https://download.open-mpi.org/release/hwloc/v2.0/hwloc-2.0.2.tar.gz"
     list_url = "http://www.open-mpi.org/software/hwloc/"
     list_depth = 2
 
+    version('2.0.2',  '71d1211eaa4b25ac7ad80cf326784e87')
+    version('2.0.1',  '442b2482bb5b81983ed256522aadbf94')
+    version('2.0.0',  '027e6928ae0b5b64c821d0a71a61cd82')
+    version('1.11.9', '4d5f5da8b1d09731d82e865ecf3fa399')
     version('1.11.8', 'a0fa1c9109a4d8b4b6568e62cc9b6e30')
     version('1.11.7', '867a5266675e5bf1ef4ab66c459653f8')
     version('1.11.6', 'b4e95eadd2fbdb6d40bbd96be6f03c84')
@@ -58,24 +47,38 @@ class Hwloc(AutotoolsPackage):
     variant('libxml2', default=True, description="Build with libxml2")
     variant('pci', default=(sys.platform != 'darwin'),
             description="Support analyzing devices on PCI bus")
+    variant('shared', default=True, description="Build shared libraries")
+    variant(
+        'cairo',
+        default=False,
+        description='Enable the Cairo back-end of hwloc\'s lstopo command'
+    )
+
+    depends_on('pkgconfig', type='build')
 
     depends_on('cuda', when='+cuda')
     depends_on('libpciaccess', when='+pci')
     depends_on('libxml2', when='+libxml2')
-    depends_on('pkg-config', type='build')
+    depends_on('cairo', when='+cairo')
+    depends_on('numactl', when='@:1.11.9 platform=linux')
 
     def url_for_version(self, version):
         return "http://www.open-mpi.org/software/hwloc/v%s/downloads/hwloc-%s.tar.gz" % (version.up_to(2), version)
 
     def configure_args(self):
-        spec = self.spec
         args = [
-            "--enable-cuda" if '+cuda' in spec else "--disable-cuda",
-            "--enable-libxml2" if '+libxml2' in spec else "--disable-libxml2",
-            "--enable-pci" if '+pci' in spec else "--disable-pci",
             # Disable OpenCL, since hwloc might pick up an OpenCL
             # library at build time that is then not found at run time
             # (Alternatively, we could require OpenCL as dependency.)
             "--disable-opencl",
         ]
+        if '@2.0.0:' in self.spec:
+            args.append('--enable-netloc')
+
+        args.extend(self.enable_or_disable('cairo'))
+        args.extend(self.enable_or_disable('cuda'))
+        args.extend(self.enable_or_disable('libxml2'))
+        args.extend(self.enable_or_disable('pci'))
+        args.extend(self.enable_or_disable('shared'))
+
         return args
diff --git a/var/spack/repos/builtin/packages/hybpiper/package.py b/var/spack/repos/builtin/packages/hybpiper/package.py
index c3e3a22b13..fba2f13a2a 100644
--- a/var/spack/repos/builtin/packages/hybpiper/package.py
+++ b/var/spack/repos/builtin/packages/hybpiper/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py
index 428f7db386..bcf4665c5d 100644
--- a/var/spack/repos/builtin/packages/hydra/package.py
+++ b/var/spack/repos/builtin/packages/hydra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/hydrogen/package.py b/var/spack/repos/builtin/packages/hydrogen/package.py
new file mode 100644
index 0000000000..9a65ea4fe3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hydrogen/package.py
@@ -0,0 +1,156 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import sys
+from spack import *
+
+
+class Hydrogen(CMakePackage):
+    """Hydrogen: Distributed-memory dense and sparse-direct linear algebra
+       and optimization library. Based on the Elemental library."""
+
+    homepage = "http://libelemental.org"
+    url      = "https://github.com/LLNL/Elemental/archive/0.99.tar.gz"
+    git      = "https://github.com/LLNL/Elemental.git"
+
+    version('develop', branch='hydrogen')
+    version('1.0', sha256='d8a97de3133f2c6b6bb4b80d32b4a4cc25eb25e0df4f0cec0f8cb19bf34ece98')
+    version('0.99', 'b678433ab1d498da47acf3dc5e056c23')
+
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    variant('hybrid', default=True,
+            description='Make use of OpenMP within MPI packing/unpacking')
+    variant('openmp_blas', default=False,
+            description='Use OpenMP for threading in the BLAS library')
+    variant('quad', default=False,
+            description='Enable quad precision')
+    variant('int64', default=False,
+            description='Use 64bit integers')
+    variant('int64_blas', default=False,
+            description='Use 64bit integers for BLAS.')
+    variant('scalapack', default=False,
+            description='Build with ScaLAPACK library')
+    variant('build_type', default='Release',
+            description='The build type to build',
+            values=('Debug', 'Release'))
+    variant('blas', default='openblas', values=('openblas', 'mkl', 'accelerate', 'essl'),
+            description='Enable the use of OpenBlas/MKL/Accelerate/ESSL')
+    variant('mpfr', default=False,
+            description='Support GNU MPFR\'s'
+            'arbitrary-precision floating-point arithmetic')
+    variant('cuda', default=False,
+            description='Builds with support for GPUs via CUDA and cuDNN')
+    variant('test', default=False,
+            description='Builds test suite')
+    variant('al', default=False,
+            description='Builds with Aluminum communication library')
+    variant('omp_taskloops', default=False,
+            description='Use OpenMP taskloops instead of parallel for loops.')
+
+    # Note that #1712 forces us to enumerate the different blas variants
+    depends_on('openblas', when='blas=openblas ~openmp_blas ~int64_blas')
+    depends_on('openblas +ilp64', when='blas=openblas ~openmp_blas +int64_blas')
+    depends_on('openblas threads=openmp', when='blas=openblas +openmp_blas ~int64_blas')
+    depends_on('openblas threads=openmp +lip64', when='blas=openblas +openmp_blas +int64_blas')
+
+    depends_on('intel-mkl', when="blas=mkl ~openmp_blas ~int64_blas")
+    depends_on('intel-mkl +ilp64', when="blas=mkl ~openmp_blas +int64_blas")
+    depends_on('intel-mkl threads=openmp', when='blas=mkl +openmp_blas ~int64_blas')
+    depends_on('intel-mkl@2017.1 +openmp +ilp64', when='blas=mkl +openmp_blas +int64_blas')
+
+    depends_on('veclibfort', when='blas=accelerate')
+    conflicts('blas=accelerate +openmp_blas')
+
+    depends_on('essl -cuda', when='blas=essl -openmp_blas ~int64_blas')
+    depends_on('essl -cuda +ilp64', when='blas=essl -openmp_blas +int64_blas')
+    depends_on('essl threads=openmp', when='blas=essl +openmp_blas ~int64_blas')
+    depends_on('essl threads=openmp +ilp64', when='blas=essl +openmp_blas +int64_blas')
+    depends_on('netlib-lapack +external-blas', when='blas=essl')
+
+    depends_on('aluminum@master', when='+al ~cuda')
+    depends_on('aluminum@master +gpu +mpi-cuda', when='+al +cuda ~nccl')
+    depends_on('aluminum@master +gpu +nccl +mpi_cuda', when='+al +cuda +nccl')
+
+    # Note that this forces us to use OpenBLAS until #1712 is fixed
+    depends_on('lapack', when='blas=openblas ~openmp_blas')
+
+    depends_on('mpi', when='~cuda')
+    depends_on('mpi +cuda', when='+cuda')
+
+    depends_on('scalapack', when='+scalapack')
+    depends_on('gmp', when='+mpfr')
+    depends_on('mpc', when='+mpfr')
+    depends_on('mpfr', when='+mpfr')
+
+    depends_on('cuda', when='+cuda')
+    depends_on('cudnn', when='+cuda')
+    depends_on('cub', when='+cuda')
+
+    conflicts('@0:0.98', msg="Hydrogen did not exist before v0.99. " +
+              "Did you mean to use Elemental instead?")
+
+    @property
+    def libs(self):
+        shared = True if '+shared' in self.spec else False
+        return find_libraries(
+            'libEl', root=self.prefix, shared=shared, recursive=True
+        )
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            '-DCMAKE_INSTALL_MESSAGE:STRING=LAZY',
+            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DBUILD_SHARED_LIBS:BOOL=%s'      % ('+shared' in spec),
+            '-DHydrogen_ENABLE_OPENMP:BOOL=%s'       % ('+hybrid' in spec),
+            '-DHydrogen_ENABLE_QUADMATH:BOOL=%s'     % ('+quad' in spec),
+            '-DHydrogen_USE_64BIT_INTS:BOOL=%s'      % ('+int64' in spec),
+            '-DHydrogen_USE_64BIT_BLAS_INTS:BOOL=%s' % ('+int64_blas' in spec),
+            '-DHydrogen_ENABLE_MPC:BOOL=%s'        % ('+mpfr' in spec),
+            '-DHydrogen_GENERAL_LAPACK_FALLBACK=ON',
+            '-DHydrogen_ENABLE_CUDA=%s' % ('+cuda' in spec),
+            '-DHydrogen_ENABLE_TESTING=%s' % ('+test' in spec),
+        ]
+
+        # Add support for OS X to find OpenMP
+        if (self.spec.satisfies('%clang')):
+            if (sys.platform == 'darwin'):
+                clang = self.compiler.cc
+                clang_bin = os.path.dirname(clang)
+                clang_root = os.path.dirname(clang_bin)
+                args.extend([
+                    '-DOpenMP_DIR={0}'.format(clang_root)])
+
+        if 'blas=openblas' in spec:
+            args.extend([
+                '-DHydrogen_USE_OpenBLAS:BOOL=%s' % ('blas=openblas' in spec),
+                '-DOpenBLAS_DIR:STRING={0}'.format(
+                    spec['openblas'].prefix)])
+        elif 'blas=mkl' in spec:
+            args.extend([
+                '-DHydrogen_USE_MKL:BOOL=%s' % ('blas=mkl' in spec)])
+        elif 'blas=accelerate' in spec:
+            args.extend(['-DHydrogen_USE_ACCELERATE:BOOL=TRUE'])
+        elif 'blas=essl' in spec:
+            args.extend([
+                '-DHydrogen_USE_ESSL:BOOL=%s' % ('blas=essl' in spec)])
+
+        if '+omp_taskloops' in spec:
+            args.extend([
+                '-DHydrogen_ENABLE_OMP_TASKLOOP:BOOL=%s' %
+                ('+omp_taskloops' in spec)])
+
+        if '+al' in spec:
+            args.extend([
+                '-DHydrogen_ENABLE_ALUMINUM:BOOL=%s' % ('+al' in spec),
+                '-DHYDROGEN_Aluminum_DIR={0}'.format(
+                    spec['aluminum'].prefix)])
+
+        return args
diff --git a/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.13.0.patch b/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.13.0.patch
new file mode 100644
index 0000000000..a793bec8fc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.13.0.patch
@@ -0,0 +1,578 @@
+From c8467e905debeff23b8403aab7184e128decbba3 Mon Sep 17 00:00:00 2001
+From: Geoffrey Malcolm Oxberry <goxberry@gmail.com>
+Date: Tue, 11 Sep 2018 17:46:30 -0700
+Subject: [PATCH] build system: patch to build macOS shared libs
+
+---
+ src/FEI_mv/fei-hypre/Makefile         | 4 ++--
+ src/FEI_mv/femli/Makefile             | 4 ++--
+ src/IJ_mv/Makefile                    | 4 ++--
+ src/config/configure.in               | 9 +++++++--
+ src/configure                         | 9 +++++++--
+ src/distributed_ls/Euclid/Makefile    | 4 ++--
+ src/distributed_ls/ParaSails/Makefile | 4 ++--
+ src/distributed_ls/pilut/Makefile     | 4 ++--
+ src/distributed_matrix/Makefile       | 4 ++--
+ src/krylov/Makefile                   | 4 ++--
+ src/lib/Makefile                      | 4 ++--
+ src/matrix_matrix/Makefile            | 4 ++--
+ src/multivector/Makefile              | 4 ++--
+ src/parcsr_block_mv/Makefile          | 4 ++--
+ src/parcsr_ls/Makefile                | 4 ++--
+ src/parcsr_mv/Makefile                | 4 ++--
+ src/seq_mv/Makefile                   | 4 ++--
+ src/sstruct_ls/Makefile               | 4 ++--
+ src/sstruct_mv/Makefile               | 4 ++--
+ src/struct_ls/Makefile                | 4 ++--
+ src/struct_mv/Makefile                | 4 ++--
+ src/test/Makefile                     | 8 +++++---
+ src/utilities/Makefile                | 4 ++--
+ 23 files changed, 59 insertions(+), 47 deletions(-)
+
+diff --git a/src/FEI_mv/fei-hypre/Makefile b/src/FEI_mv/fei-hypre/Makefile
+index 09cad91df..68e5b394b 100644
+--- a/src/FEI_mv/fei-hypre/Makefile
++++ b/src/FEI_mv/fei-hypre/Makefile
+@@ -159,7 +159,7 @@ OBJSC = ${FILESC:.c=.o}
+ OBJSCXX = ${FILESCXX:.cxx=.o}
+ OBJS = ${OBJSC} ${OBJSCXX}
+ 
+-SONAME = libHYPRE_FEI-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_FEI-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -211,7 +211,7 @@ libHYPRE_FEI.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_FEI.so: ${OBJS}
++libHYPRE_FEI.so libHYPRE_FEI.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/FEI_mv/femli/Makefile b/src/FEI_mv/femli/Makefile
+index eac52137f..2beea900e 100644
+--- a/src/FEI_mv/femli/Makefile
++++ b/src/FEI_mv/femli/Makefile
+@@ -128,7 +128,7 @@ OBJSC = ${FILES:.c=.o}
+ OBJSCXX = ${OBJSC:.cxx=.o}
+ OBJS = ${OBJSCXX:.f=.o}
+ 
+-SONAME = libHYPRE_mli-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_mli-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -156,7 +156,7 @@ libHYPRE_mli.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_mli.so: ${OBJS}
++libHYPRE_mli.so libHYPRE_mli.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/IJ_mv/Makefile b/src/IJ_mv/Makefile
+index ab014ff7d..4f92e717a 100644
+--- a/src/IJ_mv/Makefile
++++ b/src/IJ_mv/Makefile
+@@ -53,7 +53,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_IJ_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_IJ_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -84,7 +84,7 @@ libHYPRE_IJ_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_IJ_mv.so: ${OBJS}
++libHYPRE_IJ_mv.so libHYPRE_IJ_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/config/configure.in b/src/config/configure.in
+index de8a10255..8f2d2c90e 100644
+--- a/src/config/configure.in
++++ b/src/config/configure.in
+@@ -1383,6 +1383,8 @@ dnl *********************************************************************
+ if test "$hypre_using_shared" = "yes"
+ then
+    HYPRE_LIBSUFFIX=".so"
++   SHARED_SET_SONAME="-Wl,-soname,"
++   SHARED_OPTIONS="-Wl,-z,defs"
+    case $hypre_platform in
+       AIX* | aix* | Aix*) SHARED_COMPILE_FLAG="-qmkshrobj"
+                           SHARED_BUILD_FLAG="-G"
+@@ -1390,6 +1392,11 @@ dnl                          LINK_F77="${F77} -brtl"
+                           LINK_FC="${FC} -brtl"
+                           LINK_CC="${CC} -brtl"
+                           LINK_CXX="${CXX} -brtl" ;;
++      DARWIN* | darwin* | Darwin*) SHARED_COMPILE_FLAG="-fPIC"
++                                   SHARED_BUILD_FLAG="-dynamiclib -undefined dynamic_lookup"
++				   HYPRE_LIBSUFFIX=".dylib"
++				   SHARED_SET_SONAME="-install_name @rpath/"
++				   SHARED_OPTIONS="-undefined error" ;;
+                        *) SHARED_COMPILE_FLAG="-fPIC"
+                           SHARED_BUILD_FLAG="-shared" ;;
+    esac
+@@ -1405,8 +1412,6 @@ dnl   BUILD_F77_SHARED="${F77} ${SHARED_BUILD_FLAG}"
+       BUILD_CC_SHARED="${CC} ${SHARED_BUILD_FLAG}"
+    fi
+    BUILD_CXX_SHARED="${CXX} ${SHARED_BUILD_FLAG}"
+-   SHARED_SET_SONAME="-Wl,-soname,"
+-   SHARED_OPTIONS="-Wl,-z,defs"
+ fi
+ 
+ BUILD_PYTHON=0
+diff --git a/src/configure b/src/configure
+index fa3d0717a..763a62dc5 100755
+--- a/src/configure
++++ b/src/configure
+@@ -7676,12 +7676,19 @@ HYPRE_LIBSUFFIX=".a"
+ if test "$hypre_using_shared" = "yes"
+ then
+    HYPRE_LIBSUFFIX=".so"
++   SHARED_SET_SONAME="-Wl,-soname,"
++   SHARED_OPTIONS="-Wl,-z,defs"
+    case $hypre_platform in
+       AIX* | aix* | Aix*) SHARED_COMPILE_FLAG="-qmkshrobj"
+                           SHARED_BUILD_FLAG="-G"
+                           LINK_FC="${FC} -brtl"
+                           LINK_CC="${CC} -brtl"
+                           LINK_CXX="${CXX} -brtl" ;;
++      DARWIN* | darwin* | Darwin*) SHARED_COMPILE_FLAG="-fPIC"
++                                   SHARED_BUILD_FLAG="-dynamiclib -undefined dynamic_lookup"
++				   HYPRE_LIBSUFFIX=".dylib"
++				   SHARED_SET_SONAME="-install_name @rpath/"
++				   SHARED_OPTIONS="-undefined error" ;;
+                        *) SHARED_COMPILE_FLAG="-fPIC"
+                           SHARED_BUILD_FLAG="-shared" ;;
+    esac
+@@ -7696,8 +7703,6 @@ then
+       BUILD_CC_SHARED="${CC} ${SHARED_BUILD_FLAG}"
+    fi
+    BUILD_CXX_SHARED="${CXX} ${SHARED_BUILD_FLAG}"
+-   SHARED_SET_SONAME="-Wl,-soname,"
+-   SHARED_OPTIONS="-Wl,-z,defs"
+ fi
+ 
+ BUILD_PYTHON=0
+diff --git a/src/distributed_ls/Euclid/Makefile b/src/distributed_ls/Euclid/Makefile
+index 03d9db355..b8b71dddd 100644
+--- a/src/distributed_ls/Euclid/Makefile
++++ b/src/distributed_ls/Euclid/Makefile
+@@ -87,7 +87,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_Euclid-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_Euclid-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -114,7 +114,7 @@ libHYPRE_Euclid.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_Euclid.so: ${OBJS}
++libHYPRE_Euclid.so libHYPRE_Euclid.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_ls/ParaSails/Makefile b/src/distributed_ls/ParaSails/Makefile
+index fe881b1f3..78091ad88 100644
+--- a/src/distributed_ls/ParaSails/Makefile
++++ b/src/distributed_ls/ParaSails/Makefile
+@@ -59,7 +59,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_ParaSails-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_ParaSails-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -86,7 +86,7 @@ libHYPRE_ParaSails.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_ParaSails.so: ${OBJS}
++libHYPRE_ParaSails.so libHYPRE_ParaSails.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_ls/pilut/Makefile b/src/distributed_ls/pilut/Makefile
+index 2ed918e2c..333edbafa 100644
+--- a/src/distributed_ls/pilut/Makefile
++++ b/src/distributed_ls/pilut/Makefile
+@@ -49,7 +49,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_DistributedMatrixPilutSolver-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_DistributedMatrixPilutSolver-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -78,7 +78,7 @@ libHYPRE_DistributedMatrixPilutSolver.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_DistributedMatrixPilutSolver.so: ${OBJS}
++libHYPRE_DistributedMatrixPilutSolver.so libHYPRE_DistributedMatrixPilutSolver.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_matrix/Makefile b/src/distributed_matrix/Makefile
+index b8d42944c..d30908fa2 100644
+--- a/src/distributed_matrix/Makefile
++++ b/src/distributed_matrix/Makefile
+@@ -40,7 +40,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_DistributedMatrix-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_DistributedMatrix-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -69,7 +69,7 @@ libHYPRE_DistributedMatrix.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_DistributedMatrix.so: ${OBJS}
++libHYPRE_DistributedMatrix.so libHYPRE_DistributedMatrix.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/krylov/Makefile b/src/krylov/Makefile
+index 152d5153a..63d085431 100644
+--- a/src/krylov/Makefile
++++ b/src/krylov/Makefile
+@@ -55,7 +55,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_krylov-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_krylov-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -88,7 +88,7 @@ libHYPRE_krylov.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_krylov.so: ${OBJS}
++libHYPRE_krylov.so libHYPRE_krylov.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/lib/Makefile b/src/lib/Makefile
+index 72875e2c1..f49d16838 100644
+--- a/src/lib/Makefile
++++ b/src/lib/Makefile
+@@ -57,7 +57,7 @@ $(UTILITIESFILES)\
+ $(BLASFILES)\
+ $(LAPACKFILES)
+ 
+-SONAME = libHYPRE-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ SOLIBS = ${MPILIBDIRS} ${MPILIBS} ${LAPACKLIBDIRS} ${LAPACKLIBS}\
+  ${BLASLIBDIRS} ${BLASLIBS} ${LIBS} ${FLIBS}
+ 
+@@ -103,7 +103,7 @@ libHYPRE.a: ${FILES_HYPRE}
+ 	${AR} $@ $(UTILITIESFILES) $(BLASFILES) $(LAPACKFILES)
+ 	${RANLIB} $@
+ 
+-libHYPRE.so: ${FILES_HYPRE}
++libHYPRE.so libHYPRE.dylib: ${FILES_HYPRE}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${FILES_HYPRE} ${SOLIBS} ${SHARED_SET_SONAME}${SONAME} ${SHARED_OPTIONS} ${LDFLAGS}
+ 	ln -s ${SONAME} $@
+diff --git a/src/matrix_matrix/Makefile b/src/matrix_matrix/Makefile
+index 1da8ced0e..a611bee51 100644
+--- a/src/matrix_matrix/Makefile
++++ b/src/matrix_matrix/Makefile
+@@ -35,7 +35,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_MatrixMatrix-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_MatrixMatrix-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -64,7 +64,7 @@ libHYPRE_MatrixMatrix.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_MatrixMatrix.so: ${OBJS}
++libHYPRE_MatrixMatrix.so libHYPRE_MatrixMatrix.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/multivector/Makefile b/src/multivector/Makefile
+index 915cf5e0e..fce270f13 100644
+--- a/src/multivector/Makefile
++++ b/src/multivector/Makefile
+@@ -31,7 +31,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_multivector-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_multivector-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -60,7 +60,7 @@ libHYPRE_multivector.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_multivector.so: ${OBJS}
++libHYPRE_multivector.so libHYPRE_multivector.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_block_mv/Makefile b/src/parcsr_block_mv/Makefile
+index 3f1e33db1..b7559d39e 100644
+--- a/src/parcsr_block_mv/Makefile
++++ b/src/parcsr_block_mv/Makefile
+@@ -59,7 +59,7 @@ DRIVER_FILES =
+ OBJS = ${FILES:.c=.o}
+ DRIVER_OBJS = ${DRIVER_FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_block_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_block_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -114,7 +114,7 @@ libHYPRE_parcsr_block_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_block_mv.so: ${OBJS}
++libHYPRE_parcsr_block_mv.so libHYPRE_parcsr_block_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_ls/Makefile b/src/parcsr_ls/Makefile
+index 74972be17..7670387e0 100644
+--- a/src/parcsr_ls/Makefile
++++ b/src/parcsr_ls/Makefile
+@@ -133,7 +133,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -165,7 +165,7 @@ libHYPRE_parcsr_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_ls.so: ${OBJS}
++libHYPRE_parcsr_ls.so libHYPRE_parcsr_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_mv/Makefile b/src/parcsr_mv/Makefile
+index 99b4f7ba8..ff027bb30 100644
+--- a/src/parcsr_mv/Makefile
++++ b/src/parcsr_mv/Makefile
+@@ -71,7 +71,7 @@ DRIVER_FILES =\
+ OBJS = ${FILES:.c=.o}
+ DRIVER_OBJS = ${DRIVER_FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -127,7 +127,7 @@ libHYPRE_parcsr_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_mv.so: ${OBJS}
++libHYPRE_parcsr_mv.so libHYPRE_parcsr_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/seq_mv/Makefile b/src/seq_mv/Makefile
+index 6982fa067..b0692cd26 100644
+--- a/src/seq_mv/Makefile
++++ b/src/seq_mv/Makefile
+@@ -49,7 +49,7 @@ FILES =\
+ OBJS = ${FILES:.c=.o}
+ CUOBJS = ${FILES_NVCC:.cu=.o}
+ 
+-SONAME = libHYPRE_seq_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_seq_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -80,7 +80,7 @@ libHYPRE_seq_mv.a: ${OBJS} ${CUOBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_seq_mv.so: ${OBJS} ${CUOBJS}
++libHYPRE_seq_mv.so libHYPRE_seq_mv.dylib: ${OBJS} ${CUOBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/sstruct_ls/Makefile b/src/sstruct_ls/Makefile
+index 28811f8bf..463843d9a 100644
+--- a/src/sstruct_ls/Makefile
++++ b/src/sstruct_ls/Makefile
+@@ -109,7 +109,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_sstruct_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_sstruct_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -140,7 +140,7 @@ libHYPRE_sstruct_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_sstruct_ls.so: ${OBJS}
++libHYPRE_sstruct_ls.so libHYPRE_sstruct_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/sstruct_mv/Makefile b/src/sstruct_mv/Makefile
+index d9adda815..1f4dfc029 100644
+--- a/src/sstruct_mv/Makefile
++++ b/src/sstruct_mv/Makefile
+@@ -59,7 +59,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_sstruct_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_sstruct_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -90,7 +90,7 @@ libHYPRE_sstruct_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_sstruct_mv.so: ${OBJS}
++libHYPRE_sstruct_mv.so libHYPRE_sstruct_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/struct_ls/Makefile b/src/struct_ls/Makefile
+index 4653b733d..007529823 100644
+--- a/src/struct_ls/Makefile
++++ b/src/struct_ls/Makefile
+@@ -104,7 +104,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_struct_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_struct_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -135,7 +135,7 @@ libHYPRE_struct_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_struct_ls.so: ${OBJS}
++libHYPRE_struct_ls.so libHYPRE_struct_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/struct_mv/Makefile b/src/struct_mv/Makefile
+index eabf9b00f..349947a4f 100644
+--- a/src/struct_mv/Makefile
++++ b/src/struct_mv/Makefile
+@@ -66,7 +66,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_struct_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_struct_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -97,7 +97,7 @@ libHYPRE_struct_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_struct_mv.so: ${OBJS}
++libHYPRE_struct_mv.so libHYPRE_struct_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/test/Makefile b/src/test/Makefile
+index 17e8f465d..4616c6de4 100644
+--- a/src/test/Makefile
++++ b/src/test/Makefile
+@@ -40,7 +40,7 @@ F77_COMPILE_FLAGS = \
+  -I${HYPRE_BUILD_DIR}/include\
+  ${CINCLUDES}
+ 
+-MPILIBFLAGS = ${MPILIBDIRS} ${MPILIBS} ${MPIFLAGS} 
++MPILIBFLAGS = ${MPILIBDIRS} ${MPILIBS} ${MPIFLAGS}
+ LAPACKLIBFLAGS = ${LAPACKLIBDIRS} ${LAPACKLIBS}
+ BLASLIBFLAGS = ${BLASLIBDIRS} ${BLASLIBS}
+ LIBFLAGS = ${LDFLAGS} ${LIBS}
+@@ -48,6 +48,9 @@ LIBFLAGS = ${LDFLAGS} ${LIBS}
+ LFLAGS =\
+  -L${HYPRE_BUILD_DIR}/lib\
+  -lHYPRE\
++ -Wl,-rpath,${HYPRE_BUILD_DIR}/lib\
++ ${DSUPERLU_LIBS}\
++ ${SUPERLU_LIBS}\
+  ${MPILIBFLAGS}\
+  ${LAPACKLIBFLAGS}\
+  ${BLASLIBFLAGS}\
+@@ -265,7 +268,7 @@ fparcsr_mv: fparcsr_mv.f
+ 	@echo  "Building" $@ "... "
+ 	${LINK_FC} -c $@
+ 
+-fsstruct_ls: fsstruct_ls.f 
++fsstruct_ls: fsstruct_ls.f
+ 	@echo  "Building" $@ "... "
+ 	${LINK_FC} -c $@
+ 
+@@ -280,4 +283,3 @@ fstruct_ls: fstruct_ls.f
+ fstruct_mv: fstruct_mv.f
+ 	@echo  "Building" $@ "... "
+ 	${LINK_FC} -c $@
+-
+diff --git a/src/utilities/Makefile b/src/utilities/Makefile
+index 512e6d0be..c1710766a 100644
+--- a/src/utilities/Makefile
++++ b/src/utilities/Makefile
+@@ -66,7 +66,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_utilities-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_utilities-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -100,7 +100,7 @@ libHYPRE_utilities.a: ${OBJS}
+ 	${AR} $@ *.o
+ 	${RANLIB} $@
+ 
+-libHYPRE_utilities.so: ${OBJS}
++libHYPRE_utilities.so libHYPRE_utilities.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+-- 
+2.19.0
+
diff --git a/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.14.0.patch b/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.14.0.patch
new file mode 100644
index 0000000000..1d563f9a42
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hypre/darwin-shared-libs-for-hypre-2.14.0.patch
@@ -0,0 +1,553 @@
+From c5db8367db7873cabe2d7e60a577eb1eb158f364 Mon Sep 17 00:00:00 2001
+From: Geoffrey Malcolm Oxberry <goxberry@gmail.com>
+Date: Tue, 11 Sep 2018 17:46:30 -0700
+Subject: [PATCH] build system: patch to build macOS shared libs
+
+---
+ src/FEI_mv/fei-hypre/Makefile         | 4 ++--
+ src/FEI_mv/femli/Makefile             | 4 ++--
+ src/IJ_mv/Makefile                    | 4 ++--
+ src/config/configure.in               | 9 +++++++--
+ src/configure                         | 9 +++++++--
+ src/distributed_ls/Euclid/Makefile    | 4 ++--
+ src/distributed_ls/ParaSails/Makefile | 4 ++--
+ src/distributed_ls/pilut/Makefile     | 4 ++--
+ src/distributed_matrix/Makefile       | 4 ++--
+ src/krylov/Makefile                   | 4 ++--
+ src/lib/Makefile                      | 4 ++--
+ src/matrix_matrix/Makefile            | 4 ++--
+ src/multivector/Makefile              | 4 ++--
+ src/parcsr_block_mv/Makefile          | 4 ++--
+ src/parcsr_ls/Makefile                | 4 ++--
+ src/parcsr_mv/Makefile                | 4 ++--
+ src/seq_mv/Makefile                   | 4 ++--
+ src/sstruct_ls/Makefile               | 4 ++--
+ src/sstruct_mv/Makefile               | 4 ++--
+ src/struct_ls/Makefile                | 4 ++--
+ src/struct_mv/Makefile                | 4 ++--
+ src/test/Makefile                     | 1 +
+ src/utilities/Makefile                | 4 ++--
+ 23 files changed, 55 insertions(+), 44 deletions(-)
+
+diff --git a/src/FEI_mv/fei-hypre/Makefile b/src/FEI_mv/fei-hypre/Makefile
+index 09cad91df..68e5b394b 100644
+--- a/src/FEI_mv/fei-hypre/Makefile
++++ b/src/FEI_mv/fei-hypre/Makefile
+@@ -159,7 +159,7 @@ OBJSC = ${FILESC:.c=.o}
+ OBJSCXX = ${FILESCXX:.cxx=.o}
+ OBJS = ${OBJSC} ${OBJSCXX}
+ 
+-SONAME = libHYPRE_FEI-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_FEI-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -211,7 +211,7 @@ libHYPRE_FEI.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_FEI.so: ${OBJS}
++libHYPRE_FEI.so libHYPRE_FEI.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/FEI_mv/femli/Makefile b/src/FEI_mv/femli/Makefile
+index 07bf5dff3..499757ffa 100644
+--- a/src/FEI_mv/femli/Makefile
++++ b/src/FEI_mv/femli/Makefile
+@@ -129,7 +129,7 @@ OBJSC = ${FILES:.c=.o}
+ OBJSCXX = ${OBJSC:.cxx=.o}
+ OBJS = ${OBJSCXX:.f=.o}
+ 
+-SONAME = libHYPRE_mli-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_mli-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -157,7 +157,7 @@ libHYPRE_mli.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_mli.so: ${OBJS}
++libHYPRE_mli.so libHYPRE_mli.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/IJ_mv/Makefile b/src/IJ_mv/Makefile
+index ab014ff7d..4f92e717a 100644
+--- a/src/IJ_mv/Makefile
++++ b/src/IJ_mv/Makefile
+@@ -53,7 +53,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_IJ_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_IJ_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -84,7 +84,7 @@ libHYPRE_IJ_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_IJ_mv.so: ${OBJS}
++libHYPRE_IJ_mv.so libHYPRE_IJ_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/config/configure.in b/src/config/configure.in
+index c0a0e3091..c05e13cd2 100644
+--- a/src/config/configure.in
++++ b/src/config/configure.in
+@@ -1413,6 +1413,8 @@ dnl *********************************************************************
+ if test "$hypre_using_shared" = "yes"
+ then
+    HYPRE_LIBSUFFIX=".so"
++   SHARED_SET_SONAME="-Wl,-soname,"
++   SHARED_OPTIONS="-Wl,-z,defs"
+    case $hypre_platform in
+       AIX* | aix* | Aix*) SHARED_COMPILE_FLAG="-qmkshrobj"
+                           SHARED_BUILD_FLAG="-G"
+@@ -1420,6 +1422,11 @@ dnl                          LINK_F77="${F77} -brtl"
+                           LINK_FC="${FC} -brtl"
+                           LINK_CC="${CC} -brtl"
+                           LINK_CXX="${CXX} -brtl" ;;
++      DARWIN* | darwin* | Darwin*) SHARED_COMPILE_FLAG="-fPIC"
++                                   SHARED_BUILD_FLAG="-dynamiclib -undefined dynamic_lookup"
++				   HYPRE_LIBSUFFIX=".dylib"
++				   SHARED_SET_SONAME="-install_name @rpath/"
++				   SHARED_OPTIONS="-undefined error" ;;
+                        *) SHARED_COMPILE_FLAG="-fPIC"
+                           SHARED_BUILD_FLAG="-shared" ;;
+    esac
+@@ -1435,8 +1442,6 @@ dnl   BUILD_F77_SHARED="${F77} ${SHARED_BUILD_FLAG}"
+       BUILD_CC_SHARED="${CC} ${SHARED_BUILD_FLAG}"
+    fi
+    BUILD_CXX_SHARED="${CXX} ${SHARED_BUILD_FLAG}"
+-   SHARED_SET_SONAME="-Wl,-soname,"
+-   SHARED_OPTIONS="-Wl,-z,defs"
+ fi
+ 
+ BUILD_PYTHON=0
+diff --git a/src/configure b/src/configure
+index c4b2e42cf..2de08ceae 100755
+--- a/src/configure
++++ b/src/configure
+@@ -7876,12 +7876,19 @@ HYPRE_LIBSUFFIX=".a"
+ if test "$hypre_using_shared" = "yes"
+ then
+    HYPRE_LIBSUFFIX=".so"
++   SHARED_SET_SONAME="-Wl,-soname,"
++   SHARED_OPTIONS="-Wl,-z,defs"
+    case $hypre_platform in
+       AIX* | aix* | Aix*) SHARED_COMPILE_FLAG="-qmkshrobj"
+                           SHARED_BUILD_FLAG="-G"
+                           LINK_FC="${FC} -brtl"
+                           LINK_CC="${CC} -brtl"
+                           LINK_CXX="${CXX} -brtl" ;;
++      DARWIN* | darwin* | Darwin*) SHARED_COMPILE_FLAG="-fPIC"
++                                   SHARED_BUILD_FLAG="-dynamiclib -undefined dynamic_lookup"
++				   HYPRE_LIBSUFFIX=".dylib"
++				   SHARED_SET_SONAME="-install_name @rpath/"
++				   SHARED_OPTIONS="-undefined error" ;;
+                        *) SHARED_COMPILE_FLAG="-fPIC"
+                           SHARED_BUILD_FLAG="-shared" ;;
+    esac
+@@ -7896,8 +7903,6 @@ then
+       BUILD_CC_SHARED="${CC} ${SHARED_BUILD_FLAG}"
+    fi
+    BUILD_CXX_SHARED="${CXX} ${SHARED_BUILD_FLAG}"
+-   SHARED_SET_SONAME="-Wl,-soname,"
+-   SHARED_OPTIONS="-Wl,-z,defs"
+ fi
+ 
+ BUILD_PYTHON=0
+diff --git a/src/distributed_ls/Euclid/Makefile b/src/distributed_ls/Euclid/Makefile
+index 03d9db355..b8b71dddd 100644
+--- a/src/distributed_ls/Euclid/Makefile
++++ b/src/distributed_ls/Euclid/Makefile
+@@ -87,7 +87,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_Euclid-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_Euclid-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -114,7 +114,7 @@ libHYPRE_Euclid.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_Euclid.so: ${OBJS}
++libHYPRE_Euclid.so libHYPRE_Euclid.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_ls/ParaSails/Makefile b/src/distributed_ls/ParaSails/Makefile
+index fe881b1f3..78091ad88 100644
+--- a/src/distributed_ls/ParaSails/Makefile
++++ b/src/distributed_ls/ParaSails/Makefile
+@@ -59,7 +59,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_ParaSails-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_ParaSails-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -86,7 +86,7 @@ libHYPRE_ParaSails.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_ParaSails.so: ${OBJS}
++libHYPRE_ParaSails.so libHYPRE_ParaSails.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_ls/pilut/Makefile b/src/distributed_ls/pilut/Makefile
+index e24d4d224..67e00fb5b 100644
+--- a/src/distributed_ls/pilut/Makefile
++++ b/src/distributed_ls/pilut/Makefile
+@@ -50,7 +50,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_DistributedMatrixPilutSolver-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_DistributedMatrixPilutSolver-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -79,7 +79,7 @@ libHYPRE_DistributedMatrixPilutSolver.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_DistributedMatrixPilutSolver.so: ${OBJS}
++libHYPRE_DistributedMatrixPilutSolver.so libHYPRE_DistributedMatrixPilutSolver.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/distributed_matrix/Makefile b/src/distributed_matrix/Makefile
+index b8d42944c..d30908fa2 100644
+--- a/src/distributed_matrix/Makefile
++++ b/src/distributed_matrix/Makefile
+@@ -40,7 +40,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_DistributedMatrix-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_DistributedMatrix-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -69,7 +69,7 @@ libHYPRE_DistributedMatrix.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_DistributedMatrix.so: ${OBJS}
++libHYPRE_DistributedMatrix.so libHYPRE_DistributedMatrix.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/krylov/Makefile b/src/krylov/Makefile
+index bb3ec05cf..f4682b657 100644
+--- a/src/krylov/Makefile
++++ b/src/krylov/Makefile
+@@ -58,7 +58,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_krylov-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_krylov-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -91,7 +91,7 @@ libHYPRE_krylov.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_krylov.so: ${OBJS}
++libHYPRE_krylov.so libHYPRE_krylov.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/lib/Makefile b/src/lib/Makefile
+index 72875e2c1..f49d16838 100644
+--- a/src/lib/Makefile
++++ b/src/lib/Makefile
+@@ -57,7 +57,7 @@ $(UTILITIESFILES)\
+ $(BLASFILES)\
+ $(LAPACKFILES)
+ 
+-SONAME = libHYPRE-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ SOLIBS = ${MPILIBDIRS} ${MPILIBS} ${LAPACKLIBDIRS} ${LAPACKLIBS}\
+  ${BLASLIBDIRS} ${BLASLIBS} ${LIBS} ${FLIBS}
+ 
+@@ -103,7 +103,7 @@ libHYPRE.a: ${FILES_HYPRE}
+ 	${AR} $@ $(UTILITIESFILES) $(BLASFILES) $(LAPACKFILES)
+ 	${RANLIB} $@
+ 
+-libHYPRE.so: ${FILES_HYPRE}
++libHYPRE.so libHYPRE.dylib: ${FILES_HYPRE}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${FILES_HYPRE} ${SOLIBS} ${SHARED_SET_SONAME}${SONAME} ${SHARED_OPTIONS} ${LDFLAGS}
+ 	ln -s ${SONAME} $@
+diff --git a/src/matrix_matrix/Makefile b/src/matrix_matrix/Makefile
+index 1da8ced0e..a611bee51 100644
+--- a/src/matrix_matrix/Makefile
++++ b/src/matrix_matrix/Makefile
+@@ -35,7 +35,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_MatrixMatrix-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_MatrixMatrix-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -64,7 +64,7 @@ libHYPRE_MatrixMatrix.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_MatrixMatrix.so: ${OBJS}
++libHYPRE_MatrixMatrix.so libHYPRE_MatrixMatrix.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/multivector/Makefile b/src/multivector/Makefile
+index 915cf5e0e..fce270f13 100644
+--- a/src/multivector/Makefile
++++ b/src/multivector/Makefile
+@@ -31,7 +31,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_multivector-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_multivector-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -60,7 +60,7 @@ libHYPRE_multivector.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_multivector.so: ${OBJS}
++libHYPRE_multivector.so libHYPRE_multivector.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_block_mv/Makefile b/src/parcsr_block_mv/Makefile
+index bac31a5ed..eba6d2589 100644
+--- a/src/parcsr_block_mv/Makefile
++++ b/src/parcsr_block_mv/Makefile
+@@ -61,7 +61,7 @@ DRIVER_FILES =
+ OBJS = ${FILES:.c=.o}
+ DRIVER_OBJS = ${DRIVER_FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_block_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_block_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -116,7 +116,7 @@ libHYPRE_parcsr_block_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_block_mv.so: ${OBJS}
++libHYPRE_parcsr_block_mv.so libHYPRE_parcsr_block_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_ls/Makefile b/src/parcsr_ls/Makefile
+index f25eda61f..980ccf283 100644
+--- a/src/parcsr_ls/Makefile
++++ b/src/parcsr_ls/Makefile
+@@ -139,7 +139,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -171,7 +171,7 @@ libHYPRE_parcsr_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_ls.so: ${OBJS}
++libHYPRE_parcsr_ls.so libHYPRE_parcsr_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/parcsr_mv/Makefile b/src/parcsr_mv/Makefile
+index 87c697ad9..654be6dd1 100644
+--- a/src/parcsr_mv/Makefile
++++ b/src/parcsr_mv/Makefile
+@@ -73,7 +73,7 @@ DRIVER_FILES =\
+ OBJS = ${FILES:.c=.o}
+ DRIVER_OBJS = ${DRIVER_FILES:.c=.o}
+ 
+-SONAME = libHYPRE_parcsr_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_parcsr_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -129,7 +129,7 @@ libHYPRE_parcsr_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_parcsr_mv.so: ${OBJS}
++libHYPRE_parcsr_mv.so libHYPRE_parcsr_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/seq_mv/Makefile b/src/seq_mv/Makefile
+index 0f2c34d0d..da0b29a54 100644
+--- a/src/seq_mv/Makefile
++++ b/src/seq_mv/Makefile
+@@ -50,7 +50,7 @@ FILES =\
+ OBJS = ${FILES:.c=.o}
+ CUOBJS = ${FILES_NVCC:.cu=.o}
+ 
+-SONAME = libHYPRE_seq_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_seq_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -81,7 +81,7 @@ libHYPRE_seq_mv.a: ${OBJS} ${CUOBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_seq_mv.so: ${OBJS} ${CUOBJS}
++libHYPRE_seq_mv.so libHYPRE_seq_mv.dylib: ${OBJS} ${CUOBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/sstruct_ls/Makefile b/src/sstruct_ls/Makefile
+index b4511f4ab..0f2a0a1f3 100644
+--- a/src/sstruct_ls/Makefile
++++ b/src/sstruct_ls/Makefile
+@@ -111,7 +111,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_sstruct_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_sstruct_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -142,7 +142,7 @@ libHYPRE_sstruct_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_sstruct_ls.so: ${OBJS}
++libHYPRE_sstruct_ls.so libHYPRE_sstruct_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/sstruct_mv/Makefile b/src/sstruct_mv/Makefile
+index d9adda815..1f4dfc029 100644
+--- a/src/sstruct_mv/Makefile
++++ b/src/sstruct_mv/Makefile
+@@ -59,7 +59,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_sstruct_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_sstruct_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -90,7 +90,7 @@ libHYPRE_sstruct_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_sstruct_mv.so: ${OBJS}
++libHYPRE_sstruct_mv.so libHYPRE_sstruct_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/struct_ls/Makefile b/src/struct_ls/Makefile
+index 4653b733d..007529823 100644
+--- a/src/struct_ls/Makefile
++++ b/src/struct_ls/Makefile
+@@ -104,7 +104,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_struct_ls-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_struct_ls-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -135,7 +135,7 @@ libHYPRE_struct_ls.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_struct_ls.so: ${OBJS}
++libHYPRE_struct_ls.so libHYPRE_struct_ls.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/struct_mv/Makefile b/src/struct_mv/Makefile
+index eabf9b00f..349947a4f 100644
+--- a/src/struct_mv/Makefile
++++ b/src/struct_mv/Makefile
+@@ -66,7 +66,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_struct_mv-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_struct_mv-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -97,7 +97,7 @@ libHYPRE_struct_mv.a: ${OBJS}
+ 	${AR} $@ ${OBJS}
+ 	${RANLIB} $@
+ 
+-libHYPRE_struct_mv.so: ${OBJS}
++libHYPRE_struct_mv.so libHYPRE_struct_mv.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+diff --git a/src/test/Makefile b/src/test/Makefile
+index 86481720f..ec05bfcbd 100644
+--- a/src/test/Makefile
++++ b/src/test/Makefile
+@@ -52,6 +52,7 @@ LIBFLAGS = ${LDFLAGS} ${LIBS}
+ LFLAGS =\
+  -L${HYPRE_BUILD_DIR}/lib\
+  -lHYPRE\
++ -Wl,-rpath,${HYPRE_BUILD_DIR}/lib\
+  ${DSUPERLU_LIBS}\
+  ${SUPERLU_LIBS}\
+  ${MPILIBFLAGS}\
+diff --git a/src/utilities/Makefile b/src/utilities/Makefile
+index bd4a3fe67..a4993b9e4 100644
+--- a/src/utilities/Makefile
++++ b/src/utilities/Makefile
+@@ -64,7 +64,7 @@ FILES =\
+ 
+ OBJS = ${FILES:.c=.o}
+ 
+-SONAME = libHYPRE_utilities-${HYPRE_RELEASE_VERSION}.so
++SONAME = libHYPRE_utilities-${HYPRE_RELEASE_VERSION}${HYPRE_LIB_SUFFIX}
+ 
+ ##################################################################
+ # Targets
+@@ -98,7 +98,7 @@ libHYPRE_utilities.a: ${OBJS}
+ 	${AR} $@ *.o
+ 	${RANLIB} $@
+ 
+-libHYPRE_utilities.so: ${OBJS}
++libHYPRE_utilities.so libHYPRE_utilities.dylib: ${OBJS}
+ 	@echo  "Building $@ ... "
+ 	${BUILD_CC_SHARED} -o ${SONAME} ${OBJS} ${SHARED_SET_SONAME}${SONAME}
+ 	ln -s ${SONAME} $@
+-- 
+2.19.0
+
diff --git a/var/spack/repos/builtin/packages/hypre/package.py b/var/spack/repos/builtin/packages/hypre/package.py
index 8472d64337..c78cd16071 100644
--- a/var/spack/repos/builtin/packages/hypre/package.py
+++ b/var/spack/repos/builtin/packages/hypre/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import sys
@@ -33,17 +14,25 @@ class Hypre(Package):
        unstructured grid problems."""
 
     homepage = "http://computation.llnl.gov/project/linear_solvers/software.php"
-    url      = "http://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b.tar.gz"
+    url      = "https://github.com/LLNL/hypre/archive/v2.14.0.tar.gz"
+    git      = "https://github.com/LLNL/hypre.git"
 
-    version('2.12.1', 'c6fcb6d7e57cec1c7ce4a44da885068c', url='https://github.com/LLNL/hypre/archive/v2.12.1.tar.gz')
+    version('develop', branch='master')
+    version('2.15.1', '877002d49f38b6a1434955baf79eff35')
+    version('2.15.0', '4645acc49141069cae1d53de96107a08')
+    version('2.14.0', 'ecde5cc807ec45bfb647e9f28d2eaea1')
+    version('2.13.0', '4b688a5c15b6b5e3de5e045ae081b89b')
+    version('2.12.1', 'c6fcb6d7e57cec1c7ce4a44da885068c')
     version('2.11.2', 'd507943a1a3ce5681c3308e2f3a6dd34')
     version('2.11.1', '3f02ef8fd679239a6723f60b7f796519')
     version('2.10.1', 'dc048c4cabb3cd549af72591474ad674')
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
-    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', tag='xsdk-0.2.0')
 
-    # hypre does not know how to build shared libraries on Darwin
+    # Versions 2.13.0 and later can be patched to build shared
+    # libraries on Darwin; the patch for this capability does not
+    # apply to version 2.12.1 and earlier due to changes in the build system
+    # between versions 2.12.1 and 2.13.0.
     variant('shared', default=(sys.platform != 'darwin'),
             description="Build shared library (disables static library)")
     # SuperluDist have conflicting headers with those in Hypre
@@ -52,14 +41,32 @@ class Hypre(Package):
     variant('int64', default=False,
             description="Use 64bit integers")
     variant('mpi', default=True, description='Enable MPI support')
+    variant('debug', default=False,
+            description='Build debug instead of optimized version')
 
     # Patch to add ppc64le in config.guess
     patch('ibm-ppc64le.patch', when='@:2.11.1')
 
+    # Patch to build shared libraries on Darwin
+    patch('darwin-shared-libs-for-hypre-2.13.0.patch', when='+shared@2.13.0 platform=darwin')
+    patch('darwin-shared-libs-for-hypre-2.14.0.patch', when='+shared@2.14.0: platform=darwin')
+
     depends_on("mpi", when='+mpi')
     depends_on("blas")
     depends_on("lapack")
 
+    # Patch to build shared libraries on Darwin does not apply to
+    # versions before 2.13.0
+    conflicts("+shared@:2.12.99 platform=darwin")
+
+    def url_for_version(self, version):
+        if version >= Version('2.12.0'):
+            url = 'https://github.com/LLNL/hypre/archive/v{0}.tar.gz'
+        else:
+            url = 'http://computation.llnl.gov/project/linear_solvers/download/hypre-{0}.tar.gz'
+
+        return url.format(version)
+
     def install(self, spec, prefix):
         # Note: --with-(lapack|blas)_libs= needs space separated list of names
         lapack = spec['lapack'].libs
@@ -93,6 +100,11 @@ class Hypre(Package):
             configure_args.append("--without-mli")
             configure_args.append("--without-fei")
 
+        if '+debug' in self.spec:
+            configure_args.append("--enable-debug")
+        else:
+            configure_args.append("--disable-debug")
+
         # Hypre's source is staged under ./src so we'll have to manually
         # cd into it.
         with working_dir("src"):
@@ -108,3 +120,27 @@ class Hypre(Package):
                 sstruct('-in', 'test/sstruct.in.default', '-solver', '40',
                         '-rhsone')
             make("install")
+
+    @property
+    def headers(self):
+        """Export the main hypre header, HYPRE.h; all other headers can be found
+        in the same directory.
+        Sample usage: spec['hypre'].headers.cpp_flags
+        """
+        hdrs = find_headers('HYPRE', self.prefix.include, recursive=False)
+        return hdrs or None
+
+    @property
+    def libs(self):
+        """Export the hypre library.
+        Sample usage: spec['hypre'].libs.ld_flags
+        """
+        search_paths = [[self.prefix.lib, False], [self.prefix.lib64, False],
+                        [self.prefix, True]]
+        is_shared = '+shared' in self.spec
+        for path, recursive in search_paths:
+            libs = find_libraries('libHYPRE', root=path,
+                                  shared=is_shared, recursive=recursive)
+            if libs:
+                return libs
+        return None
diff --git a/var/spack/repos/builtin/packages/i3/package.py b/var/spack/repos/builtin/packages/i3/package.py
new file mode 100644
index 0000000000..123fdbb212
--- /dev/null
+++ b/var/spack/repos/builtin/packages/i3/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class I3(AutotoolsPackage):
+    """i3, improved tiling wm. i3 is a tiling window manager, completely
+    written from scratch. The target platforms are GNU/Linux and BSD operating
+    systems, our code is Free and Open Source Software (FOSS) under the BSD
+    license. i3 is primarily targeted at advanced users and developers."""
+
+    homepage = "https://i3wm.org/"
+    url      = "https://github.com/i3/i3/archive/4.14.1.tar.gz"
+
+    version('4.14.1', 'bdbb6d7bb5a647c8b7b53ed10de84cc5')
+
+    depends_on('autoconf',  type='build')
+    depends_on('automake',  type='build')
+    depends_on('libtool',   type='build')
+    depends_on('m4',        type='build')
+    depends_on('pkgconfig', type='build')
+
+    depends_on('libev')
+    depends_on('startup-notification')
+    depends_on('xcb-util-cursor')
+    depends_on('xcb-util-keysyms')
+    depends_on('xcb-util-wm')
+    depends_on('xcb-util-xrm')
+    depends_on('libxkbcommon')
+    depends_on('yajl')
+    depends_on('cairo+X')
+    depends_on('pango+X')
diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py
index 8fcf7980c8..6a78788ad5 100644
--- a/var/spack/repos/builtin/packages/ibmisc/package.py
+++ b/var/spack/repos/builtin/packages/ibmisc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/iceauth/package.py b/var/spack/repos/builtin/packages/iceauth/package.py
index a2f919be54..41f8f669a6 100644
--- a/var/spack/repos/builtin/packages/iceauth/package.py
+++ b/var/spack/repos/builtin/packages/iceauth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Iceauth(AutotoolsPackage):
     depends_on('libice')
 
     depends_on('xproto@7.0.22:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/icedtea/package.py b/var/spack/repos/builtin/packages/icedtea/package.py
index 9bc7da3102..c8a5916c7b 100644
--- a/var/spack/repos/builtin/packages/icedtea/package.py
+++ b/var/spack/repos/builtin/packages/icedtea/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -37,12 +18,11 @@ class Icedtea(AutotoolsPackage):
 
     version('3.4.0',  'eba66765b92794495e16b83f23640872')
 
-    provides('java@8', when='@3.4.0:3.99.99')
     variant('X', default=False, description="Build with GUI support.")
     variant('shenandoah', default=False,
             description="Build with the shenandoah gc. Only for version 3+")
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('gmake', type='build')
     depends_on('cups')
     depends_on('jdk', type='build')
@@ -58,7 +38,7 @@ class Icedtea(AutotoolsPackage):
     depends_on('libxcomposite', when='~X', type='build')
     depends_on('libxau', when='~X', type='build')
     depends_on('libxdmcp', when='~X', type='build')
-    depends_on('gtkplus+X', when='~X', type='build')
+    depends_on('gtkplus', when='~X', type='build')
 
     depends_on('libx11', when='+X')
     depends_on('xproto', when='+X')
@@ -71,7 +51,7 @@ class Icedtea(AutotoolsPackage):
     depends_on('libxcomposite', when='+X')
     depends_on('libxau', when='+X')
     depends_on('libxdmcp', when='+X')
-    depends_on('gtkplus+X', when='+X')
+    depends_on('gtkplus', when='+X')
 
     depends_on('freetype@2:')
     depends_on('wget', type='build')
@@ -82,6 +62,9 @@ class Icedtea(AutotoolsPackage):
     depends_on('zlib')
     depends_on('alsa-lib')
 
+    provides('java')
+    provides('java@8', when='@3.4.0:3.99.99')
+
     force_autoreconf = True
 
     resource(name='corba', placement='corba_src',
@@ -139,6 +122,20 @@ class Icedtea(AutotoolsPackage):
              url='http://icedtea.wildebeest.org/download/drops/icedtea8/3.4.0/shenandoah.tar.xz',
              when='@3.4.0')
 
+    # FIXME:
+    # 1. `extends('java')` doesn't work, you need to use `extends('icedtea')`
+    # 2. Packages cannot extend multiple packages, see #987
+    # 3. Update `YamlFilesystemView.merge` to allow a Package to completely
+    #    override how it is symlinked into a view prefix. Then, spack activate
+    #    can symlink all *.jar files to `prefix.lib.ext`
+    extendable = True
+
+    @property
+    def home(self):
+        """For compatibility with the ``jdk`` package, so that other packages
+        can say ``spec['java'].home`` regardless of the Java provider."""
+        return self.prefix
+
     def configure_args(self):
         os.environ['POTENTIAL_CXX'] = os.environ['CXX']
         os.environ['POTENTIAL_CC'] = os.environ['CC']
@@ -175,7 +172,34 @@ class Icedtea(AutotoolsPackage):
         return args
 
     def setup_environment(self, spack_env, run_env):
-        run_env.set('JAVA_HOME', self.spec.prefix)
+        """Set JAVA_HOME."""
+
+        run_env.set('JAVA_HOME', self.home)
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        spack_env.set('JAVA_HOME', self.prefix)
+        """Set JAVA_HOME and CLASSPATH.
+
+        CLASSPATH contains the installation prefix for the extension and any
+        other Java extensions it depends on."""
+
+        spack_env.set('JAVA_HOME', self.home)
+
+        class_paths = []
+        for d in dependent_spec.traverse(deptype=('build', 'run', 'test')):
+            if d.package.extends(self.spec):
+                class_paths.extend(find(d.prefix, '*.jar'))
+
+        classpath = os.pathsep.join(class_paths)
+        spack_env.set('CLASSPATH', classpath)
+
+        # For runtime environment set only the path for
+        # dependent_spec and prepend it to CLASSPATH
+        if dependent_spec.package.extends(self.spec):
+            class_paths = find(dependent_spec.prefix, '*.jar')
+            classpath = os.pathsep.join(class_paths)
+            run_env.prepend_path('CLASSPATH', classpath)
+
+    def setup_dependent_package(self, module, dependent_spec):
+        """Allows spec['java'].home to work."""
+
+        self.spec.home = self.home
diff --git a/var/spack/repos/builtin/packages/icet/package.py b/var/spack/repos/builtin/packages/icet/package.py
index d8591a2411..bf1f311d0a 100644
--- a/var/spack/repos/builtin/packages/icet/package.py
+++ b/var/spack/repos/builtin/packages/icet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,10 @@ class Icet(CMakePackage):
        sort-last parallel rendering library."""
 
     homepage = "http://icet.sandia.gov"
-    url      = "https://gitlab.kitware.com/icet/icet/repository/archive.tar.bz2?ref=IceT-2.1.1"
+    url      = "https://gitlab.kitware.com/api/v4/projects/icet%2Ficet/repository/archive.tar.bz2?sha=IceT-2.1.1"
+    git      = "https://gitlab.kitware.com/icet/icet.git"
 
-    version('develop', branch='master',
-            git='https://gitlab.kitware.com/icet/icet.git')
+    version('develop', branch='master')
     version('2.1.1', '4f971c51105a64937460d482adca2a6c')
 
     depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/ico/package.py b/var/spack/repos/builtin/packages/ico/package.py
index 7f627f5921..1d7442ddc5 100644
--- a/var/spack/repos/builtin/packages/ico/package.py
+++ b/var/spack/repos/builtin/packages/ico/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Ico(AutotoolsPackage):
     depends_on('libx11@0.99.1:')
 
     depends_on('xproto@7.0.22:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/icu4c/package.py b/var/spack/repos/builtin/packages/icu4c/package.py
index f8dcb52805..78d63b8c3b 100644
--- a/var/spack/repos/builtin/packages/icu4c/package.py
+++ b/var/spack/repos/builtin/packages/icu4c/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Icu4c(AutotoolsPackage):
     list_url = "http://download.icu-project.org/files/icu4c"
     list_depth = 2
 
+    version('60.1', '3d164a2d1bcebd1464c6160ebb8315ef')
     version('58.2', 'fac212b32b7ec7ab007a12dff1f3aea1')
     version('57.1', '976734806026a4ef8bdd17937c8898b9')
 
@@ -45,4 +27,11 @@ class Icu4c(AutotoolsPackage):
         return url.format(version.dotted, version.underscored)
 
     def configure_args(self):
-        return ['--enable-rpath']
+        args = []
+
+        # The --enable-rpath option is only needed on MacOS, and it
+        # breaks the build for xerces-c on Linux.
+        if 'platform=darwin' in self.spec:
+            args.append('--enable-rpath')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/id3lib/package.py b/var/spack/repos/builtin/packages/id3lib/package.py
index da4c513c63..23bbc99aef 100644
--- a/var/spack/repos/builtin/packages/id3lib/package.py
+++ b/var/spack/repos/builtin/packages/id3lib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/idba/package.py b/var/spack/repos/builtin/packages/idba/package.py
index d886ac0455..a7b2a455f7 100644
--- a/var/spack/repos/builtin/packages/idba/package.py
+++ b/var/spack/repos/builtin/packages/idba/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/igraph/package.py b/var/spack/repos/builtin/packages/igraph/package.py
index 4ec2e71555..35bcb1c87e 100644
--- a/var/spack/repos/builtin/packages/igraph/package.py
+++ b/var/spack/repos/builtin/packages/igraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/igvtools/igvtools.sh b/var/spack/repos/builtin/packages/igvtools/igvtools.sh
new file mode 100644
index 0000000000..82023e72b3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/igvtools/igvtools.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+# convenience wrapper for the igvtools jar file
+java $JAVA_ARGS $JAVA_OPTS -jar igvtools.jar "$@"
+
diff --git a/var/spack/repos/builtin/packages/igvtools/package.py b/var/spack/repos/builtin/packages/igvtools/package.py
new file mode 100644
index 0000000000..8e57a57fb3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/igvtools/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Igvtools(Package):
+    """IGVTools suite of command-line utilities for preprocessing data
+    files"""
+
+    homepage = "https://software.broadinstitute.org/software/igv/home"
+    url      = "http://data.broadinstitute.org/igv/projects/downloads/2.3/igvtools_2.3.98.zip"
+
+    version('2.3.98', '17ed12a213cd9cdaeb2f2a5c56d84bc4')
+
+    depends_on('java@8:')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'igvtools.jar'
+        install(jar_file, prefix.bin)
+        install_tree('genomes', prefix.genomes)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "igvtools.sh")
+        script = prefix.bin.igvtools
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = spec['jdk'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file(jar_file, join_path(prefix.bin, jar_file),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/ilmbase/package.py b/var/spack/repos/builtin/packages/ilmbase/package.py
index 75e52d66c2..996e6bd104 100644
--- a/var/spack/repos/builtin/packages/ilmbase/package.py
+++ b/var/spack/repos/builtin/packages/ilmbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/image-magick/package.py b/var/spack/repos/builtin/packages/image-magick/package.py
index 24b92132a0..354a7fd63a 100644
--- a/var/spack/repos/builtin/packages/image-magick/package.py
+++ b/var/spack/repos/builtin/packages/image-magick/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/imake/package.py b/var/spack/repos/builtin/packages/imake/package.py
index f3da05200b..47dcefa4e9 100644
--- a/var/spack/repos/builtin/packages/imake/package.py
+++ b/var/spack/repos/builtin/packages/imake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,4 +15,4 @@ class Imake(AutotoolsPackage):
     version('1.0.7', '186ca7b8ff0de8752f2a2d0426542363')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/imp/package.py b/var/spack/repos/builtin/packages/imp/package.py
new file mode 100644
index 0000000000..656e07e7e1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/imp/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Imp(CMakePackage):
+    """IMP, the Integrative Modeling Platform."""
+
+    homepage = "https://integrativemodeling.org"
+    url      = "https://github.com/salilab/imp/archive/2.8.0.tar.gz"
+
+    version('2.8.0', 'bc985d40dc63bb12e09d6d7403954645')
+
+    depends_on('python@2.7:')
+    depends_on('swig')
+    depends_on('boost@1.40:')
+    depends_on('hdf5')
+    depends_on('eigen')
diff --git a/var/spack/repos/builtin/packages/impute2/package.py b/var/spack/repos/builtin/packages/impute2/package.py
index 44993a306f..41c51a796d 100644
--- a/var/spack/repos/builtin/packages/impute2/package.py
+++ b/var/spack/repos/builtin/packages/impute2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/infernal/package.py b/var/spack/repos/builtin/packages/infernal/package.py
index f84722964d..59c2d7ce61 100644
--- a/var/spack/repos/builtin/packages/infernal/package.py
+++ b/var/spack/repos/builtin/packages/infernal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/inputproto/package.py b/var/spack/repos/builtin/packages/inputproto/package.py
index f60b08cacf..31d0732aca 100644
--- a/var/spack/repos/builtin/packages/inputproto/package.py
+++ b/var/spack/repos/builtin/packages/inputproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Inputproto(AutotoolsPackage):
 
     version('2.3.2', '6450bad6f8d5ebe354b01b734d1fd7ca')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/intel-daal/package.py b/var/spack/repos/builtin/packages/intel-daal/package.py
index d528f88461..acf84f5021 100644
--- a/var/spack/repos/builtin/packages/intel-daal/package.py
+++ b/var/spack/repos/builtin/packages/intel-daal/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelDaal(IntelPackage):
@@ -33,6 +11,14 @@ class IntelDaal(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/daal"
 
+    version('2019.0.117', 'd42fb6c3e8b31b1288049e89df37f2e8',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13577/l_daal_2019.0.117.tgz")
+    version('2018.3.222', 'e688825c563e357b7b626ece610d6a85',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13007/l_daal_2018.3.222.tgz")
+    version('2018.2.199', 'd015ff34a87a18922736b5fba0d0b0e0',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12727/l_daal_2018.2.199.tgz")
+    version('2018.1.163', '12a9586734a03a956095440161fd741a',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_daal_2018.1.163.tgz")
     version('2018.0.128', '5779e670f67c33cc1c6cdcdca5e4636e',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12072/l_daal_2018.0.128.tgz")
     version('2017.4.239', 'b47e9b92d948ee312e8a98170a1c0640',
@@ -51,36 +37,3 @@ class IntelDaal(IntelPackage):
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8687/l_daal_2016.2.181.tgz")
 
     provides('daal')
-
-    @property
-    def license_required(self):
-        # The Intel libraries are provided without requiring a license as of
-        # version 2017.2. Trying to specify the license will fail. See:
-        # https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries
-        if self.version >= Version('2017.2'):
-            return False
-        else:
-            return True
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source daal/bin/daalvars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        daalvars = os.path.join(self.prefix.daal.bin, 'daalvars.sh')
-
-        if os.path.isfile(daalvars):
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                daalvars, 'intel64'))
diff --git a/var/spack/repos/builtin/packages/intel-gpu-tools/package.py b/var/spack/repos/builtin/packages/intel-gpu-tools/package.py
index 5238e57e32..24b01fb0c6 100644
--- a/var/spack/repos/builtin/packages/intel-gpu-tools/package.py
+++ b/var/spack/repos/builtin/packages/intel-gpu-tools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -49,7 +30,7 @@ class IntelGpuTools(AutotoolsPackage):
     depends_on('flex', type='build')
     depends_on('bison', type='build')
     depends_on('python@3:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # xrandr ?
diff --git a/var/spack/repos/builtin/packages/intel-ipp/package.py b/var/spack/repos/builtin/packages/intel-ipp/package.py
index ae7a1358e1..b9bc862882 100644
--- a/var/spack/repos/builtin/packages/intel-ipp/package.py
+++ b/var/spack/repos/builtin/packages/intel-ipp/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelIpp(IntelPackage):
@@ -33,6 +11,14 @@ class IntelIpp(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-ipp"
 
+    version('2019.0.117', 'c96be6e138d32bf9b8abc789d25db71d',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13576/l_ipp_2019.0.117.tgz')
+    version('2018.3.222', '2ccc16ec002466e52f1e6e1bfe9b1149',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13006/l_ipp_2018.3.222.tgz')
+    version('2018.2.199', 'f87276b485d2f6ec070c1b41ac1ed871',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12726/l_ipp_2018.2.199.tgz')
+    version('2018.1.163', '183d4888f3d91f632b617fdd401f04ed',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_ipp_2018.1.163.tgz')
     version('2018.0.128', 'e64190bc9041b52d9eed7e8ee91bf1de',
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12071/l_ipp_2018.0.128.tgz')
     version('2017.3.196', '47e53bd1a2740041f4d0be7c36b61a18',
@@ -43,40 +29,8 @@ class IntelIpp(IntelPackage):
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11031/l_ipp_2017.1.132.tgz")
     version('2017.0.098', 'e7be757ebe351d9f9beed7efdc7b7118',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9663/l_ipp_2017.0.098.tgz")
+    # built from parallel_studio_xe_2016.3.067
     version('9.0.3.210', '0e1520dd3de7f811a6ef6ebc7aa429a3',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9067/l_ipp_9.0.3.210.tgz")
 
     provides('ipp')
-
-    @property
-    def license_required(self):
-        # The Intel libraries are provided without requiring a license as of
-        # version 2017.2. Trying to specify the license will fail. See:
-        # https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries
-        if self.version >= Version('2017.2'):
-            return False
-        else:
-            return True
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source ipp/bin/ippvars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        ippvars = os.path.join(self.prefix.ipp.bin, 'ippvars.sh')
-
-        if os.path.isfile(ippvars):
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                ippvars, 'intel64'))
diff --git a/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py
new file mode 100644
index 0000000000..72dafd7572
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-mkl-dnn/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class IntelMklDnn(CMakePackage):
+    """Intel(R) Math Kernel Library for Deep Neural Networks
+    (Intel(R) MKL-DNN)."""
+
+    homepage = "https://01.org/mkl-dnn"
+    url      = "https://github.com/01org/mkl-dnn/archive/v0.11.tar.gz"
+
+    version('0.11', 'a060a42753f633a146c3db699eeee666')
+    version('0.10', '3855ad02452a6906e3a9adc9cecef49c')
+    version('0.9',  'dfb89d8f9d0bce55e878df32544cb0ea')
+
+    depends_on('intel-mkl')
diff --git a/var/spack/repos/builtin/packages/intel-mkl/package.py b/var/spack/repos/builtin/packages/intel-mkl/package.py
index e2c2b8d46a..4b04e97d34 100644
--- a/var/spack/repos/builtin/packages/intel-mkl/package.py
+++ b/var/spack/repos/builtin/packages/intel-mkl/package.py
@@ -1,32 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import sys
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelMkl(IntelPackage):
@@ -34,6 +13,14 @@ class IntelMkl(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-mkl"
 
+    version('2019.0.117', 'd9e1b6b96fbffd4b306c7e8291f141a2',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13575/l_mkl_2019.0.117.tgz")
+    version('2018.3.222', '3e63646a4306eff95e8d0aafd53a2983',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13005/l_mkl_2018.3.222.tgz")
+    version('2018.2.199', 'fd31b656a8eb859c89495b9cc41230b4',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12725/l_mkl_2018.2.199.tgz")
+    version('2018.1.163', 'f1f7b6ddd7eb57dfe39bd4643446dc1c',
+            url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_mkl_2018.1.163.tgz")
     version('2018.0.128', '0fa23779816a0f2ee23a396fc1af9978',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12070/l_mkl_2018.0.128.tgz")
     version('2017.4.239', '3066272dd0ad3da7961b3d782e1fab3b',
@@ -46,8 +33,10 @@ class IntelMkl(IntelPackage):
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11024/l_mkl_2017.1.132.tgz")
     version('2017.0.098', '3cdcb739ab5ab1e047eb130b9ffdd8d0',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9662/l_mkl_2017.0.098.tgz")
+    # built from parallel_studio_xe_2016.3.x
     version('11.3.3.210', 'f72546df27f5ebb0941b5d21fd804e34',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9068/l_mkl_11.3.3.210.tgz")
+    # built from parallel_studio_xe_2016.2.062
     version('11.3.2.181', '536dbd82896d6facc16de8f961d17d65',
             url="http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8711/l_mkl_11.3.2.181.tgz")
 
@@ -56,7 +45,7 @@ class IntelMkl(IntelPackage):
     variant(
         'threads', default='none',
         description='Multithreading support',
-        values=('openmp', 'none'),
+        values=('openmp', 'tbb', 'none'),
         multi=False
     )
 
@@ -64,158 +53,8 @@ class IntelMkl(IntelPackage):
     provides('lapack')
     provides('scalapack')
     provides('mkl')
+    provides('fftw-api@3', when='@2017:')
 
     if sys.platform == 'darwin':
         # there is no libmkl_gnu_thread on macOS
         conflicts('threads=openmp', when='%gcc')
-
-    @property
-    def license_required(self):
-        # The Intel libraries are provided without requiring a license as of
-        # version 2017.2. Trying to specify the license will fail. See:
-        # https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries
-        if self.version >= Version('2017.2'):
-            return False
-        else:
-            return True
-
-    @property
-    def blas_libs(self):
-        spec = self.spec
-        prefix = self.prefix
-        shared = '+shared' in spec
-
-        if '+ilp64' in spec:
-            mkl_integer = ['libmkl_intel_ilp64']
-        else:
-            mkl_integer = ['libmkl_intel_lp64']
-
-        mkl_threading = ['libmkl_sequential']
-
-        omp_libs = LibraryList([])
-
-        if spec.satisfies('threads=openmp'):
-            if '%intel' in spec:
-                mkl_threading = ['libmkl_intel_thread']
-                omp_threading = ['libiomp5']
-
-                if sys.platform != 'darwin':
-                    omp_root = prefix.compilers_and_libraries.linux.lib.intel64
-                else:
-                    omp_root = prefix.lib
-                omp_libs = find_libraries(
-                    omp_threading, root=omp_root, shared=shared)
-            elif '%gcc' in spec:
-                mkl_threading = ['libmkl_gnu_thread']
-
-                gcc = Executable(self.compiler.cc)
-                libgomp = gcc('--print-file-name', 'libgomp.{0}'.format(
-                    dso_suffix), output=str)
-                omp_libs = LibraryList(libgomp)
-
-        # TODO: TBB threading: ['libmkl_tbb_thread', 'libtbb', 'libstdc++']
-
-        if sys.platform != 'darwin':
-            mkl_root = prefix.compilers_and_libraries.linux.mkl.lib.intel64
-        else:
-            mkl_root = prefix.mkl.lib
-
-        mkl_libs = find_libraries(
-            mkl_integer + ['libmkl_core'] + mkl_threading,
-            root=mkl_root,
-            shared=shared
-        )
-
-        # Intel MKL link line advisor recommends these system libraries
-        system_libs = find_system_libraries(
-            ['libpthread', 'libm', 'libdl'],
-            shared=shared
-        )
-
-        return mkl_libs + omp_libs + system_libs
-
-    @property
-    def lapack_libs(self):
-        return self.blas_libs
-
-    @property
-    def scalapack_libs(self):
-        libnames = ['libmkl_scalapack']
-
-        # Intel MKL does not directly depend on mpi but the scalapack
-        # interface does and the corresponding  BLACS library changes
-        # depending on the MPI implementation we are using. We need then to
-        # inspect the root package which asked for Scalapack and check which
-        # MPI it depends on.
-        root = self.spec.root
-        if sys.platform == 'darwin' and '^mpich' in root:
-            # MKL 2018 supports only MPICH on darwin
-            libnames.append('libmkl_blacs_mpich')
-        elif '^openmpi' in root:
-            libnames.append('libmkl_blacs_openmpi')
-        elif '^mpich@1' in root:
-            libnames.append('libmkl_blacs')
-        elif '^mpich@2:' in root:
-            libnames.append('libmkl_blacs_intelmpi')
-        elif '^mvapich2' in root:
-            libnames.append('libmkl_blacs_intelmpi')
-        elif '^mpt' in root:
-            libnames.append('libmkl_blacs_sgimpt')
-        elif '^intel-mpi' in root:
-            libnames.append('libmkl_blacs_intelmpi')
-        else:
-            raise InstallError('No MPI found for scalapack')
-
-        integer = 'ilp64' if '+ilp64' in self.spec else 'lp64'
-        mkl_root = self.prefix.mkl.lib if sys.platform == 'darwin' else \
-            self.prefix.compilers_and_libraries.linux.mkl.lib.intel64
-
-        shared = True if '+shared' in self.spec else False
-
-        libs = find_libraries(
-            ['{0}_{1}'.format(l, integer) for l in libnames],
-            root=mkl_root,
-            shared=shared
-        )
-
-        return libs
-
-    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        # set up MKLROOT for everyone using MKL package
-        if sys.platform == 'darwin':
-            mkl_lib = self.prefix.mkl.lib
-            mkl_root = self.prefix.mkl
-        else:
-            mkl_lib = self.prefix.compilers_and_libraries.linux.mkl.lib.intel64
-            mkl_root = self.prefix.compilers_and_libraries.linux.mkl
-
-        spack_env.set('MKLROOT', mkl_root)
-        spack_env.append_path('SPACK_COMPILER_EXTRA_RPATHS', mkl_lib)
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source mkl/bin/mklvars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        mklvars = os.path.join(self.prefix.mkl.bin, 'mklvars.sh')
-
-        if sys.platform == 'darwin':
-            if os.path.isfile(mklvars):
-                run_env.extend(EnvironmentModifications.from_sourcing_file(
-                    mklvars))
-        else:
-            if os.path.isfile(mklvars):
-                run_env.extend(EnvironmentModifications.from_sourcing_file(
-                    mklvars, 'intel64'))
diff --git a/var/spack/repos/builtin/packages/intel-mpi/package.py b/var/spack/repos/builtin/packages/intel-mpi/package.py
index 42b9872b30..c3ac5b68be 100644
--- a/var/spack/repos/builtin/packages/intel-mpi/package.py
+++ b/var/spack/repos/builtin/packages/intel-mpi/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelMpi(IntelPackage):
@@ -33,6 +11,14 @@ class IntelMpi(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-mpi-library"
 
+    version('2019.0.117', '8572d5fa1f26a7de8edc8b64653b0955',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13584/l_mpi_2019.0.117.tgz')
+    version('2018.3.222', 'df92593818fadff63c57418669c6083b',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13112/l_mpi_2018.3.222.tgz')
+    version('2018.2.199', '6ffeab59c83a8842537484d53e180520',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12748/l_mpi_2018.2.199.tgz')
+    version('2018.1.163', '437ce50224c5bbf98fd578a810c3e401',
+            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12414/l_mpi_2018.1.163.tgz')
     version('2018.0.128', '15b46fc6a3014595de897aa48d3a658b',
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12120/l_mpi_2018.0.128.tgz')
     version('2017.4.239', '460a9ef1b3599d60b4d696e3f0f2a14d',
@@ -43,95 +29,21 @@ class IntelMpi(IntelPackage):
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11334/l_mpi_2017.2.174.tgz')
     version('2017.1.132', 'd5e941ac2bcf7c5576f85f6bcfee4c18',
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11014/l_mpi_2017.1.132.tgz')
+    # built from parallel_studio_xe_2016.3.068
     version('5.1.3.223',  '4316e78533a932081b1a86368e890800',
             url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9278/l_mpi_p_5.1.3.223.tgz')
 
     provides('mpi')
 
-    @property
-    def license_required(self):
-        # The Intel libraries are provided without requiring a license as of
-        # version 2017.2. Trying to specify the license will fail. See:
-        # https://software.intel.com/en-us/articles/free-ipsxe-tools-and-libraries
-        if self.version >= Version('2017.2'):
-            return False
-        else:
-            return True
-
-    @property
-    def mpi_libs(self):
-        mpi_root = self.prefix.compilers_and_libraries.linux.mpi.lib64
-        query_parameters = self.spec.last_query.extra_parameters
-        libraries = ['libmpifort', 'libmpi']
-
-        if 'cxx' in query_parameters:
-            libraries = ['libmpicxx'] + libraries
-
-        return find_libraries(
-            libraries, root=mpi_root, shared=True, recurse=True
-        )
-
-    @property
-    def mpi_headers(self):
-        # recurse from self.prefix will find too many things for all the
-        # supported sub-architectures like 'mic'
-        mpi_root = self.prefix.compilers_and_libraries.linux.mpi.include64
-        return find_headers('mpi', root=mpi_root, recurse=False)
-
-    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        spack_env.set('I_MPI_CC', spack_cc)
-        spack_env.set('I_MPI_CXX', spack_cxx)
-        spack_env.set('I_MPI_F77', spack_fc)
-        spack_env.set('I_MPI_F90', spack_f77)
-        spack_env.set('I_MPI_FC', spack_fc)
-
-    def setup_dependent_package(self, module, dep_spec):
-        # Intel comes with 2 different flavors of MPI wrappers:
-        #
-        # * mpiicc, mpiicpc, and mpifort are hardcoded to wrap around
-        #   the Intel compilers.
-        # * mpicc, mpicxx, mpif90, and mpif77 allow you to set which
-        #   compilers to wrap using I_MPI_CC and friends. By default,
-        #   wraps around the GCC compilers.
-        #
-        # In theory, these should be equivalent as long as I_MPI_CC
-        # and friends are set to point to the Intel compilers, but in
-        # practice, mpicc fails to compile some applications while
-        # mpiicc works.
-        bindir = self.prefix.compilers_and_libraries.linux.mpi.intel64.bin
-
-        if self.compiler.name == 'intel':
-            self.spec.mpicc  = bindir.mpiicc
-            self.spec.mpicxx = bindir.mpiicpc
-            self.spec.mpifc  = bindir.mpiifort
-            self.spec.mpif77 = bindir.mpiifort
-        else:
-            self.spec.mpicc  = bindir.mpicc
-            self.spec.mpicxx = bindir.mpicxx
-            self.spec.mpifc  = bindir.mpif90
-            self.spec.mpif77 = bindir.mpif77
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source compilers_and_libraries/linux/mpi/intel64/bin/mpivars.sh
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        mpivars = os.path.join(
-            self.prefix.compilers_and_libraries.linux.mpi.intel64.bin,
-            'mpivars.sh')
-
-        if os.path.isfile(mpivars):
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                mpivars))
+    def setup_dependent_environment(self, *args):
+        # Handle in callback, conveying client's compilers in additional arg.
+        # CAUTION - DUP code in:
+        #   ../intel-mpi/package.py
+        #   ../intel-parallel-studio/package.py
+        self._setup_dependent_env_callback(*args, compilers_of_client={
+            'CC':   spack_cc,
+            'CXX':  spack_cxx,
+            'F77':  spack_f77,
+            'F90':  spack_fc,
+            'FC':   spack_fc,
+        })
diff --git a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
index 9828eaf6c0..666623f154 100644
--- a/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
+++ b/var/spack/repos/builtin/packages/intel-parallel-studio/package.py
@@ -1,32 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 glob
-import os
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class IntelParallelStudio(IntelPackage):
@@ -34,66 +11,87 @@ class IntelParallelStudio(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
 
-    version('professional.2018.0', '9a233854e9218937bc5f46f02b3c7542',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12062/parallel_studio_xe_2018_professional_edition.tgz')
-    version('cluster.2018.0',      'fa9baeb83dd2e8e4a464e3db38f28d0f',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12058/parallel_studio_xe_2018_cluster_edition.tgz')
-    version('composer.2018.0',     '31ba768fba6e7322957b03feaa3add28',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz')
-    version('professional.2017.4', '27398416078e1e4005afced3e9a6df7e',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz')
-    version('cluster.2017.4',      '27398416078e1e4005afced3e9a6df7e',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz')
-    version('composer.2017.4',     'd03d351809e182c481dc65e07376d9a2',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz')
-    version('professional.2017.3', '691874735458d3e88fe0bcca4438b2a9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz')
-    version('cluster.2017.3',      '691874735458d3e88fe0bcca4438b2a9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz')
-    version('composer.2017.3',     '52344df122c17ddff3687f84ceb21623',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz')
-    version('professional.2017.2', '70e54b33d940a1609ff1d35d3c56e3b3',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz')
-    version('cluster.2017.2',      '70e54b33d940a1609ff1d35d3c56e3b3',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz')
-    version('composer.2017.2',     '2891ab1ece43eb61b6ab892f07c47f01',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz')
-    version('professional.2017.1', '7f75a4a7e2c563be778c377f9d35a542',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz')
-    version('cluster.2017.1',      '7f75a4a7e2c563be778c377f9d35a542',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz')
-    version('composer.2017.1',     '1f31976931ed8ec424ac7c3ef56f5e85',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz')
-    version('professional.2017.0', '34c98e3329d6ac57408b738ae1daaa01',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz')
-    version('cluster.2017.0',      '34c98e3329d6ac57408b738ae1daaa01',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz')
-    version('composer.2017.0',     'b67da0065a17a05f110ed1d15c3c6312',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz')
-    version('professional.2016.4', '16a641a06b156bb647c8a56e71f3bb33',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz')
-    version('cluster.2016.4',      '16a641a06b156bb647c8a56e71f3bb33',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz')
-    version('composer.2016.4',      '2bc9bfc9be9c1968a6e42efb4378f40e',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz')
-    version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz')
-    version('cluster.2016.3',      'eda19bb0d0d19709197ede58f13443f3',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz')
-    version('composer.2016.3',     '3208eeabee951fc27579177b593cefe9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz')
-    version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz')
-    version('cluster.2016.2',      '70be832f2d34c9bf596a5e99d5f2d832',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz')
-    version('composer.2016.2',     '1133fb831312eb519f7da897fec223fa',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz')
-    version('professional.2015.6', 'd460f362c30017b60f85da2e51ad25bf',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz')
-    version('cluster.2015.6',      'd460f362c30017b60f85da2e51ad25bf',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz')
-    version('composer.2015.6',      'da9f8600c18d43d58fba0488844f79c9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz')
+    # As of 2016, the product comes in three "editions" that vary by scope.
+    #
+    # In Spack, select the edition via the version number in the spec, e.g.:
+    #   intel-parallel-studio@cluster.2018
+
+    # Cluster Edition (top tier; all components included)
+    version('cluster.2019.0',      'd4c249c5438c1a55640291efcc96418d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13589/parallel_studio_xe_2019_cluster_edition.tgz')
+    #
+    version('cluster.2018.3',      '7112837d20a100b895d9cd9ba9b6748d', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12998/parallel_studio_xe_2018_update3_cluster_edition.tgz')
+    version('cluster.2018.2',      '3b8d93a3fa10869dde024b739b96a9c4', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12717/parallel_studio_xe_2018_update2_cluster_edition.tgz')
+    version('cluster.2018.1',      '9c007011e0e3fc72747b58756fbf01cd', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12374/parallel_studio_xe_2018_update1_cluster_edition.tgz')
+    version('cluster.2018.0',      'fa9baeb83dd2e8e4a464e3db38f28d0f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12058/parallel_studio_xe_2018_cluster_edition.tgz')
+    #
+    version('cluster.2017.7',      '158461b000b31f0ef8169b6f0277bfb5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12856/parallel_studio_xe_2017_update7.tgz')
+    version('cluster.2017.6',      'b0bbddeec3e78a84b967c9ca70dade77', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12534/parallel_studio_xe_2017_update6.tgz')
+    version('cluster.2017.5',      'baeb8e584317fcdf1f60b8208bd4eab5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12138/parallel_studio_xe_2017_update5.tgz')
+    version('cluster.2017.4',      '27398416078e1e4005afced3e9a6df7e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz')
+    version('cluster.2017.3',      '691874735458d3e88fe0bcca4438b2a9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz')
+    version('cluster.2017.2',      '70e54b33d940a1609ff1d35d3c56e3b3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz')
+    version('cluster.2017.1',      '7f75a4a7e2c563be778c377f9d35a542', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz')
+    version('cluster.2017.0',      '34c98e3329d6ac57408b738ae1daaa01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz')
+    #
+    version('cluster.2016.4',      '16a641a06b156bb647c8a56e71f3bb33', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz')
+    version('cluster.2016.3',      'eda19bb0d0d19709197ede58f13443f3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz')
+    version('cluster.2016.2',      '70be832f2d34c9bf596a5e99d5f2d832', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz')
+    version('cluster.2016.1',      '83b260ef3fcfd4e30afbeb7eb31b6b20', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8365/parallel_studio_xe_2016_update1.tgz')
+    version('cluster.2016.0',      '00b4de9727a906a3aff468c26dd3f89c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/7997/parallel_studio_xe_2016.tgz')
+    #
+    version('cluster.2015.6',      'd460f362c30017b60f85da2e51ad25bf', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz')
+    version('cluster.2015.1',      '542b78c86beff9d7b01076a7be9c6ddc', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz')
+
+    # Professional Edition (middle tier; excluded: MPI/TAC/Cluster Checker)
+    #
+    # NB: Pre-2018 download packages for Professional are the same as for
+    # Cluster; differences manifest only in the tokens present in the license
+    # file delivered as part of the purchase.
+    version('professional.2018.3', 'e0fb828de0a5f238f775b6122cc7e2c5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12999/parallel_studio_xe_2018_update3_professional_edition.tgz')
+    version('professional.2018.2', '91ed14aeb6157d60a0ec39929d0bc778', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12718/parallel_studio_xe_2018_update2_professional_edition.tgz')
+    version('professional.2018.1', '91669ff7afbfd07868a429a122c90357', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12375/parallel_studio_xe_2018_update1_professional_edition.tgz')
+    version('professional.2018.0', '9a233854e9218937bc5f46f02b3c7542', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12062/parallel_studio_xe_2018_professional_edition.tgz')
+    #
+    version('professional.2017.7', '158461b000b31f0ef8169b6f0277bfb5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12856/parallel_studio_xe_2017_update7.tgz')
+    version('professional.2017.6', 'b0bbddeec3e78a84b967c9ca70dade77', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12534/parallel_studio_xe_2017_update6.tgz')
+    version('professional.2017.5', 'baeb8e584317fcdf1f60b8208bd4eab5', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12138/parallel_studio_xe_2017_update5.tgz')
+    version('professional.2017.4', '27398416078e1e4005afced3e9a6df7e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11537/parallel_studio_xe_2017_update4.tgz')
+    version('professional.2017.3', '691874735458d3e88fe0bcca4438b2a9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11460/parallel_studio_xe_2017_update3.tgz')
+    version('professional.2017.2', '70e54b33d940a1609ff1d35d3c56e3b3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11298/parallel_studio_xe_2017_update2.tgz')
+    version('professional.2017.1', '7f75a4a7e2c563be778c377f9d35a542', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10973/parallel_studio_xe_2017_update1.tgz')
+    version('professional.2017.0', '34c98e3329d6ac57408b738ae1daaa01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9651/parallel_studio_xe_2017.tgz')
+    #
+    version('professional.2016.4', '16a641a06b156bb647c8a56e71f3bb33', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9781/parallel_studio_xe_2016_update4.tgz')
+    version('professional.2016.3', 'eda19bb0d0d19709197ede58f13443f3', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9061/parallel_studio_xe_2016_update3.tgz')
+    version('professional.2016.2', '70be832f2d34c9bf596a5e99d5f2d832', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8676/parallel_studio_xe_2016_update2.tgz')
+    version('professional.2016.1', '83b260ef3fcfd4e30afbeb7eb31b6b20', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8365/parallel_studio_xe_2016_update1.tgz')
+    version('professional.2016.0', '00b4de9727a906a3aff468c26dd3f89c', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/7997/parallel_studio_xe_2016.tgz')
+    #
+    version('professional.2015.6', 'd460f362c30017b60f85da2e51ad25bf', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8469/parallel_studio_xe_2015_update6.tgz')
+    version('professional.2015.1', '542b78c86beff9d7b01076a7be9c6ddc', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4992/parallel_studio_xe_2015_update1.tgz')
+
+    # Composer Edition (basic tier; excluded: MPI/..., Advisor/Inspector/Vtune)
+    version('composer.2018.3',     '234223cc470717c2095456d9f048d690', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13002/parallel_studio_xe_2018_update3_composer_edition.tgz')
+    version('composer.2018.2',     '76f820f53de4c1ff998229c983cf4f53', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12722/parallel_studio_xe_2018_update2_composer_edition.tgz')
+    version('composer.2018.1',     '28cb807126d713350f4aa6f9f167448a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12381/parallel_studio_xe_2018_update1_composer_edition.tgz')
+    version('composer.2018.0',     '31ba768fba6e7322957b03feaa3add28', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz')
+    #
+    version('composer.2017.7',     '4c02a4a29a8f2424f31baa23116a1001', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12860/parallel_studio_xe_2017_update7_composer_edition.tgz')
+    version('composer.2017.6',     'd96cce0c3feef20091efde458f581a9f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12538/parallel_studio_xe_2017_update6_composer_edition.tgz')
+    # version('composer.2017.5',     -- TBD --
+    version('composer.2017.4',     'd03d351809e182c481dc65e07376d9a2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz')
+    version('composer.2017.3',     '52344df122c17ddff3687f84ceb21623', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz')
+    version('composer.2017.2',     '2891ab1ece43eb61b6ab892f07c47f01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz')
+    version('composer.2017.1',     '1f31976931ed8ec424ac7c3ef56f5e85', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz')
+    version('composer.2017.0',     'b67da0065a17a05f110ed1d15c3c6312', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz')
+    #
+    version('composer.2016.4',     '2bc9bfc9be9c1968a6e42efb4378f40e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz')
+    version('composer.2016.3',     '3208eeabee951fc27579177b593cefe9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz')
+    version('composer.2016.2',     '1133fb831312eb519f7da897fec223fa', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz')
+    #
+    # Pre-2016, the only product was "Composer XE"; dir structure is different.
+    version('composer.2015.6',     'da9f8600c18d43d58fba0488844f79c9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz')
+    version('composer.2015.1',     '85beae681ae56411a8e791a7c44a5c0a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4933/l_compxe_2015.1.133.tgz')
 
     # Generic Variants
     variant('rpath',    default=True,
@@ -137,368 +135,46 @@ class IntelParallelStudio(IntelPackage):
     variant('vtune',     default=False,
             description='Install the Intel VTune Amplifier XE')
 
-    provides('daal', when='+daal')
-
-    provides('ipp', when='+ipp')
+    provides('daal',        when='+daal')
+    provides('ipp',         when='+ipp')
 
-    provides('mkl',       when='+mkl')
-    provides('blas',      when='+mkl')
-    provides('lapack',    when='+mkl')
-    provides('scalapack', when='+mkl')
+    provides('mkl',         when='+mkl')
+    provides('blas',        when='+mkl')
+    provides('lapack',      when='+mkl')
+    provides('scalapack',   when='+mkl')
 
-    provides('mpi', when='+mpi')
+    provides('mpi',         when='+mpi')
+    provides('tbb',         when='+tbb')
 
-    provides('tbb', when='+tbb')
+    # For TBB, static linkage is not and has never been supported by Intel:
+    # https://www.threadingbuildingblocks.org/faq/there-version-tbb-provides-statically-linked-libraries
+    conflicts('+tbb',       when='~shared')
 
-    # The following components are not available in the Composer Edition
     conflicts('+advisor',   when='@composer.0:composer.9999')
     conflicts('+clck',      when='@composer.0:composer.9999')
     conflicts('+inspector', when='@composer.0:composer.9999')
     conflicts('+itac',      when='@composer.0:composer.9999')
+    conflicts('+mpi',       when='@composer.0:composer.9999')
     conflicts('+vtune',     when='@composer.0:composer.9999')
 
-    @property
-    def blas_libs(self):
-        spec = self.spec
-        prefix = self.prefix
-        shared = '+shared' in spec
-
-        if '+ilp64' in spec:
-            mkl_integer = ['libmkl_intel_ilp64']
-        else:
-            mkl_integer = ['libmkl_intel_lp64']
-
-        mkl_threading = ['libmkl_sequential']
-
-        omp_libs = LibraryList([])
-
-        if spec.satisfies('threads=openmp'):
-            if '%intel' in spec:
-                mkl_threading = ['libmkl_intel_thread']
-                omp_threading = ['libiomp5']
-
-                omp_root = prefix.compilers_and_libraries.linux.lib.intel64
-                omp_libs = find_libraries(
-                    omp_threading, root=omp_root, shared=shared)
-            elif '%gcc' in spec:
-                mkl_threading = ['libmkl_gnu_thread']
-
-                gcc = Executable(self.compiler.cc)
-                omp_libs = gcc('--print-file-name', 'libgomp.{0}'.format(
-                    dso_suffix), output=str)
-                omp_libs = LibraryList(omp_libs)
-
-        # TODO: TBB threading: ['libmkl_tbb_thread', 'libtbb', 'libstdc++']
-
-        mkl_root = prefix.compilers_and_libraries.linux.mkl.lib.intel64
-
-        mkl_libs = find_libraries(
-            mkl_integer + ['libmkl_core'] + mkl_threading,
-            root=mkl_root,
-            shared=shared
-        )
-
-        # Intel MKL link line advisor recommends these system libraries
-        system_libs = find_system_libraries(
-            ['libpthread', 'libm', 'libdl'],
-            shared=shared
-        )
-
-        return mkl_libs + omp_libs + system_libs
-
-    @property
-    def lapack_libs(self):
-        return self.blas_libs
-
-    @property
-    def scalapack_libs(self):
-        libnames = ['libmkl_scalapack']
-        if self.spec.satisfies('^openmpi'):
-            libnames.append('libmkl_blacs_openmpi')
-        elif self.spec.satisfies('^mpich@1'):
-            libnames.append('libmkl_blacs')
-        elif self.spec.satisfies('^mpich@2:'):
-            libnames.append('libmkl_blacs_intelmpi')
-        elif self.spec.satisfies('^mvapich2'):
-            libnames.append('libmkl_blacs_intelmpi')
-        elif self.spec.satisfies('^mpt'):
-            libnames.append('libmkl_blacs_sgimpt')
-        # TODO: ^intel-parallel-studio can mean intel mpi, a compiler or a lib
-        # elif self.spec.satisfies('^intel-parallel-studio'):
-        #     libnames.append('libmkl_blacs_intelmpi')
-        else:
-            raise InstallError('No MPI found for scalapack')
-
-        integer = 'ilp64' if '+ilp64' in self.spec else 'lp64'
-        mkl_root = self.prefix.compilers_and_libraries.linux.mkl.lib.intel64
-        shared = True if '+shared' in self.spec else False
-
-        libs = find_libraries(
-            ['{0}_{1}'.format(l, integer) for l in libnames],
-            root=mkl_root,
-            shared=shared
-        )
-        return libs
-
-    @property
-    def mpi_libs(self):
-        mpi_root = self.prefix.compilers_and_libraries.linux.mpi.lib64
-        query_parameters = self.spec.last_query.extra_parameters
-        libraries = ['libmpifort', 'libmpi']
-
-        if 'cxx' in query_parameters:
-            libraries = ['libmpicxx'] + libraries
-
-        return find_libraries(
-            libraries, root=mpi_root, shared=True, recurse=True
-        )
-
-    @property
-    def mpi_headers(self):
-        # recurse from self.prefix will find too many things for all the
-        # supported sub-architectures like 'mic'
-        mpi_root = self.prefix.compilers_and_libraries.linux.mpi.include64
-        return find_headers('mpi', root=mpi_root, recurse=False)
-
-    @property
-    def components(self):
-        spec = self.spec
-        edition = self.version[0]
-
-        # Intel(R) Compilers
-        components = [
-            # Common files
-            'intel-comp-',
-            'intel-openmp',
-
-            # C/C++
-            'intel-icc',
-
-            # Fortran
-            'intel-ifort',
-
-            # Parallel Studio Documentation and Licensing Files
-            'intel-psxe',
-        ]
-
-        # Intel(R) Parallel Studio XE Suite Files and Documentation
-        if edition == 'cluster':
-            components.append('intel-icsxe')
-        elif edition == 'professional':
-            components.extend(['intel-ips', 'intel-ipsc', 'intel-ipsf'])
-        elif edition == 'composer':
-            components.extend([
-                'intel-compxe', 'intel-ccompxe', 'intel-fcompxe'
-            ])
-
-        # Intel(R) Data Analytics Acceleration Library
-        if '+daal' in spec:
-            components.append('intel-daal')
-
-        # Intel(R) Debugger for Heterogeneous Compute
-        if '+gdb' in spec:
-            components.append('intel-gdb')
-
-        # Intel(R) Integrated Performance Primitives
-        if '+ipp' in spec:
-            components.extend(['intel-ipp', 'intel-crypto-ipp'])
-
-        # Intel(R) Math Kernel Library
-        if '+mkl' in spec:
-            components.append('intel-mkl')
-
-        # Intel(R) MPI Library
-        if '+mpi' in spec:
-            components.extend(['intel-mpi', 'intel-mpirt', 'intel-imb'])
-
-        # Intel(R) Threading Building Blocks
-        if '+tbb' in spec:
-            components.append('intel-tbb')
-
-        # Intel(R) Advisor
-        if '+advisor' in spec:
-            components.append('intel-advisor')
-
-        # Intel(R) Cluster Checker
-        if '+clck' in spec:
-            components.append('intel_clck')
-
-        # Intel(R) Inspector
-        if '+inspector' in spec:
-            components.append('intel-inspector')
-
-        # Intel(R) Trace Analyzer and Collector
-        if '+itac' in spec:
-            components.extend(['intel-itac', 'intel-ta', 'intel-tc'])
-
-        # Intel(R) VTune(TM) Amplifier XE
-        if '+vtune' in spec:
-            components.append('intel-vtune-amplifier-xe')
-
-        return components
-
-    @property
-    def bin_dir(self):
-        """The relative path to the bin directory with symlinks resolved."""
-
-        bin_path = os.path.join(self.prefix.bin, 'icc')
-        absolute_path = os.path.realpath(bin_path)  # resolve symlinks
-        relative_path = os.path.relpath(absolute_path, self.prefix)
-        return os.path.dirname(relative_path)
-
-    @property
-    def lib_dir(self):
-        """The relative path to the lib directory with symlinks resolved."""
-
-        lib_path = os.path.join(self.prefix.lib, 'intel64', 'libimf.a')
-        absolute_path = os.path.realpath(lib_path)  # resolve symlinks
-        relative_path = os.path.relpath(absolute_path, self.prefix)
-        return os.path.dirname(relative_path)
-
-    @property
-    def license_files(self):
-        spec = self.spec
-        year = self.version[1]
-
-        directories = [
-            'Licenses',
-            self.bin_dir
-        ]
-
-        if '+advisor' in spec:
-            advisor_dir = 'advisor_xe/licenses'
-
-            if year >= 2017:
-                advisor_dir = 'advisor/licenses'
-
-            directories.append(advisor_dir)
-
-        if '+inspector' in spec:
-            inspector_dir = 'inspector_xe/licenses'
-
-            if year >= 2017:
-                inspector_dir = 'inspector/licenses'
-
-            directories.append(inspector_dir)
-
-        if '+itac' in spec:
-            itac_dir = 'itac_{0}'.format(year)
-
-            directories.append(itac_dir)
-
-        if '+vtune' in spec:
-            vtune_dir = 'vtune_amplifier_xe/licenses'
-
-            directories.append(vtune_dir)
-
-        return [os.path.join(dir, 'license.lic') for dir in directories]
-
-    @run_after('install')
-    def filter_compiler_wrappers(self):
-        spec = self.spec
-
-        if '+mpi' in spec:
-            if '~newdtags' in spec:
-                wrappers = [
-                    'mpif77', 'mpif90', 'mpigcc', 'mpigxx',
-                    'mpiicc', 'mpiicpc', 'mpiifort'
-                ]
-                wrapper_paths = []
-                for root, dirs, files in os.walk(spec.prefix):
-                    for name in files:
-                        if name in wrappers:
-                            wrapper_paths.append(os.path.join(spec.prefix,
-                                                              root, name))
-                for wrapper in wrapper_paths:
-                    filter_file('-Xlinker --enable-new-dtags', ' ',
-                                wrapper, string=True)
-
-    @run_after('install')
-    def rpath_configuration(self):
-        spec = self.spec
-
-        if '+rpath' in spec:
-            lib_dir = os.path.join(self.prefix, self.lib_dir)
-            for compiler in ['icc', 'icpc', 'ifort']:
-                cfgfilename = os.path.join(
-                    self.prefix, self.bin_dir, '{0}.cfg'.format(compiler))
-                with open(cfgfilename, 'w') as f:
-                    f.write('-Xlinker -rpath -Xlinker {0}\n'.format(lib_dir))
-
-    @run_after('install')
-    def fix_psxevars(self):
-        """Newer versions of Intel Parallel Studio have a bug in the
-        ``psxevars.sh`` script."""
-
-        bindir = glob.glob(join_path(
-            self.prefix, 'parallel_studio*', 'bin'))[0]
-
-        filter_file('^SCRIPTPATH=.*', 'SCRIPTPATH={0}'.format(self.prefix),
-                    os.path.join(bindir, 'psxevars.sh'),
-                    os.path.join(bindir, 'psxevars.csh'))
-
-    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        if '+mpi' in self.spec:
-            spack_env.set('I_MPI_CC',  spack_cc)
-            spack_env.set('I_MPI_CXX', spack_cxx)
-            spack_env.set('I_MPI_F77', spack_fc)
-            spack_env.set('I_MPI_F90', spack_f77)
-            spack_env.set('I_MPI_FC',  spack_fc)
-
-        # set up MKLROOT for everyone using MKL package
-        if '+mkl' in self.spec:
-            mkl_root = self.prefix.compilers_and_libraries.linux.mkl.lib.intel64  # noqa
-
-            spack_env.set('MKLROOT', self.prefix)
-            spack_env.append_path('SPACK_COMPILER_EXTRA_RPATHS', mkl_root)
-
-    def setup_dependent_package(self, module, dep_spec):
-        if '+mpi' in self.spec:
-            # Intel comes with 2 different flavors of MPI wrappers:
-            #
-            # * mpiicc, mpiicpc, and mpifort are hardcoded to wrap around
-            #   the Intel compilers.
-            # * mpicc, mpicxx, mpif90, and mpif77 allow you to set which
-            #   compilers to wrap using I_MPI_CC and friends. By default,
-            #   wraps around the GCC compilers.
-            #
-            # In theory, these should be equivalent as long as I_MPI_CC
-            # and friends are set to point to the Intel compilers, but in
-            # practice, mpicc fails to compile some applications while
-            # mpiicc works.
-            bindir = self.prefix.compilers_and_libraries.linux.mpi.intel64.bin
-
-            if self.compiler.name == 'intel':
-                self.spec.mpicc  = bindir.mpiicc
-                self.spec.mpicxx = bindir.mpiicpc
-                self.spec.mpifc  = bindir.mpiifort
-                self.spec.mpif77 = bindir.mpiifort
-            else:
-                self.spec.mpicc  = bindir.mpicc
-                self.spec.mpicxx = bindir.mpicxx
-                self.spec.mpifc  = bindir.mpif90
-                self.spec.mpif77 = bindir.mpif77
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source parallel_studio_xe_2017/bin/psxevars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        psxevars = glob.glob(join_path(
-            self.prefix, 'parallel_studio*', 'bin', 'psxevars.sh'))
-
-        if psxevars:
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                psxevars[0], 'intel64'))
+    conflicts('+clck',      when='@professional.0:professional.9999')
+    conflicts('+itac',      when='@professional.0:professional.9999')
+    conflicts('+mpi',       when='@professional.0:professional.9999')
+
+    # The following components are not available before 2016
+    conflicts('+daal',      when='@professional.0:professional.2015.7')
+    conflicts('+daal',      when='@cluster.0:cluster.2015.7')
+    conflicts('+daal',      when='@composer.0:composer.2015.7')
+
+    def setup_dependent_environment(self, *args):
+        # Handle in callback, conveying client's compilers in additional arg.
+        # CAUTION - DUP code in:
+        #   ../intel-mpi/package.py
+        #   ../intel-parallel-studio/package.py
+        self._setup_dependent_env_callback(*args, compilers_of_client={
+            'CC':   spack_cc,
+            'CXX':  spack_cxx,
+            'F77':  spack_f77,
+            'F90':  spack_fc,
+            'FC':   spack_fc,
+        })
diff --git a/var/spack/repos/builtin/packages/intel-tbb/disable-tm.patch b/var/spack/repos/builtin/packages/intel-tbb/disable-tm.patch
new file mode 100644
index 0000000000..7ef0e93b78
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-tbb/disable-tm.patch
@@ -0,0 +1,15 @@
+Disable transactional memory.  This is needed for some AMD or very old
+Intel systems.  See issue #6090.
+
+diff -Naurb tbb-2018_U4.orig/include/tbb/tbb_config.h tbb-2018_U4/include/tbb/tbb_config.h
+--- tbb-2018_U4.orig/include/tbb/tbb_config.h	2018-05-30 07:35:25.000000000 -0500
++++ tbb-2018_U4/include/tbb/tbb_config.h	2018-07-24 16:26:11.662673434 -0500
+@@ -98,7 +98,7 @@
+ #define __TBB_DEFINE_MIC 1
+ #endif
+ 
+-#define __TBB_TSX_AVAILABLE  ((__TBB_x86_32 || __TBB_x86_64) && !__TBB_DEFINE_MIC)
++#define __TBB_TSX_AVAILABLE  0
+ 
+ /** Presence of compiler features **/
+ 
diff --git a/var/spack/repos/builtin/packages/intel-tbb/package.py b/var/spack/repos/builtin/packages/intel-tbb/package.py
index 05185ce297..55eaa995ac 100644
--- a/var/spack/repos/builtin/packages/intel-tbb/package.py
+++ b/var/spack/repos/builtin/packages/intel-tbb/package.py
@@ -1,29 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
+import inspect
+import platform
 
 
 class IntelTbb(Package):
@@ -34,28 +17,69 @@ class IntelTbb(Package):
     """
     homepage = "http://www.threadingbuildingblocks.org/"
 
-    # Only version-specific URL's work for TBB
-    version('2018.1', 'b2f2fa09adf44a22f4024049907f774b',
-            url='https://github.com/01org/tbb/archive/2018_U1.tar.gz')
-    version('2018.0', 'e54de69981905ad69eb9cf0226b9bf5f9a4ba065',
-            url='https://github.com/01org/tbb/archive/2018.tar.gz')
-    version('2017.8', '488f049fd107d8b1f6ba59cf4aad881172525106',
-            url='https://github.com/01org/tbb/archive/2017_U8.tar.gz')
-    version('2017.6', 'c0a722fd1ae66b40aeab25da6049086ef5f02f17',
-            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',
-            url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb2017_20161128oss_src.tgz')
-    version('4.4.4', 'd4cee5e4ca75cab5181834877738619c56afeb71',
-            url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz')
-    version('4.4.3', '80707e277f69d9b20eeebdd7a5f5331137868ce1',
-            url='https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160128oss_src_0.tgz')
+    # See url_for_version() below.
+    version('2019',   '2119f1db2f905dc5b423482d7689b7d6')
+    version('2018.6', '9a0f78db4f72356068b00f29f54ee6bc')
+    version('2018.5', 'ff3ae09f8c23892fbc3008c39f78288f')
+    version('2018.4', '5e2e6ba0e25624a94331c945856551c2')
+    version('2018.3', 'cd2e136598ffa5c136f077ee85a35b4c')
+    version('2018.2', '0b8dfe30917a54e40828eeb0ed7562ae')
+    version('2018.1', 'b2f2fa09adf44a22f4024049907f774b')
+    version('2018',   '7fb30d5ea2545f26ce02757d9ab05e6c')
+    version('2017.8', '7240f57f1aeea0e266a5e17ae68fdc16')
+    version('2017.7', '364f2a4b80e978f38a69cbf7c466b898')
+    version('2017.6', 'ec21254af4fc2a29574c272f501a3138')
+    version('2017.5', '85b41c64102c052e24d8a39f6193e599')
+    version('2017.4', '71526b2fef098515e212302d1455de7d')
+    version('2017.3', 'd7622eeaafeff8d271c7aa684bd82ddb')
+    version('2017.2', '9605cbea96998a10a186fc72c35cbd76')
+    version('2017.1', '6c0fe8aa7bc911a85e8e522e620511b3')
+    version('2017',   '9e7f9ea684ecf84ac74dcd3c6012cfa6')
+    version('4.4.6',  '20e15206f70c2651bfc964e451a443a0')
+    version('4.4.5',  '531a67cd98f9b4ec8ece95c5f8193a83')
+    version('4.4.4',  '61531b2e8684e06a621dcdca1a7a420e')
+    version('4.4.3',  '8e3e39e1fdfb3f7c3a5ac8ec1afe186e')
+    version('4.4.2',  'e92b110e8eb238741b00e3789b39969e')
+    version('4.4.1',  'a02c9958f02c1b5f3626874219979ae8')
+    version('4.4',    '1d512085221996eae6cec04e1a4cd3dd')
 
     provides('tbb')
 
-    # include patch for gcc rtm options
-    patch("tbb_gcc_rtm_key.patch", level=0)
+    conflicts('%gcc@6.1:', when='@:4.4.3',
+              msg='4.4.4 or later required for GCC >= 6.1.')
+
+    variant('shared', default=True,
+            description='Builds a shared version of TBB libraries')
+
+    variant('cxxstd',
+            default='default',
+            values=('default', '98', '11', '14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
+
+    variant('tm', default=True,
+            description='Enable use of transactional memory on x86')
+
+    # Build and install CMake config files if we're new enough.
+    depends_on('cmake@3.0.0:', type='build', when='@2017.0:')
+
+    # Deactivate use of RTM with GCC when on an OS with an elderly assembler.
+    patch("tbb_gcc_rtm_key.patch", level=0, when='%gcc@4.8.0: os=rhel6')
+    patch("tbb_gcc_rtm_key.patch", level=0, when='%gcc@4.8.0: os=scientific6')
+    patch("tbb_gcc_rtm_key.patch", level=0, when='%gcc@4.8.0: os=centos6')
+
+    # Patch cmakeConfig.cmake.in to find the libraries where we install them.
+    patch("tbb_cmakeConfig.patch", level=0, when='@2017.0:')
+
+    # Some very old systems don't support transactional memory.
+    patch("disable-tm.patch", when='~tm')
+
+    def url_for_version(self, version):
+        url = 'https://github.com/01org/tbb/archive/{0}.tar.gz'
+        if (version[0] >= 2017) and len(version) > 1:
+            return url.format('{0}_U{1}'.format(version[0], version[1]))
+        else:
+            return url.format(version)
 
     def coerce_to_spack(self, tbb_build_subdir):
         for compiler in ["icc", "gcc", "clang"]:
@@ -75,9 +99,6 @@ class IntelTbb(Package):
                         of.write(l)
 
     def install(self, spec, prefix):
-        if spec.satisfies('%gcc@6.1:') and spec.satisfies('@:4.4.3'):
-            raise InstallError('Only TBB 4.4.4 and above build with GCC 6.1!')
-
         # We need to follow TBB's compiler selection logic to get the proper
         # build + link flags but we still need to use spack's compiler wrappers
         # to accomplish this, we do two things:
@@ -100,11 +121,24 @@ class IntelTbb(Package):
         mkdirp(prefix)
         mkdirp(prefix.lib)
 
+        make_opts = []
+
+        # Static builds of TBB are enabled by including 'big_iron.inc' file
+        # See caveats in 'big_iron.inc' for limits on using TBB statically
+        # Lore states this file must be handed to make before other options
+        if '+shared' not in self.spec:
+            make_opts.append("extra_inc=big_iron.inc")
+
+        if spec.variants['cxxstd'].value != 'default':
+            make_opts.append('stdver=c++{0}'.
+                             format(spec.variants['cxxstd'].value))
+
         #
         # tbb does not have a configure script or make install target
         # we simply call make, and try to put the pieces together
         #
-        make("compiler=%s"  % (tbb_compiler))
+        make_opts.append("compiler={0}".format(tbb_compiler))
+        make(*make_opts)
 
         # install headers to {prefix}/include
         install_tree('include', prefix.include)
@@ -123,3 +157,12 @@ class IntelTbb(Package):
             fs = glob.glob(join_path("build", "*debug", lib_name + "_debug.*"))
             for f in fs:
                 install(f, prefix.lib)
+
+        if self.spec.satisfies('@2017.0:'):
+            # Generate and install the CMake Config file.
+            cmake_args = ('-DTBB_ROOT={0}'.format(prefix),
+                          '-DTBB_OS={0}'.format(platform.system()),
+                          '-P',
+                          'tbb_config_generator.cmake')
+            with working_dir(join_path(self.stage.source_path, 'cmake')):
+                inspect.getmodule(self).cmake(*cmake_args)
diff --git a/var/spack/repos/builtin/packages/intel-tbb/tbb_cmakeConfig.patch b/var/spack/repos/builtin/packages/intel-tbb/tbb_cmakeConfig.patch
new file mode 100644
index 0000000000..a7a7ec24a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-tbb/tbb_cmakeConfig.patch
@@ -0,0 +1,11 @@
+--- cmake/templates/TBBConfig.cmake.in~	2018-03-30 10:55:05.000000000 -0500
++++ cmake/templates/TBBConfig.cmake.in	2018-05-25 10:25:52.498708945 -0500
+@@ -52,7 +52,7 @@
+ 
+ @TBB_CHOOSE_COMPILER_SUBDIR@
+ 
+-get_filename_component(_tbb_lib_path "${_tbb_root}/@TBB_SHARED_LIB_DIR@/${_tbb_arch_subdir}/${_tbb_compiler_subdir}" ABSOLUTE)
++get_filename_component(_tbb_lib_path "${_tbb_root}/@TBB_SHARED_LIB_DIR@" ABSOLUTE)
+ 
+ foreach (_tbb_component ${TBB_FIND_COMPONENTS})
+     set(_tbb_release_lib "${_tbb_lib_path}/@TBB_LIB_PREFIX@${_tbb_component}.@TBB_LIB_EXT@")
diff --git a/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch b/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch
index f1a42fb52f..29f040d4a8 100644
--- a/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch
+++ b/var/spack/repos/builtin/packages/intel-tbb/tbb_gcc_rtm_key.patch
@@ -1,23 +1,11 @@
-*** build/linux.gcc.inc.orig	2017-01-10 16:54:01.000000000 -0800
---- build/linux.gcc.inc	2017-01-10 16:54:04.000000000 -0800
-***************
-*** 49,57 ****
-  endif
-  
-  # gcc 4.8 and later support RTM intrinsics, but require command line switch to enable them
-! ifneq (,$(shell gcc -dumpversion | egrep  "^(4\.[8-9]|[5-9])"))
-!     RTM_KEY = -mrtm
-! endif
-  
-  ifeq ($(cfg), release)
-          CPLUS_FLAGS = $(ITT_NOTIFY) -g -O2 -DUSE_PTHREAD
---- 49,57 ----
-  endif
-  
-  # gcc 4.8 and later support RTM intrinsics, but require command line switch to enable them
-! #ifneq (,$(shell gcc -dumpversion | egrep  "^(4\.[8-9]|[5-9])"))
-! #    RTM_KEY = -mrtm
-! #endif
-  
-  ifeq ($(cfg), release)
-          CPLUS_FLAGS = $(ITT_NOTIFY) -g -O2 -DUSE_PTHREAD
\ No newline at end of file
+--- build/linux.gcc.inc~	2016-09-15 07:00:44.000000000 -0500
++++ build/linux.gcc.inc	2018-06-07 17:32:53.181194974 -0500
+@@ -46,7 +46,7 @@
+ 
+ # gcc 4.8 and later support RTM intrinsics, but require command line switch to enable them
+ ifneq (,$(shell gcc -dumpversion | egrep  "^(4\.[8-9]|[5-9])"))
+-    RTM_KEY = -mrtm
++    RTM_KEY = # -mrtm
+ endif
+ 
+ ifeq ($(cfg), release)
diff --git a/var/spack/repos/builtin/packages/intel-xed/package.py b/var/spack/repos/builtin/packages/intel-xed/package.py
new file mode 100644
index 0000000000..3469a531fd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/intel-xed/package.py
@@ -0,0 +1,84 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os
+
+
+class IntelXed(Package):
+    """The Intel X86 Encoder Decoder library for encoding and decoding x86
+    machine instructions (64- and 32-bit).  Also includes libxed-ild,
+    a lightweight library for decoding the length of an instruction."""
+
+    homepage = "https://intelxed.github.io/"
+    git      = "https://github.com/intelxed/xed.git"
+
+    version('2018.02.14', commit='44d06033b69aef2c20ab01bfb518c52cd71bb537')
+
+    resource(name='mbuild',
+             git='https://github.com/intelxed/mbuild.git',
+             commit='bb9123152a330c7fa1ff1a502950dc199c83e177',
+             destination='')
+
+    variant('debug', default=False, description='enable debug symbols')
+
+    depends_on('python@2.7:', type='build')
+
+    mycflags = []
+
+    # Save CFLAGS for use in install.
+    def flag_handler(self, name, flags):
+        if name == 'cflags':
+            self.mycflags = flags
+        return (flags, None, None)
+
+    def install(self, spec, prefix):
+        # XED needs PYTHONPATH to find the mbuild directory.
+        mbuild_dir = join_path(self.stage.source_path, 'mbuild')
+        python_path = os.getenv('PYTHONPATH', '')
+        os.environ['PYTHONPATH'] = mbuild_dir + ':' + python_path
+
+        mfile = Executable('./mfile.py')
+
+        args = ['-j', str(make_jobs),
+                '--cc=%s' % spack_cc,
+                '--no-werror']
+
+        if '+debug' in spec:
+            args.append('--debug')
+
+        # If an optimization flag (-O...) is specified in CFLAGS, use
+        # that, else set default opt level.
+        for flag in self.mycflags:
+            if len(flag) >= 2 and flag[0:2] == '-O':
+                break
+        else:
+            args.append('--opt=2')
+
+        # Build and install static libxed.a.
+        mfile('--clean')
+        mfile(*args)
+
+        mkdirp(prefix.include)
+        mkdirp(prefix.lib)
+
+        libs = glob.glob(join_path('obj', 'lib*.a'))
+        for lib in libs:
+            install(lib, prefix.lib)
+
+        # Build and install shared libxed.so.
+        mfile('--clean')
+        mfile('--shared', *args)
+
+        libs = glob.glob(join_path('obj', 'lib*.so'))
+        for lib in libs:
+            install(lib, prefix.lib)
+
+        # Install header files.
+        hdrs = glob.glob(join_path('include', 'public', 'xed', '*.h'))  \
+            + glob.glob(join_path('obj', '*.h'))
+        for hdr in hdrs:
+            install(hdr, prefix.include)
diff --git a/var/spack/repos/builtin/packages/intel/package.py b/var/spack/repos/builtin/packages/intel/package.py
index d67550caa6..69db3e21a6 100644
--- a/var/spack/repos/builtin/packages/intel/package.py
+++ b/var/spack/repos/builtin/packages/intel/package.py
@@ -1,31 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-from spack.environment import EnvironmentModifications
 
 
 class Intel(IntelPackage):
@@ -33,78 +11,31 @@ class Intel(IntelPackage):
 
     homepage = "https://software.intel.com/en-us/intel-parallel-studio-xe"
 
-    version('18.0.0', '31ba768fba6e7322957b03feaa3add28',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz')
-    version('17.0.4', 'd03d351809e182c481dc65e07376d9a2',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz')
-    version('17.0.3', '52344df122c17ddff3687f84ceb21623',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz')
-    version('17.0.2', '2891ab1ece43eb61b6ab892f07c47f01',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz')
-    version('17.0.1', '1f31976931ed8ec424ac7c3ef56f5e85',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz')
-    version('17.0.0', 'b67da0065a17a05f110ed1d15c3c6312',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz')
-    version('16.0.4', '2bc9bfc9be9c1968a6e42efb4378f40e',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz')
-    version('16.0.3', '3208eeabee951fc27579177b593cefe9',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz')
-    version('16.0.2', '1133fb831312eb519f7da897fec223fa',
-            url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz')
+    # Same as in ../intel-parallel-studio/package.py, Composer Edition,
+    # but the version numbering in Spack differs.
+    version('18.0.3',              '234223cc470717c2095456d9f048d690', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13002/parallel_studio_xe_2018_update3_composer_edition.tgz')
+    version('18.0.2',              '76f820f53de4c1ff998229c983cf4f53', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12722/parallel_studio_xe_2018_update2_composer_edition.tgz')
+    version('18.0.1',              '28cb807126d713350f4aa6f9f167448a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12381/parallel_studio_xe_2018_update1_composer_edition.tgz')
+    version('18.0.0',              '31ba768fba6e7322957b03feaa3add28', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12067/parallel_studio_xe_2018_composer_edition.tgz')
+    #
+    version('17.0.7',              '4c02a4a29a8f2424f31baa23116a1001', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12860/parallel_studio_xe_2017_update7_composer_edition.tgz')
+    version('17.0.6',              'd96cce0c3feef20091efde458f581a9f', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/12538/parallel_studio_xe_2017_update6_composer_edition.tgz')
+    # version('17.0.5',              -- TBD --
+    version('17.0.4',              'd03d351809e182c481dc65e07376d9a2', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11541/parallel_studio_xe_2017_update4_composer_edition.tgz')
+    version('17.0.3',              '52344df122c17ddff3687f84ceb21623', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11464/parallel_studio_xe_2017_update3_composer_edition.tgz')
+    version('17.0.2',              '2891ab1ece43eb61b6ab892f07c47f01', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/11302/parallel_studio_xe_2017_update2_composer_edition.tgz')
+    version('17.0.1',              '1f31976931ed8ec424ac7c3ef56f5e85', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/10978/parallel_studio_xe_2017_update1_composer_edition.tgz')
+    version('17.0.0',              'b67da0065a17a05f110ed1d15c3c6312', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9656/parallel_studio_xe_2017_composer_edition.tgz')
+    #
+    version('16.0.4',              '2bc9bfc9be9c1968a6e42efb4378f40e', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9785/parallel_studio_xe_2016_composer_edition_update4.tgz')
+    version('16.0.3',              '3208eeabee951fc27579177b593cefe9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/9063/parallel_studio_xe_2016_composer_edition_update3.tgz')
+    version('16.0.2',              '1133fb831312eb519f7da897fec223fa', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8680/parallel_studio_xe_2016_composer_edition_update2.tgz')
+    #
+    # Grandfathered release; different directory structure.
+    version('15.0.6',              'da9f8600c18d43d58fba0488844f79c9', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/8432/l_compxe_2015.6.233.tgz')
+    version('15.0.1',              '85beae681ae56411a8e791a7c44a5c0a', url='http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/4933/l_compxe_2015.1.133.tgz')
 
     variant('rpath', default=True, description='Add rpath to .cfg files')
 
-    components = [
-        # Common files
-        'intel-comp-',
-        'intel-openmp',
-
-        # C/C++
-        'intel-icc',
-
-        # Fortran
-        'intel-ifort',
-    ]
-
-    @property
-    def license_files(self):
-        return [
-            'Licenses/license.lic',
-            join_path('compilers_and_libraries', 'linux', 'bin',
-                      'intel64', 'license.lic')
-        ]
-
-    @run_after('install')
-    def rpath_configuration(self):
-        if '+rpath' in self.spec:
-            bin_dir = join_path(self.prefix, 'compilers_and_libraries',
-                                'linux', 'bin', 'intel64')
-            lib_dir = join_path(self.prefix, 'compilers_and_libraries',
-                                'linux', 'compiler', 'lib', 'intel64_lin')
-            for compiler in ['icc', 'icpc', 'ifort']:
-                cfgfilename = join_path(bin_dir, '{0}.cfg'.format(compiler))
-                with open(cfgfilename, 'w') as f:
-                    f.write('-Xlinker -rpath -Xlinker {0}\n'.format(lib_dir))
-
-    def setup_environment(self, spack_env, run_env):
-        """Adds environment variables to the generated module file.
-
-        These environment variables come from running:
-
-        .. code-block:: console
-
-           $ source bin/compilervars.sh intel64
-        """
-        # NOTE: Spack runs setup_environment twice, once pre-build to set up
-        # the build environment, and once post-installation to determine
-        # the environment variables needed at run-time to add to the module
-        # file. The script we need to source is only present post-installation,
-        # so check for its existence before sourcing.
-        # TODO: At some point we should split setup_environment into
-        # setup_build_environment and setup_run_environment to get around
-        # this problem.
-        compilervars = os.path.join(self.prefix.bin, 'compilervars.sh')
-
-        if os.path.isfile(compilervars):
-            run_env.extend(EnvironmentModifications.from_sourcing_file(
-                compilervars, 'intel64'))
+    # Since the current package is a subset of 'intel-parallel-studio',
+    # all remaining Spack actions are handled in the package class.
diff --git a/var/spack/repos/builtin/packages/intltool/package.py b/var/spack/repos/builtin/packages/intltool/package.py
index 0c84d3b516..dea21ab25a 100644
--- a/var/spack/repos/builtin/packages/intltool/package.py
+++ b/var/spack/repos/builtin/packages/intltool/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,6 +20,12 @@ class Intltool(AutotoolsPackage):
     depends_on('perl-xml-parser', type=('build', 'run'))
     depends_on('perl@5.8.1:',     type=('build', 'run'))
 
+    # patch for "Unescaped left brace in regex is illegal here in regex"
+    # warnings witn perl 5.22 and errors with perl 5.26 and newer
+    patch('https://launchpadlibrarian.net/216052398/intltool-perl-5.22.patch',
+          sha256='ca9d6562f29f06c64150f50369a24402b7aa01a3a0dc73dce55106f3224330a1',
+          level=0)
+
     def check(self):
         # `make check` passes but causes `make install` to fail
         pass
diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py
index 96b5a455c9..eee53a9911 100644
--- a/var/spack/repos/builtin/packages/ior/package.py
+++ b/var/spack/repos/builtin/packages/ior/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/iozone/package.py b/var/spack/repos/builtin/packages/iozone/package.py
index c75595ba14..09124c2196 100644
--- a/var/spack/repos/builtin/packages/iozone/package.py
+++ b/var/spack/repos/builtin/packages/iozone/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/iperf2/package.py b/var/spack/repos/builtin/packages/iperf2/package.py
new file mode 100644
index 0000000000..3e9498ddf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/iperf2/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Iperf2(AutotoolsPackage):
+    """This code is a continuation based from the no longer maintained iperf
+    2.0.5 code base. Iperf 2.0.5 is still widely deployed and used by many for
+    testing networks and for qualifying networking products."""
+
+    homepage = "https://sourceforge.net/projects/iperf2"
+    url      = "https://downloads.sourceforge.net/project/iperf2/iperf-2.0.12.tar.gz"
+
+    version('2.0.12', 'e501e26b9289097086ce0c44a42b10bc')
diff --git a/var/spack/repos/builtin/packages/iperf3/package.py b/var/spack/repos/builtin/packages/iperf3/package.py
new file mode 100644
index 0000000000..16cf48f157
--- /dev/null
+++ b/var/spack/repos/builtin/packages/iperf3/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Iperf3(AutotoolsPackage):
+    """The iperf series of tools perform active measurements to determine the
+    maximum achievable bandwidth on IP networks. iperf2 is a separately
+    maintained project."""
+
+    homepage = "https://software.es.net/iperf/"
+    url      = "https://github.com/esnet/iperf/archive/3.6.tar.gz"
+
+    version('3.6', '5082ffc4141abc1bac7cbd59337ff409')
diff --git a/var/spack/repos/builtin/packages/ipopt/package.py b/var/spack/repos/builtin/packages/ipopt/package.py
index a9502a3e85..64930c5ca7 100644
--- a/var/spack/repos/builtin/packages/ipopt/package.py
+++ b/var/spack/repos/builtin/packages/ipopt/package.py
@@ -1,36 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Ipopt(Package):
+class Ipopt(AutotoolsPackage):
     """Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a
        software package for large-scale nonlinear optimization."""
     homepage = "https://projects.coin-or.org/Ipopt"
     url      = "http://www.coin-or.org/download/source/Ipopt/Ipopt-3.12.4.tgz"
 
+    version('3.12.10', 'e1a3ad09e41edbfe41948555ece0bdc78757a5ca764b6be5a9a127af2e202d2e')
+    version('3.12.9', '8ff3fe1a8560896fc5559839a87c2530cac4ed231b0806e487bfd3cf2d294ab8')
+    version('3.12.8', '62c6de314220851b8f4d6898b9ae8cf0a8f1e96b68429be1161f8550bb7ddb03')
     version('3.12.7', '2a36e4a04717a8ed7012ac7d1253ae4ffbc1a8fd')
     version('3.12.6', 'ed4072427fab786fcf6082fe7e6f6c2ed9b5e6f8')
     version('3.12.5', '3f63ddfff517235ead17af6cceb426ca858dda37')
@@ -44,17 +28,26 @@ class Ipopt(Package):
             description="Build with Coin Harwell Subroutine Libraries")
     variant('metis', default=False,
             description="Build with METIS partitioning support")
+    variant('debug', default=False,
+            description="Build debug instead of optimized version")
 
     depends_on("blas")
     depends_on("lapack")
-    depends_on("pkg-config", type='build')
+    depends_on("pkgconfig", type='build')
     depends_on("mumps+double~mpi")
     depends_on('coinhsl', when='+coinhsl')
-    depends_on('metis@4.0:4.999', when='+metis')
+    depends_on('metis@4.0:', when='+metis')
 
     patch('ipopt_ppc_build.patch', when='arch=ppc64le')
 
-    def install(self, spec, prefix):
+    flag_handler = build_system_flags
+    build_directory = 'spack-build'
+
+    # IPOPT does not build correctly in parallel on OS X
+    parallel = False
+
+    def configure_args(self):
+        spec = self.spec
         # Dependency directories
         blas_dir = spec['blas'].prefix
         lapack_dir = spec['lapack'].prefix
@@ -68,8 +61,8 @@ class Ipopt(Package):
         blas_lib = spec['blas'].libs.ld_flags
         lapack_lib = spec['lapack'].libs.ld_flags
 
-        configure_args = [
-            "--prefix=%s" % prefix,
+        args = [
+            "--prefix=%s" % self.prefix,
             "--with-mumps-incdir=%s" % mumps_dir.include,
             "--with-mumps-lib=%s" % mumps_libcmd,
             "--enable-shared",
@@ -81,18 +74,21 @@ class Ipopt(Package):
         ]
 
         if 'coinhsl' in spec:
-            configure_args.extend([
+            args.extend([
                 '--with-hsl-lib=%s' % spec['coinhsl'].libs.ld_flags,
                 '--with-hsl-incdir=%s' % spec['coinhsl'].prefix.include])
 
         if 'metis' in spec:
-            configure_args.extend([
+            args.extend([
                 '--with-metis-lib=%s' % spec['metis'].libs.ld_flags,
                 '--with-metis-incdir=%s' % spec['metis'].prefix.include])
 
-        configure(*configure_args)
+        # The IPOPT configure file states that '--enable-debug' implies
+        # '--disable-shared', but adding '--enable-shared' overrides
+        # '--disable-shared' and builds a shared library with debug symbols
+        if '+debug' in spec:
+            args.append('--enable-debug')
+        else:
+            args.append('--disable-debug')
 
-        # IPOPT does not build correctly in parallel on OS X
-        make(parallel=False)
-        make("test", parallel=False)
-        make("install", parallel=False)
+        return args
diff --git a/var/spack/repos/builtin/packages/isaac-server/package.py b/var/spack/repos/builtin/packages/isaac-server/package.py
index 3bfad09f98..f8451ad443 100644
--- a/var/spack/repos/builtin/packages/isaac-server/package.py
+++ b/var/spack/repos/builtin/packages/isaac-server/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,14 @@ class IsaacServer(CMakePackage):
 
     homepage = "http://computationalradiationphysics.github.io/isaac/"
     url      = "https://github.com/ComputationalRadiationPhysics/isaac/archive/v1.3.0.tar.gz"
+    git      = "https://github.com/ComputationalRadiationPhysics/isaac.git"
+
+    maintainers = ['ax3l']
 
-    version('develop', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/isaac.git')
-    version('master', branch='master',
-            git='https://github.com/ComputationalRadiationPhysics/isaac.git')
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('1.4.0', '3ad05c8fad4673366077204c5d39285f')
+    version('1.3.3', '7aeebaf0c5a77e2cb9bea066750e369b')
     version('1.3.2', 'c557daa74de52fd79e734c9758fca38b')
     version('1.3.1', '7fe075f9af68d05355eaba0e224f20ca')
     version('1.3.0', 'c8a794da9bb998ef0e75449bfece1a12')
@@ -49,7 +33,7 @@ class IsaacServer(CMakePackage):
     depends_on('libwebsockets@2.1.1:', type='link')
     # depends_on('gstreamer@1.0', when='+gstreamer')
 
-    # Until the pull request is merged: https://github.com/ComputationalRadiationPhysics/isaac/pull/70
+    # https://github.com/ComputationalRadiationPhysics/isaac/pull/70
     patch('jpeg.patch', when='@:1.3.1')
 
     root_cmakelists_dir = 'server'
diff --git a/var/spack/repos/builtin/packages/isaac/package.py b/var/spack/repos/builtin/packages/isaac/package.py
index 4c05faeb26..c8f3793fc6 100644
--- a/var/spack/repos/builtin/packages/isaac/package.py
+++ b/var/spack/repos/builtin/packages/isaac/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,13 @@ class Isaac(CMakePackage):
 
     homepage = "http://computationalradiationphysics.github.io/isaac/"
     url      = "https://github.com/ComputationalRadiationPhysics/isaac/archive/v1.3.0.tar.gz"
+    git      = "https://github.com/ComputationalRadiationPhysics/isaac.git"
+
+    maintainers = ['ax3l']
 
-    version('develop', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/isaac.git')
-    version('master', branch='master',
-            git='https://github.com/ComputationalRadiationPhysics/isaac.git')
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('1.4.0', '3ad05c8fad4673366077204c5d39285f')
     version('1.3.3', '7aeebaf0c5a77e2cb9bea066750e369b')
     version('1.3.2', 'c557daa74de52fd79e734c9758fca38b')
     version('1.3.1', '7fe075f9af68d05355eaba0e224f20ca')
@@ -51,7 +34,7 @@ class Isaac(CMakePackage):
     depends_on('boost@1.56.0:', type='link')
     depends_on('boost@1.65.1:', type='link', when='^cuda@9:')
     depends_on('cuda@7.0:', type='link', when='+cuda')
-    # depends_on('alpaka', when='+alpaka')
+    # depends_on('alpaka@0.3', when='+alpaka')
     depends_on('icet', type='link')
     depends_on('mpi', type='link')
 
diff --git a/var/spack/repos/builtin/packages/isl/package.py b/var/spack/repos/builtin/packages/isl/package.py
index 4c25f3ec97..cca2ba21f3 100644
--- a/var/spack/repos/builtin/packages/isl/package.py
+++ b/var/spack/repos/builtin/packages/isl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,12 @@ class Isl(AutotoolsPackage):
     sets and relations of integer points bounded by affine constraints."""
 
     homepage = "http://isl.gforge.inria.fr"
-    url      = "http://isl.gforge.inria.fr/isl-0.18.tar.bz2"
+    url      = "http://isl.gforge.inria.fr/isl-0.19.tar.bz2"
 
-    version('0.18', '11436d6b205e516635b666090b94ab32')
-    version('0.14', 'acd347243fca5609e3df37dba47fd0bb')
+    version('0.19', sha256='d59726f34f7852a081fbd3defd1ab2136f174110fc2e0c8d10bb122173fa9ed8')
+    version('0.18', sha256='6b8b0fd7f81d0a957beb3679c81bbb34ccc7568d5682844d8924424a0dadcb1b')
+    version('0.15', sha256='8ceebbf4d9a81afa2b4449113cee4b7cb14a687d7a549a963deb5e2a41458b6b')
+    version('0.14', sha256='7e3c02ff52f8540f6a85534f54158968417fd676001651c8289c705bd0228f36')
 
     depends_on('gmp')
 
diff --git a/var/spack/repos/builtin/packages/itstool/package.py b/var/spack/repos/builtin/packages/itstool/package.py
index 00e273bb2f..b0858df2b9 100644
--- a/var/spack/repos/builtin/packages/itstool/package.py
+++ b/var/spack/repos/builtin/packages/itstool/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/itsx/package.py b/var/spack/repos/builtin/packages/itsx/package.py
index 84dc525740..6d4414db12 100644
--- a/var/spack/repos/builtin/packages/itsx/package.py
+++ b/var/spack/repos/builtin/packages/itsx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/jackcess/package.py b/var/spack/repos/builtin/packages/jackcess/package.py
new file mode 100644
index 0000000000..d55357bccf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jackcess/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Jackcess(Package):
+    """Jackcess is a pure Java library for reading from and writing to
+    MS Access databases (currently supporting versions 2000-2016)."""
+
+    homepage = "http://jackcess.sourceforge.net/"
+    url      = "https://sourceforge.net/projects/jackcess/files/jackcess/2.1.12/jackcess-2.1.12.jar"
+
+    version('2.1.12',   '7d051d8dd93f2fe7e5e86389ea380619', expand=False)
+    version('1.2.14.3', 'ef778421c1385ac9ab4aa7edfb954caa', expand=False)
+
+    extends('jdk')
+    depends_on('java', type='run')
+    depends_on('commons-lang@2.6', when='@2.1.12', type='run')
+    depends_on('commons-lang@2.4', when='@1.2.14.3', type='run')
+    depends_on('commons-logging@1.1.3', when='@2.1.12', type='run')
+    depends_on('commons-logging@1.1.1', when='@1.2.14.3', type='run')
+
+    def install(self, spec, prefix):
+        install('jackcess-{0}.jar'.format(self.version), prefix)
diff --git a/var/spack/repos/builtin/packages/jags/package.py b/var/spack/repos/builtin/packages/jags/package.py
index 248f4019d6..0916d85f72 100644
--- a/var/spack/repos/builtin/packages/jags/package.py
+++ b/var/spack/repos/builtin/packages/jags/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,15 +11,18 @@ class Jags(AutotoolsPackage):
        Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC)
        simulation not wholly unlike BUGS"""
 
+    tags = ['mcmc', 'Gibbs sampler']
+
     homepage = "http://mcmc-jags.sourceforge.net/"
     url = "https://downloads.sourceforge.net/project/mcmc-jags/JAGS/4.x/Source/JAGS-4.2.0.tar.gz"
 
+    version('4.3.0', 'd88dff326603deee39ce7fa4234c5a43')
     version('4.2.0', '9e521b3cfb23d3290a8c6bc0b79bf426')
 
     depends_on('blas')
     depends_on('lapack')
 
     def configure_args(self):
-        args = ['--with-blas=-L%s' % self.spec['blas'].prefix.lib,
-                '--with-lapack=-L%s' % self.spec['lapack'].prefix.lib]
+        args = ['--with-blas=%s' % self.spec['blas'].libs.ld_flags,
+                '--with-lapack=%s' % self.spec['lapack'].libs.ld_flags]
         return args
diff --git a/var/spack/repos/builtin/packages/jansson/package.py b/var/spack/repos/builtin/packages/jansson/package.py
index e3e2d56cff..c929eaa865 100644
--- a/var/spack/repos/builtin/packages/jansson/package.py
+++ b/var/spack/repos/builtin/packages/jansson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class Jansson(CMakePackage):
 
     homepage = "http://www.digip.org/jansson/"
     url      = "https://github.com/akheron/jansson/archive/v2.9.tar.gz"
+    maintainers = ['ax3l']
 
     version('2.9', 'd2db25c437b359fc5a065ed938962237')
 
diff --git a/var/spack/repos/builtin/packages/jasper/package.py b/var/spack/repos/builtin/packages/jasper/package.py
index 5739f902a1..6b0fc9c866 100644
--- a/var/spack/repos/builtin/packages/jasper/package.py
+++ b/var/spack/repos/builtin/packages/jasper/package.py
@@ -1,58 +1,102 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Jasper(AutotoolsPackage):
+class Jasper(Package):
     """Library for manipulating JPEG-2000 images"""
 
     homepage = "https://www.ece.uvic.ca/~frodo/jasper/"
-    url = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip"
+    url      = "https://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.14.tar.gz"
+    list_url = homepage
 
-    version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754')
+    version('2.0.14',  '23561b51da8eb5d0dc85b91eff3d9a7f',
+            url="https://www.ece.uvic.ca/~frodo/jasper/software/jasper-2.0.14.tar.gz")
+    version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754',
+            url="https://www.ece.uvic.ca/~frodo/jasper/software/jasper-1.900.1.zip")
 
-    variant('shared', default=True,
-            description='Builds shared versions of the libraries')
-    variant('debug', default=False,
-            description='Builds debug versions of the libraries')
+    variant('jpeg',   default=True,  description='Enable the use of the JPEG library')
+    variant('opengl', default=False, description='Enable the use of the OpenGL and GLUT libraries')
+    variant('shared', default=True,  description='Enable the building of shared libraries')
+    variant('build_type', default='Release', description='CMake build type', values=('Debug', 'Release'))
+
+    depends_on('cmake@2.8.11:', type='build', when='@2:')
+    depends_on('jpeg', when='+jpeg')
+    depends_on('gl', when='+opengl')
+
+    # Fixes a bug where an assertion fails when certain JPEG-2000
+    # files with an alpha channel are processed.
+    # See: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=469786
+    patch('fix_alpha_channel_assert_fail.patch', when='@1.900.1')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = std_cmake_args
+        args.append('-DJAS_ENABLE_DOC=false')
 
-    depends_on('jpeg')
+        if '+jpeg' in spec:
+            args.append('-DJAS_ENABLE_LIBJPEG=true')
+        else:
+            args.append('-DJAS_ENABLE_LIBJPEG=false')
 
-    # Fixes a bug (still in upstream as of v.1.900.1) where an assertion fails
-    # when certain JPEG-2000 files with an alpha channel are processed
-    # see: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=469786
-    patch('fix_alpha_channel_assert_fail.patch')
+        if '+opengl' in spec:
+            args.append('-DJAS_ENABLE_OPENGL=true')
+        else:
+            args.append('-DJAS_ENABLE_OPENGL=false')
+
+        if '+shared' in spec:
+            args.append('-DJAS_ENABLE_SHARED=true')
+        else:
+            args.append('-DJAS_ENABLE_SHARED=false')
+
+        return args
 
     def configure_args(self):
         spec = self.spec
-        args = ['--mandir={0}'.format(spec.prefix.man)]
+        args = [
+            '--prefix={0}'.format(self.prefix)
+        ]
+
+        if '+jpeg' in spec:
+            args.append('--enable-libjpeg')
+        else:
+            args.append('--disable-libjpeg')
+
+        if '+opengl' in spec:
+            args.append('--enable-opengl')
+        else:
+            args.append('--disable-opengl')
 
         if '+shared' in spec:
             args.append('--enable-shared')
+        else:
+            args.append('--disable-shared')
 
-        if '+debug' not in spec:
+        if 'build_type=Debug' in spec:
+            args.append('--enable-debug')
+        else:
             args.append('--disable-debug')
 
         return args
+
+    @when('@2:')
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *self.cmake_args())
+            make()
+            if self.run_tests:
+                make('test')
+            make('install')
+
+    @when('@:1')
+    def install(self, spec, prefix):
+        configure(*self.configure_args())
+        make()
+        if self.run_tests:
+            make('check')
+        make('install')
+        if self.run_tests:
+            make('installcheck')
diff --git a/var/spack/repos/builtin/packages/jbigkit/package.py b/var/spack/repos/builtin/packages/jbigkit/package.py
new file mode 100644
index 0000000000..66dd1b202c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jbigkit/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Jbigkit(MakefilePackage):
+    """JBIG-Kit is a software implementation of
+    the JBIG1 data compression standard."""
+
+    homepage = "http://www.cl.cam.ac.uk/~mgk25/jbigkit/"
+    url      = "http://www.cl.cam.ac.uk/~mgk25/jbigkit/download/jbigkit-2.1.tar.gz"
+
+    version('2.1', 'ebcf09bed9f14d7fa188d3bd57349522')
+    version('1.6', 'ce196e45f293d40ba76af3dc981ccfd7')
+
+    build_directory = 'libjbig'
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('libjbig/Makefile')
+        makefile.filter('CC = .*', 'CC = cc')
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            mkdir(prefix.include)
+            for f in ['jbig85.h', 'jbig_ar.h', 'jbig.h']:
+                install(f, prefix.include)
+            mkdir(prefix.lib)
+            for f in ['libjbig85.a', 'libjbig.a']:
+                install(f, prefix.lib)
+            mkdir(prefix.bin)
+            for f in ['tstcodec', 'tstcodec85']:
+                install(f, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/jchronoss/package.py b/var/spack/repos/builtin/packages/jchronoss/package.py
new file mode 100644
index 0000000000..dc8763b064
--- /dev/null
+++ b/var/spack/repos/builtin/packages/jchronoss/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Jchronoss(CMakePackage):
+    """ JCHRONOSS aims to help HPC application testing process
+     to scale as much as the application does. """
+
+    homepage = "http://jchronoss.hpcframework.com"
+    url      = "http://fs.paratools.com/mpc/contrib/apps/jchronoss/JCHRONOSS-1.2.tar.gz"
+
+    version('1.2',   'f083ca453537e4f60ad17d266bbab1f1')
+    version('1.1.1', '2d78a0998efec20e7726af19fff76a72')
+    version('1.1',   'a8ba0b21b18548874b8ab2a6ca6e1081')
+    version('1.0',   '78d81e00248e21f4adea4a1ccfd6156b')
+
+    variant("realtime", default=False, description="Enable Real-Time support")
+    variant("openmp", default=False, description="Enable OpenMP constructs")
+    variant("ncurses", default=False, description="Enable ncurses-based tool")
+    variant('color', default=False, description='Enable colour-themed output')
+
+    depends_on("libxml2")
+    depends_on("libwebsockets", when="+realtime")
+    depends_on("libev", when="+realtime")
+    depends_on("ncurses", when="+ncurses")
+
+    def cmake_args(self):
+        args = ["-DSPACK_DRIVEN=ON"]
+
+        if '+color' in self.spec:
+            args.append("-DENABLE_COLOR=yes")
+        if '+openmp' in self.spec:
+            args.append("-DENABLE_OPENMP=yes")
+        if '+ncurses' in self.spec:
+            args.append("-DENABLE_PLUGIN_NCURSES=yes")
+        if '+realtime' in self.spec:
+            args.append("-DENABLE_PLUGIN_SERVER=yes")
+
+        return args
diff --git a/var/spack/repos/builtin/packages/jdk/package.py b/var/spack/repos/builtin/packages/jdk/package.py
index 9c221fa364..0204572f25 100644
--- a/var/spack/repos/builtin/packages/jdk/package.py
+++ b/var/spack/repos/builtin/packages/jdk/package.py
@@ -1,79 +1,178 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-#
-# Author: Justin Too <too1@llnl.gov>
-#
-import distutils.dir_util
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.util.prefix import Prefix
 from spack import *
 
+import llnl.util.tty as tty
+import os
+
 
 class Jdk(Package):
-    """The Java Development Kit (JDK) released by Oracle Corporation
-       in the form of a binary product aimed at Java developers."""
+    """The Java Development Kit (JDK) released by Oracle Corporation in the
+    form of a binary product aimed at Java developers. Includes a complete JRE
+    plus tools for developing, debugging, and monitoring Java applications."""
+
     homepage = "http://www.oracle.com/technetwork/java/javase/downloads/index.html"
 
+    maintainers = ['justintoo']
+
     # Oracle requires that you accept their License Agreement in order
     # to access the Java packages in download.oracle.com. In order to
     # automate this process, we need to utilize these additional curl
-    # commandline options.
-    #
-    # See http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux
+    # command-line options. See:
+    # http://stackoverflow.com/questions/10268583/how-to-automate-download-and-installation-of-java-jdk-on-linux
     curl_options = [
         '-j',  # junk cookies
         '-H',  # specify required License Agreement cookie
-        'Cookie: oraclelicense=accept-securebackup-cookie']
+        'Cookie: oraclelicense=accept-securebackup-cookie'
+    ]
 
-    # For instructions on how to find the magic URL, see:
-    # https://gist.github.com/P7h/9741922
-    # https://linuxconfig.org/how-to-install-java-se-development-kit-on-debian-linux
-    version('8u141-b15', '8cf4c4e00744bfafc023d770cb65328c', curl_options=curl_options,
+    # To add the latest version, go to the homepage listed above,
+    # click "JDK Download", click "Accept License Agreement", right-click the
+    # Linux .tar.gz link, and select Copy Link Address. The checksum can be
+    # found in a link above. The build number can be deciphered from the URL.
+    # Alternatively, run `bin/java -version` after extracting. Replace '+'
+    # symbol in version with '_', otherwise it will be interpreted as a variant
+    version('11.0.1', sha256='e7fd856bacad04b6dbf3606094b6a81fa9930d6dbb044bbd787be7ea93abc885', curl_options=curl_options,
+            url='http://download.oracle.com/otn-pub/java/jdk/11.0.1+13/90cf5d8f270a4347a95050320eef3fb7/jdk-11.0.1_linux-x64_bin.tar.gz')
+    version('10.0.2_13', sha256='6633c20d53c50c20835364d0f3e172e0cbbce78fff81867488f22a6298fa372b', curl_options=curl_options,
+            url='http://download.oracle.com/otn-pub/java/jdk/10.0.2+13/19aef61b38124481863b1413dce1855f/jdk-10.0.2_linux-x64_bin.tar.gz')
+    version('10.0.1_10', 'ae8ed645e6af38432a56a847597ac61d4283b7536688dbab44ab536199d1e5a4', curl_options=curl_options,
+            url='http://download.oracle.com/otn-pub/java/jdk/10.0.1+10/fb4372174a714e6b8c52526dc134031e/jdk-10.0.1_linux-x64_bin.tar.gz')
+    version('1.8.0_181-b13', 'ef599e322eee42f6769991dd3e3b1a31', curl_options=curl_options, 
+            url='http://download.oracle.com/otn-pub/java/jdk/8u181-b13/96a7b8442fe848ef90c96a2fad6ed6d1/jdk-8u181-linux-x64.tar.gz')
+    version('1.8.0_172-b11', 'eda2945e8c02b84adbf78f46c37b71c1', curl_options=curl_options,
+            url='http://download.oracle.com/otn-pub/java/jdk/8u172-b11/a58eab1ec242421181065cdc37240b08/jdk-8u172-linux-x64.tar.gz')
+    version('1.8.0_141-b15', '8cf4c4e00744bfafc023d770cb65328c', curl_options=curl_options,
             url='http://download.oracle.com/otn-pub/java/jdk/8u141-b15/336fa29ff2bb4ef291e347e091f7f4a7/jdk-8u141-linux-x64.tar.gz')
-    version('8u131-b11', '75b2cb2249710d822a60f83e28860053', curl_options=curl_options,
+    version('1.8.0_131-b11', '75b2cb2249710d822a60f83e28860053', curl_options=curl_options,
             url='http://download.oracle.com/otn-pub/java/jdk/8u131-b11/d54c1d3a095b4ff2b6607d096fa80163/jdk-8u131-linux-x64.tar.gz')
-    version('8u92-b14',  '65a1cc17ea362453a6e0eb4f13be76e4', curl_options=curl_options)
-    version('8u73-b02',  '1b0120970aa8bc182606a16bf848a686', curl_options=curl_options)
-    version('8u66-b17',  '88f31f3d642c3287134297b8c10e61bf', 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-b0', '6152f8a7561acf795ca4701daa10a965')
-
-    provides('java@8', when='@8u0:8u999')
-    provides('java@7', when='@7u0:7u999')
-
-    def url_for_version(self, version):
-        url = "http://download.oracle.com/otn-pub/java/jdk/{0}/jdk-{1}-linux-x64.tar.gz"
-        version = str(version)
-        minor_version = version[:version.index('-')]
-        return url.format(version, minor_version)
+    version('1.8.0_92-b14', '65a1cc17ea362453a6e0eb4f13be76e4', curl_options=curl_options)
+    version('1.8.0_73-b02', '1b0120970aa8bc182606a16bf848a686', curl_options=curl_options)
+    version('1.8.0_66-b17', '88f31f3d642c3287134297b8c10e61bf', curl_options=curl_options)
+    version('1.7.0_80-b0', '6152f8a7561acf795ca4701daa10a965', curl_options=curl_options)
+
+    provides('java')
+    provides('java@11', when='@11.0:11.999')
+    provides('java@10', when='@10.0:10.999')
+    provides('java@9',  when='@9.0:9.999')
+    provides('java@8',  when='@1.8.0:1.8.999')
+    provides('java@7',  when='@1.7.0:1.7.999')
+
+    # FIXME:
+    # 1. `extends('java')` doesn't work, you need to use `extends('jdk')`
+    # 2. Packages cannot extend multiple packages, see #987
+    # 3. Update `YamlFilesystemView.merge` to allow a Package to completely
+    #    override how it is symlinked into a view prefix. Then, spack activate
+    #    can symlink all *.jar files to `prefix.lib.ext`
+    extendable = True
+
+    @property
+    def home(self):
+        """Most of the time, ``JAVA_HOME`` is simply ``spec['java'].prefix``.
+        However, if the user is using an externally installed JDK, it may be
+        symlinked. For example, on macOS, the ``java`` executable can be found
+        in ``/usr/bin``, but ``JAVA_HOME`` is actually
+        ``/Library/Java/JavaVirtualMachines/jdk-10.0.1.jdk/Contents/Home``.
+        Users may not know the actual installation directory and add ``/usr``
+        to their ``packages.yaml`` unknowingly. Run ``java_home`` if it exists
+        to determine exactly where it is installed. Specify which version we
+        are expecting in case multiple Java versions are installed.
+        See ``man java_home`` for more details."""
+
+        prefix = self.prefix
+        java_home = prefix.libexec.java_home
+        if os.path.exists(java_home):
+            java_home = Executable(java_home)
+            version = str(self.version.up_to(2))
+            prefix = java_home('--version', version, output=str).strip()
+            prefix = Prefix(prefix)
+
+        return prefix
+
+    @property
+    def libs(self):
+        """Depending on the version number and whether the full JDK or just
+        the JRE was installed, Java libraries can be in several locations:
+
+        * ``lib/libjvm.so``
+        * ``jre/lib/libjvm.dylib``
+
+        Search recursively to find the correct library location."""
+
+        return find_libraries(['libjvm'], root=self.home, recursive=True)
+
+    @run_before('install')
+    def macos_check(self):
+        if self.spec.satisfies('platform=darwin'):
+            msg = """\
+Spack's JDK package only supports Linux. If you need to install JDK on macOS,
+manually download the .dmg from:
+
+    {0}
+
+and double-click to install. Once JDK is installed, you can tell Spack where
+to find it like so. To find the JDK installation directory, run:
+
+    $ /usr/libexec/java_home
+
+If you have multiple versions of JDK installed, you can specify a particular
+version to search for with the --version flag. To find the exact version
+number, run:
+
+    $ java -version
+
+If the version number contains a '+' symbol, replace it with '_', otherwise
+Spack will think it is a variant. Add JDK as an external package by running:
+
+    $ spack config edit packages
+
+and adding entries for each installation:
+
+    packages:
+        jdk:
+            paths:
+                jdk@10.0.1_10:    /path/to/jdk/Home
+                jdk@1.7.0_45-b18: /path/to/jdk/Home
+            buildable: False""".format(self.homepage)
+
+            tty.die(msg)
 
     def install(self, spec, prefix):
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix)
 
     def setup_environment(self, spack_env, run_env):
-        run_env.set('JAVA_HOME', self.spec.prefix)
+        """Set JAVA_HOME."""
+
+        run_env.set('JAVA_HOME', self.home)
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        spack_env.set('JAVA_HOME', self.spec.prefix)
+        """Set JAVA_HOME and CLASSPATH.
+
+        CLASSPATH contains the installation prefix for the extension and any
+        other Java extensions it depends on."""
+
+        spack_env.set('JAVA_HOME', self.home)
+
+        class_paths = []
+        for d in dependent_spec.traverse(deptype=('build', 'run', 'test')):
+            if d.package.extends(self.spec):
+                class_paths.extend(find(d.prefix, '*.jar'))
+
+        classpath = os.pathsep.join(class_paths)
+        spack_env.set('CLASSPATH', classpath)
+
+        # For runtime environment set only the path for
+        # dependent_spec and prepend it to CLASSPATH
+        if dependent_spec.package.extends(self.spec):
+            class_paths = find(dependent_spec.prefix, '*.jar')
+            classpath = os.pathsep.join(class_paths)
+            run_env.prepend_path('CLASSPATH', classpath)
+
+    def setup_dependent_package(self, module, dependent_spec):
+        """Allows spec['java'].home to work."""
+
+        self.spec.home = self.home
diff --git a/var/spack/repos/builtin/packages/jellyfish/package.py b/var/spack/repos/builtin/packages/jellyfish/package.py
index e6d65838a1..a90438d633 100644
--- a/var/spack/repos/builtin/packages/jellyfish/package.py
+++ b/var/spack/repos/builtin/packages/jellyfish/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,12 @@ class Jellyfish(AutotoolsPackage):
        DNA."""
 
     homepage = "http://www.cbcb.umd.edu/software/jellyfish/"
-    url      = "http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz"
+    url      = "https://github.com/gmarcais/Jellyfish/releases/download/v2.2.7/jellyfish-2.2.7.tar.gz"
+    list_url = "http://www.cbcb.umd.edu/software/jellyfish/"
 
-    version('1.1.11', 'dc994ea8b0896156500ea8c648f24846')
+    version('2.2.7', 'f741192d9061f28e34cb67c86a1027ab')
+    version('1.1.11', 'dc994ea8b0896156500ea8c648f24846',
+            url='http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz')
 
     depends_on('perl', type=('build', 'run'))
     depends_on('python', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py
index 0534c72ed5..25d75d5541 100644
--- a/var/spack/repos/builtin/packages/jemalloc/package.py
+++ b/var/spack/repos/builtin/packages/jemalloc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/jmol/package.py b/var/spack/repos/builtin/packages/jmol/package.py
index 0688d63816..3ea84eb7bc 100644
--- a/var/spack/repos/builtin/packages/jmol/package.py
+++ b/var/spack/repos/builtin/packages/jmol/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Jmol(Package):
@@ -38,7 +18,7 @@ class Jmol(Package):
     depends_on('java', type='run')
 
     def install(self, spec, prefix):
-        copy_tree('jmol-{0}'.format(self.version), prefix)
+        install_tree('jmol-{0}'.format(self.version), prefix)
 
     def setup_environment(self, spack_env, run_env):
         run_env.prepend_path('PATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/jq/package.py b/var/spack/repos/builtin/packages/jq/package.py
index 1d7d912a91..87db91d292 100644
--- a/var/spack/repos/builtin/packages/jq/package.py
+++ b/var/spack/repos/builtin/packages/jq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/json-c/package.py b/var/spack/repos/builtin/packages/json-c/package.py
index 5076650d69..420fe695e2 100644
--- a/var/spack/repos/builtin/packages/json-c/package.py
+++ b/var/spack/repos/builtin/packages/json-c/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,16 @@ class JsonC(AutotoolsPackage):
     homepage = "https://github.com/json-c/json-c/wiki"
     url      = "https://s3.amazonaws.com/json-c_releases/releases/json-c-0.12.1.tar.gz"
 
+    version('0.13.1', '04969ad59cc37bddd83741a08b98f350')
     version('0.12.1', '55f7853f7d8cf664554ce3fa71bf1c7d')
     version('0.11',   'aa02367d2f7a830bf1e3376f77881e98')
 
     depends_on('autoconf', type='build')
 
     parallel = False
+
+    @when('@0.12.1 %gcc@7:')
+    def patch(self):
+        filter_file('-Wextra',
+                    '-Wextra -Wno-error=implicit-fallthrough',
+                    'Makefile.in')
diff --git a/var/spack/repos/builtin/packages/json-cwx/package.py b/var/spack/repos/builtin/packages/json-cwx/package.py
index bd331acb03..2f3d928bbf 100644
--- a/var/spack/repos/builtin/packages/json-cwx/package.py
+++ b/var/spack/repos/builtin/packages/json-cwx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/json-glib/package.py b/var/spack/repos/builtin/packages/json-glib/package.py
new file mode 100644
index 0000000000..f69aa247fc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/json-glib/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class JsonGlib(AutotoolsPackage):
+    """JSON-GLib is a library for reading and parsing JSON using GLib and
+    GObject data types and API."""
+
+    homepage = "https://developer.gnome.org/json-glib"
+    url      = "https://ftp.gnome.org/pub/gnome/sources/json-glib/1.2/json-glib-1.2.8.tar.xz"
+
+    version('1.2.8', 'ff31e7d0594df44318e12facda3d086e')
+
+    depends_on('glib')
diff --git a/var/spack/repos/builtin/packages/jsoncpp/package.py b/var/spack/repos/builtin/packages/jsoncpp/package.py
index 3b486bf356..f8bf532e53 100644
--- a/var/spack/repos/builtin/packages/jsoncpp/package.py
+++ b/var/spack/repos/builtin/packages/jsoncpp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,8 +23,7 @@ class Jsoncpp(CMakePackage):
                     'MinSizeRel', 'Coverage'))
 
     depends_on('cmake@3.1:', type='build')
-    # TODO: Add a 'test' deptype
-    # depends_on('python', type='test')
+    depends_on('python', type='test')
 
     def cmake_args(self):
         return ['-DBUILD_SHARED_LIBS=ON']
diff --git a/var/spack/repos/builtin/packages/judy/package.py b/var/spack/repos/builtin/packages/judy/package.py
index 87b061bd33..7b17e2e163 100644
--- a/var/spack/repos/builtin/packages/judy/package.py
+++ b/var/spack/repos/builtin/packages/judy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py
index fa6aaf3f95..c9e3a23cb2 100644
--- a/var/spack/repos/builtin/packages/julia/package.py
+++ b/var/spack/repos/builtin/packages/julia/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
@@ -30,18 +11,18 @@ import sys
 
 class Julia(Package):
     """The Julia Language: A fresh approach to technical computing"""
+
     homepage = "http://julialang.org"
     url      = "https://github.com/JuliaLang/julia/releases/download/v0.4.3/julia-0.4.3-full.tar.gz"
+    git      = "https://github.com/JuliaLang/julia.git"
 
-    version('master',
-            git='https://github.com/JuliaLang/julia.git', branch='master')
-    version('release-0.5',
-            git='https://github.com/JuliaLang/julia.git', branch='release-0.5')
-    version('0.5.2', '8c3fff150a6f96cf0536fb3b4eaa5cbb', preferred=True)
+    version('master', branch='master')
+    version('0.6.2', '255d80bc8d56d5f059fe18f0798e32f6')
+    version('release-0.5', branch='release-0.5')
+    version('0.5.2', '8c3fff150a6f96cf0536fb3b4eaa5cbb')
     version('0.5.1', 'bce119b98f274e0f07ce01498c463ad5')
     version('0.5.0', 'b61385671ba74767ab452363c43131fb')
-    version('release-0.4',
-            git='https://github.com/JuliaLang/julia.git', branch='release-0.4')
+    version('release-0.4', branch='release-0.4')
     version('0.4.7', '75a7a7dd882b7840829d8f165e9b9078')
     version('0.4.6', 'd88db18c579049c23ab8ef427ccedf5d')
     version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6')
@@ -66,7 +47,7 @@ class Julia(Package):
     # Build-time dependencies:
     # depends_on("awk")
     depends_on("m4", type="build")
-    # depends_on("pkg-config")
+    # depends_on("pkgconfig")
 
     # Combined build-time and run-time dependencies:
     # (Yes, these are run-time dependencies used by Julia's package manager.)
diff --git a/var/spack/repos/builtin/packages/k8/package.py b/var/spack/repos/builtin/packages/k8/package.py
new file mode 100644
index 0000000000..efdcb06af9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/k8/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import sys
+import os
+from spack import *
+
+
+class K8(Package):
+    """K8 is a Javascript shell based on Google's V8 Javascript engine."""
+
+    homepage = "https://github.com/attractivechaos/k8"
+    url      = "https://github.com/attractivechaos/k8/releases/download/v0.2.4/k8-0.2.4.tar.bz2"
+
+    version('0.2.4', 'edc5579ff18842a2a59aa92ce8bab8b4')
+
+    depends_on('zlib', type='run')
+
+    def install(self, spec, prefix):
+        if (sys.platform == 'darwin'):
+            os.rename('k8-Darwin', 'k8')
+
+        if (sys.platform != 'darwin'):
+            os.rename('k8-Linux', 'k8')
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/kahip/package.py b/var/spack/repos/builtin/packages/kahip/package.py
index 30565a5180..29c6adae77 100644
--- a/var/spack/repos/builtin/packages/kahip/package.py
+++ b/var/spack/repos/builtin/packages/kahip/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# Copyright (c) 2017 Christian Schulz
-# Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is released as part of Spack under the LGPL license
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE file for the LLNL notice and LGPL.
-#
-# License
-# -------
-# 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import os
@@ -44,8 +24,9 @@ class Kahip(SConsPackage):
 
     homepage  = 'http://algo2.iti.kit.edu/documents/kahip/index.html'
     url       = 'http://algo2.iti.kit.edu/schulz/software_releases/KaHIP_2.00.tar.gz'
+    git       = 'https://github.com/schulzchristian/KaHIP.git'
 
-    version('develop', git='https://github.com/schulzchristian/KaHIP.git')
+    version('develop', branch='master')
     version('2.00', '0a66b0a604ad72cfb7e3dce00e2c9fdfac82b855')
 
     depends_on('argtable')
diff --git a/var/spack/repos/builtin/packages/kaiju/package.py b/var/spack/repos/builtin/packages/kaiju/package.py
new file mode 100644
index 0000000000..621c81969c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kaiju/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Kaiju(MakefilePackage):
+    """Kaiju is a program for the taxonomic classification
+    of high-throughput sequencing reads."""
+
+    homepage = "https://github.com/bioinformatics-centre/kaiju"
+    url      = "https://github.com/bioinformatics-centre/kaiju/archive/v1.6.2.zip"
+
+    version('1.6.2', '0bd85368954837aa31f3de8b87ea410b')
+
+    build_directory = 'src'
+
+    depends_on('perl-io-compress', type='run')
+    depends_on('py-htseq', type='run')
+
+    def edit(self, spec, prefix):
+        # Replace ftp:// with https://
+        makedb = FileFilter('util/makeDB.sh')
+        makedb.filter('ftp://', 'https://', string=True)
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/kaks-calculator/package.py b/var/spack/repos/builtin/packages/kaks-calculator/package.py
index 622e499e7f..f9244acc3b 100644
--- a/var/spack/repos/builtin/packages/kaks-calculator/package.py
+++ b/var/spack/repos/builtin/packages/kaks-calculator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/kaldi/package.py b/var/spack/repos/builtin/packages/kaldi/package.py
index bb2481d879..6b3457f12a 100644
--- a/var/spack/repos/builtin/packages/kaldi/package.py
+++ b/var/spack/repos/builtin/packages/kaldi/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 from os.path import join
 from fnmatch import fnmatch
 import os
@@ -35,11 +15,11 @@ class Kaldi(Package):    # Does not use Autotools
     Kaldi is intended for use by speech recognition researchers."""
 
     homepage = "https://github.com/kaldi-asr/kaldi"
-    url      = "https://github.com/kaldi-asr/kaldi/archive/master.zip"
+    git      = "https://github.com/kaldi-asr/kaldi.git"
 
-    version('master', git='https://github.com/kaldi-asr/kaldi.git')
-    version('c024e8', git='https://github.com/kaldi-asr/kaldi.git',
-            commit='c024e8aa0a727bf76c91a318f76a1f8b0b59249e')
+    version('master')
+    version('2018-07-11', commit='6f2140b032b0108bc313eefdca65151289642773')
+    version('2015-10-07', commit='c024e8aa0a727bf76c91a318f76a1f8b0b59249e')
 
     variant('shared', default=True,
             description='build shared libraries')
@@ -53,18 +33,16 @@ class Kaldi(Package):    # Does not use Autotools
     depends_on('sph2pipe', type='run')
     depends_on('sctk', type='run')
     depends_on('speex', type='run')
-    depends_on('openfst@1.4.1-patch', when='@c024e8')
+    depends_on('openfst@1.4.1-patch', when='@2015-10-07')
+    depends_on('openfst@1.6.0:', when='@2018-07-11')
     depends_on('openfst')
 
-    patch('openfst-1.4.1.patch', when='@c024e8')
+    patch('openfst-1.4.1.patch', when='@2015-10-07')
 
     def install(self, spec, prefix):
         configure_args = ['--fst-root=' + spec['openfst'].prefix]
-
-        if spec.satisfies('c024e8'):
-            configure_args.append('--speex-root=' + spec['speex'].prefix)
-            configure_args.append('--fst-version=' +
-                                  str(spec['openfst'].version))
+        configure_args.append('--fst-version=' + str(spec['openfst'].version))
+        configure_args.append('--speex-root=' + spec['speex'].prefix)
 
         if '~shared' in spec:
             configure_args.append('--static')
@@ -96,13 +74,18 @@ class Kaldi(Package):    # Does not use Autotools
             make()
 
             mkdirp(prefix.bin)
-            for root, dirs, files in os.walk('bin'):
+            for root, dirs, files in os.walk('.'):
                 for name in files:
+                    if name.endswith(".so") or name.endswith(".cc") \
+                            or name.endswith(".pptx"):
+                        continue
+                    if "configure" is name:
+                        continue
                     if os.access(join(root, name), os.X_OK):
                         install(join(root, name), prefix.bin)
 
             mkdir(prefix.lib)
-            copy_tree('lib', prefix.lib)
+            install_tree('lib', prefix.lib)
 
             for root, dirs, files in os.walk('.'):
                 for name in files:
diff --git a/var/spack/repos/builtin/packages/kallisto/package.py b/var/spack/repos/builtin/packages/kallisto/package.py
index 1d0cb35a18..c537ca6ad4 100644
--- a/var/spack/repos/builtin/packages/kallisto/package.py
+++ b/var/spack/repos/builtin/packages/kallisto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/karma/package.py b/var/spack/repos/builtin/packages/karma/package.py
new file mode 100644
index 0000000000..b1a45f6919
--- /dev/null
+++ b/var/spack/repos/builtin/packages/karma/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Karma(Package):
+    """Karma is a toolkit for interprocess communications, authentication,
+    encryption, graphics display, user interface and manipulating the Karma
+    network data structure. It contains KarmaLib (the structured libraries
+    and API) and a large number of modules (applications)
+    to perform many standard tasks. """
+
+    homepage = "https://www.atnf.csiro.au/computing/software/karma/"
+    url      = "ftp://ftp.atnf.csiro.au/pub/software/karma/karma-1.7.25-common.tar.bz2"
+
+    version('1.7.25-common', sha256='afda682d79c0923df5a6c447a32b09294da1582933abae3205c008104da54fbd')
+
+    depends_on('libx11', type=('build', 'run'))
+    depends_on('libxaw', type=('build', 'run'))
+
+    phases = ['install']
+
+    resource(
+                name='karma-linux',
+                url='ftp://ftp.atnf.csiro.au/pub/software/karma/karma-1.7.25-amd64_Linux_libc6.3.tar.bz2',
+                sha256='effc3ed61c28b966b357147d90357d03c22d743c6af6edb49a863c6eb625a441',
+                destination='./'
+               )
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('LIBRARY_PATH', self.prefix.lib)
+        run_env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib)
+
+    def install(self, spec, prefix):
+        install_tree('./karma-1.7.25/amd64_Linux_libc6.3/bin', prefix.bin)
+        install_tree('./karma-1.7.25/amd64_Linux_libc6.3/lib', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/kbproto/package.py b/var/spack/repos/builtin/packages/kbproto/package.py
index fa210e9101..05b6f5e665 100644
--- a/var/spack/repos/builtin/packages/kbproto/package.py
+++ b/var/spack/repos/builtin/packages/kbproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Kbproto(AutotoolsPackage):
 
     version('1.0.7', '19acc5f02ae80381e216f443134e0bbb')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/kdiff3/package.py b/var/spack/repos/builtin/packages/kdiff3/package.py
index 4d60416497..93f1e097fd 100644
--- a/var/spack/repos/builtin/packages/kdiff3/package.py
+++ b/var/spack/repos/builtin/packages/kdiff3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/kealib/cmake.patch b/var/spack/repos/builtin/packages/kealib/cmake.patch
new file mode 100644
index 0000000000..97d7f8cc27
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kealib/cmake.patch
@@ -0,0 +1,73 @@
+# HG changeset patch
+# User Sam Gillingham <gillingham.sam@gmail.com>
+# Date 1526963592 -36000
+# Node ID d103fef327d47ba31826007f9c9ab02c1f354330
+# Parent  a4e63dbb642c83516104ea82cec0e45c4caffd54
+More work on making out of tree builds work
+
+diff --git a/trunk/CMakeLists.txt b/trunk/CMakeLists.txt
+--- a/trunk/CMakeLists.txt
++++ b/trunk/CMakeLists.txt
+@@ -20,14 +20,6 @@
+   set (WINDOWS ${WIN32})
+ endif()
+ 
+-set (PROJECT_BINARY_DIR bin)
+-set (PROJECT_LIBRARY_DIR lib)
+-set (PROJECT_SOURCE_DIR src)
+-set (PROJECT_TEST_DIR tests)
+-set (PROJECT_HEADER_DIR include)
+-set (PROJECT_TOOLS_DIR tools)
+-set (PROJECT_GDAL_DIR gdal)
+-
+ # The version number.
+ set (LIBKEA_HG_VERSION 289)
+ set (LIBKEA_VERSION_MAJOR 1)
+@@ -160,8 +152,8 @@
+ 
+ ###############################################################################
+ # Setup configure file
+-configure_file ( "${PROJECT_HEADER_DIR}/kea-config.h.in" "${PROJECT_HEADER_DIR}/libkea/kea-config.h" )
+-configure_file ( "${PROJECT_TOOLS_DIR}/kea-config.in" "${PROJECT_BINARY_DIR}/kea-config" )
++configure_file ( "${PROJECT_SOURCE_DIR}/include/kea-config.h.in" "${PROJECT_BINARY_DIR}/include/libkea/kea-config.h" )
++configure_file ( "${PROJECT_SOURCE_DIR}/tools/kea-config.in" "${PROJECT_BINARY_DIR}/bin/kea-config" )
+ ###############################################################################
+ 
+ ###############################################################################
+@@ -173,11 +165,12 @@
+ ###############################################################################
+ # Build library
+ 
+-include_directories ("${PROJECT_HEADER_DIR}")
++include_directories ("${PROJECT_SOURCE_DIR}/include")
++include_directories ("${PROJECT_BINARY_DIR}/include") # for kea-config.h
+ include_directories(${HDF5_INCLUDE_DIR})
+-add_subdirectory ("${PROJECT_SOURCE_DIR}")
++add_subdirectory ("${PROJECT_SOURCE_DIR}/src")
+ if (LIBKEA_WITH_GDAL)
+-	add_subdirectory ("${PROJECT_GDAL_DIR}")
++	add_subdirectory ("${PROJECT_SOURCE_DIR}/gdal")
+ endif(LIBKEA_WITH_GDAL)
+ ###############################################################################
+ 
+@@ -191,7 +184,7 @@
+ ###############################################################################
+ # Installation
+ 
+-install (FILES "${PROJECT_BINARY_DIR}/kea-config" DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
++install (FILES "${PROJECT_BINARY_DIR}/bin/kea-config" DESTINATION bin PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+ ###############################################################################
+ 
+ ###############################################################################
+diff --git a/trunk/src/CMakeLists.txt b/trunk/src/CMakeLists.txt
+--- a/trunk/src/CMakeLists.txt
++++ b/trunk/src/CMakeLists.txt
+@@ -38,7 +38,7 @@
+ ###############################################################################
+ # Testing
+ # exe needs to be in 'src' otherwise it doesn't work
+-add_executable (test1 ${PROJECT_TEST_DIR}/test1.cpp)
++add_executable (test1 ${PROJECT_SOURCE_DIR}/src/tests/test1.cpp)
+ target_link_libraries (test1 ${LIBKEA_LIB_NAME})
+ if(NOT WIN32)
+     # set rpath so the text exe finds hdf5. Really only needed
diff --git a/var/spack/repos/builtin/packages/kealib/package.py b/var/spack/repos/builtin/packages/kealib/package.py
index 3b24a08393..92ca45f5ba 100644
--- a/var/spack/repos/builtin/packages/kealib/package.py
+++ b/var/spack/repos/builtin/packages/kealib/package.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Kealib(CMakePackage):
-    """An HDF5 Based Raster File Format
+    """An HDF5 Based Raster File Format.
 
     KEALib provides an implementation of the GDAL data model.
     The format supports raster attribute tables, image pyramids,
@@ -41,18 +22,39 @@ class Kealib(CMakePackage):
 
     Development work on this project has been funded by Landcare Research.
     """
-    homepage = "http://kealib.org/"
-    url      = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.5.tar.gz"
+    homepage = "http://www.kealib.org/"
+    url      = "https://bitbucket.org/chchrsc/kealib/get/kealib-1.4.10.tar.gz"
+    hg       = "https://bitbucket.org/chchrsc/kealib"
 
-    version('1.4.5', '112e9c42d980b2d2987a3c15d0833a5d')
+    version('develop', hg=hg)
+    version('1.4.10', '5684aeb2085a67a4270c73e79d4ab768')
+    version('1.4.9',  'a095d0b9d6de1d609ffaf242e00cc2b6')
+    version('1.4.8',  '1af2514c908f9168ff6665cc012815ad')
+    version('1.4.7',  '6139e31e50f552247ddf98f489948893')
 
-    depends_on('hdf5')
     depends_on('cmake@2.8.10:', type='build')
+    depends_on('hdf5+cxx+hl')
+
+    patch('cmake.patch', when='@1.4.7')
 
-    root_cmakelists_dir = 'trunk'
+    @property
+    def root_cmakelists_dir(self):
+        if self.version >= Version('1.4.9'):
+            return '.'
+        else:
+            return 'trunk'
 
     def cmake_args(self):
-        return [
-            '-DHDF5_INCLUDE_DIR=%s' % self.spec['hdf5'].prefix.include,
-            '-DHDF5_LIB_PATH=%s' % self.spec['hdf5'].prefix.lib,
-        ]
+        spec = self.spec
+
+        if self.version >= Version('1.4.9'):
+            return [
+                '-DHDF5_ROOT={0}'.format(spec['hdf5'].prefix)
+            ]
+        else:
+            return [
+                '-DHDF5_INCLUDE_DIR={0}'.format(
+                    spec['hdf5'].headers.directories[0]),
+                '-DHDF5_LIB_PATH={0}'.format(
+                    spec['hdf5'].libs.directories[0])
+            ]
diff --git a/var/spack/repos/builtin/packages/kentutils/package.py b/var/spack/repos/builtin/packages/kentutils/package.py
index 3fdd495a17..11680cecec 100644
--- a/var/spack/repos/builtin/packages/kentutils/package.py
+++ b/var/spack/repos/builtin/packages/kentutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Kentutils(MakefilePackage):
     """Jim Kent command line bioinformatic utilities"""
 
     homepage = "https://github.com/ENCODE-DCC/kentUtils"
-    url      = "https://github.com/ENCODE-DCC/kentUtils"
+    git      = "https://github.com/ENCODE-DCC/kentUtils.git"
 
-    version('302.1', git='https://github.com/ENCODE-DCC/kentUtils.git', commit='d8376c5d52a161f2267346ed3dc94b5dce74c2f9')
+    version('302.1', commit='d8376c5d52a161f2267346ed3dc94b5dce74c2f9')
 
     depends_on('libpng')
     depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/kibana/package.py b/var/spack/repos/builtin/packages/kibana/package.py
new file mode 100644
index 0000000000..c47e75bd5b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kibana/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Kibana(Package):
+    """Kibana lets you visualize your Elasticsearch data and navigate the
+    Elastic Stack"""
+
+    homepage = "https://www.elastic.co/products/kibana"
+    url      = "https://artifacts.elastic.co/downloads/kibana/kibana-6.4.0-linux-x86_64.tar.gz"
+
+    version('6.4.0', sha256='df2056105a08c206a1adf9caed09a152a53429a0f1efc1ba3ccd616092d78aee')
+
+    depends_on('jdk', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('.', join_path(prefix, '.'))
diff --git a/var/spack/repos/builtin/packages/kim-api/package.py b/var/spack/repos/builtin/packages/kim-api/package.py
new file mode 100644
index 0000000000..f8141813f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kim-api/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class KimApi(CMakePackage):
+    """OpenKIM is an online framework for making molecular simulations
+       reliable, reproducible, and portable. Computer implementations of
+       inter-atomic models are archived in OpenKIM, verified for coding
+       integrity, and tested by computing their predictions for a variety
+       of material properties. Models conforming to the KIM application
+       programming interface (API) work seamlessly with major simulation
+       codes that have adopted the KIM API standard.
+    """
+    homepage = "https://openkim.org/"
+    git      = "https://github.com/openkim/kim-api"
+
+    version('develop', branch='master')
+    version('2.0rc1', commit="c2ab409ec0154ebd85d20a0a1a0bd2ba6ea95a9c") 
+
+    def cmake_args(self):
+        args = ['-DBUILD_MODULES=OFF']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/kmergenie/package.py b/var/spack/repos/builtin/packages/kmergenie/package.py
index 7f64892d70..e3c122bdad 100644
--- a/var/spack/repos/builtin/packages/kmergenie/package.py
+++ b/var/spack/repos/builtin/packages/kmergenie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/kokkos/package.py b/var/spack/repos/builtin/packages/kokkos/package.py
index e1ebf79eca..6de38510c4 100644
--- a/var/spack/repos/builtin/packages/kokkos/package.py
+++ b/var/spack/repos/builtin/packages/kokkos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,13 +12,121 @@ class Kokkos(Package):
 
     homepage = "https://github.com/kokkos/kokkos"
     url      = "https://github.com/kokkos/kokkos/archive/2.03.00.tar.gz"
+    git      = "https://github.com/kokkos/kokkos.git"
 
+    version('develop', branch='develop')
+    version('2.7.00',  'b357f9374c1008754babb4495f95e392')
+    version('2.5.00',  '2db83c56587cb83b772d0c81a3228a21')
+    version('2.04.11', 'd4849cee6eb9001d61c30f1d9fe74336')
+    version('2.04.04', '2c6d1c2569b91c9fcd4117296438e65c')
+    version('2.04.00', 'd99ac790ff5f29545d8eb53de90c0a85')
+    version('2.03.13', '3874a159a517384541ea5b52f85501ba')
+    version('2.03.05', '8727d783453f719eec392e10a36b49fd')
     version('2.03.00', 'f205d659d4304747759fabfba32d43c3')
+    version('2.02.15', 'de41e38f452a50bb03363c519fe20769')
+    version('2.02.07', 'd5baeea70109249f7dca763074ffb202')
 
+    variant('serial', default=True, description="enable Serial backend (default)")
     variant('qthreads', default=False, description="enable Qthreads backend")
     variant('cuda', default=False, description="enable Cuda backend")
+    variant('openmp', default=False, description="enable OpenMP backend")
+
+    # Compilation options
+    variant('pic', default=False,
+            description="enable position independent code (-fPIC flag)")
+
+    # Kokkos options
+    variant('aggressive_vectorization', default=False,
+            description="set aggressive_vectorization Kokkos option")
+    variant('disable_profiling', default=False,
+            description="set disable_profiling Kokkos option")
+    variant('disable_dualview_modify_check', default=False,
+            description="set disable_dualview_modify_check Kokkos option")
+    variant('enable_profile_load_print', default=False,
+            description="set enable_profile_load_print Kokkos option")
+    variant('compiler_warnings', default=False,
+            description="set compiler_warnings Kokkos option")
+    variant('disable_deprecated_code', default=False,
+            description="set disable_deprecated_code Kokkos option")
+    variant('enable_eti', default=False,
+            description="set enable_eti Kokkos option")
+
+    # CUDA options
+    variant('force_uvm', default=False,
+            description="set force_uvm Kokkos CUDA option")
+    variant('use_ldg', default=False,
+            description="set use_ldg Kokkos CUDA option")
+    variant('rdc', default=False,
+            description="set rdc Kokkos CUDA option")
+    variant('enable_lambda', default=False,
+            description="set enable_lambda Kokkos CUDA option")
+
+    gpu_values = ('Kepler30', 'Kepler32', 'Kepler35', 'Kepler37',
+                  'Maxwell50', 'Maxwell52', 'Maxwell53',
+                  'Pascal60', 'Pascal61',
+                  'Volta70', 'Volta72')
+
+    cuda_options = ('force_uvm', 'use_ldg', 'rdc', 'enable_lambda')
+
+    # Host architecture variant
+    variant(
+        'host_arch',
+        default=None,
+        values=('AMDAVX', 'ARMv80', 'ARMv81', 'ARMv8-ThunderX',
+                'Power7', 'Power8', 'Power9',
+                'WSM', 'SNB', 'HSW', 'BDW', 'SKX', 'KNC', 'KNL'),
+        description='Set the host architecture to use'
+    )
 
-    depends_on('hwloc')
+    # GPU architecture variant
+    variant(
+        'gpu_arch',
+        default=None,
+        values=gpu_values,
+        description='Set the GPU architecture to use'
+    )
+
+    # Checks on Kokkos version and Kokkos options
+    conflicts('+aggressive_vectorization', when='@:2.0.99',)
+    conflicts('+disable_profiling', when='@:2.0.99',)
+    conflicts('+disable_dualview_modify_check', when='@:2.03.04',)
+    conflicts('+enable_profile_load_print', when='@:2.03.04',)
+    conflicts('+compiler_warnings', when='@:2.03.14',)
+    conflicts('+disable_deprecated_code', when='@:2.5.99',)
+    conflicts('+enable_eti', when='@:2.6.99',)
+
+    # Check that we haven't specified a gpu architecture
+    # without specifying CUDA
+    for p in gpu_values:
+        conflicts('gpu_arch={0}'.format(p), when='~cuda',
+            msg='Must specify CUDA backend to use a GPU architecture.')
+
+    # Check that we haven't specified a Kokkos CUDA option
+    # without specifying CUDA
+    conflicts('+force_uvm', when='~cuda',
+        msg='Must enable CUDA to use force_uvm.')
+    conflicts('+use_ldg', when='~cuda',
+        msg='Must enable CUDA to use use_ldg.')
+    conflicts('+rdc', when='~cuda',
+        msg='Must enable CUDA to use rdc.')
+    conflicts('+enable_lambda', when='~cuda',
+        msg='Must enable CUDA to use enable_lambda.')
+
+    # Check that we haven't asked for a GPU architecture that
+    # the revision of kokkos does not support
+    conflicts('gpu_arch=Volta70', when='@:2.5.99')
+    conflicts('gpu_arch=Volta72', when='@:2.5.99')
+
+    # conflicts on kokkos version and cuda enabled
+    # see kokkos issue #1296
+    # https://github.com/kokkos/kokkos/issues/1296
+    conflicts('+cuda', when='@2.5.00:develop',
+        msg='Kokkos build system has issue when CUDA enabled'
+        ' in version 2.5.00 through 2.7.00, and develop until '
+        'issue #1296 is resolved.')
+
+    # Specify that v1.x is required as v2.x has API changes
+    depends_on('hwloc@:1')
     depends_on('qthreads', when='+qthreads')
     depends_on('cuda', when='+cuda')
 
@@ -48,13 +137,67 @@ class Kokkos(Package):
             g_args = [
                 '--prefix=%s' % prefix,
                 '--with-hwloc=%s' % spec['hwloc'].prefix,
-                '--with-serial',
-                '--with-openmp',
             ]
-            if 'qthreads' in spec:
+            arch_args = []
+            kokkos_options_args = []
+            cuda_options_args = []
+
+            # PIC
+            if '+pic' in spec:
+                g_args.append('--cxxflags=-fPIC')
+
+            # Backends
+            if '+serial' in spec:
+                g_args.append('--with-serial')
+            if '+openmp' in spec:
+                g_args.append('--with-openmp')
+            if '+qthreads' in spec:
                 g_args.append('--with-qthreads=%s' % spec['qthreads'].prefix)
-            if 'cuda' in spec:
+            if '+cuda' in spec:
                 g_args.append('--with-cuda=%s' % spec['cuda'].prefix)
+            # Host architectures
+            host_arch = spec.variants['host_arch'].value
+            # GPU architectures
+            gpu_arch  = spec.variants['gpu_arch'].value
+            if host_arch:
+                arch_args.append(host_arch)
+            if gpu_arch:
+                arch_args.append(gpu_arch)
+            # Combined architecture flags
+            if arch_args:
+                g_args.append('--arch={0}'.format(','.join(arch_args)))
+
+            # CUDA options
+            if '+force_uvm' in spec:
+                cuda_options_args.append('force_uvm')
+            if '+use_ldg' in spec:
+                cuda_options_args.append('use_ldg')
+            if '+rdc' in spec:
+                cuda_options_args.append('rdc')
+            if '+enable_lambda' in spec:
+                cuda_options_args.append('enable_lambda')
+            if cuda_options_args:
+                g_args.append('--with-cuda-options={0}'
+                              .format(','.join(cuda_options_args)))
+
+            # Kokkos options
+            if '+aggressive_vectorization' in spec:
+                kokkos_options_args.append('aggressive_vectorization')
+            if '+disable_profiling' in spec:
+                kokkos_options_args.append('disable_profiling')
+            if '+disable_dualview_modify_check' in spec:
+                kokkos_options_args.append('disable_dualview_modify_check')
+            if '+enable_profile_load_print' in spec:
+                kokkos_options_args.append('enable_profile_load_print')
+            if '+compiler_warnings' in spec:
+                kokkos_options_args.append('compiler_warnings')
+            if '+disable_deprecated_code' in spec:
+                kokkos_options_args.append('disable_deprecated_code')
+            if '+enable_eti' in spec:
+                kokkos_options_args.append('enable_eti')
+            if kokkos_options_args:
+                g_args.append('--with-options={0}'
+                              .format(','.join(kokkos_options_args)))
 
             generate(*g_args)
             make()
diff --git a/var/spack/repos/builtin/packages/kraken/package.py b/var/spack/repos/builtin/packages/kraken/package.py
index 3994c8c138..4c32e153da 100644
--- a/var/spack/repos/builtin/packages/kraken/package.py
+++ b/var/spack/repos/builtin/packages/kraken/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/krb5/package.py b/var/spack/repos/builtin/packages/krb5/package.py
new file mode 100644
index 0000000000..70c7b4aac4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/krb5/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Krb5(AutotoolsPackage):
+    """Network authentication protocol"""
+
+    homepage = "https://kerberos.org"
+    url      = "https://kerberos.org/dist/krb5/1.16/krb5-1.16.1.tar.gz"
+
+    version('1.16.1', '848e9b80d6aaaa798e3f3df24b83c407')
+
+    depends_on('openssl')
+
+    configure_directory = 'src'
+    build_directory = 'src'
+
+    def configure_args(self):
+        args = ['--disable-debug',
+                '--disable-dependency-tracking',
+                '--disable-silent-rules',
+                '--without-system-verto']
+        return args
diff --git a/var/spack/repos/builtin/packages/krims/package.py b/var/spack/repos/builtin/packages/krims/package.py
index f64092de6c..fe40186d21 100644
--- a/var/spack/repos/builtin/packages/krims/package.py
+++ b/var/spack/repos/builtin/packages/krims/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,15 +10,16 @@ class Krims(CMakePackage):
     """The bucket of Krimskrams every C or C++ project needs"""
 
     homepage = "http://lazyten.org/krims"
-    url = "https://github.com/lazyten/krims/archive/v0.2.1.tar.gz"
+    url      = "https://github.com/lazyten/krims/archive/v0.2.1.tar.gz"
+    git      = "https://github.com/lazyten/krims.git"
+
     maintainers = ['mfherbst']
 
     #
     # Versions
     #
+    version("develop", branch="master")
     version("0.2.1", "bf219656fd81c342a4782bad7d7beed0")
-    version("develop", git="https://github.com/lazyten/krims.git",
-            branch="master")
 
     #
     # Variants
diff --git a/var/spack/repos/builtin/packages/kripke/package.py b/var/spack/repos/builtin/packages/kripke/package.py
index d2030cbcfe..c8614d933c 100644
--- a/var/spack/repos/builtin/packages/kripke/package.py
+++ b/var/spack/repos/builtin/packages/kripke/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,8 @@ class Kripke(CMakePackage):
     """Kripke is a simple, scalable, 3D Sn deterministic particle
        transport proxy/mini app.
     """
-    homepage = "https://codesign.llnl.gov/kripke.php"
-    url      = "https://codesign.llnl.gov/downloads/kripke-openmp-1.1.tar.gz"
+    homepage = "https://computation.llnl.gov/projects/co-design/kripke"
+    url      = "https://computation.llnl.gov/projects/co-design/download/kripke-openmp-1.1.tar.gz"
 
     tags = ['proxy-app']
     version('1.1', '7fe6f2b26ed983a6ce5495ab701f85bf')
diff --git a/var/spack/repos/builtin/packages/kvasir-mpl/package.py b/var/spack/repos/builtin/packages/kvasir-mpl/package.py
new file mode 100644
index 0000000000..7561fc17cc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kvasir-mpl/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class KvasirMpl(Package):
+    """Kvasir metaprogramming library"""
+
+    homepage = "https://github.com/kvasir-io/mpl"
+    git      = "https://github.com/kvasir-io/mpl.git"
+
+    version('develop', branch='development')
+
+    def install(self, spec, prefix):
+        install_tree('src', prefix.include)
diff --git a/var/spack/repos/builtin/packages/kvtree/package.py b/var/spack/repos/builtin/packages/kvtree/package.py
new file mode 100644
index 0000000000..8f1c64607d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/kvtree/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Kvtree(CMakePackage):
+    """KVTree provides a fully extensible C datastructure modeled after perl
+    hashes."""
+
+    homepage = "https://github.com/ECP-VeloC/KVTree"
+    url      = "https://github.com/ECP-VeloC/KVTree/archive/v1.0.1.zip"
+    git      = "https://github.com/ecp-veloc/kvtree.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('1.0.2', sha256='6b54f4658e5ebab747c0c2472b1505ac1905eefc8a0b2a97d8776f800ee737a3')
+
+    variant('mpi', default=True, description="Build with MPI message packing")
+    depends_on('mpi', when='+mpi')
+
+    def cmake_args(self):
+        args = []
+        if self.spec.satisfies('+mpi'):
+            args.append("-DMPI=ON")
+            args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        else:
+            args.append("-DMPI=OFF")
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DKVTREE_LINK_STATIC=ON")
+        return args
diff --git a/var/spack/repos/builtin/packages/laghos/package.py b/var/spack/repos/builtin/packages/laghos/package.py
index 0e889782e6..deab6d8f0b 100644
--- a/var/spack/repos/builtin/packages/laghos/package.py
+++ b/var/spack/repos/builtin/packages/laghos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,15 +14,21 @@ class Laghos(MakefilePackage):
     """
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    homepage = "https://codesign.llnl.gov/laghos.php"
-    git      = "https://github.com/CEED/Laghos"
+    homepage = "https://computation.llnl.gov/projects/co-design/laghos"
     url      = "https://github.com/CEED/Laghos/archive/v1.0.tar.gz"
+    git      = "https://github.com/CEED/Laghos.git"
+
+    version('develop', branch='master')
+    version('1.1', sha256='53b9bfe2af263c63eb4544ca1731dd26f40b73a0d2775a9883db51821bf23b7f')
+    version('1.0', '4c091e115883c79bed81c557ef16baff')
+
+    variant('metis', default=True, description='Enable/disable METIS support')
 
-    version('1.0', '107c2f693936723e764a4d404d33d44a')
-    version('develop', git=git, branch='master')
+    depends_on('mfem@develop+mpi+metis', when='@develop+metis')
+    depends_on('mfem@develop+mpi~metis', when='@develop~metis')
 
-    depends_on('mpi')
-    depends_on('mfem@laghos-v1.0', when='@1.0')
+    depends_on('mfem@laghos-v1.0,3.3.2:+mpi+metis', when='@1.0:+metis')
+    depends_on('mfem@laghos-v1.0,3.3.2:+mpi~metis', when='@1.0:~metis')
 
     @property
     def build_targets(self):
@@ -49,13 +36,24 @@ class Laghos(MakefilePackage):
         spec = self.spec
 
         targets.append('MFEM_DIR=%s' % spec['mfem'].prefix)
-        targets.append('CONFIG_MK=%s' % join_path(spec['mfem'].prefix,
-                       'share/mfem/config.mk'))
-        targets.append('TEST_MK=%s' % join_path(spec['mfem'].prefix,
-                       'share/mfem/test.mk'))
+        targets.append('CONFIG_MK=%s' % spec['mfem'].package.config_mk)
+        targets.append('TEST_MK=%s' % spec['mfem'].package.test_mk)
+        targets.append('CXX=%s' % spec['mpi'].mpicxx)
 
         return targets
 
+    # See lib/spack/spack/build_systems/makefile.py
+    def check(self):
+        targets = []
+        spec = self.spec
+
+        targets.append('MFEM_DIR=%s' % spec['mfem'].prefix)
+        targets.append('CONFIG_MK=%s' % spec['mfem'].package.config_mk)
+        targets.append('TEST_MK=%s' % spec['mfem'].package.test_mk)
+
+        with working_dir(self.build_directory):
+            make('test', *targets)
+
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         install('laghos', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py
index 7eeea42773..5743d39189 100644
--- a/var/spack/repos/builtin/packages/lammps/package.py
+++ b/var/spack/repos/builtin/packages/lammps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-#
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import datetime as dt
 
@@ -35,10 +16,17 @@ class Lammps(CMakePackage):
     """
     homepage = "http://lammps.sandia.gov/"
     url      = "https://github.com/lammps/lammps/archive/patch_1Sep2017.tar.gz"
+    git      = "https://github.com/lammps/lammps.git"
+
+    tags = ['ecp', 'ecp-apps']
 
+    version('develop', branch='master')
+    version('20180822', sha256='9f8942ca3f8e81377ae88ccfd075da4e27d0dd677526085e1a807777c8324074')
+    version('20180629', '6d5941863ee25ad2227ff3b7577d5e7c')
+    version('20180316', '25bad35679583e0dd8cb8753665bb84b')
+    version('20180222', '4d0513e3183bd57721814d217fdaf957')
     version('20170922', '4306071f919ec7e759bda195c26cfd9a')
     version('20170901', '767e7f07289663f033474dfe974974e7')
-    version('develop', git='https://github.com/lammps/lammps', branch='master')
 
     def url_for_version(self, version):
         vdate = dt.datetime.strptime(str(version), "%Y%m%d")
@@ -68,7 +56,9 @@ class Lammps(CMakePackage):
     depends_on('netcdf+mpi', when='+user-netcdf')
     depends_on('blas', when='+user-atc')
     depends_on('lapack', when='+user-atc')
-    depends_on('latte', when='+latte')
+    depends_on('latte@1.0.1', when='@:20180222+latte')
+    depends_on('latte@1.1.1:', when='@20180316:20180628+latte')
+    depends_on('latte@1.2.1:', when='@20180629:+latte')
     depends_on('blas', when='+latte')
     depends_on('lapack', when='+latte')
     depends_on('python', when='+python')
@@ -76,7 +66,7 @@ class Lammps(CMakePackage):
     depends_on('mpi', when='+user-h5md')
     depends_on('hdf5', when='+user-h5md')
 
-    conflicts('+body', when='+poems')
+    conflicts('+body', when='+poems@:20180628')
     conflicts('+latte', when='@:20170921')
     conflicts('+python', when='~lib')
     conflicts('+qeq', when='~manybody')
@@ -93,15 +83,25 @@ class Lammps(CMakePackage):
     def cmake_args(self):
         spec = self.spec
 
+        mpi_prefix = 'ENABLE'
+        pkg_prefix = 'ENABLE'
+        if spec.satisfies('@20180629:'):
+            mpi_prefix = 'BUILD'
+            pkg_prefix = 'PKG'
+
         args = [
             '-DBUILD_SHARED_LIBS={0}'.format(
                 'ON' if '+lib' in spec else 'OFF'),
-            '-DENABLE_MPI={0}'.format(
+            '-D{0}_MPI={1}'.format(
+                mpi_prefix,
                 'ON' if '+mpi' in spec else 'OFF')
         ]
 
+        if spec.satisfies('@20180629:+lib'):
+            args.append('-DBUILD_LIB=ON')
+
         for pkg in self.supported_packages:
-            opt = '-DENABLE_{0}'.format(pkg.upper())
+            opt = '-D{0}_{1}'.format(pkg_prefix, pkg.upper())
             if '+{0}'.format(pkg) in spec:
                 args.append('{0}=ON'.format(opt))
             else:
diff --git a/var/spack/repos/builtin/packages/last/package.py b/var/spack/repos/builtin/packages/last/package.py
index 34054313f7..9e0ac55850 100644
--- a/var/spack/repos/builtin/packages/last/package.py
+++ b/var/spack/repos/builtin/packages/last/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lastz/package.py b/var/spack/repos/builtin/packages/lastz/package.py
new file mode 100644
index 0000000000..1b438c81b6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lastz/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lastz(MakefilePackage):
+    """LASTZ is a program for aligning DNA sequences, a pairwise aligner."""
+
+    homepage = "https://lastz.github.io/lastz"
+    url      = "https://github.com/lastz/lastz/archive/1.04.00.tar.gz"
+
+    version('1.04.00', sha256='a4c2c7a77430387e96dbc9f5bdc75874334c672be90f5720956c0f211abf9f5a')
+
+    def install(self, spec, prefix):
+        make('install', 'LASTZ_INSTALL={0}'.format(prefix.bin))
diff --git a/var/spack/repos/builtin/packages/latte/package.py b/var/spack/repos/builtin/packages/latte/package.py
index 7e3c9afa61..fe7b75b8a8 100644
--- a/var/spack/repos/builtin/packages/latte/package.py
+++ b/var/spack/repos/builtin/packages/latte/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,9 +11,15 @@ class Latte(CMakePackage):
     """Open source density functional tight binding molecular dynamics."""
 
     homepage = "https://github.com/lanl/latte"
-    url      = "https://github.com/lanl/latte/tarball/v1.0"
+    url      = "https://github.com/lanl/latte/tarball/v1.2.1"
+    git      = "https://github.com/lanl/latte.git"
+
+    tags = ['ecp', 'ecp-apps']
 
-    version('develop', git='https://github.com/lanl/latte', branch='master')
+    version('develop', branch='master')
+    version('1.2.1', '56db44afaba2a89e6ca62ac565c3c012')
+    version('1.2.0', 'b9bf8f84a0e0cf7b0e278a1bc7751b3d')
+    version('1.1.1', 'ab11867ba6235189681cf6e50a50cc50')
     version('1.0.1', 'd0b99edbcf7a19abe0a68a192d6f6234')
 
     variant('mpi', default=True,
@@ -60,4 +47,9 @@ class Latte(CMakePackage):
         if '+progress' in self.spec:
             options.append('-DPROGRESS=yes')
 
+        blas_list = ';'.join(self.spec['blas'].libs)
+        lapack_list = ';'.join(self.spec['lapack'].libs)
+        options.append('-DBLAS_LIBRARIES={0}'.format(blas_list))
+        options.append('-DLAPACK_LIBRARIES={0}'.format(lapack_list))
+
         return options
diff --git a/var/spack/repos/builtin/packages/launchmon/package.py b/var/spack/repos/builtin/packages/launchmon/package.py
index 5697a1f370..2042d0bb27 100644
--- a/var/spack/repos/builtin/packages/launchmon/package.py
+++ b/var/spack/repos/builtin/packages/launchmon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lazyten/package.py b/var/spack/repos/builtin/packages/lazyten/package.py
index 4827b9495e..20099f549a 100644
--- a/var/spack/repos/builtin/packages/lazyten/package.py
+++ b/var/spack/repos/builtin/packages/lazyten/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -30,15 +11,16 @@ class Lazyten(CMakePackage):
     """Lightweight linear algebra library based on lazy matrices"""
 
     homepage = "http://lazyten.org"
-    url = "https://github.com/lazyten/lazyten/archive/v0.4.1.tar.gz"
+    url      = "https://github.com/lazyten/lazyten/archive/v0.4.1.tar.gz"
+    git      = "https://github.com/lazyten/lazyten.git"
+
     maintainers = ['mfherbst']
 
     #
     # Versions
     #
+    version("develop", branch="master")
     version('0.4.1', 'd06f7996144e1bf1b0aee82c2af36e83')
-    version("develop", git="https://github.com/lazyten/lazyten.git",
-            branch="master")
 
     #
     # Variants
diff --git a/var/spack/repos/builtin/packages/lbann/package.py b/var/spack/repos/builtin/packages/lbann/package.py
index 5e65566cb2..148b097051 100644
--- a/var/spack/repos/builtin/packages/lbann/package.py
+++ b/var/spack/repos/builtin/packages/lbann/package.py
@@ -1,27 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import sys
 from spack import *
 
 
@@ -32,39 +15,167 @@ class Lbann(CMakePackage):
 
     homepage = "http://software.llnl.gov/lbann/"
     url      = "https://github.com/LLNL/lbann/archive/v0.91.tar.gz"
+    git      = "https://github.com/LLNL/lbann.git"
 
-    version('develop', git='https://github.com/LLNL/lbann.git', branch="develop")
+    version('develop', branch='develop')
+    version('0.95', sha256='d310b986948b5ee2bedec36383a7fe79403721c8dc2663a280676b4e431f83c2')
+    version('0.94', sha256='567e99b488ebe6294933c98a212281bffd5220fc13a0a5cd8441f9a3761ceccf')
+    version('0.93', '1913a25a53d4025fa04c16f14afdaa55')
+    version('0.92', 'c0eb1595a7c74640e96f280beb497564')
     version('0.91', '83b0ec9cd0b7625d41dfb06d2abd4134')
 
     variant('gpu', default=False, description='Builds with support for GPUs via CUDA and cuDNN')
+    variant('nccl', default=False, description='Builds with support for NCCL communication lib')
     variant('opencv', default=True, description='Builds with support for image processing routines with OpenCV')
     variant('seq_init', default=False, description='Force serial initialization of weight matrices.')
-    variant('dtype', default=4, description='Size (bits) of floating point representation for weights')
+    variant('dtype', default='float',
+            description='Type for floating point representation of weights',
+            values=('float', 'double'))
     variant('build_type', default='Release',
             description='The build type to build',
             values=('Debug', 'Release'))
+    variant('al', default=True, description='Builds with support for Aluminum Library')
+    variant('conduit', default=False, description='Builds with support for Conduit Library')
+
+    # It seems that there is a need for one statement per version bounds
+    depends_on('hydrogen +openmp_blas +shared +int64', when='@:0.90,0.95: ~al')
+    depends_on('hydrogen +openmp_blas +shared +int64 +al', when='@:0.90,0.95: +al')
+
+    depends_on('hydrogen +openmp_blas +shared +int64 build_type=Debug',
+               when='build_type=Debug @:0.90,0.95: ~al')
+    depends_on('hydrogen +openmp_blas +shared +int64 build_type=Debug +al',
+               when='build_type=Debug @:0.90,0.95: +al')
+
+    depends_on('hydrogen +openmp_blas +shared +int64 +cuda',
+               when='+gpu @:0.90,0.95: ~al')
+    depends_on('hydrogen +openmp_blas +shared +int64 +cuda +al',
+               when='+gpu @:0.90,0.95: +al')
+
+    depends_on('hydrogen +openmp_blas +shared +int64 +cuda build_type=Debug',
+               when='build_type=Debug @:0.90,0.95: +gpu')
+    depends_on('hydrogen +openmp_blas +shared +int64 +cuda build_type=Debug +al',
+               when='build_type=Debug @:0.90,0.95: +gpu +al')
+
+    # Older versions depended on Elemental not Hydrogen
+    depends_on('elemental +openmp_blas +shared +int64', when='@0.91:0.94')
+    depends_on('elemental +openmp_blas +shared +int64 build_type=Debug',
+               when='build_type=Debug @0.91:0.94')
+
+    depends_on('aluminum@master', when='@:0.90,0.95: +al ~gpu')
+    depends_on('aluminum@master +gpu +mpi-cuda', when='@:0.90,0.95: +al +gpu ~nccl')
+    depends_on('aluminum@master +gpu +nccl +mpi_cuda', when='@:0.90,0.95: +al +gpu +nccl')
 
-    depends_on('elemental +openmp_blas +shared +int64')
-    depends_on('elemental +openmp_blas +shared +int64 build_type=Debug', 
-               when=('build_type=Debug'))
     depends_on('cuda', when='+gpu')
     depends_on('cudnn', when='+gpu')
     depends_on('cub', when='+gpu')
-    depends_on('mpi')
+    depends_on('mpi', when='~gpu')
+    depends_on('mpi +cuda', when='+gpu')
     depends_on('hwloc')
-    depends_on('opencv@3.2.0: +openmp +core +highgui +imgproc +jpeg +png +tiff +zlib ~eigen', when='+opencv')
+
+    # LBANN wraps OpenCV calls in OpenMP parallel loops, build without OpenMP
+    # Additionally disable video related options, they incorrectly link in a
+    # bad OpenMP library when building with clang or Intel compilers
+    depends_on('opencv@3.2.0: +core +highgui +imgproc +jpeg +png +tiff +zlib '
+               '+fast-math +powerpc +vsx ~calib3d ~cuda ~dnn ~eigen'
+               '~features2d ~flann ~gtk ~ipp ~ipp_iw ~jasper ~java ~lapack ~ml'
+               '~openmp ~opencl ~opencl_svm ~openclamdblas ~openclamdfft'
+               '~pthreads_pf ~python ~qt ~stitching ~superres ~ts ~video'
+               '~videostab ~videoio ~vtk', when='+opencv')
+
     depends_on('protobuf@3.0.2:')
     depends_on('cnpy')
+    depends_on('nccl', when='+gpu +nccl')
 
-    def cmake_args(self):
+    depends_on('conduit@master +hdf5', when='+conduit')
+
+    @property
+    def common_config_args(self):
         spec = self.spec
         # Environment variables
-        CPPFLAGS = []
-        CPPFLAGS.append('-DLBANN_SET_EL_RNG')
+        cppflags = []
+        cppflags.append('-DLBANN_SET_EL_RNG -ldl')
 
-        args = [
+        return [
             '-DCMAKE_INSTALL_MESSAGE=LAZY',
-            '-DCMAKE_CXX_FLAGS=%s' % ' '.join(CPPFLAGS),
+            '-DCMAKE_CXX_FLAGS=%s' % ' '.join(cppflags),
+            '-DLBANN_VERSION=spack',
+            '-DCNPY_DIR={0}'.format(spec['cnpy'].prefix),
+        ]
+
+    # Get any recent versions or non-numeric version
+    # Note that develop > numeric and non-develop < numeric
+    @when('@:0.90,0.94:')
+    def cmake_args(self):
+        spec = self.spec
+        args = self.common_config_args
+        args.extend([
+            '-DLBANN_WITH_TOPO_AWARE:BOOL=%s' % ('+gpu +nccl' in spec),
+            '-DLBANN_SEQUENTIAL_INITIALIZATION:BOOL=%s' %
+            ('+seq_init' in spec),
+            '-DLBANN_WITH_TBINF=OFF',
+            '-DLBANN_WITH_VTUNE=OFF',
+            '-DLBANN_DATATYPE={0}'.format(spec.variants['dtype'].value),
+            '-DLBANN_VERBOSE=0'])
+
+        if self.spec.satisfies('@:0.90') or self.spec.satisfies('@0.95:'):
+            args.extend([
+                '-DHydrogen_DIR={0}/CMake/hydrogen'.format(
+                    spec['hydrogen'].prefix)])
+        elif self.spec.satisfies('@0.94'):
+            args.extend([
+                '-DElemental_DIR={0}/CMake/elemental'.format(
+                    spec['elemental'].prefix)])
+
+        if '+al' in spec:
+            args.extend(['-DLBANN_WITH_ALUMINUM:BOOL=%s' % ('+al' in spec),
+                         '-DAluminum_DIR={0}'.format(spec['aluminum'].prefix)])
+
+        if '+conduit' in spec:
+            args.extend(['-DLBANN_CONDUIT_DIR:BOOL=%s' % ('+conduit' in spec),
+                         '-DLBANN_CONDUIT_DIR={0}'.format(
+                             spec['conduit'].prefix)])
+
+        # Add support for OpenMP
+        if (self.spec.satisfies('%clang')):
+            if (sys.platform == 'darwin'):
+                clang = self.compiler.cc
+                clang_bin = os.path.dirname(clang)
+                clang_root = os.path.dirname(clang_bin)
+                args.extend([
+                    '-DOpenMP_CXX_FLAGS=-fopenmp=libomp',
+                    '-DOpenMP_CXX_LIB_NAMES=libomp',
+                    '-DOpenMP_libomp_LIBRARY={0}/lib/libomp.dylib'.format(
+                        clang_root)])
+
+        if '+opencv' in spec:
+            args.extend(['-DOpenCV_DIR:STRING={0}'.format(
+                spec['opencv'].prefix)])
+
+        if '+gpu' in spec:
+            args.extend([
+                '-DLBANN_WITH_CUDA:BOOL=%s' % ('+gpu' in spec),
+                '-DLBANN_WITH_SOFTMAX_CUDA:BOOL=%s' % ('+gpu' in spec),
+                '-DCUDA_TOOLKIT_ROOT_DIR={0}'.format(
+                    spec['cuda'].prefix)])
+            args.extend([
+                '-DLBANN_WITH_CUDNN:BOOL=%s' % ('+gpu' in spec),
+                '-DcuDNN_DIR={0}'.format(
+                    spec['cudnn'].prefix)])
+            args.extend(['-DCUB_DIR={0}'.format(
+                spec['cub'].prefix)])
+            if '+nccl' in spec:
+                args.extend([
+                    '-DLBANN_WITH_NCCL:BOOL=%s' % ('+gpu +nccl' in spec),
+                    '-DNCCL_DIR={0}'.format(
+                        spec['nccl'].prefix)])
+
+        return args
+
+    @when('@0.91:0.93')
+    def cmake_args(self):
+        spec = self.spec
+        args = self.common_config_args
+        args.extend([
             '-DWITH_CUDA:BOOL=%s' % ('+gpu' in spec),
             '-DWITH_CUDNN:BOOL=%s' % ('+gpu' in spec),
             '-DELEMENTAL_USE_CUBLAS:BOOL=%s' % (
@@ -72,14 +183,16 @@ class Lbann(CMakePackage):
             '-DWITH_TBINF=OFF',
             '-DWITH_VTUNE=OFF',
             '-DElemental_DIR={0}'.format(spec['elemental'].prefix),
-            '-DCNPY_DIR={0}'.format(spec['cnpy'].prefix),
             '-DELEMENTAL_MATH_LIBS={0}'.format(
                 spec['elemental'].libs),
             '-DSEQ_INIT:BOOL=%s' % ('+seq_init' in spec),
-            '-DDATATYPE={0}'.format(int(spec.variants['dtype'].value)),
             '-DVERBOSE=0',
-            '-DLBANN_HOME=.',
-            '-DLBANN_VER=spack']
+            '-DLBANN_HOME=.'])
+
+        if spec.variants['dtype'].value == 'float':
+            args.extend(['-DDATATYPE=4'])
+        elif spec.variants['dtype'].value == 'double':
+            args.extend(['-DDATATYPE=8'])
 
         if '+opencv' in spec:
             args.extend(['-DOpenCV_DIR:STRING={0}'.format(
@@ -89,7 +202,7 @@ class Lbann(CMakePackage):
             args.extend(['-DcuDNN_DIR={0}'.format(
                 spec['cudnn'].prefix)])
 
-        if '+cudnn' in spec:
+        if '+cub' in spec:
             args.extend(['-DCUB_DIR={0}'.format(
                 spec['cub'].prefix)])
 
diff --git a/var/spack/repos/builtin/packages/lbxproxy/package.py b/var/spack/repos/builtin/packages/lbxproxy/package.py
index 6b5c4d0bc7..6548807b1a 100644
--- a/var/spack/repos/builtin/packages/lbxproxy/package.py
+++ b/var/spack/repos/builtin/packages/lbxproxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -48,5 +29,5 @@ class Lbxproxy(AutotoolsPackage):
     depends_on('xtrans', type='build')
     depends_on('xproxymanagementprotocol', type='build')
     depends_on('bigreqsproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/lbzip2/package.py b/var/spack/repos/builtin/packages/lbzip2/package.py
new file mode 100644
index 0000000000..6103ce00e3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lbzip2/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lbzip2(AutotoolsPackage):
+    """Multi-threaded compression utility with support for bzip2
+       compressed file format"""
+
+    homepage = "http://lbzip2.org/"
+    url      = "http://archive.lbzip2.org/lbzip2-2.5.tar.gz"
+
+    version('2.5', sha256='46c75ee93cc95eedc6005625442b2b8e59a2bef3ba80987d0491f055185650e9')
diff --git a/var/spack/repos/builtin/packages/lcals/package.py b/var/spack/repos/builtin/packages/lcals/package.py
index bd12081130..e697be8989 100644
--- a/var/spack/repos/builtin/packages/lcals/package.py
+++ b/var/spack/repos/builtin/packages/lcals/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import platform
@@ -35,8 +16,8 @@ class Lcals(MakefilePackage):
         by Frank H. McMahon, UCRL-53745.). The suite contains facilities to
         generate timing statistics and reports."""
 
-    homepage = "https://codesign.llnl.gov/LCALS-downloads/"
-    url = "https://codesign.llnl.gov/LCALS-downloads/lcals-v1.0.2.tgz"
+    homepage = "https://computation.llnl.gov/projects/co-design/lcals"
+    url      = "https://computation.llnl.gov/projects/co-design/download/lcals-v1.0.2.tgz"
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/lcms/package.py b/var/spack/repos/builtin/packages/lcms/package.py
index 816cc3f005..e68e96bdc9 100644
--- a/var/spack/repos/builtin/packages/lcms/package.py
+++ b/var/spack/repos/builtin/packages/lcms/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,11 @@ class Lcms(AutotoolsPackage):
     """Little cms is a color management library. Implements fast
        transforms between ICC profiles. It is focused on speed, and is
        portable across several platforms (MIT license)."""
+
     homepage = "http://www.littlecms.com"
-    url      = "http://downloads.sourceforge.net/project/lcms/lcms/2.8/lcms2-2.8.tar.gz"
+    url      = "http://downloads.sourceforge.net/project/lcms/lcms/2.9/lcms2-2.9.tar.gz"
 
+    version('2.9', '8de1b7724f578d2995c8fdfa35c3ad0e')
     version('2.8', '87a5913f1a52464190bb655ad230539c')
     version('2.6', 'f4c08d38ceade4a664ebff7228910a33')
 
diff --git a/var/spack/repos/builtin/packages/ldc-bootstrap/package.py b/var/spack/repos/builtin/packages/ldc-bootstrap/package.py
index 6e3288f085..5cff31e35d 100644
--- a/var/spack/repos/builtin/packages/ldc-bootstrap/package.py
+++ b/var/spack/repos/builtin/packages/ldc-bootstrap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ldc/package.py b/var/spack/repos/builtin/packages/ldc/package.py
index 8dd2052fca..26a9d61ccd 100644
--- a/var/spack/repos/builtin/packages/ldc/package.py
+++ b/var/spack/repos/builtin/packages/ldc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Ldc(CMakePackage):
     """
 
     homepage = "https://dlang.org/"
-    url = "https://github.com/ldc-developers/ldc/releases/download/v0.17.4/ldc-0.17.4-src.tar.gz"
+    url      = "https://github.com/ldc-developers/ldc/releases/download/v1.3.0/ldc-1.3.0-src.tar.gz"
 
     version('1.3.0', '537d992a361b0fd0440b24a5145c9107')
 
diff --git a/var/spack/repos/builtin/packages/legion/package.py b/var/spack/repos/builtin/packages/legion/package.py
index 0ec388994f..4ae0cf533c 100644
--- a/var/spack/repos/builtin/packages/legion/package.py
+++ b/var/spack/repos/builtin/packages/legion/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -42,8 +23,11 @@ class Legion(CMakePackage):
     """
     homepage = "http://legion.stanford.edu/"
     url      = "https://github.com/StanfordLegion/legion/tarball/legion-17.02.0"
+    git      = "https://github.com/StanfordLegion/legion.git"
 
-    version('develop', git='https://github.com/StanfordLegion/legion', branch='master')
+    version('develop', branch='master')
+    version('18.05.0', 'ab5ac8cd4aa4c91e6187bf1333a031bf')
+    version('18.02.0', '14937b386100347b051a5fc514636353')
     version('17.10.0', 'ebfc974dc82a9d7f3ba53242ecae62e1')
     version('17.08.0', 'acc1ea8c564c4a382a015e0c9cf94574')
     version('17.02.0', '31ac3004e2fb0996764362d2b6f6844a')
diff --git a/var/spack/repos/builtin/packages/leveldb/package.py b/var/spack/repos/builtin/packages/leveldb/package.py
index db61668021..e06f347e23 100644
--- a/var/spack/repos/builtin/packages/leveldb/package.py
+++ b/var/spack/repos/builtin/packages/leveldb/package.py
@@ -1,32 +1,13 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import glob
 from spack import *
 
 
-class Leveldb(Package):
+class Leveldb(MakefilePackage):
     """LevelDB is a fast key-value storage library written at Google
     that provides an ordered mapping from string keys to string values."""
 
@@ -39,21 +20,14 @@ class Leveldb(Package):
     depends_on("snappy")
 
     def install(self, spec, prefix):
-        make()
-
-        mkdirp(prefix.include)
-        mkdirp(prefix.lib)
-        mkdirp(join_path(prefix.lib, 'pkgconfig'))
-
-        cp = which('cp')
+        mkdirp(prefix.lib.pkgconfig)
 
-        # cp --preserve=links libleveldb.* prefix/lib
-        args = glob.glob('out-shared/libleveldb.*') \
-            + glob.glob('out-static/libleveldb.*')
-        args.append(prefix.lib)
-        cp('--preserve=links', *args)
+        libraries  = glob.glob('out-shared/libleveldb.*')
+        libraries += glob.glob('out-static/libleveldb.*')
+        for library in libraries:
+            install(library, prefix.lib)
 
-        cp('-r', 'include/leveldb', prefix.include)
+        install_tree('include', prefix.include)
 
         with open(join_path(prefix.lib, 'pkgconfig', 'leveldb.pc'), 'w') as f:
             f.write('prefix={0}\n'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/lftp/package.py b/var/spack/repos/builtin/packages/lftp/package.py
index 47b4706776..1525298538 100644
--- a/var/spack/repos/builtin/packages/lftp/package.py
+++ b/var/spack/repos/builtin/packages/lftp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,7 @@ class Lftp(AutotoolsPackage):
 
     version('4.8.1', '419b27c016d968a0226b2e5df1454c22')
     version('4.7.7', 'ddc71b3b11a1af465e829075ae14b3ff')
+    version('4.6.4', 'f84ecfc368b7afcc56fe7d3da2457d12')
 
     depends_on('expat')
     depends_on('libiconv')
diff --git a/var/spack/repos/builtin/packages/libaec/package.py b/var/spack/repos/builtin/packages/libaec/package.py
index 814f7760c5..2a40d3f602 100644
--- a/var/spack/repos/builtin/packages/libaec/package.py
+++ b/var/spack/repos/builtin/packages/libaec/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class Libaec(CMakePackage):
     """
 
     homepage = 'https://gitlab.dkrz.de/k202009/libaec'
-    url = 'https://gitlab.dkrz.de/k202009/libaec/repository/archive.tar.gz?ref=v1.0.2'
+    url = 'https://gitlab.dkrz.de/api/v4/projects/k202009%2Flibaec/repository/archive.tar.gz?sha=v1.0.2'
     list_url = 'https://gitlab.dkrz.de/k202009/libaec/tags'
 
     provides('szip')
diff --git a/var/spack/repos/builtin/packages/libaio/package.py b/var/spack/repos/builtin/packages/libaio/package.py
index 2a617c0518..56872455cd 100644
--- a/var/spack/repos/builtin/packages/libaio/package.py
+++ b/var/spack/repos/builtin/packages/libaio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Libaio(Package):
     """This is the linux native Asynchronous I/O interface library."""
 
     homepage = "http://lse.sourceforge.net/io/aio.html"
-    url      = "https://ftp.de.debian.org/debian/pool/main/liba/libaio/libaio_0.3.110.orig.tar.gz"
+    url      = "https://debian.inf.tu-dresden.de/debian/pool/main/liba/libaio/libaio_0.3.110.orig.tar.gz"
 
     version('0.3.110', '2a35602e43778383e2f4907a4ca39ab8')
 
diff --git a/var/spack/repos/builtin/packages/libapplewm/package.py b/var/spack/repos/builtin/packages/libapplewm/package.py
index 146596081f..373b373487 100644
--- a/var/spack/repos/builtin/packages/libapplewm/package.py
+++ b/var/spack/repos/builtin/packages/libapplewm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Libapplewm(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('applewmproto@1.4:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # Crashes with this error message on Linux:
diff --git a/var/spack/repos/builtin/packages/libarchive/package.py b/var/spack/repos/builtin/packages/libarchive/package.py
index f06f09b391..08c743e724 100644
--- a/var/spack/repos/builtin/packages/libarchive/package.py
+++ b/var/spack/repos/builtin/packages/libarchive/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class Libarchive(AutotoolsPackage):
     homepage = "http://www.libarchive.org"
     url      = "http://www.libarchive.org/downloads/libarchive-3.1.2.tar.gz"
 
+    version('3.3.2', '4583bd6b2ebf7e0e8963d90879eb1b27')
     version('3.2.1', 'afa257047d1941a565216edbf0171e72')
     version('3.1.2', 'efad5a503f66329bb9d2f4308b5de98a')
     version('3.1.1', '1f3d883daf7161a0065e42a15bbf168f')
diff --git a/var/spack/repos/builtin/packages/libassuan/package.py b/var/spack/repos/builtin/packages/libassuan/package.py
index 8a56551ff5..7f28942a53 100644
--- a/var/spack/repos/builtin/packages/libassuan/package.py
+++ b/var/spack/repos/builtin/packages/libassuan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Libassuan(AutotoolsPackage):
        protocol."""
 
     homepage = "https://gnupg.org/software/libassuan/index.html"
-    url = "https://gnupg.org/ftp/gcrypt/libassuan/libassuan-2.4.3.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/libassuan/libassuan-2.4.5.tar.bz2"
 
+    version('2.4.5', '4f22bdb70d424cfb41b64fd73b7e1e45')
     version('2.4.3', '8e01a7c72d3e5d154481230668e6eb5a')
 
     depends_on('libgpg-error')
diff --git a/var/spack/repos/builtin/packages/libatomic-ops/package.py b/var/spack/repos/builtin/packages/libatomic-ops/package.py
index df12c000f3..a629eab02d 100644
--- a/var/spack/repos/builtin/packages/libatomic-ops/package.py
+++ b/var/spack/repos/builtin/packages/libatomic-ops/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libbeagle/package.py b/var/spack/repos/builtin/packages/libbeagle/package.py
index 4d064a063b..a4f9352e72 100644
--- a/var/spack/repos/builtin/packages/libbeagle/package.py
+++ b/var/spack/repos/builtin/packages/libbeagle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,8 +21,13 @@ class Libbeagle(AutotoolsPackage):
     depends_on('m4',       type='build')
 
     depends_on('subversion', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('java', type='build')
 
     def url_for_version(self, version):
         url = "https://github.com/beagle-dev/beagle-lib/archive/beagle_release_{0}.tar.gz"
         return url.format(version.underscored)
+
+    def setup_environment(self, spack_env, run_env):
+        prefix = self.prefix
+        run_env.prepend_path('BEAST_LIB', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/libbeato/package.py b/var/spack/repos/builtin/packages/libbeato/package.py
new file mode 100644
index 0000000000..0cc0a19a13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libbeato/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libbeato(AutotoolsPackage):
+    """libbeato is a C library containing routines for various uses in Genomics,
+    and includes a copy of the freeware portion of the C library
+    from UCSC's Genome Browser Group."""
+
+    homepage = "https://github.com/CRG-Barcelona/libbeato"
+    url      = "https://github.com/CRG-Barcelona/libbeato/archive/master.tar.gz"
+
+    version('master', 'ee6f0f0f3f09c4f601fcfed3b13e7395')
diff --git a/var/spack/repos/builtin/packages/libbsd/package.py b/var/spack/repos/builtin/packages/libbsd/package.py
index f9b8a291ca..4587d29e1f 100644
--- a/var/spack/repos/builtin/packages/libbsd/package.py
+++ b/var/spack/repos/builtin/packages/libbsd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libbson/package.py b/var/spack/repos/builtin/packages/libbson/package.py
index 39a606cf73..92f5a26f14 100644
--- a/var/spack/repos/builtin/packages/libbson/package.py
+++ b/var/spack/repos/builtin/packages/libbson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,10 @@ class Libbson(AutotoolsPackage):
     homepage = "https://github.com/mongodb/libbson"
     url      = "https://github.com/mongodb/libbson/releases/download/1.7.0/libbson-1.7.0.tar.gz"
 
+    maintainers = ['michaelkuhn']
+
+    version('1.9.1', 'f91f59fc5a0cbba94d4d32dad1bd0cfd')
+    version('1.8.1', '42601455cf7f450b46f62c4e6115c440')
     version('1.8.0', '8b3c64570eec721f951831958e707a5a')
     version('1.7.0', 'e196ad77dd8458ebc1166e6135030b63')
     version('1.6.3', 'b7bdb314197106fcfb4af105a582d343')
diff --git a/var/spack/repos/builtin/packages/libcanberra/package.py b/var/spack/repos/builtin/packages/libcanberra/package.py
index f7b8a78659..6c6fd99ae1 100644
--- a/var/spack/repos/builtin/packages/libcanberra/package.py
+++ b/var/spack/repos/builtin/packages/libcanberra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -55,7 +36,7 @@ class Libcanberra(AutotoolsPackage):
 
     depends_on('libvorbis')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     def configure_args(self):
         args = ['--enable-static']
diff --git a/var/spack/repos/builtin/packages/libcap/package.py b/var/spack/repos/builtin/packages/libcap/package.py
index af7c363bf0..234c1846b4 100644
--- a/var/spack/repos/builtin/packages/libcap/package.py
+++ b/var/spack/repos/builtin/packages/libcap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libceed/occaFree-0.2.diff b/var/spack/repos/builtin/packages/libceed/occaFree-0.2.diff
new file mode 100644
index 0000000000..060710d4ad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libceed/occaFree-0.2.diff
@@ -0,0 +1,41 @@
+diff --git a/backends/occa/ceed-occa-basis.c b/backends/occa/ceed-occa-basis.c
+index 85ec292..86a46ee 100644
+--- a/backends/occa/ceed-occa-basis.c
++++ b/backends/occa/ceed-occa-basis.c
+@@ -293,10 +293,6 @@ static int CeedBasisDestroy_Occa(CeedBasis basis) {
+   const Ceed ceed = basis->ceed;
+   CeedBasis_Occa *data = basis->data;
+   dbg("[CeedBasis][Destroy]");
+-  occaFree(data->kZero);
+-  occaFree(data->kInterp);
+-  occaFree(data->kGrad);
+-  occaFree(data->kWeight);
+   occaFree(data->qref1d);
+   occaFree(data->qweight1d);
+   occaFree(data->interp1d);
+diff --git a/backends/occa/ceed-occa-qfunction.c b/backends/occa/ceed-occa-qfunction.c
+index a2776c3..abf7de0 100644
+--- a/backends/occa/ceed-occa-qfunction.c
++++ b/backends/occa/ceed-occa-qfunction.c
+@@ -154,7 +154,6 @@ static int CeedQFunctionDestroy_Occa(CeedQFunction qf) {
+   CeedQFunction_Occa *data=qf->data;
+   free(data->oklPath);
+   dbg("[CeedQFunction][Destroy]");
+-  occaFree(data->kQFunctionApply);
+   if (data->ready) {
+     if (!data->op) occaFree(data->d_q);
+     occaFree(data->d_u);
+diff --git a/backends/occa/ceed-occa-restrict.c b/backends/occa/ceed-occa-restrict.c
+index 6b7786c..c5360dc 100644
+--- a/backends/occa/ceed-occa-restrict.c
++++ b/backends/occa/ceed-occa-restrict.c
+@@ -95,9 +95,6 @@ static int CeedElemRestrictionDestroy_Occa(CeedElemRestriction r) {
+   const Ceed ceed = r->ceed;
+   CeedElemRestriction_Occa *data = r->data;
+   dbg("[CeedElemRestriction][Destroy]");
+-  for (int i=0; i<9; i++) {
+-    occaFree(data->kRestrict[i]);
+-  }
+   ierr = CeedFree(&data); CeedChk(ierr);
+   return 0;
+ }
diff --git a/var/spack/repos/builtin/packages/libceed/package.py b/var/spack/repos/builtin/packages/libceed/package.py
new file mode 100644
index 0000000000..54bb7b495f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libceed/package.py
@@ -0,0 +1,60 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libceed(Package):
+    """The CEED API Library: Code for Efficient Extensible Discretizations."""
+
+    homepage = "https://github.com/CEED/libCEED"
+    git      = "https://github.com/CEED/libCEED.git"
+
+    version('develop', branch='master')
+    version('0.2', tag='v0.2')
+    version('0.1', tag='v0.1')
+
+    variant('occa', default=True, description='Enable OCCA backends')
+    variant('cuda', default=False, description='Enable CUDA support')
+    variant('debug', default=False, description='Enable debug build')
+
+    depends_on('occa@v1.0.0-alpha.5,develop', when='+occa')
+    depends_on('occa@develop', when='@develop+occa')
+    depends_on('occa+cuda', when='+occa+cuda')
+    depends_on('occa~cuda', when='+occa~cuda')
+
+    # occa: do not occaFree kernels
+    # Repeated creation and freeing of kernels appears to expose a caching
+    # bug in Occa.
+    patch('occaFree-0.2.diff', when='@0.2')
+
+    phases = ['build', 'install']
+
+    def build(self, spec, prefix):
+        # Note: The occa package exports OCCA_DIR in the environment
+
+        makeopts = ['V=1']
+        makeopts += ['NDEBUG=%s' % ('' if '+debug' in spec else '1')]
+        make(*makeopts)
+
+        if self.run_tests:
+            make('prove', *makeopts, parallel=False)
+
+    def install(self, spec, prefix):
+        make('install', 'prefix=%s' % prefix, parallel=False)
+
+    @when('@0.1')
+    def install(self, spec, prefix):
+        mkdirp(prefix.include)
+        install('ceed.h', prefix.include)
+        mkdirp(prefix.lib)
+        install('libceed.%s' % dso_suffix, prefix.lib)
+        filter_file('^prefix=.*$', 'prefix=%s' % prefix, 'ceed.pc')
+        filter_file('^includedir=\$\{prefix\}$',
+                    'includedir=${prefix}/include', 'ceed.pc')
+        filter_file('^libdir=\$\{prefix\}$', 'libdir=${prefix}/lib', 'ceed.pc')
+        filter_file('Version:.*$', 'Version: 0.1', 'ceed.pc')
+        mkdirp(prefix.lib.pkgconfig)
+        install('ceed.pc', prefix.lib.pkgconfig)
diff --git a/var/spack/repos/builtin/packages/libcerf/package.py b/var/spack/repos/builtin/packages/libcerf/package.py
index f119f96832..ecf35f87f4 100644
--- a/var/spack/repos/builtin/packages/libcerf/package.py
+++ b/var/spack/repos/builtin/packages/libcerf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/libcheck/package.py b/var/spack/repos/builtin/packages/libcheck/package.py
new file mode 100644
index 0000000000..19553b8b6a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libcheck/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libcheck(CMakePackage):
+    """A unit testing framework for C."""
+
+    homepage = "https://libcheck.github.io/check/index.html"
+    url      = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz"
+
+    version('0.12.0', '31b17c6075820a434119592941186f70')
+    version('0.11.0', '9b90522b31f5628c2e0f55dda348e558')
+    version('0.10.0', '53c5e5c77d090e103a17f3ed7fd7d8b8')
diff --git a/var/spack/repos/builtin/packages/libcint/package.py b/var/spack/repos/builtin/packages/libcint/package.py
new file mode 100644
index 0000000000..1698dbb3ce
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libcint/package.py
@@ -0,0 +1,63 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libcint(CMakePackage):
+    """Library for analytical Gaussian integrals for quantum chemistry."""
+
+    homepage    = "https://github.com/sunqm/libcint"
+    url         = "https://github.com/sunqm/libcint/archive/v3.0.4.tar.gz"
+    maintainers = ['mfherbst']
+
+    #
+    # Versions
+    #
+    version('3.0.13', sha256='ee64f0bc7fb6073063ac3c9bbef8951feada141e197b1a5cc389c8cccf8dc360')
+    version('3.0.12', sha256='7409ef41f1465cf4c1ae9834dfc0b0585c0fdc63b55d8ee8b8a7a6d5e31f309d')
+    version('3.0.11', sha256='4c9c24d4bd4791391848f19a4be5177137aca27a8e0375574101a7a1261157cf')
+    version('3.0.10', sha256='aac6d9630dc4c62840f03262166e877d3aeaf27b6b33498fb490fa3428f12fe4')
+    version('3.0.8',  sha256='ca94772f74aaf7b8ad4d7c1b09578c9115ec909c3d8b82dacc908c351c631c35')
+    version('3.0.7',  sha256='e603cd90567c6116d4f704ea66a010b447c11052e90db1d91488adc187142ead')
+    version('3.0.6',  sha256='a7d6d46de9be044409270b27727a1d620d21b5fda6aa7291548938e1ced25404')
+    version('3.0.5',  sha256='7bde241ce83c00b89c80459e3af5734d40925d8fd9fcaaa7245f61b08192c722')
+    version('3.0.4',  sha256='0f25ef7ad282dd7a20e4decf283558e4f949243a5423ff4c0cd875276c310c47')
+
+    #
+    # Variants
+    #
+    variant('f12', default=True,
+            description="Enable explicitly correlated f12 integrals.")
+    variant('coulomb_erf', default=True,
+            description="Enable attenuated coulomb operator integrals.")
+    variant('test', default=False, description="Build test programs")
+    variant('shared', default=True,
+            description="Build the shared library")
+
+    #
+    # Dependencies and conflicts
+    #
+    depends_on('cmake@2.6:', type="build")
+    depends_on('blas')
+    depends_on('python', type=("build", "test"), when="+test")
+    depends_on('py-numpy', type=("build", "test"), when="+test")
+
+    # Libcint tests only work with a shared libcint library
+    conflicts('+test~shared')
+
+    #
+    # Settings and cmake cache
+    #
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            "-DWITH_COULOMB_ERF=" + str("+coulomb_erf" in spec),
+            "-DWITH_F12=" + str("+f12" in spec),
+            "-DBUILD_SHARED_LIBS=" + str("+shared" in spec),
+            "-DENABLE_TEST=" + str("+test" in spec),
+            "-DENABLE_EXAMPLE=OFF",  # Requires fortran compiler
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/libcircle/package.py b/var/spack/repos/builtin/packages/libcircle/package.py
index 98778ea9a4..5bd6bf719f 100644
--- a/var/spack/repos/builtin/packages/libcircle/package.py
+++ b/var/spack/repos/builtin/packages/libcircle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libconfig/package.py b/var/spack/repos/builtin/packages/libconfig/package.py
index e62ec6bd83..9dea0cd4c8 100644
--- a/var/spack/repos/builtin/packages/libconfig/package.py
+++ b/var/spack/repos/builtin/packages/libconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Libconfig(AutotoolsPackage):
     """C/C++ Configuration File Library"""
 
     homepage = "http://www.hyperrealm.com/libconfig/"
-    url      = "https://github.com/hyperrealm/libconfig/archive/v1.6.tar.gz"
+    url      = "https://github.com/hyperrealm/libconfig/archive/v1.5.tar.gz"
 
     force_autoreconf = True
     # there is currently a build error with version 1.6, see:
diff --git a/var/spack/repos/builtin/packages/libcroco/package.py b/var/spack/repos/builtin/packages/libcroco/package.py
new file mode 100644
index 0000000000..eefc188457
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libcroco/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libcroco(AutotoolsPackage):
+    """Libcroco is a standalone css2 parsing and manipulation library."""
+
+    homepage = "https://developer.gnome.org/libcroco"
+    url      = "http://ftp.gnome.org/pub/gnome/sources/libcroco/0.6/libcroco-0.6.12.tar.xz"
+
+    version('0.6.12', 'bc0984fce078ba2ce29f9500c6b9ddce')
+
+    depends_on('glib')
+    depends_on('libxml2')
diff --git a/var/spack/repos/builtin/packages/libctl/package.py b/var/spack/repos/builtin/packages/libctl/package.py
index fc729d6db8..ae68dc5bef 100644
--- a/var/spack/repos/builtin/packages/libctl/package.py
+++ b/var/spack/repos/builtin/packages/libctl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libdivsufsort/package.py b/var/spack/repos/builtin/packages/libdivsufsort/package.py
index 1e679eb2ec..2ac8d6f65e 100644
--- a/var/spack/repos/builtin/packages/libdivsufsort/package.py
+++ b/var/spack/repos/builtin/packages/libdivsufsort/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libdmx/package.py b/var/spack/repos/builtin/packages/libdmx/package.py
index c89323935f..9514dc9f00 100644
--- a/var/spack/repos/builtin/packages/libdmx/package.py
+++ b/var/spack/repos/builtin/packages/libdmx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libdmx(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('dmxproto@2.2.99.1:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py
index 521e097dc8..ca4e26577c 100644
--- a/var/spack/repos/builtin/packages/libdrm/package.py
+++ b/var/spack/repos/builtin/packages/libdrm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -39,7 +20,7 @@ class Libdrm(Package):
     version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6')
     version('2.4.33', '86e4e3debe7087d5404461e0032231c8')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('libpciaccess@0.10:', when=(sys.platform != 'darwin'))
     depends_on('libpthread-stubs')
 
diff --git a/var/spack/repos/builtin/packages/libdwarf/package.py b/var/spack/repos/builtin/packages/libdwarf/package.py
index 970a4502b4..a473b2c83a 100644
--- a/var/spack/repos/builtin/packages/libdwarf/package.py
+++ b/var/spack/repos/builtin/packages/libdwarf/package.py
@@ -1,28 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
+import os
 
 # Only build certain parts of dwarf because the other ones break.
 dwarf_dirs = ['libdwarf', 'dwarfdump2']
@@ -44,11 +27,14 @@ class Libdwarf(Package):
     url      = "http://www.prevanders.net/libdwarf-20160507.tar.gz"
     list_url = homepage
 
+    version('20180129', 'c5e90fad4640f0d713ae8b986031f959')
     version('20160507', 'ae32d6f9ece5daf05e2d4b14822ea811')
     version('20130729', '4cc5e48693f7b93b7aa0261e63c0e21d')
     version('20130207', '64b42692e947d5180e162e46c689dfbf')
     version('20130126', 'ded74a5e90edb5a12aac3c29d260c5db')
+    depends_on("elfutils@0.163", when='@20160507', type='link')
     depends_on("elf", type='link')
+    depends_on('zlib', type='link')
 
     parallel = False
 
@@ -56,49 +42,71 @@ class Libdwarf(Package):
         filter_file(r'^typedef struct Elf Elf;$', '', 'libdwarf/libdwarf.h.in')
 
     def install(self, spec, prefix):
-
-        # elfutils contains a dwarf.h that conflicts with libdwarf's
-        # TODO: we should remove this when we can modify the include order
-        hide_list = []
-        if spec.satisfies('^elfutils'):
-            dwarf_h = join_path(spec['elfutils'].prefix, 'include/dwarf.h')
-            hide_list.append(dwarf_h)
-        with hide_files(*hide_list):
-            # dwarf build does not set arguments for ar properly
-            make.add_default_arg('ARFLAGS=rcs')
-
-            # Dwarf doesn't provide an install, so we have to do it.
-            mkdirp(prefix.bin, prefix.include, prefix.lib, prefix.man.man1)
-
-            with working_dir('libdwarf'):
-                extra_config_args = []
-
-                # this is to prevent picking up system /usr/include/libelf.h
-                if spec.satisfies('^libelf'):
-                    libelf_inc_dir = join_path(spec['libelf'].prefix,
-                                               'include/libelf')
-                    extra_config_args.append('CFLAGS=-I{0}'.format(
-                                             libelf_inc_dir))
-                configure("--prefix=" + prefix, "--enable-shared",
-                          *extra_config_args)
-                make()
-
-                install('libdwarf.a',  prefix.lib)
-                install('libdwarf.so', prefix.lib)
-                install('libdwarf.h',  prefix.include)
-                install('dwarf.h',     prefix.include)
-
-            if spec.satisfies('@20130126:20130729'):
-                dwarfdump_dir = 'dwarfdump2'
-            else:
-                dwarfdump_dir = 'dwarfdump'
-            with working_dir(dwarfdump_dir):
-                configure("--prefix=" + prefix)
-
-                # This makefile has strings of copy commands that
-                # cause a race in parallel
-                make(parallel=False)
-
-                install('dwarfdump',      prefix.bin)
-                install('dwarfdump.conf', prefix.lib)
-                install('dwarfdump.1',    prefix.man.man1)
+        # dwarf build does not set arguments for ar properly
+        make.add_default_arg('ARFLAGS=rcs')
+
+        # Dwarf doesn't provide an install, so we have to do it.
+        mkdirp(prefix.bin, prefix.include, prefix.lib, prefix.man.man1)
+
+        with working_dir('libdwarf'):
+            extra_config_args = []
+
+            # this is to prevent picking up system /usr/include/libelf.h
+            if spec.satisfies('^libelf'):
+                libelf_inc_dir = join_path(spec['libelf'].prefix,
+                                           'include/libelf')
+                extra_config_args.append(
+                    'CFLAGS=-I{0} -Wl,-L{1} -Wl,-lelf'.format(
+                        libelf_inc_dir, spec['libelf'].prefix.lib))
+            configure("--prefix=" + prefix, "--enable-shared",
+                      *extra_config_args)
+            filter_file(r'^dwfzlib\s*=\s*-lz',
+                        'dwfzlib=-L{0} -lz'.format(
+                            self.spec['zlib'].prefix.lib),
+                        'Makefile')
+            make()
+
+            libdwarf_name = 'libdwarf.{0}'.format(dso_suffix)
+            libdwarf1_name = 'libdwarf.{0}'.format(dso_suffix) + ".1"
+            install('libdwarf.a',  prefix.lib)
+            install('libdwarf.so', join_path(prefix.lib, libdwarf1_name))
+            if spec.satisfies('@20160507:'):
+                with working_dir(prefix.lib):
+                    os.symlink(libdwarf1_name, libdwarf_name)
+            install('libdwarf.h',  prefix.include)
+            install('dwarf.h',     prefix.include)
+
+            # It seems like fix_darwin_install_name can't be used
+            # here directly; the install name of the library in
+            # the stage directory must be fixed in order for dyld
+            # to locate it on Darwin when spack builds dwarfdump
+            if sys.platform == 'darwin':
+                install_name_tool = which('install_name_tool')
+                install_name_tool('-id',
+                                  join_path('..', 'libdwarf',
+                                            'libdwarf.so'),
+                                  'libdwarf.so')
+
+        if spec.satisfies('@20130126:20130729'):
+            dwarfdump_dir = 'dwarfdump2'
+        else:
+            dwarfdump_dir = 'dwarfdump'
+        with working_dir(dwarfdump_dir):
+            configure("--prefix=" + prefix)
+            filter_file(r'^dwfzlib\s*=\s*-lz',
+                        'dwfzlib=-L{0} -lz'.format(
+                            self.spec['zlib'].prefix.lib),
+                        'Makefile')
+
+            # This makefile has strings of copy commands that
+            # cause a race in parallel
+            make(parallel=False)
+
+            install('dwarfdump',      prefix.bin)
+            install('dwarfdump.conf', prefix.lib)
+            install('dwarfdump.1',    prefix.man.man1)
+
+    @run_after('install')
+    def darwin_fix(self):
+        if sys.platform == 'darwin':
+            fix_darwin_install_name(self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/libedit/package.py b/var/spack/repos/builtin/packages/libedit/package.py
index 42a09fd540..b253397ee4 100644
--- a/var/spack/repos/builtin/packages/libedit/package.py
+++ b/var/spack/repos/builtin/packages/libedit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libelf/package.py b/var/spack/repos/builtin/packages/libelf/package.py
index 5d433c19d5..b843966310 100644
--- a/var/spack/repos/builtin/packages/libelf/package.py
+++ b/var/spack/repos/builtin/packages/libelf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libemos/package.py b/var/spack/repos/builtin/packages/libemos/package.py
index 8db882d4be..02d953c4ab 100644
--- a/var/spack/repos/builtin/packages/libemos/package.py
+++ b/var/spack/repos/builtin/packages/libemos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,31 +12,37 @@ class Libemos(CMakePackage):
 
     homepage = "https://software.ecmwf.int/wiki/display/EMOS/Emoslib"
     url      = "https://software.ecmwf.int/wiki/download/attachments/3473472/libemos-4.4.2-Source.tar.gz"
+    list_url = "https://software.ecmwf.int/wiki/display/EMOS/Releases"
 
+    version('4.5.1', 'eec1ef4de841df3c68c08fa94d7939ff')
+    version('4.5.0', '0ad8962a73e3ca90a8094561adc81276')
+    version('4.4.9', '24d098cd062d443a544fe17727726285')
     version('4.4.7', '395dcf21cf06872f772fb6b73d8e67b9')
     version('4.4.2', 'f15a9aff0f40861f3f046c9088197376')
 
-    variant('eccodes', default=False,
-            description="Use eccodes instead of grib-api for GRIB decoding")
+    variant('grib', default='eccodes', values=('eccodes', 'grib-api'),
+            description='Specify GRIB backend')
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo', 'Production'))
 
-    depends_on('eccodes', when='+eccodes')
-    depends_on('grib-api', when='~eccodes')
+    depends_on('eccodes', when='grib=eccodes')
+    depends_on('grib-api', when='grib=grib-api')
     depends_on('fftw+float+double')
     depends_on('cmake@2.8.11:', type='build')
+    depends_on('pkgconfig', type='build')
+
+    conflicts('grib=eccodes', when='@:4.4.1',
+              msg='Eccodes is supported starting version 4.4.2')
 
     def cmake_args(self):
-        spec = self.spec
         args = []
 
-        if spec.satisfies('+eccodes'):
+        if self.spec.variants['grib'].value == 'eccodes':
             args.append('-DENABLE_ECCODES=ON')
-            args.append('-DECCODES_PATH=%s' % spec['eccodes'].prefix)
         else:
-            args.append('-DENABLE_ECCODES=OFF')
-            args.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
+            if self.spec.satisfies('@4.4.2:'):
+                args.append('-DENABLE_ECCODES=OFF')
 
         # To support long pathnames that spack generates
         args.append('-DCMAKE_Fortran_FLAGS=-ffree-line-length-none')
diff --git a/var/spack/repos/builtin/packages/libepoxy/package.py b/var/spack/repos/builtin/packages/libepoxy/package.py
index 9f29a701a0..a8fcb945b1 100644
--- a/var/spack/repos/builtin/packages/libepoxy/package.py
+++ b/var/spack/repos/builtin/packages/libepoxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,6 +10,18 @@ class Libepoxy(AutotoolsPackage):
     """Epoxy is a library for handling OpenGL function pointer management for
     you."""
     homepage = "https://github.com/anholt/libepoxy"
-    url      = "https://github.com/anholt/libepoxy/releases/download/v1.3.1/libepoxy-1.3.1.tar.bz2"
+    url      = "https://github.com/anholt/libepoxy/releases/download/1.4.3/libepoxy-1.4.3.tar.xz"
+    list_url = "https://github.com/anholt/libepoxy/releases"
 
+    version('1.4.3', 'af4c3ce0fb1143bdc4e43f85695a9bed')
     version('1.3.1', '96f6620a9b005a503e7b44b0b528287d')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('meson')
+    depends_on('mesa')
+
+    def configure_args(self):
+        # Disable egl, otherwise configure fails with:
+        # error: Package requirements (egl) were not met
+        # Package 'egl', required by 'virtual:world', not found
+        return ['--enable-egl=no']
diff --git a/var/spack/repos/builtin/packages/libev/package.py b/var/spack/repos/builtin/packages/libev/package.py
new file mode 100644
index 0000000000..26eec70d3e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libev/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libev(AutotoolsPackage):
+    """A full-featured and high-performance event loop that is loosely modelled
+    after libevent, but without its limitations and bugs."""
+
+    homepage = "http://software.schmorp.de/pkg/libev.html"
+    url      = "http://dist.schmorp.de/libev/libev-4.24.tar.gz"
+    git      = "https://github.com/enki/libev.git"
+    list_url = "http://dist.schmorp.de/libev/Attic/"
+
+    version('develop', branch='master')
+    version('4.24', '94459a5a22db041dec6f98424d6efe54')
+
+    depends_on('autoconf', type='build', when='@develop')
+    depends_on('automake', type='build', when='@develop')
+    depends_on('libtool',  type='build', when='@develop')
+    depends_on('m4',       type='build', when='@develop')
diff --git a/var/spack/repos/builtin/packages/libevent/package.py b/var/spack/repos/builtin/packages/libevent/package.py
index 562bb212f9..49cda592fb 100644
--- a/var/spack/repos/builtin/packages/libevent/package.py
+++ b/var/spack/repos/builtin/packages/libevent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libevpath/package.py b/var/spack/repos/builtin/packages/libevpath/package.py
index 64c2fb44e3..b27b8c6b70 100644
--- a/var/spack/repos/builtin/packages/libevpath/package.py
+++ b/var/spack/repos/builtin/packages/libevpath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,17 +14,32 @@ class Libevpath(CMakePackage):
     """
 
     homepage = "https://github.com/GTkorvo/evpath"
-    url = "https://github.com/GTkorvo/evpath/archive/v4.1.1.tar.gz"
+    url      = "https://github.com/GTkorvo/evpath/archive/v4.1.1.tar.gz"
+    git      = "https://github.com/GTkorvo/evpath.git"
 
-    version('develop', git='https://github.com/GTkorvo/evpath.git',
-            branch='master')
+    version('develop', branch='master')
+    version('4.4.0', 'd8630eb358ec90ae2d188e0e6c74022a')
+    version('4.2.4', '757ce010a6b7564dc62d3c79edd861d5')
     version('4.2.1', 'f928dc0dee41668afc91634c7051ce1a')
     version('4.1.2', '1a187f55431c991ae7040e3ff041d75c')
     version('4.1.1', '65a8db820f396ff2926e3d31908d123d')
 
+    variant('enet_transport', default=False, description='Build an ENET transport for EVpath')
+
+    depends_on('gtkorvo-enet', when='@4.4.0: +enet_transport')
+    depends_on('gtkorvo-enet@1.3.13', when='@:4.2.4 +enet_transport')
     depends_on('libffs')
 
     def cmake_args(self):
-        args = ["-DENABLE_TESTING=0", "-DTARGET_CNL=1",
-                "-DBUILD_SHARED_STATIC=STATIC"]
+        args = ["-DTARGET_CNL=1"]
+        if self.spec.satisfies('@4.4.0:'):
+            args.append("-DBUILD_SHARED_LIBS=OFF")
+        else:
+            args.append("-DENABLE_BUILD_STATIC=STATIC")
+
+        if self.run_tests:
+            args.append('-DENABLE_TESTING=1')
+        else:
+            args.append('-DENABLE_TESTING=0')
+
         return args
diff --git a/var/spack/repos/builtin/packages/libfabric/package.py b/var/spack/repos/builtin/packages/libfabric/package.py
index 01e139824a..3644b6205c 100644
--- a/var/spack/repos/builtin/packages/libfabric/package.py
+++ b/var/spack/repos/builtin/packages/libfabric/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,21 +11,27 @@ class Libfabric(AutotoolsPackage):
        fabric communication services to applications."""
 
     homepage = "https://libfabric.org/"
-    url      = "https://github.com/ofiwg/libfabric/releases/download/v1.5.0/libfabric-1.5.0.tar.gz"
+    url      = "https://github.com/ofiwg/libfabric/releases/download/v1.6.1/libfabric-1.6.1.tar.gz"
+    git = "https://github.com/ofiwg/libfabric.git"
 
+    version('develop', branch='master')
+    version('1.6.1', 'ff78dc9fcbf273a119c737a4e1df46d1')
+    version('1.6.0', '91d63ab3c0b9724a4db660019f928cab')
+    version('1.5.3', '1fe07e972fe487c6a3e44c0fb68b49a2')
     version('1.5.0', 'fda3e9b31ebe184f5157288d059672d6')
+    version('1.4.2', '2009c8e0817060fb99606ddbf6c5ccf8')
 
     fabrics = ('psm',
                'psm2',
                'sockets',
                'verbs',
                'usnic',
-               'mxm',
                'gni',
                'xpmem',
                'udp',
                'rxm',
-               'rxd')
+               'rxd',
+               'mlx')
 
     variant(
        'fabrics',
@@ -54,6 +41,21 @@ class Libfabric(AutotoolsPackage):
        multi=True
     )
 
+    depends_on('rdma-core', when='fabrics=verbs')
+    depends_on('opa-psm2', when='fabrics=psm2')
+    depends_on('psm', when='fabrics=psm')
+    depends_on('ucx', when='fabrics=mlx')
+
+    depends_on('m4', when='@develop', type='build')
+    depends_on('autoconf', when='@develop', type='build')
+    depends_on('automake', when='@develop', type='build')
+    depends_on('libtool', when='@develop', type='build')
+
+    @when('@develop')
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen.sh')
+
     def configure_args(self):
         args = []
 
diff --git a/var/spack/repos/builtin/packages/libffi/package.py b/var/spack/repos/builtin/packages/libffi/package.py
index f87060118d..b43eb91619 100644
--- a/var/spack/repos/builtin/packages/libffi/package.py
+++ b/var/spack/repos/builtin/packages/libffi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,3 +18,8 @@ class Libffi(AutotoolsPackage):
     # version('3.1', 'f5898b29bbfd70502831a212d9249d10',url =
     # "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug
     # $(lib64) instead of ${lib64} in libffi.pc
+
+    @property
+    def headers(self):
+        # The headers are probably in self.prefix.lib but we search everywhere
+        return find_headers('ffi', self.prefix, recursive=True)
diff --git a/var/spack/repos/builtin/packages/libffs/package.py b/var/spack/repos/builtin/packages/libffs/package.py
index ee7a690214..1500777652 100644
--- a/var/spack/repos/builtin/packages/libffs/package.py
+++ b/var/spack/repos/builtin/packages/libffs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,20 +15,30 @@ class Libffs(CMakePackage):
     """
 
     homepage = "http://www.cc.gatech.edu/systems/projects/FFS"
-    url = "https://github.com/GTkorvo/ffs/archive/v1.1.tar.gz"
+    url      = "https://github.com/GTkorvo/ffs/archive/v1.1.tar.gz"
+    git      = "https://github.com/GTkorvo/ffs.git"
 
-    version('develop', git='https://github.com/GTkorvo/ffs.git',
-            branch='master')
+    version('develop', branch='master')
+    version('1.5',   'c41c5f5f448b627740deecd695b7bbf8')
     version('1.1.1', 'aa1c8ad5cf35e8cf76735e3a60891509')
-    version('1.1', '561c6b3abc53e12b3c01192e8ef2ffbc')
+    version('1.1',   '561c6b3abc53e12b3c01192e8ef2ffbc')
 
-    depends_on('flex')
-    depends_on('bison')
+    depends_on('flex', type='build', when='@:1.4')
+    depends_on('bison', type='build', when='@:1.4')
+    depends_on('gtkorvo-cercs-env', type='build', when='@:1.4')
     depends_on('gtkorvo-atl')
     depends_on('gtkorvo-dill')
-    depends_on('gtkorvo-cercs-env')
 
     def cmake_args(self):
-        args = ["-DENABLE_TESTING=0", "-DTARGET_CNL=1",
-                "-DBUILD_SHARED_STATIC=STATIC"]
+        args = ["-DTARGET_CNL=1"]
+        if self.spec.satisfies('@1.5:'):
+            args.append("-DBUILD_SHARED_LIBS=OFF")
+        else:
+            args.append("-DENABLE_BUILD_STATIC=STATIC")
+
+        if self.run_tests:
+            args.append('-DENABLE_TESTING=0')
+        else:
+            args.append('-DENABLE_TESTING=0')
+
         return args
diff --git a/var/spack/repos/builtin/packages/libfontenc/package.py b/var/spack/repos/builtin/packages/libfontenc/package.py
index c5bc0478b2..579cbf3f9d 100644
--- a/var/spack/repos/builtin/packages/libfontenc/package.py
+++ b/var/spack/repos/builtin/packages/libfontenc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Libfontenc(AutotoolsPackage):
     depends_on('zlib')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libfs/package.py b/var/spack/repos/builtin/packages/libfs/package.py
index 95d5708d2f..ace282f7fb 100644
--- a/var/spack/repos/builtin/packages/libfs/package.py
+++ b/var/spack/repos/builtin/packages/libfs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libfs(AutotoolsPackage):
     depends_on('xproto@7.0.17:', type='build')
     depends_on('fontsproto', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libgcrypt/package.py b/var/spack/repos/builtin/packages/libgcrypt/package.py
index 053f62f9fc..dbc4bf5022 100644
--- a/var/spack/repos/builtin/packages/libgcrypt/package.py
+++ b/var/spack/repos/builtin/packages/libgcrypt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Libgcrypt(AutotoolsPackage):
        key algorithms, large integer functions, random numbers and a lot
        of supporting functions. """
     homepage = "http://www.gnu.org/software/libgcrypt/"
-    url = "https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.7.6.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/libgcrypt/libgcrypt-1.8.1.tar.bz2"
 
+    version('1.8.1', 'b21817f9d850064d2177285f1073ec55')
     version('1.7.6', '54e180679a7ae4d090f8689ca32b654c')
     version('1.6.2', 'b54395a93cb1e57619943c082da09d5f')
 
diff --git a/var/spack/repos/builtin/packages/libgd/package.py b/var/spack/repos/builtin/packages/libgd/package.py
index 22eb66d1c3..89178e649a 100644
--- a/var/spack/repos/builtin/packages/libgd/package.py
+++ b/var/spack/repos/builtin/packages/libgd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -50,7 +31,7 @@ class Libgd(AutotoolsPackage):
     depends_on('libtool', type='build')
     depends_on('m4', type='build')
     depends_on('gettext', type='build')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     depends_on('libiconv')
     depends_on('libpng')
diff --git a/var/spack/repos/builtin/packages/libgeotiff/package.py b/var/spack/repos/builtin/packages/libgeotiff/package.py
new file mode 100644
index 0000000000..e7a76d2eec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libgeotiff/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libgeotiff(AutotoolsPackage):
+    """GeoTIFF represents an effort by over 160 different remote sensing, GIS,
+    cartographic, and surveying related companies and organizations to
+    establish a TIFF based interchange format for georeferenced raster imagery.
+    """
+
+    homepage = "https://trac.osgeo.org/geotiff/"
+    url      = "http://download.osgeo.org/geotiff/libgeotiff/libgeotiff-1.4.2.tar.gz"
+
+    version('1.4.2', '96ab80e0d4eff7820579957245d844f8')
+
+    variant('zlib', default=True, description='Include zlib support')
+    variant('jpeg', default=True, description='Include jpeg support')
+    variant('proj', default=True, description='Use PROJ.4 library')
+
+    depends_on('zlib', when='+zlib')
+    depends_on('jpeg', when='+jpeg')
+    depends_on('libtiff')
+    depends_on('proj', when='+proj')
+
+    def configure_args(self):
+        spec = self.spec
+
+        args = [
+            '--with-libtiff={0}'.format(spec['libtiff'].prefix),
+        ]
+
+        if '+zlib' in spec:
+            args.append('--with-zlib={0}'.format(spec['zlib'].prefix))
+        else:
+            args.append('--with-zlib=no')
+
+        if '+jpeg' in spec:
+            args.append('--with-jpeg={0}'.format(spec['jpeg'].prefix))
+        else:
+            args.append('--with-jpeg=no')
+
+        if '+proj' in spec:
+            args.append('--with-proj={0}'.format(spec['proj'].prefix))
+        else:
+            args.append('--with-proj=no')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py
index 9ea82790ac..dfeecb1918 100644
--- a/var/spack/repos/builtin/packages/libgit2/package.py
+++ b/var/spack/repos/builtin/packages/libgit2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Libgit2(CMakePackage):
     homepage = "https://libgit2.github.com/"
     url      = "https://github.com/libgit2/libgit2/archive/v0.24.2.tar.gz"
 
+    version('0.26.0', '6ea75a8a5745a7b2a14d3ed94486e761')
     version('0.24.2', '735661b5b73e3c120d13e2bae21e49b3')
 
     depends_on('cmake@2.8:', type='build')
diff --git a/var/spack/repos/builtin/packages/libgpg-error/package.py b/var/spack/repos/builtin/packages/libgpg-error/package.py
index ea97c9e13e..e094fbf4dc 100644
--- a/var/spack/repos/builtin/packages/libgpg-error/package.py
+++ b/var/spack/repos/builtin/packages/libgpg-error/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libgpuarray/package.py b/var/spack/repos/builtin/packages/libgpuarray/package.py
index 3bc1100c81..a9a40b8312 100644
--- a/var/spack/repos/builtin/packages/libgpuarray/package.py
+++ b/var/spack/repos/builtin/packages/libgpuarray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,17 @@ class Libgpuarray(CMakePackage):
     homepage = "http://deeplearning.net/software/libgpuarray/"
     url      = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz"
 
+    version('0.7.5', '2534011464555c3e99d14231db965c20')
+    version('0.7.4', '19f57cd381175162048c8154f5251546')
+    version('0.7.3', 'cb44aeb8482330974abdb36b0a477e5d')
+    version('0.7.2', '0f9d7748501bc5c71bf04aae2285ac4e')
+    version('0.7.1', '7eb5bb6689ddbc386a9d498f5c0027fb')
+    version('0.7.0', 'f71b066f21ef7666f3a851e96c26f52e')
+    version('0.6.9', '7f75c39f1436c920ed9c5ffde5631fc0')
     version('0.6.2', '7f163bd5f48f399cd6e608ee3d528ee4')
     version('0.6.1', 'cfcd1b54447f9d55b05514df62c70ae2')
     version('0.6.0', '98a4ec1b4c8f225f0b89c18b899a000b')
 
     depends_on('cuda')
     depends_on('cmake@3:', type='build')
-
-    extends('python')
+    depends_on('libcheck')
diff --git a/var/spack/repos/builtin/packages/libgridxc/package.py b/var/spack/repos/builtin/packages/libgridxc/package.py
new file mode 100644
index 0000000000..a4d7d3ccdf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libgridxc/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libgridxc(Package):
+    """A library to compute the exchange and correlation energy and potential
+       in spherical (i.e. an atom) or periodic systems."""
+
+    homepage = "https://launchpad.net/libgridxc"
+    url      = "https://launchpad.net/libgridxc/trunk/0.7/+download/libgridxc-0.7.6.tgz"
+
+    version('0.7.6', 'a593f845d7565a168f1cf515a0a89879')
+
+    phases = ['configure', 'install']
+
+    def configure(self, spec, prefix):
+        sh = which('sh')
+        with working_dir('build', create=True):
+            sh('../src/config.sh')
+            copy('../extra/fortran.mk', 'fortran.mk')
+
+    def install(self, spec, prefix):
+        with working_dir('build'):
+            make('PREFIX=%s' % self.prefix, 'FC=fc')
diff --git a/var/spack/repos/builtin/packages/libgtextutils/package.py b/var/spack/repos/builtin/packages/libgtextutils/package.py
index be6759e91e..535bb7694e 100644
--- a/var/spack/repos/builtin/packages/libgtextutils/package.py
+++ b/var/spack/repos/builtin/packages/libgtextutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libharu/package.py b/var/spack/repos/builtin/packages/libharu/package.py
index 3542582df8..9193de7e96 100644
--- a/var/spack/repos/builtin/packages/libharu/package.py
+++ b/var/spack/repos/builtin/packages/libharu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -34,11 +15,17 @@ class Libharu(AutotoolsPackage):
 
     homepage = "http://libharu.org"
     url      = "https://github.com/libharu/libharu/archive/RELEASE_2_3_0.tar.gz"
+    git      = "https://github.com/libharu/libharu.git"
 
+    version('master', branch='master')
     version('2.3.0', '4f916aa49c3069b3a10850013c507460')
     version('2.2.0', 'b65a6fc33a0bdad89bec6b7def101f01')
-    version('master', branch='master',
-            git='https://github.com/libharu/libharu.git')
+
+    depends_on('libtool', type=('build'))
+    depends_on('autoconf', type=('build'))
+    depends_on('automake', type=('build'))
+    depends_on('libpng')
+    depends_on('zlib')
 
     def autoreconf(self, spec, prefix):
         """execute their autotools wrapper script"""
@@ -46,6 +33,16 @@ class Libharu(AutotoolsPackage):
             bash = which('bash')
             bash('./buildconf.sh', '--force')
 
+    def configure_args(self):
+        """Point to spack-installed zlib and libpng"""
+        spec = self.spec
+        args = []
+
+        args.append('--with-zlib={0}'.format(spec['zlib'].prefix))
+        args.append('--with-png={0}'.format(spec['libpng'].prefix))
+
+        return args
+
     def url_for_version(self, version):
         url = 'https://github.com/libharu/libharu/archive/RELEASE_{0}.tar.gz'
         return url.format(version.underscored)
diff --git a/var/spack/repos/builtin/packages/libhio/0001-configury-fix-a-problem-with-bz2-configury.patch b/var/spack/repos/builtin/packages/libhio/0001-configury-fix-a-problem-with-bz2-configury.patch
new file mode 100644
index 0000000000..b5cf61bdc6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libhio/0001-configury-fix-a-problem-with-bz2-configury.patch
@@ -0,0 +1,38 @@
+From 3a7b7432a7354661d0a971b074c30529f5db457c Mon Sep 17 00:00:00 2001
+From: Howard Pritchard <howardp@lanl.gov>
+Date: Sat, 10 Mar 2018 13:51:41 -0800
+Subject: [PATCH] configury: fix a problem with bz2 configury
+
+turns out by default spack wants to use a non-default
+location bz2, or we have to turn it off.  either way
+the bz2 configury is wrong and needs to be fixed.
+
+Signed-off-by: Howard Pritchard <howardp@lanl.gov>
+
+diff --git a/m4/hio_check_bz2.m4 b/m4/hio_check_bz2.m4
+index 3a373ad1..b7dfdb75 100644
+--- a/m4/hio_check_bz2.m4
++++ b/m4/hio_check_bz2.m4
+@@ -1,9 +1,9 @@
+ # -*- mode: shell-script -*-
+-# Copyright 2015-2016 Los Alamos National Security, LLC. All rights
++# Copyright 2015-2018 Los Alamos National Security, LLC. All rights
+ #                     reserved.
+ 
+ AC_DEFUN([HIO_CHECK_BZ2],[
+-    AC_ARG_WITH(bz2, [AS_HELP_STRING([--with-external-bz2=PATH],
++    AC_ARG_WITH(external-bz2, [AS_HELP_STRING([--with-external_bz2=PATH],
+                                      [use external bzip2. pass yes to use default version @<:@default=no@:>@])],
+                 [], [with_external_bz2=no])
+ 
+@@ -14,6 +14,7 @@ AC_DEFUN([HIO_CHECK_BZ2],[
+             else
+                 LDFLAGS="$LDFLAGS -L$with_external_bz2/lib64"
+             fi
++            LIBS="$LIBS -lbz2"
+         fi
+ 
+         AC_CHECK_LIB([bz2],[BZ2_bzBuffToBuffCompress],[hio_have_bz2=1])
+-- 
+2.4.0.rc3.16.g0ab00b9
+
diff --git a/var/spack/repos/builtin/packages/libhio/0001-hdf5-make-docs-optional.patch b/var/spack/repos/builtin/packages/libhio/0001-hdf5-make-docs-optional.patch
new file mode 100644
index 0000000000..588edec602
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libhio/0001-hdf5-make-docs-optional.patch
@@ -0,0 +1,37 @@
+From 6aec1b94fe84f2fe3a82e3ff338fd4721c84db34 Mon Sep 17 00:00:00 2001
+From: Howard Pritchard <howardp@lanl.gov>
+Date: Mon, 12 Mar 2018 14:19:28 -0700
+Subject: [PATCH] hdf5: make docs optional
+
+With the current makefile, configuring in hdf5
+hio plugin always ends up trying to generate docs.
+Make generating hdf5/hio plugin docs optional with
+
+make docs
+
+Signed-off-by: Howard Pritchard <howardp@lanl.gov>
+
+diff --git a/hdf5-hio/Makefile.am b/hdf5-hio/Makefile.am
+index e4c93b77..1733866d 100644
+--- a/hdf5-hio/Makefile.am
++++ b/hdf5-hio/Makefile.am
+@@ -1,6 +1,6 @@
+ # -*- Makefile.am -*-
+ #
+-# Copyright (c) 2014-2016 Los Alamos National Security, LLC. All rights
++# Copyright (c) 2014-2018 Los Alamos National Security, LLC. All rights
+ #                         reserved.
+ # $COPYRIGHT$
+ #
+@@ -11,7 +11,7 @@
+ 
+ ACLOCAL_AMFLAGS=-I m4
+ 
+-SUBDIRS = src test doc
++SUBDIRS = src test
+ 
+ EXTRA_DIST =
+ DISTCLEANFILES =
+-- 
+2.4.0.rc3.16.g0ab00b9
+
diff --git a/var/spack/repos/builtin/packages/libhio/0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch b/var/spack/repos/builtin/packages/libhio/0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch
new file mode 100644
index 0000000000..f9b8b8e163
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libhio/0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch
@@ -0,0 +1,31 @@
+From f6f806c2ea46866c9490d2d2ddc3f119666d26d4 Mon Sep 17 00:00:00 2001
+From: Howard Pritchard <hppritcha@gmail.com>
+Date: Mon, 17 Sep 2018 05:05:01 -0600
+Subject: [PATCH] spack: fix for spack to work on non-cray systems
+
+or when one wants to use Open MPI on a cray system with spack.
+The problem is that when using an MPI with spack, its going to
+use a long value for the CC and CXX variables.  This confused
+the libhio configury, resulting in it being built without mpi
+support, leading to failure of xexec to properly compile, etc.
+
+This commit fixes that problem.
+
+Signed-off-by: Howard Pritchard <hppritcha@gmail.com>
+
+diff --git a/configure.ac b/configure.ac
+index afab5553..62d35c85 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -37,7 +37,7 @@ if ( test -n "$XTOS_VERSION" || test -n "$CRAYPE_DIR" ) && (test -z $CC || test
+     if test ! -n "$LD" ; then
+         LD=ld
+     fi
+-elif test ${MPICC} = "mpicc" ; then
++elif test -n "$MPICC" ; then
+     CC=${MPICC}
+     CXX=${MPICXX}
+     hio_use_mpi=1
+-- 
+1.8.3.1
+
diff --git a/var/spack/repos/builtin/packages/libhio/package.py b/var/spack/repos/builtin/packages/libhio/package.py
index db74e7c546..64224b6528 100644
--- a/var/spack/repos/builtin/packages/libhio/package.py
+++ b/var/spack/repos/builtin/packages/libhio/package.py
@@ -1,40 +1,62 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 from spack import *
 
 
 class Libhio(AutotoolsPackage):
-    """
-    A library for writing to hierarchical data store systems.
+    """libHIO is a flexible, high-performance parallel IO package developed
+       at LANL.  libHIO supports IO to either a conventional PFS or to Cray
+       DataWarp with management of Cray DataWarp space and stage-in and
+       stage-out from and to the PFS.
     """
 
-    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"
+    homepage = "https://github.com/hpc/libhio"
+    url      = "https://github.com/hpc/libhio/releases/download/hio.1.4.1.0/libhio-1.4.1.0.tar.bz2"
 
-    version('1.3.0.1', 'c073541de8dd70aeb8878bd00d6d877f')
+    #
+    # We don't include older versions since they are missing features
+    # needed by current and future consumers of libhio
+    #
+    version('1.4.1.2', '38c7d33210155e5796b16d536d1b5cfe')
+    version('1.4.1.0', '6ef566fd8cf31fdcd05fab01dd3fae44')
+
+    #
+    # main users of libhio thru spack will want to use HFDF5 plugin,
+    # so make hdf5 variant a default
+    #
+    variant('hdf5', default=True, description='Enable HDF5 support')
 
     depends_on("json-c")
     depends_on("bzip2")
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
+    depends_on('mpi')
+
+    #
+    # libhio depends on hdf5+mpi if hdf5 is being used since it
+    # autodetects the presence of an MPI and/or uses mpicc by default to build
+    depends_on('hdf5+mpi', when='+hdf5')
+
+    #
+    # wow, we need to patch libhio
+    #
+    patch('0001-configury-fix-a-problem-with-bz2-configury.patch', when="@1.4.1.0")
+    patch('0001-hdf5-make-docs-optional.patch', when="@1.4.1.0")
+    patch('0001-spack-fix-for-spack-to-work-on-non-cray-systems.patch', when="@1.4.1.2")
+
+    def autoreconf(self, spec, prefix):
+        autoreconf = which('autoreconf')
+        autoreconf('-ifv')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        args.append('--with-external_bz2={0}'.format(spec['bzip2'].prefix))
+        if '+hdf5' in spec:
+            args.append('--with-hdf5={0}'.format(spec['hdf5'].prefix))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/libiberty/package.py b/var/spack/repos/builtin/packages/libiberty/package.py
new file mode 100644
index 0000000000..166979d30c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libiberty/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+# Libiberty has two homes: binutils and gcc.  This package uses the
+# binutils tarfile but only builds the libiberty subdirectory.  This
+# is useful for other packages that want the demangling functions
+# without the rest of binutils.
+
+class Libiberty(AutotoolsPackage):
+    """The libiberty.a library from GNU binutils.  Libiberty provides
+    demangling and support functions for the GNU toolchain."""
+
+    homepage = "https://www.gnu.org/software/binutils/"
+    url      = "https://ftpmirror.gnu.org/binutils/binutils-2.31.1.tar.xz"
+
+    version('2.31.1', '5b7c9d4ce96f507d95c1b9a255e52418')
+    version('2.30',   'ffc476dd46c96f932875d1b2e27e929f')
+    version('2.29.1', 'acc9cd826edb9954ac7cecb81c727793')
+    version('2.28.1', 'a3bf359889e4b299fce1f4cb919dc7b6')
+
+    variant('pic', default=False,
+            description='Compile with position independent code.')
+
+    # Configure and build just libiberty.
+    configure_directory = 'libiberty'
+
+    # Set default cflags (-g -O2), add -fPIC if requested, and move to
+    # the configure line.
+    def flag_handler(self, name, flags):
+        if name != 'cflags':
+            return (flags, None, None)
+
+        if '-g' not in flags:
+            flags.append('-g')
+
+        for flag in flags:
+            if flag.startswith('-O'):
+                break
+        else:
+            flags.append('-O2')
+
+        if '+pic' in self.spec:
+            flags.append(self.compiler.pic_flag)
+
+        return (None, None, flags)
+
+    def configure_args(self):
+        args = ['--enable-install-libiberty']
+        return args
diff --git a/var/spack/repos/builtin/packages/libice/package.py b/var/spack/repos/builtin/packages/libice/package.py
index 4ffc67ed9c..501fe81677 100644
--- a/var/spack/repos/builtin/packages/libice/package.py
+++ b/var/spack/repos/builtin/packages/libice/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Libice(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libiconv/package.py b/var/spack/repos/builtin/packages/libiconv/package.py
index 1e3d29a4df..b435f19f1e 100644
--- a/var/spack/repos/builtin/packages/libiconv/package.py
+++ b/var/spack/repos/builtin/packages/libiconv/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import shutil
 
 
 class Libiconv(AutotoolsPackage):
@@ -31,7 +11,7 @@ class Libiconv(AutotoolsPackage):
     and the iconv program for character set conversion."""
 
     homepage = "https://www.gnu.org/software/libiconv/"
-    url      = "http://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.15.tar.gz"
+    url      = "https://ftpmirror.gnu.org/libiconv/libiconv-1.15.tar.gz"
 
     version('1.15', 'ace8b5f2db42f7b3b3057585e80d9808')
     version('1.14', 'e34509b1623cec449dfeb73d7ce9c6c6')
@@ -40,10 +20,12 @@ class Libiconv(AutotoolsPackage):
     # of C11 any more and thus might not exist.
     patch('gets.patch', when='@1.14')
 
+    conflicts('@1.14', when='%gcc@5:')
+
     def configure_args(self):
         args = ['--enable-extra-encodings']
 
         # A hack to patch config.guess in the libcharset sub directory
-        shutil.copyfile('./build-aux/config.guess',
-                        'libcharset/build-aux/config.guess')
+        copy('./build-aux/config.guess',
+             'libcharset/build-aux/config.guess')
         return args
diff --git a/var/spack/repos/builtin/packages/libint/package.py b/var/spack/repos/builtin/packages/libint/package.py
index 8fa0906658..1ea8031dec 100644
--- a/var/spack/repos/builtin/packages/libint/package.py
+++ b/var/spack/repos/builtin/packages/libint/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -64,11 +45,10 @@ class Libint(AutotoolsPackage):
     @property
     def optflags(self):
         flags = '-O2'
-
         # Optimizations for the Intel compiler, suggested by CP2K
+        # See ../libxc/package.py for rationale and doc.
         if '%intel' in self.spec:
-            # -xSSE2 will make it usable on old architecture
-            flags += ' -xSSE2 -xAVX -axCORE-AVX2 -ipo'
+            flags += ' -xSSE4.2 -axAVX,CORE-AVX2 -ipo'
 
         return flags
 
diff --git a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
index 2264147362..e57b8b84d2 100644
--- a/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
+++ b/var/spack/repos/builtin/packages/libjpeg-turbo/package.py
@@ -1,41 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class LibjpegTurbo(AutotoolsPackage):
+class LibjpegTurbo(Package):
     """libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to
        accelerate baseline JPEG compression and decompression. libjpeg is a
        library that implements JPEG image encoding, decoding and
        transcoding."""
+    # https://github.com/libjpeg-turbo/libjpeg-turbo/blob/master/BUILDING.md
+    homepage = "https://libjpeg-turbo.org/"
+    url      = "https://github.com/libjpeg-turbo/libjpeg-turbo/archive/1.5.90.tar.gz"
 
-    homepage = "http://libjpeg-turbo.virtualgl.org"
-    url      = "http://downloads.sourceforge.net/libjpeg-turbo/libjpeg-turbo-1.3.1.tar.gz"
-
-    version('1.5.0', '3fc5d9b6a8bce96161659ae7a9939257')
-    version('1.3.1', '2c3a68129dac443a72815ff5bb374b05')
+    version('1.5.90', '85f7f9c377b70cbf48e61726097d4efa')
+    version('1.5.3', '5b7549d440b86c98a517355c102d155e')
+    version('1.5.0', 'eff98ac84de05eafc65ae96caa6e23e9')
+    version('1.3.1', '5e4bc19c3cb602bcab1296b9bee5124c')
 
     provides('jpeg')
 
@@ -45,3 +28,27 @@ class LibjpegTurbo(AutotoolsPackage):
     # TODO: Implement the selection between two supported assemblers.
     # depends_on("yasm", type='build')
     depends_on("nasm", type='build')
+    depends_on('autoconf', type='build', when="@1.3.1:1.5.3")
+    depends_on('automake', type='build', when="@1.3.1:1.5.3")
+    depends_on('libtool', type='build', when="@1.3.1:1.5.3")
+    depends_on('cmake', type='build', when="@1.5.90:")
+
+    @property
+    def libs(self):
+        return find_libraries("libjpeg*", root=self.prefix, recursive=True)
+
+    @when('@1.3.1:1.5.3')
+    def install(self, spec, prefix):
+        autoreconf('-ifv')
+        configure('--prefix=%s' % prefix)
+        make()
+        make('install')
+
+    @when('@1.5.90:')
+    def install(self, spec, prefix):
+        cmake_args = ['-GUnix Makefiles']
+        cmake_args.extend(std_cmake_args)
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make('install')
diff --git a/var/spack/repos/builtin/packages/libjpeg/package.py b/var/spack/repos/builtin/packages/libjpeg/package.py
index bd789200cb..908b6f6bea 100644
--- a/var/spack/repos/builtin/packages/libjpeg/package.py
+++ b/var/spack/repos/builtin/packages/libjpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,15 @@ class Libjpeg(AutotoolsPackage):
     alongside various utilities for handling JPEG data."""
 
     homepage = "http://www.ijg.org"
-    url      = "http://www.ijg.org/files/jpegsrc.v9b.tar.gz"
+    url      = "http://www.ijg.org/files/jpegsrc.v9c.tar.gz"
 
+    version('9c', '93c62597eeef81a84d988bccbda1e990')
     version('9b', '6a9996ce116ec5c52b4870dbcd6d3ddb')
     version('9a', '3353992aecaee1805ef4109aadd433e7')
 
     provides('jpeg')
+
+    def check(self):
+        # Libjpeg has both 'check' and 'test' targets that are aliases.
+        # Only need to run the tests once.
+        make('check')
diff --git a/var/spack/repos/builtin/packages/libksba/package.py b/var/spack/repos/builtin/packages/libksba/package.py
index a9f498e3d3..48be52968f 100644
--- a/var/spack/repos/builtin/packages/libksba/package.py
+++ b/var/spack/repos/builtin/packages/libksba/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/liblbxutil/package.py b/var/spack/repos/builtin/packages/liblbxutil/package.py
index 90be9b3cdd..32c49195d3 100644
--- a/var/spack/repos/builtin/packages/liblbxutil/package.py
+++ b/var/spack/repos/builtin/packages/liblbxutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,7 +16,7 @@ class Liblbxutil(AutotoolsPackage):
 
     depends_on('xextproto@7.0.99.1:', type='build')
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # There is a bug in the library that causes the following messages:
diff --git a/var/spack/repos/builtin/packages/liblockfile/install_as_nonroot.patch b/var/spack/repos/builtin/packages/liblockfile/install_as_nonroot.patch
new file mode 100644
index 0000000000..66c6f994eb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/liblockfile/install_as_nonroot.patch
@@ -0,0 +1,46 @@
+--- liblockfile-1.14/Makefile.in	2017-01-17 13:21:05.000000000 +0000
++++ liblockfile-1.14/Makefile.in	2018-03-28 07:20:45.054312625 +0000
+@@ -49,35 +49,33 @@ xlockfile.o:	lockfile.c
+ 		$(CC) $(CFLAGS) -c lockfile.c -o xlockfile.o
+ 
+ install_static:	static install_common
+-		install -d -m 755 -g root -p $(libdir)
++		install -d -m 755 -p $(libdir)
+ 		install -m 644 liblockfile.a $(libdir)
+ 
+ install_shared:	shared install_static install_common
+-		install -d -m 755 -g root -p $(libdir)
++		install -d -m 755 -p $(libdir)
+ 		install -m 755 liblockfile.so \
+ 			$(libdir)/liblockfile.so.$(SOVER)
+ 		ln -s liblockfile.so.$(SOVER) $(libdir)/liblockfile.so.$(MAJOR)
+ 		ln -s liblockfile.so.$(SOVER) $(libdir)/liblockfile.so
+-		if test "$(DESTDIR)" = ""; then @LDCONFIG@; fi
+ 
+ install_common:
+-		install -d -m 755 -g root -p $(includedir)
+-		install -d -m 755 -g root -p $(bindir)
+-		install -d -m 755 -g root -p $(mandir)/man1
+-		install -d -m 755 -g root -p $(mandir)/man3
++		install -d -m 755 -p $(includedir)
++		install -d -m 755 -p $(bindir)
++		install -d -m 755 -p $(mandir)/man1
++		install -d -m 755 -p $(mandir)/man3
+ 		install -m 644 lockfile.h maillock.h $(includedir)
+ 		if [ "$(MAILGROUP)" != "" ]; then\
+ 		  install -g $(MAILGROUP) -m 2755 dotlockfile $(bindir);\
+ 		else \
+-		  install -g root -m 755 dotlockfile $(bindir); \
++		  install -m 755 dotlockfile $(bindir); \
+ 		fi
+ 		install -m 644 *.1 $(mandir)/man1
+ 		install -m 644 *.3 $(mandir)/man3
+ 
+ install_nfslib:	nfslib
+-		install -d -m 755 -g root -p $(nfslockdir)
++		install -d -m 755 -p $(nfslockdir)
+ 		install -m 755 nfslock.so.$(NFSVER) $(nfslockdir)
+-		if test "$(DESTDIR)" = ""; then @LDCONFIG@; fi
+ 
+ clean:
+ 		rm -f *.a *.o *.so *.so.* dotlockfile
diff --git a/var/spack/repos/builtin/packages/liblockfile/package.py b/var/spack/repos/builtin/packages/liblockfile/package.py
new file mode 100644
index 0000000000..1598a026a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/liblockfile/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Liblockfile(AutotoolsPackage):
+    """NFS-safe locking library"""
+
+    homepage = "https://github.com/miquels/liblockfile"
+    url      = "https://github.com/miquels/liblockfile/archive/v1.14.tar.gz"
+
+    version('1.14', '24ce9dbb34d7f508a52a91f762746ce3')
+
+    patch('install_as_nonroot.patch')
+
+    def configure_args(self):
+        args = ['--enable-shared']
+        return args
diff --git a/var/spack/repos/builtin/packages/libmatheval/guile-2.0.patch b/var/spack/repos/builtin/packages/libmatheval/guile-2.0.patch
new file mode 100644
index 0000000000..18bacb44ca
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libmatheval/guile-2.0.patch
@@ -0,0 +1,197 @@
+--- libmatheval-1.1.11-v/configure	2018-07-13 11:16:19.115719477 +0200
++++ libmatheval-1.1.11/configure	2018-07-13 11:33:07.914093005 +0200
+@@ -640,6 +640,7 @@
+ GUILE_CFLAGS
+ GUILE_TOOLS
+ GUILE_CONFIG
++GUILE_EFFECTIVE_VERSION
+ GUILE
+ AUTOM4TE
+ YFLAGS
+@@ -4831,21 +4832,6 @@
+ 
+ 
+ 
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+-
+ # Check whether --with-gnu-ld was given.
+ if test "${with_gnu_ld+set}" = set; then :
+   withval=$with_gnu_ld; test "$withval" = no || with_gnu_ld=yes
+@@ -12267,8 +12253,9 @@
+  break
+ fi
+ done
++# start patch
+ 
+-
++CPPFLAGS="$GUILE_CFLAGS  -DSCM_ENABLE_DEPRECATED=0 $CPPFLAGS"
+ ac_fn_c_check_type "$LINENO" "scm_t_bits" "ac_cv_type_scm_t_bits" "#include <libguile.h>
+ "
+ if test "x$ac_cv_type_scm_t_bits" = xyes; then :
+@@ -12276,14 +12263,15 @@
+ $as_echo "#define HAVE_SCM_T_BITS 1" >>confdefs.h
+ 
+ fi
+-
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_c_define_gsubr in -lguile" >&5
+-$as_echo_n "checking for scm_c_define_gsubr in -lguile... " >&6; }
+-if ${ac_cv_lib_guile_scm_c_define_gsubr+:} false; then :
++GUILE_EFFECTIVE_VERSION=2.0
++as_ac_Lib=`$as_echo "ac_cv_lib_guile-$GUILE_EFFECTIVE_VERSION''_scm_c_define_gsubr" | $as_tr_sh`
++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_c_define_gsubr in -lguile-$GUILE_EFFECTIVE_VERSION" >&5
++$as_echo_n "checking for scm_c_define_gsubr in -lguile-$GUILE_EFFECTIVE_VERSION... " >&6; }
++if eval \${$as_ac_Lib+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lguile $GUILE_LDFLAGS $LIBS"
++LIBS="-lguile-$GUILE_EFFECTIVE_VERSION $GUILE_LDFLAGS $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -12303,29 +12291,31 @@
+ }
+ _ACEOF
+ if ac_fn_c_try_link "$LINENO"; then :
+-  ac_cv_lib_guile_scm_c_define_gsubr=yes
++  eval "$as_ac_Lib=yes"
+ else
+-  ac_cv_lib_guile_scm_c_define_gsubr=no
++  eval "$as_ac_Lib=no"
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+     conftest$ac_exeext conftest.$ac_ext
+ LIBS=$ac_check_lib_save_LIBS
+ fi
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_guile_scm_c_define_gsubr" >&5
+-$as_echo "$ac_cv_lib_guile_scm_c_define_gsubr" >&6; }
+-if test "x$ac_cv_lib_guile_scm_c_define_gsubr" = xyes; then :
++eval ac_res=\$$as_ac_Lib
++	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
++$as_echo "$ac_res" >&6; }
++if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
+ 
+ $as_echo "#define HAVE_SCM_C_DEFINE_GSUBR 1" >>confdefs.h
+ 
+ fi
+ 
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_make_gsubr in -lguile" >&5
+-$as_echo_n "checking for scm_make_gsubr in -lguile... " >&6; }
+-if ${ac_cv_lib_guile_scm_make_gsubr+:} false; then :
++as_ac_Lib=`$as_echo "ac_cv_lib_guile-$GUILE_EFFECTIVE_VERSION''_scm_make_gsubr" | $as_tr_sh`
++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_make_gsubr in -lguile-$GUILE_EFFECTIVE_VERSION" >&5
++$as_echo_n "checking for scm_make_gsubr in -lguile-$GUILE_EFFECTIVE_VERSION... " >&6; }
++if eval \${$as_ac_Lib+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lguile $GUILE_LDFLAGS $LIBS"
++LIBS="-lguile-$GUILE_EFFECTIVE_VERSION $GUILE_LDFLAGS $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -12345,29 +12335,31 @@
+ }
+ _ACEOF
+ if ac_fn_c_try_link "$LINENO"; then :
+-  ac_cv_lib_guile_scm_make_gsubr=yes
++  eval "$as_ac_Lib=yes"
+ else
+-  ac_cv_lib_guile_scm_make_gsubr=no
++  eval "$as_ac_Lib=no"
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+     conftest$ac_exeext conftest.$ac_ext
+ LIBS=$ac_check_lib_save_LIBS
+ fi
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_guile_scm_make_gsubr" >&5
+-$as_echo "$ac_cv_lib_guile_scm_make_gsubr" >&6; }
+-if test "x$ac_cv_lib_guile_scm_make_gsubr" = xyes; then :
++eval ac_res=\$$as_ac_Lib
++	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
++$as_echo "$ac_res" >&6; }
++if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
+ 
+ $as_echo "#define HAVE_SCM_MAKE_GSUBR 1" >>confdefs.h
+ 
+ fi
+ 
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_num2dbl in -lguile" >&5
+-$as_echo_n "checking for scm_num2dbl in -lguile... " >&6; }
+-if ${ac_cv_lib_guile_scm_num2dbl+:} false; then :
++as_ac_Lib=`$as_echo "ac_cv_lib_guile-$GUILE_EFFECTIVE_VERSION''_scm_num2dbl" | $as_tr_sh`
++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for scm_num2dbl in -lguile-$GUILE_EFFECTIVE_VERSION" >&5
++$as_echo_n "checking for scm_num2dbl in -lguile-$GUILE_EFFECTIVE_VERSION... " >&6; }
++if eval \${$as_ac_Lib+:} false; then :
+   $as_echo_n "(cached) " >&6
+ else
+   ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lguile $GUILE_LDFLAGS $LIBS"
++LIBS="-lguile-$GUILE_EFFECTIVE_VERSION $GUILE_LDFLAGS $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h.  */
+ 
+@@ -12387,22 +12379,25 @@
+ }
+ _ACEOF
+ if ac_fn_c_try_link "$LINENO"; then :
+-  ac_cv_lib_guile_scm_num2dbl=yes
++  eval "$as_ac_Lib=yes"
+ else
+-  ac_cv_lib_guile_scm_num2dbl=no
++  eval "$as_ac_Lib=no"
+ fi
+ rm -f core conftest.err conftest.$ac_objext \
+     conftest$ac_exeext conftest.$ac_ext
+ LIBS=$ac_check_lib_save_LIBS
+ fi
+-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_guile_scm_num2dbl" >&5
+-$as_echo "$ac_cv_lib_guile_scm_num2dbl" >&6; }
+-if test "x$ac_cv_lib_guile_scm_num2dbl" = xyes; then :
++eval ac_res=\$$as_ac_Lib
++	       { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_res" >&5
++$as_echo "$ac_res" >&6; }
++if eval test \"x\$"$as_ac_Lib"\" = x"yes"; then :
+ 
+ $as_echo "#define HAVE_SCM_NUM2DBL 1" >>confdefs.h
+ 
+ fi
+ 
++# end patch
++# end patch
+ 
+ ac_config_files="$ac_config_files Makefile doc/Makefile lib/Makefile"
+ 
+--- libmatheval-1.1.11-v/tests/matheval.c.bak	2018-07-13 12:43:21.718862366 +0200
++++ libmatheval-1.1.11/tests/matheval.c	2018-07-13 12:46:34.162597100 +0200
+@@ -51,7 +51,7 @@
+ 
+ /* Guile interface for libmatheval library.  Procedures below are simple
+  * wrappers for corresponding libmatheval procedures. */
+-static scm_sizet evaluator_destroy_scm(SCM evaluator_smob);
++static size_t    evaluator_destroy_scm(SCM evaluator_smob);
+ static SCM      evaluator_create_scm(SCM string);
+ static SCM      evaluator_evaluate_scm(SCM evaluator_smob, SCM count,
+ 				       SCM names, SCM values);
+@@ -122,7 +122,7 @@
+ }
+ 
+ /* Wrapper for evaluator_destroy() procedure from libmatheval library. */
+-static          scm_sizet
++static          size_t
+ evaluator_destroy_scm(SCM evaluator_smob)
+ {
+ 	SCM_ASSERT((SCM_NIMP(evaluator_smob)
diff --git a/var/spack/repos/builtin/packages/libmatheval/guile-2.2.patch b/var/spack/repos/builtin/packages/libmatheval/guile-2.2.patch
new file mode 100644
index 0000000000..394f9ebdef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libmatheval/guile-2.2.patch
@@ -0,0 +1,20 @@
+--- libmatheval-1.1.11/Makefile.in.orig	2018-07-13 17:42:03.426339145 +0200
++++ libmatheval-1.1.11/Makefile.in	2018-07-13 17:42:24.190310979 +0200
+@@ -316,7 +316,7 @@
+ MAINTAINERCLEANFILES = Makefile.in aclocal.m4 configure config.h.in	\
+ config.log config.status stamp-h.in $(AUX_DIST)
+ 
+-SUBDIRS = doc lib tests
++SUBDIRS = doc lib 
+ pkgconfigdir = $(libdir)/pkgconfig
+ pkgconfig_DATA = libmatheval.pc
+ all: config.h
+@@ -863,7 +863,7 @@
+ .PHONY: beauty dist-hook
+ 
+ beauty:
+-	-for dir in lib tests; do cd $$dir; $(MAKE) $@; cd ..; done
++	-for dir in lib ; do cd $$dir; $(MAKE) $@; cd ..; done
+ 
+ dist-hook:
+ 	for file in $(AUX_DIST); do \
diff --git a/var/spack/repos/builtin/packages/libmatheval/package.py b/var/spack/repos/builtin/packages/libmatheval/package.py
index f0992c4b42..da39d24515 100644
--- a/var/spack/repos/builtin/packages/libmatheval/package.py
+++ b/var/spack/repos/builtin/packages/libmatheval/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,18 @@ class Libmatheval(AutotoolsPackage):
     compute symbolic derivatives and output expressions to strings."""
 
     homepage = "https://www.gnu.org/software/libmatheval/"
-    url      = "https://ftp.gnu.org/gnu/libmatheval/libmatheval-1.1.11.tar.gz"
+    url      = "https://ftpmirror.gnu.org/libmatheval/libmatheval-1.1.11.tar.gz"
 
     version('1.1.11', '595420ea60f6ddd75623847f46ca45c4')
 
     # Only needed for unit tests, but configure crashes without it
     depends_on('guile', type='build')
+
+    depends_on('flex')
+
+    # guile 2.0 provides a deprecated interface for the unit test using guile
+    patch('guile-2.0.patch', when='^guile@2.0')
+
+    # guile 2.2 does not support deprecated functions any longer
+    # the patch skips the unit tests
+    patch('guile-2.2.patch', when='^guile@2.2:')
diff --git a/var/spack/repos/builtin/packages/libmaxminddb/package.py b/var/spack/repos/builtin/packages/libmaxminddb/package.py
new file mode 100644
index 0000000000..abe154bb01
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libmaxminddb/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libmaxminddb(AutotoolsPackage):
+    """C library for the MaxMind DB file format"""
+
+    homepage = "https://github.com/maxmind/libmaxminddb"
+    url      = "https://github.com/maxmind/libmaxminddb/releases/download/1.3.2/libmaxminddb-1.3.2.tar.gz"
+
+    version('1.3.2', '67a861965b30d045bf29a2126bcc05ed')
+
+    def configure_args(self):
+        args = ['--disable-debug',
+                '--disable-dependency-tracking',
+                '--disable-silent-rules']
+        return args
diff --git a/var/spack/repos/builtin/packages/libmesh/package.py b/var/spack/repos/builtin/packages/libmesh/package.py
index 20603a6589..d21e056b33 100644
--- a/var/spack/repos/builtin/packages/libmesh/package.py
+++ b/var/spack/repos/builtin/packages/libmesh/package.py
@@ -1,56 +1,212 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Libmesh(Package):
+class Libmesh(AutotoolsPackage):
     """The libMesh library provides a framework for the numerical simulation of
        partial differential equations using arbitrary unstructured
        discretizations on serial and parallel platforms."""
 
     homepage = "http://libmesh.github.io/"
     url      = "https://github.com/libMesh/libmesh/releases/download/v1.0.0/libmesh-1.0.0.tar.bz2"
+    git      = "https://github.com/libMesh/libmesh.git"
 
+    version('1.3.0', sha256='a8cc2cd44f42b960989dba10fa438b04af5798c46db0b4ec3ed29591b8359786')
+    version('1.2.1', sha256='11c22c7d96874a17de6b8c74caa45d6745d40bf3610e88b2bd28fd3381f5ba70')
     version('1.0.0', 'cb464fc63ea0b71b1e69fa3f5d4f93a4')
 
+    # support for libraries that are only available through the bundled copies:
+    # TODO libMesh 1.2.1 gained the ability to specify a path to capnproto
+    variant('capnproto', default=False, description='Compile with the bundled capnproto serialization library')
+    variant('exodusii', default=False, description='Compile with the bundled ExodusII output library')
+    variant('fparser', default=False, description='Compile with the bundled fparser function parser library')
+    variant('gmv', default=False, description='Compile with the bundled gmv format IO library')
+    variant('laspack', default=False, description='Compile with the bundled laspack interative solver library')
+    variant('libhilbert', default=False, description='Compile with the bundled libHilbert partitioning library')
+    variant('metaphysicl', default=False, description='Compile with the bundled metaphysicl AD library')
+    variant('metis', default=False, description='Compile with the bundled METIS graph partitioning library')
+    variant('nanoflann', default=False, description='Compile with the bundled nanoflann graph library')
+    variant('nemesis', default=False, description='Compile with the bundled nemesis IO library')
+    variant('netcdf', default=False, description='Compile with the bundled NETCDF IO library')
+    # TODO the copy of parmetis bundled with libMesh assumes that we use the
+    # bundled copy of metis, but previous versions of this build script use an
+    # external metis installation. Be conservative and completely disable
+    # parmetis support to preserve the old behavior (and to prevent compiling
+    # with two different copies of metis).
+    #
+    # variant('parmetis', default=False,
+    #         description='Compile with the bundled PARMETIS graph library')
+    variant('qhull', default=False, description='Compile with the bundled qhull mesh generation library')
+    variant('sfc', default=False, description='Compile with the bundled sfcurves partitioning library')
+    variant('tetgen', default=False, description='Compile with the bundled tetgen mesh generation library')
+    variant('triangle', default=False, description='Compile with the bundled Triangle mesh generation library')
+
+    # support for libraries that may be externally installed:
+    variant('boost', default=False, description='Compile with components dependent on boost')
+    variant('eigen', default=False, description='support for dense linear algebra with Eigen')
+    variant('hdf5', default=False, description='Compile with support for HDF5 files')
+    variant('slepc', default=False, description='Compile with support for the SLEPc eigensolver')
+
+    # other features:
+    variant('debug', default=False, description='Compile with support for debugging')
     variant('mpi', default=True, description='Enables MPI parallelism')
+    # While it is possible to configure libMesh to use openMP with neither
+    # pthreads nor TBB, no openMP code can actually be reached without enabling
+    # pthreads as well. Hence, since enabling openMP while disabling pthreads
+    # is not useful, we include openMP in the same variant to make it clear
+    # which scheduler is ultimately used.
+    variant('threads', default='none',
+            description='Enable threading support (with a particular '
+            'scheduler, in the case of openmp and tbb)',
+            values=('none', 'pthreads', 'tbb', 'openmp'), multi=False)
 
-    depends_on('mpi', when='+mpi')
+    conflicts('+metaphysicl', when='@:1.2.999',
+              msg='The interface to metaphysicl is not available in libMesh '
+              'versions older than 1.3.0. Please explicitly disable this '
+              'variant.')
 
-    # Parallel version of libmesh needs parallel solvers
+    depends_on('boost', when='+boost')
+    # The Scotch dependency of Eigen is not used by libMesh. Since Scotch can
+    # only be used with certain versions of flex it conflicts with several
+    # versions of GCC, so explicitly disable it.
+    depends_on('eigen~scotch', when='+eigen')
+    depends_on('hdf5+mpi', when='+hdf5+mpi')
+    depends_on('mpi', when='+mpi')
+    depends_on('mpi', when='+slepc')
+    # compilation dependencies depend on perl
+    depends_on('perl')
     depends_on('petsc+mpi', when='+mpi')
+    depends_on('petsc+metis', when='+metis')
+    depends_on('slepc', when='+slepc')
+    depends_on('tbb', when='threads=tbb')
+
+    def configure_args(self):
+        options = []
+
+        # GLIBCXX debugging is not, by default, supported by other libraries,
+        # so unconditionally disable it for libmesh
+        options.append('--enable-glibcxx-debugging=no')
+
+        # All bundled dependencies are explicitly disabled, so we do not need
+        # to perform this check:
+        options.append('--disable-strict-lgpl')
+
+        # The Hinnant unique pointer implementation is incompatible with boost
+        # (and not necessary with C++11 support), so unconditionally disable
+        # it:
+        options.append('--disable-hinnant-unique-ptr')
+        # libMesh does not allow for us to specify an installation location for
+        # zlib, an undocumented dependency of gzstreams: hence we must
+        # unconditionally disable gzstreams.
+        options.append('--enable-gzstreams=no')
+        # Similarly, since we cannot specify a location for bzip2 or xz, so
+        # disable them to avoid picking up system installations:
+        options.append('--disable-bzip2')
+        options.append('--disable-xz')
+        # TODO enable GDB backtracing. Disable for now to avoid picking up the
+        # system gdb installation:
+        options.append('--without-gdb-command')
+
+        # TODO add X11 as a dependency to get tecplot working
+        options.append('--enable-tecio=no')
+        options.append('--enable-tecplot=no')
+
+        # handle the bundled libraries that are not themselves dependencies of
+        # other bundled libaries:
+        for bundled_library in ['capnproto', 'exodusii', 'fparser', 'gmv',
+                                'laspack', 'libHilbert', 'metaphysicl',
+                                'nanoflann', 'nemesis', 'parmetis', 'qhull',
+                                'sfc', 'tetgen', 'triangle']:
+            if '+' + bundled_library.lower() in self.spec:
+                options.append('--enable-' + bundled_library + "=yes")
+            else:
+                options.append('--enable-' + bundled_library + "=no")
+
+        # and the ones which are dependencies of other bundled libraries:
+        if '+exodusii' in self.spec or '+netcdf' in self.spec:
+            options.append('--enable-netcdf=yes')
+        else:
+            options.append('--enable-netcdf=no')
+
+        # handle external library dependencies:
+        if '+boost' in self.spec:
+            options.append('--with-boost=%s' % self.spec['boost'].prefix)
+        else:
+            options.append('--enable-boost=no')
+
+        if '+eigen' in self.spec:
+            options.append('--with-eigen=%s' % self.spec['eigen'].prefix)
+        else:
+            options.append('--enable-eigen=no')
+
+        if '+hdf5' in self.spec:
+            options.append('--with-hdf5=%s' % self.spec['hdf5'].prefix)
+        else:
+            options.append('--enable-hdf5=no')
+            # This is necessary with libMesh 1.2.1 to prevent a configure
+            # error:
+            if '+netcdf' not in self.spec:
+                options.append('--disable-netcdf-4')
+
+        if '+metis' in self.spec:
+            options.append('--with-metis=PETSc')
+
+        if '+petsc' in self.spec:
+            options.append('--enable-petsc=yes')
+            options.append('PETSC_DIR=%s' % self.spec['petsc'].prefix)
+        else:
+            options.append('--enable-petsc=no')
+
+        if '+slepc' in self.spec:
+            options.append('SLEPC_DIR=%s' % self.spec['slepc'].prefix)
+        else:
+            options.append('--enable-slepc=no')
+
+        # and, finally, other things:
+        if '+debug' in self.spec:
+            options.append('--with-methods=dbg')
+        else:
+            options.append('--with-methods=opt')
+
+        if '+mpi' in self.spec:
+            options.append('CC=%s' % self.spec['mpi'].mpicc)
+            options.append('CXX=%s' % self.spec['mpi'].mpicxx)
+            options.append('--with-mpi=%s' % self.spec['mpi'].prefix)
+        else:
+            options.append('--disable-mpi')
+            # libMesh will try to link with the system MPI library unless we
+            # provide explicit overrides
+            options.append('CC=%s' % self.compiler.cc)
+            options.append('CXX=%s' % self.compiler.cxx)
+
+        if 'threads=openmp' in self.spec:
+            # OpenMP cannot be used if pthreads is not available: see
+            # parallel/threads_pthread.h and parallel/threads.h
+            options.append('--enable-openmp=yes')
+            options.append('--with-thread-model=pthread')
+            options.append('--enable-pthreads=yes')
+        else:
+            options.append('--enable-openmp=no')
 
-    def install(self, spec, prefix):
-        config_args = ["--prefix=%s" % prefix]
+        if 'threads=pthreads' in self.spec:
+            options.append('--with-thread-model=pthread')
+            options.append('--enable-pthreads=yes')
+        else:
+            if 'threads=openmp' not in self.spec:
+                options.append('--enable-pthreads=no')
 
-        if '+mpi' in spec:
-            config_args.append('CC=%s' % spec['mpi'].mpicc)
-            config_args.append('CXX=%s' % spec['mpi'].mpicxx)
-            config_args.append('PETSC_DIR=%s' % spec['petsc'].prefix)
+        if 'threads=tbb' in self.spec:
+            options.append('--with-thread-model=tbb')
+            options.append('--enable-tbb=yes')
+            options.append('--with-tbb=%s' % self.spec['tbb'].prefix)
+        else:
+            options.append('--enable-tbb=no')
 
-        configure(*config_args)
+        return options
 
-        make()
-        make('install')
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.append_flags('PERL', self.spec['perl'].command.path)
diff --git a/var/spack/repos/builtin/packages/libmng/package.py b/var/spack/repos/builtin/packages/libmng/package.py
index 95542361ef..e4e11c9594 100644
--- a/var/spack/repos/builtin/packages/libmng/package.py
+++ b/var/spack/repos/builtin/packages/libmng/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libmongoc/package.py b/var/spack/repos/builtin/packages/libmongoc/package.py
index 5050dd0336..2f1dc4d7f7 100644
--- a/var/spack/repos/builtin/packages/libmongoc/package.py
+++ b/var/spack/repos/builtin/packages/libmongoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,10 @@ class Libmongoc(AutotoolsPackage):
     homepage = "https://github.com/mongodb/mongo-c-driver"
     url      = "https://github.com/mongodb/mongo-c-driver/releases/download/1.7.0/mongo-c-driver-1.7.0.tar.gz"
 
+    maintainers = ['michaelkuhn']
+
+    version('1.9.1', '86f98ace1a5f073eea6875a96761b198')
+    version('1.8.1', '52d54a4107a2da20c1a1b28bc1ff9d44')
     version('1.8.0', '8c271a16ff30f6d4f5e134f699f7360f')
     version('1.7.0', '21acf3584e92631422bc91e9e3cf4f76')
     version('1.6.3', '0193610cf1d98aae7008f272a1000972')
@@ -41,12 +26,25 @@ class Libmongoc(AutotoolsPackage):
     variant('snappy', default=True, description='Enable Snappy support.')
     variant('zlib', default=True, description='Enable zlib support.')
 
+    patch('https://github.com/mongodb/mongo-c-driver/pull/466.patch', sha256='713a872217d11aba04a774785a2824d26b566543c270a1fa386114f5200fda20', when='@1.8.1')
+
+    depends_on('autoconf', type='build', when='@1.8.1')
+    depends_on('automake', type='build', when='@1.8.1')
+    depends_on('libtool', type='build', when='@1.8.1')
+    depends_on('m4', type='build', when='@1.8.1')
+    depends_on('pkgconfig', type='build')
+
     depends_on('libbson')
 
     depends_on('openssl', when='+ssl')
     depends_on('snappy', when='+snappy')
     depends_on('zlib', when='+zlib')
 
+    @property
+    def force_autoreconf(self):
+        # Run autoreconf due to build system patch
+        return self.spec.satisfies('@1.8.1')
+
     def configure_args(self):
         spec = self.spec
 
@@ -61,12 +59,15 @@ class Libmongoc(AutotoolsPackage):
             args.append('--enable-ssl=no')
 
         if spec.satisfies('@1.7.0:'):
-            # --with-{snappy,zlib}=system are currently broken and cause
-            # configure to not find the dependencies. We still want to
-            # explicitly disable them when appropriate.
+            # --with-{snappy,zlib}=system are broken for versions < 1.8.1
             if '+snappy' not in spec:
                 args.append('--with-snappy=no')
+            elif spec.satisfies('@1.8.1:'):
+                args.append('--with-snappy=system')
+
             if '+zlib' not in spec:
                 args.append('--with-zlib=no')
+            elif spec.satisfies('@1.8.1:'):
+                args.append('--with-zlib=system')
 
         return args
diff --git a/var/spack/repos/builtin/packages/libmonitor/package.py b/var/spack/repos/builtin/packages/libmonitor/package.py
index 7ec87ca453..314f195af9 100644
--- a/var/spack/repos/builtin/packages/libmonitor/package.py
+++ b/var/spack/repos/builtin/packages/libmonitor/package.py
@@ -1,38 +1,77 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Libmonitor(AutotoolsPackage):
-    """Libmonitor is a library for process and thread control."""
+    """Libmonitor is a library providing callback functions for the
+    begin and end of processes and threads.  It provides a layer on
+    which to build process monitoring tools and profilers."""
+
     homepage = "https://github.com/HPCToolkit/libmonitor"
-    version('20130218', git='https://github.com/HPCToolkit/libmonitor.git',
-            commit='4f2311e')
+    git      = "https://github.com/HPCToolkit/libmonitor.git"
+
+    version('master', branch='master')
+    version('2018.07.18', commit='d28cc1d3c08c02013a68a022a57a6ac73db88166',
+            preferred=True)
+    version('2013.02.18', commit='4f2311e413fd90583263d6f20453bbe552ccfef3')
+
+    # Configure for Rice HPCToolkit.
+    variant('hpctoolkit', default=False,
+            description='Configure for HPCToolkit')
+
+    variant('bgq', default=False,
+            description='Configure for Blue Gene/Q')
+
+    # Configure for Krell and OpenSpeedshop.
     variant('krellpatch', default=False,
-            description="build with openspeedshop based patch.")
+            description="Build with openspeedshop based patch.")
+
+    patch('libmonitorkrell-0000.patch', when='@2013.02.18+krellpatch')
+    patch('libmonitorkrell-0001.patch', when='@2013.02.18+krellpatch')
+    patch('libmonitorkrell-0002.patch', when='@2013.02.18+krellpatch')
+
+    signals = 'SIGBUS, SIGSEGV, SIGPROF, 36, 37, 38'
+
+    # Set default cflags (-g -O2) and move to the configure line.
+    def flag_handler(self, name, flags):
+        if name != 'cflags':
+            return (flags, None, None)
+
+        if '-g' not in flags:
+            flags.append('-g')
+        for flag in flags:
+            if flag.startswith('-O'):
+                break
+        else:
+            flags.append('-O2')
+
+        return (None, None, flags)
+
+    def configure_args(self):
+        args = []
+
+        if '+hpctoolkit' in self.spec:
+            args.append('--enable-client-signals=%s' % self.signals)
+
+        # TODO: Spack has trouble finding cross-compilers; the +bgq variant
+        # manually specifies the appropriate compiler to build for BGQ (by
+        # setting that here, Spack's choice of CC is overridden).
+        # If the user manually defines an entry in compilers.yaml, the bgq
+        # variant should not be required if the user specifies the bgq
+        # architecture for the libmonitor package. See #8860
+        # TODO: users want to build this for the backend and dependents for the
+        # frontend. Spack ought to make that easy by finding the appropriate
+        # compiler for each if the root and libmonitor are designated to build
+        # on the frontend and backend, respectively. As of now though, there
+        # is an issue with compiler concretization such that spack will attempt
+        # to assign the compiler chosen for libmonitor to the root (unless the
+        # user specifies the compiler for each in addition to the arch).
+        # See #8859
+        if '+bgq' in self.spec:
+            args.append('CC=powerpc64-bgq-linux-gcc')
 
-    patch('libmonitorkrell-0000.patch', when='@20130218+krellpatch')
-    patch('libmonitorkrell-0001.patch', when='@20130218+krellpatch')
-    patch('libmonitorkrell-0002.patch', when='@20130218+krellpatch')
+        return args
diff --git a/var/spack/repos/builtin/packages/libnbc/package.py b/var/spack/repos/builtin/packages/libnbc/package.py
index 67ac5da744..daf7b95c57 100644
--- a/var/spack/repos/builtin/packages/libnbc/package.py
+++ b/var/spack/repos/builtin/packages/libnbc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libnl/package.py b/var/spack/repos/builtin/packages/libnl/package.py
new file mode 100644
index 0000000000..1eabb45108
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libnl/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Libnl(AutotoolsPackage):
+    """libnl - Netlink Protocol Library Suite"""
+
+    homepage = "https://www.infradead.org/~tgr/libnl/"
+    url      = "https://github.com/thom311/libnl/releases/download/libnl3_3_0/libnl-3.3.0.tar.gz"
+
+    version('3.3.0', 'ab3ef137cad95bdda5ff0ffa5175dfa5')
+    version('3.2.25', '03f74d0cd5037cadc8cdfa313bbd195c')
+
+    depends_on('bison', type='build')
+    depends_on('flex', type='build')
+    depends_on('m4', type='build')
+
+    conflicts('platform=darwin', msg='libnl requires FreeBSD or Linux')
diff --git a/var/spack/repos/builtin/packages/libnova/package.py b/var/spack/repos/builtin/packages/libnova/package.py
new file mode 100644
index 0000000000..63745e8dd4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libnova/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libnova(AutotoolsPackage):
+    """"libnova is a general purpose, double precision, Celestial Mechanics,
+        Astrometry and Astrodynamics library."""
+
+    homepage = "http://libnova.sourceforge.net"
+    url      = "https://sourceforge.net/projects/libnova/files/libnova/v%200.15.0/libnova-0.15.0.tar.gz/download"
+
+    version('0.15.0', '756fdb55745cb78511f83a62c25f3be4')
+
+    depends_on('m4')
+    depends_on('autoconf')
+    depends_on('automake')
+    depends_on('libtool')
+
+    force_autoreconf = True
diff --git a/var/spack/repos/builtin/packages/libogg/package.py b/var/spack/repos/builtin/packages/libogg/package.py
index e2c38e7759..bdb5700cc9 100644
--- a/var/spack/repos/builtin/packages/libogg/package.py
+++ b/var/spack/repos/builtin/packages/libogg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/liboldx/package.py b/var/spack/repos/builtin/packages/liboldx/package.py
index f03e0bfe88..210f12a1af 100644
--- a/var/spack/repos/builtin/packages/liboldx/package.py
+++ b/var/spack/repos/builtin/packages/liboldx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Liboldx(AutotoolsPackage):
 
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libpcap/package.py b/var/spack/repos/builtin/packages/libpcap/package.py
index 02221b371e..5956353568 100644
--- a/var/spack/repos/builtin/packages/libpcap/package.py
+++ b/var/spack/repos/builtin/packages/libpcap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,3 +13,6 @@ class Libpcap(AutotoolsPackage):
     url      = "http://www.tcpdump.org/release/libpcap-1.8.1.tar.gz"
 
     version('1.8.1', '3d48f9cd171ff12b0efd9134b52f1447')
+
+    depends_on('flex', type='build')
+    depends_on('bison', type='build')
diff --git a/var/spack/repos/builtin/packages/libpciaccess/package.py b/var/spack/repos/builtin/packages/libpciaccess/package.py
index 7c4efde8ca..ad30ebd082 100644
--- a/var/spack/repos/builtin/packages/libpciaccess/package.py
+++ b/var/spack/repos/builtin/packages/libpciaccess/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Libpciaccess(AutotoolsPackage):
     version('0.13.4', 'cc1fad87da60682af1d5fa43a5da45a4')
 
     depends_on('libtool', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libpfm4/package.py b/var/spack/repos/builtin/packages/libpfm4/package.py
index 3e30ead2dc..32d72371b9 100644
--- a/var/spack/repos/builtin/packages/libpfm4/package.py
+++ b/var/spack/repos/builtin/packages/libpfm4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,30 @@ class Libpfm4(MakefilePackage):
     homepage = "http://perfmon2.sourceforge.net"
     url      = "https://downloads.sourceforge.net/project/perfmon2/libpfm4/libpfm-4.8.0.tar.gz"
 
+    version('4.10.1', 'd8f66cb9bfa7e1434434e0de6409db5b')
+    version('4.9.0', '42ad4a2e5b8e1f015310db8535739c73')
     version('4.8.0', '730383896db92e12fb2cc10f2d41dd43')
 
     # Fails to build libpfm4 with intel compiler version 16 and 17
     conflicts('%intel@16:17')
 
+    # Set default optimization level (-O2) if not specified.
+    def flag_handler(self, name, flags):
+        if name == 'cflags':
+            for flag in flags:
+                if flag.startswith('-O'):
+                    break
+            else:
+                flags.append('-O2')
+
+        return (flags, None, None)
+
+    # Remove -Werror from CFLAGS.  Given the large space of platform,
+    # compiler, version, we don't want to fail the build over a stray
+    # warning.
+    def patch(self):
+        filter_file('-Werror', '', 'config.mk')
+
     @property
     def install_targets(self):
         return ['DESTDIR={0}'.format(self.prefix),
diff --git a/var/spack/repos/builtin/packages/libpipeline/package.py b/var/spack/repos/builtin/packages/libpipeline/package.py
index a242862b34..b5528d7dc3 100644
--- a/var/spack/repos/builtin/packages/libpipeline/package.py
+++ b/var/spack/repos/builtin/packages/libpipeline/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,5 @@ class Libpipeline(AutotoolsPackage):
 
     version('1.4.2', '30cec7bcd6fee723adea6a54389f3da2')
 
-    depends_on('pkg-config', type='build')
-    # TODO: Add a 'test' deptype
-    # See https://github.com/spack/spack/issues/1279
-    # depends_on('check', type='test')
+    depends_on('pkgconfig', type='build')
+    depends_on('check', type='test')
diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py
index a328bd44f8..e9e9d9e56f 100644
--- a/var/spack/repos/builtin/packages/libpng/package.py
+++ b/var/spack/repos/builtin/packages/libpng/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,11 +10,13 @@ class Libpng(AutotoolsPackage):
     """libpng is the official PNG reference library."""
 
     homepage = "http://www.libpng.org/pub/png/libpng.html"
-    url      = "http://download.sourceforge.net/libpng/libpng-1.6.29.tar.gz"
+    url      = "http://download.sourceforge.net/libpng/libpng-1.6.34.tar.gz"
     list_url = "https://sourceforge.net/projects/libpng/files/"
     list_depth = 2
 
+    version('1.6.34', '03fbc5134830240104e96d3cda648e71')
     version('1.6.29', '68553080685f812d1dd7a6b8215c37d8')
+    version('1.6.28', '897ccec1ebfb0922e83c2bfaa1be8748')
     version('1.6.27', '58698519e9f6126c1caeefc28dbcbd5f')
     # From http://www.libpng.org/pub/png/libpng.html (2017-01-04)
     #     Virtually all libpng versions through 1.6.26, 1.5.27,
@@ -57,7 +40,12 @@ class Libpng(AutotoolsPackage):
             # not honored, see
             #   https://sourceforge.net/p/libpng/bugs/210/#33f1
             # '--with-zlib=' + self.spec['zlib'].prefix,
-            'CFLAGS={0}'.format(self.spec['zlib'].headers.include_flags),
+            'CPPFLAGS={0}'.format(self.spec['zlib'].headers.include_flags),
             'LDFLAGS={0}'.format(self.spec['zlib'].libs.search_flags)
         ]
         return args
+
+    def check(self):
+        # Libpng has both 'check' and 'test' targets that are aliases.
+        # Only need to run the tests once.
+        make('check')
diff --git a/var/spack/repos/builtin/packages/libpsl/package.py b/var/spack/repos/builtin/packages/libpsl/package.py
index 75722c63fd..88d843bb1e 100644
--- a/var/spack/repos/builtin/packages/libpsl/package.py
+++ b/var/spack/repos/builtin/packages/libpsl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Libpsl(AutotoolsPackage):
     depends_on('icu4c')
 
     depends_on('gettext', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('python@2.7:', type='build')
 
     depends_on('valgrind~mpi~boost', type='test')
diff --git a/var/spack/repos/builtin/packages/libpthread-stubs/package.py b/var/spack/repos/builtin/packages/libpthread-stubs/package.py
index 286120d908..1cc977316b 100644
--- a/var/spack/repos/builtin/packages/libpthread-stubs/package.py
+++ b/var/spack/repos/builtin/packages/libpthread-stubs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libquo/package.py b/var/spack/repos/builtin/packages/libquo/package.py
index 08006c4295..4677798391 100644
--- a/var/spack/repos/builtin/packages/libquo/package.py
+++ b/var/spack/repos/builtin/packages/libquo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,16 +13,24 @@ class Libquo(AutotoolsPackage):
     single- and multi-threaded libraries."""
 
     homepage = "https://github.com/lanl/libquo"
-    url      = "https://github.com/lanl/libquo/archive/v1.2.9.tar.gz"
+    url      = "http://lanl.github.io/libquo/dists/libquo-1.3.tar.gz"
+    git      = "https://github.com/lanl/libquo.git"
 
-    version('develop', git='https://github.com/lanl/libquo', branch='master')
-    version('1.3', '3ff74162837425a15ecf695ca0201e4a')
-    version('1.2.9', 'ca82ab33f13e2b89983f81e7c02e98c2')
+    version('develop', branch='master')
+    version('1.3',   '1a1fb83d2c9e99ef5d5fcd71037ef8e8')
+    version('1.2.9', '85907cfbdb8b1e57fc5fcf3bced7cfa8')
 
     depends_on('mpi')
-    depends_on('autoconf', type='build')
-    depends_on('automake', type='build')
-    depends_on('libtool', type='build')
+
+    depends_on('m4',       when='@develop', type='build')
+    depends_on('autoconf', when='@develop', type='build')
+    depends_on('automake', when='@develop', type='build')
+    depends_on('libtool',  when='@develop', type='build')
+
+    @when('@develop')
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen')
 
     def configure_args(self):
         return [
diff --git a/var/spack/repos/builtin/packages/librom/package.py b/var/spack/repos/builtin/packages/librom/package.py
new file mode 100644
index 0000000000..e00792e777
--- /dev/null
+++ b/var/spack/repos/builtin/packages/librom/package.py
@@ -0,0 +1,57 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Librom(AutotoolsPackage):
+    """libROM: library for computing large-scale reduced order models"""
+
+    homepage = "https://github.com/LLNL/libROM"
+    git      = "https://github.com/LLNL/libROM.git"
+
+    version('develop', branch='master')
+
+    depends_on('lapack')
+    depends_on('mpi')
+    depends_on('zlib')
+    depends_on('libszip')
+    depends_on('hdf5')
+    depends_on('perl')
+    depends_on('graphviz')
+    depends_on('doxygen')
+    depends_on('boost')
+
+    def configure_args(self):
+        spec = self.spec
+        args = ['--with-lapack={0}'.format(spec['lapack'].prefix),
+                '--with-lapack-libs={0}'.format(spec['lapack'].libs.ld_flags),
+                '--with-zlib={0}'.format(spec['zlib'].prefix),
+                '--with-szlib={0}'.format(spec['libszip'].prefix),
+                '--with-hdf5={0}'.format(spec['hdf5'].prefix),
+                '--with-MPICC={0}'.format(spec['mpi'].mpicc),
+                '--with-mpi-include={0}'.format(spec['mpi'].prefix.include),
+                '--with-mpi-libs={0}'.format(spec['mpi'].libs.ld_flags),
+                '--with-perl={0}'.format(spec['perl'].prefix),
+                '--with-doxygen={0}'.format(spec['doxygen'].prefix)]
+        return args
+
+    # TODO(oxberry1@llnl.gov): Submit PR upstream that implements
+    # install phase in autotools
+    def install(self, spec, prefix):
+        mkdirp(self.spec.prefix.lib)
+        install('libROM.a', join_path(self.spec.prefix.lib, 'libROM.a'))
+
+        mkdirp(self.spec.prefix.include)
+        for f in glob.glob('*.h'):
+            install(f, join_path(self.spec.prefix.include, f))
+
+        mkdirp(self.spec.prefix.share)
+        install('libROM_Design_and_Theory.pdf',
+                join_path(self.spec.prefix.share,
+                          'libROM_Design_and_Theory.pdf'))
+
+        install_tree('docs', self.spec.prefix.share.docs)
diff --git a/var/spack/repos/builtin/packages/libsharp/package.py b/var/spack/repos/builtin/packages/libsharp/package.py
new file mode 100644
index 0000000000..a80eb7f58f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libsharp/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libsharp(AutotoolsPackage):
+    """Libsharp is a code library for spherical harmonic transforms (SHTs) and
+    spin-weighted spherical harmonic transforms, which evolved from the libpsht
+    library."""
+
+    variant('openmp', default=True, description='Build with openmp support')
+    variant('mpi', default=True, description='Build with MPI support')
+
+    homepage = "https://github.com/Libsharp/libsharp"
+    git      = "https://github.com/Libsharp/libsharp.git"
+
+    version('1.0.0', commit='cc4753ff4b0ef393f0d4ada41a175c6d1dd85d71')
+    version('2018-01-17', commit='593d4eba67d61827191c32fb94bf235cb31205e1')
+
+    depends_on('autoconf', type='build')
+    depends_on('mpi', when='+mpi')
+
+    def autoreconf(self, spec, prefix):
+        """Generate autotools configuration"""
+        bash = which('bash')
+        bash('autoconf')
+
+    def configure_args(self):
+        args = []
+        if '+openmp' not in self.spec:
+            args.append("--disable-openmp")
+        if '+mpi' not in self.spec:
+            args.append("--disable-mpi")
+        return args
+
+    def install(self, spec, prefix):
+        install_tree('auto/include', join_path(prefix, 'include'))
+        install_tree('auto/lib', join_path(prefix, 'lib'))
diff --git a/var/spack/repos/builtin/packages/libshm/package.py b/var/spack/repos/builtin/packages/libshm/package.py
new file mode 100644
index 0000000000..3e52739131
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libshm/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libshm(Package):
+    """Libshm is a header library
+    making an easy C++11 access to a shared memory."""
+
+    homepage = "https://github.com/afeldman/libshm"
+    git      = "https://github.com/afeldman/libshm.git"
+
+    version('master')
+
+    def install(self, spec, prefix):
+        install_tree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/libsigcpp/package.py b/var/spack/repos/builtin/packages/libsigcpp/package.py
new file mode 100644
index 0000000000..32a3674fd6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libsigcpp/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libsigcpp(AutotoolsPackage):
+    """Libsigc++ is a C++ library for typesafe callbacks"""
+
+    homepage = "https://libsigcplusplus.github.io/libsigcplusplus/index.html"
+    url      = "https://ftp.acc.umu.se/pub/GNOME/sources/libsigc++/2.0/libsigc++-2.0.3.tar.gz"
+
+    version('2.9.3', '0e5630fd0557ee80b5e5cbbcebaa2594')
+    version('2.1.1', '5ae4d6da9a408c90e86c776673c38972')
+    version('2.0.3', '57c6887dd46ce0bd312a4823589db5d8')
+
+    def url_for_version(self, version):
+        """Handle version-based custom URLs."""
+        url = "https://ftp.acc.umu.se/pub/GNOME/sources/libsigc++"
+        ext = '.tar.gz' if version < Version('2.2.10') else '.tar.xz'
+        return url + "/%s/libsigc++-%s%s" % (version.up_to(2), version, ext)
diff --git a/var/spack/repos/builtin/packages/libsigsegv/package.py b/var/spack/repos/builtin/packages/libsigsegv/package.py
index f13710bff9..68c88a11aa 100644
--- a/var/spack/repos/builtin/packages/libsigsegv/package.py
+++ b/var/spack/repos/builtin/packages/libsigsegv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Libsigsegv(AutotoolsPackage):
     """GNU libsigsegv is a library for handling page faults in user mode."""
 
     homepage = "https://www.gnu.org/software/libsigsegv/"
-    url      = "https://ftp.gnu.org/gnu/libsigsegv/libsigsegv-2.11.tar.gz"
+    url      = "https://ftpmirror.gnu.org/libsigsegv/libsigsegv-2.11.tar.gz"
 
     patch('patch.new_config_guess', when='@2.10')
 
diff --git a/var/spack/repos/builtin/packages/libsm/package.py b/var/spack/repos/builtin/packages/libsm/package.py
index 602f5daa56..50e0fb3fca 100644
--- a/var/spack/repos/builtin/packages/libsm/package.py
+++ b/var/spack/repos/builtin/packages/libsm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Libsm(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libsodium/package.py b/var/spack/repos/builtin/packages/libsodium/package.py
index e62319e439..c7c1a2191a 100644
--- a/var/spack/repos/builtin/packages/libsodium/package.py
+++ b/var/spack/repos/builtin/packages/libsodium/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class Libsodium(AutotoolsPackage):
     url      = "https://download.libsodium.org/libsodium/releases/libsodium-1.0.13.tar.gz"
     list_url = "https://download.libsodium.org/libsodium/releases/old"
 
+    version('1.0.15', '070373e73a0b10bd96f412e1732ebc42')
     version('1.0.13', 'f38aac160a4bd05f06f743863e54e499')
     version('1.0.12', 'c308e3faa724b630b86cc0aaf887a5d4')
     version('1.0.11', 'b58928d035064b2a46fb564937b83540')
diff --git a/var/spack/repos/builtin/packages/libspatialindex/package.py b/var/spack/repos/builtin/packages/libspatialindex/package.py
index 69183c8131..9f1a27c60d 100644
--- a/var/spack/repos/builtin/packages/libspatialindex/package.py
+++ b/var/spack/repos/builtin/packages/libspatialindex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libsplash/package.py b/var/spack/repos/builtin/packages/libsplash/package.py
index b710dae58c..37a7c09b0e 100644
--- a/var/spack/repos/builtin/packages/libsplash/package.py
+++ b/var/spack/repos/builtin/packages/libsplash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,11 +17,12 @@ class Libsplash(CMakePackage):
 
     homepage = "https://github.com/ComputationalRadiationPhysics/libSplash"
     url      = "https://github.com/ComputationalRadiationPhysics/libSplash/archive/v1.4.0.tar.gz"
+    git      = "https://github.com/ComputationalRadiationPhysics/libSplash.git"
+    maintainers = ['ax3l']
 
-    version('develop', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/libSplash.git')
-    version('master', branch='master',
-            git='https://github.com/ComputationalRadiationPhysics/libSplash.git')
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('1.7.0', '22dea94734fe4f4c5f4e875ce70900d3')
     version('1.6.0', 'c05bce95abfe1ae4cd9d9817acf58d94')
     version('1.5.0', 'c1efec4c20334242c8a3b6bfdc0207e3')
     version('1.4.0', '2de37bcef6fafa1960391bf44b1b50e0')
@@ -50,6 +32,23 @@ class Libsplash(CMakePackage):
     variant('mpi', default=True,
             description='Enable parallel I/O (one-file aggregation) support')
 
-    depends_on('hdf5@1.8.6:')
-    depends_on('hdf5+mpi', when='+mpi')
+    depends_on('cmake@3.10.0:', type='build', when='@1.7.0:')
+    depends_on('hdf5@1.8.6: ~mpi', when='~mpi')
+    depends_on('hdf5@1.8.6: +mpi', when='+mpi')
     depends_on('mpi', when='+mpi')
+
+    patch('root_cmake_1.7.0.patch', when='@1.7.0')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = []
+
+        if spec.satisfies('@1.7.0:'):
+            args += [
+                '-DSplash_USE_MPI:BOOL={0}'.format(
+                    'ON' if '+mpi' in spec else 'OFF'),
+                '-DSplash_USE_PARALLEL:BOOL={0}'.format(
+                    'ON' if '+mpi' in spec else 'OFF')
+            ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/libsplash/root_cmake_1.7.0.patch b/var/spack/repos/builtin/packages/libsplash/root_cmake_1.7.0.patch
new file mode 100644
index 0000000000..788e24925d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libsplash/root_cmake_1.7.0.patch
@@ -0,0 +1,15 @@
+diff --git CMakeLists.txt CMakeLists.txt
+index 4846ff7..5e102ce 100644
+--- libSplash-1.7.0/CMakeLists.txt
++++ libSplash-1.7.0/CMakeLists.txt
+@@ -392,7 +392,8 @@ install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/tools/splash2xdmf.py DESTINATION bin)
+ #
+ enable_testing()
+ 
+-if($ENV{USER} STREQUAL root)
++# OpenMPI root guard: https://github.com/open-mpi/ompi/issues/4451
++if("$ENV{USER}" STREQUAL "root")
+     set(MPI_ALLOW_ROOT --allow-run-as-root)
+ endif()
+ set(MPI_TEST_EXE ${MPIEXEC_EXECUTABLE} ${MPI_ALLOW_ROOT} ${MPIEXEC_NUMPROC_FLAG})
+
diff --git a/var/spack/repos/builtin/packages/libssh/package.py b/var/spack/repos/builtin/packages/libssh/package.py
new file mode 100644
index 0000000000..511e2779a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libssh/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libssh(CMakePackage):
+    """libssh: the SSH library"""
+
+    homepage = "https://www.libssh.org"
+    url      = "https://red.libssh.org/attachments/download/218/libssh-0.7.5.tar.xz"
+
+    version('0.7.5', 'd3fc864208bf607ad87cdee836894feb')
+
+    depends_on('openssl')
+    depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/libssh2/package.py b/var/spack/repos/builtin/packages/libssh2/package.py
index 030e7aeab5..bf56dc36b1 100644
--- a/var/spack/repos/builtin/packages/libssh2/package.py
+++ b/var/spack/repos/builtin/packages/libssh2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class Libssh2(CMakePackage):
     homepage = "https://www.libssh2.org/"
     url      = "https://www.libssh2.org/download/libssh2-1.7.0.tar.gz"
 
+    version('1.8.0', '3d1147cae66e2959ea5441b183de1b1c')
     version('1.7.0', 'b01662a210e94cccf2f76094db7dac5c')
     version('1.4.3', '071004c60c5d6f90354ad1b701013a0b')  # CentOS7
 
diff --git a/var/spack/repos/builtin/packages/libsvm/package.py b/var/spack/repos/builtin/packages/libsvm/package.py
index 564775c91c..2c35ef7dce 100644
--- a/var/spack/repos/builtin/packages/libsvm/package.py
+++ b/var/spack/repos/builtin/packages/libsvm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libszip/package.py b/var/spack/repos/builtin/packages/libszip/package.py
index 2f4b570fec..feef66a655 100644
--- a/var/spack/repos/builtin/packages/libszip/package.py
+++ b/var/spack/repos/builtin/packages/libszip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,11 +17,11 @@ class Libszip(AutotoolsPackage):
     homepage = "https://support.hdfgroup.org/doc_resource/SZIP/"
     url      = "https://support.hdfgroup.org/ftp/lib-external/szip/2.1.1/src/szip-2.1.1.tar.gz"
     list_url = "https://support.hdfgroup.org/ftp/lib-external/szip"
-    list_depth = 2
+    list_depth = 3
 
     provides('szip')
 
-    version('2.1.1', 'dd579cf0f26d44afd10a0ad7291fc282')
+    version('2.1.1', '5addbf2a5b1bf928b92c47286e921f72')
     version('2.1',   '902f831bcefb69c6b635374424acbead')
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/libtermkey/package.py b/var/spack/repos/builtin/packages/libtermkey/package.py
index 6b8b6b58bd..28a6aa5552 100644
--- a/var/spack/repos/builtin/packages/libtermkey/package.py
+++ b/var/spack/repos/builtin/packages/libtermkey/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libtiff/package.py b/var/spack/repos/builtin/packages/libtiff/package.py
index a28d553429..3a2efbfb5c 100644
--- a/var/spack/repos/builtin/packages/libtiff/package.py
+++ b/var/spack/repos/builtin/packages/libtiff/package.py
@@ -1,39 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Libtiff(AutotoolsPackage):
-    """libtiff graphics format library"""
+    """LibTIFF - Tag Image File Format (TIFF) Library and Utilities."""
+
     homepage = "http://www.simplesystems.org/libtiff/"
-    url      = "http://download.osgeo.org/libtiff/tiff-4.0.8.tar.gz"
+    url      = "http://download.osgeo.org/libtiff/tiff-4.0.9.tar.gz"
 
+    version('4.0.9', '54bad211279cc93eb4fca31ba9bfdc79')
     version('4.0.8', '2a7d1c1318416ddf36d5f6fa4600069b')
     version('4.0.7', '77ae928d2c6b7fb46a21c3a29325157b')
     version('4.0.6', 'd1d2e940dea0b5ad435f21f03d96dd72')
     version('4.0.3', '051c1068e6a0627f461948c365290410')
+    version('3.9.7', '626102f448ba441d42e3212538ad67d2')
 
     depends_on('jpeg')
     depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/libtool/flag_space.patch b/var/spack/repos/builtin/packages/libtool/flag_space.patch
new file mode 100644
index 0000000000..4ec1fc8c98
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libtool/flag_space.patch
@@ -0,0 +1,19 @@
+diff --git a/m4/libtool.m4 b/m4/libtool.m4
+index b55a6e57..26febc87 100644
+--- a/m4/libtool.m4
++++ b/m4/libtool.m4
+@@ -7557,10 +7557,11 @@ if AC_TRY_EVAL(ac_compile); then
+     case $prev$p in
+ 
+     -L* | -R* | -l*)
+-       # Some compilers place space between "-{L,R}" and the path.
++       # Some compilers place space between "-{L,R,l}" and the path (value).
+        # Remove the space.
+-       if test x-L = "$p" ||
+-          test x-R = "$p"; then
++       if test x-L = x"$p" ||
++          test x-R = x"$p" ||
++          test x-l = x"$p"; then
+ 	 prev=$p
+ 	 continue
+        fi
diff --git a/var/spack/repos/builtin/packages/libtool/package.py b/var/spack/repos/builtin/packages/libtool/package.py
index eca530ce0c..37c6f2a876 100644
--- a/var/spack/repos/builtin/packages/libtool/package.py
+++ b/var/spack/repos/builtin/packages/libtool/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,15 +10,30 @@ class Libtool(AutotoolsPackage):
     """libtool -- library building part of autotools."""
 
     homepage = 'https://www.gnu.org/software/libtool/'
-    url = 'http://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz'
+    url      = 'https://ftpmirror.gnu.org/libtool/libtool-2.4.2.tar.gz'
 
+    version('develop', git='https://git.savannah.gnu.org/git/libtool.git',
+            branch='master', submodules=True)
     version('2.4.6', 'addf44b646ddb4e3919805aa88fa7c5e')
     version('2.4.2', 'd2f3b7d4627e69e13514a40e72a24d50')
 
     depends_on('m4@1.4.6:', type='build')
+    depends_on('autoconf', type='build', when='@develop')
+    depends_on('automake', type='build', when='@develop')
+    depends_on('help2man', type='build', when='@develop')
+    depends_on('xz', type='build', when='@develop')
+    depends_on('texinfo', type='build', when='@develop')
+
+    # Fix parsing of compiler output when collecting predeps and postdeps
+    # http://lists.gnu.org/archive/html/bug-libtool/2016-03/msg00003.html
+    patch('flag_space.patch', when='@develop')
 
     build_directory = 'spack-build'
 
+    @when('@develop')
+    def autoreconf(self, spec, prefix):
+        Executable('./bootstrap')()
+
     def _make_executable(self, name):
         return Executable(join_path(self.prefix.bin, name))
 
@@ -46,8 +42,25 @@ class Libtool(AutotoolsPackage):
                               join_path(self.prefix.share, 'aclocal'))
 
     def setup_dependent_package(self, module, dependent_spec):
-        # Automake is very likely to be a build dependency,
-        # so we add the tools it provides to the dependent module
-        executables = ['libtoolize', 'libtool']
+        # Automake is very likely to be a build dependency, so we add
+        # the tools it provides to the dependent module. Some build
+        # systems differentiate between BSD libtool (e.g., Darwin) and
+        # GNU libtool, so also add 'glibtool' and 'glibtoolize' to the
+        # list of executables. See Homebrew:
+        # https://github.com/Homebrew/homebrew-core/blob/master/Formula/libtool.rb
+        executables = ['libtoolize', 'libtool', 'glibtoolize', 'glibtool']
         for name in executables:
             setattr(module, name, self._make_executable(name))
+
+    @run_after('install')
+    def post_install(self):
+        # Some platforms name GNU libtool and GNU libtoolize
+        # 'glibtool' and 'glibtoolize', respectively, to differentiate
+        # them from BSD libtool and BSD libtoolize. On these BSD
+        # platforms, build systems sometimes expect to use the assumed
+        # GNU commands glibtool and glibtoolize instead of the BSD
+        # variant; this happens frequently, for instance, on Darwin
+        symlink(join_path(self.prefix.bin, 'libtool'),
+                join_path(self.prefix.bin, 'glibtool'))
+        symlink(join_path(self.prefix.bin, 'libtoolize'),
+                join_path(self.prefix.bin, 'glibtoolize'))
diff --git a/var/spack/repos/builtin/packages/libunistring/package.py b/var/spack/repos/builtin/packages/libunistring/package.py
index a4250bc8ee..5653a0eba5 100644
--- a/var/spack/repos/builtin/packages/libunistring/package.py
+++ b/var/spack/repos/builtin/packages/libunistring/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,7 @@ class Libunistring(AutotoolsPackage):
     and for manipulating C strings according to the Unicode standard."""
 
     homepage = "https://www.gnu.org/software/libunistring/"
-    url      = "http://ftp.gnu.org/gnu/libunistring/libunistring-0.9.7.tar.xz"
+    url      = "https://ftpmirror.gnu.org/libunistring/libunistring-0.9.7.tar.xz"
 
     version('0.9.7', '82e0545363d111bfdfec2ddbfe62ffd3')
     version('0.9.6', 'cb09c398020c27edac10ca590e9e9ef3')
diff --git a/var/spack/repos/builtin/packages/libunwind/package.py b/var/spack/repos/builtin/packages/libunwind/package.py
index 9c8c0574b1..201c31af52 100644
--- a/var/spack/repos/builtin/packages/libunwind/package.py
+++ b/var/spack/repos/builtin/packages/libunwind/package.py
@@ -1,34 +1,39 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Libunwind(AutotoolsPackage):
     """A portable and efficient C programming interface (API) to determine
        the call-chain of a program."""
+
     homepage = "http://www.nongnu.org/libunwind/"
     url      = "http://download.savannah.gnu.org/releases/libunwind/libunwind-1.1.tar.gz"
 
+    version('1.3-rc1', 'f09b670de5db6430a3de666e6aed60e3')
+    version('1.2.1', '06ba9e60d92fd6f55cd9dadb084df19e', preferred=True)
     version('1.1', 'fb4ea2f6fbbe45bf032cd36e586883ce')
+
+    variant('xz', default=False,
+            description='Support xz (lzma) compressed symbol tables.')
+
+    depends_on('xz', type='link', when='+xz')
+
+    conflicts('platform=darwin',
+              msg='Non-GNU libunwind needs ELF libraries Darwin does not have')
+
+    provides('unwind')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        if '+xz' in spec:
+            args.append('--enable-minidebuginfo')
+        else:
+            args.append('--disable-minidebuginfo')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py
index 750730b6ed..e50030468b 100644
--- a/var/spack/repos/builtin/packages/libuuid/package.py
+++ b/var/spack/repos/builtin/packages/libuuid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libuv/package.py b/var/spack/repos/builtin/packages/libuv/package.py
index d88b2306aa..5fd2121580 100644
--- a/var/spack/repos/builtin/packages/libuv/package.py
+++ b/var/spack/repos/builtin/packages/libuv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libvorbis/package.py b/var/spack/repos/builtin/packages/libvorbis/package.py
index 6a3561fb1a..9c526dba0f 100644
--- a/var/spack/repos/builtin/packages/libvorbis/package.py
+++ b/var/spack/repos/builtin/packages/libvorbis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class Libvorbis(AutotoolsPackage):
 
     depends_on('libogg')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     # `make check` crashes when run in parallel
     parallel = False
diff --git a/var/spack/repos/builtin/packages/libvterm/package.py b/var/spack/repos/builtin/packages/libvterm/package.py
index 5ed4d0b74e..aef6d23d27 100644
--- a/var/spack/repos/builtin/packages/libvterm/package.py
+++ b/var/spack/repos/builtin/packages/libvterm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libwebsockets/package.py b/var/spack/repos/builtin/packages/libwebsockets/package.py
index 0b02793554..94f0982ba1 100644
--- a/var/spack/repos/builtin/packages/libwebsockets/package.py
+++ b/var/spack/repos/builtin/packages/libwebsockets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Libwebsockets(CMakePackage):
 
     homepage = "https://github.com/warmcat/libwebsockets"
     url      = "https://github.com/warmcat/libwebsockets/archive/v2.1.0.tar.gz"
+    maintainers = ['ax3l']
 
     version('2.2.1', '1f641cde2ab3687db3d553f68fe0f620')
     version('2.1.1', '674684ffb90d4a0bcf7a075eb7b90192')
diff --git a/var/spack/repos/builtin/packages/libwindowswm/package.py b/var/spack/repos/builtin/packages/libwindowswm/package.py
index ffbff1f652..26a5bdb066 100644
--- a/var/spack/repos/builtin/packages/libwindowswm/package.py
+++ b/var/spack/repos/builtin/packages/libwindowswm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Libwindowswm(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('windowswmproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libx11/package.py b/var/spack/repos/builtin/packages/libx11/package.py
index 9658fab352..8f49422985 100644
--- a/var/spack/repos/builtin/packages/libx11/package.py
+++ b/var/spack/repos/builtin/packages/libx11/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,6 +22,15 @@ class Libx11(AutotoolsPackage):
     depends_on('xtrans', type='build')
     depends_on('kbproto', type=('build', 'link'))
     depends_on('inputproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
     depends_on('perl', type='build')
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libX11', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
+        return None
diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py
index 64f9a3a526..4c5acaf985 100644
--- a/var/spack/repos/builtin/packages/libxau/package.py
+++ b/var/spack/repos/builtin/packages/libxau/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Libxau(AutotoolsPackage):
     version('1.0.8', 'a85cd601d82bc79c0daa280917572e20')
 
     depends_on('xproto', type=('build', 'link'))
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxaw/package.py b/var/spack/repos/builtin/packages/libxaw/package.py
index 7470ce2f72..327c8c6088 100644
--- a/var/spack/repos/builtin/packages/libxaw/package.py
+++ b/var/spack/repos/builtin/packages/libxaw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Libxaw(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxaw3d/package.py b/var/spack/repos/builtin/packages/libxaw3d/package.py
index 13137d622f..85b53d2bfc 100644
--- a/var/spack/repos/builtin/packages/libxaw3d/package.py
+++ b/var/spack/repos/builtin/packages/libxaw3d/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Libxaw3d(AutotoolsPackage):
     depends_on('libxext')
     depends_on('libxpm')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py
index d92ba97e73..bdb5fcabd2 100644
--- a/var/spack/repos/builtin/packages/libxc/package.py
+++ b/var/spack/repos/builtin/packages/libxc/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Libxc(Package):
+class Libxc(AutotoolsPackage):
     """Libxc is a library of exchange-correlation functionals for
     density-functional theory."""
 
@@ -52,7 +33,7 @@ class Libxc(Package):
         # Libxc installs both shared and static libraries.
         # If a client ask for static explicitly then return
         # the static libraries
-        shared = False if 'static' in query_parameters else True
+        shared = ('static' not in query_parameters)
 
         # Libxc has a fortran90 interface: give clients the
         # possibility to query for it
@@ -60,34 +41,46 @@ class Libxc(Package):
             libraries = ['libxcf90'] + libraries
 
         return find_libraries(
-            libraries, root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
 
-    def install(self, spec, prefix):
-        # Optimizations for the Intel compiler, suggested by CP2K
+    def setup_environment(self, spack_env, run_env):
         optflags = '-O2'
         if self.compiler.name == 'intel':
-            optflags += ' -xAVX -axCORE-AVX2 -ipo'
+            # Optimizations for the Intel compiler, suggested by CP2K
+            #
+            # Note that not every lowly login node has advanced CPUs:
+            #
+            #   $ icc  -xAVX -axCORE-AVX2 -ipo hello.c
+            #   $ ./a.out
+            #   Please verify that both the operating system and the \
+            #   processor support Intel(R) AVX instructions.
+            #
+            # NB: The same flags are applied in:
+            #   - ../libint/package.py
+            #
+            # Related:
+            #   - ../fftw/package.py        variants: simd, fma
+            #   - ../c-blosc/package.py     variant:  avx2
+            #   - ../r-rcppblaze/package.py AVX* in "info" but not in code?
+            #   - ../openblas/package.py    variants: cpu_target!?!
+            #   - ../cp2k/package.py
+            #
+            # Documentation at:
+            # https://software.intel.com/en-us/cpp-compiler-18.0-developer-guide-and-reference-ax-qax
+            #
+            optflags += ' -xSSE4.2 -axAVX,CORE-AVX2 -ipo'
             if which('xiar'):
-                env['AR'] = 'xiar'
-
-        if 'CFLAGS' in env and env['CFLAGS']:
-            env['CFLAGS'] += ' ' + optflags
-        else:
-            env['CFLAGS'] = optflags
+                spack_env.set('AR', 'xiar')
 
-        if 'FCFLAGS' in env and env['FCFLAGS']:
-            env['FCFLAGS'] += ' ' + optflags
-        else:
-            env['FCFLAGS'] = optflags
+        spack_env.append_flags('CFLAGS',  optflags)
+        spack_env.append_flags('FCFLAGS', optflags)
 
-        configure('--prefix={0}'.format(prefix),
-                  '--enable-shared')
-
-        make()
+    def configure_args(self):
+        args = ['--enable-shared']
+        return args
 
+    def check(self):
         # libxc provides a testsuite, but many tests fail
         # http://www.tddft.org/pipermail/libxc/2013-February/000032.html
-        # make('check')
-
-        make('install')
+        pass
diff --git a/var/spack/repos/builtin/packages/libxcb/package.py b/var/spack/repos/builtin/packages/libxcb/package.py
index cbca3bfd39..91f6d3f648 100644
--- a/var/spack/repos/builtin/packages/libxcb/package.py
+++ b/var/spack/repos/builtin/packages/libxcb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,20 +13,30 @@ class Libxcb(AutotoolsPackage):
     extensibility."""
 
     homepage = "https://xcb.freedesktop.org/"
-    url      = "https://xcb.freedesktop.org/dist/libxcb-1.11.tar.gz"
+    url      = "https://xcb.freedesktop.org/dist/libxcb-1.13.tar.gz"
 
-    version('1.12', '95eee7c28798e16ba5443f188b27a476')
-    version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb')
+    version('1.13',   '3ba7fe0a7d60650bfb73fbf623aa57cc')
+    version('1.12',   '95eee7c28798e16ba5443f188b27a476')
     version('1.11.1', '118623c15a96b08622603a71d8789bf3')
+    version('1.11',   '1698dd837d7e6e94d029dbe8b3a82deb')
 
     depends_on('libpthread-stubs')
     depends_on('libxau@0.99.2:')
     depends_on('libxdmcp')
 
+    # libxcb 1.X requires xcb-proto >= 1.X
     depends_on('xcb-proto', type='build')
+    depends_on('xcb-proto@1.13:', when='@1.13:1.13.999', type='build')
+    depends_on('xcb-proto@1.12:', when='@1.12:1.12.999', type='build')
+    depends_on('xcb-proto@1.11:', when='@1.11:1.11.999', type='build')
+
     # TODO: uncomment once build deps can be resolved separately
-    # depends_on('python@2:2.8', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    # See #7646, #4145, #4063, and #2548 for details
+    # libxcb 1.13 added Python 3 support
+    # depends_on('python', type='build')
+    # depends_on('python@2:2.8', when='@:1.12', type='build')
+
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def patch(self):
diff --git a/var/spack/repos/builtin/packages/libxcomposite/package.py b/var/spack/repos/builtin/packages/libxcomposite/package.py
index b408a08394..d0a9a2f971 100644
--- a/var/spack/repos/builtin/packages/libxcomposite/package.py
+++ b/var/spack/repos/builtin/packages/libxcomposite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Libxcomposite(AutotoolsPackage):
 
     depends_on('libx11')
     depends_on('libxfixes')
-
+    depends_on('fixesproto@0.4:', type='build')
     depends_on('compositeproto@0.4:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxcursor/package.py b/var/spack/repos/builtin/packages/libxcursor/package.py
index ec6b4d28f1..1160708781 100644
--- a/var/spack/repos/builtin/packages/libxcursor/package.py
+++ b/var/spack/repos/builtin/packages/libxcursor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxcursor(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('fixesproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxdamage/package.py b/var/spack/repos/builtin/packages/libxdamage/package.py
index 948e266aba..bb1684c364 100644
--- a/var/spack/repos/builtin/packages/libxdamage/package.py
+++ b/var/spack/repos/builtin/packages/libxdamage/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxdamage(AutotoolsPackage):
     depends_on('damageproto@1.1:', type='build')
     depends_on('fixesproto', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxdmcp/package.py b/var/spack/repos/builtin/packages/libxdmcp/package.py
index 093aa90dd3..f3fbc87ef4 100644
--- a/var/spack/repos/builtin/packages/libxdmcp/package.py
+++ b/var/spack/repos/builtin/packages/libxdmcp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,5 +15,5 @@ class Libxdmcp(AutotoolsPackage):
     version('1.1.2', 'ab0d6a38f0344a05d698ec7d48cfa5a8')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxevie/package.py b/var/spack/repos/builtin/packages/libxevie/package.py
index 0ad59c24ee..a1ceb23dbb 100644
--- a/var/spack/repos/builtin/packages/libxevie/package.py
+++ b/var/spack/repos/builtin/packages/libxevie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxevie(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
     depends_on('evieext', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxext/package.py b/var/spack/repos/builtin/packages/libxext/package.py
index 2ecdad7be5..a4e7b9234c 100644
--- a/var/spack/repos/builtin/packages/libxext/package.py
+++ b/var/spack/repos/builtin/packages/libxext/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Libxext(AutotoolsPackage):
 
     depends_on('xproto@7.0.13:', type='build')
     depends_on('xextproto@7.1.99:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxfixes/package.py b/var/spack/repos/builtin/packages/libxfixes/package.py
index 5c18e389f1..cfcaa5f466 100644
--- a/var/spack/repos/builtin/packages/libxfixes/package.py
+++ b/var/spack/repos/builtin/packages/libxfixes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxfixes(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('fixesproto@5.0:', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxfont/package.py b/var/spack/repos/builtin/packages/libxfont/package.py
index 4d08c4db71..1fef06a9bb 100644
--- a/var/spack/repos/builtin/packages/libxfont/package.py
+++ b/var/spack/repos/builtin/packages/libxfont/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Libxfont(AutotoolsPackage):
     depends_on('xtrans', type='build')
     depends_on('xproto', type='build')
     depends_on('fontsproto@2.1.3:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxfont2/package.py b/var/spack/repos/builtin/packages/libxfont2/package.py
index b2a6a793cd..ee3f0ac054 100644
--- a/var/spack/repos/builtin/packages/libxfont2/package.py
+++ b/var/spack/repos/builtin/packages/libxfont2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Libxfont2(AutotoolsPackage):
     depends_on('xtrans', type='build')
     depends_on('xproto', type='build')
     depends_on('fontsproto@2.1.3:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxfontcache/package.py b/var/spack/repos/builtin/packages/libxfontcache/package.py
index d113cda057..a48a671dc1 100644
--- a/var/spack/repos/builtin/packages/libxfontcache/package.py
+++ b/var/spack/repos/builtin/packages/libxfontcache/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxfontcache(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('fontcacheproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxft/package.py b/var/spack/repos/builtin/packages/libxft/package.py
index 63f9236302..baa61ba7f0 100644
--- a/var/spack/repos/builtin/packages/libxft/package.py
+++ b/var/spack/repos/builtin/packages/libxft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Libxft(AutotoolsPackage):
     depends_on('libx11')
     depends_on('libxrender@0.8.2:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxi/package.py b/var/spack/repos/builtin/packages/libxi/package.py
index a16be21fba..3c474aaf4b 100644
--- a/var/spack/repos/builtin/packages/libxi/package.py
+++ b/var/spack/repos/builtin/packages/libxi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,10 +14,14 @@ class Libxi(AutotoolsPackage):
 
     version('1.7.6', 'f3828f9d7893068f6f6f10fe15b31afa')
 
+    depends_on('pkgconfig', type='build')
     depends_on('libx11@1.6:')
     depends_on('libxext@1.0.99.1:')
     depends_on('libxfixes@5:')
 
+    # transient build dependency (from libxfixes), i.e. shouldn't be needed?
+    depends_on('fixesproto@5.0:', type='build')
+
     depends_on('xproto@7.0.13:', type='build')
     depends_on('xextproto@7.0.3:', type='build')
     depends_on('inputproto@2.2.99.1:', type='build')
diff --git a/var/spack/repos/builtin/packages/libxinerama/package.py b/var/spack/repos/builtin/packages/libxinerama/package.py
index 74ec63f266..151d74eb79 100644
--- a/var/spack/repos/builtin/packages/libxinerama/package.py
+++ b/var/spack/repos/builtin/packages/libxinerama/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxinerama(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('xineramaproto@1.1.99.1:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxkbcommon/package.py b/var/spack/repos/builtin/packages/libxkbcommon/package.py
new file mode 100644
index 0000000000..d864c4b786
--- /dev/null
+++ b/var/spack/repos/builtin/packages/libxkbcommon/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Libxkbcommon(AutotoolsPackage):
+    """xkbcommon is a library to handle keyboard descriptions, including
+    loading them from disk, parsing them and handling their state. It's mainly
+    meant for client toolkits, window systems, and other system
+    applications."""
+
+    homepage = "https://xkbcommon.org/"
+    url      = "https://github.com/xkbcommon/libxkbcommon/archive/xkbcommon-0.8.0.tar.gz"
+
+    version('0.8.0', '0d9738fb2ed2dcc6e2c6920d94e135ce')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+    depends_on('bison',    type='build')
+    depends_on('xkbdata')
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+        args.append('--with-xkb-config-root={0}'
+                    .format(spec['xkbdata'].prefix))
+        return args
diff --git a/var/spack/repos/builtin/packages/libxkbfile/package.py b/var/spack/repos/builtin/packages/libxkbfile/package.py
index c345a8a362..e1730005f9 100644
--- a/var/spack/repos/builtin/packages/libxkbfile/package.py
+++ b/var/spack/repos/builtin/packages/libxkbfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Libxkbfile(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('kbproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxkbui/package.py b/var/spack/repos/builtin/packages/libxkbui/package.py
index eb34053918..168fb2fa3d 100644
--- a/var/spack/repos/builtin/packages/libxkbui/package.py
+++ b/var/spack/repos/builtin/packages/libxkbui/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Libxkbui(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxkbfile')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py
index 87bbb965b8..eb2409ebf2 100644
--- a/var/spack/repos/builtin/packages/libxml2/package.py
+++ b/var/spack/repos/builtin/packages/libxml2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,11 @@ class Libxml2(AutotoolsPackage):
     """Libxml2 is the XML C parser and toolkit developed for the Gnome
        project (but usable outside of the Gnome platform), it is free
        software available under the MIT License."""
+
     homepage = "http://xmlsoft.org"
-    url      = "http://xmlsoft.org/sources/libxml2-2.9.2.tar.gz"
+    url      = "http://xmlsoft.org/sources/libxml2-2.9.8.tar.gz"
 
+    version('2.9.8', 'b786e353e2aa1b872d70d5d1ca0c740d')
     version('2.9.4', 'ae249165c173b1ff386ee8ad676815f5')
     version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788')
     version('2.7.8', '8127a65e8c3b08856093099b52599c86')
@@ -44,7 +27,7 @@ class Libxml2(AutotoolsPackage):
     depends_on('zlib')
     depends_on('xz')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     def configure_args(self):
         spec = self.spec
@@ -60,3 +43,7 @@ class Libxml2(AutotoolsPackage):
             args.append('--without-python')
 
         return args
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.prepend_path('CPATH', self.prefix.include.libxml2)
+        run_env.prepend_path('CPATH', self.prefix.include.libxml2)
diff --git a/var/spack/repos/builtin/packages/libxmu/package.py b/var/spack/repos/builtin/packages/libxmu/package.py
index bb3f168d6a..854946016b 100644
--- a/var/spack/repos/builtin/packages/libxmu/package.py
+++ b/var/spack/repos/builtin/packages/libxmu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Libxmu(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxp/package.py b/var/spack/repos/builtin/packages/libxp/package.py
index f18d4b89c9..d5260e0039 100644
--- a/var/spack/repos/builtin/packages/libxp/package.py
+++ b/var/spack/repos/builtin/packages/libxp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxp(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('printproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxpm/package.py b/var/spack/repos/builtin/packages/libxpm/package.py
index 11ede1fe88..6eb7b81af7 100644
--- a/var/spack/repos/builtin/packages/libxpm/package.py
+++ b/var/spack/repos/builtin/packages/libxpm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,7 +23,7 @@ class Libxpm(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def setup_environment(self, spack_env, run_env):
diff --git a/var/spack/repos/builtin/packages/libxpresent/package.py b/var/spack/repos/builtin/packages/libxpresent/package.py
index 286bf89fb8..3dbc97145e 100644
--- a/var/spack/repos/builtin/packages/libxpresent/package.py
+++ b/var/spack/repos/builtin/packages/libxpresent/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxpresent(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('presentproto@1.0:', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxprintapputil/package.py b/var/spack/repos/builtin/packages/libxprintapputil/package.py
index a6d2838d4d..a1207a4323 100644
--- a/var/spack/repos/builtin/packages/libxprintapputil/package.py
+++ b/var/spack/repos/builtin/packages/libxprintapputil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxprintapputil(AutotoolsPackage):
     depends_on('libxau')
 
     depends_on('printproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxprintutil/package.py b/var/spack/repos/builtin/packages/libxprintutil/package.py
index 9bd765e1b6..0bbb53d62f 100644
--- a/var/spack/repos/builtin/packages/libxprintutil/package.py
+++ b/var/spack/repos/builtin/packages/libxprintutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxprintutil(AutotoolsPackage):
     depends_on('libxau')
 
     depends_on('printproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxrandr/package.py b/var/spack/repos/builtin/packages/libxrandr/package.py
index 2ee8f76acb..29167ef0a1 100644
--- a/var/spack/repos/builtin/packages/libxrandr/package.py
+++ b/var/spack/repos/builtin/packages/libxrandr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Libxrandr(AutotoolsPackage):
     depends_on('randrproto@1.5:', type='build')
     depends_on('xextproto', type='build')
     depends_on('renderproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxrender/package.py b/var/spack/repos/builtin/packages/libxrender/package.py
index 49ed107daa..ac46c46ce8 100644
--- a/var/spack/repos/builtin/packages/libxrender/package.py
+++ b/var/spack/repos/builtin/packages/libxrender/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Libxrender(AutotoolsPackage):
     depends_on('libx11@1.6:')
 
     depends_on('renderproto@0.9:', type=('build', 'link'))
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxres/package.py b/var/spack/repos/builtin/packages/libxres/package.py
index eb691f8835..f5a8758d3d 100644
--- a/var/spack/repos/builtin/packages/libxres/package.py
+++ b/var/spack/repos/builtin/packages/libxres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxres(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('resourceproto@1.0:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxscrnsaver/package.py b/var/spack/repos/builtin/packages/libxscrnsaver/package.py
index ec68e8d395..242ddbd50f 100644
--- a/var/spack/repos/builtin/packages/libxscrnsaver/package.py
+++ b/var/spack/repos/builtin/packages/libxscrnsaver/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Libxscrnsaver(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('scrnsaverproto@1.2:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxshmfence/package.py b/var/spack/repos/builtin/packages/libxshmfence/package.py
index fea8c64fdd..c0206fa598 100644
--- a/var/spack/repos/builtin/packages/libxshmfence/package.py
+++ b/var/spack/repos/builtin/packages/libxshmfence/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,10 +14,11 @@ class Libxshmfence(AutotoolsPackage):
     using file descriptor passing."""
 
     homepage = "https://cgit.freedesktop.org/xorg/lib/libxshmfence/"
-    url      = "http://xorg.freedesktop.org/archive/individual/lib/libxshmfence-1.2.tar.gz"
+    url      = "https://www.x.org/archive/individual/lib/libxshmfence-1.3.tar.bz2"
 
-    version('1.2', 'f0b30c0fc568b22ec524859ee28556f1')
+    version('1.3', '42dda8016943dc12aff2c03a036e0937')
+    version('1.2', '66662e76899112c0f99e22f2fc775a7e')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxslt/package.py b/var/spack/repos/builtin/packages/libxslt/package.py
index cbb04c0ee2..cdd361928f 100644
--- a/var/spack/repos/builtin/packages/libxslt/package.py
+++ b/var/spack/repos/builtin/packages/libxslt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libxsmm/package.py b/var/spack/repos/builtin/packages/libxsmm/package.py
index ec1fa2f0bc..0786ec051c 100644
--- a/var/spack/repos/builtin/packages/libxsmm/package.py
+++ b/var/spack/repos/builtin/packages/libxsmm/package.py
@@ -1,41 +1,25 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
 
-class Libxsmm(Package):
+class Libxsmm(MakefilePackage):
     '''Library targeting Intel Architecture
     for small, dense or sparse matrix multiplications,
     and small convolutions.'''
 
     homepage = 'https://github.com/hfp/libxsmm'
-    url      = 'https://github.com/hfp/libxsmm/archive/1.8.1.tar.gz'
-
-    version('develop', git='https://github.com/hfp/libxsmm.git')
+    url      = 'https://github.com/hfp/libxsmm/archive/1.9.tar.gz'
+    git      = 'https://github.com/hfp/libxsmm.git'
 
+    version('develop', branch='master')
+    version('1.9',   'a001a491d9b98239bc2bfd906bd09d90')
+    version('1.8.3', '3415928340929c3a29773934de05c978')
+    version('1.8.2', '8f11ece699244c28dcb6742969a2ccd4')
     version('1.8.1', 'ece51ec767580f4542f509655daa5ec0')
     version('1.8',   '2d513afbdad99e5d04c6c4ab4c9bb25b')
     version('1.7.1', 'a938335b1c2c90616dc72c2c1a5824ab')
@@ -60,17 +44,19 @@ class Libxsmm(Package):
             description='Unoptimized with call-trace (LIBXSMM_TRACE).')
     variant('header-only', default=False,
             description='Produce header-only installation')
+    conflicts('+header-only', when='@:1.6.2',
+              msg='Header-only is available since v1.6.2!')
 
     @property
     def libs(self):
         result = find_libraries(['libxsmm', 'libxsmmf'], root=self.prefix,
-                                recurse=True)
+                                recursive=True)
         if len(result) == 0:
             result = find_libraries(['libxsmm', 'libxsmmf'], root=self.prefix,
-                                    shared=False, recurse=True)
+                                    shared=False, recursive=True)
         return result
 
-    def patch(self):
+    def edit(self, spec, prefix):
         kwargs = {'ignore_absent': False, 'backup': False, 'string': True}
         makefile = FileFilter('Makefile.inc')
 
@@ -83,26 +69,7 @@ class Libxsmm(Package):
         makefile.filter('FC = ifort',       'FC ?= ifort', **kwargs)
         makefile.filter('FC = gfortran',    'FC ?= gfortran', **kwargs)
 
-    def manual_install(self, prefix):
-        spec = self.spec
-        install_tree('include', prefix.include)
-        if '~header-only' in spec:
-            install_tree('lib', prefix.lib)
-        doc_path = prefix.share + '/libxsmm/doc'
-        mkdirp(doc_path)
-        for doc_file in glob('documentation/*.md'):
-            install(doc_file, doc_path)
-        for doc_file in glob('documentation/*.pdf'):
-            install(doc_file, doc_path)
-        install('README.md', doc_path)
-        install('LICENSE', doc_path)
-
-    def install(self, spec, prefix):
-        if '+header-only' in spec and '@1.6.2:' not in spec:
-            raise InstallError(
-                "The variant +header-only is only available " +
-                "for versions @1.6.2:")
-
+    def build(self, spec, prefix):
         # include symbols by default
         make_args = ['SYM=1']
 
@@ -118,4 +85,21 @@ class Libxsmm(Package):
             make_args += ['TRACE=1']
 
         make(*make_args)
-        self.manual_install(prefix)
+
+    def install(self, spec, prefix):
+        install_tree('include', prefix.include)
+        if '+header-only' in spec:
+            install_tree('src', prefix.src)
+        else:
+            install_tree('lib', prefix.lib)
+        mkdirp(prefix.doc)
+        for doc_file in glob(join_path('documentation', '*.md')):
+            install(doc_file, prefix.doc)
+        for doc_file in glob(join_path('documentation', '*.pdf')):
+            install(doc_file, prefix.doc)
+        if '@1.8.2:' in spec:
+            install('LICENSE.md', prefix.doc)
+        else:
+            install('README.md', prefix.doc)
+            install('LICENSE', prefix.doc)
+        install('version.txt', prefix.doc)
diff --git a/var/spack/repos/builtin/packages/libxstream/package.py b/var/spack/repos/builtin/packages/libxstream/package.py
index 00b7c0be32..df27052dbc 100644
--- a/var/spack/repos/builtin/packages/libxstream/package.py
+++ b/var/spack/repos/builtin/packages/libxstream/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libxt/package.py b/var/spack/repos/builtin/packages/libxt/package.py
index b3e2ac4e63..65746869a0 100644
--- a/var/spack/repos/builtin/packages/libxt/package.py
+++ b/var/spack/repos/builtin/packages/libxt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,11 @@ class Libxt(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('kbproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
+
+    @property
+    def libs(self):
+        return find_libraries(
+            'libXt', root=self.prefix, shared=True, recursive=True
+        )
diff --git a/var/spack/repos/builtin/packages/libxtrap/package.py b/var/spack/repos/builtin/packages/libxtrap/package.py
index 83405cf48d..9a7f3ac1ff 100644
--- a/var/spack/repos/builtin/packages/libxtrap/package.py
+++ b/var/spack/repos/builtin/packages/libxtrap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -48,5 +29,5 @@ class Libxtrap(AutotoolsPackage):
 
     depends_on('trapproto', type='build')
     depends_on('xextproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxtst/package.py b/var/spack/repos/builtin/packages/libxtst/package.py
index 9b6b4093ba..2bd5d8cefd 100644
--- a/var/spack/repos/builtin/packages/libxtst/package.py
+++ b/var/spack/repos/builtin/packages/libxtst/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,5 +31,5 @@ class Libxtst(AutotoolsPackage):
     depends_on('xextproto@7.0.99.3:', type='build')
     depends_on('inputproto', type='build')
     depends_on('fixesproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxv/package.py b/var/spack/repos/builtin/packages/libxv/package.py
index e29ec91b84..773f6eee2a 100644
--- a/var/spack/repos/builtin/packages/libxv/package.py
+++ b/var/spack/repos/builtin/packages/libxv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxv(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('videoproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxvmc/package.py b/var/spack/repos/builtin/packages/libxvmc/package.py
index 42e56618a4..a3ca179a86 100644
--- a/var/spack/repos/builtin/packages/libxvmc/package.py
+++ b/var/spack/repos/builtin/packages/libxvmc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxvmc(AutotoolsPackage):
 
     depends_on('xextproto', type='build')
     depends_on('videoproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxxf86dga/package.py b/var/spack/repos/builtin/packages/libxxf86dga/package.py
index f92ff7fb63..45ad7a1540 100644
--- a/var/spack/repos/builtin/packages/libxxf86dga/package.py
+++ b/var/spack/repos/builtin/packages/libxxf86dga/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxxf86dga(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
     depends_on('xf86dgaproto@2.0.99.2:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxxf86misc/package.py b/var/spack/repos/builtin/packages/libxxf86misc/package.py
index 8b161008f8..a8abde1e66 100644
--- a/var/spack/repos/builtin/packages/libxxf86misc/package.py
+++ b/var/spack/repos/builtin/packages/libxxf86misc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxxf86misc(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
     depends_on('xf86miscproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libxxf86vm/package.py b/var/spack/repos/builtin/packages/libxxf86vm/package.py
index 6b2cf951ed..4ec5eae3e0 100644
--- a/var/spack/repos/builtin/packages/libxxf86vm/package.py
+++ b/var/spack/repos/builtin/packages/libxxf86vm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Libxxf86vm(AutotoolsPackage):
     depends_on('xproto', type='build')
     depends_on('xextproto', type='build')
     depends_on('xf86vidmodeproto@2.2.99.1:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/libyogrt/package.py b/var/spack/repos/builtin/packages/libyogrt/package.py
index f48ce80e83..5d63913911 100644
--- a/var/spack/repos/builtin/packages/libyogrt/package.py
+++ b/var/spack/repos/builtin/packages/libyogrt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/libzip/package.py b/var/spack/repos/builtin/packages/libzip/package.py
index c193caae7f..c40bc283e1 100644
--- a/var/spack/repos/builtin/packages/libzip/package.py
+++ b/var/spack/repos/builtin/packages/libzip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lighttpd/package.py b/var/spack/repos/builtin/packages/lighttpd/package.py
new file mode 100644
index 0000000000..7824d9392b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lighttpd/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Lighttpd(CMakePackage):
+    """a secure, fast, compliant and very flexible web-server"""
+
+    homepage = "https://www.lighttpd.net"
+    url      = "https://download.lighttpd.net/lighttpd/releases-1.4.x/lighttpd-1.4.50.tar.gz"
+
+    version('1.4.50', sha256='c9a9f175aca6db22ebebbc47de52c54a99bbd1dce8d61bb75103609a3d798235')
+    version('1.4.49', sha256='8b744baf9f29c386fff1a6d2e435491e726cb8d29cfdb1fe20ab782ee2fc2ac7')
+
+    def cmake_args(self):
+        return ["-DSBINDIR=bin"]
diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py
index edba82da40..c7f8403f47 100644
--- a/var/spack/repos/builtin/packages/likwid/package.py
+++ b/var/spack/repos/builtin/packages/likwid/package.py
@@ -1,45 +1,29 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
+import os
 
 
 class Likwid(Package):
     """Likwid is a simple to install and use toolsuite of command line
     applications for performance oriented programmers. It works for Intel and
-    AMD processors on the Linux operating system."""
+    AMD processors on the Linux operating system. This version uses the
+    perf_event backend which reduces the feature set but allows user installs.
+    See https://github.com/RRZE-HPC/likwid/wiki/TutorialLikwidPerf#feature-limitations
+    for information."""
 
     homepage = "https://github.com/RRZE-HPC/likwid"
     url      = "https://github.com/RRZE-HPC/likwid/archive/4.1.2.tar.gz"
 
     maintainers = ['davydden']
 
-    version('4.3.0', 'f6bdf12513af95bd6eefa9c68644e724')
-    version('4.2.1', 'c408ddcf0317cdd894af4c580cd74294')
-    version('4.2.0', 'e41ff334b8f032a323d941ce32907a75')
-    version('4.1.2', 'a857ce5bd23e31d96e2963fe81cb38f0')
+    version('4.3.2', '2cf00e220dfe22c8d9b6e44f7534e11d')
+    version('4.3.1', 'ff28250f622185688bf5e2e0975368ea')
+    version('4.3.0', '7f8f6981d7d341fce2621554323f8c8b')
 
     # NOTE: There is no way to use an externally provided hwloc with Likwid.
     # The reason is that the internal hwloc is patched to contain extra
@@ -64,10 +48,11 @@ class Likwid(Package):
     @run_before('install')
     def filter_sbang(self):
         # Filter sbang before install so Spack's sbang hook can fix it up
-        perl = join_path(self.spec['perl'].prefix.bin, 'perl')
         files = ['perl/feedGnuplot'] + glob.glob('filters/*')
 
-        filter_file('^#!/usr/bin/perl', '#!{0}'.format(perl), *files)
+        filter_file('^#!/usr/bin/perl',
+                    '#!{0}'.format(self.spec['perl'].command.path),
+                    *files)
 
     def install(self, spec, prefix):
         if self.compiler.name not in self.supported_compilers:
@@ -83,8 +68,16 @@ class Likwid(Package):
                     prefix,
                     'config.mk')
 
-        filter_file('^INSTALL_CHOWN.*',
-                    'INSTALL_CHOWN = -o $(USER)',
+        # FIXME: once https://github.com/spack/spack/issues/4432 is
+        # resolved, install as root by default and remove this
+        filter_file('^ACCESSMODE .*',
+                    'ACCESSMODE = perf_event',
+                    'config.mk')
+        filter_file('^BUILDFREQ .*',
+                    'BUILDFREQ = false',
+                    'config.mk')
+        filter_file('^BUILDDAEMON .*',
+                    'BUILDDAEMON = false',
                     'config.mk')
 
         if spec.satisfies('^lua'):
@@ -104,5 +97,6 @@ class Likwid(Package):
                             spec['lua'].prefix.bin),
                         'config.mk')
 
+        env['PWD'] = os.getcwd()
         make()
         make('install')
diff --git a/var/spack/repos/builtin/packages/linkphase3/package.py b/var/spack/repos/builtin/packages/linkphase3/package.py
index 4cba38115a..2aed38c49c 100644
--- a/var/spack/repos/builtin/packages/linkphase3/package.py
+++ b/var/spack/repos/builtin/packages/linkphase3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class Linkphase3(Package):
     """Haplotype reconstruction in pedigreed populations."""
 
     homepage = "https://github.com/tdruet/LINKPHASE3"
-    url      = "https://github.com/tdruet/LINKPHASE3"
+    git      = "https://github.com/tdruet/LINKPHASE3.git"
 
-    version('2017-06-14', commit='559913593fc818bb1adb29796a548cf5bf323827',
-            git='https://github.com/tdruet/LINKPHASE3.git')
+    version('2017-06-14', commit='559913593fc818bb1adb29796a548cf5bf323827')
 
     def install(self, spec, prefix):
         fortran = Executable(self.compiler.fc)
diff --git a/var/spack/repos/builtin/packages/linux-headers/package.py b/var/spack/repos/builtin/packages/linux-headers/package.py
index 224c502121..1ad8e9687a 100644
--- a/var/spack/repos/builtin/packages/linux-headers/package.py
+++ b/var/spack/repos/builtin/packages/linux-headers/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/listres/package.py b/var/spack/repos/builtin/packages/listres/package.py
index 783b4f48d6..62a953fb61 100644
--- a/var/spack/repos/builtin/packages/listres/package.py
+++ b/var/spack/repos/builtin/packages/listres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Listres(AutotoolsPackage):
     depends_on('libxmu')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/llvm-lld/package.py b/var/spack/repos/builtin/packages/llvm-lld/package.py
deleted file mode 100644
index ff27c21f94..0000000000
--- a/var/spack/repos/builtin/packages/llvm-lld/package.py
+++ /dev/null
@@ -1,48 +0,0 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 LlvmLld(CMakePackage):
-    """lld - The LLVM Linker
-       lld is a new set of modular code for creating linker tools."""
-    homepage = "http://lld.llvm.org"
-    url      = "http://llvm.org/releases/3.4/lld-3.4.src.tar.gz"
-
-    version('3.4', '3b6a17e58c8416c869c14dd37682f78e')
-
-    depends_on('llvm')
-    depends_on('cmake@2.8:', type='build')
-
-    def cmake_args(self):
-        if 'CXXFLAGS' in env and env['CXXFLAGS']:
-            env['CXXFLAGS'] += ' ' + self.compiler.cxx11_flag
-        else:
-            env['CXXFLAGS'] = self.compiler.cxx11_flag
-
-        return [
-            '-DLLD_PATH_TO_LLVM_BUILD=%s' % self.spec['llvm'].prefix,
-            '-DLLVM_MAIN_SRC_DIR=%s' % self.spec['llvm'].prefix,
-        ]
diff --git a/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py b/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py
index 2526cd4d03..bc274649f6 100644
--- a/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py
+++ b/var/spack/repos/builtin/packages/llvm-openmp-ompt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,19 +13,14 @@ class LlvmOpenmpOmpt(CMakePackage):
        changes for OMPT, the OpenMP Tools interface"""
 
     homepage = "https://github.com/OpenMPToolsInterface/LLVM-openmp"
+    git      = "https://github.com/OpenMPToolsInterface/LLVM-openmp.git"
 
-    # towards_tr4 branch
-    version('towards_tr4', branch='towards_tr4',
-            git='https://github.com/OpenMPToolsInterface/LLVM-openmp.git')
-
-    version('3.9.2b2',
-            git='https://github.com/OpenMPToolsInterface/LLVM-openmp.git',
-            commit='5cdca5dd3c0c336d42a335ca7cff622e270c9d47')
+    # tr6_forwards branch
+    version('tr6_forwards', branch='tr6_forwards')
+    version('3.9.2b2', commit='5cdca5dd3c0c336d42a335ca7cff622e270c9d47')
 
     # align-to-tr-rebased branch
-    version('3.9.2b',
-            git='https://github.com/OpenMPToolsInterface/LLVM-openmp.git',
-            commit='982a08bcf3df9fb5afc04ac3bada47f19cc4e3d3')
+    version('3.9.2b', commit='982a08bcf3df9fb5afc04ac3bada47f19cc4e3d3')
 
     # variant for building llvm-openmp-ompt as a stand alone library
     variant('standalone', default=False,
@@ -79,9 +55,9 @@ class LlvmOpenmpOmpt(CMakePackage):
                      '-DCMAKE_BUILD_WITH_INSTALL_RPATH=true',
                      '-DLIBOMP_USE_DEBUGGER=false'])
 
-        # Build llvm-openmp-ompt using the toward_tr4 branch
+        # Build llvm-openmp-ompt using the tr6_forwards branch
         # This requires the version to be 5.0 (50)
-        if '@towards_tr4' in self.spec:
+        if '@tr6_forwards' in self.spec:
                 cmake_args.extend(
                     ['-DLIBOMP_OMP_VERSION=50'])
 
diff --git a/var/spack/repos/builtin/packages/llvm/package.py b/var/spack/repos/builtin/packages/llvm/package.py
index 48f767aa17..8ec8d7fc37 100644
--- a/var/spack/repos/builtin/packages/llvm/package.py
+++ b/var/spack/repos/builtin/packages/llvm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,6 +31,7 @@ class Llvm(CMakePackage):
     variant('clang', default=True,
             description="Build the LLVM C/C++/Objective-C compiler frontend")
     variant('lldb', default=True, description="Build the LLVM debugger")
+    variant('lld', default=True, description="Build the LLVM linker")
     variant('internal_unwind', default=True,
             description="Build the libcxxabi libunwind")
     variant('polly', default=True,
@@ -80,13 +62,15 @@ class Llvm(CMakePackage):
     depends_on('cmake@3.4.3:', type='build')
 
     # Universal dependency
-    depends_on('python@2.7:2.8')  # Seems not to support python 3.X.Y
+    depends_on('python@2.7:2.8', when='@:4.999')
+    depends_on('python')
     depends_on('py-lit', type=('build', 'run'))
 
     # lldb dependencies
     depends_on('ncurses', when='+lldb')
     depends_on('swig', when='+lldb')
     depends_on('libedit', when='+lldb')
+    depends_on('py-six', when='@5.0.0: +lldb +python')
 
     # gold support
     depends_on('binutils+gold', when='+gold')
@@ -97,6 +81,8 @@ class Llvm(CMakePackage):
 
     base_url = 'http://llvm.org/releases/%%(version)s/%(pkg)s-%%(version)s.src.tar.xz'
     llvm_url = base_url % {'pkg': 'llvm'}
+    # Flang uses its own fork of llvm.
+    flang_llvm_url = 'https://github.com/flang-compiler/llvm.git'
 
     resources = {
         'compiler-rt': {
@@ -141,6 +127,12 @@ class Llvm(CMakePackage):
             'placement': 'lldb',
             'variant': '+lldb',
         },
+        'lld': {
+            'url':  base_url % {'pkg': 'lld'},
+            'destination': 'tools',
+            'placement': 'lld',
+            'variant': '+lld',
+        },
         'polly': {
             'url':  base_url % {'pkg': 'polly'},
             'destination': 'tools',
@@ -156,7 +148,7 @@ class Llvm(CMakePackage):
     }
     releases = [
         {
-            'version': 'trunk',
+            'version': 'develop',
             'repo': 'http://llvm.org/svn/llvm-project/llvm/trunk',
             'resources': {
                 'compiler-rt': 'http://llvm.org/svn/llvm-project/compiler-rt/trunk',
@@ -167,10 +159,91 @@ class Llvm(CMakePackage):
                 'cfe': 'http://llvm.org/svn/llvm-project/cfe/trunk',
                 'clang-tools-extra': 'http://llvm.org/svn/llvm-project/clang-tools-extra/trunk',
                 'lldb': 'http://llvm.org/svn/llvm-project/lldb/trunk',
+                'lld': 'http://llvm.org/svn/llvm-project/lld/trunk',
                 'libunwind': 'http://llvm.org/svn/llvm-project/libunwind/trunk',
             }
         },
         {
+            'version': '7.0.0',
+            'md5': 'e0140354db83cdeb8668531b431398f0',
+            'resources': {
+                'compiler-rt': '3b759c47076298363f4443395e0e51c1',
+                'openmp': '8800aac08f2f9dad0ebf66e0e152bd63',
+                'polly': 'ff689bbfdca3ea812d195f60e63d8346',
+                'libcxx': '5ef835bf8c9f49611af4d5f3362d9658',
+                'libcxxabi': 'f04adafa019f4f5cce9550007da251c1',
+                'cfe': '2ac5d8d78be681e31611c5e546e11174',
+                'clang-tools-extra': 'e98b37a5911cd556775cba0868a56981',
+                'lldb': '76338963b3ccc4f9dccc923716207310',
+                'lld': '5eb148c3064acff71d8e5856163c8323',
+                'libunwind': 'e585a3e4ae6045f2561bc8a8fcd0bfbb'
+            }
+        },
+        {
+            'version': '6.0.1',
+            'md5': 'c88c98709300ce2c285391f387fecce0',
+            'resources': {
+                'compiler-rt': '99bf8bcb68ba96dda74f6aee6c55f639',
+                'openmp': '4826402ae3633c36c51ba4d0e5527d30',
+                'polly': '4e5937753d1f77e2c0feca485fc7f9da',
+                'libcxx': '2c13cd0136ab6f8060a4cde85b5f86e2',
+                'libcxxabi': '41764959176d5fcc7baee8cd22ed1705',
+                'cfe': '4e419bd4e3b55aa06d872320f754bd85',
+                'clang-tools-extra': '431cba2b652e9c227a59a6d681388160',
+                'lldb': '482eba39e78c75a83216cf2d5b7a54b4',
+                'lld': '31cc580b32be124972c40c19c0839fed',
+                'libunwind': '569eed6f508af4c4c053b1112e6f3d0b'
+            }
+        },
+        {
+            'version': '6.0.0',
+            'md5': '788a11a35fa62eb008019b37187d09d2',
+            'resources': {
+                'compiler-rt': 'ba6368e894b5528e527d86a69d8533c6',
+                'openmp': 'eb6b8d0318a950a8192933a3b500585d',
+                'polly': 'e5808a3a1ed1c23f56dd1854b86689d0',
+                'libcxx': '4ecad7dfd8ea636205d3ffef028df73a',
+                'libcxxabi': '9d06327892fc5d8acec4ef2e2821ab3d',
+                'cfe': '121b3896cb0c7765d690acc5d9495d24',
+                'clang-tools-extra': '6b1d543116dab5a3caba10091d983743',
+                'lldb': '1ec6498066e273b7261270f344b68121',
+                'lld': '7ab2612417477b03538f11cd8b5e12f8',
+                'libunwind': '022a4ee2c3bf7b6d151e0444f66aca64'
+            }
+        },
+        {
+            'version': '5.0.2',
+            'md5': 'c5e980edf7f22d66f0f7561b35c1e195',
+            'resources': {
+                'compiler-rt': '22728d702a64ffc6d073d1dda25a1eb9',
+                'openmp': 'ad214f7f46d671f9b73d75e9d54e4594',
+                'polly': '5777f1248633ebc2b81ffe6ecb8cf4b1',
+                'libcxx': '93e7942c01cdd5bce5378bc3926f97ea',
+                'libcxxabi': '855ada029899c95cd6a852f13ed0ea71',
+                'cfe': '1cd6ee1b74331fb37c27b4a2a1802c97',
+                'clang-tools-extra': 'd4d0d9637fa1e47daf3f51e743d8f138',
+                'lldb': '9d0addd1a28a4c155b8f69919e7bbff7',
+                'lld': '7b7e2371cd250aec54879ae13b441382',
+                'libunwind': '5b2a11e475fe8e7f3725792ba66da086',
+            }
+        },
+        {
+            'version': '5.0.1',
+            'md5': '3a4ec6dcbc71579eeaec7cb157fe2168',
+            'resources': {
+                'compiler-rt': '6329380d643fb5dc5f5abdd0d5eecd70',
+                'openmp': '7f9c8f6aecd97df9c18187157ed2f813',
+                'polly': '49c49fb61b0e73855fc21a60db9f5ab3',
+                'libcxx': 'a9dd49822f2c82cef9a9240d1714a67c',
+                'libcxxabi': '60972ef307539aa517c9878d45b43452',
+                'cfe': 'e4daa278d8f252585ab73d196484bf11',
+                'clang-tools-extra': 'c2bd3733c183b033b49f7a416c6dca36',
+                'lldb': 'd64078681215b5935614b6b83b2d1463',
+                'lld': 'a873c7fdaac647613d8eed2cb03d82de',
+                'libunwind': 'ccf48200065481244d3d09828d54e87f',
+            }
+        },
+        {
             'version': '5.0.0',
             'md5': '5ce9c5ad55243347ea0fdb4c16754be0',
             'resources': {
@@ -182,6 +255,7 @@ class Llvm(CMakePackage):
                 'cfe': '699c448c6d6d0edb693c87beb1cc8c6e',
                 'clang-tools-extra': '0cda05d1a61becb393eb63746963d7f5',
                 'lldb': '8de19973d044ca2cfe325d4625a5cfef',
+                'lld': 'a39cbecced3263feab9139b47118e062',
                 'libunwind': '98fb2c677068c6f36727fb1d5397bca3',
             }
         },
@@ -197,6 +271,7 @@ class Llvm(CMakePackage):
                 'cfe': 'a6c7b3e953f8b93e252af5917df7db97',
                 'clang-tools-extra': 'cfd46027a0ab7eed483dfcc803e86bd9',
                 'lldb': '908bdd777d3b527a914ba360477b8ab3',
+                'lld': '39cd3512cddcfd7d37ef12066c961660',
                 'libunwind': 'b72ec95fb784e61f15d6196414b92f5e',
             }
         },
@@ -212,6 +287,7 @@ class Llvm(CMakePackage):
                 'cfe': '756e17349fdc708c62974b883bf72d37',
                 'clang-tools-extra': '99e711337ec3e9a8bb36e8dd62b2cd6e',
                 'lldb': 'bd41ba7fcca55d2a554409bbccd34d2d',
+                'lld': 'e5784656e0f38e3578f10ff7551d3896',
                 'libunwind': '0c3534eaa11c0cae33a1dcf5f36ce287',
             }
         },
@@ -227,6 +303,7 @@ class Llvm(CMakePackage):
                 'cfe': '45713ec5c417ed9cad614cd283d786a1',
                 'clang-tools-extra': '1a01d545a064fcbc46a2f05f6880d3d7',
                 'lldb': '91399402f287d3f637db1207113deecb',
+                'lld': '6254dd138e23b098df4ef7840c11e2c8',
                 'libunwind': 'f273dd0ed638ad0601b23176a36f187b',
             }
         },
@@ -242,6 +319,7 @@ class Llvm(CMakePackage):
                 'cfe': '29e1d86bee422ab5345f5e9fb808d2dc',
                 'clang-tools-extra': 'f4f663068c77fc742113211841e94d5e',
                 'lldb': '968d053c3c3d7297983589164c6999e9',
+                'lld': 'c23c895c0d855a0dc426af686538a95e',
                 'libunwind': '3e5c87c723a456be599727a444b1c166',
             }
         },
@@ -257,6 +335,7 @@ class Llvm(CMakePackage):
                 'cfe': '4ff2f8844a786edb0220f490f7896080',
                 'clang-tools-extra': '6e49f285d0b366cc3cab782d8c92d382',
                 'lldb': '9e4787b71be8e432fffd31e13ac87623',
+                'lld': '68cd069bf99c71ebcfbe01d557c0e14d',
                 'libunwind': 'd66e2387e1d37a8a0c8fe6a0063a3bab',
             }
         },
@@ -272,6 +351,7 @@ class Llvm(CMakePackage):
                 'cfe': 'cc99e7019bb74e6459e80863606250c5',
                 'clang-tools-extra': 'c2344f50e0eea0b402f0092a80ddc036',
                 'lldb': 'a5da35ed9cc8c8817ee854e3dbfba00e',
+                'lld': 'de33b5c6c77698ee2f8d024fbffb8df1',
                 'libunwind': '162ade468607f153cca12be90b5194fa',
             }
         },
@@ -287,6 +367,7 @@ class Llvm(CMakePackage):
                 'cfe': '0acd026b5529164197563d135a8fd83e',
                 'clang-tools-extra': '5d49ff745037f061a7c86aeb6a24c3d2',
                 'lldb': 'a106d8a0d21fc84d76953822fbaf3398',
+                'lld': '6c3794e30fbe118a601fb694627f34f8',
                 'libunwind': '814bd52c9247c5d04629658fbcb3ab8c',
             }
         },
@@ -302,6 +383,7 @@ class Llvm(CMakePackage):
                 'cfe': '8f9d27335e7331cf0a4711e952f21f01',
                 'clang-tools-extra': 'd5a87dacb65d981a427a536f6964642e',
                 'lldb': 'e5931740400d1dc3e7db4c7ba2ceff68',
+                'lld': '91bd593a67293d84dad0bf11845546c2',
                 'libunwind': '9a75392eb7eb8ed5c0840007e212baf5',
             }
         },
@@ -316,6 +398,7 @@ class Llvm(CMakePackage):
                 'cfe': 'ff862793682f714bb7862325b9c06e20',
                 'clang-tools-extra': '3ebc1dc41659fcec3db1b47d81575e06',
                 'lldb': '51e5eb552f777b950bb0ff326e60d5f0',
+                'lld': '7143cc4fa88851a9f9b9a03621fbb387',
             }
         },
         {
@@ -329,12 +412,54 @@ class Llvm(CMakePackage):
                 'cfe': '93f9532f8f7e6f1d8e5c1116907051cb',
                 'clang-tools-extra': 'f13f31ed3038acadc6fa63fef812a246',
                 'lldb': 'cc5ea8a414c62c33e760517f8929a204',
+                'lld': '173be02b7ff4e5e31fbb0a591a03d7a3',
+            }
+        },
+    ]
+
+    # Flang uses its own fork of clang (renamed flang-driver).
+    flang_resources = {
+        'flang-driver': {
+            'git': 'https://github.com/flang-compiler/flang-driver.git',
+            'destination': 'tools',
+            'placement': 'clang'
+        },
+        'openmp': {
+            'git': 'https://github.com/llvm-mirror/openmp.git',
+            'destination': 'projects',
+            'placement': 'openmp'
+        }
+    }
+
+    flang_releases = [
+        {
+            'version': 'develop',
+            'branch': 'release_60',
+            'resources': {
+                'flang-driver': 'release_60',
+                'openmp': 'release_60',
             }
         },
+        {
+            'version': '20180612',
+            'commit': 'f26a3ece4ccd68a52f5aa970ec42837ee0743296',
+            'resources': {
+                'flang-driver': 'e079fa68cb35a53c88c41a1939f90b94d539e984',
+                'openmp': 'd5aa29cb3bcf51289d326b4e565613db8aff65ef'
+            }
+        },
+        {
+            'version': 'ppc64le-20180612',
+            'commit': '4158932a46eb2f06a166f22a4a52ae48c7d2949e',
+            'resources': {
+                'flang-driver': '50c1828a134d5a0f1553b355bf0946db48b0aa6d',
+                'openmp': '29b515e1e6d26b5b0d32d47d28dcdb4b8a11470d'
+            }
+        }
     ]
 
     for release in releases:
-        if release['version'] == 'trunk':
+        if release['version'] == 'develop':
             version(release['version'], svn=release['repo'])
 
             for name, repo in release['resources'].items():
@@ -356,15 +481,67 @@ class Llvm(CMakePackage):
                                          resources[name].get('variant', "")),
                          placement=resources[name].get('placement', None))
 
+    for release in flang_releases:
+        if release['version'] == 'develop':
+            version('flang-' + release['version'], git=flang_llvm_url, branch=release['branch'])
+
+            for name, branch in release['resources'].items():
+                flang_resource = flang_resources[name]
+                resource(name=name,
+                         git=flang_resource['git'],
+                         branch=branch,
+                         destination=flang_resource['destination'],
+                         placement=flang_resource['placement'],
+                         when='@flang-' + release['version'])
+
+        else:
+            version('flang-' + release['version'], git=flang_llvm_url, commit=release['commit'])
+
+            for name, commit in release['resources'].items():
+                flang_resource = flang_resources[name]
+                resource(name=name,
+                         git=flang_resource['git'],
+                         commit=commit,
+                         destination=flang_resource['destination'],
+                         placement=flang_resource['placement'],
+                         when='@flang-' + release['version'])
+
     conflicts('+clang_extra', when='~clang')
     conflicts('+lldb',        when='~clang')
 
+    # LLVM 4 and 5 does not build with GCC 8
+    conflicts('%gcc@8:',      when='@:5')
+
     # Github issue #4986
     patch('llvm_gcc7.patch', when='@4.0.0:4.0.1+lldb %gcc@7.0:')
 
+    @run_before('cmake')
+    def check_darwin_lldb_codesign_requirement(self):
+        if not self.spec.satisfies('+lldb platform=darwin'):
+            return
+        codesign = which('codesign')
+        mkdir('tmp')
+        llvm_check_file = join_path('tmp', 'llvm_check')
+        copy('/usr/bin/false', llvm_check_file)
+
+        try:
+            codesign('-f', '-s', 'lldb_codesign', '--dryrun',
+                     llvm_check_file)
+
+        except ProcessError:
+            explanation = ('The "lldb_codesign" identity must be available'
+                           ' to build LLVM with LLDB. See https://llvm.org/'
+                           'svn/llvm-project/lldb/trunk/docs/code-signing'
+                           '.txt for details on how to create this identity.')
+            raise RuntimeError(explanation)
+
     def setup_environment(self, spack_env, run_env):
         spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag)
 
+        if '+clang' in self.spec:
+            run_env.set('CC', join_path(self.spec.prefix.bin, 'clang'))
+            run_env.set('CXX', join_path(self.spec.prefix.bin, 'clang++'))
+
     def cmake_args(self):
         spec = self.spec
 
@@ -385,11 +562,15 @@ class Llvm(CMakePackage):
                                '-DLLVM_POLLY_BUILD:Bool=OFF',
                                '-DLLVM_POLLY_LINK_INTO_TOOLS:Bool=OFF'])
 
+        if '+python' in spec and '+lldb' in spec and spec.satisfies('@5.0.0:'):
+            cmake_args.append('-DLLDB_USE_SYSTEM_SIX:Bool=TRUE')
         if '+clang' not in spec:
             cmake_args.append('-DLLVM_EXTERNAL_CLANG_BUILD:Bool=OFF')
         if '+lldb' not in spec:
             cmake_args.extend(['-DLLVM_EXTERNAL_LLDB_BUILD:Bool=OFF',
                                '-DLLVM_TOOL_LLDB_BUILD:Bool=OFF'])
+        if '+lld' not in spec:
+            cmake_args.append('-DLLVM_TOOL_LLD_BUILD:Bool=OFF')
         if '+internal_unwind' not in spec:
             cmake_args.append('-DLLVM_EXTERNAL_LIBUNWIND_BUILD:Bool=OFF')
         if '+libcxx' in spec:
@@ -408,7 +589,15 @@ class Llvm(CMakePackage):
             cmake_args.append('-DLLVM_LINK_LLVM_DYLIB:Bool=ON')
 
         if '+all_targets' not in spec:  # all is default on cmake
-            targets = ['CppBackend', 'NVPTX', 'AMDGPU']
+
+            if spec.version < Version('3.9.0'):
+                targets = ['CppBackend', 'NVPTX', 'AMDGPU']
+            else:
+                # Starting in 3.9.0 CppBackend is no longer a target (see
+                # LLVM_ALL_TARGETS in llvm's top-level CMakeLists.txt for
+                # the complete list of targets)
+                targets = ['NVPTX', 'AMDGPU']
+
             if 'x86' in spec.architecture.target.lower():
                 targets.append('X86')
             elif 'arm' in spec.architecture.target.lower():
@@ -416,7 +605,7 @@ class Llvm(CMakePackage):
             elif 'aarch64' in spec.architecture.target.lower():
                 targets.append('AArch64')
             elif 'sparc' in spec.architecture.target.lower():
-                targets.append('sparc')
+                targets.append('Sparc')
             elif ('ppc' in spec.architecture.target.lower() or
                   'power' in spec.architecture.target.lower()):
                 targets.append('PowerPC')
@@ -433,7 +622,9 @@ class Llvm(CMakePackage):
         with working_dir(self.build_directory):
             # When building shared libraries these need to be installed first
             make('install-LLVMTableGen')
-            make('install-LLVMDemangle')
+            if self.spec.version >= Version('4.0.0'):
+                # LLVMDemangle target was added in 4.0.0
+                make('install-LLVMDemangle')
             make('install-LLVMSupport')
 
     @run_after('install')
diff --git a/var/spack/repos/builtin/packages/lmdb/package.py b/var/spack/repos/builtin/packages/lmdb/package.py
index fb147403d9..2900dc6bd6 100644
--- a/var/spack/repos/builtin/packages/lmdb/package.py
+++ b/var/spack/repos/builtin/packages/lmdb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lmod/package.py b/var/spack/repos/builtin/packages/lmod/package.py
index 73cfcd2b88..f9ba114cf7 100644
--- a/var/spack/repos/builtin/packages/lmod/package.py
+++ b/var/spack/repos/builtin/packages/lmod/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -38,6 +19,9 @@ class Lmod(AutotoolsPackage):
     homepage = 'https://www.tacc.utexas.edu/research-development/tacc-projects/lmod'
     url      = 'https://github.com/TACC/Lmod/archive/7.4.11.tar.gz'
 
+    version('7.8', sha256='40388380a36a00c3ce929a9f88c8fffc93deeabf87a7c3f8864a82acad38c3ba')
+    version('7.7.29', 'bd3f171995e6863505e8a958d158ced1')
+    version('7.7.13', 'e1d222fa04148707dceb08c82d7e9fa5')
     version('7.7',    '8ac594401716c6d1b40cac22bc1030ca')
     version('7.6.14', '60726c991038b6337fbb27b6a333a2d4')
     version('7.4.11', '70c55ba0ba3877b6d8df536ee7ea6d49')
@@ -52,7 +36,7 @@ class Lmod(AutotoolsPackage):
     version('6.3.7',  '0fa4d5a24c41cae03776f781aa2dedc1')
     version('6.0.1',  '91abf52fe5033bd419ffe2842ebe7af9')
 
-    depends_on('lua@5.2:')
+    depends_on('lua@5.1:')
     depends_on('lua-luaposix', type=('build', 'run'))
     depends_on('lua-luafilesystem', type=('build', 'run'))
     depends_on('tcl', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/lndir/package.py b/var/spack/repos/builtin/packages/lndir/package.py
index 071ce420d8..35a2517af0 100644
--- a/var/spack/repos/builtin/packages/lndir/package.py
+++ b/var/spack/repos/builtin/packages/lndir/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,4 +16,4 @@ class Lndir(AutotoolsPackage):
     version('1.0.3', '7173b2e4832658d319c2980a7c834205')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/log4cplus/package.py b/var/spack/repos/builtin/packages/log4cplus/package.py
new file mode 100644
index 0000000000..d759f2f6d3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/log4cplus/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Log4cplus(CMakePackage):
+    """log4cplus is a simple to use C++ logging API
+    providing thread-safe, flexible, and arbitrarily
+    granular control over log management and configuration."""
+
+    homepage = "https://sourceforge.net/projects/log4cplus/"
+    url      = "https://download.sourceforge.net/project/log4cplus/log4cplus-stable/2.0.1/log4cplus-2.0.1.tar.bz2"
+
+    version('2.0.1', 'ec01c03241ebd31127a44d1880830d8f')
+    version('1.2.1', 'e4e6c38b065b70b5d6efc238a5106bc9')
+    version('1.2.0', 'e250f0f431c0723f8b625323e7b6465d')
diff --git a/var/spack/repos/builtin/packages/log4cxx/package.py b/var/spack/repos/builtin/packages/log4cxx/package.py
index b2bf7a4e35..a88e9cccbb 100644
--- a/var/spack/repos/builtin/packages/log4cxx/package.py
+++ b/var/spack/repos/builtin/packages/log4cxx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,8 +14,9 @@ class Log4cxx(AutotoolsPackage):
 
     version('0.10.0', 'b30ffb8da3665178e68940ff7a61084c')
 
-    depends_on('libxml2')
     depends_on('apr-util')
+    depends_on('apr')
+    depends_on('zip')
 
     build_directory = 'spack-build'
 
@@ -44,4 +26,5 @@ class Log4cxx(AutotoolsPackage):
 
     def configure_args(self):
         args = ['--disable-static']
+
         return args
diff --git a/var/spack/repos/builtin/packages/loki/package.py b/var/spack/repos/builtin/packages/loki/package.py
new file mode 100644
index 0000000000..1f4cac66f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/loki/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Loki(MakefilePackage):
+    """Loki is a C++ library of designs, containing flexible implementations
+    of common design patterns and idioms."""
+
+    homepage = "http://loki-lib.sourceforge.net"
+    url      = "https://downloads.sourceforge.net/project/loki-lib/Loki/Loki%200.1.7/loki-0.1.7.tar.bz2"
+
+    version('0.1.7', '33a24bcbb99fa2ec8fcbbab65649f3f6')
+
+    variant('shared', default=True, description="Build shared libraries")
+
+    def build(self, spec, prefix):
+        if '+shared' in spec:
+            make('-C', 'src', 'build-shared')
+        else:
+            make('-C', 'src', 'build-static')
+
+    def install(self, spec, prefix):
+        make('-C', 'include', 'install', 'prefix={0}'.format(prefix))
+        if '+shared' in spec:
+            make('-C', 'src', 'install-shared', 'prefix={0}'.format(prefix))
+        else:
+            make('-C', 'src', 'install-static', 'prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/lordec/package.py b/var/spack/repos/builtin/packages/lordec/package.py
new file mode 100644
index 0000000000..f02ec371b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lordec/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lordec(MakefilePackage):
+    """LoRDEC is a program to correct sequencing errors in long reads from
+    3rd generation sequencing with high error rate, and is especially
+    intended for PacBio reads."""
+
+    homepage = "http://www.atgc-montpellier.fr/lordec/"
+    url      = "https://gite.lirmm.fr/lordec/lordec-releases/uploads/e3116a5f251e46e47f7a3b7ddb2bd7f6/lordec-src_0.8.tar.gz"
+
+    version('0.8', 'd5a57db681d1cd31c516aa780ce53f9d')
+
+    depends_on('boost')
+    depends_on('cmake@3.1.0:', type='build')
+
+    build_targets = ['clean', 'all']
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/lrslib/package.py b/var/spack/repos/builtin/packages/lrslib/package.py
index 586750b9bf..05b7941fd9 100644
--- a/var/spack/repos/builtin/packages/lrslib/package.py
+++ b/var/spack/repos/builtin/packages/lrslib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/lrzip/package.py b/var/spack/repos/builtin/packages/lrzip/package.py
index 531cba2b87..bacc3a2f01 100644
--- a/var/spack/repos/builtin/packages/lrzip/package.py
+++ b/var/spack/repos/builtin/packages/lrzip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,10 @@ class Lrzip(Package):
     but not both."""
 
     homepage = 'http://lrzip.kolivas.org'
-    url = 'https://github.com/ckolivas/lrzip/archive/v0.630.tar.gz'
+    url      = 'https://github.com/ckolivas/lrzip/archive/v0.630.tar.gz'
+    git      = 'https://github.com/ckolivas/lrzip.git'
 
-    version('master', git='https://github.com/ckolivas/lrzip.git')
+    version('master', branch='master')
     version('0.630', '3ca7f1d1365aa105089d1fbfc6b0924a')
     version('0.621', '1f07227b39ae81a98934411e8611e341')
     version('0.616', 'd40bdb046d0807ef602e36b1e9782cc0')
diff --git a/var/spack/repos/builtin/packages/lsof/package.py b/var/spack/repos/builtin/packages/lsof/package.py
new file mode 100644
index 0000000000..b03afeb004
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lsof/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Lsof(Package):
+    """Lsof displays information about files open to Unix processes."""
+
+    homepage = "https://people.freebsd.org/~abe/"
+    url      = "https://www.mirrorservice.org/sites/lsof.itap.purdue.edu/pub/tools/unix/lsof/lsof_4.89.tar.gz"
+
+    version('4.89', '8afbaff3ee308edc130bdc5df0801c8f')
+
+    def install(self, spec, prefix):
+        tar = which('tar')
+        tar('xf', 'lsof_{0}_src.tar'.format(self.version))
+
+        with working_dir('lsof_{0}_src'.format(self.version)):
+            configure = Executable('./Configure')
+            configure('-n', 'linux')
+
+            make()
+
+            mkdir(prefix.bin)
+            install('lsof', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/ltrace/package.py b/var/spack/repos/builtin/packages/ltrace/package.py
new file mode 100644
index 0000000000..3e18f659ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ltrace/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ltrace(AutotoolsPackage):
+    """Ltrace intercepts and records dynamic library calls which are called
+    by an executed process and the signals received by that process. It
+    can also intercept and print the system calls executed by the program."""
+
+    homepage = "https://www.ltrace.org"
+    url      = "https://www.ltrace.org/ltrace_0.7.3.orig.tar.bz2"
+
+    version('0.7.3', 'b3dd199af8f18637f7d4ef97fdfb9d14')
+
+    conflicts('platform=darwin', msg='ltrace runs only on Linux.')
diff --git a/var/spack/repos/builtin/packages/lua-bitlib/package.py b/var/spack/repos/builtin/packages/lua-bitlib/package.py
index 014eb77e43..55a04311c2 100644
--- a/var/spack/repos/builtin/packages/lua-bitlib/package.py
+++ b/var/spack/repos/builtin/packages/lua-bitlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
diff --git a/var/spack/repos/builtin/packages/lua-jit/package.py b/var/spack/repos/builtin/packages/lua-jit/package.py
index 2005936110..be3d28e4c8 100644
--- a/var/spack/repos/builtin/packages/lua-jit/package.py
+++ b/var/spack/repos/builtin/packages/lua-jit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/lua-lpeg/package.py b/var/spack/repos/builtin/packages/lua-lpeg/package.py
index aa9a491e4b..1d57d0bc9c 100644
--- a/var/spack/repos/builtin/packages/lua-lpeg/package.py
+++ b/var/spack/repos/builtin/packages/lua-lpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/lua-luafilesystem/package.py b/var/spack/repos/builtin/packages/lua-luafilesystem/package.py
index 7194654838..1611a64b3a 100644
--- a/var/spack/repos/builtin/packages/lua-luafilesystem/package.py
+++ b/var/spack/repos/builtin/packages/lua-luafilesystem/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lua-luaposix/package.py b/var/spack/repos/builtin/packages/lua-luaposix/package.py
index 5cc81d6e65..8d9ad7f832 100644
--- a/var/spack/repos/builtin/packages/lua-luaposix/package.py
+++ b/var/spack/repos/builtin/packages/lua-luaposix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/lua-mpack/package.py b/var/spack/repos/builtin/packages/lua-mpack/package.py
index ffdb953428..f6cca90e0d 100644
--- a/var/spack/repos/builtin/packages/lua-mpack/package.py
+++ b/var/spack/repos/builtin/packages/lua-mpack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/lua/package.py b/var/spack/repos/builtin/packages/lua/package.py
index 46d1e5c094..ceb816a5d7 100644
--- a/var/spack/repos/builtin/packages/lua/package.py
+++ b/var/spack/repos/builtin/packages/lua/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -49,6 +30,8 @@ class Lua(Package):
 
     depends_on('ncurses')
     depends_on('readline')
+    # luarocks needs unzip for some packages (e.g. lua-luaposix)
+    depends_on('unzip', type='run')
 
     resource(
         name="luarocks",
@@ -64,28 +47,41 @@ class Lua(Package):
         else:
             target = 'linux'
         make('INSTALL_TOP=%s' % prefix,
-             'MYCFLAGS=%s' % (
-                 self.compiler.pic_flag),
              'MYLDFLAGS=-L%s -L%s' % (
                  spec['readline'].prefix.lib,
                  spec['ncurses'].prefix.lib),
              'MYLIBS=-lncursesw',
-             'CC=%s -std=gnu99' % spack_cc,
+             'CC=%s -std=gnu99 %s' % (spack_cc,
+                                      self.compiler.pic_flag),
              target)
         make('INSTALL_TOP=%s' % prefix,
-             'MYCFLAGS=%s' % (
-                 self.compiler.pic_flag),
-             'MYLDFLAGS=-L%s -L%s' % (
-                 spec['readline'].prefix.lib,
-                 spec['ncurses'].prefix.lib),
-             'MYLIBS=-lncursesw',
-             'CC=%s -std=gnu99' % spack_cc,
              'install')
 
         static_to_shared_library(join_path(prefix.lib, 'liblua.a'),
                                  arguments=['-lm'], version=self.version,
                                  compat_version=self.version.up_to(2))
 
+        # compatibility with ax_lua.m4 from autoconf-archive
+        # https://www.gnu.org/software/autoconf-archive/ax_lua.html
+        with working_dir(prefix.lib):
+            # e.g., liblua.so.5.1.5
+            src_path = 'liblua.{0}.{1}'.format(dso_suffix,
+                                               str(self.version.up_to(3)))
+
+            # For lua version 5.1.X, the symlinks should be:
+            # liblua5.1.so
+            # liblua51.so
+            # liblua-5.1.so
+            # liblua-51.so
+            version_formats = [str(self.version.up_to(2)),
+                               Version(str(self.version.up_to(2))).joined]
+            for version_str in version_formats:
+                for joiner in ['', '-']:
+                    dest_path = 'liblua{0}{1}.{2}'.format(joiner,
+                                                          version_str,
+                                                          dso_suffix)
+                    os.symlink(src_path, dest_path)
+
         with working_dir(os.path.join('luarocks', 'luarocks')):
             configure('--prefix=' + prefix, '--with-lua=' + prefix)
             make('build')
@@ -102,6 +98,7 @@ class Lua(Package):
                 deptypes=('build', 'run'), deptype_query='run'):
             if d.package.extends(self.spec):
                 lua_paths.append(os.path.join(d.prefix, self.lua_lib_dir))
+                lua_paths.append(os.path.join(d.prefix, self.lua_lib64_dir))
                 lua_paths.append(os.path.join(d.prefix, self.lua_share_dir))
 
         lua_patterns = []
@@ -112,6 +109,7 @@ class Lua(Package):
 
         # Always add this package's paths
         for p in (os.path.join(self.spec.prefix, self.lua_lib_dir),
+                  os.path.join(self.spec.prefix, self.lua_lib64_dir),
                   os.path.join(self.spec.prefix, self.lua_share_dir)):
             self.append_paths(lua_patterns, lua_cpatterns, p)
 
@@ -156,6 +154,10 @@ class Lua(Package):
         return os.path.join('lib', 'lua', str(self.version.up_to(2)))
 
     @property
+    def lua_lib64_dir(self):
+        return os.path.join('lib64', 'lua', str(self.version.up_to(2)))
+
+    @property
     def lua_share_dir(self):
         return os.path.join('share', 'lua', str(self.version.up_to(2)))
 
diff --git a/var/spack/repos/builtin/packages/luit/package.py b/var/spack/repos/builtin/packages/luit/package.py
index 47eb6be44c..4969375a19 100644
--- a/var/spack/repos/builtin/packages/luit/package.py
+++ b/var/spack/repos/builtin/packages/luit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,7 +20,7 @@ class Luit(Package):
     depends_on('libfontenc')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/lulesh/package.py b/var/spack/repos/builtin/packages/lulesh/package.py
index 489a175108..614d8cf933 100644
--- a/var/spack/repos/builtin/packages/lulesh/package.py
+++ b/var/spack/repos/builtin/packages/lulesh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,10 @@ class Lulesh(MakefilePackage):
     code to only solve a Sedov blast problem with analytic answer
     """
     tags = ['proxy-app']
-    homepage = "https://codesign.llnl.gov/lulesh.php"
-    url      = "https://codesign.llnl.gov/lulesh/lulesh2.0.3.tgz"
+    homepage = "https://computation.llnl.gov/projects/co-design/lulesh"
+    git      = "https://github.com/LLNL/LULESH.git"
 
-    version('2.0.3', '336644a8750f71c7c6b9d2960976e7aa')
+    version('2.0.3', tag='2.0.3')
 
     variant('mpi', default=True, description='Build with MPI support')
     variant('openmp', default=True, description='Build with OpenMP support')
diff --git a/var/spack/repos/builtin/packages/lumpy-sv/package.py b/var/spack/repos/builtin/packages/lumpy-sv/package.py
new file mode 100644
index 0000000000..709f7d0f4c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lumpy-sv/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class LumpySv(MakefilePackage):
+    """A probabilistic framework for structural variant discovery."""
+
+    homepage = "https://github.com/arq5x/lumpy-sv"
+    url      = "https://github.com/arq5x/lumpy-sv/archive/0.2.13.tar.gz"
+
+    version('0.2.13', '36929d29fc3a171d3abbe1d93f9f3b50')
+
+    depends_on('htslib')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('export CXX .*', '')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/lwgrp/package.py b/var/spack/repos/builtin/packages/lwgrp/package.py
index aa742230ac..76926714d1 100644
--- a/var/spack/repos/builtin/packages/lwgrp/package.py
+++ b/var/spack/repos/builtin/packages/lwgrp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lwm2/package.py b/var/spack/repos/builtin/packages/lwm2/package.py
index 4858391f2a..58c6d73f94 100644
--- a/var/spack/repos/builtin/packages/lwm2/package.py
+++ b/var/spack/repos/builtin/packages/lwm2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Lwm2(AutotoolsPackage):
        measurements from a program.
     """
     homepage = "https://jay.grs.rwth-aachen.de/redmine/projects/lwm2"
+    hg       = "https://jay.grs.rwth-aachen.de/hg/lwm2"
 
-    version('torus', hg='https://jay.grs.rwth-aachen.de/hg/lwm2', revision='torus')
+    version('torus', revision='torus')
 
     depends_on("papi")
     depends_on("mpi")
diff --git a/var/spack/repos/builtin/packages/lz4/package.py b/var/spack/repos/builtin/packages/lz4/package.py
index 2c8d0977ae..fed8c3bfe2 100644
--- a/var/spack/repos/builtin/packages/lz4/package.py
+++ b/var/spack/repos/builtin/packages/lz4/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
 class Lz4(Package):
@@ -34,10 +16,11 @@ class Lz4(Package):
     homepage = "http://lz4.github.io/lz4/"
     url      = "https://github.com/lz4/lz4/archive/v1.7.5.tar.gz"
 
+    version('1.8.1.2', '343538e69ba752a386c669b1a28111e2')
     version('1.7.5', 'c9610c5ce97eb431dddddf0073d919b9')
     version('1.3.1', '42b09fab42331da9d3fb33bd5c560de9')
 
-    # depends_on('valgrind', type='test')
+    depends_on('valgrind', type='test')
 
     def url_for_version(self, version):
         url = "https://github.com/lz4/lz4/archive"
@@ -48,7 +31,15 @@ class Lz4(Package):
             return "{0}/r{1}.tar.gz".format(url, version.joined)
 
     def install(self, spec, prefix):
-        make()
+        if sys.platform != "darwin":
+            make('MOREFLAGS=-lrt')  # fixes make error on CentOS6
+        else:
+            make()
         if self.run_tests:
             make('test')  # requires valgrind to be installed
         make('install', 'PREFIX={0}'.format(prefix))
+
+    @run_after('install')
+    def darwin_fix(self):
+        if sys.platform == 'darwin':
+            fix_darwin_install_name(self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/lzma/package.py b/var/spack/repos/builtin/packages/lzma/package.py
index 3e256d54b0..a5abb82ff7 100644
--- a/var/spack/repos/builtin/packages/lzma/package.py
+++ b/var/spack/repos/builtin/packages/lzma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/lzo/package.py b/var/spack/repos/builtin/packages/lzo/package.py
index ded3a32375..f5b4fe8060 100644
--- a/var/spack/repos/builtin/packages/lzo/package.py
+++ b/var/spack/repos/builtin/packages/lzo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/m4/package.py b/var/spack/repos/builtin/packages/m4/package.py
index f3cb8122f5..926758a766 100644
--- a/var/spack/repos/builtin/packages/m4/package.py
+++ b/var/spack/repos/builtin/packages/m4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,13 +10,18 @@ class M4(AutotoolsPackage):
     """GNU M4 is an implementation of the traditional Unix macro processor."""
 
     homepage = "https://www.gnu.org/software/m4/m4.html"
-    url      = "https://ftp.gnu.org/gnu/m4/m4-1.4.18.tar.gz"
+    url      = "https://ftpmirror.gnu.org/m4/m4-1.4.18.tar.gz"
 
     version('1.4.18', 'a077779db287adf4e12a035029002d28')
     version('1.4.17', 'a5e9954b1dae036762f7b13673a2cf76')
 
     patch('gnulib-pgi.patch', when='@1.4.18')
     patch('pgi.patch', when='@1.4.17')
+    # from: https://github.com/Homebrew/homebrew-core/blob/master/Formula/m4.rb
+    # Patch credit to Jeremy Huddleston Sequoia <jeremyhu@apple.com>
+    patch('secure_snprintf.patch', when='platform_os = highsierra')
+    # https://bugzilla.redhat.com/show_bug.cgi?id=1573342
+    patch('https://src.fedoraproject.org/rpms/m4/raw/5d147168d4b93f38a4833f5dd1d650ad88af5a8a/f/m4-1.4.18-glibc-change-work-around.patch', sha256='fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8', when='@1.4.18')
 
     variant('sigsegv', default=True,
             description="Build the libsigsegv dependency")
diff --git a/var/spack/repos/builtin/packages/m4/secure_snprintf.patch b/var/spack/repos/builtin/packages/m4/secure_snprintf.patch
new file mode 100644
index 0000000000..da3ae5ba0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/m4/secure_snprintf.patch
@@ -0,0 +1,15 @@
+With format string strictness, High Sierra also enforces that %n isn't used
+in dynamic format strings, but we should just disable its use on darwin in
+general.
+
+--- a/lib/vasnprintf.c.orig	2017-06-22 15:19:15.000000000 -0700
++++ b/lib/vasnprintf.c	2017-06-22 15:20:20.000000000 -0700
+@@ -4869,7 +4869,7 @@ VASNPRINTF (DCHAR_T *resultbuf, size_t *
+ #endif
+                   *fbp = dp->conversion;
+ #if USE_SNPRINTF
+-# if !(((__GLIBC__ > 2 || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 3)) && !defined __UCLIBC__) || ((defined _WIN32 || defined __WIN32__) && ! defined __CYGWIN__))
++# if !defined(__APPLE__) && !(((__GLIBC__ > 2 || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 3)) && !defined __UCLIBC__) || ((defined _WIN32 || defined __WIN32__) && ! defined __CYGWIN__))
+                 fbp[1] = '%';
+                 fbp[2] = 'n';
+                 fbp[3] = '\0';
diff --git a/var/spack/repos/builtin/packages/macsio/package.py b/var/spack/repos/builtin/packages/macsio/package.py
index f17cec4350..09d4f50c50 100644
--- a/var/spack/repos/builtin/packages/macsio/package.py
+++ b/var/spack/repos/builtin/packages/macsio/package.py
@@ -1,41 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Macsio(CMakePackage):
-    """A Multi-purpose, Application-Centric, Scalable I/O Proxy Application
-    """
+    """A Multi-purpose, Application-Centric, Scalable I/O Proxy Application."""
+
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    homepage = "http://llnl.github.io/MACSio"
-    url = "https://github.com/LLNL/MACSio/archive/1.0.tar.gz"
+    homepage = "https://computation.llnl.gov/projects/co-design/macsio"
+    url      = "https://github.com/LLNL/MACSio/archive/v1.1.tar.gz"
+    git      = "https://github.com/LLNL/MACSio.git"
 
+    version('develop', branch='master')
+
+    version('1.1', sha256='a86249b0f10647c0b631773db69568388094605ec1a0af149d9e61e95e6961ec')
     version('1.0', '90e8e00ea84af2a47bee387ad331dbde')
-    version('develop', git='https://github.com/LLNL/MACSio.git',
-            branch='master')
 
     variant('mpi', default=True, description="Build MPI plugin")
     variant('silo', default=True, description="Build with SILO plugin")
@@ -52,7 +35,7 @@ class Macsio(CMakePackage):
     depends_on('json-cwx')
     depends_on('mpi', when="+mpi")
     depends_on('silo', when="+silo")
-    depends_on('hdf5', when="+hdf5")
+    depends_on('hdf5+hl', when="+hdf5")
     # depends_on('hdf5+szip', when="+szip")
     depends_on('exodusii', when="+exodus")
     # pdb is packaged with silo
@@ -114,3 +97,7 @@ class Macsio(CMakePackage):
                               .format(spec['netcdf'].prefix))
 
         return cmake_args
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('spack-build/macsio/macsio', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/mad-numdiff/package.py b/var/spack/repos/builtin/packages/mad-numdiff/package.py
index 8d687e2258..660fe03203 100644
--- a/var/spack/repos/builtin/packages/mad-numdiff/package.py
+++ b/var/spack/repos/builtin/packages/mad-numdiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,6 +12,7 @@ class MadNumdiff(CMakePackage):
 
     homepage = "https://github.com/quinoacomputing/ndiff"
     url      = "https://github.com/quinoacomputing/ndiff/tarball/20150724"
+    git      = "https://github.com/quinoacomputing/ndiff.git"
 
-    version('develop', git='https://github.com/quinoacomputing/ndiff', branch='master')
+    version('develop', branch='master')
     version('20150724', '7723c0f2499aea8fd960377c5bed28d8')
diff --git a/var/spack/repos/builtin/packages/mafft/package.py b/var/spack/repos/builtin/packages/mafft/package.py
index 2b46cf9332..f2b75416bf 100644
--- a/var/spack/repos/builtin/packages/mafft/package.py
+++ b/var/spack/repos/builtin/packages/mafft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py
index 540abd6c1d..bd35327480 100644
--- a/var/spack/repos/builtin/packages/magics/package.py
+++ b/var/spack/repos/builtin/packages/magics/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -33,48 +14,86 @@ class Magics(CMakePackage):
 
     homepage = "https://software.ecmwf.int/wiki/display/MAGP/Magics"
     url      = "https://software.ecmwf.int/wiki/download/attachments/3473464/Magics-2.29.0-Source.tar.gz"
+    list_url = "https://software.ecmwf.int/wiki/display/MAGP/Releases"
 
-    # Maintainers of Magics do not keep tarballs of minor releases. Once the
-    # next minor released is published the previous one becomes unavailable.
-    # That is why the preferred version is the latest stable one.
+    # The policy on which minor releases remain available and which get deleted
+    # after a newer version becomes available is unclear.
+    version('2.34.3', 'b4180bc4114ffd723b80728947f50c17')
+    version('2.34.1', '1ecc5cc20cb0c3f2f0b9171626f09d53')
+    version('2.33.0', '8d513fd2244f2974b3517a8b30dd51f6')
     version('2.32.0', 'e17956fffce9ea826cf994f8d275e0f5')
+    version('2.31.0', '3564dca9e1b4af096fd631906f5e6c89')
+    version('2.29.6', '56d2c31ca75162e5e86ef75d355e87f1')
     version('2.29.4', '91c561f413316fb665b3bb563f3878d1')
-    version('2.29.0', 'db20a4d3c51a2da5657c31ae3de59709', preferred=True)
+    version('2.29.0', 'db20a4d3c51a2da5657c31ae3de59709')
 
     # The patch reorders includes and adds namespaces where necessary to
     # resolve ambiguity of invocations of isnan and isinf functions. The
     # patch is not needed since the version 2.29.1
     patch('resolve_isnan_ambiguity.patch', when='@2.29.0')
 
-    variant('bufr', default=False, description='Enable BUFR support')
+    variant('grib', default='eccodes', values=('eccodes', 'grib-api'),
+            description='Specify GRIB backend')
     variant('netcdf', default=False, description='Enable NetCDF support')
-    variant('cairo', default=True, description='Enable cairo support[png/jpeg]')
+    variant('cairo', default=False,
+            description='Enable cairo support[png/jpeg]')
+    variant('python', default=False, description='Enable Python interface')
+    variant('fortran', default=False, description='Enable Fortran interface')
     variant('metview', default=False, description='Enable metview support')
     variant('qt', default=False, description='Enable metview support with qt')
-    variant('eccodes', default=False, description='Use eccodes instead of grib-api')
+    variant('bufr', default=False, description='Enable BUFR support')
+
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo', 'Production'))
 
+    # Build dependencies
     depends_on('cmake@2.8.11:', type='build')
-    depends_on('pkg-config', type='build')
-
-    # Currently python is only necessary to run
-    # building preprocessing scripts.
-    depends_on('python', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('python@:2', type='build')
     depends_on('perl', type='build')
     depends_on('perl-xml-parser', type='build')
-    depends_on('eccodes', when='+eccodes')
-    depends_on('grib-api', when='~eccodes')
+
+    # Non-optional dependencies
     depends_on('proj')
     depends_on('boost')
     depends_on('expat')
-    depends_on('pango', when='+cairo')
+
+    # Magics (at least up to version 2.34.3) should directly and
+    # unconditionally depend on zlib, which is not reflected neither in the
+    # installation instructions nor explicitly stated in the cmake script:
+    # zlib is pulled as a dependency of png. The dependency on png is formally
+    # optional and depends on an unofficial flag ENABLE_PNG, which is
+    # redundant, because png is used only when ENABLE_CAIRO=ON. The problem is
+    # that files that make calls to png library get compiled and linked
+    # unconditionally, which makes png a non-optional dependency (and
+    # ENABLE_PNG always has to be set to ON).
+    depends_on('zlib')
+    depends_on('libpng')
+
+    # GRIB support is non-optional, regardless of what the instruction says.
+    depends_on('eccodes', when='grib=eccodes')
+    depends_on('grib-api', when='grib=grib-api')
+
+    # Optional dependencies
     depends_on('netcdf-cxx', when='+netcdf')
-    depends_on('libemos', when='+bufr')
+    depends_on('pango', when='+cairo')
+    depends_on('libemos grib=eccodes', when='+bufr grib=eccodes')
+    depends_on('libemos grib=grib-api', when='+bufr grib=grib-api')
     depends_on('qt', when='+metview+qt')
 
-    conflicts('+eccodes', when='@:2.29.0')
+    extends('python', when='+python')
+    # Python 2 is required for running the building scripts. Since we can't
+    # have two different versions of Python at the same time, we haven't even
+    # tested if the Python interface supports Python 3.
+    depends_on('python', when='+python', type=('link', 'run'))
+    depends_on('py-numpy', when='+python', type=('build', 'run'))
+    depends_on('swig', when='+python', type='build')
+
+    conflicts('grib=eccodes', when='@:2.29.0',
+              msg='Eccodes is supported starting version 2.29.1')
+    conflicts('+python', when='@:2.28',
+              msg='Python interface is supported starting version 2.29.0')
 
     # Replace system python and perl by spack versions:
     def patch(self):
@@ -84,50 +103,51 @@ class Magics(CMakePackage):
             filter_file('#!/usr/bin/python', '#!/usr/bin/env python', pyfile)
 
     def cmake_args(self):
-        spec = self.spec
         args = [
             '-DENABLE_ODB=OFF',
-            '-DENABLE_PYTHON=OFF',
-            '-DBOOST_ROOT=%s' % spec['boost'].prefix,
-            '-DPROJ4_PATH=%s' % spec['proj'].prefix,
-            '-DENABLE_TESTS=OFF',
+            '-DENABLE_SPOT=OFF'
         ]
 
-        if '+bufr' in spec:
-            args.append('-DENABLE_BUFR=ON')
-            args.append('-DLIBEMOS_PATH=%s' % spec['libemos'].prefix)
+        if self.spec.variants['grib'].value == 'eccodes':
+            args.append('-DENABLE_ECCODES=ON')
         else:
-            args.append('-DENABLE_BUFR=OFF')
+            if self.spec.satisfies('@2.29.1:'):
+                args.append('-DENABLE_ECCODES=OFF')
 
-        if '+netcdf' in spec:
+        if '+netcdf' in self.spec:
             args.append('-DENABLE_NETCDF=ON')
-            args.append('-DNETCDF_PATH=%s' % spec['netcdf-cxx'].prefix)
         else:
             args.append('-DENABLE_NETCDF=OFF')
 
-        if '+cairo' in spec:
+        if '+cairo' in self.spec:
             args.append('-DENABLE_CAIRO=ON')
         else:
             args.append('-DENABLE_CAIRO=OFF')
 
-        if '+metview' in spec:
-            if '+qt' in spec:
+        if '+python' in self.spec:
+            args.append('-DENABLE_PYTHON=ON')
+        else:
+            if self.spec.satisfies('@2.29.0:'):
+                args.append('-DENABLE_PYTHON=OFF')
+
+        if '+fortran' in self.spec:
+            args.append('-DENABLE_FORTRAN=ON')
+        else:
+            args.append('-DENABLE_FORTRAN=OFF')
+
+        if '+bufr' in self.spec:
+            args.append('-DENABLE_BUFR=ON')
+        else:
+            args.append('-DENABLE_BUFR=OFF')
+
+        if '+metview' in self.spec:
+            if '+qt' in self.spec:
                 args.append('-DENABLE_METVIEW=ON')
-                if spec['qt'].version[0] == 5:
+                if self.spec['qt'].satisfies('@5:'):
                     args.append('-DENABLE_QT5=ON')
             else:
                 args.append('-DENABLE_METVIEW_NO_QT=ON')
         else:
             args.append('-DENABLE_METVIEW=OFF')
 
-        if '+eccodes' in spec:
-            args.append('-DENABLE_ECCODES=ON')
-            args.append('-DECCODES_PATH=%s' % spec['eccodes'].prefix)
-        else:
-            args.append('-DENABLE_ECCODES=OFF')
-            args.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix)
-
-        if (self.compiler.f77 is None) or (self.compiler.fc is None):
-            args.append('-DENABLE_FORTRAN=OFF')
-
         return args
diff --git a/var/spack/repos/builtin/packages/magma/magma-2.3.0-gcc-4.8.patch b/var/spack/repos/builtin/packages/magma/magma-2.3.0-gcc-4.8.patch
new file mode 100644
index 0000000000..f734a5f16a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/magma/magma-2.3.0-gcc-4.8.patch
@@ -0,0 +1,24 @@
+diff -ru magma-2.3.0/testing/testings.h magma-2.3.0-patched/testing/testings.h
+--- magma-2.3.0/testing/testings.h	2017-11-14 21:34:00.000000000 -0800
++++ magma-2.3.0-patched/testing/testings.h	2018-03-23 20:41:16.459934643 -0700
+@@ -269,4 +269,20 @@
+     typename blas::traits<FloatT>::real_t* sigma,
+     FloatT* A, magma_int_t lda );
+ 
++// This overload for the case sigma = nullptr is a workaround for an issue
++// when building with gcc 4.8.5. This is not an issue with gcc 4.9.2.
++template< typename FloatT >
++void magma_generate_matrix(
++    magma_opts& opts,
++    magma_int_t m, magma_int_t n,
++    std::nullptr_t sigma,
++    FloatT* A, magma_int_t lda )
++{
++    magma_generate_matrix<FloatT>(
++        opts,
++        m, n,
++        (typename blas::traits<FloatT>::real_t*) sigma,
++        A, lda );
++}
++
+ #endif /* TESTINGS_H */
diff --git a/var/spack/repos/builtin/packages/magma/package.py b/var/spack/repos/builtin/packages/magma/package.py
index bccac28497..7a28a3bd85 100644
--- a/var/spack/repos/builtin/packages/magma/package.py
+++ b/var/spack/repos/builtin/packages/magma/package.py
@@ -1,49 +1,40 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Serban Maerean, serban@us.ibm.com, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
 from spack import *
 
 
 class Magma(CMakePackage):
-    """The MAGMA project aims to develop a dense linear algebra library
-    similar to LAPACK but for heterogeneous/hybrid architectures,
-    starting with current "Multicore+GPU" systems.
+    """The MAGMA project aims to develop a dense linear algebra library similar to
+       LAPACK but for heterogeneous/hybrid architectures, starting with current
+       "Multicore+GPU" systems.
     """
 
     homepage = "http://icl.cs.utk.edu/magma/"
     url = "http://icl.cs.utk.edu/projectsfiles/magma/downloads/magma-2.2.0.tar.gz"
 
-    version('2.2.0', '6c1ebf4cdf63eb302ff6258ff8c49217')
+    version('2.4.0', sha256='4eb839b1295405fd29c8a6f5b4ed578476010bf976af46573f80d1169f1f9a4f')
+    version('2.3.0', sha256='010a4a057d7aa1e57b9426bffc0958f3d06913c9151463737e289e67dd9ea608')
+    version('2.2.0', sha256='df5d4ace417e5bf52694eae0d91490c6bde4cde1b0da98e8d400c5c3a70d83a2')
 
     variant('fortran', default=True,
             description='Enable Fortran bindings support')
+    variant('shared', default=True,
+            description='Enable shared library')
 
+    depends_on('blas')
     depends_on('lapack')
-    depends_on('cuda@9.0:', when='%gcc@6.0:6.9.9')
-    depends_on('cuda@8.0:', when='%gcc@5.0:')
+    depends_on('cuda')
+
+    conflicts('%gcc@6:', when='^cuda@:8')
+    conflicts('%gcc@7:', when='^cuda@:9')
+
     patch('ibm-xl.patch', when='@2.2:%xl')
     patch('ibm-xl.patch', when='@2.2:%xl_r')
+    patch('magma-2.3.0-gcc-4.8.patch', when='@2.3.0%gcc@:4.8')
 
     def cmake_args(self):
         spec = self.spec
@@ -52,10 +43,17 @@ class Magma(CMakePackage):
         options.extend([
             '-DCMAKE_INSTALL_PREFIX=%s' % prefix,
             '-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix,
-            '-DLAPACK_LIBRARIES=%s;%s' % (spec['blas'].libs,
-                                          spec['lapack'].libs)
+            '-DBLAS_LIBRARIES=%s' % spec['blas'].libs.joined(';'),
+            # As of MAGMA v2.3.0, CMakeLists.txt does not use the variable
+            # BLAS_LIBRARIES, but only LAPACK_LIBRARIES, so we need to
+            # explicitly add blas to LAPACK_LIBRARIES.
+            '-DLAPACK_LIBRARIES=%s' %
+            (spec['lapack'].libs + spec['blas'].libs).joined(';')
         ])
 
+        options += ['-DBUILD_SHARED_LIBS=%s' %
+                    ('ON' if ('+shared' in spec) else 'OFF')]
+
         if '+fortran' in spec:
             options.extend([
                 '-DUSE_FORTRAN=yes'
@@ -66,8 +64,16 @@ class Magma(CMakePackage):
                 ])
 
         if spec.satisfies('^cuda@9.0:'):
-            options.extend([
-                '-DGPU_TARGET=sm30'
-            ])
+            if '@:2.2.0' in spec:
+                options.extend(['-DGPU_TARGET=sm30'])
+            else:
+                options.extend(['-DGPU_TARGET=sm_30'])
 
         return options
+
+    @run_after('install')
+    def post_install(self):
+        install('magmablas/atomics.cuh', self.prefix.include)
+        install('control/magma_threadsetting.h', self.prefix.include)
+        install('control/pthread_barrier.h', self.prefix.include)
+        install('control/magma_internal.h', self.prefix.include)
diff --git a/var/spack/repos/builtin/packages/makedepend/package.py b/var/spack/repos/builtin/packages/makedepend/package.py
index 41edb6ed69..9dd5ea50f5 100644
--- a/var/spack/repos/builtin/packages/makedepend/package.py
+++ b/var/spack/repos/builtin/packages/makedepend/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,4 +15,4 @@ class Makedepend(AutotoolsPackage):
     version('1.0.5', 'efb2d7c7e22840947863efaedc175747')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/mallocmc/package.py b/var/spack/repos/builtin/packages/mallocmc/package.py
index ed8ba9bdeb..d5d4faa21c 100644
--- a/var/spack/repos/builtin/packages/mallocmc/package.py
+++ b/var/spack/repos/builtin/packages/mallocmc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,11 +20,12 @@ class Mallocmc(CMakePackage):
 
     homepage = "https://github.com/ComputationalRadiationPhysics/mallocMC"
     url      = "https://github.com/ComputationalRadiationPhysics/mallocMC/archive/2.2.0crp.tar.gz"
+    git      = "https://github.com/ComputationalRadiationPhysics/mallocMC.git"
+
+    maintainers = ['ax3l']
 
-    version('develop', branch='dev',
-            git='https://github.com/ComputationalRadiationPhysics/mallocMC.git')
-    version('master', branch='master',
-            git='https://github.com/ComputationalRadiationPhysics/mallocMC.git')
+    version('develop', branch='dev')
+    version('master', branch='master')
     version('2.2.0crp', '3e5c5fc963d1a9abc829ff701504e54c')
     version('2.1.0crp', 'd2bd2644012b64a246048575e9a9051c')
     version('2.0.1crp', '1f674d5d1ae05446d9a4e4b65465dca0')
diff --git a/var/spack/repos/builtin/packages/man-db/package.py b/var/spack/repos/builtin/packages/man-db/package.py
index 7a6a03731e..634815260d 100644
--- a/var/spack/repos/builtin/packages/man-db/package.py
+++ b/var/spack/repos/builtin/packages/man-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/manta/package.py b/var/spack/repos/builtin/packages/manta/package.py
new file mode 100644
index 0000000000..74f717920a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/manta/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Manta(CMakePackage):
+    """Structural variant and indel caller for mapped sequencing data"""
+
+    homepage = "https://github.com/Illumina/manta"
+    url      = "https://github.com/Illumina/manta/releases/download/v1.3.2/manta-1.3.2.release_src.tar.bz2"
+
+    depends_on('boost@1.58.0:', type='build')
+    depends_on('cmake@2.8.12:', type='build')
+    depends_on('python@2.7.0:2.7.999', type=('build', 'run'))
+
+    version('1.4.0', '582d10f3bc56aecfa5c24931af3742b4')
+    version('1.3.2', '83f43fe1a12605c1e9803d1020b24bd1')
+    version('1.3.1', 'e315caff775878872ee300ed34e8adae')
+    version('1.3.0', '1243e2bb58ca7c9d69bbfbe528f492ec')
diff --git a/var/spack/repos/builtin/packages/maq/package.py b/var/spack/repos/builtin/packages/maq/package.py
new file mode 100644
index 0000000000..222b56827d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/maq/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Maq(AutotoolsPackage):
+    """Maq is a software that builds mapping assemblies from short reads
+       generated by the next-generation sequencing machines."""
+
+    homepage = "http://maq.sourceforge.net/"
+    url      = "https://downloads.sourceforge.net/project/maq/maq/0.7.1/maq-0.7.1.tar.bz2"
+    list_url = "https://sourceforge.net/projects/maq/files/maq/"
+
+    version('0.7.1', '51130f6c8257c133719adacdd1433f35')
+    version('0.5.0', '854e2bee32d5237236d4c68c0ed7c52d')
+
+    conflicts('%gcc@4.7.0:', when='@0.7.1')
diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py
index 53203f585a..c2ec90f299 100644
--- a/var/spack/repos/builtin/packages/mariadb/package.py
+++ b/var/spack/repos/builtin/packages/mariadb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/masa/package.py b/var/spack/repos/builtin/packages/masa/package.py
index e0e7c00cde..a269d0362c 100644
--- a/var/spack/repos/builtin/packages/masa/package.py
+++ b/var/spack/repos/builtin/packages/masa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,12 +12,11 @@ class Masa(AutotoolsPackage):
        provides a suite of manufactured solutions for the software
        verification of partial differential equation solvers in multiple
        dimensions."""
+
     homepage = "https://github.com/manufactured-solutions/MASA"
-    url      = "https://github.com/manufactured-solutions/MASA.git"
+    git      = "https://github.com/manufactured-solutions/MASA.git"
 
-    version('master',
-            git='https://github.com/manufactured-solutions/MASA.git',
-            tag='master')
+    version('master', tag='master')
 
     variant('fortran', default=True,
             description='Compile with Fortran interfaces')
diff --git a/var/spack/repos/builtin/packages/masurca/package.py b/var/spack/repos/builtin/packages/masurca/package.py
new file mode 100644
index 0000000000..4aeb00e0dd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/masurca/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Masurca(Package):
+    """MaSuRCA is whole genome assembly software. It combines the efficiency
+       of the de Bruijn graph and Overlap-Layout-Consensus (OLC)
+       approaches."""
+
+    homepage = "http://www.genome.umd.edu/masurca.html"
+    url      = "ftp://ftp.genome.umd.edu/pub/MaSuRCA/latest/MaSuRCA-3.2.3.tar.gz"
+
+    version('3.2.6', 'f068f91e33fd7381de406a7a954bfe01')
+    version('3.2.3', 'd9b4419adfe6b64e42ce986253a50ff5')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('boost')
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        installer = Executable('./install.sh')
+        installer()
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/matio/package.py b/var/spack/repos/builtin/packages/matio/package.py
index 8569893375..89be615244 100644
--- a/var/spack/repos/builtin/packages/matio/package.py
+++ b/var/spack/repos/builtin/packages/matio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/matlab/package.py b/var/spack/repos/builtin/packages/matlab/package.py
index c61bbe05d6..d9f3a9476c 100644
--- a/var/spack/repos/builtin/packages/matlab/package.py
+++ b/var/spack/repos/builtin/packages/matlab/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import subprocess
@@ -41,8 +22,8 @@ class Matlab(Package):
     mirror so that Spack can find it. For instructions on how to set up a
     mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
 
-    homepage = "https://www.mathworks.com/products/matlab.html"
-
+    homepage = "https://www.mathworks.com/products/matlab.html" 
+    version('R2018b', sha256='8cfcddd3878d3a69371c4e838773bcabf12aaf0362cc2e1ae7e8820845635cac')
     version('R2016b', 'b0e0b688894282139fa787b5a86a5cf7')
 
     variant(
@@ -80,15 +61,15 @@ class Matlab(Package):
         }
 
         # Store values requested by the installer in a file
-        with open('spack_installer_input.txt', 'w') as inputFile:
+        with open('spack_installer_input.txt', 'w') as input_file:
             for key in config:
-                inputFile.write('{0}={1}\n'.format(key, config[key]))
+                input_file.write('{0}={1}\n'.format(key, config[key]))
 
     def install(self, spec, prefix):
         self.configure(spec, prefix)
 
         # Run silent installation script
         # Full path required
-        inputFile = join_path(self.stage.source_path,
-                              'spack_installer_input.txt')
-        subprocess.call(['./install', '-inputFile', inputFile])
+        input_file = join_path(
+            self.stage.source_path, 'spack_installer_input.txt')
+        subprocess.call(['./install', '-inputFile', input_file])
diff --git a/var/spack/repos/builtin/packages/maven/package.py b/var/spack/repos/builtin/packages/maven/package.py
index 425e5abaab..58cfe004d7 100644
--- a/var/spack/repos/builtin/packages/maven/package.py
+++ b/var/spack/repos/builtin/packages/maven/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Maven(Package):
@@ -39,4 +19,4 @@ class Maven(Package):
 
     def install(self, spec, prefix):
         # install pre-built distribution
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/maverick/package.py b/var/spack/repos/builtin/packages/maverick/package.py
index b898beafb7..047540cce1 100644
--- a/var/spack/repos/builtin/packages/maverick/package.py
+++ b/var/spack/repos/builtin/packages/maverick/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mawk/package.py b/var/spack/repos/builtin/packages/mawk/package.py
index 2749736796..864e76b8f3 100644
--- a/var/spack/repos/builtin/packages/mawk/package.py
+++ b/var/spack/repos/builtin/packages/mawk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mbedtls/package.py b/var/spack/repos/builtin/packages/mbedtls/package.py
index 12687ea5a8..f6ea6c5dbe 100644
--- a/var/spack/repos/builtin/packages/mbedtls/package.py
+++ b/var/spack/repos/builtin/packages/mbedtls/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mc/package.py b/var/spack/repos/builtin/packages/mc/package.py
new file mode 100644
index 0000000000..38037f1707
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mc/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mc(AutotoolsPackage):
+    """The GNU Midnight Commander is a visual file manager."""
+
+    homepage = "https://midnight-commander.org"
+    url      = "http://ftp.midnight-commander.org/mc-4.8.20.tar.bz2"
+
+    version('4.8.20', 'dcfc7aa613c62291a0f71f6b698d8267')
+
+    depends_on('ncurses')
+    depends_on('pkgconfig', type='build')
+    depends_on('glib@2.14:')
+    depends_on('libssh2@1.2.5:')
+
+    def setup_environment(self, spack_env, run_env):
+        # Fix compilation bug on macOS by pretending we don't have utimensat()
+        # https://github.com/MidnightCommander/mc/pull/130
+        if 'darwin' in self.spec.architecture:
+            env['ac_cv_func_utimensat'] = 'no'
+
+    def configure_args(self):
+        args = [
+            '--disable-debug',
+            '--disable-dependency-tracking',
+            '--disable-silent-rules',
+            '--without-x',
+            '--with-screen=ncurses',
+            '--enable-vfs-sftp'
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/mcl/package.py b/var/spack/repos/builtin/packages/mcl/package.py
index 4644cc39ac..91352caac2 100644
--- a/var/spack/repos/builtin/packages/mcl/package.py
+++ b/var/spack/repos/builtin/packages/mcl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mdtest/package.py b/var/spack/repos/builtin/packages/mdtest/package.py
index 519aed704c..56bede2f87 100644
--- a/var/spack/repos/builtin/packages/mdtest/package.py
+++ b/var/spack/repos/builtin/packages/mdtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Mdtest(Package):
        and directories and then reports the performance."""
 
     homepage = "https://github.com/LLNL/mdtest"
+    git      = "https://github.com/LLNL/mdtest.git"
 
-    version('1.9.3', git='https://github.com/LLNL/mdtest.git', commit='49f3f0')
+    version('1.9.3', commit='49f3f0')
 
     depends_on('mpi')
 
diff --git a/var/spack/repos/builtin/packages/med/package.py b/var/spack/repos/builtin/packages/med/package.py
new file mode 100644
index 0000000000..95d3794ced
--- /dev/null
+++ b/var/spack/repos/builtin/packages/med/package.py
@@ -0,0 +1,52 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Med(CMakePackage):
+    """The MED file format is a specialization of the HDF5 standard."""
+
+    homepage = "http://docs.salome-platform.org/latest/dev/MEDCoupling/med-file.html"
+    url = "http://files.salome-platform.org/Salome/other/med-3.2.0.tar.gz"
+
+    maintainers = ['likask']
+
+    version('3.2.0', 'eb61df92f0624feb6328f517cd756a23')
+
+    variant('api23', default=True, description='Enable API2.3')
+
+    depends_on('mpi')
+    depends_on('hdf5@:1.8.19+mpi')
+
+    # FIXME This is minimal installation.
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        if '+api23' in spec:
+            options.extend([
+                '-DCMAKE_CXX_FLAGS:STRING=-DMED_API_23=1',
+                '-DCMAKE_C_FLAGS:STRING=-DMED_API_23=1',
+                '-DMED_API_23=1'])
+
+        options.extend([
+            '-DMEDFILE_USE_MPI=YES'
+            '-DMEDFILE_BUILD_TESTS={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+            '-DMEDFILE_BUILD_PYTHON=OFF',
+            '-DMEDFILE_INSTALL_DOC=OFF',
+            '-DMEDFILE_BUILD_SHARED_LIBS=OFF',
+            '-DMEDFILE_BUILD_STATIC_LIBS=ON',
+            '-DCMAKE_Fortran_COMPILER='])
+
+        options.extend([
+            '-DHDF5_ROOT_DIR=%s' % spec['hdf5'].prefix,
+            '-DMPI_ROOT_DIR=%s' % spec['mpi'].prefix])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/meep/package.py b/var/spack/repos/builtin/packages/meep/package.py
index 79c50a8123..3a125c8bb9 100644
--- a/var/spack/repos/builtin/packages/meep/package.py
+++ b/var/spack/repos/builtin/packages/meep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mefit/package.py b/var/spack/repos/builtin/packages/mefit/package.py
new file mode 100644
index 0000000000..ce21fc9261
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mefit/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mefit(Package):
+    """This pipeline will merge overlapping paired-end reads, calculate
+    merge statistics, and filter reads for quality."""
+
+    homepage = "https://github.com/nisheth/MeFiT"
+    git      = "https://github.com/nisheth/MeFiT.git"
+
+    version('1.0', commit='0733326d8917570bbf70ff5c0f710bf66c13db09')
+
+    depends_on('py-numpy')
+    depends_on('py-htseq')
+    depends_on('jellyfish')
+    depends_on('casper %gcc@4.8.5')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/megahit/package.py b/var/spack/repos/builtin/packages/megahit/package.py
new file mode 100644
index 0000000000..d753c611ab
--- /dev/null
+++ b/var/spack/repos/builtin/packages/megahit/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Megahit(MakefilePackage):
+    """MEGAHIT: An ultra-fast single-node solution for
+    large and complex metagenomics assembly via succinct de Bruijn graph"""
+
+    homepage = "https://github.com/voutcn/megahit"
+    url      = "https://github.com/voutcn/megahit/archive/v1.1.3.tar.gz"
+
+    version('1.1.3', '2962a781a22c0884fa97b95f740ed2fe')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('megahit', prefix.bin)
+        install('megahit_asm_core', prefix.bin)
+        install('megahit_sdbg_build', prefix.bin)
+        install('megahit_toolkit', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/memaxes/package.py b/var/spack/repos/builtin/packages/memaxes/package.py
index 581454ef06..3b5e7f8733 100644
--- a/var/spack/repos/builtin/packages/memaxes/package.py
+++ b/var/spack/repos/builtin/packages/memaxes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/meme/package.py b/var/spack/repos/builtin/packages/meme/package.py
index 224410e85e..b7b66f3b04 100644
--- a/var/spack/repos/builtin/packages/meme/package.py
+++ b/var/spack/repos/builtin/packages/meme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,22 +14,24 @@ class Meme(AutotoolsPackage):
     homepage = "http://meme-suite.org"
     url      = "http://meme-suite.org/meme-software/4.11.4/meme_4.11.4.tar.gz"
 
+    version('4.12.0', '40d282cc33f7dedb06b24b9f34ac15c1')
     version('4.11.4', '371f513f82fa0888205748e333003897')
 
     variant('mpi', default=True, description='Enable MPI support')
+    variant('image-magick', default=False, description='Enable image-magick for png output')
 
     depends_on('zlib', type=('link'))
-    depends_on('libxml2', type=('link'))
-    depends_on('libxslt', type=('link'))
     depends_on('libgcrypt', type=('link'))
     depends_on('perl', type=('build', 'run'))
     depends_on('python@2.7:', type=('build', 'run'))
     depends_on('mpi', when='+mpi')
+    depends_on('image-magick', type=('build', 'run'), when='+image-magick')
+    depends_on('perl-xml-parser', type=('build', 'run'))
 
-    # disable mpi support
     def configure_args(self):
         spec = self.spec
-        args = []
+        # have meme build its own versions of libxml2/libxslt, see #6736
+        args = ['--enable-build-libxml2', '--enable-build-libxslt']
         if '~mpi' in spec:
             args += ['--enable-serial']
         return args
diff --git a/var/spack/repos/builtin/packages/memkind/package.py b/var/spack/repos/builtin/packages/memkind/package.py
new file mode 100644
index 0000000000..097a642f13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/memkind/package.py
@@ -0,0 +1,49 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Memkind(AutotoolsPackage):
+    """The memkind library is a user extensible heap manager built on top of
+    jemalloc which enables control of memory characteristics and a partitioning
+    of the heap between kinds of memory. The kinds of memory are defined by
+    operating system memory policies that have been applied to virtual address
+    ranges. Memory characteristics supported by memkind without user extension
+    include control of NUMA and page size features. The jemalloc non-standard
+    interface has been extended to enable specialized arenas to make requests
+    for virtual memory from the operating system through the memkind partition
+    interface. Through the other memkind interfaces the user can control and
+    extend memory partition features and allocate memory while selecting
+    enabled features."""
+
+    homepage = "https://github.com/memkind/memkind"
+    url      = "https://github.com/memkind/memkind/archive/v1.7.0.tar.gz"
+
+    version('1.7.0', 'bfbbb9226d40fd12ae1822a8be4c9207')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+    depends_on('numactl')
+
+    phases = ['build_jemalloc', 'autoreconf', 'configure', 'build',
+              'install']
+
+    def patch(self):
+        with open('VERSION', 'w') as version_file:
+            version_file.write('{0}\n'.format(self.version))
+
+    def build_jemalloc(self, spec, prefix):
+        if os.path.exists('build_jemalloc.sh'):
+            bash = which('bash')
+            bash('./build_jemalloc.sh')
+
+    def autoreconf(self, spec, prefix):
+        if os.path.exists('autogen.sh'):
+            bash = which('bash')
+            bash('./autogen.sh')
diff --git a/var/spack/repos/builtin/packages/meraculous/package.py b/var/spack/repos/builtin/packages/meraculous/package.py
new file mode 100644
index 0000000000..cb9c96eff7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/meraculous/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Meraculous(CMakePackage):
+    """Meraculous is a while genome assembler for Next Generation Sequencing
+       data geared for large genomes."""
+
+    homepage = "http://jgi.doe.gov/data-and-tools/meraculous/"
+    url      = "https://downloads.sourceforge.net/project/meraculous20/Meraculous-v2.2.4.tar.gz"
+    git      = "https://bitbucket.org/berkeleylab/genomics-meraculous2.git"
+
+    version('2.2.5.1', branch='release-2.2.5.1')
+    version('2.2.4', '349feb6cb178643a46e4b092c87bad3a')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('boost@1.5.0:')
+    depends_on('gnuplot@3.7:')
+    depends_on('perl-log-log4perl', type=('build', 'run'))
+
+    conflicts('%gcc@6.0.0:', when='@2.2.4')
+
+    def patch(self):
+        edit = FileFilter('CMakeLists.txt')
+        edit.filter("-static-libstdc\+\+", "")
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('MERACULOUS_ROOT', self.prefix)
+        run_env.prepend_path('PERL5LIB', self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/mercurial/package.py b/var/spack/repos/builtin/packages/mercurial/package.py
index 4ecd3332a9..aaabdd6c01 100644
--- a/var/spack/repos/builtin/packages/mercurial/package.py
+++ b/var/spack/repos/builtin/packages/mercurial/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from llnl.util import tty
 
@@ -39,6 +20,7 @@ class Mercurial(PythonPackage):
         'mercurial.httpclient', 'mercurial.pure'
     ]
 
+    version('4.4.1', '37974a416d1d9525e1375c92025b16d9')
     version('4.1.2', '934c99808bdc8385e074b902d59b0d93')
     version('3.9.1', '3759dd10edb8c1a6dfb8ff0ce82658ce')
     version('3.9',   'e2b355da744e94747daae3a5339d28a0')
@@ -47,7 +29,8 @@ class Mercurial(PythonPackage):
     version('3.8.2', 'c38daa0cbe264fc621dc3bb05933b0b3')
     version('3.8.1', '172a8c588adca12308c2aca16608d7f4')
 
-    depends_on('python@2.6:2.8')
+    depends_on('python@2.6:2.8', when='@:4.2.99')
+    depends_on('python@2.7:2.8,3.5:3.5.999,3.6.2:', when='@4.3:')
     depends_on('py-docutils', type='build')
     depends_on('py-pygments', type=('build', 'run'))
     depends_on('py-certifi',  type=('build', 'run'))
@@ -84,8 +67,8 @@ class Mercurial(PythonPackage):
         hgrc_filename = join_path(etc_dir, 'hgrc')
 
         # Use certifi to find the location of the CA certificate
-        certificate = python('-c', 'import certifi; print certifi.where()',
-                             output=str)
+        print_str = self.spec['python'].package.print_string('certifi.where()')
+        certificate = python('-c', 'import certifi; ' + print_str)
 
         if not certificate:
             tty.warn('CA certificate not found. You may not be able to '
diff --git a/var/spack/repos/builtin/packages/mesa-glu/package.py b/var/spack/repos/builtin/packages/mesa-glu/package.py
index b450728e75..efd45dfa39 100644
--- a/var/spack/repos/builtin/packages/mesa-glu/package.py
+++ b/var/spack/repos/builtin/packages/mesa-glu/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,3 +17,13 @@ class MesaGlu(AutotoolsPackage):
     variant('mesa', default=True,
        description='Usually depends on mesa, disable for accelerated OpenGL')
     depends_on('mesa', when='+mesa')
+
+    provides('glu@1.3')
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libGLU', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
diff --git a/var/spack/repos/builtin/packages/mesa/package.py b/var/spack/repos/builtin/packages/mesa/package.py
index af8c20ae52..2823a98260 100644
--- a/var/spack/repos/builtin/packages/mesa/package.py
+++ b/var/spack/repos/builtin/packages/mesa/package.py
@@ -1,27 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is released as part of spack under the LGPL license.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import sys
 from spack import *
 
 
@@ -36,6 +18,7 @@ class Mesa(AutotoolsPackage):
     _oldurlfmt = "https://mesa.freedesktop.org/archive/older-versions/{0}.x/{1}/mesa-{1}.tar.xz"
     list_depth = 2
 
+    version('18.1.2', 'a2d4f031eb6bd6111d44d84004476918')
     version('17.2.3', 'a7dca71afbc7294cb7d505067fd44ef6')
     version('17.2.2', '1a157b5baefb5adf9f4fbb8a6632d74c')
     version('17.1.5', '6cf936fbcaadd98924298a7009e8265d')
@@ -46,6 +29,10 @@ class Mesa(AutotoolsPackage):
     version('12.0.6', '1a3d4fea0656c208db59289e4ed33b3f')
     version('12.0.3', '1113699c714042d8c4df4766be8c57d8')
 
+    provides('gl@:4.5', when='@17:')
+    provides('gl@:4.4', when='@13:')
+    provides('gl@:4.3', when='@12:')
+
     variant('swrender', default=True,
             description="Build with (gallium) software rendering.")
     variant('hwrender', default=False,
@@ -54,12 +41,13 @@ class Mesa(AutotoolsPackage):
             description="Use llvm for rendering pipes.")
 
     # General dependencies
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('flex@2.5.35:', type='build')
     depends_on('bison@2.4.1:', type='build')
-    depends_on('binutils', type='build')
+    depends_on('binutils', type='build', when=(sys.platform != 'darwin'))
     depends_on('python@2.6.4:', type='build')
     depends_on('py-mako@0.3.4:', type='build')
+    depends_on('py-argparse', type='build')
     depends_on('gettext')
     depends_on('icu4c')
     depends_on('expat')
@@ -76,6 +64,7 @@ class Mesa(AutotoolsPackage):
     depends_on('libxfixes')
     depends_on('libxv')
     depends_on('libxvmc')
+    depends_on('zlib@1.2.3:')
 
     # For DRI and hardware acceleration
     depends_on('dri2proto@2.6:', type='build', when='+hwrender')
@@ -86,6 +75,8 @@ class Mesa(AutotoolsPackage):
     depends_on('llvm@:3.9.1+link_dylib', when='@13:13.99+llvm')
     depends_on('llvm+link_dylib', when='+llvm')
     depends_on('libelf', when='+llvm')
+    depends_on('damageproto', when='+hwrender')
+    depends_on('fixesproto', when='+hwrender')
 
     def url_for_version(self, version):
         """Handle Mesa version-based custom URLs."""
@@ -190,3 +181,16 @@ class Mesa(AutotoolsPackage):
                 configure(*options)
             else:
                 raise
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libGL', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
+
+    @when('^python@3:')
+    def setup_environment(self, spack_env, run_env):
+        # this avoids an "import site" error in the build
+        spack_env.unset('PYTHONHOME')
diff --git a/var/spack/repos/builtin/packages/meshkit/package.py b/var/spack/repos/builtin/packages/meshkit/package.py
index 9db76fc4d8..9ed67edc96 100644
--- a/var/spack/repos/builtin/packages/meshkit/package.py
+++ b/var/spack/repos/builtin/packages/meshkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/meson/package.py b/var/spack/repos/builtin/packages/meson/package.py
index 046d9b2dea..7ede3c996d 100644
--- a/var/spack/repos/builtin/packages/meson/package.py
+++ b/var/spack/repos/builtin/packages/meson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/mesquite/package.py b/var/spack/repos/builtin/packages/mesquite/package.py
index b23f1294ce..2abaa589b9 100644
--- a/var/spack/repos/builtin/packages/mesquite/package.py
+++ b/var/spack/repos/builtin/packages/mesquite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/metabat/package.py b/var/spack/repos/builtin/packages/metabat/package.py
new file mode 100644
index 0000000000..d8be2b90ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/metabat/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Metabat(SConsPackage):
+    """MetaBAT, an efficient tool for accurately reconstructing single
+    genomes from complex microbial communities."""
+
+    homepage = "https://bitbucket.org/berkeleylab/metabat"
+    url      = "https://bitbucket.org/berkeleylab/metabat/get/v2.12.1.tar.gz"
+
+    version('2.12.1', 'c032f47a8b24e58a5a9fefe52cb6e0f8')
+
+    depends_on('boost@1.55.0:', type=('build', 'run'))
+    depends_on('perl', type='run')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('BOOST_ROOT', self.spec['boost'].prefix)
+
+    def install_args(self, spec, prefix):
+        return ["PREFIX={0}".format(prefix)]
+
+    @run_after('build')
+    def fix_perl_scripts(self):
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'aggregateBinDepths.pl')
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'aggregateContigOverlapsByBin.pl')
diff --git a/var/spack/repos/builtin/packages/metaphysicl/package.py b/var/spack/repos/builtin/packages/metaphysicl/package.py
index 52548f7b4c..bfa0157cad 100644
--- a/var/spack/repos/builtin/packages/metaphysicl/package.py
+++ b/var/spack/repos/builtin/packages/metaphysicl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py
index 20e601fbd8..ad03293d29 100644
--- a/var/spack/repos/builtin/packages/metis/package.py
+++ b/var/spack/repos/builtin/packages/metis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import glob
@@ -45,12 +26,25 @@ class Metis(Package):
     version('4.0.3', 'd3848b454532ef18dc83e4fb160d1e10')
 
     variant('shared', default=True, description='Enables the build of shared libraries.')
-    variant('debug', default=False, description='Builds the library in debug mode.')
-    variant('gdb', default=False, description='Enables gdb support.')
-
+    variant('gdb', default=False, description='Enables gdb support (version 5+).')
     variant('int64', default=False, description='Sets the bit width of METIS\'s index type to 64.')
     variant('real64', default=False, description='Sets the bit width of METIS\'s real type to 64.')
 
+    # For Metis version 5:, the build system is CMake, provide the
+    # `build_type` variant.
+    variant('build_type', default='Release',
+            description='The build type for the installation (only Debug or'
+            ' Release allowed for version 4).',
+            values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'))
+
+    # Prior to version 5, the (non-cmake) build system only knows about
+    # 'build_type=Debug|Release'.
+    conflicts('@:4.999', when='build_type=RelWithDebInfo')
+    conflicts('@:4.999', when='build_type=MinSizeRel')
+    conflicts('@:4.999', when='+gdb')
+    conflicts('@:4.999', when='+int64')
+    conflicts('@:4.999', when='+real64')
+
     depends_on('cmake@2.8:', when='@5:', type='build')
 
     patch('install_gklib_defs_rename.patch', when='@5:')
@@ -87,12 +81,10 @@ class Metis(Package):
     @when('@:4')
     def install(self, spec, prefix):
         # Process library spec and options
-        if any('+{0}'.format(v) in spec for v in ['gdb', 'int64', 'real64']):
-            raise InstallError('METIS@:4 does not support the following '
-                               'variants: gdb, int64, real64.')
-
-        options = ['COPTIONS={0}'.format(self.compiler.pic_flag)]
-        if '+debug' in spec:
+        options = []
+        if '+shared' in spec:
+            options.append('COPTIONS={0}'.format(self.compiler.pic_flag))
+        if spec.variants['build_type'].value == 'Debug':
             options.append('OPTFLAGS=-g -O0')
         make(*options)
 
@@ -135,8 +127,8 @@ class Metis(Package):
 
         # Set up and run tests on installation
         ccompile('-I%s' % prefix.include, '-L%s' % prefix.lib,
-                 self.compiler.cc_rpath_arg +
-                 '%s' % (prefix.lib if '+shared' in spec else ''),
+                 (self.compiler.cc_rpath_arg + prefix.lib
+                  if '+shared' in spec else ''),
                  join_path('Programs', 'io.o'), join_path('Test', 'mtest.c'),
                  '-o', '%s/mtest' % prefix.bin, '-lmetis', '-lm')
 
@@ -185,6 +177,11 @@ class Metis(Package):
         options.append('-DGKLIB_PATH:PATH=%s/GKlib' % source_directory)
         options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
 
+        # Normally this is available via the 'CMakePackage' object, but metis
+        # IS-A 'Package' (not a 'CMakePackage') to support non-cmake metis@:5.
+        build_type = spec.variants['build_type'].value
+        options.extend(['-DCMAKE_BUILD_TYPE:STRING={0}'.format(build_type)])
+
         if '+shared' in spec:
             options.append('-DSHARED:BOOL=ON')
         else:
@@ -196,9 +193,6 @@ class Metis(Package):
                     rpath_options.append(o)
             for o in rpath_options:
                 options.remove(o)
-        if '+debug' in spec:
-            options.extend(['-DDEBUG:BOOL=ON',
-                            '-DCMAKE_BUILD_TYPE:STRING=Debug'])
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
@@ -208,11 +202,11 @@ class Metis(Package):
             make('install')
 
             # install GKlib headers, which will be needed for ParMETIS
-            GKlib_dist = join_path(prefix.include, 'GKlib')
-            mkdirp(GKlib_dist)
+            gklib_dist = join_path(prefix.include, 'GKlib')
+            mkdirp(gklib_dist)
             hfiles = glob.glob(join_path(source_directory, 'GKlib', '*.h'))
             for hfile in hfiles:
-                install(hfile, GKlib_dist)
+                install(hfile, gklib_dist)
 
         if self.run_tests:
             # FIXME: On some systems, the installed binaries for METIS cannot
diff --git a/var/spack/repos/builtin/packages/mfem/mfem-3.3-3.4-petsc-3.9.patch b/var/spack/repos/builtin/packages/mfem/mfem-3.3-3.4-petsc-3.9.patch
new file mode 100644
index 0000000000..dcf4870a25
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mfem/mfem-3.3-3.4-petsc-3.9.patch
@@ -0,0 +1,71 @@
+diff --git a/examples/petsc/rc_ex3p b/examples/petsc/rc_ex3p
+index 2cbe07ef2..c585d9b52 100644
+--- a/examples/petsc/rc_ex3p
++++ b/examples/petsc/rc_ex3p
+@@ -6,4 +6,4 @@
+ # it needs PETSc configured with MUMPS
+ 
+ -solver_pc_type cholesky
+--solver_pc_factor_mat_solver_package mumps
++-solver_pc_factor_mat_solver_type mumps
+diff --git a/examples/petsc/rc_ex3p_bddc b/examples/petsc/rc_ex3p_bddc
+index ea887bb29..2e1eba0d5 100644
+--- a/examples/petsc/rc_ex3p_bddc
++++ b/examples/petsc/rc_ex3p_bddc
+@@ -16,7 +16,7 @@
+ #-pc_bddc_adaptive_threshold 10
+ 
+ # Customization of the local solvers
+-#-pc_bddc_neumann_pc_factor_mat_solver_package mumps
+-#-pc_bddc_dirichlet_pc_factor_mat_solver_package mumps
++#-pc_bddc_neumann_pc_factor_mat_solver_type mumps
++#-pc_bddc_dirichlet_pc_factor_mat_solver_type mumps
+ #-pc_bddc_coarse_pc_type cholesky
+-#-pc_bddc_coarse_pc_factor_mat_solver_package mumps
++#-pc_bddc_coarse_pc_factor_mat_solver_type mumps
+diff --git a/examples/petsc/rc_ex4p b/examples/petsc/rc_ex4p
+index f734f35fe..64fbe9427 100644
+--- a/examples/petsc/rc_ex4p
++++ b/examples/petsc/rc_ex4p
+@@ -2,4 +2,4 @@
+ # it needs PETSc configured with MUMPS
+ 
+ -solver_pc_type cholesky
+--solver_pc_factor_mat_solver_package mumps
++-solver_pc_factor_mat_solver_type mumps
+diff --git a/examples/petsc/rc_ex4p_bddc b/examples/petsc/rc_ex4p_bddc
+index 9507ad431..e8ef99db7 100644
+--- a/examples/petsc/rc_ex4p_bddc
++++ b/examples/petsc/rc_ex4p_bddc
+@@ -13,7 +13,7 @@
+ #-pc_bddc_adaptive_threshold 10
+ 
+ # Customization of the local solvers
+-#-pc_bddc_neumann_pc_factor_mat_solver_package mumps
+-#-pc_bddc_dirichlet_pc_factor_mat_solver_package mumps
++#-pc_bddc_neumann_pc_factor_mat_solver_type mumps
++#-pc_bddc_dirichlet_pc_factor_mat_solver_type mumps
+ #-pc_bddc_coarse_pc_type cholesky
+-#-pc_bddc_coarse_pc_factor_mat_solver_package mumps
++#-pc_bddc_coarse_pc_factor_mat_solver_type mumps
+diff --git a/examples/petsc/rc_ex5p_bddc b/examples/petsc/rc_ex5p_bddc
+index b243c53c8..a4bc899c3 100644
+--- a/examples/petsc/rc_ex5p_bddc
++++ b/examples/petsc/rc_ex5p_bddc
+@@ -28,13 +28,13 @@
+ # local solvers (needs PETSc compiled with support for SuiteSparse)
+ # default solvers will fail
+ -prec_pc_bddc_neumann_pc_type lu
+--prec_pc_bddc_neumann_pc_factor_mat_solver_package umfpack
++-prec_pc_bddc_neumann_pc_factor_mat_solver_type umfpack
+ -prec_pc_bddc_dirichlet_pc_type lu
+--prec_pc_bddc_dirichlet_pc_factor_mat_solver_package umfpack
++-prec_pc_bddc_dirichlet_pc_factor_mat_solver_type umfpack
+ 
+ # coarse solver (needs PETSc compiled with support for MUMPS)
+ # default solver may fail
+--prec_pc_bddc_coarse_pc_factor_mat_solver_package mumps
++-prec_pc_bddc_coarse_pc_factor_mat_solver_type mumps
+ -prec_pc_bddc_coarse_pc_type cholesky
+ 
+ # deluxe scaling (needs PETSc compiled with support for MUMPS)
diff --git a/var/spack/repos/builtin/packages/mfem/mfem-3.4.patch b/var/spack/repos/builtin/packages/mfem/mfem-3.4.patch
new file mode 100644
index 0000000000..465e0525ea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mfem/mfem-3.4.patch
@@ -0,0 +1,36 @@
+diff --git a/config/test.mk b/config/test.mk
+index 4821b084d..62479fc63 100644
+--- a/config/test.mk
++++ b/config/test.mk
+@@ -14,11 +14,13 @@
+ # Colors used below:
+ # green    '\033[0;32m'
+ # red      '\033[0;31m'
++# yellow   '\033[0;33m'
+ # no color '\033[0m'
+ COLOR_PRINT = if [ -t 1 ]; then \
+    printf $(1)$(2)'\033[0m'$(3); else printf $(2)$(3); fi
+ PRINT_OK = $(call COLOR_PRINT,'\033[0;32m',OK,"  ($$1 $$2)\n")
+ PRINT_FAILED = $(call COLOR_PRINT,'\033[0;31m',FAILED,"  ($$1 $$2)\n")
++PRINT_SKIP = $(call COLOR_PRINT,'\033[0;33m',SKIP,"\n")
+ 
+ # Timing support
+ define TIMECMD_detect
+diff --git a/examples/pumi/makefile b/examples/pumi/makefile
+index 2f98eeca7..5ff652aca 100644
+--- a/examples/pumi/makefile
++++ b/examples/pumi/makefile
+@@ -51,6 +51,13 @@ endif
+ MFEM_TESTS = EXAMPLES
+ include $(MFEM_TEST_MK)
+ 
++ifneq (,$(filter test%,$(MAKECMDGOALS)))
++   ifeq (,$(wildcard ../../data/pumi))
++      $(info PUMI data directory not found. The PUMI tests will be SKIPPED.)
++      mfem-test = printf "   $(3) [$(2) $(1) ... ]: "; $(PRINT_SKIP)
++   endif
++endif
++
+ # Testing: Parallel vs. serial runs
+ RUN_MPI_NP = $(MFEM_MPIEXEC) $(MFEM_MPIEXEC_NP)
+ RUN_MPI = $(RUN_MPI_NP) $(MFEM_MPI_NP)
diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py
index 3afbd4ca2f..d6f55b6566 100644
--- a/var/spack/repos/builtin/packages/mfem/package.py
+++ b/var/spack/repos/builtin/packages/mfem/package.py
@@ -1,43 +1,33 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 re
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import os
+import shutil
 
 
 class Mfem(Package):
     """Free, lightweight, scalable C++ library for finite element methods."""
 
+    tags = ['FEM', 'finite elements', 'high-order', 'AMR', 'HPC']
+
     homepage = 'http://www.mfem.org'
-    url      = 'https://github.com/mfem/mfem'
+    git      = 'https://github.com/mfem/mfem.git'
+
+    maintainers = ['goxberry', 'tzanio', 'markcmiller86', 'acfisher',
+                   'v-dobrev']
+
+    # Recommended mfem builds to test when updating this file: see the shell
+    # script 'test_builds.sh' in the same directory as this file.
 
     # mfem is downloaded from a URL shortener at request of upstream
     # author Tzanio Kolev <tzanio@llnl.gov>.  See here:
     #     https://github.com/mfem/mfem/issues/53
     #
     # The following procedure should be used to verify security when a
-    # new verison is added:
+    # new version is added:
     #
     # 1. Verify that no checksums on old versions have changed.
     #
@@ -51,13 +41,20 @@ class Mfem(Package):
     # If this quick verification procedure fails, additional discussion
     # will be required to verify the new version.
 
-    version('3.3.2', 
-            '01a762a5d0a2bc59ce4e2f59009045a4',
-            url='https://goo.gl/Kd7Jk8', extension='.tar.gz',
+    # 'develop' is a special version that is always larger (or newer) than any
+    # other version.
+    version('develop', branch='master')
+
+    version('3.4.0',
+            '4e73e4fe0482636de3c5dc983cd395839a83cb16f6f509bd88b053e8b3858e05',
+            url='https://bit.ly/mfem-3-4', extension='.tar.gz',
             preferred=True)
 
-    version('laghos-v1.0', git='https://github.com/mfem/mfem',
-            tag='laghos-v1.0')
+    version('3.3.2',
+            'b70fa3c5080b9ec514fc05f4a04ff74322b99ac4ecd6d99c229f0ed5188fc0ce',
+            url='https://goo.gl/Kd7Jk8', extension='.tar.gz')
+
+    version('laghos-v1.0', tag='laghos-v1.0')
 
     version('3.3',
             'b17bd452593aada93dc0fee748fcfbbf4f04ce3e7d77fdd0341cc9103bcacd0b',
@@ -71,8 +68,19 @@ class Mfem(Package):
             '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57',
             url='http://goo.gl/xrScXn', extension='.tar.gz')
 
+    variant('static', default=True,
+        description='Build static library')
+    variant('shared', default=False,
+        description='Build shared library')
     variant('mpi', default=True,
         description='Enable MPI parallelism')
+    # Can we make the default value for 'metis' to depend on the 'mpi' value?
+    variant('metis', default=True,
+        description='Enable METIS support')
+    # TODO: The 'hypre' variant is the same as 'mpi', we may want to remove it.
+    #       For now, keep the 'hypre' variant while ignoring its setting. This
+    #       is done to preserve compatibility with other packages that refer to
+    #       it, e.g. xSDK.
     variant('hypre', default=True,
         description='Required for MPI parallelism')
     variant('openmp', default=False,
@@ -83,12 +91,17 @@ class Mfem(Package):
             ' May cause minor performance issues.'))
     variant('superlu-dist', default=False,
         description='Enable MPI parallel, sparse direct solvers')
+    # Placeholder for STRUMPACK, support added in mfem v3.3.2:
+    # variant('strumpack', default=False,
+    #     description='Enable support for STRUMPACK')
     variant('suite-sparse', default=False,
         description='Enable serial, sparse direct solvers')
     variant('petsc', default=False,
-        description='Enable PETSc solvers, preconditioners, etc..')
+        description='Enable PETSc solvers, preconditioners, etc.')
     variant('sundials', default=False,
         description='Enable Sundials time integrators')
+    variant('pumi', default=False,
+        description='Enable functionality based on PUMI')
     variant('mpfr', default=False,
         description='Enable precise, 1D quadrature rules')
     variant('lapack', default=False,
@@ -97,43 +110,87 @@ class Mfem(Package):
         description='Build debug instead of optimized version')
     variant('netcdf', default=False,
         description='Enable Cubit/Genesis reader')
+    variant('conduit', default=False,
+        description='Enable binary data I/O using Conduit')
     variant('gzstream', default=True,
         description='Support zip\'d streams for I/O')
+    variant('gnutls', default=False,
+        description='Enable secure sockets using GnuTLS')
+    variant('libunwind', default=False,
+        description='Enable backtrace on error support using Libunwind')
+    variant('timer', default='auto',
+        values=('auto', 'std', 'posix', 'mac', 'mpi'),
+        description='Timing functions to use in mfem::StopWatch')
     variant('examples', default=False,
         description='Build and install examples')
     variant('miniapps', default=False,
         description='Build and install miniapps')
 
-    conflicts('+mpi', when='~hypre')
-    conflicts('+suite-sparse', when='~lapack')
-    conflicts('+superlu-dist', when='@:3.1')
+    conflicts('+shared', when='@:3.3.2')
+    conflicts('~static~shared')
+    conflicts('~threadsafe', when='+openmp')
+
     conflicts('+netcdf', when='@:3.1')
+    conflicts('+superlu-dist', when='@:3.1')
+    conflicts('+gnutls', when='@:3.1')
+    conflicts('+gzstream', when='@:3.2')
+    conflicts('+mpfr', when='@:3.2')
+    conflicts('+petsc', when='@:3.2')
+    conflicts('+sundials', when='@:3.2')
+    conflicts('+pumi', when='@:3.3.2')
+    conflicts('timer=mac', when='@:3.3.0')
+    conflicts('timer=mpi', when='@:3.3.0')
+    conflicts('~metis+mpi', when='@:3.3.0')
+    conflicts('+metis~mpi', when='@:3.3.0')
+    conflicts('+conduit', when='@:3.3.2')
+
+    conflicts('+superlu-dist', when='~mpi')
+    conflicts('+petsc', when='~mpi')
+    conflicts('+pumi', when='~mpi')
+    conflicts('timer=mpi', when='~mpi')
+
+    conflicts('+pumi', when='+shared')
 
-    depends_on('hypre', when='+hypre')
+    depends_on('mpi', when='+mpi')
+    depends_on('hypre@2.10.0:2.13.999', when='@:3.3.999+mpi')
+    depends_on('hypre', when='@3.4:+mpi')
+
+    depends_on('metis', when='+metis')
     depends_on('blas', when='+lapack')
-    depends_on('blas', when='+suite-sparse')
     depends_on('lapack', when='+lapack')
-    depends_on('lapack', when='+suite-sparse')
-
-    depends_on('mpi', when='+mpi')
-    depends_on('metis')
-    depends_on('parmetis', when='+superlu-dist')
-    depends_on('metis@5:', when='+superlu-dist')
-    depends_on('metis@5:', when='+suite-sparse ^suite-sparse@4.5:')
 
-    depends_on('sundials@2.7:+hypre', when='+sundials')
+    depends_on('sundials@2.7.0', when='@:3.3.0+sundials~mpi')
+    depends_on('sundials@2.7.0+mpi+hypre', when='@:3.3.0+sundials+mpi')
+    depends_on('sundials@2.7.0:', when='@3.3.2:+sundials~mpi')
+    depends_on('sundials@2.7.0:+mpi+hypre', when='@3.3.2:+sundials+mpi')
+    depends_on('pumi', when='+pumi')
     depends_on('suite-sparse', when='+suite-sparse')
-    depends_on('superlu-dist', when='@3.2: +superlu-dist')
-    depends_on('petsc@3.8:', when='+petsc')
-
+    depends_on('superlu-dist', when='+superlu-dist')
+    # The PETSc tests in MFEM will fail if PETSc is not configured with
+    # SuiteSparse and MUMPS. On the other hand, if we require the variants
+    # '+suite-sparse+mumps' of PETSc, the xsdk package concretization fails.
+    depends_on('petsc@3.8:+mpi+double+hypre', when='+petsc')
+    # Recommended when building outside of xsdk:
+    # depends_on('petsc@3.8:+mpi+double+hypre+suite-sparse+mumps',
+    #            when='+petsc')
     depends_on('mpfr', when='+mpfr')
-    depends_on('netcdf', when='@3.2: +netcdf')
-    depends_on('zlib', when='@3.2: +netcdf')
-    depends_on('hdf5', when='@3.2: +netcdf')
-    depends_on('libunwind', when='+debug')
+    depends_on('netcdf', when='+netcdf')
+    depends_on('unwind', when='+libunwind')
     depends_on('zlib', when='+gzstream')
+    depends_on('gnutls', when='+gnutls')
+    depends_on('conduit@0.3.1:', when='+conduit')
+    depends_on('conduit+mpi', when='+conduit+mpi')
+
+    patch('mfem_ppc_build.patch', when='@3.2:3.3.0 arch=ppc64le')
+    patch('mfem-3.4.patch', when='@3.4.0')
+    patch('mfem-3.3-3.4-petsc-3.9.patch',
+          when='@3.3.0:3.4.0 +petsc ^petsc@3.9.0:')
 
-    patch('mfem_ppc_build.patch', when='@3.2:3.3 arch=ppc64le')
+    phases = ['configure', 'build', 'install']
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.unset('MFEM_DIR')
+        spack_env.unset('MFEM_BUILD_DIR')
 
     #
     # Note: Although MFEM does support CMake configuration, MFEM
@@ -142,144 +199,230 @@ class Mfem(Package):
     # likely to be up to date in supporting *all* of MFEM's
     # configuration options. So, don't use CMake
     #
-    def install(self, spec, prefix):
+    def configure(self, spec, prefix):
 
         def yes_no(varstr):
             return 'YES' if varstr in self.spec else 'NO'
 
-        metis5_str = 'NO'
-        if '+superlu-dist' in spec or  \
-            spec.satisfies('+suite-sparse ^suite-sparse@4.5:') or \
-                spec['metis'].satisfies('@5:'):
-                metis5_str = 'YES'
+        # We need to add rpaths explicitly to allow proper export of link flags
+        # from within MFEM.
+
+        # Similar to spec[pkg].libs.ld_flags but prepends rpath flags too.
+        def ld_flags_from_library_list(libs_list):
+            flags = ['-Wl,-rpath,%s' % dir for dir in libs_list.directories]
+            flags += [libs_list.ld_flags]
+            return ' '.join(flags)
+
+        def ld_flags_from_dirs(pkg_dirs_list, pkg_libs_list):
+            flags = ['-Wl,-rpath,%s' % dir for dir in pkg_dirs_list]
+            flags += ['-L%s' % dir for dir in pkg_dirs_list]
+            flags += ['-l%s' % lib for lib in pkg_libs_list]
+            return ' '.join(flags)
+
+        def find_optional_library(name, prefix):
+            for shared in [True, False]:
+                for path in ['lib64', 'lib']:
+                    lib = find_libraries(name, join_path(prefix, path),
+                                         shared=shared, recursive=False)
+                    if lib:
+                        return lib
+            return LibraryList([])
 
-        threadsafe_str = 'NO'
-        if '+openmp' in spec or '+threadsafe' in spec:
-            threadsafe_str = 'YES'
+        metis5_str = 'NO'
+        if ('+metis' in spec) and spec['metis'].satisfies('@5:'):
+            metis5_str = 'YES'
 
         options = [
             'PREFIX=%s' % prefix,
             'MFEM_USE_MEMALLOC=YES',
             'MFEM_DEBUG=%s' % yes_no('+debug'),
+            # NOTE: env['CXX'] is the spack c++ compiler wrapper. The real
+            # compiler is defined by env['SPACK_CXX'].
             'CXX=%s' % env['CXX'],
-            'MFEM_USE_LIBUNWIND=%s' % yes_no('+debug'),
+            'MFEM_USE_LIBUNWIND=%s' % yes_no('+libunwind'),
             'MFEM_USE_GZSTREAM=%s' % yes_no('+gzstream'),
+            'MFEM_USE_METIS=%s' % yes_no('+metis'),
             'MFEM_USE_METIS_5=%s' % metis5_str,
-            'MFEM_THREAD_SAFE=%s' % threadsafe_str,
+            'MFEM_THREAD_SAFE=%s' % yes_no('+threadsafe'),
             'MFEM_USE_MPI=%s' % yes_no('+mpi'),
             'MFEM_USE_LAPACK=%s' % yes_no('+lapack'),
             'MFEM_USE_SUPERLU=%s' % yes_no('+superlu-dist'),
             'MFEM_USE_SUITESPARSE=%s' % yes_no('+suite-sparse'),
             'MFEM_USE_SUNDIALS=%s' % yes_no('+sundials'),
             'MFEM_USE_PETSC=%s' % yes_no('+petsc'),
+            'MFEM_USE_PUMI=%s' % yes_no('+pumi'),
             'MFEM_USE_NETCDF=%s' % yes_no('+netcdf'),
             'MFEM_USE_MPFR=%s' % yes_no('+mpfr'),
-            'MFEM_USE_OPENMP=%s' % yes_no('+openmp')]
+            'MFEM_USE_GNUTLS=%s' % yes_no('+gnutls'),
+            'MFEM_USE_OPENMP=%s' % yes_no('+openmp'),
+            'MFEM_USE_CONDUIT=%s' % yes_no('+conduit')]
+
+        cxxflags = spec.compiler_flags['cxxflags']
+        if cxxflags:
+            # The cxxflags are set by the spack c++ compiler wrapper. We also
+            # set CXXFLAGS explicitly, for clarity, and to properly export the
+            # cxxflags in the variable MFEM_CXXFLAGS in config.mk.
+            options += ['CXXFLAGS=%s' % ' '.join(cxxflags)]
+
+        if '~static' in spec:
+            options += ['STATIC=NO']
+        if '+shared' in spec:
+            options += ['SHARED=YES', 'PICFLAG=%s' % self.compiler.pic_flag]
 
         if '+mpi' in spec:
             options += ['MPICXX=%s' % spec['mpi'].mpicxx]
+            hypre = spec['hypre']
+            # The hypre package always links with 'blas' and 'lapack'.
+            all_hypre_libs = hypre.libs + hypre['lapack'].libs + \
+                hypre['blas'].libs
+            options += [
+                'HYPRE_OPT=-I%s' % hypre.prefix.include,
+                'HYPRE_LIB=%s' % ld_flags_from_library_list(all_hypre_libs)]
 
-        if '+hypre' in spec:
+        if '+metis' in spec:
             options += [
-                'HYPRE_DIR=%s' % spec['hypre'].prefix,
-                'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include,
-                'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib + ' -lHYPRE']
+                'METIS_OPT=-I%s' % spec['metis'].prefix.include,
+                'METIS_LIB=%s' %
+                ld_flags_from_dirs([spec['metis'].prefix.lib], ['metis'])]
 
         if '+lapack' in spec:
-            lapack_lib = (spec['lapack'].libs + spec['blas'].libs).ld_flags  # NOQA: ignore=E501
+            lapack_blas = spec['lapack'].libs + spec['blas'].libs
             options += [
-                'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include,
-                'LAPACK_LIB=%s' % lapack_lib]
+                # LAPACK_OPT is not used
+                'LAPACK_LIB=%s' % ld_flags_from_library_list(lapack_blas)]
 
         if '+superlu-dist' in spec:
-            metis_lib = '-L%s -lparmetis -lmetis' % spec['parmetis'].prefix.lib
-            options += [
-                'METIS_DIR=%s' % spec['parmetis'].prefix,
-                'METIS_OPT=-I%s' % spec['parmetis'].prefix.include,
-                'METIS_LIB=%s' % metis_lib]
-            superlu_lib = '-L%s' % spec['superlu-dist'].prefix.lib
-            superlu_lib += ' -lsuperlu_dist'
+            lapack_blas = spec['lapack'].libs + spec['blas'].libs
             options += [
-                'SUPERLU_DIR=%s' % spec['superlu-dist'].prefix,
-                'SUPERLU_OPT=-I%s' % spec['superlu-dist'].prefix.include,
-                'SUPERLU_LIB=%s' % superlu_lib]
-        else:
-            metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib
-            options += [
-                'METIS_DIR=%s' % spec['metis'].prefix,
-                'METIS_OPT=-I%s' % spec['metis'].prefix.include,
-                'METIS_LIB=%s' % metis_lib]
+                'SUPERLU_OPT=-I%s -I%s' %
+                (spec['superlu-dist'].prefix.include,
+                 spec['parmetis'].prefix.include),
+                'SUPERLU_LIB=-L%s -L%s -lsuperlu_dist -lparmetis %s' %
+                (spec['superlu-dist'].prefix.lib,
+                 spec['parmetis'].prefix.lib,
+                 ld_flags_from_library_list(lapack_blas))]
 
         if '+suite-sparse' in spec:
-            ssp = spec['suite-sparse'].prefix
-            ss_lib = '-L%s' % ssp.lib
-            if '@3.2:' in spec:
-                ss_lib += ' -lklu -lbtf'
-            ss_lib += (' -lumfpack -lcholmod -lcolamd' +
-                       ' -lamd -lcamd -lccolamd -lsuitesparseconfig')
-            no_rt = spec.satisfies('platform=darwin')
-            if not no_rt:
-                ss_lib += ' -lrt'
-            ss_lib += (' ' + metis_lib + ' ' + lapack_lib)
+            ss_spec = 'suite-sparse:' + self.suitesparse_components
             options += [
-                'SUITESPARSE_DIR=%s' % ssp,
-                'SUITESPARSE_OPT=-I%s' % ssp.include,
-                'SUITESPARSE_LIB=%s' % ss_lib]
+                'SUITESPARSE_OPT=-I%s' % spec[ss_spec].prefix.include,
+                'SUITESPARSE_LIB=%s' %
+                ld_flags_from_library_list(spec[ss_spec].libs)]
 
         if '+sundials' in spec:
-            sundials_libs = (
-                '-lsundials_arkode -lsundials_cvode'
-                ' -lsundials_nvecserial -lsundials_kinsol')
-            if '+mpi' in spec:
-                sundials_libs += (
-                    ' -lsundials_nvecparhyp -lsundials_nvecparallel')
+            sun_spec = 'sundials:' + self.sundials_components
             options += [
-                'SUNDIALS_DIR=%s' % spec['sundials'].prefix,
-                'SUNDIALS_OPT=-I%s' % spec['sundials'].prefix.include,
-                'SUNDIALS_LIB=-L%s %s' % (spec['sundials'].prefix.lib,
-                                          sundials_libs)]
+                'SUNDIALS_OPT=%s' % spec[sun_spec].headers.cpp_flags,
+                'SUNDIALS_LIB=%s' %
+                ld_flags_from_library_list(spec[sun_spec].libs)]
 
         if '+petsc' in spec:
-            f = open('%s/lib/pkgconfig/PETSc.pc' % spec['petsc'].prefix, 'r')
-            for line in f:
-                if re.search('^\s*Cflags: ', line):
-                    petsc_opts = re.sub('^\s*Cflags: (.*)', '\\1', line)
-                elif re.search('^\s*Libs.*: ', line):
-                    petsc_libs = re.sub('^\s*Libs.*: (.*)', '\\1', line)
-            f.close()
+            # options += ['PETSC_DIR=%s' % spec['petsc'].prefix]
             options += [
-                'PETSC_DIR=%s' % spec['petsc'].prefix,
-                'PETSC_OPT=%s' % petsc_opts,
-                'PETSC_LIB=-L%s -lpetsc %s' %
-                (spec['petsc'].prefix.lib, petsc_libs)]
+                'PETSC_OPT=%s' % spec['petsc'].headers.cpp_flags,
+                'PETSC_LIB=%s' %
+                ld_flags_from_library_list(spec['petsc'].libs)]
+
+        if '+pumi' in spec:
+            options += ['PUMI_DIR=%s' % spec['pumi'].prefix]
 
         if '+netcdf' in spec:
-            np = spec['netcdf'].prefix
-            zp = spec['zlib'].prefix
-            h5p = spec['hdf5'].prefix
-            nlib = '-L%s -lnetcdf ' % np.lib
-            nlib += '-L%s -lhdf5_hl -lhdf5 ' % h5p.lib
-            nlib += '-L%s -lz' % zp.lib
             options += [
-                'NETCDF_DIR=%s' % np,
-                'HDF5_DIR=%s' % h5p,
-                'ZLIB_DIR=%s' % zp,
-                'NETCDF_OPT=-I%s' % np.include,
-                'NETCDF_LIB=%s' % nlib]
+                'NETCDF_OPT=-I%s' % spec['netcdf'].prefix.include,
+                'NETCDF_LIB=%s' %
+                ld_flags_from_dirs([spec['netcdf'].prefix.lib], ['netcdf'])]
+
+        if '+gzstream' in spec:
+            if "@:3.3.2" in spec:
+                options += ['ZLIB_DIR=%s' % spec['zlib'].prefix]
+            else:
+                options += [
+                    'ZLIB_OPT=-I%s' % spec['zlib'].prefix.include,
+                    'ZLIB_LIB=%s' %
+                    ld_flags_from_library_list(spec['zlib'].libs)]
 
         if '+mpfr' in spec:
-            options += ['MPFR_LIB=-L%s -lmpfr' % spec['mpfr'].prefix.lib]
+            options += [
+                'MPFR_OPT=-I%s' % spec['mpfr'].prefix.include,
+                'MPFR_LIB=%s' %
+                ld_flags_from_dirs([spec['mpfr'].prefix.lib], ['mpfr'])]
+
+        if '+gnutls' in spec:
+            options += [
+                'GNUTLS_OPT=-I%s' % spec['gnutls'].prefix.include,
+                'GNUTLS_LIB=%s' %
+                ld_flags_from_dirs([spec['gnutls'].prefix.lib], ['gnutls'])]
+
+        if '+libunwind' in spec:
+            libunwind = spec['unwind']
+            headers = find_headers('libunwind', libunwind.prefix.include)
+            headers.add_macro('-g')
+            libs = find_optional_library('libunwind', libunwind.prefix)
+            # When mfem uses libunwind, it also needs 'libdl'.
+            libs += LibraryList(find_system_libraries('libdl'))
+            options += [
+                'LIBUNWIND_OPT=%s' % headers.cpp_flags,
+                'LIBUNWIND_LIB=%s' % ld_flags_from_library_list(libs)]
 
         if '+openmp' in spec:
-            options += ['OPENMP_OPT = %s' % self.compiler.openmp_flag]
+            options += ['OPENMP_OPT=%s' % self.compiler.openmp_flag]
+
+        timer_ids = {'std': '0', 'posix': '2', 'mac': '4', 'mpi': '6'}
+        timer = spec.variants['timer'].value
+        if timer != 'auto':
+            options += ['MFEM_TIMER_TYPE=%s' % timer_ids[timer]]
+
+        if '+conduit' in spec:
+            conduit = spec['conduit']
+            headers = HeaderList(find(conduit.prefix.include, 'conduit.hpp',
+                                      recursive=True))
+            conduit_libs = ['libconduit', 'libconduit_relay',
+                            'libconduit_blueprint']
+            libs = find_libraries(conduit_libs, conduit.prefix.lib,
+                                  shared=('+shared' in conduit))
+            libs += LibraryList(find_system_libraries('libdl'))
+            if '+hdf5' in conduit:
+                hdf5 = conduit['hdf5']
+                headers += find_headers('hdf5', hdf5.prefix.include)
+                libs += hdf5.libs
+            options += [
+                'CONDUIT_OPT=%s' % headers.cpp_flags,
+                'CONDUIT_LIB=%s' % ld_flags_from_library_list(libs)]
+
+        make('config', *options, parallel=False)
+        make('info', parallel=False)
 
-        make('config', *options)
+    def build(self, spec, prefix):
         make('lib')
 
-        if self.run_tests:
-            make('check')
+    @run_after('build')
+    def check_or_test(self):
+        # Running 'make check' or 'make test' may fail if MFEM_MPIEXEC or
+        # MFEM_MPIEXEC_NP are not set appropriately.
+        if not self.run_tests:
+            # check we can build ex1 (~mpi) or ex1p (+mpi).
+            make('-C', 'examples', 'ex1p' if ('+mpi' in self.spec) else 'ex1',
+                 parallel=False)
+            # make('check', parallel=False)
+        else:
+            make('all')
+            make('test', parallel=False)
+
+    def install(self, spec, prefix):
+        make('install', parallel=False)
 
-        make('install')
+        # TODO: The way the examples and miniapps are being installed is not
+        # perfect. For example, the makefiles do not work.
+
+        install_em = ('+examples' in spec) or ('+miniapps' in spec)
+        if install_em and ('+shared' in spec):
+            make('examples/clean', 'miniapps/clean')
+            # This is a hack to get the examples and miniapps to link with the
+            # installed shared mfem library:
+            with working_dir('config'):
+                os.rename('config.mk', 'config.mk.orig')
+                copy(str(self.config_mk), 'config.mk')
+                shutil.copystat('config.mk.orig', 'config.mk')
 
         if '+examples' in spec:
             make('examples')
@@ -288,3 +431,64 @@ class Mfem(Package):
         if '+miniapps' in spec:
             make('miniapps')
             install_tree('miniapps', join_path(prefix, 'miniapps'))
+
+        if install_em:
+            install_tree('data', join_path(prefix, 'data'))
+
+    @property
+    def suitesparse_components(self):
+        """Return the SuiteSparse components needed by MFEM."""
+        ss_comps = 'umfpack,cholmod,colamd,amd,camd,ccolamd,suitesparseconfig'
+        if self.spec.satisfies('@3.2:'):
+            ss_comps = 'klu,btf,' + ss_comps
+        return ss_comps
+
+    @property
+    def sundials_components(self):
+        """Return the SUNDIALS components needed by MFEM."""
+        sun_comps = 'arkode,cvode,nvecserial,kinsol'
+        if '+mpi' in self.spec:
+            sun_comps += ',nvecparhyp,nvecparallel'
+        return sun_comps
+
+    @property
+    def headers(self):
+        """Export the main mfem header, mfem.hpp.
+        """
+        hdrs = HeaderList(find(self.prefix.include, 'mfem.hpp',
+                               recursive=False))
+        return hdrs or None
+
+    @property
+    def libs(self):
+        """Export the mfem library file.
+        """
+        libs = find_libraries('libmfem', root=self.prefix.lib,
+                              shared=('+shared' in self.spec), recursive=False)
+        return libs or None
+
+    @property
+    def config_mk(self):
+        """Export the location of the config.mk file.
+           This property can be accessed using spec['mfem'].package.config_mk
+        """
+        dirs = [self.prefix, self.prefix.share.mfem]
+        for d in dirs:
+            f = join_path(d, 'config.mk')
+            if os.access(f, os.R_OK):
+                return FileList(f)
+        return FileList(find(self.prefix, 'config.mk', recursive=True))
+
+    @property
+    def test_mk(self):
+        """Export the location of the test.mk file.
+           This property can be accessed using spec['mfem'].package.test_mk.
+           In version 3.3.2 and newer, the location of test.mk is also defined
+           inside config.mk, variable MFEM_TEST_MK.
+        """
+        dirs = [self.prefix, self.prefix.share.mfem]
+        for d in dirs:
+            f = join_path(d, 'test.mk')
+            if os.access(f, os.R_OK):
+                return FileList(f)
+        return FileList(find(self.prefix, 'test.mk', recursive=True))
diff --git a/var/spack/repos/builtin/packages/mfem/test_builds.sh b/var/spack/repos/builtin/packages/mfem/test_builds.sh
new file mode 100755
index 0000000000..125fa0055c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mfem/test_builds.sh
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+builds=(
+    # preferred version:
+    'mfem'
+    'mfem~mpi~metis~gzstream'
+    'mfem+mpi+superlu-dist+suite-sparse+petsc \
+        +sundials+pumi+mpfr+netcdf+gzstream+gnutls+libunwind \
+        ^hypre~internal-superlu ^petsc+suite-sparse+mumps'
+    'mfem~mpi+suite-sparse+sundials+mpfr+netcdf \
+        +gzstream+gnutls+libunwind'
+    # develop version:
+    'mfem@develop+shared~static'
+    'mfem@develop+shared~static~mpi~metis~gzstream'
+    # TODO: Replace '^conduit~python~hdf5' with '^conduit~python' when conduit
+    # is fixed to accept '^hdf5+mpi'.
+    # NOTE: Skip PUMI since it conflicts with '+shared'.
+    'mfem@develop+shared~static+mpi \
+        +superlu-dist+suite-sparse+petsc+sundials+mpfr+netcdf+gzstream \
+        +gnutls+libunwind+conduit ^hypre~internal-superlu \
+        ^petsc+suite-sparse+mumps ^conduit~python~hdf5'
+    # TODO: The options '^netcdf~mpi ^hdf5@1.8.19~mpi' are added just to make
+    # conduit happy.
+    'mfem@develop+shared~static~mpi \
+        +suite-sparse+sundials+mpfr+netcdf+gzstream+gnutls+libunwind \
+        +conduit ^conduit~python ^netcdf~mpi ^hdf5@1.8.19~mpi'
+)
+
+builds2=(
+    # preferred version
+    'mfem+superlu-dist'
+    'mfem+suite-sparse~mpi'
+    'mfem+suite-sparse'
+    'mfem+sundials~mpi'
+    'mfem+sundials'
+    'mfem+pumi'
+    'mfem+netcdf~mpi'
+    'mfem+netcdf'
+    'mfem+mpfr'
+    'mfem+gnutls'
+    'mfem+petsc+mpi ^hypre~internal-superlu ^petsc+suite-sparse+mumps'
+    # develop version
+    'mfem@develop+superlu-dist'
+    'mfem@develop+suite-sparse~mpi'
+    'mfem@develop+suite-sparse'
+    'mfem@develop+sundials~mpi'
+    'mfem@develop+sundials'
+    'mfem@develop+pumi'
+    'mfem@develop+netcdf~mpi'
+    'mfem@develop+netcdf'
+    'mfem@develop+mpfr'
+    'mfem@develop+gnutls'
+    'mfem@develop+conduit~mpi ^conduit~python'
+    'mfem@develop+conduit ^conduit~python'
+    'mfem@develop+petsc+mpi ^hypre~internal-superlu \
+        ^petsc+suite-sparse+mumps'
+)
+
+trap 'printf "\nScript interrupted.\n"; exit 33' INT
+
+SEP='=========================================================================='
+sep='--------------------------------------------------------------------------'
+
+for bld in "${builds[@]}" "${builds2[@]}"; do
+    printf "\n%s\n" "${SEP}"
+    printf "    %s\n" "${bld}"
+    printf "%s\n" "${SEP}"
+    eval bbb="\"${bld}\""
+    spack spec -I $bbb || exit 1
+    printf "%s\n" "${sep}"
+    spack install --test=root $bbb || exit 2
+done
+
+# Uninstall all mfem builds:
+# spack uninstall --all mfem
diff --git a/var/spack/repos/builtin/packages/microbiomeutil/package.py b/var/spack/repos/builtin/packages/microbiomeutil/package.py
index 319148f71d..64952c6165 100644
--- a/var/spack/repos/builtin/packages/microbiomeutil/package.py
+++ b/var/spack/repos/builtin/packages/microbiomeutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/minced/package.py b/var/spack/repos/builtin/packages/minced/package.py
new file mode 100644
index 0000000000..c237ad2737
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minced/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Minced(Package):
+    """MinCED is a program to find Clustered Regularly Interspaced Short
+    Palindromic Repeats (CRISPRs) in full genomes or environmental datasets
+    such as metagenomes, in which sequence size can be anywhere from 100 to
+    800 bp."""
+
+    homepage = "https://github.com/ctSkennerton/minced"
+    url      = "https://github.com/ctSkennerton/minced/archive/0.2.0.tar.gz"
+
+    version('0.2.0', '32544f5a523f10fece6a127699e11245')
+
+    depends_on('java', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        make()
+        install('minced', prefix)
+        install('minced.jar', prefix)
diff --git a/var/spack/repos/builtin/packages/mindthegap/package.py b/var/spack/repos/builtin/packages/mindthegap/package.py
new file mode 100644
index 0000000000..11dbdb8ac5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mindthegap/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mindthegap(CMakePackage):
+    """MindTheGap is a software that performs integrated detection and
+       assembly of genomic insertion variants in NGS read datasets with
+       respect to a reference genome."""
+
+    homepage = "https://gatb.inria.fr/software/mind-the-gap/"
+    git      = "https://github.com/GATB/MindTheGap.git"
+
+    version('2.0.2', tags='v2.0.2', submodules=True)
+
+    depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/miniaero/package.py b/var/spack/repos/builtin/packages/miniaero/package.py
index da1421963f..46907a0fc8 100644
--- a/var/spack/repos/builtin/packages/miniaero/package.py
+++ b/var/spack/repos/builtin/packages/miniaero/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,12 +13,11 @@ class Miniaero(MakefilePackage):
     """
 
     homepage = "http://mantevo.org"
-    url      = "https://github.com/Mantevo/miniAero.git"
+    git      = "https://github.com/Mantevo/miniAero.git"
 
     tags = ['proxy-app']
 
-    version('2016-11-11', git='https://github.com/Mantevo/miniAero.git',
-            commit='f46d135479a5be19ec5d146ccaf0e581aeff4596')
+    version('2016-11-11', commit='f46d135479a5be19ec5d146ccaf0e581aeff4596')
 
     depends_on('kokkos')
 
diff --git a/var/spack/repos/builtin/packages/miniamr/package.py b/var/spack/repos/builtin/packages/miniamr/package.py
index 1740ab461c..0a0147e50e 100644
--- a/var/spack/repos/builtin/packages/miniamr/package.py
+++ b/var/spack/repos/builtin/packages/miniamr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,10 +13,11 @@ class Miniamr(MakefilePackage):
     """
 
     homepage = "https://mantevo.org"
-    url      = "https://github.com/Mantevo/miniAMR/archive/v1.4.tar.gz"
+    url      = "https://github.com/Mantevo/miniAMR/archive/v1.4.0.tar.gz"
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
+    version('1.4.1', sha256='dd8e8d9fd0768cb4f2c5d7fe6989dfa6bb95a8461f04deaccdbb50b0dd51e97a')
     version('1.4.0', '3aab0247047a94e343709cf2e51cc46e')
 
     variant('mpi', default=True, description='Build with MPI support')
@@ -59,8 +41,8 @@ class Miniamr(MakefilePackage):
     def install(self, spec, prefix):
         # Manual installation
         mkdir(prefix.bin)
-        mkdir(prefix.doc)
+        mkdir(prefix.docs)
 
         install('ref/ma.x', prefix.bin)
         # Install Support Documents
-        install('ref/README', prefix.doc)
+        install('ref/README', prefix.docs)
diff --git a/var/spack/repos/builtin/packages/miniasm/package.py b/var/spack/repos/builtin/packages/miniasm/package.py
new file mode 100644
index 0000000000..8c32b90555
--- /dev/null
+++ b/var/spack/repos/builtin/packages/miniasm/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Miniasm(MakefilePackage):
+    """Miniasm is a very fast OLC-based de novo assembler for noisy long
+    reads."""
+
+    homepage = "http://www.example.co://github.com/lh3/miniasm"
+    git      = "https://github.com/lh3/miniasm.git"
+
+    version('2018-3-30', commit='55cf0189e2f7d5bda5868396cebe066eec0a9547')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/miniconda2/package.py b/var/spack/repos/builtin/packages/miniconda2/package.py
index 7433b2d731..c5c5fb3f40 100644
--- a/var/spack/repos/builtin/packages/miniconda2/package.py
+++ b/var/spack/repos/builtin/packages/miniconda2/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from six.moves.urllib.parse import urlparse
 from os.path import split
 
 
@@ -33,12 +13,15 @@ class Miniconda2(Package):
     homepage = "https://conda.io/miniconda.html"
     url      = "https://repo.continuum.io/miniconda/Miniconda2-4.3.11-Linux-x86_64.sh"
 
+    version('4.5.11', sha256='0e23e8d0a1a14445f78960a66b363b464b889ee3b0e3f275b7ffb836df1cb0c6', expand=False)
+    version('4.5.4', '8a1c02f6941d8778f8afad7328265cf5', expand=False)
+    version('4.3.30', 'bd1655b4b313f7b2a1f2e15b7b925d03', expand=False)
     version('4.3.14', '8cb075cf5462480980ef2373ad9fad38', expand=False)
     version('4.3.11', 'd573980fe3b5cdf80485add2466463f5', expand=False)
 
     def install(self, spec, prefix):
-        # peel the name of the script out of the url
-        result = urlparse(self.url)
-        dir, script = split(result.path)
+        # peel the name of the script out of the pathname of the
+        # downloaded file
+        dir, script = split(self.stage.archive_file)
         bash = which('bash')
         bash(script, '-b', '-f', '-p', self.prefix)
diff --git a/var/spack/repos/builtin/packages/miniconda3/package.py b/var/spack/repos/builtin/packages/miniconda3/package.py
index faaa786b6c..cf47b424c5 100644
--- a/var/spack/repos/builtin/packages/miniconda3/package.py
+++ b/var/spack/repos/builtin/packages/miniconda3/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from six.moves.urllib.parse import urlparse
 from os.path import split
 
 
@@ -33,12 +13,15 @@ class Miniconda3(Package):
     homepage = "https://conda.io/miniconda.html"
     url      = "https://repo.continuum.io/miniconda/Miniconda3-4.3.11-Linux-x86_64.sh"
 
+    version('4.5.11', sha256='ea4594241e13a2671c5b158b3b813f0794fe58d514795fbf72a1aad24db918cf', expand=False)
+    version('4.5.4', 'a946ea1d0c4a642ddf0c3a26a18bb16d', expand=False)
+    version('4.3.30', '0b80a152332a4ce5250f3c09589c7a81', expand=False)
     version('4.3.14', 'fc6fc37479e3e3fcf3f9ba52cae98991', expand=False)
     version('4.3.11', '1924c8d9ec0abf09005aa03425e9ab1a', expand=False)
 
     def install(self, spec, prefix):
-        # peel the name of the script out of the url
-        result = urlparse(self.url)
-        dir, script = split(result.path)
+        # peel the name of the script out of the pathname of the
+        # downloaded file
+        dir, script = split(self.stage.archive_file)
         bash = which('bash')
         bash(script, '-b', '-f', '-p', self.prefix)
diff --git a/var/spack/repos/builtin/packages/minife/package.py b/var/spack/repos/builtin/packages/minife/package.py
index 0757a8c6db..00279455d3 100644
--- a/var/spack/repos/builtin/packages/minife/package.py
+++ b/var/spack/repos/builtin/packages/minife/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/minighost/package.py b/var/spack/repos/builtin/packages/minighost/package.py
index f397306645..c4cf78f5a9 100644
--- a/var/spack/repos/builtin/packages/minighost/package.py
+++ b/var/spack/repos/builtin/packages/minighost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import tarfile
 
@@ -54,17 +35,16 @@ class Minighost(MakefilePackage):
         if '+mpi' in self.spec:
             targets.append('PROTOCOL=-D_MG_MPI')
             targets.append('FC={0}'.format(self.spec['mpi'].mpif77))
-            targets.append('CC={0}'.format(self.spec['mpi'].mpicc))
-            targets.append(
-                'LIBS=-lm -lgfortran -lmpi_usempi -lmpi_mpifh -lmpi')
+            # CC is only used for linking, use it to pull in the right f77 libs
+            targets.append('CC={0}'.format(self.spec['mpi'].mpif77))
         else:
             targets.append('PROTOCOL=-D_MG_SERIAL')
             targets.append('FC=f77')
             targets.append('CC=cc')
-            targets.append('LIBS=-lm -lgfortran')
 
         if '%gcc' in self.spec:
             targets.append('COMPILER_SUITE=gnu')
+            targets.append('LIBS=-lm -lgfortran')
         elif '%cce' in self.spec:
             targets.append('COMPILER_SUITE=cray')
         elif '%intel' in self.spec:
diff --git a/var/spack/repos/builtin/packages/minigmg/package.py b/var/spack/repos/builtin/packages/minigmg/package.py
index 8cbd35faff..730ae4df5c 100644
--- a/var/spack/repos/builtin/packages/minigmg/package.py
+++ b/var/spack/repos/builtin/packages/minigmg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/minimap2/package.py b/var/spack/repos/builtin/packages/minimap2/package.py
index 17abaaeafa..92da1ac170 100644
--- a/var/spack/repos/builtin/packages/minimap2/package.py
+++ b/var/spack/repos/builtin/packages/minimap2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/minimd/package.py b/var/spack/repos/builtin/packages/minimd/package.py
index a9a6d90aa2..34192f64d2 100644
--- a/var/spack/repos/builtin/packages/minimd/package.py
+++ b/var/spack/repos/builtin/packages/minimd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import glob
 import tarfile
diff --git a/var/spack/repos/builtin/packages/miniqmc/package.py b/var/spack/repos/builtin/packages/miniqmc/package.py
new file mode 100644
index 0000000000..f243b6a8fb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/miniqmc/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Miniqmc(CMakePackage):
+    """A simplified real space QMC code for algorithm development,
+       performance portability testing, and computer science experiments
+    """
+
+    homepage = "https://github.com/QMCPACK/miniqmc"
+    url      = "https://github.com/QMCPACK/miniqmc/archive/0.2.0.tar.gz"
+
+    version('0.4.0', sha256='41ddb5de6dcc85404344c80dc7538aedf5e1f1eb0f2a67ebac069209f7dd11e4')
+    version('0.3.0', sha256='3ba494ba1055df91e157cb426d1fbe4192aa3f04b019277d9e571d057664d5a9')
+    version('0.2.0', 'b96bacaf48b8e9c0de05d04a95066bc1')
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    depends_on('mpi')
+    depends_on('lapack')
+
+    def cmake_args(self):
+        args = [
+            '-DCMAKE_CXX_COMPILER=%s' % self.spec['mpi'].mpicxx,
+            '-DCMAKE_C_COMPILER=%s' % self.spec['mpi'].mpicc
+        ]
+        return args
+
+    def install(self, spec, prefix):
+        install_tree(join_path('spack-build', 'bin'), prefix.bin)
+        install_tree(join_path('spack-build', 'lib'), prefix.lib)
diff --git a/var/spack/repos/builtin/packages/minisign/package.py b/var/spack/repos/builtin/packages/minisign/package.py
new file mode 100755
index 0000000000..a380fedd15
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minisign/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Minisign(CMakePackage):
+    """Minisign is a dead simple tool to sign files and verify signatures."""
+
+    homepage = "https://jedisct1.github.io/minisign/"
+    url = "https://github.com/jedisct1/minisign/archive/0.7.tar.gz"
+
+    version('0.7', 'd634202555c4f499e8ef9d6848d6f4ca')
+
+    depends_on('libsodium')
diff --git a/var/spack/repos/builtin/packages/minismac2d/package.py b/var/spack/repos/builtin/packages/minismac2d/package.py
index 4e961fac94..e793337868 100644
--- a/var/spack/repos/builtin/packages/minismac2d/package.py
+++ b/var/spack/repos/builtin/packages/minismac2d/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -49,7 +30,7 @@ class Minismac2d(MakefilePackage):
             'CPP=cpp',
             'FC={0}'.format(self.spec['mpi'].mpifc),
             'LD={0}'.format(self.spec['mpi'].mpifc),
-            'MPIDIR=-I{0}/include'.format(self.spec['mpi'].prefix),
+            'MPIDIR=-I{0}'.format(self.spec['mpi'].headers.directories[0]),
             'CPPFLAGS=-P -traditional  -DD_PRECISION',
             'FFLAGS=-O3 -c -g -DD_PRECISION',
             'LDFLAGS=-O3',
diff --git a/var/spack/repos/builtin/packages/minitri/package.py b/var/spack/repos/builtin/packages/minitri/package.py
index 6451a8b86a..570d4b44a4 100644
--- a/var/spack/repos/builtin/packages/minitri/package.py
+++ b/var/spack/repos/builtin/packages/minitri/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/minivite/package.py b/var/spack/repos/builtin/packages/minivite/package.py
new file mode 100644
index 0000000000..f39a6f4f5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minivite/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Minivite(MakefilePackage):
+    """miniVite is a proxy application that implements a single phase of
+       Louvain method in distributed memory for graph community detection.
+    """
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "http://hpc.pnl.gov/people/hala/grappolo.html"
+    git      = "https://github.com/Exa-Graph/miniVite.git"
+
+    version('develop', branch='master')
+    version('1.0', tag='v1.0')
+
+    variant('openmp', default=True, description='Build with OpenMP support')
+    variant('opt', default=True, description='Optimization flags')
+
+    depends_on('mpi')
+
+    @property
+    def build_targets(self):
+        targets = []
+        cxxflags = ['-std=c++11 -g -DCHECK_NUM_EDGES -DPRINT_EXTRA_NEDGES']
+        ldflags = []
+
+        if '+openmp' in self.spec:
+            cxxflags.append(self.compiler.openmp_flag)
+            ldflags.append(self.compiler.openmp_flag)
+        if '+opt' in self.spec:
+            cxxflags.append(' -O3 ')
+
+        targets.append('CXXFLAGS={0}'.format(' '.join(cxxflags)))
+        targets.append('OPTFLAGS={0}'.format(' '.join(ldflags)))
+        targets.append('CXX={0}'.format(self.spec['mpi'].mpicxx))
+
+        return targets
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('dspl', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/minixyce/package.py b/var/spack/repos/builtin/packages/minixyce/package.py
index 6273838f7e..b014203cc5 100644
--- a/var/spack/repos/builtin/packages/minixyce/package.py
+++ b/var/spack/repos/builtin/packages/minixyce/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/minuit/LASymMatrix.h.patch b/var/spack/repos/builtin/packages/minuit/LASymMatrix.h.patch
new file mode 100644
index 0000000000..645d2ccd35
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minuit/LASymMatrix.h.patch
@@ -0,0 +1,117 @@
+commit 62772d5fb0c6c7661c7acaa73d21de4205579d73
+Author: Paul Chelarescu <paulchelarescu@gmail.com>
+Date:   Fri Jun 22 15:34:20 2018 +0200
+
+    Patched LASymMatrix.h
+
+diff --git a/Minuit/LASymMatrix.h b/Minuit/LASymMatrix.h
+index 755eb11..976c0de 100644
+--- a/Minuit/LASymMatrix.h
++++ b/Minuit/LASymMatrix.h
+@@ -16,6 +16,7 @@
+ // #include <iostream>
+ 
+ #include "Minuit/StackAllocator.h"
++#include <cstring>
+ //extern StackAllocator StackAllocatorHolder::get();
+ 
+ int mndaxpy(unsigned int, double, const double*, int, double*, int);
+@@ -37,7 +38,7 @@ public:
+ 
+   LASymMatrix(unsigned int n) : theSize(n*(n+1)/2), theNRow(n), theData((double*)StackAllocatorHolder::get().allocate(sizeof(double)*n*(n+1)/2)) {
+ //     assert(theSize>0);
+-    memset(theData, 0, theSize*sizeof(double));
++    std::memset(theData, 0, theSize*sizeof(double));
+ //     std::cout<<"LASymMatrix(unsigned int n), n= "<<n<<std::endl;
+   }
+ 
+@@ -52,7 +53,7 @@ public:
+   LASymMatrix(const LASymMatrix& v) : 
+     theSize(v.size()), theNRow(v.nrow()), theData((double*)StackAllocatorHolder::get().allocate(sizeof(double)*v.size())) {
+ //     std::cout<<"LASymMatrix(const LASymMatrix& v)"<<std::endl;
+-    memcpy(theData, v.data(), theSize*sizeof(double));
++    std::memcpy(theData, v.data(), theSize*sizeof(double));
+   }
+ 
+   LASymMatrix& operator=(const LASymMatrix& v) {
+@@ -60,7 +61,7 @@ public:
+ //     std::cout<<"theSize= "<<theSize<<std::endl;
+ //     std::cout<<"v.size()= "<<v.size()<<std::endl;
+     assert(theSize == v.size());
+-    memcpy(theData, v.data(), theSize*sizeof(double));
++    std::memcpy(theData, v.data(), theSize*sizeof(double));
+     return *this;
+   }
+ 
+@@ -69,7 +70,7 @@ public:
+     theSize(v.obj().size()), theNRow(v.obj().nrow()), theData((double*)StackAllocatorHolder::get().allocate(sizeof(double)*v.obj().size())) {
+ //     std::cout<<"LASymMatrix(const ABObj<sym, LASymMatrix, T>& v)"<<std::endl;
+     //std::cout<<"allocate "<<theSize<<std::endl;    
+-    memcpy(theData, v.obj().data(), theSize*sizeof(double));
++    std::memcpy(theData, v.obj().data(), theSize*sizeof(double));
+     mndscal(theSize, double(v.f()), theData, 1);
+     //std::cout<<"theData= "<<theData[0]<<" "<<theData[1]<<std::endl;
+   } 
+@@ -105,7 +106,7 @@ public:
+ 
+   template<class T>
+   LASymMatrix(const ABObj<sym, MatrixInverse<sym, ABObj<sym, LASymMatrix, T>, T>, T>& inv) : theSize(inv.obj().obj().obj().size()), theNRow(inv.obj().obj().obj().nrow()), theData((double*)StackAllocatorHolder::get().allocate(sizeof(double)*inv.obj().obj().obj().size())) {
+-    memcpy(theData, inv.obj().obj().obj().data(), theSize*sizeof(double));
++    std::memcpy(theData, inv.obj().obj().obj().data(), theSize*sizeof(double));
+     mndscal(theSize, double(inv.obj().obj().f()), theData, 1);
+     invert(*this);
+     mndscal(theSize, double(inv.f()), theData, 1);
+@@ -236,7 +237,7 @@ public:
+       assert(theSize == v.obj().size());
+     }
+     //std::cout<<"theData= "<<theData[0]<<" "<<theData[1]<<std::endl;
+-    memcpy(theData, v.obj().data(), theSize*sizeof(double));
++    std::memcpy(theData, v.obj().data(), theSize*sizeof(double));
+     (*this) *= v.f();
+     return *this;
+   }
+@@ -251,7 +252,7 @@ public:
+       LASymMatrix tmp(something.obj());
+       tmp *= something.f();
+       assert(theSize == tmp.size());
+-      memcpy(theData, tmp.data(), theSize*sizeof(double)); 
++      std::memcpy(theData, tmp.data(), theSize*sizeof(double)); 
+     }
+     //std::cout<<"template<class A, class T> LASymMatrix& operator=(const ABObj<sym, ABObj<sym, A, T>, T>& something)"<<std::endl;
+     return *this;
+@@ -270,7 +271,7 @@ public:
+       tmp += sum.obj().b();
+       tmp *= sum.f();
+       assert(theSize == tmp.size());
+-      memcpy(theData, tmp.data(), theSize*sizeof(double));
++      std::memcpy(theData, tmp.data(), theSize*sizeof(double));
+     }
+     return *this;
+   }
+@@ -290,7 +291,7 @@ public:
+       tmp += sum.obj().a();
+       tmp *= sum.f();
+       assert(theSize == tmp.size());
+-      memcpy(theData, tmp.data(), theSize*sizeof(double));
++      std::memcpy(theData, tmp.data(), theSize*sizeof(double));
+     }
+     //std::cout<<"leaving LASymMatrix& operator=(const ABObj<sym, ABSum<ABObj<sym, LASymMatrix..."<<std::endl;
+     return *this;
+@@ -302,7 +303,7 @@ public:
+       theSize = inv.obj().obj().obj().size();
+       theNRow = inv.obj().obj().obj().nrow();
+       theData = (double*)StackAllocatorHolder::get().allocate(sizeof(double)*theSize);
+-      memcpy(theData, inv.obj().obj().obj().data(), theSize*sizeof(double));
++      std::memcpy(theData, inv.obj().obj().obj().data(), theSize*sizeof(double));
+       (*this) *= inv.obj().obj().f();
+       invert(*this);
+       (*this) *= inv.f();
+@@ -311,7 +312,7 @@ public:
+       invert(tmp);
+       tmp *= double(inv.f());
+       assert(theSize == tmp.size());
+-      memcpy(theData, tmp.data(), theSize*sizeof(double));
++      std::memcpy(theData, tmp.data(), theSize*sizeof(double));
+     }
+     return *this;
+   }
diff --git a/var/spack/repos/builtin/packages/minuit/package.py b/var/spack/repos/builtin/packages/minuit/package.py
new file mode 100644
index 0000000000..54b4644866
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minuit/package.py
@@ -0,0 +1,47 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Minuit(AutotoolsPackage):
+    """MINUIT is a physics analysis tool for function minimization."""
+
+    homepage = "https://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/home.html"
+    url      = "http://www.cern.ch/mathlibs/sw/5_34_14/Minuit2/Minuit2-5.34.14.tar.gz"
+    list_url = "https://seal.web.cern.ch/seal/snapshot/work-packages/mathlibs/minuit/release/download.html"
+
+    version('5.34.14', '7fc00378a2ed1f731b719d4837d62d6a')
+    version('5.28.00', '536a1d29e5cc9bd4499d17d665021370')
+    version('5.27.02', 'b54673f2b9b62a8ff4e6937a2ed8fda5')
+    version('5.24.00', '9a915e56bee1e8986a719aa80e7b05d6')
+    version('5.22.00', '2cbc34907bfe202c7a779e9713355846')
+    version('5.21.06', 'b431ed129abb6c5020fd58d53cb8d27c')
+    version('5.20.00', '3083d31e3764de45d477d082d60f2c29')
+    version('5.18.00', 'a8764e7213fe811e56d5b6e5f3a91f5e')
+    version('5.16.00', '6ea5feca06fca365d324bcfe16db7f08')
+    version('5.14.00', 'b7452867b01c76cd115c696336c202d2')
+    version('5.12.00', '36726b8c6fcddf4f0837c900461a1d3c')
+    version('5.10.00', 'dfc7afc0add70deaca105ff549f5a786')
+    version('5.08.00', '1cc8da07c4a247c877f39acf8d76ba02')
+    version('1.7.9', '10fd518fc778317fdadbc4ef6f7ce8e4')
+    version('1.7.6', '6a9a8341557de154274caff810686364')
+    version('1.7.1', 'd202a1cf58662e9833f2967b4dc8808e')
+    version('1.6.3', '955f560d0fb17bd7f081eddd7080fad6')
+    version('1.6.0', '6992d70fc8fded50be49b6b358b58507')
+    version('1.5.2', '31a0698febe59edd70aa001c4d7a56f8')
+    version('1.5.0', 'bc502c66af071fcdc0a2ae45a8740c75')
+
+    def url_for_version(self, version):
+        if version > Version('5.0.0'):
+            url = "http://www.cern.ch/mathlibs/sw/{0}/Minuit2/Minuit2-{1}.tar.gz"
+            return url.format(version.underscored, version)
+        else:
+            url = "http://seal.web.cern.ch/seal/minuit/releases/Minuit-{0}.tar.gz"
+            return url.format(version.underscored)
+
+    patch('sprintf.cxx.patch', when='@5.08.00:5.18.00')
+    patch('sprintf.patch', when='@:1.7.9')
+    patch('LASymMatrix.h.patch', when='@:1.7.6')
diff --git a/var/spack/repos/builtin/packages/minuit/sprintf.cxx.patch b/var/spack/repos/builtin/packages/minuit/sprintf.cxx.patch
new file mode 100644
index 0000000000..f6bf81cbc3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minuit/sprintf.cxx.patch
@@ -0,0 +1,10 @@
+--- a/src/MnUserTransformation.cxx	2008-01-17 15:05:38.000000000 +0100
++++ b/src/MnUserTransformation.cxx	2018-06-22 13:44:02.629389848 +0200
+@@ -11,6 +11,7 @@
+ #include "Minuit2/MnUserCovariance.h"
+ 
+ #include <algorithm>
++#include <cstdio>
+ 
+ namespace ROOT {
+ 
diff --git a/var/spack/repos/builtin/packages/minuit/sprintf.patch b/var/spack/repos/builtin/packages/minuit/sprintf.patch
new file mode 100644
index 0000000000..be49ed772a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/minuit/sprintf.patch
@@ -0,0 +1,10 @@
+--- a/src/MnUserTransformation.cpp	2018-06-22 11:35:34.476798087 +0200
++++ b/src/MnUserTransformation.cpp	2018-06-22 11:08:01.729725829 +0200
+@@ -2,6 +2,7 @@
+ #include "Minuit/MnUserCovariance.h"
+ 
+ #include <algorithm>
++#include <cstdio>
+ 
+ class MnParStr {
+ 
diff --git a/var/spack/repos/builtin/packages/mira/package.py b/var/spack/repos/builtin/packages/mira/package.py
new file mode 100644
index 0000000000..f842ed8860
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mira/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mira(AutotoolsPackage):
+    """MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome
+       and EST/RNASeq projects."""
+
+    homepage = "http://sourceforge.net/projects/mira-assembler/"
+    url      = "https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2"
+
+    version('4.0.2', '1921b426910653a34a6dbb37346f28ea')
+
+    depends_on('boost@1.46:')
+    depends_on('expat@2.0.1:')
+    depends_on('gperftools')
+
+    conflicts('%gcc@6:', when='@:4.0.2')
+
+    def patch(self):
+        with working_dir(join_path('src', 'progs')):
+            edit = FileFilter('quirks.C')
+            edit.filter('#include <boost/filesystem.hpp>',
+                        '#include <boost/filesystem.hpp>\n#include <iostream>')
+
+    def configure_args(self):
+        args = ['--with-boost=%s' % self.spec['boost'].prefix,
+                '--with-expat=%s' % self.spec['expat'].prefix]
+        return args
diff --git a/var/spack/repos/builtin/packages/mirdeep/package.py b/var/spack/repos/builtin/packages/mirdeep/package.py
deleted file mode 100644
index 28981eade5..0000000000
--- a/var/spack/repos/builtin/packages/mirdeep/package.py
+++ /dev/null
@@ -1,67 +0,0 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 glob
-
-
-class Mirdeep(Package):
-    """miRDeep2 is a completely overhauled tool which discovers microRNA genes
-       by analyzing sequenced RNAs."""
-
-    homepage = "https://www.mdc-berlin.de/8551903/en/"
-    url      = "https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep2_0_0_8.zip"
-
-    version('2.0.0.8', 'a707f7d7ad4a2975fb8b2e78c5bcf483')
-
-    depends_on('perl', type=('build', 'run'))
-    depends_on('perl-pdf-api2', type=('build', 'run'))
-    depends_on('bowtie')
-    depends_on('viennarna')
-    depends_on('squid')
-    depends_on('randfold')
-
-    def url_for_version(self, version):
-        url = 'https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep{0}.zip'
-        return url.format(version.underscored)
-
-    def patch(self):
-        with working_dir('src'):
-            files = glob.iglob("*.pl")
-            for file in files:
-                change = FileFilter(file)
-                change.filter('usr/bin/perl', 'usr/bin/env perl')
-                change.filter('perl -W', 'perl')
-                change.filter("../Rfam_for_miRDeep.fa",
-                              "Rfam_for_miRDeep.fa")
-                change.filter("../install_successful",
-                              "install_successful")
-
-    def install(self, spec, prefix):
-        install_tree('src', prefix.bin)
-        install('Rfam_for_miRDeep.fa', prefix.bin)
-        # miRDeep looks for the install_sucessful file to check if you used
-        # their automated install script which we'll just be kind of hacking
-        # around
-        touch(prefix.bin.install_successful)
diff --git a/var/spack/repos/builtin/packages/mirdeep2/package.py b/var/spack/repos/builtin/packages/mirdeep2/package.py
new file mode 100644
index 0000000000..cf85705750
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mirdeep2/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Mirdeep2(Package):
+    """miRDeep2 is a completely overhauled tool which discovers microRNA genes
+       by analyzing sequenced RNAs."""
+
+    homepage = "https://www.mdc-berlin.de/8551903/en/"
+    url      = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_0_0_8.zip"
+
+    version('0.0.8', 'a707f7d7ad4a2975fb8b2e78c5bcf483')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('perl-pdf-api2', type=('build', 'run'))
+    depends_on('bowtie')
+    depends_on('viennarna')
+    depends_on('squid')
+    depends_on('randfold')
+
+    def url_for_version(self, version):
+        url = 'https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_{0}.zip'
+        return url.format(version.underscored)
+
+    def patch(self):
+        with working_dir('src'):
+            files = glob.iglob("*.pl")
+            for file in files:
+                change = FileFilter(file)
+                change.filter('usr/bin/perl', 'usr/bin/env perl')
+                change.filter('perl -W', 'perl')
+                change.filter("../Rfam_for_miRDeep.fa",
+                              "Rfam_for_miRDeep.fa")
+                change.filter("../install_successful",
+                              "install_successful")
+
+    def install(self, spec, prefix):
+        install_tree('src', prefix.bin)
+        install('Rfam_for_miRDeep.fa', prefix.bin)
+        # miRDeep looks for the install_sucessful file to check if you used
+        # their automated install script which we'll just be kind of hacking
+        # around
+        touch(prefix.bin.install_successful)
diff --git a/var/spack/repos/builtin/packages/mitofates/DirichletRegulator_fast.patch b/var/spack/repos/builtin/packages/mitofates/DirichletRegulator_fast.patch
new file mode 100644
index 0000000000..85e836878e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mitofates/DirichletRegulator_fast.patch
@@ -0,0 +1,13 @@
+--- a/bin/modules/DirichletRegulator_fast.pm	2014-10-23 01:59:55.000000000 -0500
++++ b/bin/modules/DirichletRegulator_fast.pm	2018-07-11 11:19:07.814358134 -0500
+@@ -10,9 +10,7 @@
+ use strict;
+ use warnings;
+ use FindBin qw($Bin);
+-use Inline (Config => 
+-	      DIRECTORY => "$Bin/modules/_Inline/",
+-            );
++use Inline;
+ use Inline 'C';
+ 
+ # Sub-routin: DirichletParser
diff --git a/var/spack/repos/builtin/packages/mitofates/package.py b/var/spack/repos/builtin/packages/mitofates/package.py
index 0ba5535b3d..beefab38e1 100644
--- a/var/spack/repos/builtin/packages/mitofates/package.py
+++ b/var/spack/repos/builtin/packages/mitofates/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import glob
 
 
 class Mitofates(Package):
@@ -35,7 +17,33 @@ class Mitofates(Package):
     version('1.2', 'aaac42a8e8c7318a4abde9df3a4b72d1')
 
     depends_on('libsvm')
+    depends_on('perl', type='run')
+    depends_on('perl-inline-c', type='run')
+    depends_on('perl-perl6-slurp', type='run')
+    depends_on('perl-math-cephes', type='run')
+
+    # The DirichletRegulator_fast.pm sets the perl Inline directory
+    # to be inside the deployed source (which won't be writable by
+    # the end user of site wide deployed software.
+    # Removing that config entry will cause the inline module to auto
+    # create a directory in the user's homedir instead
+    patch('DirichletRegulator_fast.patch')
+
+    def patch(self):
+        perlscripts = FileFilter('MitoFates.pl')
+        perlscripts.filter('#!/usr/bin/perl', '#!/usr/bin/env perl')
+
+        # other perl module files probably should get this filter too
+        with working_dir(join_path(self.stage.source_path, 'bin/modules')):
+            perlmodules = glob.glob('*.pm')
+            filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', *perlmodules)
 
     def install(self, spec, prefix):
         install_tree('bin', prefix.bin)
         install('MitoFates.pl', prefix)
+        chmod = which('chmod')
+        chmod('+x', join_path(prefix, 'MitoFates.pl'))
+
+    def setup_environment(self, spack_env, run_env):
+        # We want the main MitoFates.pl script in the path
+        run_env.prepend_path('PATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/mitos/package.py b/var/spack/repos/builtin/packages/mitos/package.py
index 1cc402590b..bfefd762e9 100644
--- a/var/spack/repos/builtin/packages/mitos/package.py
+++ b/var/spack/repos/builtin/packages/mitos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class Mitos(CMakePackage):
 
     homepage = "https://github.com/llnl/Mitos"
     url      = "https://github.com/LLNL/Mitos/archive/v0.9.1.tar.gz"
+    git      = "https://github.com/llnl/Mitos.git"
 
-    version('0.9.2',
-            git='https://github.com/llnl/Mitos.git',
-            commit='8cb143a2e8c00353ff531a781a9ca0992b0aaa3d')
+    version('0.9.2', commit='8cb143a2e8c00353ff531a781a9ca0992b0aaa3d')
     version('0.9.1', 'c6cb57f3cae54f5157affd97ef7ef79e')
 
     depends_on('dyninst@8.2.1:')
diff --git a/var/spack/repos/builtin/packages/mkfontdir/package.py b/var/spack/repos/builtin/packages/mkfontdir/package.py
index f1f12b514e..1a907d79ce 100644
--- a/var/spack/repos/builtin/packages/mkfontdir/package.py
+++ b/var/spack/repos/builtin/packages/mkfontdir/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Mkfontdir(AutotoolsPackage):
 
     depends_on('mkfontscale', type='run')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/mkfontscale/package.py b/var/spack/repos/builtin/packages/mkfontscale/package.py
index 9e8945f045..b1ad4f492c 100644
--- a/var/spack/repos/builtin/packages/mkfontscale/package.py
+++ b/var/spack/repos/builtin/packages/mkfontscale/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Mkfontscale(AutotoolsPackage):
     depends_on('freetype')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/mlhka/package.py b/var/spack/repos/builtin/packages/mlhka/package.py
index 85a23d5edd..303c868ba3 100644
--- a/var/spack/repos/builtin/packages/mlhka/package.py
+++ b/var/spack/repos/builtin/packages/mlhka/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class Mlhka(Package):
        and divergence data."""
 
     homepage = "https://wright.eeb.utoronto.ca"
-    url      = "https://github.com/rossibarra/MLHKA"
+    git      = "https://github.com/rossibarra/MLHKA.git"
 
-    version('2.1', git='https://github.com/rossibarra/MLHKA.git',
-            commit='e735ddd39073af58da21b00b27dea203736e5467')
+    version('2.1', commit='e735ddd39073af58da21b00b27dea203736e5467')
 
     def install(self, spec, prefix):
         cxx = which('c++')
diff --git a/var/spack/repos/builtin/packages/moab/package.py b/var/spack/repos/builtin/packages/moab/package.py
index 8e84f63b2c..0f7bad2143 100644
--- a/var/spack/repos/builtin/packages/moab/package.py
+++ b/var/spack/repos/builtin/packages/moab/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -60,6 +41,7 @@ class Moab(AutotoolsPackage):
     variant('irel', default=False, description='Enable irel interface')
     variant('fbigeom', default=False, description='Enable fbigeom interface')
     variant('coupler', default=True, description='Enable mbcoupler tool')
+    variant('dagmc', default=False, description='Enable dagmc tool')
 
     variant("debug", default=False, description='enable debug symbols')
     variant('shared', default=False,
@@ -80,6 +62,7 @@ class Moab(AutotoolsPackage):
     # depends_on('vtk', when='+vtk')
 
     depends_on('blas')
+    depends_on('lapack')
     depends_on('mpi', when='+mpi')
     depends_on('hdf5', when='+hdf5')
     depends_on('hdf5+mpi', when='+hdf5+mpi')
@@ -124,6 +107,9 @@ class Moab(AutotoolsPackage):
 #       else:
 #           options.append('--without-mpi')
 
+        options.append('--with-blas=%s' % spec['blas'].libs.ld_flags)
+        options.append('--with-lapack=%s' % spec['lapack'].libs.ld_flags)
+
         if '+hdf5' in spec:
             options.append('--with-hdf5=%s' % spec['hdf5'].prefix)
         else:
@@ -158,6 +144,11 @@ class Moab(AutotoolsPackage):
         else:
             options.append('--disable-mbcoupler')
 
+        if '+dagmc' in spec:
+            options.append('--enable-dagmc')
+        else:
+            options.append('--disable-dagmc')
+
         if '+metis' in spec:
             options.append('--with-metis=%s' % spec['metis'].prefix)
         else:
diff --git a/var/spack/repos/builtin/packages/modern-wheel/package.py b/var/spack/repos/builtin/packages/modern-wheel/package.py
new file mode 100644
index 0000000000..4e3b9b8322
--- /dev/null
+++ b/var/spack/repos/builtin/packages/modern-wheel/package.py
@@ -0,0 +1,45 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import sys
+
+
+class ModernWheel(CMakePackage):
+    """C++ utility collection. Provides various facilities of common use in
+    modern codebases like dynamic linking helpers, loadable plugins facilities
+    and misc patterns."""
+
+    homepage = "https://github.com/alalazo/modern_wheel"
+    url      = "https://github.com/alalazo/modern_wheel/archive/1.2.tar.gz"
+
+    version('1.2', 'dc440099c52b6af3b8ddff6fd7730aff')
+    version('1.1', '289455239ad19497b7db55aacb299ca8')
+    version('1.0', '503dc3e7da2b422c4295e4afcba09dfb')
+
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+    # Test implementation files cause some issues on darwin,
+    # needs to be investigated.
+    variant('test',   default=sys.platform != 'darwin',
+            description='Enables the build of unit tests')
+
+    # FindBoost shipped with CMake up to version 3.10.2 (latest one
+    # up to now) is known to be unable to detect Boost >= 1.66.0.
+    # This issue will be probably fixed in CMake >= 3.11.0:
+    # https://gitlab.kitware.com/cmake/cmake/issues/17575
+    # Until then, just assume that we cannot correctly configure
+    # ModernWheel with Boost >= 1.66.0.
+    depends_on('boost           +system +filesystem', when='@:1.1.999')
+    depends_on('boost@:1.65.999 +system +filesystem', when='@1.2:')
+
+    def cmake_args(self):
+        spec = self.spec
+        return [
+            '-DBUILD_UNIT_TEST:BOOL={0}'.format(
+                'ON' if '+test' in spec else 'OFF'),
+            '-DBUILD_SHARED_LIBS:BOOL={0}'.format(
+                'ON' if '+shared' in spec else 'OFF'),
+        ]
diff --git a/var/spack/repos/builtin/packages/mofem-cephas/package.py b/var/spack/repos/builtin/packages/mofem-cephas/package.py
new file mode 100644
index 0000000000..7ddacfb780
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-cephas/package.py
@@ -0,0 +1,81 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class MofemCephas(CMakePackage):
+    """mofem-cephas core library"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    git      = "https://bitbucket.org/likask/mofem-cephas.git"
+
+    maintainers = ['likask']
+
+    version('develop', branch='develop', submodules=True)
+    version('0.8.7', tag='v0.8.7', submodules=True)
+
+    # This option can be only used for development of core lib
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking to source')
+    variant('adol-c', default=True, description='Compile with Adol-C')
+    variant('tetgen', default=True, description='Compile with Tetgen')
+    variant('med', default=True, description='Compile with Med')
+    variant('slepc', default=False, description='Compile with Slepc')
+
+    depends_on("mpi")
+    depends_on("boost")
+    depends_on("parmetis")
+    # Fixed version of hdf5, to remove some problems with dependent
+    # packages, f.e. MED format
+    depends_on("hdf5@:1.8.19+hl+mpi")
+    depends_on("petsc@:3.9.2+mumps+mpi")
+    depends_on('slepc', when='+slepc')
+    depends_on("moab")
+    # Upper bound set to ADOL-C until issues with memory leaks
+    # for versions 2.6: fully resolved
+    depends_on("adol-c@2.5.2~examples", when="+adol-c")
+    depends_on("tetgen", when="+tetgen")
+    depends_on("med", when='+med')
+
+    extendable = True
+
+    root_cmakelists_dir = 'mofem'
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DPETSC_DIR=%s' % spec['petsc'].prefix,
+            '-DPETSC_ARCH=',
+            '-DMOAB_DIR=%s' % spec['moab'].prefix,
+            '-DBOOST_DIR=%s' % spec['boost'].prefix])
+
+        # build tests
+        options.append('-DMOFEM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        # variant packages
+        if '+adol-c' in spec:
+            options.append('-DADOL-C_DIR=%s' % spec['adol-c'].prefix)
+
+        if '+tetgen' in spec:
+            options.append('-DTETGEN_DIR=%s' % spec['tetgen'].prefix)
+
+        if '+med' in spec:
+            options.append('-DMED_DIR=%s' % spec['med'].prefix)
+
+        if '+slepc' in spec:
+            options.append('-DSLEPC_DIR=%s' % spec['slepc'].prefix)
+
+        # copy users modules, i.e. stand alone vs linked users modules
+        options.append(
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO'))
+        return options
diff --git a/var/spack/repos/builtin/packages/mofem-fracture-module/package.py b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py
new file mode 100644
index 0000000000..f573d7def1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-fracture-module/package.py
@@ -0,0 +1,87 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class MofemFractureModule(CMakePackage):
+    """mofem fracture module"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    git = "https://bitbucket.org/likask/mofem_um_fracture_mechanics.git"
+
+    maintainers = ['likask']
+
+    version('develop', branch='develop')
+    version('0.9.42', tag='v0.9.42')
+
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking')
+
+    extends('mofem-cephas')
+    depends_on("mofem-users-modules", type=('build', 'link', 'run'))
+
+    # The CMakeLists.txt installed with mofem-cephas package set cmake
+    # environment to install extension from extension repository. It searches
+    # for modules in user provides paths, for example in Spack source path.Also
+    # it finds all cmake exported targets installed in lib directory, which are
+    # built with dependent extensions, f.e.mofem - users - modules or others if
+    # needed.
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        spec = self.spec
+        return spec['mofem-cephas'].prefix.users_modules
+
+    def cmake_args(self):
+        spec = self.spec
+        source = self.stage.source_path
+
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DEXTERNAL_MODULES_BUILD=YES',
+            '-DUM_INSTALL_BREFIX=%s' % spec['mofem-users-modules'].prefix,
+            '-DEXTERNAL_MODULE_SOURCE_DIRS=%s' % source,
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO')])
+
+        # Set module version
+        if self.spec.version == Version('develop'):
+            options.extend([
+                '-DFM_VERSION_MAJOR=%s' % 0,
+                '-DFM_VERSION_MINOR=%s' % 0,
+                '-DFM_VERSION_BUILD=%s' % 0])
+        else:
+            options.extend([
+                '-DFM_VERSION_MAJOR=%s' % self.spec.version[0],
+                '-DFM_VERSION_MINOR=%s' % self.spec.version[1],
+                '-DFM_VERSION_BUILD=%s' % self.spec.version[2]])
+
+        # build tests
+        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        return options
+
+    # This function is not needed to run code installed by extension, nor in
+    # the install process. However for users like to have access to source code
+    # to play and make with it. Having source code at hand one can compile in
+    # own build directory it in mofem-cephas view when the extension is
+    # activated.
+    @run_after('install')
+    def copy_source_code(self):
+        source = self.stage.source_path
+        prefix = self.prefix
+        install_tree(source, prefix.ext_users_modules.fracture_mechanics)
diff --git a/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py
new file mode 100644
index 0000000000..b967a45e7f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-minimal-surface-equation/package.py
@@ -0,0 +1,75 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class MofemMinimalSurfaceEquation(CMakePackage):
+    """mofem minimal surface equation"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    git      = "https://bitbucket.org/likask/mofem_um_minimal_surface_equation.git"
+
+    maintainers = ['likask']
+
+    version('develop', branch='develop')
+    version('0.3.9', tag='v0.3.9')
+
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking')
+
+    extends('mofem-cephas')
+    depends_on("mofem-users-modules", type=('build', 'link', 'run'))
+
+    # The CMakeLists.txt installed with mofem - cephas package set cmake
+    # environment to install extension from extension repository.It searches
+    # for modules in user provides paths, for example in Spack source path.Also
+    # it finds all cmake exported targets installed in lib directory, which are
+    # built with dependent extensions, f.e.mofem - users - modules or others if
+    # needed.
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        spec = self.spec
+        return spec['mofem-cephas'].prefix.users_modules
+
+    def cmake_args(self):
+        spec = self.spec
+        source = self.stage.source_path
+
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DEXTERNAL_MODULES_BUILD=YES',
+            '-DUM_INSTALL_BREFIX=%s' % spec['mofem-users-modules'].prefix,
+            '-DEXTERNAL_MODULE_SOURCE_DIRS=%s' % source,
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO')])
+
+        # build tests
+        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        return options
+
+    # This function is not needed to run code installed by extension, nor in
+    # the install process. However for users like to have access to source code
+    # to play and make with it. Having source code at hand one can compile in
+    # own build directory it in mofem-cephas view when the extension is
+    # activated.
+    @run_after('install')
+    def copy_source_code(self):
+        source = self.stage.source_path
+        prefix = self.prefix
+        install_tree(source, prefix.ext_users_modules.minimal_surface_equation)
diff --git a/var/spack/repos/builtin/packages/mofem-users-modules/package.py b/var/spack/repos/builtin/packages/mofem-users-modules/package.py
new file mode 100644
index 0000000000..8ddec392d0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mofem-users-modules/package.py
@@ -0,0 +1,66 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class MofemUsersModules(CMakePackage):
+    """MofemUsersModules creates installation environment for user-provided
+    modules and extends of mofem-cephas package. The CMakeList.txt file for
+    user modules is located in mofem-cephas/user_modules prefix.
+    MofemUsersModules itself does not contain any code (is a dummy with a
+    single dummy version). It provide sources location of users modules, i.e.
+    mofem-fracture-module. Those are kept as a stand-alone package (instead
+    of resources) as they have different versions and developers. One can
+    install the extension, f.e. spack installs extension spack install
+    mofem-fracture-module. Next, create a symlink to run the code, f.e. spack
+    view symlink um_view mofem-cephas, and activate the extension, i.e. spack
+    activate um_view mofem-minimal-surface-equation. Basic mofem
+    functionality is available when with spack install mofem-users-modules,
+    it provides simple examples for calculating elasticity problems,
+    magnetostatics, saturated and unsaturated flow and a couple more. For
+    more information how to work with Spack and MoFEM see
+    http://mofem.eng.gla.ac.uk/mofem/html/install_spack.html"""
+
+    homepage = "http://mofem.eng.gla.ac.uk"
+    url = "https://bitbucket.org/likask/mofem-joseph/downloads/users_modules_dummy"
+    version('1.0', '5a8b22c9cdcad7bbad92b1590d55edb1', expand=False)
+
+    maintainers = ['likask']
+
+    variant('copy_user_modules', default=True,
+        description='Copy user modules directory instead linking')
+
+    extends('mofem-cephas')
+
+    @property
+    def root_cmakelists_dir(self):
+        """The relative path to the directory containing CMakeLists.txt
+
+        This path is relative to the root of the extracted tarball,
+        not to the ``build_directory``. Defaults to the current directory.
+
+        :return: directory containing CMakeLists.txt
+        """
+        spec = self.spec
+        return spec['mofem-cephas'].prefix.users_modules
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        # obligatory options
+        options.extend([
+            '-DWITH_SPACK=YES',
+            '-DSTAND_ALLONE_USERS_MODULES=%s' %
+            ('YES' if '+copy_user_modules' in spec else 'NO')])
+
+        # build tests
+        options.append('-DMOFEM_UM_BUILD_TETS={0}'.format(
+            'ON' if self.run_tests else 'OFF'))
+
+        return options
diff --git a/var/spack/repos/builtin/packages/molcas/package.py b/var/spack/repos/builtin/packages/molcas/package.py
index 7c4958cc94..38d7c1be2d 100644
--- a/var/spack/repos/builtin/packages/molcas/package.py
+++ b/var/spack/repos/builtin/packages/molcas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/mono/package.py b/var/spack/repos/builtin/packages/mono/package.py
index a2f841ceb1..b3a7161b4d 100644
--- a/var/spack/repos/builtin/packages/mono/package.py
+++ b/var/spack/repos/builtin/packages/mono/package.py
@@ -1,27 +1,8 @@
-###############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -47,6 +28,7 @@ class Mono(AutotoolsPackage):
     depends_on('libiconv')
     depends_on('perl', type=('build'))
 
+    version('5.4.1.7', '28a82df5d0b7854b387d4f21d852ac70')
     version('5.4.0.167', '103c7a737632046a9e9a0b039d752ee1')
     version('5.0.1.1', '17692c7a797f95ee6f9a0987fda3d486')
     version('4.8.0.524', 'baeed5b8139a85ad7e291d402a4bcccb')
diff --git a/var/spack/repos/builtin/packages/mosh/package.py b/var/spack/repos/builtin/packages/mosh/package.py
index de15e46bde..23d9cd0f1c 100644
--- a/var/spack/repos/builtin/packages/mosh/package.py
+++ b/var/spack/repos/builtin/packages/mosh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,6 +25,7 @@ class Mosh(AutotoolsPackage):
     depends_on('zlib')
     depends_on('openssl')
 
+    depends_on('pkgconfig', type='build')
     depends_on('perl', type='run')
 
     build_directory = 'spack-build'
diff --git a/var/spack/repos/builtin/packages/mothur/package.py b/var/spack/repos/builtin/packages/mothur/package.py
index e19ee30f98..ad66649025 100644
--- a/var/spack/repos/builtin/packages/mothur/package.py
+++ b/var/spack/repos/builtin/packages/mothur/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,9 @@ class Mothur(MakefilePackage):
     homepage = "https://github.com/mothur/mothur"
     url      = "https://github.com/mothur/mothur/archive/v1.39.5.tar.gz"
 
+    version('1.40.5', 'd57847849fdb961c3f66c9b9fdf3057b')
     version('1.39.5', '1f826ea4420e6822fc0db002c5940b92')
 
-    variant('mpi', default=True, description='Enable MPI parallel support')
-
-    depends_on('mpi', when='+mpi')
     depends_on('boost')
     depends_on('readline')
 
diff --git a/var/spack/repos/builtin/packages/motif/package.py b/var/spack/repos/builtin/packages/motif/package.py
new file mode 100644
index 0000000000..fdafcc065a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/motif/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Motif(AutotoolsPackage):
+    """"
+    Motif - Graphical user interface (GUI)
+    specification and the widget toolkit
+    """
+    homepage = "http://motif.ics.com/"
+    url = "http://cfhcable.dl.sourceforge.net/project/motif/Motif 2.3.8 Source Code/motif-2.3.8.tar.gz"
+
+    version('2.3.8', '7572140bb52ba21ec2f0c85b2605e2b1')
+
+    depends_on("flex")
+    depends_on("libx11")
+    depends_on("libxt")
+    depends_on("libxext")
+    depends_on("libxft")
+    depends_on("libxcomposite")
+    depends_on("libxfixes")
+    depends_on("xbitmaps")
diff --git a/var/spack/repos/builtin/packages/motioncor2/package.py b/var/spack/repos/builtin/packages/motioncor2/package.py
index 304e369d99..91f1a493ce 100644
--- a/var/spack/repos/builtin/packages/motioncor2/package.py
+++ b/var/spack/repos/builtin/packages/motioncor2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -36,15 +17,24 @@ class Motioncor2(Package):
     to keep up with automated data collection."""
 
     homepage = "http://msg.ucsf.edu/em/software"
-    url      = "http://msg.ucsf.edu/MotionCor2/MotionCor2-1.0.2.tar.gz"
+    url      = "http://msg.ucsf.edu/MotionCor2/MotionCor2-1.1.0.zip"
 
-    version('1.0.2',        'f2f4c5b09170ab8480ca657f14cdba2b')
-    version('1.0.1',        '73d94a80abdef9bf37bbc80fbbe76622')
-    version('1.0.0',        '490f4df8daa9f5ddb9eec3962ba3ddf5')
+    version('1.1.0',
+            '6e37e7ed63a9f0aab5d794b2604d5ba79333960bb9440a1a218630b03dbeaeac')
+    version('1.0.5',
+            '4efa55af25644bcff1ca7882419267b8c094c9cc6155b37d2c204b154c56f5a8',
+            url='http://msg.ucsf.edu/MotionCor2/MotionCor2-1.0.5.tar.gz')
+    version('1.0.4',
+            'c75738160ac18d3f27c33677e78e63313d8ec2b023b5a46173428c3fa0451a94',
+            url='http://msg.ucsf.edu/MotionCor2/MotionCor2-1.0.4.tar.gz')
 
     depends_on('cuda@8.0:8.99', type='run')
+    # libtiff.so.3 is required
+    depends_on('libtiff@3.0:3.99', type='run')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         for files in glob("MotionCor2_*"):
             install(files, prefix.bin)
+        with working_dir(prefix.bin):
+            symlink('MotionCor2_{0}'.format(spec.version), 'MotionCor2')
diff --git a/var/spack/repos/builtin/packages/mount-point-attributes/package.py b/var/spack/repos/builtin/packages/mount-point-attributes/package.py
new file mode 100644
index 0000000000..1a82e18b6c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mount-point-attributes/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class MountPointAttributes(AutotoolsPackage):
+    """Library to turn expensive, non-scalable file system calls into simple
+       string comparison operations."""
+
+    homepage = "https://github.com/LLNL/MountPointAttributes"
+    url = 'https://github.com/LLNL/MountPointAttributes/files/2270601/mountpointattr-1.1.tar.gz'
+
+    version('1.1', 'c9f0e7f5a3e16b9a022e5948712ecb2a')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
diff --git a/var/spack/repos/builtin/packages/mozjs/package.py b/var/spack/repos/builtin/packages/mozjs/package.py
index b0e98772af..08c467b763 100644
--- a/var/spack/repos/builtin/packages/mozjs/package.py
+++ b/var/spack/repos/builtin/packages/mozjs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Mozjs(AutotoolsPackage):
             url="http://ftp.mozilla.org/pub/js/js185-1.0.0.tar.gz")
 
     depends_on('perl@5.6:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('python@2.7.3:2.8', type='build')
     depends_on('nspr', when='@:27')
     depends_on('libffi@3.0.9:')
diff --git a/var/spack/repos/builtin/packages/mpark-variant/package.py b/var/spack/repos/builtin/packages/mpark-variant/package.py
new file mode 100644
index 0000000000..ad1704d6f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mpark-variant/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class MparkVariant(CMakePackage):
+    """C++17 `std::variant` for C++11/14/17"""
+
+    homepage = "https://mpark.github.io/variant"
+    url      = "https://github.com/mpark/variant/archive/v1.3.0.tar.gz"
+    maintainers = ['ax3l']
+
+    version('1.3.0', '368b7d6f1a07bd6ee26ff518258dc71c')
+
+    conflicts('%gcc@:4.7')
+    conflicts('%clang@:3.5')
diff --git a/var/spack/repos/builtin/packages/mpc/package.py b/var/spack/repos/builtin/packages/mpc/package.py
index 749794015a..1e1763d0df 100644
--- a/var/spack/repos/builtin/packages/mpc/package.py
+++ b/var/spack/repos/builtin/packages/mpc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,20 +10,28 @@ class Mpc(AutotoolsPackage):
     """Gnu Mpc is a C library for the arithmetic of complex numbers
        with arbitrarily high precision and correct rounding of the
        result."""
+
     homepage = "http://www.multiprecision.org"
-    url      = "https://ftp.gnu.org/gnu/mpc/mpc-1.0.2.tar.gz"
+    url      = "https://ftpmirror.gnu.org/mpc/mpc-1.1.0.tar.gz"
+    list_url = "http://www.multiprecision.org/mpc/download.html"
 
+    version('1.1.0', '4125404e41e482ec68282a2e687f6c73')
     version('1.0.3', 'd6a1d5f8ddea3abd2cc3e98f58352d26')
     version('1.0.2', '68fadff3358fb3e7976c7a398a0af4c3')
 
-    depends_on('gmp@4.3.2:')   # mpir is a drop-in replacement for this
-    depends_on('mpfr@2.4.2:')  # Could also be built against mpir
+    # Could also be built against mpir instead
+    depends_on('gmp@4.3.2:')
+    depends_on('gmp@5.0.0:', when='@1.1.0:')
+    depends_on('mpfr@2.4.2:')
+    depends_on('mpfr@3.0.0:', when='@1.1.0:')
 
     def url_for_version(self, version):
         if version < Version("1.0.1"):
-            return "http://www.multiprecision.org/mpc/download/mpc-%s.tar.gz" % version
+            url = "http://www.multiprecision.org/mpc/download/mpc-{0}.tar.gz"
         else:
-            return "https://ftp.gnu.org/gnu/mpc/mpc-%s.tar.gz" % version
+            url = "https://ftp.gnu.org/gnu/mpc/mpc-{0}.tar.gz"
+
+        return url.format(version)
 
     def configure_args(self):
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/mpe2/package.py b/var/spack/repos/builtin/packages/mpe2/package.py
index d5041d7a32..470a29d8b2 100644
--- a/var/spack/repos/builtin/packages/mpe2/package.py
+++ b/var/spack/repos/builtin/packages/mpe2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mpest/package.py b/var/spack/repos/builtin/packages/mpest/package.py
index c5cba773dd..25e7e4f156 100644
--- a/var/spack/repos/builtin/packages/mpest/package.py
+++ b/var/spack/repos/builtin/packages/mpest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mpfr/package.py b/var/spack/repos/builtin/packages/mpfr/package.py
index 01006dd72a..3ddf429f52 100644
--- a/var/spack/repos/builtin/packages/mpfr/package.py
+++ b/var/spack/repos/builtin/packages/mpfr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,18 +11,33 @@ class Mpfr(AutotoolsPackage):
        floating-point computations with correct rounding."""
 
     homepage = "http://www.mpfr.org"
-    url      = "https://ftp.gnu.org/gnu/mpfr/mpfr-3.1.5.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/mpfr/mpfr-4.0.1.tar.bz2"
 
+    version('4.0.1', '8c21d8ac7460493b2b9f3ef3cc610454')
+    version('4.0.0', 'ef619f3bb68039e35c4a219e06be72d0')
+    version('3.1.6', '320c28198def956aeacdb240b46b8969')
     version('3.1.5', 'b1d23a55588e3b2a13e3be66bc69fd8d')
     version('3.1.4', 'b8a2f6b0e68bef46e53da2ac439e1cf4')
     version('3.1.3', '5fdfa3cfa5c86514ee4a241a1affa138')
     version('3.1.2', 'ee2c3ac63bf0c2359bf08fc3ee094c19')
 
     # mpir is a drop-in replacement for gmp
-    depends_on('gmp@4.1.0:')  # 4.2.3 or higher is recommended
+    depends_on('gmp@4.1:')  # 4.2.3 or higher is recommended
+    depends_on('gmp@5.0:', when='@4.0.0:')  # http://www.mpfr.org/mpfr-4.0.0/
+
+    # Check the Bugs section of old release pages for patches.
+    # http://www.mpfr.org/mpfr-X.Y.Z/#bugs
+    patches = {
+        '3.1.6': '66a5d58364113a21405fc53f4a48f4e8',
+        '3.1.5': '1dc5fe65feb5607b89fe0f410d53b627',
+        '3.1.4': 'd124381573404fe83654c7d5a79aeabf',
+        '3.1.3': 'ebd1d835e0ae2fd8a9339210ccd1d0a8',
+        '3.1.2': '9f96a5c7cac1d6cd983ed9cf7d997074',
+    }
 
-    patch('vasprintf.patch', when='@3.1.5')
-    patch('strtofr.patch',   when='@3.1.5')
+    for ver, checksum in patches.items():
+        patch('http://www.mpfr.org/mpfr-{0}/allpatches'.format(ver),
+              when='@' + ver, sha256=checksum)
 
     def configure_args(self):
         args = [
diff --git a/var/spack/repos/builtin/packages/mpfr/strtofr.patch b/var/spack/repos/builtin/packages/mpfr/strtofr.patch
deleted file mode 100644
index 01878bf1b0..0000000000
--- a/var/spack/repos/builtin/packages/mpfr/strtofr.patch
+++ /dev/null
@@ -1,92 +0,0 @@
-diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES
---- mpfr-3.1.5-a/PATCHES	2016-12-19 22:11:17.022676737 +0000
-+++ mpfr-3.1.5-b/PATCHES	2016-12-19 22:11:17.094676820 +0000
-@@ -0,0 +1 @@
-+strtofr
-diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION
---- mpfr-3.1.5-a/VERSION	2016-12-15 08:35:46.544430346 +0000
-+++ mpfr-3.1.5-b/VERSION	2016-12-19 22:11:17.094676820 +0000
-@@ -1 +1 @@
--3.1.5-p1
-+3.1.5-p2
-diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h
---- mpfr-3.1.5-a/src/mpfr.h	2016-12-15 08:35:46.540430340 +0000
-+++ mpfr-3.1.5-b/src/mpfr.h	2016-12-19 22:11:17.090676815 +0000
-@@ -27,7 +27,7 @@
- #define MPFR_VERSION_MAJOR 3
- #define MPFR_VERSION_MINOR 1
- #define MPFR_VERSION_PATCHLEVEL 5
--#define MPFR_VERSION_STRING "3.1.5-p1"
-+#define MPFR_VERSION_STRING "3.1.5-p2"
- 
- /* Macros dealing with MPFR VERSION */
- #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c))
-diff -Naurd mpfr-3.1.5-a/src/strtofr.c mpfr-3.1.5-b/src/strtofr.c
---- mpfr-3.1.5-a/src/strtofr.c	2016-09-27 07:58:15.000000000 +0000
-+++ mpfr-3.1.5-b/src/strtofr.c	2016-12-19 22:11:17.066676788 +0000
-@@ -743,11 +743,14 @@
-          of the pstr_size most significant digits of pstr->mant, with
-          equality in case exact is non-zero. */
- 
--      /* test if rounding is possible, and if so exit the loop */
--      if (exact || mpfr_can_round_raw (result, ysize,
--                                       (pstr->negative) ? -1 : 1,
--                                       ysize_bits - err - 1,
--                                       MPFR_RNDN, rnd, MPFR_PREC(x)))
-+      /* test if rounding is possible, and if so exit the loop.
-+         Note: we also need to be able to determine the correct ternary value,
-+         thus we use the MPFR_PREC(x) + (rnd == MPFR_RNDN) trick.
-+         For example if result = xxx...xxx111...111 and rnd = RNDN,
-+         then we know the correct rounding is xxx...xx(x+1), but we cannot know
-+         the correct ternary value. */
-+      if (exact || mpfr_round_p (result, ysize, ysize_bits - err - 1,
-+                                 MPFR_PREC(x) + (rnd == MPFR_RNDN)))
-         break;
- 
-     next_loop:
-diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c
---- mpfr-3.1.5-a/src/version.c	2016-12-15 08:35:46.544430346 +0000
-+++ mpfr-3.1.5-b/src/version.c	2016-12-19 22:11:17.094676820 +0000
-@@ -25,5 +25,5 @@
- const char *
- mpfr_get_version (void)
- {
--  return "3.1.5-p1";
-+  return "3.1.5-p2";
- }
-diff -Naurd mpfr-3.1.5-a/tests/tstrtofr.c mpfr-3.1.5-b/tests/tstrtofr.c
---- mpfr-3.1.5-a/tests/tstrtofr.c	2016-09-27 07:58:14.000000000 +0000
-+++ mpfr-3.1.5-b/tests/tstrtofr.c	2016-12-19 22:11:17.066676788 +0000
-@@ -1191,6 +1191,24 @@
-   mpfr_clears (e, x1, x2, (mpfr_ptr) 0);
- }
- 
-+/* Note: the number is 5^47/2^9. */
-+static void
-+bug20161217 (void)
-+{
-+  mpfr_t fp, z;
-+  static const char * num = "0.1387778780781445675529539585113525390625e31";
-+  int inex;
-+
-+  mpfr_init2 (fp, 110);
-+  mpfr_init2 (z, 110);
-+  inex = mpfr_strtofr (fp, num, NULL, 10, MPFR_RNDN);
-+  MPFR_ASSERTN(inex == 0);
-+  mpfr_set_str_binary (z, "10001100001000010011110110011101101001010000001011011110010001010100010100100110111101000010001011001100001101E-9");
-+  MPFR_ASSERTN(mpfr_equal_p (fp, z));
-+  mpfr_clear (fp);
-+  mpfr_clear (z);
-+}
-+
- int
- main (int argc, char *argv[])
- {
-@@ -1205,6 +1223,7 @@
-   test20100310 ();
-   bug20120814 ();
-   bug20120829 ();
-+  bug20161217 ();
- 
-   tests_end_mpfr ();
-   return 0;
diff --git a/var/spack/repos/builtin/packages/mpfr/vasprintf.patch b/var/spack/repos/builtin/packages/mpfr/vasprintf.patch
deleted file mode 100644
index e1576d5976..0000000000
--- a/var/spack/repos/builtin/packages/mpfr/vasprintf.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-diff -Naurd mpfr-3.1.5-a/PATCHES mpfr-3.1.5-b/PATCHES
---- mpfr-3.1.5-a/PATCHES	2016-12-15 08:35:46.476430238 +0000
-+++ mpfr-3.1.5-b/PATCHES	2016-12-15 08:35:46.544430346 +0000
-@@ -0,0 +1 @@
-+vasprintf
-diff -Naurd mpfr-3.1.5-a/VERSION mpfr-3.1.5-b/VERSION
---- mpfr-3.1.5-a/VERSION	2016-09-27 07:58:14.000000000 +0000
-+++ mpfr-3.1.5-b/VERSION	2016-12-15 08:35:46.544430346 +0000
-@@ -1 +1 @@
--3.1.5
-+3.1.5-p1
-diff -Naurd mpfr-3.1.5-a/src/mpfr.h mpfr-3.1.5-b/src/mpfr.h
---- mpfr-3.1.5-a/src/mpfr.h	2016-09-27 07:58:15.000000000 +0000
-+++ mpfr-3.1.5-b/src/mpfr.h	2016-12-15 08:35:46.540430340 +0000
-@@ -27,7 +27,7 @@
- #define MPFR_VERSION_MAJOR 3
- #define MPFR_VERSION_MINOR 1
- #define MPFR_VERSION_PATCHLEVEL 5
--#define MPFR_VERSION_STRING "3.1.5"
-+#define MPFR_VERSION_STRING "3.1.5-p1"
- 
- /* Macros dealing with MPFR VERSION */
- #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c))
-diff -Naurd mpfr-3.1.5-a/src/vasprintf.c mpfr-3.1.5-b/src/vasprintf.c
---- mpfr-3.1.5-a/src/vasprintf.c	2016-09-27 07:58:15.000000000 +0000
-+++ mpfr-3.1.5-b/src/vasprintf.c	2016-12-15 08:35:46.520430308 +0000
-@@ -1593,7 +1593,7 @@
-         }
-       else if (spec.spec == 'f' || spec.spec == 'F')
-         {
--          if (spec.prec == -1)
-+          if (spec.prec < 0)
-             spec.prec = 6;
-           if (regular_fg (np, p, spec, NULL) == -1)
-             goto error;
-diff -Naurd mpfr-3.1.5-a/src/version.c mpfr-3.1.5-b/src/version.c
---- mpfr-3.1.5-a/src/version.c	2016-09-27 07:58:15.000000000 +0000
-+++ mpfr-3.1.5-b/src/version.c	2016-12-15 08:35:46.544430346 +0000
-@@ -25,5 +25,5 @@
- const char *
- mpfr_get_version (void)
- {
--  return "3.1.5";
-+  return "3.1.5-p1";
- }
-diff -Naurd mpfr-3.1.5-a/tests/tsprintf.c mpfr-3.1.5-b/tests/tsprintf.c
---- mpfr-3.1.5-a/tests/tsprintf.c	2016-09-27 07:58:14.000000000 +0000
-+++ mpfr-3.1.5-b/tests/tsprintf.c	2016-12-15 08:35:46.520430308 +0000
-@@ -1251,6 +1251,25 @@
-   check_emin_aux (MPFR_EMIN_MIN);
- }
- 
-+static void
-+test20161214 (void)
-+{
-+  mpfr_t x;
-+  char buf[32];
-+  const char s[] = "0x0.fffffffffffff8p+1024";
-+  int r;
-+
-+  mpfr_init2 (x, 64);
-+  mpfr_set_str (x, s, 16, MPFR_RNDN);
-+  r = mpfr_snprintf (buf, 32, "%.*RDf", -2, x);
-+  MPFR_ASSERTN(r == 316);
-+  r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN + 1, x);
-+  MPFR_ASSERTN(r == 316);
-+  r = mpfr_snprintf (buf, 32, "%.*RDf", INT_MIN, x);
-+  MPFR_ASSERTN(r == 316);
-+  mpfr_clear (x);
-+}
-+
- int
- main (int argc, char **argv)
- {
-@@ -1271,6 +1290,7 @@
-   mixed ();
-   check_emax ();
-   check_emin ();
-+  test20161214 ();
- 
- #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE)
- #if MPFR_LCONV_DPTS
diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpibash/package.py
index f5476328b7..f4157ca66f 100644
--- a/var/spack/repos/builtin/packages/mpibash/package.py
+++ b/var/spack/repos/builtin/packages/mpibash/package.py
@@ -1,56 +1,28 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Mpibash(Package):
+class Mpibash(AutotoolsPackage):
     """Parallel scripting right from the Bourne-Again Shell (Bash)"""
-    homepage = "http://www.ccs3.lanl.gov/~pakin/software/mpibash-4.3.html"
 
-    version('4.3', '81348932d5da294953e15d4814c74dd1',
-            url="http://ftp.gnu.org/gnu/bash/bash-4.3.tar.gz")
+    homepage = "https://github.com/lanl/MPI-Bash"
+    url      = "https://github.com/lanl/MPI-Bash/releases/download/v1.2/mpibash-1.2.tar.gz"
 
-    # patch -p1 < ../mpibash-4.3.patch
-    patch('mpibash-4.3.patch', level=1, when='@4.3')
-
-    # above patch modifies configure.ac
-    depends_on('autoconf', type='build')
+    version('1.2', 'b81001fb234ed79c4e5bf2f7efee3529')
 
+    depends_on('bash@4.4:')
     # uses MPI_Exscan which is in MPI-1.2 and later
     depends_on('mpi@1.2:')
 
     depends_on('libcircle')
 
-    def install(self, spec, prefix):
-        # run autoconf to rebuild configure
-        autoconf = which('autoconf')
-        autoconf()
-
-        configure("--prefix=" + prefix,
-                  "CC=mpicc")
-
-        make(parallel=False)
-
-        make("install")
+    def configure_args(self):
+        args = [
+            "--with-bashdir={0}".format(self.spec['bash'].prefix.include.bash),
+            "CC={0}".format(self.spec['mpi'].mpicc)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/mpiblast/package.py b/var/spack/repos/builtin/packages/mpiblast/package.py
index eebb7da1fb..c358075f1e 100644
--- a/var/spack/repos/builtin/packages/mpiblast/package.py
+++ b/var/spack/repos/builtin/packages/mpiblast/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mpich/package.py b/var/spack/repos/builtin/packages/mpich/package.py
index 74234f46ae..aea92872f0 100644
--- a/var/spack/repos/builtin/packages/mpich/package.py
+++ b/var/spack/repos/builtin/packages/mpich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -31,10 +12,13 @@ class Mpich(AutotoolsPackage):
     the Message Passing Interface (MPI) standard."""
 
     homepage = "http://www.mpich.org"
-    url = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
+    url      = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
+    git      = "https://github.com/pmodels/mpich.git"
     list_url = "http://www.mpich.org/static/downloads/"
     list_depth = 1
 
+    version('develop', submodules=True)
+    version('3.2.1', 'e175452f4d61646a52c73031683fc375')
     version('3.2',   'f414cfa77099cd1fa1a5ae4e22db508a')
     version('3.1.4', '2ab544607986486562e076b83937bba2')
     version('3.1.3', '93cb17f91ac758cbf9174ecb03563778')
@@ -42,7 +26,6 @@ class Mpich(AutotoolsPackage):
     version('3.1.1', '40dc408b1e03cc36d80209baaa2d32b7')
     version('3.1',   '5643dd176499bfb7d25079aaff25f2ec')
     version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
-    version('develop', git='git://github.com/pmodels/mpich')
 
     variant('hydra', default=True,  description='Build the hydra process manager')
     variant('pmi',   default=True,  description='Build with PMI support')
@@ -71,10 +54,16 @@ spack package at this time.''',
     provides('mpi@:3.0', when='@3:')
     provides('mpi@:1.3', when='@1:')
 
+    filter_compiler_wrappers(
+        'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
+    )
+
     # fix MPI_Barrier segmentation fault
     # see https://lists.mpich.org/pipermail/discuss/2016-May/004764.html
     # and https://lists.mpich.org/pipermail/discuss/2016-June/004768.html
-    patch('mpich32_clang.patch', when='@3.2%clang')
+    patch('mpich32_clang.patch', when='@3.2:3.2.0%clang')
+
+    depends_on('findutils', type='build')
 
     depends_on('libfabric', when='netmod=ofi')
 
@@ -169,34 +158,3 @@ spack package at this time.''',
         config_args.append(device_config)
 
         return config_args
-
-    @run_after('install')
-    def filter_compilers(self):
-        """Run after install to make the MPI compilers use the
-        compilers that Spack built the package with.
-
-        If this isn't done, they'll have CC, CXX, F77, and FC set
-        to Spack's generic cc, c++, f77, and f90.  We want them to
-        be bound to whatever compiler they were built with."""
-
-        mpicc = join_path(self.prefix.bin, 'mpicc')
-        mpicxx = join_path(self.prefix.bin, 'mpicxx')
-        mpif77 = join_path(self.prefix.bin, 'mpif77')
-        mpif90 = join_path(self.prefix.bin, 'mpif90')
-
-        # Substitute Spack compile wrappers for the real
-        # underlying compiler
-        kwargs = {
-            'ignore_absent': True,
-            'backup': False,
-            'string': True
-        }
-        filter_file(env['CC'],  self.compiler.cc,  mpicc,  **kwargs)
-        filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs)
-        filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs)
-        filter_file(env['FC'],  self.compiler.fc,  mpif90, **kwargs)
-
-        # Remove this linking flag if present
-        # (it turns RPATH into RUNPATH)
-        for wrapper in (mpicc, mpicxx, mpif77, mpif90):
-            filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs)
diff --git a/var/spack/repos/builtin/packages/mpifileutils/package.py b/var/spack/repos/builtin/packages/mpifileutils/package.py
index f1bb7e3f39..8257587f1b 100644
--- a/var/spack/repos/builtin/packages/mpifileutils/package.py
+++ b/var/spack/repos/builtin/packages/mpifileutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,14 +18,22 @@ class Mpifileutils(AutotoolsPackage):
 
     homepage = "https://github.com/hpc/mpifileutils"
     url      = "https://github.com/hpc/mpifileutils/releases/download/v0.6/mpifileutils-0.6.tar.gz"
+    git      = "https://github.com/hpc/mpifileutils.git"
 
+    version('develop', branch='master')
+    version('0.8', '1082600e7ac4e6b2c13d91bbec40cffb')
     version('0.7', 'c081f7f72c4521dddccdcf9e087c5a2b')
     version('0.6', '620bcc4966907481f1b1a965b28fc9bf')
 
     depends_on('mpi')
     depends_on('libcircle')
     depends_on('lwgrp')
-    depends_on('dtcmp')
+
+    # need precise version of dtcmp, since DTCMP_Segmented_exscan added
+    # in v1.0.3 but renamed in v1.1.0 and later
+    depends_on('dtcmp@1.0.3',  when='@:0.7')
+    depends_on('dtcmp@1.1.0:', when='@0.8:')
+
     depends_on('libarchive')
 
     variant('xattr', default=True,
diff --git a/var/spack/repos/builtin/packages/mpilander/package.py b/var/spack/repos/builtin/packages/mpilander/package.py
new file mode 100644
index 0000000000..6f53f4d59a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mpilander/package.py
@@ -0,0 +1,45 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Mpilander(CMakePackage):
+    """There can only be one (MPI process)!"""
+
+    homepage = "https://github.com/MPILander/MPILander"
+    git      = "https://github.com/MPILander/MPILander.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+
+    # variant('cuda', default=False, description='Enable CUDA support')
+    # variant(
+    #     'schedulers',
+    #     description='List of supported schedulers',
+    #     values=('alps', 'lsf', 'tm', 'slurm', 'sge', 'loadleveler'),
+    #     multi=True
+    # )
+
+    depends_on('cmake@3.9.2:', type='build')
+
+    provides('mpi@:3.1')
+
+    # compiler support
+    conflicts('%gcc@:4.7')
+    conflicts('%clang@:3.8')
+    conflicts('%intel@:16')
+
+    def cmake_args(self):
+        args = [
+            # tests and examples
+            '-DBUILD_TESTING:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+            '-DBUILD_EXAMPLES:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/mpileaks/package.py b/var/spack/repos/builtin/packages/mpileaks/package.py
index cbf330666a..291df5da34 100644
--- a/var/spack/repos/builtin/packages/mpileaks/package.py
+++ b/var/spack/repos/builtin/packages/mpileaks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mpip/package.py b/var/spack/repos/builtin/packages/mpip/package.py
index a641217622..172207885c 100644
--- a/var/spack/repos/builtin/packages/mpip/package.py
+++ b/var/spack/repos/builtin/packages/mpip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/mpir/package.py b/var/spack/repos/builtin/packages/mpir/package.py
index 14be170a3a..6e79df36e1 100644
--- a/var/spack/repos/builtin/packages/mpir/package.py
+++ b/var/spack/repos/builtin/packages/mpir/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,11 @@ class Mpir(Package):
 
     homepage = "https://github.com/wbhart/mpir"
     url      = "https://github.com/wbhart/mpir/archive/mpir-2.7.0.tar.gz"
+    git      = "https://github.com/wbhart/mpir.git"
 
+    version('develop', branch='master')
     version('2.7.0', '985b5d57bd0e74c74125ee885b9c8f71')
     version('2.6.0', 'ec17d6a7e026114ceb734b2466aa0a91')
-    version('develop', git='https://github.com/wbhart/mpir.git')
 
     # This setting allows mpir to act as a drop-in replacement for gmp
     variant('gmp_compat',        default=False,
diff --git a/var/spack/repos/builtin/packages/mpix-launch-swift/package.py b/var/spack/repos/builtin/packages/mpix-launch-swift/package.py
index a56337fdd4..83d3d28799 100644
--- a/var/spack/repos/builtin/packages/mpix-launch-swift/package.py
+++ b/var/spack/repos/builtin/packages/mpix-launch-swift/package.py
@@ -1,41 +1,20 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
-class MpixLaunchSwift(Package):
+class MpixLaunchSwift(MakefilePackage):
     """Library that allows a child MPI application to be launched
     inside a subset of processes in a parent MPI application.
     """
 
     homepage = "https://bitbucket.org/kshitijvmehta/mpix_launch_swift"
-    url = "https://kshitijvmehta@bitbucket.org/kshitijvmehta/mpix_launch_swift.git"
+    git      = "https://kshitijvmehta@bitbucket.org/kshitijvmehta/mpix_launch_swift.git"
 
-    version('develop', git='https://kshitijvmehta@bitbucket.org/kshitijvmehta/mpix_launch_swift.git',
-            branch='envs')
+    version('develop', branch='envs')
 
     depends_on('stc')
     depends_on('tcl')
@@ -43,5 +22,4 @@ class MpixLaunchSwift(Package):
     depends_on('swig', type='build')
 
     def install(self, spec, prefix):
-        make()
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/mrbayes/package.py b/var/spack/repos/builtin/packages/mrbayes/package.py
index 9361c3cc0e..79701d2a03 100644
--- a/var/spack/repos/builtin/packages/mrbayes/package.py
+++ b/var/spack/repos/builtin/packages/mrbayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class Mrbayes(AutotoolsPackage):
        of model parameters."""
 
     homepage = "http://mrbayes.sourceforge.net"
-    url      = "https://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.6/mrbayes-3.2.6.tar.gz"
+    git      = "https://github.com/NBISweden/MrBayes.git"
 
-    version('3.2.6', '95f9822f24be47b976bf87540b55d1fe')
+    version('2017-11-22', commit='8a9adb11bcc538cb95d91d57568dff383f924503')
 
     variant('mpi', default=True, description='Enable MPI parallel support')
     variant('beagle', default=True, description='Enable BEAGLE library for speed benefits')
@@ -48,8 +29,6 @@ class Mrbayes(AutotoolsPackage):
     depends_on('libbeagle', when='+beagle')
     depends_on('mpi', when='+mpi')
 
-    configure_directory = 'src'
-
     def configure_args(self):
         args = []
         if '~beagle' in self.spec:
diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py
index 6569934817..14e2fc8200 100644
--- a/var/spack/repos/builtin/packages/mrnet/package.py
+++ b/var/spack/repos/builtin/packages/mrnet/package.py
@@ -1,47 +1,33 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Mrnet(AutotoolsPackage):
     """The MRNet Multi-Cast Reduction Network."""
+
     homepage = "http://paradyn.org/mrnet"
     url      = "http://ftp.cs.wisc.edu/pub/paradyn/mrnet/mrnet_5.0.1.tar.gz"
+    git      = "https://github.com/dyninst/mrnet.git"
     list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet"
 
-    version('5.0.1-2', git='https://github.com/dyninst/mrnet.git',
-            commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9')
+    version('5.0.1-3', branch='master')
+    version('5.0.1-2', commit='20b1eacfc6d680d9f6472146d2dfaa0f900cc2e9')
     version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd')
     version('4.1.0', '5a248298b395b329e2371bf25366115c')
     version('4.0.0', 'd00301c078cba57ef68613be32ceea2f')
 
+    variant('cti', default=False,
+            description="Build the MRNet with the CTI startup option")
     variant('lwthreads', default=False,
             description="Also build the MRNet LW threadsafe libraries")
     parallel = False
 
     depends_on("boost")
+    depends_on("cti", when='+cti')
 
     def configure_args(self):
         spec = self.spec
@@ -51,5 +37,11 @@ class Mrnet(AutotoolsPackage):
         # lwthreads variant is present
         if '+lwthreads' in spec:
             config_args.append('--enable-ltwt-threadsafe')
-
+        # Build the MRNet with CTI based start-up when
+        # the cti variant is present
+        if '+cti' in spec:
+            config_args.append('--with-startup=cray-cti')
+            cti = self.spec['cti'].prefix
+            config_args.append('--with-craycti-inc=-I%s/include' % cti)
+            config_args.append('--with-craycti-lib=-I%s/lib' % cti)
         return config_args
diff --git a/var/spack/repos/builtin/packages/mrtrix3/package.py b/var/spack/repos/builtin/packages/mrtrix3/package.py
index f5daeabf5a..fc99abfc9a 100644
--- a/var/spack/repos/builtin/packages/mrtrix3/package.py
+++ b/var/spack/repos/builtin/packages/mrtrix3/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import distutils.dir_util
 
 
 class Mrtrix3(Package):
@@ -33,10 +13,9 @@ class Mrtrix3(Package):
        density."""
 
     homepage = "http://www.mrtrix.org/"
-    url      = "https://github.com/MRtrix3/mrtrix3"
+    git      = "https://github.com/MRtrix3/mrtrix3.git"
 
-    version('2017-09-25', commit='72aca89e3d38c9d9e0c47104d0fb5bd2cbdb536d',
-            git='https://github.com/MRtrix3/mrtrix3.git')
+    version('2017-09-25', commit='72aca89e3d38c9d9e0c47104d0fb5bd2cbdb536d')
 
     depends_on('python@2.7:', type=('build', 'run'))
     depends_on('py-numpy', type=('build', 'run'))
@@ -54,9 +33,7 @@ class Mrtrix3(Package):
         build = Executable('./build')
         configure()
         build()
-        # install_tree('.', prefix) does not work since the prefix
-        # directory already exists by this point
-        distutils.dir_util.copy_tree('.', prefix)
+        install_tree('.', prefix)
 
     def setup_environment(self, spac_env, run_env):
         run_env.prepend_path('PATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/mscgen/package.py b/var/spack/repos/builtin/packages/mscgen/package.py
new file mode 100644
index 0000000000..f926b539af
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mscgen/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Mscgen(AutotoolsPackage):
+    """Mscgen is a small program that parses Message Sequence Chart descriptions
+    and produces PNG, SVG, EPS or server side image maps (ismaps) as the
+    output."""
+
+    homepage = "http://www.mcternan.me.uk/mscgen/"
+    url      = "http://www.mcternan.me.uk/mscgen/software/mscgen-src-0.20.tar.gz"
+
+    version('0.20', '65c90fb5150d7176b65b793f0faa7377')
+
+    depends_on('flex')
+    depends_on('bison')
+    depends_on('pkgconf')
+    depends_on('libgd')
diff --git a/var/spack/repos/builtin/packages/msgpack-c/package.py b/var/spack/repos/builtin/packages/msgpack-c/package.py
index bf78e8d931..49cd4f765d 100644
--- a/var/spack/repos/builtin/packages/msgpack-c/package.py
+++ b/var/spack/repos/builtin/packages/msgpack-c/package.py
@@ -1,35 +1,27 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class MsgpackC(CMakePackage):
     """A small, fast binary interchange format convertible to/from JSON"""
     homepage = "http://www.msgpack.org"
-    url      = "https://github.com/msgpack/msgpack-c/archive/cpp-1.4.1.tar.gz"
+    url      = "https://github.com/msgpack/msgpack-c/archive/cpp-3.0.1.tar.gz"
 
+    version('3.0.1', 'a79f05f0dc5637c161805d6c0e9bfbe7')
     version('1.4.1', 'e2fd3a7419b9bc49e5017fdbefab87e0')
 
     depends_on('cmake@2.8.12:', type='build')
+    depends_on('googletest', type='test')
+
+    def cmake_args(self):
+        args = [
+            "-DCMAKE_CXX_FLAGS=-Wno-implicit-fallthrough",
+            "-DCMAKE_C_FLAGS=-Wno-implicit-fallthrough",
+            '-DMSGPACK_BUILD_TESTS:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF')
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/mshadow/package.py b/var/spack/repos/builtin/packages/mshadow/package.py
index cd9ecfce86..3dde91770c 100644
--- a/var/spack/repos/builtin/packages/mshadow/package.py
+++ b/var/spack/repos/builtin/packages/mshadow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,10 @@ class Mshadow(Package):
     in C++/CUDA."""
 
     homepage = "https://github.com/dmlc/mshadow"
-    url      = "https://github.com/dmlc/mshadow/archive/v1.1.tar.gz"
+    git      = "https://github.com/dmlc/mshadow.git"
 
-    version('master', git='https://github.com/dmlc/mshadow.git', branch='master')
-    version('20170721', git='https://github.com/dmlc/mshadow.git',
-            commit='20b54f068c1035f0319fa5e5bbfb129c450a5256')
+    version('master', branch='master')
+    version('20170721', commit='20b54f068c1035f0319fa5e5bbfb129c450a5256')
 
     def install(self, spec, prefix):
         install_tree('mshadow', prefix.include.mshadow)
diff --git a/var/spack/repos/builtin/packages/msmc/package.py b/var/spack/repos/builtin/packages/msmc/package.py
new file mode 100644
index 0000000000..7acde0f400
--- /dev/null
+++ b/var/spack/repos/builtin/packages/msmc/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Msmc(MakefilePackage):
+    """This software implements MSMC, a method to infer population size
+       and gene flow from multiple genome sequences"""
+
+    homepage = "https://github.com/stschiff/msmc"
+    url      = "https://github.com/stschiff/msmc/archive/v1.1.0.tar.gz"
+
+    version('1.1.0', sha256='989064400fe392ca3d2ac1a253ce7edf1801b6a7eeb77bbf2ff7bf67910216c4')
+
+    depends_on('gsl', type=('build', 'run'))
+    depends_on('dmd', type='build')
+
+    def edit(self, spec, prefix):
+        filter_file('dmd',
+                    join_path(self.spec['dmd'].prefix.linux.bin64, 'dmd'),
+                    'Makefile', string=True)
+
+    def build(self, spec, prefix):
+        gsllibdir = self.spec['gsl'].prefix.lib
+        libgsl = join_path(gsllibdir, 'libgsl.a')
+        libgslcblas = join_path(gsllibdir, 'libgslcblas.a')
+        make('GSL={0} {1}'.format(libgsl, libgslcblas))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install_tree('build', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/multitail/package.py b/var/spack/repos/builtin/packages/multitail/package.py
index 9c9ef2cca0..5857fbd751 100644
--- a/var/spack/repos/builtin/packages/multitail/package.py
+++ b/var/spack/repos/builtin/packages/multitail/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/multiverso/package.py b/var/spack/repos/builtin/packages/multiverso/package.py
index 8993ce1b4d..5d1a27e153 100644
--- a/var/spack/repos/builtin/packages/multiverso/package.py
+++ b/var/spack/repos/builtin/packages/multiverso/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,10 @@ class Multiverso(CMakePackage):
 
     homepage = "https://github.com/Microsoft/Multiverso"
     url      = "https://github.com/Microsoft/Multiverso/archive/v0.2.tar.gz"
+    git      = "https://github.com/Microsoft/Multiverso.git"
 
-    version('master', git='https://github.com/Microsoft/Multiverso.git',
-            branch='master')
-    version('143187', git='https://github.com/Microsoft/Multiverso.git',
-            commit='143187575d1cfa410100037b8aea2e767e0af637')
+    version('master', branch='master')
+    version('143187', commit='143187575d1cfa410100037b8aea2e767e0af637')
     version('0.2', '483ca7524fea14a311389e421f2bc098')
 
     depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/mummer/package.py b/var/spack/repos/builtin/packages/mummer/package.py
index 8aabf502f9..a698f27463 100644
--- a/var/spack/repos/builtin/packages/mummer/package.py
+++ b/var/spack/repos/builtin/packages/mummer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mumps/examples.patch b/var/spack/repos/builtin/packages/mumps/examples.patch
new file mode 100644
index 0000000000..78003935a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mumps/examples.patch
@@ -0,0 +1,41 @@
+--- a/examples/Makefile
++++ b/examples/Makefile
+@@ -27,32 +27,32 @@
+ LIBSMUMPS = $(libdir)/libsmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
+ 
+ ssimpletest:  $(LIBSMUMPS)  $$@.o
+-	$(FL) -o $@ $(OPTL) ssimpletest.o  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ ssimpletest.o  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ LIBDMUMPS = $(libdir)/libdmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
+ 
+ dsimpletest: $(LIBDMUMPS)  $$@.o 
+-	$(FL) -o $@ $(OPTL) dsimpletest.o  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ dsimpletest.o  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ LIBCMUMPS = $(libdir)/libcmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
+ 
+ csimpletest: $(LIBCMUMPS)  $$@.o
+-	$(FL) -o $@ $(OPTL) csimpletest.o  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ csimpletest.o  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ LIBZMUMPS = $(libdir)/libzmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
+ 
+ zsimpletest: $(LIBZMUMPS)  $$@.o
+-	$(FL) -o $@ $(OPTL) zsimpletest.o  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ zsimpletest.o  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ c_example:	$(LIBDMUMPS) $$@.o
+-	$(FL) -o $@ $(OPTL) $@.o $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ $@.o $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ multiple_arithmetics_example:	$(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $$@.o
+-	$(FL) -o $@ $(OPTL) $@.o $(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
++	$(FL) -o $@ $@.o $(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
+ 
+ 
+ .SUFFIXES: .c .F .o
diff --git a/var/spack/repos/builtin/packages/mumps/mumps-5.0.2-spectrum-mpi-xl.patch b/var/spack/repos/builtin/packages/mumps/mumps-5.0.2-spectrum-mpi-xl.patch
deleted file mode 100644
index d2bd17cb44..0000000000
--- a/var/spack/repos/builtin/packages/mumps/mumps-5.0.2-spectrum-mpi-xl.patch
+++ /dev/null
@@ -1,75 +0,0 @@
-diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1-patched/MUMPS_5.0.1/Makefile
---- ./Makefile	2015-07-23 13:08:29.000000000 -0400
-+++ ./Makefile	2016-12-05 14:08:30.788638382 -0500
-@@ -62,7 +62,7 @@
- $(libdir)/libpord$(PLAT)$(LIBEXT):
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cd $(LPORDDIR); \
--	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
-+	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" SAR="$(SAR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
- 	fi;
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cp $(LPORDDIR)/libpord$(LIBEXT) $@; \
-diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1-patched/PORD/lib/MUMPS_5.0.1/Makefile
---- ./PORD/lib/Makefile	2015-07-23 13:08:29.000000000 -0400
-+++ ./PORD/lib/Makefile	2016-12-05 11:26:24.785317467 -0500
-@@ -25,7 +25,7 @@
- 	$(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o
- 
- libpord$(LIBEXT):$(OBJS)
--	$(AR)$@ $(OBJS)
-+	$(SAR)$@ $(OBJS)
- 	$(RANLIB) $@
- 
- clean:
-diff -Naur MUMPS_5.0.1/examples/Makefile MUMPS_5.0.1-patched/examples/Makefile
---- ./examples/Makefile	2015-07-23 13:08:32.000000000 -0400
-+++ ./examples/Makefile	2016-12-05 14:36:10.692857906 -0500
-@@ -25,37 +25,30 @@
- 
- LIBSMUMPS = $(libdir)/libsmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--ssimpletest:  $(LIBSMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) ssimpletest.o  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+ssimpletest:  $(LIBSMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include ssimpletest.F  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBDMUMPS = $(libdir)/libdmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--dsimpletest: $(LIBDMUMPS)  $$@.o 
--	$(FL) -o $@ $(OPTL) dsimpletest.o  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+dsimpletest: $(LIBDMUMPS)  $$@.F 
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include dsimpletest.F  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBCMUMPS = $(libdir)/libcmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--csimpletest: $(LIBCMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) csimpletest.o  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+csimpletest: $(LIBCMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include csimpletest.F  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBZMUMPS = $(libdir)/libzmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--zsimpletest: $(LIBZMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) zsimpletest.o  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+zsimpletest: $(LIBZMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include zsimpletest.F  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
--c_example:	$(LIBDMUMPS) $$@.o
--	$(FL) -o $@ $(OPTL) $@.o $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
--
--
--.SUFFIXES: .c .F .o
--.F.o:
--	$(FC) $(OPTF) $(INCS) -I. -I$(topdir)/include -c $*.F $(OUTF)$*.o
--.c.o:
--	$(CC) $(OPTC) $(INCS) $(CDEFS) -I. -I$(topdir)/include -I$(topdir)/src -c $*.c $(OUTC)$*.o
-+c_example:	$(LIBDMUMPS) $$@.c
-+	$(CC) -o $@ $(OPTC) $(INCS) -I. -I$(topdir)/include c_example.c $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- $(libdir)/libsmumps$(PLAT)$(LIBEXT):
diff --git a/var/spack/repos/builtin/packages/mumps/mumps-5.1.1-spectrum-mpi-xl.patch b/var/spack/repos/builtin/packages/mumps/mumps-5.1.1-spectrum-mpi-xl.patch
deleted file mode 100644
index 8d9c1fb93a..0000000000
--- a/var/spack/repos/builtin/packages/mumps/mumps-5.1.1-spectrum-mpi-xl.patch
+++ /dev/null
@@ -1,79 +0,0 @@
-diff -Naur MUMPS_5.0.1/Makefile MUMPS_5.0.1-patched/MUMPS_5.0.1/Makefile
---- ./Makefile	2015-07-23 13:08:29.000000000 -0400
-+++ ./Makefile	2016-12-05 14:08:30.788638382 -0500
-@@ -62,7 +62,7 @@
- $(libdir)/libpord$(PLAT)$(LIBEXT):
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cd $(LPORDDIR); \
--	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" AR="$(AR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
-+	  $(MAKE) CC="$(CC)" CFLAGS="$(OPTC)" SAR="$(SAR)" RANLIB="$(RANLIB)" OUTC="$(OUTC)" LIBEXT=$(LIBEXT); \
- 	fi;
- 	if [ "$(LPORDDIR)" != "" ] ; then \
- 	  cp $(LPORDDIR)/libpord$(LIBEXT) $@; \
-diff -Naur MUMPS_5.0.1/PORD/lib/Makefile MUMPS_5.0.1-patched/PORD/lib/MUMPS_5.0.1/Makefile
---- ./PORD/lib/Makefile	2015-07-23 13:08:29.000000000 -0400
-+++ ./PORD/lib/Makefile	2016-12-05 11:26:24.785317467 -0500
-@@ -25,7 +25,7 @@
- 	$(CC) $(COPTIONS) -c $*.c $(OUTC)$*.o
- 
- libpord$(LIBEXT):$(OBJS)
--	$(AR)$@ $(OBJS)
-+	$(SAR)$@ $(OBJS)
- 	$(RANLIB) $@
- 
- clean:
---- ./examples/Makefile	2017-06-07 15:40:49.366671322 -0400
-+++ ./examples/Makefile	2017-06-07 15:47:55.666685772 -0400
-@@ -26,40 +26,33 @@
- 
- LIBSMUMPS = $(libdir)/libsmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--ssimpletest:  $(LIBSMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) ssimpletest.o  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+ssimpletest:  $(LIBSMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include ssimpletest.F  $(LIBSMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBDMUMPS = $(libdir)/libdmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--dsimpletest: $(LIBDMUMPS)  $$@.o 
--	$(FL) -o $@ $(OPTL) dsimpletest.o  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+dsimpletest: $(LIBDMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include dsimpletest.F  $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBCMUMPS = $(libdir)/libcmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--csimpletest: $(LIBCMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) csimpletest.o  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+csimpletest: $(LIBCMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include csimpletest.F  $(LIBCMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- LIBZMUMPS = $(libdir)/libzmumps$(PLAT)$(LIBEXT) $(LIBMUMPS_COMMON)
- 
--zsimpletest: $(LIBZMUMPS)  $$@.o
--	$(FL) -o $@ $(OPTL) zsimpletest.o  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+zsimpletest: $(LIBZMUMPS)  $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include zsimpletest.F  $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
--c_example:	$(LIBDMUMPS) $$@.o
--	$(FL) -o $@ $(OPTL) $@.o $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
-+c_example:	$(LIBDMUMPS) $$@.c
-+	$(CC) -o $@ $(OPTC) $(INCS) -I. -I$(topdir)/include c_example.c $(LIBDMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
--multiple_arithmetics_example:	$(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $$@.o
--	$(FL) -o $@ $(OPTL) $@.o $(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
--
--
--.SUFFIXES: .c .F .o
--.F.o:
--	$(FC) $(OPTF) $(INCS) -I. -I$(topdir)/include -c $*.F $(OUTF)$*.o
--.c.o:
--	$(CC) $(OPTC) $(INCS) $(CDEFS) -I. -I$(topdir)/include -I$(topdir)/src -c $*.c $(OUTC)$*.o
-+multiple_arithmetics_example:	$(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $$@.F
-+	$(FC) -o $@ $(OPTF) $(INCS) -I. -I$(topdir)/include multiple_arithmetics_example.F $(LIBSMUMPS) $(LIBDMUMPS) $(LIBCMUMPS) $(LIBZMUMPS) $(LORDERINGS) $(LIBS) $(LIBBLAS) $(LIBOTHERS)
- 
- 
- $(libdir)/libsmumps$(PLAT)$(LIBEXT):
diff --git a/var/spack/repos/builtin/packages/mumps/package.py b/var/spack/repos/builtin/packages/mumps/package.py
index cf3c4bbd1e..5ddd6606b4 100644
--- a/var/spack/repos/builtin/packages/mumps/package.py
+++ b/var/spack/repos/builtin/packages/mumps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import sys
@@ -69,10 +50,7 @@ class Mumps(Package):
     depends_on('scalapack', when='+mpi')
     depends_on('mpi', when='+mpi')
 
-    patch('mumps-5.0.2-spectrum-mpi-xl.patch', when='@5.0.2%xl^spectrum-mpi')
-    patch('mumps-5.0.2-spectrum-mpi-xl.patch', when='@5.0.2%xl_r^spectrum-mpi')
-    patch('mumps-5.1.1-spectrum-mpi-xl.patch', when='@5.1.1%xl^spectrum-mpi')
-    patch('mumps-5.1.1-spectrum-mpi-xl.patch', when='@5.1.1%xl_r^spectrum-mpi')
+    patch('examples.patch', when='@5.1.1%clang^spectrum-mpi')
 
     # this function is not a patch function because in case scalapack
     # is needed it uses self.spec['scalapack'].fc_link set by the
@@ -85,16 +63,26 @@ class Mumps(Package):
             raise RuntimeError(
                 'You cannot use the variants parmetis or ptscotch without mpi')
 
-        lapack_blas = (self.spec['lapack'].libs +
-                       self.spec['blas'].libs)
-        makefile_conf = ["LIBBLAS = %s" % lapack_blas.ld_flags]
+        # The makefile variables LIBBLAS, LSCOTCH, LMETIS, and SCALAP are only
+        # used to link the examples, so if building '+shared' there is no need
+        # to explicitly link with the respective libraries because we make sure
+        # the mumps shared libraries are already linked with them. See also the
+        # comment below about 'inject_libs'. This behaviour may cause problems
+        # if building '+shared' and the used libraries were build static
+        # without the PIC option.
+        shared = '+shared' in self.spec
+
+        lapack_blas = (self.spec['lapack'].libs + self.spec['blas'].libs)
+        makefile_conf = ["LIBBLAS = %s" %
+                         lapack_blas.ld_flags if not shared else '']
 
         orderings = ['-Dpord']
 
         if '+ptscotch' in self.spec or '+scotch' in self.spec:
             makefile_conf.extend([
                 "ISCOTCH = -I%s" % self.spec['scotch'].prefix.include,
-                "LSCOTCH = {0}".format(self.spec['scotch'].libs.ld_flags)
+                "LSCOTCH = {0}".format(
+                    self.spec['scotch'].libs.ld_flags if not shared else '')
             ])
 
             orderings.append('-Dscotch')
@@ -104,22 +92,37 @@ class Mumps(Package):
         if '+parmetis' in self.spec and '+metis' in self.spec:
             makefile_conf.extend([
                 "IMETIS = -I%s" % self.spec['parmetis'].prefix.include,
-                "LMETIS = -L%s -l%s -L%s -l%s" % (
+                ("LMETIS = -L%s -l%s -L%s -l%s" % (
                     self.spec['parmetis'].prefix.lib, 'parmetis',
-                    self.spec['metis'].prefix.lib, 'metis')
+                    self.spec['metis'].prefix.lib, 'metis')) if not shared
+                else 'LMETIS ='
             ])
 
             orderings.append('-Dparmetis')
         elif '+metis' in self.spec:
             makefile_conf.extend([
                 "IMETIS = -I%s" % self.spec['metis'].prefix.include,
-                "LMETIS = -L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')
+                ("LMETIS = -L%s -l%s" % (
+                    self.spec['metis'].prefix.lib, 'metis')) if not shared
+                else 'LMETIS ='
             ])
 
             orderings.append('-Dmetis')
 
         makefile_conf.append("ORDERINGSF = %s" % (' '.join(orderings)))
 
+        # Determine which compiler suite we are using
+        using_gcc = self.compiler.name == "gcc"
+        using_pgi = self.compiler.name == "pgi"
+        using_intel = self.compiler.name == "intel"
+        using_xl = self.compiler.name in ['xl', 'xl_r']
+
+        # The llvm compiler suite does not contain a Fortran compiler by
+        # default.  Its possible that a Spack user may have configured
+        # ~/.spack/<platform>/compilers.yaml for using xlf.
+        using_xlf = using_xl or \
+            (spack_f77.endswith('xlf') or spack_f77.endswith('xlf_r'))
+
         # when building shared libs need -fPIC, otherwise
         # /usr/bin/ld: graph.o: relocation R_X86_64_32 against `.rodata.str1.1'
         # can not be used when making a shared object; recompile with -fPIC
@@ -127,45 +130,47 @@ class Mumps(Package):
         # TODO: test this part, it needs a full blas, scalapack and
         # partitionning environment with 64bit integers
 
+        opt_level = '3' if using_xl else ''
+
         if '+int64' in self.spec:
-            if self.compiler.name == "xl" or self.compiler.name == "xl_r":
-                makefile_conf.extend(
-                    ['OPTF    = -O3',
-                     'OPTL    = %s -O3' % fpic,
-                     'OPTC    = %s -O3-DINTSIZE64' % fpic])
+            if using_xlf:
+                makefile_conf.append('OPTF = -O%s' % opt_level)
             else:
-                makefile_conf.extend(
-                    # the fortran compilation flags most probably are
-                    # working only for intel and gnu compilers this is
-                    # perhaps something the compiler should provide
-                    ['OPTF    = %s -O  -DALLOW_NON_INIT %s' % (fpic, '-fdefault-integer-8' if self.compiler.name == "gcc" else '-i8'),  # noqa
-                     'OPTL    = %s -O ' % fpic,
-                     'OPTC    = %s -O -DINTSIZE64' % fpic])
+                # the fortran compilation flags most probably are
+                # working only for intel and gnu compilers this is
+                # perhaps something the compiler should provide
+                makefile_conf.extend([
+                    'OPTF = %s -O  -DALLOW_NON_INIT %s' % (
+                        fpic,
+                        '-fdefault-integer-8' if using_gcc
+                                              else '-i8'),  # noqa
+                ])
+
+            makefile_conf.extend([
+                'OPTL = %s -O%s' % (fpic, opt_level),
+                'OPTC = %s -O%s -DINTSIZE64' % (fpic, opt_level)
+            ])
         else:
-            if self.compiler.name == "xl" or self.compiler.name == "xl_r":
-                makefile_conf.extend(
-                    ['OPTF    = -O3 -qfixed',
-                     'OPTL    = %s -O3' % fpic,
-                     'OPTC    = %s -O3' % fpic])
+            if using_xlf:
+                makefile_conf.append('OPTF = -O%s -qfixed' % opt_level)
             else:
-                makefile_conf.extend(
-                    ['OPTF    = %s -O  -DALLOW_NON_INIT' % fpic,
-                     'OPTL    = %s -O ' % fpic,
-                     'OPTC    = %s -O ' % fpic])
+                makefile_conf.append('OPTF = %s -O%s -DALLOW_NON_INIT' % (
+                    fpic, opt_level))
+
+            makefile_conf.extend([
+                'OPTL = %s -O%s' % (fpic, opt_level),
+                'OPTC = %s -O%s' % (fpic, opt_level)
+            ])
 
         if '+mpi' in self.spec:
-            scalapack = self.spec['scalapack'].libs
+            scalapack = self.spec['scalapack'].libs if not shared \
+                else LibraryList([])
             makefile_conf.extend(
                 ['CC = {0}'.format(self.spec['mpi'].mpicc),
                  'FC = {0}'.format(self.spec['mpi'].mpifc),
+                 'FL = {0}'.format(self.spec['mpi'].mpifc),
                  "SCALAP = %s" % scalapack.ld_flags,
                  "MUMPS_TYPE = par"])
-            if (self.spec.satisfies('%xl_r' or '%xl')) and self.spec.satisfies('^spectrum-mpi'):  # noqa
-                makefile_conf.extend(
-                    ['FL = {0}'.format(self.spec['mpi'].mpicc)])
-            else:
-                makefile_conf.extend(
-                    ['FL = {0}'.format(self.spec['mpi'].mpifc)])
         else:
             makefile_conf.extend(
                 ["CC = cc",
@@ -175,35 +180,64 @@ class Mumps(Package):
 
         # 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' or self.compiler.name == 'pgi':
+        if using_intel or using_pgi:
             # 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")
         else:
-            if self.compiler.name != "xl" and self.compiler.name != "xl_r":
-                makefile_conf.append("CDEFS   = -DAdd_")
+            if not using_xlf:
+                makefile_conf.append("CDEFS = -DAdd_")
 
         if '+shared' in self.spec:
+            # All Mumps libraries will be linked with 'inject_libs'.
+            inject_libs = []
+            if '+mpi' in self.spec:
+                inject_libs += [self.spec['scalapack'].libs.ld_flags]
+            if '+ptscotch' in self.spec or '+scotch' in self.spec:
+                inject_libs += [self.spec['scotch'].libs.ld_flags]
+            if '+parmetis' in self.spec and '+metis' in self.spec:
+                inject_libs += [
+                    "-L%s -l%s -L%s -l%s" % (
+                        self.spec['parmetis'].prefix.lib, 'parmetis',
+                        self.spec['metis'].prefix.lib, 'metis')]
+            elif '+metis' in self.spec:
+                inject_libs += [
+                    "-L%s -l%s" % (self.spec['metis'].prefix.lib, 'metis')]
+            inject_libs += [lapack_blas.ld_flags]
+            inject_libs = ' '.join(inject_libs)
+
             if sys.platform == 'darwin':
                 # Building dylibs with mpif90 causes segfaults on 10.8 and
                 # 10.10. Use gfortran. (Homebrew)
                 makefile_conf.extend([
                     'LIBEXT=.dylib',
-                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@) -undefined dynamic_lookup -o ' % (os.environ['FC'], prefix.lib),  # noqa
+                    'AR=%s -dynamiclib -Wl,-install_name -Wl,%s/$(notdir $@)'
+                    ' -undefined dynamic_lookup %s -o ' %
+                    (os.environ['FC'], prefix.lib, inject_libs),
                     'RANLIB=echo'
                 ])
             else:
+                if using_xlf:
+                    build_shared_flag = "qmkshrobj"
+                else:
+                    build_shared_flag = "shared"
+
                 makefile_conf.extend([
                     'LIBEXT=.so',
-                    'AR=$(FL) -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib,  # noqa
-                    'RANLIB=echo'
+                    'AR=link_cmd() { $(FL) -%s -Wl,-soname '
+                    '-Wl,%s/$(notdir $@) -o "$$@" %s; }; link_cmd ' %
+                    (build_shared_flag, prefix.lib, inject_libs),
+                    'RANLIB=ls'
                 ])
+                # When building libpord, read AR from Makefile.inc instead of
+                # going through the make command line - this prevents various
+                # problems with the substring "$$@".
+                filter_file(' AR="\$\(AR\)"', '', 'Makefile')
+                filter_file('^(INCLUDES = -I../include)',
+                            '\\1\ninclude ../../Makefile.inc',
+                            join_path('PORD', 'lib', 'Makefile'))
 
-                if self.compiler.name == 'xl' or self.compiler.name == 'xl_r':
-                    makefile_conf.extend([
-                        'SAR=/bin/xlc -shared -Wl,-soname -Wl,%s/$(notdir $@) -o' % prefix.lib  # noqa
-                    ])
         else:
             makefile_conf.extend([
                 'LIBEXT  = .a',
@@ -222,24 +256,17 @@ class Mumps(Package):
                 fh.write(makefile_inc)
 
     def install(self, spec, prefix):
-        make_libs = []
-
-        # the choice to compile ?examples is to have kind of a sanity
-        # check on the libraries generated.
-        if '+float' in spec:
-            make_libs.append('sexamples')
-            if '+complex' in spec:
-                make_libs.append('cexamples')
-
-        if '+double' in spec:
-            make_libs.append('dexamples')
-            if '+complex' in spec:
-                make_libs.append('zexamples')
-
         self.write_makefile_inc()
 
         # Build fails in parallel
-        make(*make_libs, parallel=False)
+        # That is why we split the builds of 's', 'c', 'd', and/or 'z' which
+        # can be build one after the other, each using a parallel build.
+        letters_variants = [
+            ['s', '+float'], ['c', '+complex+float'],
+            ['d', '+double'], ['z', '+complex+double']]
+        for l, v in letters_variants:
+            if v in spec:
+                make(l + 'examples')
 
         install_tree('lib', prefix.lib)
         install_tree('include', prefix.include)
@@ -253,12 +280,28 @@ class Mumps(Package):
 
         # FIXME: extend the tests to mpirun -np 2 when build with MPI
         # FIXME: use something like numdiff to compare output files
-        with working_dir('examples'):
-            if '+float' in spec:
-                os.system('./ssimpletest < input_simpletest_real')
-                if '+complex' in spec:
-                    os.system('./csimpletest < input_simpletest_real')
-            if '+double' in spec:
-                os.system('./dsimpletest < input_simpletest_real')
-                if '+complex' in spec:
-                    os.system('./zsimpletest < input_simpletest_cmplx')
+        # Note: In some cases, when 'mpi' is enabled, the examples below cannot
+        # be run without 'mpirun', so we enabled the tests only if explicitly
+        # requested with the Spack '--test' option.
+        if self.run_tests:
+            with working_dir('examples'):
+                if '+float' in spec:
+                    ssimpletest = Executable('./ssimpletest')
+                    ssimpletest(input='input_simpletest_real')
+                    if '+complex' in spec:
+                        csimpletest = Executable('./csimpletest')
+                        csimpletest(input='input_simpletest_cmplx')
+                if '+double' in spec:
+                    dsimpletest = Executable('./dsimpletest')
+                    dsimpletest(input='input_simpletest_real')
+                    if '+complex' in spec:
+                        zsimpletest = Executable('./zsimpletest')
+                        zsimpletest(input='input_simpletest_cmplx')
+
+    @property
+    def libs(self):
+        component_libs = ['*mumps*', 'pord']
+        return find_libraries(['lib' + comp for comp in component_libs],
+                              root=self.prefix.lib,
+                              shared=('+shared' in self.spec),
+                              recursive=False) or None
diff --git a/var/spack/repos/builtin/packages/munge/package.py b/var/spack/repos/builtin/packages/munge/package.py
index f53fa5953e..cca523acb0 100644
--- a/var/spack/repos/builtin/packages/munge/package.py
+++ b/var/spack/repos/builtin/packages/munge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/muparser/auto_ptr.patch b/var/spack/repos/builtin/packages/muparser/auto_ptr.patch
new file mode 100644
index 0000000000..7e39ea603f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/muparser/auto_ptr.patch
@@ -0,0 +1,52 @@
+diff --git a/include/muParserBase.h b/include/muParserBase.h
+index beb15bb..685f59f 100644
+--- a/include/muParserBase.h
++++ b/include/muParserBase.h
+@@ -288,7 +288,7 @@ private:
+     mutable stringbuf_type  m_vStringBuf; ///< String buffer, used for storing string function arguments

+     stringbuf_type  m_vStringVarBuf;

+ 

+-    std::auto_ptr<token_reader_type> m_pTokenReader; ///< Managed pointer to the token reader object.

++    std::unique_ptr<token_reader_type> m_pTokenReader; ///< Managed pointer to the token reader object.

+ 

+     funmap_type  m_FunDef;         ///< Map of function names and pointers.

+     funmap_type  m_PostOprtDef;    ///< Postfix operator callbacks

+diff --git a/include/muParserToken.h b/include/muParserToken.h
+index fc91d78..0cca469 100644
+--- a/include/muParserToken.h
++++ b/include/muParserToken.h
+@@ -69,7 +69,7 @@ namespace mu
+       TString m_strTok;   ///< Token string

+       TString m_strVal;   ///< Value for string variables

+       value_type m_fVal;  ///< the value 

+-      std::auto_ptr<ParserCallback> m_pCallback;

++      std::unique_ptr<ParserCallback> m_pCallback;

+ 

+   public:

+ 

+diff --git a/src/muParserTest.cpp b/src/muParserTest.cpp
+index 4006b27..8feaa2c 100644
+--- a/src/muParserTest.cpp
++++ b/src/muParserTest.cpp
+@@ -1258,7 +1258,7 @@ namespace mu
+ 

+       try

+       {

+-        std::auto_ptr<Parser> p1;

++        std::unique_ptr<Parser> p1;

+         Parser  p2, p3;   // three parser objects

+                           // they will be used for testing copy and assignment operators

+         // p1 is a pointer since i'm going to delete it in order to test if

+diff --git a/src/muParserTokenReader.cpp b/src/muParserTokenReader.cpp
+index 8da1e40..49cee68 100644
+--- a/src/muParserTokenReader.cpp
++++ b/src/muParserTokenReader.cpp
+@@ -147,7 +147,7 @@ namespace mu
+   */

+   ParserTokenReader* ParserTokenReader::Clone(ParserBase *a_pParent) const

+   {

+-    std::auto_ptr<ParserTokenReader> ptr(new ParserTokenReader(*this));

++    std::unique_ptr<ParserTokenReader> ptr(new ParserTokenReader(*this));

+     ptr->SetParent(a_pParent);

+     return ptr.release();

+   }

diff --git a/var/spack/repos/builtin/packages/muparser/package.py b/var/spack/repos/builtin/packages/muparser/package.py
index 8c65207dc5..fe16e5617e 100644
--- a/var/spack/repos/builtin/packages/muparser/package.py
+++ b/var/spack/repos/builtin/packages/muparser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,40 @@ class Muparser(Package):
     homepage = "http://muparser.beltoforion.de/"
     url      = "https://github.com/beltoforion/muparser/archive/v2.2.5.tar.gz"
 
+    version('2.2.6.1', '410d29b4c58d1cdc2fc9ed1c1c7f67fe')
+    # 2.2.6 presents itself as 2.2.5, don't add it to Spack
+    # version('2.2.6', 'f197b2815ca0422b2091788a78f2dc8a')
     version('2.2.5', '02dae671aa5ad955fdcbcd3fee313fb7')
 
+    # Replace std::auto_ptr by std::unique_ptr
+    # https://github.com/beltoforion/muparser/pull/46
+    patch('auto_ptr.patch',
+          when='@2.2.5')
+
+    depends_on('cmake@3.1.0:', when='@2.2.6:', type='build')
+
+    # Cmake build since 2.2.6
+    @when('@2.2.6:')
+    def install(self, spec, prefix):
+        cmake_args = [
+            '-DENABLE_SAMPLES=OFF',
+            '-DENABLE_OPENMP=OFF',
+            '-DBUILD_SHARED_LIBS=ON'
+        ]
+
+        cmake_args.extend(std_cmake_args)
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make('install')
+
+    @when('@2.2.5')
     def install(self, spec, prefix):
         options = ['--disable-debug',
+                   '--disable-samples',
                    '--disable-dependency-tracking',
+                   'CXXFLAGS={0}'.format(self.compiler.cxx11_flag),
                    '--prefix=%s' % prefix]
 
         configure(*options)
diff --git a/var/spack/repos/builtin/packages/muscle/package.py b/var/spack/repos/builtin/packages/muscle/package.py
index 7ba57284c6..71c835613f 100644
--- a/var/spack/repos/builtin/packages/muscle/package.py
+++ b/var/spack/repos/builtin/packages/muscle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/muse/package.py b/var/spack/repos/builtin/packages/muse/package.py
index 3c3616854e..89a3402e9f 100644
--- a/var/spack/repos/builtin/packages/muse/package.py
+++ b/var/spack/repos/builtin/packages/muse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/muster/package.py b/var/spack/repos/builtin/packages/muster/package.py
index d926c90d8e..88a7d06560 100644
--- a/var/spack/repos/builtin/packages/muster/package.py
+++ b/var/spack/repos/builtin/packages/muster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mvapich2/ad_lustre_rwcontig_open_source.patch b/var/spack/repos/builtin/packages/mvapich2/ad_lustre_rwcontig_open_source.patch
deleted file mode 100644
index ff85845cf8..0000000000
--- a/var/spack/repos/builtin/packages/mvapich2/ad_lustre_rwcontig_open_source.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/mpi/romio/adio/ad_lustre/ad_lustre_rwcontig.c	2013-12-10 12:05:44.806417000 -0800
-+++ b/src/mpi/romio/adio/ad_lustre/ad_lustre_rwcontig.c	2013-12-10 11:53:03.295622000 -0800
-@@ -8,7 +8,7 @@
-  *   Copyright (C) 2008 Sun Microsystems, Lustre group
-  */
- 
--#define _XOPEN_SOURCE 600
-+//#define _XOPEN_SOURCE 600
- #include <stdlib.h>
- #include <malloc.h>
- #include "ad_lustre.h"
diff --git a/var/spack/repos/builtin/packages/mvapich2/package.py b/var/spack/repos/builtin/packages/mvapich2/package.py
index 4454907b74..44b064d256 100644
--- a/var/spack/repos/builtin/packages/mvapich2/package.py
+++ b/var/spack/repos/builtin/packages/mvapich2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import sys
 
 from spack import *
@@ -41,20 +22,18 @@ class Mvapich2(AutotoolsPackage):
     url = "http://mvapich.cse.ohio-state.edu/download/mvapich/mv2/mvapich2-2.2.tar.gz"
     list_url = "http://mvapich.cse.ohio-state.edu/downloads/"
 
-    # Newer alpha release
+    version('2.3rc2', '6fcf22fe2a16023b462ef57614daa357')
+    version('2.3rc1', '386d79ae36b2136d203826465ad8b6cc')
     version('2.3a', '87c3fbf8a755b53806fa9ecb21453445')
 
     # Prefer the latest stable release
-    version('2.2', '939b65ebe5b89a5bc822cdab0f31f96e', preferred=True)
+    version('2.3', sha256='01d5fb592454ddd9ecc17e91c8983b6aea0e7559aa38f410b111c8ef385b50dd', preferred=True)
+    version('2.2', '939b65ebe5b89a5bc822cdab0f31f96e')
     version('2.1', '0095ceecb19bbb7fb262131cb9c2cdd6')
     version('2.0', '9fbb68a4111a8b6338e476dc657388b4')
-    version('1.9', '5dc58ed08fd3142c260b70fe297e127c')
-
-    patch('ad_lustre_rwcontig_open_source.patch', when='@1.9')
 
     provides('mpi')
-    provides('mpi@:2.2', when='@1.9')  # MVAPICH2-1.9 supports MPI 2.2
-    provides('mpi@:3.0', when='@2.0:')  # MVAPICH2-2.0 supports MPI 3.0
+    provides('mpi@:3.0')
 
     variant('debug', default=False,
             description='Enable debug info and error messages at run-time')
@@ -62,6 +41,9 @@ class Mvapich2(AutotoolsPackage):
     variant('cuda', default=False,
             description='Enable CUDA extension')
 
+    variant('regcache', default=True,
+            description='Enable memory registration cache')
+
     # Accepted values are:
     #   single      - No threads (MPI_THREAD_SINGLE)
     #   funneled    - Only the main thread calls MPI (MPI_THREAD_FUNNELED)
@@ -103,16 +85,44 @@ class Mvapich2(AutotoolsPackage):
         )
     )
 
+    variant(
+        'alloca',
+        default=False,
+        description='Use alloca to allocate temporary memory if available'
+    )
+
+    variant(
+        'file_systems',
+        description='List of the ROMIO file systems to activate',
+        values=('lustre', 'gpfs', 'nfs', 'ufs'),
+        multi=True
+    )
+
+    depends_on('findutils', type='build')
     depends_on('bison', type='build')
     depends_on('libpciaccess', when=(sys.platform != 'darwin'))
     depends_on('cuda', when='+cuda')
+    depends_on('psm', when='fabrics=psm')
+    depends_on('rdma-core', when='fabrics=mrail')
+    depends_on('rdma-core', when='fabrics=nemesisib')
+    depends_on('rdma-core', when='fabrics=nemesistcpib')
+    depends_on('rdma-core', when='fabrics=nemesisibtcp')
+
+    filter_compiler_wrappers(
+        'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
+    )
 
-    def url_for_version(self, version):
-        base_url = "http://mvapich.cse.ohio-state.edu/download"
-        if version < Version('2.0'):
-            return "%s/mvapich2/mv2/mvapich2-%s.tar.gz" % (base_url, version)
-        else:
-            return "%s/mvapich/mv2/mvapich2-%s.tar.gz"  % (base_url, version)
+    @property
+    def libs(self):
+        query_parameters = self.spec.last_query.extra_parameters
+        libraries = ['libmpi']
+
+        if 'cxx' in query_parameters:
+            libraries = ['libmpicxx'] + libraries
+
+        return find_libraries(
+            libraries, root=self.prefix, shared=True, recursive=True
+        )
 
     @property
     def process_manager_options(self):
@@ -122,20 +132,17 @@ class Mvapich2(AutotoolsPackage):
         for x in ('hydra', 'gforker', 'remshell'):
             if 'process_managers={0}'.format(x) in spec:
                 other_pms.append(x)
-        opts = ['--with-pm=%s' % ':'.join(other_pms)]
+
+        opts = []
+        if len(other_pms) > 0:
+            opts = ['--with-pm=%s' % ':'.join(other_pms)]
 
         # See: http://slurm.schedmd.com/mpi_guide.html#mvapich2
         if 'process_managers=slurm' in spec:
-            if self.version > Version('2.0'):
-                opts = [
-                    '--with-pmi=pmi2',
-                    '--with-pm=slurm'
-                ]
-            else:
-                opts = [
-                    '--with-pmi=slurm',
-                    '--with-pm=no'
-                ]
+            opts = [
+                '--with-pmi=pmi2',
+                '--with-pm=slurm'
+            ]
 
         return opts
 
@@ -144,7 +151,10 @@ class Mvapich2(AutotoolsPackage):
         opts = []
         # From here on I can suppose that only one variant has been selected
         if 'fabrics=psm' in self.spec:
-            opts = ["--with-device=ch3:psm"]
+            opts = [
+                "--with-device=ch3:psm",
+                "--with-psm={0}".format(self.spec['psm'].prefix)
+            ]
         elif 'fabrics=sock' in self.spec:
             opts = ["--with-device=ch3:sock"]
         elif 'fabrics=nemesistcpib' in self.spec:
@@ -156,12 +166,31 @@ class Mvapich2(AutotoolsPackage):
         elif 'fabrics=nemesis' in self.spec:
             opts = ["--with-device=ch3:nemesis"]
         elif 'fabrics=mrail' in self.spec:
-            opts = ["--with-device=ch3:mrail", "--with-rdma=gen2"]
+            opts = ["--with-device=ch3:mrail", "--with-rdma=gen2",
+                    "--disable-mcast"]
+        return opts
+
+    @property
+    def file_system_options(self):
+        spec = self.spec
+
+        fs = []
+        for x in ('lustre', 'gpfs', 'nfs', 'ufs'):
+            if 'file_systems={0}'.format(x) in spec:
+                fs.append(x)
+
+        opts = []
+        if len(fs) > 0:
+            opts.append('--with-file-system=%s' % '+'.join(fs))
+
         return opts
 
     def setup_environment(self, spack_env, run_env):
         spec = self.spec
-        if 'process_managers=slurm' in spec and spec.satisfies('@2.0:'):
+        # mvapich2 configure fails when F90 and F90FLAGS are set
+        spack_env.unset('F90')
+        spack_env.unset('F90FLAGS')
+        if 'process_managers=slurm' in spec:
             run_env.set('SLURM_MPI_TYPE', 'pmi2')
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
@@ -201,13 +230,16 @@ class Mvapich2(AutotoolsPackage):
         args = [
             '--enable-shared',
             '--enable-romio',
-            '-disable-silent-rules',
+            '--disable-silent-rules',
+            '--disable-new-dtags',
             '--enable-fortran=all',
             "--enable-threads={0}".format(spec.variants['threads'].value),
             "--with-ch3-rank-bits={0}".format(
                 spec.variants['ch3_rank_bits'].value),
         ]
 
+        args.extend(self.enable_or_disable('alloca'))
+
         if '+debug' in self.spec:
             args.extend([
                 '--disable-fast',
@@ -228,36 +260,12 @@ class Mvapich2(AutotoolsPackage):
         else:
             args.append('--disable-cuda')
 
+        if '+regcache' in self.spec:
+            args.append('--enable-registration-cache')
+        else:
+            args.append('--disable-registration-cache')
+
         args.extend(self.process_manager_options)
         args.extend(self.network_options)
+        args.extend(self.file_system_options)
         return args
-
-    @run_after('install')
-    def filter_compilers(self):
-        """Run after install to make the MPI compilers use the
-           compilers that Spack built the package with.
-
-           If this isn't done, they'll have CC, CXX, F77, and FC set
-           to Spack's generic cc, c++, f77, and f90.  We want them to
-           be bound to whatever compiler they were built with.
-        """
-        bin = self.prefix.bin
-        mpicc = join_path(bin, 'mpicc')
-        mpicxx = join_path(bin, 'mpicxx')
-        mpif77 = join_path(bin, 'mpif77')
-        mpif90 = join_path(bin, 'mpif90')
-        mpifort = join_path(bin, 'mpifort')
-
-        # Substitute Spack compile wrappers for the real
-        # underlying compiler
-        kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
-        filter_file(env['CC'], self.compiler.cc, mpicc, **kwargs)
-        filter_file(env['CXX'], self.compiler.cxx, mpicxx, **kwargs)
-        filter_file(env['F77'], self.compiler.f77, mpif77, **kwargs)
-        filter_file(env['FC'], self.compiler.fc, mpif90, **kwargs)
-        filter_file(env['FC'], self.compiler.fc, mpifort, **kwargs)
-
-        # Remove this linking flag if present
-        # (it turns RPATH into RUNPATH)
-        for wrapper in (mpicc, mpicxx, mpif77, mpif90, mpifort):
-            filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs)
diff --git a/var/spack/repos/builtin/packages/mxml/package.py b/var/spack/repos/builtin/packages/mxml/package.py
index c1e0a8f968..05a27c20e3 100644
--- a/var/spack/repos/builtin/packages/mxml/package.py
+++ b/var/spack/repos/builtin/packages/mxml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py
index 00443ec633..cc1e5861ba 100644
--- a/var/spack/repos/builtin/packages/mxnet/package.py
+++ b/var/spack/repos/builtin/packages/mxnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,8 @@ class Mxnet(MakefilePackage):
     homepage = "http://mxnet.io"
     url      = "https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz"
 
+    version('1.3.0', 'c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2',
+            url='https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz')
     version('0.10.0.post2',  '7819d511cf4a6efad681e6662fa966e4',
             url="https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz")
     version('0.10.0.post1',  '16d540f407cd22285555b3ab22040032',
@@ -43,6 +26,7 @@ class Mxnet(MakefilePackage):
     variant('opencv', default=True, description='Enable OpenCV support')
     variant('openmp', default=False, description='Enable OpenMP support')
     variant('profiler', default=False, description='Enable Profiler (for verification and debug only).')
+    variant('python', default=True, description='Install python bindings')
 
     depends_on('dmlc-core@20170508')
     depends_on('dmlc-core+openmp', when='+openmp')
@@ -50,29 +34,45 @@ class Mxnet(MakefilePackage):
     depends_on('mshadow@20170721')
     depends_on('ps-lite@20170328')
     depends_on('nnvm~shared@20170418')
-    depends_on('openblas')
+    depends_on('blas')
     depends_on('cudnn', when='+cuda')
     depends_on('cudnn', when='+cuda')
     depends_on('cub', when='+cuda')
     depends_on('opencv+core+imgproc+highgui+jpeg+png+tiff~eigen~ipp@3.0:', when='+opencv')
 
+    # python extensions
+    depends_on('python@2.7:', type=('build', 'run'), when='+python')
+    depends_on('py-setuptools', type='build', when='+python')
+    extends('python', when='+python')
+
     patch('makefile.patch', when='@0.10:0.11')
 
     def build(self, spec, prefix):
-        filter_file('export CC = gcc', '', 'make/config.mk', string=True)
-        filter_file('export CXX = g++', '', 'make/config.mk', string=True)
+        # copy template configuration file
+        copy('make/config.mk', 'config.mk')
+
+        # remove compiler overrides
+        filter_file('export CC = gcc', '', 'config.mk', string=True)
+        filter_file('export CXX = g++', '', 'config.mk', string=True)
+
+        # add blas prefix to include paths
+        filter_file(
+            '-I$(NNVM_PATH)/include',
+            '-I$(NNVM_PATH)/include -I%s/include' % spec['blas'].prefix,
+            'Makefile', string=True
+        )
+
+        # mxnet comes with its own version of nnvm and dmlc.
+        # building it will fail if we use the spack paths
 
         args = [
             'CC=%s' % self.compiler.cc,
             'CXX=%s' % self.compiler.cxx,
-            'DMLC_CORE=%s' % spec['dmlc-core'].prefix,
             'MSHADOW_PATH=%s' % spec['mshadow'].prefix,
             'PS_PATH=%s' % spec['ps-lite'].prefix,
-            'NNVM_PATH=%s' % spec['nnvm'].prefix,
             'USE_OPENMP=%s' % ('1' if '+openmp' in spec else '0'),
             'USE_CUDA=%s' % ('1' if '+cuda' in spec else '0'),
             'USE_CUDNN=%s' % ('1' if '+cuda' in spec else '0'),
-            'CUB_INCLUDE=%s' % spec['cub'].prefix.include,
             'USE_OPENCV=%s' % ('1' if '+opencv' in spec else '0'),
             'USE_PROFILER=%s' % ('1' if '+profiler' in spec else '0'),
         ]
@@ -86,16 +86,27 @@ class Mxnet(MakefilePackage):
                         '-lopencv_core -lopencv_imgproc -lopencv_imgcodecs',
                         'Makefile', string=True)
 
-        # TODO: Add more BLAS support
-        args.append('USE_BLAS=openblas')
+        if 'openblas' in spec:
+            args.extend(['USE_BLAS=openblas'])
+        elif 'atlas' in spec or 'cblas' in spec:
+            args.extend(['USE_BLAS=atlas'])
+        else:
+            args.extend(['USE_BLAS=blas'])
 
         if '+cuda' in spec:
             args.extend(['USE_CUDA_PATH=%s' % spec['cuda'].prefix,
-                         'CUDNN_PATH=%s' % spec['cudnn'].prefix])
+                         'CUDNN_PATH=%s' % spec['cudnn'].prefix,
+                         'CUB_INCLUDE=%s' % spec['cub'].prefix.include])
 
         make(*args)
 
     def install(self, spec, prefix):
+        # mxnet is just a shared library -- no need to install a bin tree
+
         install_tree('include', prefix.include)
         install_tree('lib', prefix.lib)
-        install_tree('bin', prefix.bin)
+
+        # install python bindings
+        if '+python' in spec:
+            python = which('python')
+            python('python/setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/nag/package.py b/var/spack/repos/builtin/packages/nag/package.py
index 226cd90353..8c72d36a40 100644
--- a/var/spack/repos/builtin/packages/nag/package.py
+++ b/var/spack/repos/builtin/packages/nag/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -30,7 +11,8 @@ class Nag(Package):
     """The NAG Fortran Compiler."""
     homepage = "http://www.nag.com/nagware/np.asp"
 
-    version('6.1', '0040d2254258223c78a6a4ab4829d7e0')
+    version('6.2', '8b119cc3296969bbd68b781f625de272')
+    version('6.1', '9b3cc0f8703c79f6231ae12359535119')
     version('6.0', '3fa1e7f7b51ef8a23e6c687cdcad9f96')
 
     # Licensing
diff --git a/var/spack/repos/builtin/packages/nalu-wind/package.py b/var/spack/repos/builtin/packages/nalu-wind/package.py
new file mode 100644
index 0000000000..0b3414ad85
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nalu-wind/package.py
@@ -0,0 +1,84 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import sys
+
+
+class NaluWind(CMakePackage):
+    """Nalu-Wind: Wind energy focused variant of Nalu."""
+
+    homepage = "https://github.com/exawind/nalu-wind"
+    git      = "https://github.com/exawind/nalu-wind.git"
+
+    maintainers = ['jrood-nrel']
+
+    tags = ['ecp', 'ecp-apps']
+
+    version('master', branch='master')
+
+    variant('openfast', default=False,
+            description='Compile with OpenFAST support')
+    variant('tioga', default=False,
+            description='Compile with Tioga support')
+    variant('hypre', default=False,
+            description='Compile with Hypre support')
+    variant('shared', default=(sys.platform != 'darwin'),
+            description='Build Trilinos as shared library')
+    variant('pic', default=True,
+            description='Position independent code')
+
+    depends_on('mpi')
+    depends_on('yaml-cpp@0.5.3:')
+    depends_on('trilinos+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards~hypre@master,develop', when='+shared')
+    # Cannot build Trilinos as a shared library with STK on Darwin
+    # https://github.com/trilinos/Trilinos/issues/2994
+    depends_on('trilinos~shared+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards~hypre@master,develop', when='~shared')
+    depends_on('openfast+cxx', when='+openfast')
+    depends_on('tioga', when='+tioga')
+    depends_on('hypre+mpi+int64', when='+hypre')
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        options.extend([
+            '-DTrilinos_DIR:PATH=%s' % spec['trilinos'].prefix,
+            '-DYAML_DIR:PATH=%s' % spec['yaml-cpp'].prefix,
+            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DMPI_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DMPI_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DMPI_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % (
+                'ON' if '+pic' in spec else 'OFF'),
+        ])
+
+        if '+openfast' in spec:
+            options.extend([
+                '-DENABLE_OPENFAST:BOOL=ON',
+                '-DOpenFAST_DIR:PATH=%s' % spec['openfast'].prefix
+            ])
+        else:
+            options.append('-DENABLE_OPENFAST:BOOL=OFF')
+
+        if '+tioga' in spec:
+            options.extend([
+                '-DENABLE_TIOGA:BOOL=ON',
+                '-DTIOGA_DIR:PATH=%s' % spec['tioga'].prefix
+            ])
+        else:
+            options.append('-DENABLE_TIOGA:BOOL=OFF')
+
+        if '+hypre' in spec:
+            options.extend([
+                '-DENABLE_HYPRE:BOOL=ON',
+                '-DHYPRE_DIR:PATH=%s' % spec['hypre'].prefix
+            ])
+        else:
+            options.append('-DENABLE_HYPRE:BOOL=OFF')
+
+        return options
diff --git a/var/spack/repos/builtin/packages/nalu/package.py b/var/spack/repos/builtin/packages/nalu/package.py
index 36dd317009..5e009d7e01 100644
--- a/var/spack/repos/builtin/packages/nalu/package.py
+++ b/var/spack/repos/builtin/packages/nalu/package.py
@@ -1,52 +1,43 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
 class Nalu(CMakePackage):
     """Nalu: a generalized unstructured massively parallel low Mach flow code
-       designed to support a variety of energy applications of interest (most
-       notably Wind ECP) built on the Sierra Toolkit and Trilinos solver
-       Tpetra/Epetra stack
+       designed to support a variety of energy applications of interest
+       built on the Sierra Toolkit and Trilinos solver Tpetra/Epetra stack
     """
 
     homepage = "https://github.com/NaluCFD/Nalu"
-    url      = "https://github.com/NaluCFD/Nalu.git"
+    git      = "https://github.com/NaluCFD/Nalu.git"
 
-    maintainers = ['jrood-nrel']
+    version('master', branch='master')
 
     variant('openfast', default=False,
             description='Compile with OpenFAST support')
+    variant('tioga', default=False,
+            description='Compile with Tioga support')
+    variant('hypre', default=False,
+            description='Compile with Hypre support')
+    variant('shared', default=(sys.platform != 'darwin'),
+            description='Build Trilinos as shared library')
+    variant('pic', default=True,
+            description='Position independent code')
 
-    version('master',
-            git='https://github.com/NaluCFD/Nalu.git', branch='master')
-
-    # Currently Nalu only builds static libraries; To be fixed soon
-    depends_on('yaml-cpp+pic~shared@0.5.3:')
-    depends_on('trilinos~shared+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards@master,12.12.1:')
+    depends_on('mpi')
+    depends_on('yaml-cpp@0.5.3:')
+    depends_on('trilinos+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards~hypre@master,develop', when='+shared')
+    # Cannot build Trilinos as a shared library with STK on Darwin
+    # https://github.com/trilinos/Trilinos/issues/2994
+    depends_on('trilinos~shared+exodus+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+shards~hypre@master,develop', when='~shared')
     depends_on('openfast+cxx', when='+openfast')
+    depends_on('tioga', when='+tioga')
+    depends_on('hypre+mpi+int64', when='+hypre')
 
     def cmake_args(self):
         spec = self.spec
@@ -55,12 +46,32 @@ class Nalu(CMakePackage):
         options.extend([
             '-DTrilinos_DIR:PATH=%s' % spec['trilinos'].prefix,
             '-DYAML_DIR:PATH=%s' % spec['yaml-cpp'].prefix,
-            '-DENABLE_INSTALL:BOOL=ON'
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % (
+                'ON' if '+pic' in spec else 'OFF'),
         ])
 
         if '+openfast' in spec:
             options.extend([
+                '-DENABLE_OPENFAST:BOOL=ON',
                 '-DOpenFAST_DIR:PATH=%s' % spec['openfast'].prefix
             ])
+        else:
+            options.append('-DENABLE_OPENFAST:BOOL=OFF')
+
+        if '+tioga' in spec:
+            options.extend([
+                '-DENABLE_TIOGA:BOOL=ON',
+                '-DTIOGA_DIR:PATH=%s' % spec['tioga'].prefix
+            ])
+        else:
+            options.append('-DENABLE_TIOGA:BOOL=OFF')
+
+        if '+hypre' in spec:
+            options.extend([
+                '-DENABLE_HYPRE:BOOL=ON',
+                '-DHYPRE_DIR:PATH=%s' % spec['hypre'].prefix
+            ])
+        else:
+            options.append('-DENABLE_HYPRE:BOOL=OFF')
 
         return options
diff --git a/var/spack/repos/builtin/packages/namd/package.py b/var/spack/repos/builtin/packages/namd/package.py
index 54d165525b..a7e82fd1d0 100644
--- a/var/spack/repos/builtin/packages/namd/package.py
+++ b/var/spack/repos/builtin/packages/namd/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import platform
-import shutil
 import sys
 import os
 from spack import *
@@ -44,7 +24,7 @@ class Namd(MakefilePackage):
     variant('interface', default='none', values=('none', 'tcl', 'python'),
             description='Enables TCL and/or python interface')
 
-    depends_on('charm')
+    depends_on('charmpp')
 
     depends_on('fftw@:2.99', when="fftw=2")
     depends_on('fftw@3:', when="fftw=3")
@@ -58,8 +38,8 @@ class Namd(MakefilePackage):
 
     def _copy_arch_file(self, lib):
         config_filename = 'arch/{0}.{1}'.format(self.arch, lib)
-        shutil.copy('arch/Linux-x86_64.{0}'.format(lib),
-                    config_filename)
+        copy('arch/Linux-x86_64.{0}'.format(lib),
+             config_filename)
         if lib == 'tcl':
             filter_file(r'-ltcl8\.5',
                         '-ltcl{0}'.format(self.spec['tcl'].version.up_to(2)),
diff --git a/var/spack/repos/builtin/packages/nano/package.py b/var/spack/repos/builtin/packages/nano/package.py
index 200c47a7b3..bbb2523d5a 100644
--- a/var/spack/repos/builtin/packages/nano/package.py
+++ b/var/spack/repos/builtin/packages/nano/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nanoflann/package.py b/var/spack/repos/builtin/packages/nanoflann/package.py
index 13c5797d69..f042e8e4b9 100644
--- a/var/spack/repos/builtin/packages/nanoflann/package.py
+++ b/var/spack/repos/builtin/packages/nanoflann/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nanopb/package.py b/var/spack/repos/builtin/packages/nanopb/package.py
new file mode 100644
index 0000000000..1b8472f3d7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nanopb/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Nanopb(CMakePackage):
+    """Nanopb is a small code-size Protocol Buffers implementation
+    in ansi C."""
+
+    homepage = "https://jpa.kapsi.fi/nanopb/"
+    url      = "https://github.com/nanopb/nanopb/archive/0.3.9.1.tar.gz"
+
+    version('0.3.9.1', '08d71b315819626366b0303f8658fc68')
+
+    depends_on('protobuf', type=('build'))
+    depends_on('py-protobuf', type=('build'))
diff --git a/var/spack/repos/builtin/packages/nasm/package.py b/var/spack/repos/builtin/packages/nasm/package.py
index 2979ad43f5..3604b1ec28 100644
--- a/var/spack/repos/builtin/packages/nasm/package.py
+++ b/var/spack/repos/builtin/packages/nasm/package.py
@@ -1,34 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Nasm(AutotoolsPackage):
     """NASM (Netwide Assembler) is an 80x86 assembler designed for
-       portability and modularity. It includes a disassembler as well."""
+    portability and modularity. It includes a disassembler as well."""
+
     homepage = "http://www.nasm.us"
-    url      = "http://www.nasm.us/pub/nasm/releasebuilds/2.11.06/nasm-2.11.06.tar.xz"
+    url      = "http://www.nasm.us/pub/nasm/releasebuilds/2.13.03/nasm-2.13.03.tar.xz"
+    list_url = "http://www.nasm.us/pub/nasm/releasebuilds"
+    list_depth = 1
 
+    version('2.13.03', 'd5ca2ad7121ccbae69dd606b1038532c')
     version('2.11.06', '2b958e9f5d200641e6fc9564977aecc5')
+
+    # Fix compilation with GCC 8
+    # https://bugzilla.nasm.us/show_bug.cgi?id=3392461
+    patch('https://src.fedoraproject.org/rpms/nasm/raw/0cc3eb244bd971df81a7f02bc12c5ec259e1a5d6/f/0001-Remove-invalid-pure_func-qualifiers.patch', level=1, sha256='ac9f315d204afa6b99ceefa1fe46d4eed2b8a23c7315d32d33c0f378d930e950', when='@2.13.03 %gcc@8:')
diff --git a/var/spack/repos/builtin/packages/nauty/package.py b/var/spack/repos/builtin/packages/nauty/package.py
index ef032ad7c9..a350ff207d 100644
--- a/var/spack/repos/builtin/packages/nauty/package.py
+++ b/var/spack/repos/builtin/packages/nauty/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
 from spack import *
@@ -74,7 +55,7 @@ class Nauty(AutotoolsPackage):
     depends_on('autoconf',  type='build', when='@2.6r7')
     depends_on('automake',  type='build', when='@2.6r7')
     depends_on('libtool',  type='build', when='@2.6r7')
-    depends_on('pkg-config',  type='build')
+    depends_on('pkgconfig',  type='build')
     depends_on('help2man', type='build')
     depends_on('zlib')
     depends_on('gmp')
diff --git a/var/spack/repos/builtin/packages/ncbi-magicblast/package.py b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py
new file mode 100644
index 0000000000..b0e9c3434a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ncbi-magicblast/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NcbiMagicblast(AutotoolsPackage):
+    """Magic-BLAST is a tool for mapping large next-generation RNA or DNA
+    sequencing runs against a whole genome or transcriptome. """
+
+    homepage = "https://ncbi.github.io/magicblast/"
+    url      = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.3.0/ncbi-magicblast-1.3.0-src.tar.gz"
+
+    version('1.3.0', '2615b919c1fe1bf7dc3d816392ab4420')
+
+    depends_on('lmdb')
+    configure_directory = 'c++'
+
+    def configure_args(self):
+        return ['--without-internal']
diff --git a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py
index 57b918cde8..8dd04b5586 100644
--- a/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py
+++ b/var/spack/repos/builtin/packages/ncbi-rmblastn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ncbi-toolkit/package.py b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py
new file mode 100644
index 0000000000..3f1bc0d543
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ncbi-toolkit/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NcbiToolkit(AutotoolsPackage):
+    """NCBI C++ Toolkit"""
+
+    homepage = "https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/"
+    url      = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--21_0_0.tar.gz"
+
+    version('21_0_0', '14e021e08b1a78ac9cde98d0cab92098')
+
+    depends_on('boost@1.35.0:')
+    depends_on('bzip2')
+    depends_on('libjpeg')
+    depends_on('libpng')
+    depends_on('libtiff')
+    depends_on('libxml2')
+    depends_on('libxslt@1.1.14:')
+    depends_on('lzo')
+    depends_on('pcre')
+    depends_on('giflib')
+    depends_on('sqlite@3.6.6:')
+    depends_on('zlib')
+    depends_on('samtools')
+    depends_on('bamtools')
+
+    def configure_args(self):
+        return ['--without-sybase', '--without-fastcgi']
+
+    def patch(self):
+        with working_dir(join_path('src', 'util', 'image')):
+            filter_file(r'jpeg_start_compress(&cinfo, true)',
+                        'jpeg_start_compress(&cinfo, TRUE)',
+                        'image_io_jpeg.cpp', string=True)
+
+    def build(self, spec, prefix):
+        compiler_version = self.compiler.version.joined
+
+        with working_dir(join_path(
+                'GCC{0}-DebugMT64'.format(compiler_version), 'build')):
+            make('all_r')
diff --git a/var/spack/repos/builtin/packages/nccl/package.py b/var/spack/repos/builtin/packages/nccl/package.py
index e1ac486e16..5ea2b9689c 100644
--- a/var/spack/repos/builtin/packages/nccl/package.py
+++ b/var/spack/repos/builtin/packages/nccl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,9 @@ class Nccl(MakefilePackage):
     homepage = "https://github.com/NVIDIA/nccl"
     url      = "https://github.com/NVIDIA/nccl/archive/v1.3.4-1.tar.gz"
 
+    version('2.3.5-5',
+            sha256='bac9950b4d3980c25baa8e3e4541d2dfb4d21edf32ad3b89022d04920357142f')
+    version('2.2', '5b9ce7fbdce0fde68e0f66318e6ff422')
     version('1.3.4-1', '5b9ce7fbdce0fde68e0f66318e6ff422')
     version('1.3.0-1', 'f6fb1d56913a7d212ca0c300e76f01fb')
 
@@ -42,4 +26,7 @@ class Nccl(MakefilePackage):
 
     @property
     def install_targets(self):
-        return ['PREFIX={0}'.format(self.prefix), 'install']
+        if self.version >= Version('2.3.5-5'):
+            return ['PREFIX={0}'.format(self.prefix), 'src.install']
+        else:
+            return ['PREFIX={0}'.format(self.prefix), 'install']
diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py
index e710faa034..69736cc34b 100644
--- a/var/spack/repos/builtin/packages/nccmp/package.py
+++ b/var/spack/repos/builtin/packages/nccmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ncdu/package.py b/var/spack/repos/builtin/packages/ncdu/package.py
index a95fc5b1ca..d77478c618 100644
--- a/var/spack/repos/builtin/packages/ncdu/package.py
+++ b/var/spack/repos/builtin/packages/ncdu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,8 @@ class Ncdu(Package):
     homepage = "http://dev.yorhel.nl/ncdu"
     url      = "http://dev.yorhel.nl/download/ncdu-1.11.tar.gz"
 
+    version('1.13', sha256='f4d9285c38292c2de05e444d0ba271cbfe1a705eee37c2b23ea7c448ab37255a')
+    version('1.12', sha256='820e4e4747a2a2ec7a2e9f06d2f5a353516362c22496a10a9834f871b877499a')
     version('1.11', '9e44240a5356b029f05f0e70a63c4d12')
     version('1.10', '7535decc8d54eca811493e82d4bfab2d')
     version('1.9', '93258079db897d28bb8890e2db89b1fb')
diff --git a/var/spack/repos/builtin/packages/ncftp/package.py b/var/spack/repos/builtin/packages/ncftp/package.py
index 704affdad3..2b9e417aa8 100644
--- a/var/spack/repos/builtin/packages/ncftp/package.py
+++ b/var/spack/repos/builtin/packages/ncftp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ncl/package.py b/var/spack/repos/builtin/packages/ncl/package.py
index 25b903e4c7..8a231761fd 100644
--- a/var/spack/repos/builtin/packages/ncl/package.py
+++ b/var/spack/repos/builtin/packages/ncl/package.py
@@ -1,31 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
-import shutil
 import tempfile
 
 
@@ -37,15 +17,16 @@ class Ncl(Package):
 
     homepage = "https://www.ncl.ucar.edu"
 
-    version('6.4.0', 'a981848ddcaf1c263279648265f24766',
-            url='https://www.earthsystemgrid.org/download/fileDownload.html?logicalFileId=86b9bec2-fa01-11e6-a976-00c0f03d5b7c',
-            extension='tar.gz')
+    url = "https://github.com/NCAR/ncl/archive/6.4.0.tar.gz"
+
+    version('6.5.0', '133446f3302eddf237db56bf349e1ebf228240a7320699acc339a3d7ee414591')
+    version('6.4.0', 'd891452cda7bb25afad9b6c876c73986')
 
     patch('spack_ncl.patch')
-    # Make ncl compile with hdf5 1.10
-    patch('hdf5.patch')
-    # ymake-filter's buffer may overflow
-    patch('ymake-filter.patch')
+    # Make ncl compile with hdf5 1.10 (upstream as of 6.5.0)
+    patch('hdf5.patch', when="@6.4.0")
+    # ymake-filter's buffer may overflow (upstream as of 6.5.0)
+    patch('ymake-filter.patch', when="@6.4.0")
 
     # This installation script is implemented according to this manual:
     # http://www.ncl.ucar.edu/Download/build_from_src.shtml
@@ -106,6 +87,8 @@ class Ncl(Package):
         placement='triangle_src',
         when='+triangle')
 
+    sanity_check_is_file = ['bin/ncl']
+
     def patch(self):
         # Make configure scripts use Spack's tcsh
         files = ['Configure'] + glob.glob('config/*')
@@ -261,8 +244,8 @@ class Ncl(Package):
             triangle_src = join_path(self.stage.source_path, 'triangle_src')
             triangle_dst = join_path(self.stage.source_path, 'ni', 'src',
                                      'lib', 'hlu')
-            shutil.copy(join_path(triangle_src, 'triangle.h'), triangle_dst)
-            shutil.copy(join_path(triangle_src, 'triangle.c'), triangle_dst)
+            copy(join_path(triangle_src, 'triangle.h'), triangle_dst)
+            copy(join_path(triangle_src, 'triangle.c'), triangle_dst)
 
     @staticmethod
     def delete_files(*filenames):
diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py
index 2aea5aed2c..6b46596b6e 100644
--- a/var/spack/repos/builtin/packages/nco/package.py
+++ b/var/spack/repos/builtin/packages/nco/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -60,3 +41,10 @@ class Nco(AutotoolsPackage):
     def configure_args(self):
         spec = self.spec
         return ['--{0}-doc'.format('enable' if '+doc' in spec else 'disable')]
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+        spack_env.set('NETCDF_INC', spec['netcdf'].prefix.include)
+        spack_env.set('NETCDF_LIB', spec['netcdf'].prefix.lib)
+        spack_env.set('ANTLR_ROOT', spec['antlr'].prefix)
+        spack_env.set('UDUNITS2_PATH', spec['udunits2'].prefix)
diff --git a/var/spack/repos/builtin/packages/ncurses/package.py b/var/spack/repos/builtin/packages/ncurses/package.py
index 06ffc0b650..56218a9306 100644
--- a/var/spack/repos/builtin/packages/ncurses/package.py
+++ b/var/spack/repos/builtin/packages/ncurses/package.py
@@ -1,32 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 from os.path import exists, join
 from os import makedirs
-from shutil import copy
 
 
 class Ncurses(AutotoolsPackage):
@@ -37,15 +17,18 @@ class Ncurses(AutotoolsPackage):
     SYSV-curses enhancements over BSD curses."""
 
     homepage = "http://invisible-island.net/ncurses/ncurses.html"
-    url      = "http://ftp.gnu.org/pub/gnu/ncurses/ncurses-6.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/ncurses/ncurses-6.1.tar.gz"
 
+    version('6.1', '98c889aaf8d23910d2b92d65be2e737a')
     version('6.0', 'ee13d052e1ead260d7c28071f46eefb1')
     version('5.9', '8cb9c412e5f2d96bc6f459aa8c6282a1')
 
     variant('symlinks', default=False,
             description='Enables symlinks. Needed on AFS filesystem.')
+    variant('termlib', default=False,
+            description='Enables termlib needs for gnutls in emacs.')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     patch('patch_gcc_5.txt', when='@6.0%gcc@5.0:')
     patch('sed_pgi.patch',   when='@:6.0')
@@ -71,6 +54,12 @@ class Ncurses(AutotoolsPackage):
         if '+symlinks' in self.spec:
             opts.append('--enable-symlinks')
 
+        if '+termlib' in self.spec:
+            opts.extend(('--with-termlib',
+                         '--enable-termcap',
+                         '--enable-getcap',
+                         '--enable-tcap-names'))
+
         prefix = '--prefix={0}'.format(prefix)
 
         configure = Executable('../configure')
@@ -100,9 +89,9 @@ class Ncurses(AutotoolsPackage):
             if not exists(path):
                 makedirs(path)
             for header in headers:
-                copy(header, path)
+                install(header, path)
 
     @property
     def libs(self):
         return find_libraries(
-            ['libncurses', 'libncursesw'], root=self.prefix, recurse=True)
+            ['libncurses', 'libncursesw'], root=self.prefix, recursive=True)
diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py
index 5dd160e50c..f37115fe96 100644
--- a/var/spack/repos/builtin/packages/ncview/package.py
+++ b/var/spack/repos/builtin/packages/ncview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ndiff/package.py b/var/spack/repos/builtin/packages/ndiff/package.py
index 176a3463d3..ab997d1daa 100644
--- a/var/spack/repos/builtin/packages/ndiff/package.py
+++ b/var/spack/repos/builtin/packages/ndiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nek5000/package.py b/var/spack/repos/builtin/packages/nek5000/package.py
new file mode 100644
index 0000000000..a952029a86
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nek5000/package.py
@@ -0,0 +1,234 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import numbers
+import os
+
+
+def is_integral(x):
+    """Any integer value"""
+    try:
+        return isinstance(int(x), numbers.Integral) and \
+            not isinstance(x, bool) and int(x) > 0
+    except ValueError:
+        return False
+
+
+class Nek5000(Package):
+    """A fast and scalable high-order solver for computational fluid
+       dynamics"""
+
+    homepage = "https://nek5000.mcs.anl.gov/"
+    url      = "https://github.com/Nek5000/Nek5000/releases/download/v17.0/Nek5000-v17.0.tar.gz"
+    git      = "https://github.com/Nek5000/Nek5000.git"
+
+    tags = ['cfd', 'flow', 'hpc', 'solver', 'navier-stokes',
+            'spectral-elements', 'fluid', 'ecp', 'ecp-apps']
+
+    version('develop', branch='master')
+    version('17.0', '6a13bfad2ce023897010dd88f54a0a87')
+
+    # MPI, Profiling and Visit variants
+    variant('mpi',       default=True, description='Build with MPI.')
+    variant('profiling', default=True, description='Build with profiling data.')
+    variant('visit',     default=False, description='Build with Visit.')
+
+    # TODO: add a variant 'blas' or 'external-blas' to enable the usage of
+    #       Spack installed/configured blas.
+
+    # Variant for MAXNEL, we need to read this from user
+    variant(
+        'MAXNEL',
+        default=150000,
+        description='Maximum number of elements for Nek5000 tools.',
+        values=is_integral
+    )
+
+    # Variants for Nek tools
+    variant('genbox',   default=True, description='Build genbox tool.')
+    variant('int_tp',   default=True, description='Build int_tp tool.')
+    variant('n2to3',    default=True, description='Build n2to3 tool.')
+    variant('postnek',  default=True, description='Build postnek tool.')
+    variant('reatore2', default=True, description='Build reatore2 tool.')
+    variant('genmap',   default=True, description='Build genmap tool.')
+    variant('nekmerge', default=True, description='Build nekmerge tool.')
+    variant('prenek',   default=True, description='Build prenek tool.')
+
+    # Dependencies
+    depends_on('mpi', when="+mpi")
+    depends_on('libx11', when="+prenek")
+    depends_on('libx11', when="+postnek")
+    # libxt is needed for X11/Intrinsic.h but not for linking
+    depends_on('libxt', when="+prenek")
+    depends_on('xproto', when="+prenek")
+    depends_on('libxt', when="+postnek")
+    depends_on('visit', when="+visit")
+
+    @run_before('install')
+    def fortran_check(self):
+        if not self.compiler.f77:
+            msg = 'Cannot build Nek5000 without a Fortran 77 compiler.'
+            raise RuntimeError(msg)
+
+    @run_after('install')
+    def test_install(self):
+        with working_dir('short_tests/eddy'):
+            os.system(join_path(self.prefix.bin, 'makenek') + ' eddy_uv')
+            if not os.path.isfile(join_path(os.getcwd(), 'nek5000')):
+                msg = 'Cannot build example: short_tests/eddy.'
+                raise RuntimeError(msg)
+
+    def install(self, spec, prefix):
+        tools_dir   = 'tools'
+        bin_dir     = 'bin'
+
+        # Do not use the Spack compiler wrappers.
+        # Use directly the compilers:
+        fc  = self.compiler.f77
+        cc  = self.compiler.cc
+
+        fflags = spec.compiler_flags['fflags']
+        cflags = spec.compiler_flags['cflags']
+        if ('+prenek' in spec) or ('+postnek' in spec):
+            libx11_h = find_headers('Xlib', spec['libx11'].prefix.include,
+                                    recursive=True)
+            if not libx11_h:
+                raise RuntimeError('Xlib.h not found in %s' %
+                                   spec['libx11'].prefix.include)
+            cflags += ['-I%s' % os.path.dirname(libx11_h.directories[0])]
+
+            xproto_h = find_headers('X', spec['xproto'].prefix.include,
+                                    recursive=True)
+            if not xproto_h:
+                raise RuntimeError('X.h not found in %s' %
+                                   spec['xproto'].prefix.include)
+            cflags += ['-I%s' % os.path.dirname(xproto_h.directories[0])]
+
+            libxt_h = find_headers('Intrinsic', spec['libxt'].prefix.include,
+                                   recursive=True)
+            if not libxt_h:
+                raise RuntimeError('X11/Intrinsic.h not found in %s' %
+                                   spec['libxt'].prefix.include)
+            cflags += ['-I%s' % os.path.dirname(libxt_h.directories[0])]
+        if self.compiler.name in ['xl', 'xl_r']:
+            # Use '-qextname' to add underscores.
+            # Use '-WF,-qnotrigraph' to fix an error about a string: '... ??'
+            fflags += ['-qextname', '-WF,-qnotrigraph']
+        fflags = ' '.join(fflags)
+        cflags = ' '.join(cflags)
+
+        # Build the tools, maketools copy them to Nek5000/bin by default.
+        # We will then install Nek5000/bin under prefix after that.
+        with working_dir(tools_dir):
+            # Update the maketools script to use correct compilers
+            filter_file(r'^#FC\s*=.*', 'FC="{0}"'.format(fc), 'maketools')
+            filter_file(r'^#CC\s*=.*', 'CC="{0}"'.format(cc), 'maketools')
+            if fflags:
+                filter_file(r'^#FFLAGS=.*', 'FFLAGS="{0}"'.format(fflags),
+                            'maketools')
+            if cflags:
+                filter_file(r'^#CFLAGS=.*', 'CFLAGS="{0}"'.format(cflags),
+                            'maketools')
+
+            if self.compiler.name in ['xl', 'xl_r']:
+                # Patch 'maketools' to use '-qextname' when checking for
+                # underscore becasue 'xl'/'xl_r' use this option to enable the
+                # addition of the underscore.
+                filter_file(r'^\$FC -c ', '$FC -qextname -c ', 'maketools')
+
+            libx11_lib = find_libraries('libX11', spec['libx11'].prefix.lib,
+                                        shared=True, recursive=True)
+            if not libx11_lib:
+                libx11_lib = \
+                    find_libraries('libX11', spec['libx11'].prefix.lib64,
+                                   shared=True, recursive=True)
+            if not libx11_lib:
+                raise RuntimeError('libX11 not found in %s/{lib,lib64}' %
+                                   spec['libx11'].prefix)
+            # There is no other way to set the X11 library path except brute
+            # force:
+            filter_file(r'-L\$\(X\)', libx11_lib.search_flags,
+                        join_path('prenek', 'makefile'))
+            filter_file(r'-L\$\(X\)', libx11_lib.search_flags,
+                        join_path('postnek', 'makefile'))
+
+            if self.compiler.name in ['xl', 'xl_r']:
+                # Use '-qextname' when compiling mxm.f
+                filter_file('\$\(OLAGS\)', '-qextname $(OLAGS)',
+                            join_path('postnek', 'makefile'))
+            # Define 'rename_' function that calls 'rename'
+            with open(join_path('postnek', 'xdriver.c'), 'a') as xdriver:
+                xdriver.write('\nvoid rename_(char *from, char *to)\n{\n'
+                              '   rename(from, to);\n}\n')
+
+            maxnel = self.spec.variants['MAXNEL'].value
+            filter_file(r'^#MAXNEL\s*=.*', 'MAXNEL=' + maxnel, 'maketools')
+
+            maketools = Executable('./maketools')
+
+            # Build the tools
+            if '+genbox' in spec:
+                maketools('genbox')
+            # "ERROR: int_tp does not exist!"
+            # if '+int_tp' in spec:
+            #     maketools('int_tp')
+            if '+n2to3' in spec:
+                maketools('n2to3')
+            if '+postnek' in spec:
+                maketools('postnek')
+            if '+reatore2' in spec:
+                maketools('reatore2')
+            if '+genmap' in spec:
+                maketools('genmap')
+            if '+nekmerge' in spec:
+                maketools('nekmerge')
+            if '+prenek' in spec:
+                maketools('prenek')
+
+        with working_dir(bin_dir):
+            if '+mpi' in spec:
+                fc  = spec['mpi'].mpif77
+                cc  = spec['mpi'].mpicc
+            else:
+                filter_file(r'^#MPI=0', 'MPI=0', 'makenek')
+
+            if '+profiling' not in spec:
+                filter_file(r'^#PROFILING=0', 'PROFILING=0', 'makenek')
+
+            if '+visit' in spec:
+                filter_file(r'^#VISIT=1', 'VISIT=1', 'makenek')
+                filter_file(r'^#VISIT_INSTALL=.*', 'VISIT_INSTALL=\"' +
+                            spec['visit'].prefix.bin + '\"', 'makenek')
+
+            # Update the makenek to use correct compilers and
+            # Nek5000 source.
+            filter_file(r'^#FC\s*=.*', 'FC="{0}"'.format(fc), 'makenek')
+            filter_file(r'^#CC\s*=.*', 'CC="{0}"'.format(cc), 'makenek')
+            filter_file(r'^#SOURCE_ROOT\s*=\"\$H.*',  'SOURCE_ROOT=\"' +
+                        prefix.bin.Nek5000 + '\"',  'makenek')
+            if fflags:
+                filter_file(r'^#FFLAGS=.*', 'FFLAGS="{0}"'.format(fflags),
+                            'makenek')
+            if cflags:
+                filter_file(r'^#CFLAGS=.*', 'CFLAGS="{0}"'.format(cflags),
+                            'makenek')
+
+        with working_dir('core'):
+            if self.compiler.name in ['xl', 'xl_r']:
+                # Patch 'core/makenek.inc' and 'makefile.template' to use
+                # '-qextname' when checking for underscore becasue 'xl'/'xl_r'
+                # use this option to enable the addition of the underscore.
+                filter_file(r'^\$FCcomp -c ', '$FCcomp -qextname -c ',
+                            'makenek.inc')
+                filter_file(r'\$\(FC\) -c \$\(L0\)',
+                            '$(FC) -c -qextname $(L0)', 'makefile.template')
+
+        # Install Nek5000/bin in prefix/bin
+        install_tree(bin_dir, prefix.bin)
+
+        # Copy Nek5000 source to prefix/bin
+        install_tree('../Nek5000', prefix.bin.Nek5000)
diff --git a/var/spack/repos/builtin/packages/nekbone/package.py b/var/spack/repos/builtin/packages/nekbone/package.py
index 3d419b9156..ff34fc25ac 100644
--- a/var/spack/repos/builtin/packages/nekbone/package.py
+++ b/var/spack/repos/builtin/packages/nekbone/package.py
@@ -1,27 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -33,32 +13,50 @@ class Nekbone(Package):
        the spectral element method."""
 
     homepage = "https://github.com/Nek5000/Nekbone"
-    url = "https://github.com/Nek5000/Nekbone/tarball/v17.0"
+    url      = "https://github.com/Nek5000/Nekbone/archive/v17.0.tar.gz"
+    git      = "https://github.com/Nek5000/Nekbone.git"
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
-    version('17.0', 'cc339684547614a0725959e41839fec1')
-    version('develop', git='https://github.com/Nek5000/Nekbone.git')
+    version('develop', branch='master')
+    version('17.0', sha256='ae361cc61368a924398a28a296f675b7f0c4a9516788a7f8fa3c09d787cdf69b')
 
-    depends_on('mpi')
+    # Variants
+    variant('mpi', default=True, description='Build with MPI')
 
-    def install(self, spec, prefix):
+    # dependencies
+    depends_on('mpi', when='+mpi')
+
+    @run_before('install')
+    def fortran_check(self):
+        if not self.compiler.fc:
+            msg = 'Nekbone can not be built without a Fortran compiler.'
+            raise RuntimeError(msg)
 
-        working_dirs = ['example1', 'example2', 'example3', 'nek_comm',
-                        'nek_delay', 'nek_mgrid']
+    def install(self, spec, prefix):
         mkdir(prefix.bin)
 
-        for wdir in working_dirs:
-            with working_dir('test/' + wdir):
-                makenec = FileFilter('makenek')
-                makenec.filter('CC.*', 'CC=' + self.spec['mpi'].mpicc)
-                makenec.filter('FF77.*', 'FF77=' + self.spec['mpi'].mpif77)
-                makenek = Executable('./makenek')
-                path = join_path(prefix.bin,  wdir)
-                makenek('ex1', '../../src')
-                mkdir(path)
-                install('nekbone', path)
-                install('nekpmpi', path)
-                install('data.rea', path)
-                install('SIZE', path)
-                install('README', path)
+        fc = self.compiler.fc
+        cc = self.compiler.cc
+        if '+mpi' in spec:
+            fc = spec['mpi'].mpif77
+            cc = spec['mpi'].mpicc
+
+        # Install Nekbone in prefix.bin
+        install_tree(self.stage.source_path, prefix.bin.Nekbone)
+
+        # Install scripts in prefix.bin
+        nekpmpi = 'test/example1/nekpmpi'
+        makenek = 'test/example1/makenek'
+
+        install(makenek, prefix.bin)
+        install(nekpmpi, prefix.bin)
+
+        with working_dir(prefix.bin):
+            filter_file(r'^SOURCE_ROOT\s*=.*', 'SOURCE_ROOT=\"' +
+                        prefix.bin.Nekbone + '/src\"', 'makenek')
+            filter_file(r'^CC\s*=.*', 'CC=\"' + cc + '\"', 'makenek')
+            filter_file(r'^F77\s*=.*', 'F77=\"' + fc + '\"', 'makenek')
+
+            if '+mpi' not in spec:
+                filter_file(r'^#IFMPI=\"false\"', 'IFMPI=\"false\"', 'makenek')
diff --git a/var/spack/repos/builtin/packages/nekcem/package.py b/var/spack/repos/builtin/packages/nekcem/package.py
new file mode 100644
index 0000000000..c1b981e0c1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nekcem/package.py
@@ -0,0 +1,111 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+import json
+
+
+class Nekcem(Package):
+    """Spectral-element solver for Maxwell's equations, drift-diffusion
+       equations, and more."""
+
+    # Links to homepage and git
+    homepage = "https://nekcem.mcs.anl.gov"
+    git      = "https://github.com/NekCEM/NekCEM.git"
+
+    # Variants
+    variant('mpi', default=True, description='Build with MPI')
+
+    # We only have a development version
+    version('develop')
+    version('0b8bedd', commit='0b8beddfdcca646bfcc866dfda1c5f893338399b')
+
+    # dependencies
+    depends_on('mpi', when='+mpi')
+    depends_on('blas')
+    depends_on('lapack')
+
+    @run_before('install')
+    def fortran_check(self):
+        if not self.compiler.fc:
+            msg = 'NekCEM can not be built without a Fortran compiler.'
+            raise RuntimeError(msg)
+
+    @run_after('install')
+    def test_install(self):
+        nekcem_test = join_path(self.prefix.bin, 'NekCEM', 'tests', '2dboxpec')
+        with working_dir(nekcem_test):
+            makenek = Executable(join_path(self.prefix.bin, 'makenek'))
+            makenek(os.path.basename(nekcem_test))
+            if not os.path.isfile('nekcem'):
+                msg = 'Cannot build example: %s' % nekcem_test
+                raise RuntimeError(msg)
+
+    def install(self, spec, prefix):
+        bin_dir = 'bin'
+        nek = 'nek'
+        configurenek = 'configurenek'
+        makenek = 'makenek'
+
+        fc = self.compiler.f77
+        cc = self.compiler.cc
+
+        fflags = spec.compiler_flags['fflags']
+        cflags = spec.compiler_flags['cflags']
+        ldflags = spec.compiler_flags['ldflags']
+
+        if '+mpi' in spec:
+            fc = spec['mpi'].mpif77
+            cc = spec['mpi'].mpicc
+
+        with working_dir(bin_dir):
+            fflags = ['-O3'] + fflags
+            cflags = ['-O3'] + cflags
+            fflags += ['-I.']
+            cflags += ['-I.', '-DGLOBAL_LONG_LONG']
+
+            if self.compiler.name == 'gcc' or self.compiler.name == 'clang':
+                # assuming 'clang' uses 'gfortran'
+                fflags += ['-fdefault-real-8', '-fdefault-double-8']
+                cflags += ['-DUNDERSCORE']
+            elif self.compiler.name == 'intel':
+                fflags += ['-r8']
+                cflags += ['-DUNDERSCORE']
+            elif self.compiler.name == 'xl' or self.compiler.name == 'xl_r':
+                fflags += ['-qrealsize=8']
+                cflags += ['-DPREFIX=jl_', '-DIBM']
+            elif self.compiler.name == 'pgi':
+                fflags += ['-r8']
+                cflags += ['-DUNDERSCORE']
+
+            if '+mpi' in spec:
+                fflags += ['-DMPI', '-DMPIIO']
+                cflags += ['-DMPI', '-DMPIIO']
+            blas_lapack = spec['lapack'].libs + spec['blas'].libs
+            pthread_lib = find_system_libraries('libpthread')
+            ldflags += (blas_lapack + pthread_lib).ld_flags.split()
+            all_arch = {
+                'spack-arch': {
+                    'FC': fc, 'FFLAGS': fflags,
+                    'CC': cc, 'CFLAGS': cflags,
+                    'LD': fc, 'LDFLAGS': ldflags
+                }
+            }
+            os.rename('arch.json', 'arch.json.orig')
+            with open('arch.json', 'w') as file:
+                file.write(json.dumps(all_arch))
+            filter_file(r'^ARCH=.*$', 'ARCH=spack-arch', 'makenek')
+            filter_file(r'^NEK=.*', 'NEK="%s"' % prefix.bin.NekCEM,
+                        'makenek')
+
+        # Install NekCEM in prefix/bin
+        install_tree('../NekCEM', prefix.bin.NekCEM)
+        # Create symlinks to makenek, nek and configurenek scripts
+        with working_dir(prefix.bin):
+            os.symlink(os.path.join('NekCEM', bin_dir, makenek), makenek)
+            os.symlink(
+                os.path.join('NekCEM', bin_dir, configurenek), configurenek)
+            os.symlink(os.path.join('NekCEM', bin_dir, nek), nek)
diff --git a/var/spack/repos/builtin/packages/nektar/package.py b/var/spack/repos/builtin/packages/nektar/package.py
new file mode 100644
index 0000000000..3e04b1c2b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nektar/package.py
@@ -0,0 +1,56 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Nektar(CMakePackage):
+    """Nektar++: Spectral/hp Element Framework"""
+
+    homepage = "https://www.nektar.info/"
+    url      = "https://gitlab.nektar.info/nektar/nektar/-/archive/v4.4.1/nektar-v4.4.1.tar.bz2"
+
+    version('4.4.1', '1be7d061c3cafd9a0f1eb8d281d99b89')
+
+    variant('mpi', default=True, description='Builds with mpi support')
+    variant('fftw', default=True, description='Builds with fftw support')
+    variant('arpack', default=True, description='Builds with arpack support')
+    variant('hdf5', default=True, description='Builds with hdf5 support')
+    variant('scotch', default=False,
+            description='Builds with scotch partitioning support')
+
+    depends_on('cmake@2.8.8:', type='build', when="~hdf5")
+    depends_on('cmake@3.2:', type='build', when="+hdf5")
+
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('boost@1.56.0: +iostreams')
+    depends_on('tinyxml', when='platform=darwin')
+
+    depends_on('mpi', when='+mpi')
+    depends_on('fftw@3.0: +mpi', when="+mpi+fftw")
+    depends_on('fftw@3.0: ~mpi', when="~mpi+fftw")
+    depends_on('arpack-ng +mpi', when="+arpack+mpi")
+    depends_on('arpack-ng ~mpi', when="+arpack~mpi")
+    depends_on('hdf5 +mpi +hl', when="+mpi+hdf5")
+    depends_on('scotch ~mpi ~metis', when="~mpi+scotch")
+    depends_on('scotch +mpi ~metis', when="+mpi+scotch")
+
+    conflicts("+hdf5", when="~mpi",
+              msg="Nektar's hdf5 output is for parallel builds only")
+
+    def cmake_args(self):
+        args = []
+
+        def hasfeature(feature):
+            return 'ON' if feature in self.spec else 'OFF'
+
+        args.append('-DNEKTAR_USE_MPI=%s' % hasfeature('+mpi'))
+        args.append('-DNEKTAR_USE_FFTW=%s' % hasfeature('+fftw'))
+        args.append('-DNEKTAR_USE_ARPACK=%s' % hasfeature('+arpack'))
+        args.append('-DNEKTAR_USE_HDF5=%s' % hasfeature('+hdf5'))
+        args.append('-DNEKTAR_USE_SCOTCH=%s' % hasfeature('+scotch'))
+        args.append('-DNEKTAR_USE_PETSC=OFF')
+        return args
diff --git a/var/spack/repos/builtin/packages/neovim/package.py b/var/spack/repos/builtin/packages/neovim/package.py
index 0f26daf83f..b626f34984 100644
--- a/var/spack/repos/builtin/packages/neovim/package.py
+++ b/var/spack/repos/builtin/packages/neovim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,6 +13,10 @@ class Neovim(CMakePackage):
     homepage = "http://neovim.io"
     url      = "https://github.com/neovim/neovim/archive/v0.2.0.tar.gz"
 
+    version('0.3.1', '5405bced1c929ebc245c75409cd6c7ef')
+    version('0.3.0', 'e5fdb2025757c337c17449c296eddf5b')
+    version('0.2.2', '44b69f8ace88b646ec890670f1e462c4')
+    version('0.2.1', 'f4271f22d2a46fa18dace42849c56a98')
     version('0.2.0', '9af7f61f9f0b1a2891147a479d185aa2')
 
     depends_on('lua@5.1:5.2')
@@ -44,10 +29,11 @@ class Neovim(CMakePackage):
     depends_on('libvterm')
     depends_on('unibilium')
     depends_on('msgpack-c')
+    depends_on('gperf')
 
     def cmake_args(self):
-        # FIXME: Add arguments other than
-        # FIXME: CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE
-        # FIXME: If not needed delete this function
         args = []
+        if self.version >= Version('0.2.1'):
+            args = ['-DPREFER_LUA=ON']
+
         return args
diff --git a/var/spack/repos/builtin/packages/nest/package.py b/var/spack/repos/builtin/packages/nest/package.py
new file mode 100644
index 0000000000..a62838dc7d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nest/package.py
@@ -0,0 +1,151 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Nest(CMakePackage):
+    """NEST is a simulator for spiking neural network models
+
+    It focuses on the dynamics, size and structure of neural systems rather
+    than on the exact morphology of individual neurons."""
+
+    homepage = "http://www.nest-simulator.org"
+    url      = "https://github.com/nest/nest-simulator/releases/download/v2.12.0/nest-2.12.0.tar.gz"
+
+    version('2.14.0', sha256='d6316d6c9153100a3220488abfa738958c4b65bf2622bd15540e4aa81e79f17f')
+    version('2.12.0', sha256='bac578f38bb0621618ee9d5f2f1febfee60cddc000ff32e51a5f5470bb3df40d')
+    version('2.10.0', sha256='2b6fc562cd6362e812d94bb742562a5a685fb1c7e08403765dbe123d59b0996c')
+    version('2.8.0',  sha256='d47325b27a5599b6ea58a3c4ef06656e7c5a4941c4e94dec6a5c2fa956209915')
+    version('2.6.0',  sha256='5fe4924bc57d0c7dd820aa371de935eedf7e813832c0eee2c976b33c9a8db4cf')
+    version('2.4.2',  sha256='8f86e58c1a12b733ffabd8b0400326e5a3494a458149ea8ebe9f19674d05b91b')
+
+    variant('python', default=True,
+            description='Build the PyNest interface')
+    variant('mpi', default=True,
+            description='Build with MPI bindings')
+    variant('openmp', default=True,
+            description='"Enable OpenMP support"')
+    variant('optimize', default=True,
+            description='Build with MPI bindings')
+    variant('modules', default=False,
+            description='Enables external module support')
+    variant('gsl',     default=True,
+            description="Enable GNU Scientific Library")
+    variant('shared',   default=True,
+            description="Build shared libraries")
+    # TODO add variants for neurosim and music when these are in spack
+
+    conflicts('~gsl', when='@:2.10.99',
+              msg='Option only introduced for non-ancient versions.')
+    conflicts('~shared', when='@:2.10.99',
+              msg='Option only introduced for non-ancient versions.')
+    conflicts('~openmp', when='@:2.10.99',
+              msg='Option only introduced for non-ancient versions.')
+
+    depends_on('python@2.6:',       when='+python', type=('build', 'run'))
+    depends_on('py-numpy',          when='+python', type=('build', 'run'))
+    depends_on('py-cython@0.19.2:', when='+python', type='build')
+    depends_on('py-nose',           when='+python', type='test')
+    depends_on('py-setuptools',     when='+python', type='build')
+
+    depends_on('mpi', when='+mpi')
+
+    depends_on('doxygen', type='build')
+
+    depends_on('gsl', when='+gsl')
+    depends_on('readline')
+    depends_on('libtool')
+    depends_on('pkgconfig', type='build')
+
+    extends('python', when='+python')
+
+    # Before 2.12.0 it was an autotools package
+    @when('@:2.10.99')
+    def cmake(self, spec, prefix):
+        pass
+
+    @when('@:2.10.99')
+    def build(self, spec, prefix):
+        pass
+
+    @when('@:2.10.99')
+    def install(self, spec, prefix):
+        configure_args = ["CXXFLAGS=-std=c++03",
+                          "--prefix=" + prefix,
+                          "--with-openmp"]
+        if '+python' in spec:
+            configure_args.append("--with-python")
+        else:
+            configure_args.append("--without-python")
+        if '+mpi' in spec:
+            configure_args.append("--with-mpi")
+        else:
+            configure_args.append("--without-mpi")
+        if '+optimize' in spec:
+            configure_args.append("--with-optimize")
+        else:
+            configure_args.append("--without-optimize")
+
+        configure(*configure_args)
+
+        make()
+        make("install")
+
+    def cmake_args(self):
+        args = []
+
+        if '+mpi' in self.spec:
+            args.append('-Dwith-mpi=ON')
+        else:
+            args.append('-Dwith-mpi=OFF')
+
+        if '+python':
+            version = self.spec['python'].version[0]
+            args.append('-Dwith-python={0}'.format(version))
+            args.append('-Dcythonize-pynest=' + self.spec['py-cython'].prefix)
+        else:
+            args.append('-Dwith-python=OFF')
+            args.append('-Dcythonize-pynest=OFF')
+
+        if '+optimize' in self.spec:
+            args.append('-Dwith-optimize=ON')
+        else:
+            args.append('-Dwith-optimize=OFF')
+
+        if '+gsl' in self.spec:
+            cmake_options.append('-Dwith-gsl=' + self.spec['gsl'].prefix)
+        else:
+            cmake_options.append('-Dwith-gsl=OFF')
+
+        if '+openmp' in self.spec:
+            cmake_options.append('-Dwith-openmp=ON')
+        else:
+            cmake_options.append('-Dwith-openmp=OFF')
+
+        if '+shared' in self.spec:
+            cmake_options.append('-Dstatic-libraries=OFF')
+        else:
+            cmake_options.append('-Dstatic-libraries=ON')
+
+        return args
+
+    @when('@:2.14.0+modules')
+    @run_after('install')
+    def install_headers(self):
+        # copy source files to installation folder for older versions
+        # (these are needed for modules to build against)
+        # see https://github.com/nest/nest-simulator/pull/844
+        path_headers = join_path(prefix, "include", "nest")
+
+        mkdirp(path_headers)
+
+        for suffix in ["h", "hpp"]:
+            for f in find_headers('*.{0}'.format(suffix),
+                                  self.stage.source_path, recursive=True):
+                install(f, path_headers)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set("NEST_INSTALL_DIR", self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
index 916c8f301a..07ecd2f22a 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,3 +18,10 @@ class NetcdfCxx(AutotoolsPackage):
     version('4.2', 'd32b20c00f144ae6565d9e98d9f6204c')
 
     depends_on('netcdf')
+
+    @property
+    def libs(self):
+        shared = True
+        return find_libraries(
+            'libnetcdf_c++', root=self.prefix, shared=shared, recursive=True
+        )
diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
index 0e15d67bc1..8d228cc3c0 100644
--- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,3 +21,13 @@ class NetcdfCxx4(AutotoolsPackage):
     depends_on('libtool', type='build')
 
     force_autoreconf = True
+
+    def configure_args(self):
+        return ['CPPFLAGS=-I' + self.spec['netcdf'].prefix.include]
+
+    @property
+    def libs(self):
+        shared = True
+        return find_libraries(
+            'libnetcdf_c++4', root=self.prefix, shared=shared, recursive=True
+        )
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/nag.patch b/var/spack/repos/builtin/packages/netcdf-fortran/nag.patch
new file mode 100644
index 0000000000..458c18813e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/nag.patch
@@ -0,0 +1,31 @@
+diff --git a/configure b/configure
+index 06ac8b0..d518a1a 100755
+--- a/configure
++++ b/configure
+@@ -10657,6 +10657,8 @@ _LT_EOF
+ 	lf95*)				# Lahey Fortran 8.1
+ 	  whole_archive_flag_spec=
+ 	  tmp_sharedflag='--shared' ;;
++	nagfor*)
++	  tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+ 	  tmp_addflag= ;;
+@@ -14252,6 +14254,8 @@ _LT_EOF
+ 	lf95*)				# Lahey Fortran 8.1
+ 	  whole_archive_flag_spec_F77=
+ 	  tmp_sharedflag='--shared' ;;
++	nagfor*)
++	  tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+ 	  tmp_addflag= ;;
+@@ -17142,6 +17146,8 @@ _LT_EOF
+ 	lf95*)				# Lahey Fortran 8.1
+ 	  whole_archive_flag_spec_FC=
+ 	  tmp_sharedflag='--shared' ;;
++	nagfor*)
++	  tmp_sharedflag='-Wl,-shared' ;;
+ 	xl[cC]* | bgxl[cC]* | mpixl[cC]*) # IBM XL C 8.0 on PPC (deal with xlf below)
+ 	  tmp_sharedflag='-qmkshrobj'
+ 	  tmp_addflag= ;;
diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
index f62db6eca0..64d4eca2a0 100644
--- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py
+++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,13 @@ class NetcdfFortran(AutotoolsPackage):
 
     depends_on('netcdf')
 
+    # The default libtool.m4 is too old to handle NAG compiler properly:
+    # https://github.com/Unidata/netcdf-fortran/issues/94
+    patch('nag.patch', when='@:4.4.4%nag')
+
+    def configure_args(self):
+        return ['CPPFLAGS=-I' + self.spec['netcdf'].prefix.include]
+
     @property
     def libs(self):
         libraries = ['libnetcdff']
@@ -46,5 +34,5 @@ class NetcdfFortran(AutotoolsPackage):
         shared = 'shared' in query_parameters
 
         return find_libraries(
-            libraries, root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf/package.py
index f12e2941c8..8a806dbf95 100644
--- a/var/spack/repos/builtin/packages/netcdf/package.py
+++ b/var/spack/repos/builtin/packages/netcdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import numbers
@@ -45,6 +26,7 @@ class Netcdf(AutotoolsPackage):
 
     # Version 4.4.1.1 is having problems in tests
     #    https://github.com/Unidata/netcdf-c/issues/343
+    version('4.6.1', 'ee81c593efc8a6229d9bcb350b6d7849')
     version('4.4.1.1', '503a2d6b6035d116ed53b1d80c811bda')
     # netcdf@4.4.1 can crash on you (in real life and in tests).  See:
     #    https://github.com/Unidata/netcdf-c/issues/282
@@ -152,10 +134,10 @@ class Netcdf(AutotoolsPackage):
                   r'\1{0}\2'.format(max_vars))
 
     def configure_args(self):
-        CFLAGS = []
-        CPPFLAGS = []
-        LDFLAGS = []
-        LIBS = []
+        cflags = []
+        cppflags = []
+        ldflags = []
+        libs = []
 
         config_args = ['--enable-v2',
                        '--enable-utilities',
@@ -176,7 +158,7 @@ class Netcdf(AutotoolsPackage):
         if '~shared' in self.spec:
             # We don't have shared libraries but we still want it to be
             # possible to use this library in shared builds
-            CFLAGS.append(self.compiler.pic_flag)
+            cflags.append(self.compiler.pic_flag)
 
         config_args += self.enable_or_disable('dap')
         # config_args += self.enable_or_disable('cdmremote')
@@ -188,10 +170,10 @@ class Netcdf(AutotoolsPackage):
             # undefined reference to `SSL_CTX_use_certificate_chain_file
             curl = self.spec['curl']
             curl_libs = curl.libs
-            LIBS.append(curl_libs.link_flags)
-            LDFLAGS.append(curl_libs.search_flags)
+            libs.append(curl_libs.link_flags)
+            ldflags.append(curl_libs.search_flags)
             # TODO: figure out how to get correct flags via headers.cpp_flags
-            CPPFLAGS.append('-I' + curl.prefix.include)
+            cppflags.append('-I' + curl.prefix.include)
 
         if self.spec.satisfies('@4.4:'):
             if '+mpi' in self.spec:
@@ -203,16 +185,16 @@ class Netcdf(AutotoolsPackage):
         # are removed. Variables CPPFLAGS, LDFLAGS, and LD_LIBRARY_PATH must be
         # used instead.
         hdf5_hl = self.spec['hdf5:hl']
-        CPPFLAGS.append(hdf5_hl.headers.cpp_flags)
-        LDFLAGS.append(hdf5_hl.libs.search_flags)
+        cppflags.append(hdf5_hl.headers.cpp_flags)
+        ldflags.append(hdf5_hl.libs.search_flags)
 
         if '+parallel-netcdf' in self.spec:
             config_args.append('--enable-pnetcdf')
             pnetcdf = self.spec['parallel-netcdf']
-            CPPFLAGS.append(pnetcdf.headers.cpp_flags)
+            cppflags.append(pnetcdf.headers.cpp_flags)
             # TODO: change to pnetcdf.libs.search_flags once 'parallel-netcdf'
             # package gets custom implementation of 'libs'
-            LDFLAGS.append('-L' + pnetcdf.prefix.lib)
+            ldflags.append('-L' + pnetcdf.prefix.lib)
         else:
             config_args.append('--disable-pnetcdf')
 
@@ -222,26 +204,26 @@ class Netcdf(AutotoolsPackage):
         config_args += self.enable_or_disable('hdf4')
         if '+hdf4' in self.spec:
             hdf4 = self.spec['hdf']
-            CPPFLAGS.append(hdf4.headers.cpp_flags)
+            cppflags.append(hdf4.headers.cpp_flags)
             # TODO: change to hdf4.libs.search_flags once 'hdf'
             # package gets custom implementation of 'libs' property.
-            LDFLAGS.append('-L' + hdf4.prefix.lib)
+            ldflags.append('-L' + hdf4.prefix.lib)
             # TODO: change to self.spec['jpeg'].libs.link_flags once the
             # implementations of 'jpeg' virtual package get 'jpeg_libs'
             # property.
-            LIBS.append('-ljpeg')
+            libs.append('-ljpeg')
             if '+szip' in hdf4:
                 # This should also come from hdf4.libs
-                LIBS.append('-lsz')
+                libs.append('-lsz')
 
         # Fortran support
         # In version 4.2+, NetCDF-C and NetCDF-Fortran have split.
         # Use the netcdf-fortran package to install Fortran support.
 
-        config_args.append('CFLAGS=' + ' '.join(CFLAGS))
-        config_args.append('CPPFLAGS=' + ' '.join(CPPFLAGS))
-        config_args.append('LDFLAGS=' + ' '.join(LDFLAGS))
-        config_args.append('LIBS=' + ' '.join(LIBS))
+        config_args.append('CFLAGS=' + ' '.join(cflags))
+        config_args.append('CPPFLAGS=' + ' '.join(cppflags))
+        config_args.append('LDFLAGS=' + ' '.join(ldflags))
+        config_args.append('LIBS=' + ' '.join(libs))
 
         return config_args
 
diff --git a/var/spack/repos/builtin/packages/netgauge/package.py b/var/spack/repos/builtin/packages/netgauge/package.py
index f850a22c2c..69557c8cb9 100644
--- a/var/spack/repos/builtin/packages/netgauge/package.py
+++ b/var/spack/repos/builtin/packages/netgauge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/netgen/package.py b/var/spack/repos/builtin/packages/netgen/package.py
index 9d6c4de81a..c67ed8cced 100644
--- a/var/spack/repos/builtin/packages/netgen/package.py
+++ b/var/spack/repos/builtin/packages/netgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,12 +24,13 @@ class Netgen(AutotoolsPackage):
     variant("gui", default=False, description='enable gui')
     variant("metis", default=False, description='use metis for partitioning')
 
+    depends_on('zlib')
     depends_on('mpi', when='+mpi')
     depends_on('oce+X11', when='+oce')
     depends_on('metis', when='+metis')
 
     def url_for_version(self, version):
-        url = "https://gigenet.dl.sourceforge.net/project/netgen-mesher/netgen-mesher/{0}/netgen-{1}.tar.gz"
+        url = "http://gigenet.dl.sourceforge.net/project/netgen-mesher/netgen-mesher/{0}/netgen-{1}.tar.gz"
         return url.format(version.up_to(2), version)
 
     def configure_args(self):
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/ibm-xl.patch b/var/spack/repos/builtin/packages/netlib-lapack/ibm-xl.patch
index c9598a4e7c..c6fba2a028 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/ibm-xl.patch
+++ b/var/spack/repos/builtin/packages/netlib-lapack/ibm-xl.patch
@@ -1,6 +1,17 @@
-diff -Naur lapack-3.6.1/CMAKE/CheckLAPACKCompilerFlags.cmake lapack-3.6.1-patched/CMAKE/CheckLAPACKCompilerFlags.cmake
---- lapack-3.6.1/CMAKE/CheckLAPACKCompilerFlags.cmake	2017-01-27 17:14:37.414854283 -0500
-+++ lapack-3.6.1-patched/CMAKE/CheckLAPACKCompilerFlags.cmake	2017-01-27 17:14:24.754719546 -0500
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -62,7 +62,7 @@
+     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fp-model strict")
+   endif()
+   if("${CMAKE_Fortran_COMPILER}" MATCHES "xlf")
+-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict=none")
++    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict")
+   endif()
+ # Delete libmtsk in linking sequence for Sun/Oracle Fortran Compiler.
+ # This library is not present in the Sun package SolarisStudio12.3-linux-x86-bin
+
+--- a/CMAKE/CheckLAPACKCompilerFlags.cmake
++++ b/CMAKE/CheckLAPACKCompilerFlags.cmake
 @@ -43,12 +43,6 @@
    if( "${CMAKE_Fortran_FLAGS}" MATCHES "-qflttrap=[a-zA-Z:]:enable" )
      set( FPE_EXIT TRUE )
@@ -14,3 +25,18 @@ diff -Naur lapack-3.6.1/CMAKE/CheckLAPACKCompilerFlags.cmake lapack-3.6.1-patche
  
  # HP Fortran
  elseif( CMAKE_Fortran_COMPILER_ID STREQUAL "HP" )
+
+--- a/CBLAS/CMakeLists.txt
++++ b/CBLAS/CMakeLists.txt
+@@ -12,8 +12,8 @@
+                          SYMBOL_NAMESPACE "F77_")
+ if(NOT FortranCInterface_GLOBAL_FOUND OR NOT FortranCInterface_MODULE_FOUND)
+   message(WARNING "Reverting to pre-defined include/lapacke_mangling.h")
+-  configure_file(include/lapacke_mangling_with_flags.h.in
+-                 ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h)
++  configure_file(include/cblas_mangling_with_flags.h.in
++                 ${LAPACK_BINARY_DIR}/include/cblas_mangling.h)
+ endif()
+ 
+ include_directories(include ${LAPACK_BINARY_DIR}/include)
+
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/package.py b/var/spack/repos/builtin/packages/netlib-lapack/package.py
index 8166b75bf5..b5080d0ba8 100644
--- a/var/spack/repos/builtin/packages/netlib-lapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-lapack/package.py
@@ -1,31 +1,12 @@
-#############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class NetlibLapack(Package):
+class NetlibLapack(CMakePackage):
     """LAPACK version 3.X is a comprehensive FORTRAN library that does
     linear algebra operations including matrix inversions, least squared
     solutions to linear sets of equations, eigenvector analysis, singular
@@ -36,6 +17,10 @@ class NetlibLapack(Package):
     homepage = "http://www.netlib.org/lapack/"
     url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
 
+    version('3.8.0', '96591affdbf58c450d45c1daa540dbd2',
+            url='http://www.netlib.org/lapack/lapack-3.8.0.tar.gz')
+    version('3.7.1', 'dcdeeed73de152c4643ccc5b1aeb453c')
+    version('3.7.0', '697bb8d67c7d336a0f339cc9dd0fa72f')
     version('3.6.1', '421b2cb72e15f237e144428f9c460ee0')
     version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101')
     version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
@@ -44,23 +29,47 @@ class NetlibLapack(Package):
     version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
     version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
 
-    variant('debug', default=False, description='Activates the Debug build type')
     variant('shared', default=True, description="Build shared library version")
     variant('external-blas', default=False,
             description='Build lapack with an external blas')
 
     variant('lapacke', default=True,
             description='Activates the build of the LAPACKE C interface')
+    variant('xblas', default=False,
+            description='Builds extended precision routines using XBLAS')
 
-    patch('ibm-xl.patch', when='@3:6%xl')
-    patch('ibm-xl.patch', when='@3:6%xl_r')
+    patch('ibm-xl.patch', when='@3.7: %xl')
+    patch('ibm-xl.patch', when='@3.7: %xl_r')
+
+    # https://github.com/Reference-LAPACK/lapack/issues/228
+    # TODO: update 'when' once the version of lapack
+    # containing the fix is released and added to Spack.
+    patch('undefined_declarations.patch', when='@3.8.0:')
+
+    # https://github.com/Reference-LAPACK/lapack/pull/268
+    # TODO: update 'when' once the version of lapack
+    # containing the fix is released and added to Spack.
+    patch('testing.patch', when='@3.7.0:')
 
     # virtual dependency
     provides('blas', when='~external-blas')
     provides('lapack')
 
-    depends_on('cmake', type='build')
     depends_on('blas', when='+external-blas')
+    depends_on('netlib-xblas+fortran+plain_blas', when='+xblas')
+    depends_on('python@2.7:', type='test')
+
+    # We need to run every phase twice in order to get static and shared
+    # versions of the libraries. When ~shared, we run the default
+    # implementations of the CMakePackage's phases and get only one building
+    # directory 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF (see
+    # implementations of self.build_directory and self.cmake_args() below).
+    # When +shared, we run the overridden methods for the phases, each
+    # running the default implementation twice with different values for
+    # self._building_shared. As a result, we get two building directories:
+    # 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF and
+    # 'spack-build-shared' with -DBUILD_SHARED_LIBS:BOOL=ON.
+    _building_shared = False
 
     def patch(self):
         # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
@@ -73,61 +82,124 @@ class NetlibLapack(Package):
     @property
     def blas_libs(self):
         shared = True if '+shared' in self.spec else False
+        query_parameters = self.spec.last_query.extra_parameters
+        query2libraries = {
+            tuple(): ['libblas'],
+            ('c', 'fortran'): [
+                'libcblas',
+                'libblas',
+            ],
+            ('c',): [
+                'libcblas',
+            ],
+            ('fortran',): [
+                'libblas',
+            ]
+        }
+        key = tuple(sorted(query_parameters))
+        libraries = query2libraries[key]
         return find_libraries(
-            'libblas', root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
 
     @property
     def lapack_libs(self):
         shared = True if '+shared' in self.spec else False
+        query_parameters = self.spec.last_query.extra_parameters
+        query2libraries = {
+            tuple(): ['liblapack'],
+            ('c', 'fortran'): [
+                'liblapacke',
+                'liblapack',
+            ],
+            ('c',): [
+                'liblapacke',
+            ],
+            ('fortran',): [
+                'liblapack',
+            ]
+        }
+        key = tuple(sorted(query_parameters))
+        libraries = query2libraries[key]
         return find_libraries(
-            'liblapack', root=self.prefix, shared=shared, recurse=True
+            libraries, root=self.prefix, shared=shared, recursive=True
         )
 
-    def install_one(self, spec, prefix, shared):
-        cmake_args = [
-            '-DBUILD_SHARED_LIBS:BOOL=%s' % ('ON' if shared else 'OFF'),
-            '-DCMAKE_BUILD_TYPE:STRING=%s' % (
-                'Debug' if '+debug' in spec else 'Release'),
-            '-DLAPACKE:BOOL=%s' % ('ON' if '+lapacke' in spec else 'OFF')]
-        if spec.satisfies('@3.6.0:'):
-            cmake_args.extend(['-DCBLAS=ON'])  # always build CBLAS
+    @property
+    def headers(self):
+        include_dir = self.spec.prefix.include
+        cblas_h = join_path(include_dir, 'cblas.h')
+        lapacke_h = join_path(include_dir, 'lapacke.h')
+        return HeaderList([cblas_h, lapacke_h])
 
-        if self.compiler.name == 'intel':
+    @property
+    def build_directory(self):
+        return join_path(self.stage.source_path,
+                         'spack-build-shared' if self._building_shared
+                         else 'spack-build-static')
+
+    def cmake_args(self):
+        args = ['-DBUILD_SHARED_LIBS:BOOL=' +
+                ('ON' if self._building_shared else 'OFF')]
+
+        if self.spec.satisfies('+lapacke'):
+            args.extend(['-DLAPACKE:BOOL=ON', '-DLAPACKE_WITH_TMG:BOOL=ON'])
+        else:
+            args.extend(['-DLAPACKE:BOOL=OFF', '-DLAPACKE_WITH_TMG:BOOL=OFF'])
+
+        if self.spec.satisfies('@3.6.0:'):
+            args.append('-DCBLAS=ON')  # always build CBLAS
+
+        if self.spec.satisfies('%intel'):
             # Intel compiler finds serious syntax issues when trying to
             # build CBLAS and LapackE
-            cmake_args.extend(['-DCBLAS=OFF'])
-            cmake_args.extend(['-DLAPACKE:BOOL=OFF'])
+            args.extend(['-DCBLAS=OFF', '-DLAPACKE:BOOL=OFF'])
 
-        if self.compiler.name == 'xl' or self.compiler.name == 'xl_r':
+        if self.spec.satisfies('%xl') or self.spec.satisfies('%xl_r'):
             # use F77 compiler if IBM XL
-            cmake_args.extend([
-                '-DCMAKE_Fortran_COMPILER=%s' % self.compiler.f77,
-                '-DCMAKE_Fortran_FLAGS=-qzerosize'
-            ])
+            args.extend(['-DCMAKE_Fortran_COMPILER=' + self.compiler.f77,
+                         '-DCMAKE_Fortran_FLAGS=' +
+                         (' '.join(self.spec.compiler_flags['fflags'])) +
+                         " -O3 -qnohot"])
 
         # deprecated routines are commonly needed by, for example, suitesparse
         # Note that OpenBLAS spack is built with deprecated routines
-        cmake_args.extend(['-DBUILD_DEPRECATED:BOOL=ON'])
+        args.append('-DBUILD_DEPRECATED:BOOL=ON')
+
+        if self.spec.satisfies('+external-blas'):
+            args.extend(['-DUSE_OPTIMIZED_BLAS:BOOL=ON',
+                         '-DBLAS_LIBRARIES:PATH=' +
+                         self.spec['blas'].libs.joined(';')])
+
+        if self.spec.satisfies('+xblas'):
+            args.extend(['-DXBLAS_INCLUDE_DIR=' +
+                         self.spec['netlib-xblas'].prefix.include,
+                         '-DXBLAS_LIBRARY=' +
+                         self.spec['netlib-xblas'].libs.joined(';')])
+
+        args.append('-DBUILD_TESTING:BOOL=' +
+                    ('ON' if self.run_tests else 'OFF'))
 
-        if '+external-blas' in spec:
-            cmake_args.extend([
-                '-DUSE_OPTIMIZED_BLAS:BOOL=ON',
-                '-DBLAS_LIBRARIES:PATH=%s' % spec['blas'].libs.joined(';')
-            ])
+        return args
 
-        cmake_args.extend(std_cmake_args)
+    # Build, install, and check both static and shared versions of the
+    # libraries when +shared
+    @when('+shared')
+    def cmake(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).cmake(spec, prefix)
 
-        build_dir = 'spack-build' + ('-shared' if shared else '-static')
-        with working_dir(build_dir, create=True):
-            cmake('..', *cmake_args)
-            make()
-            make("install")
+    @when('+shared')
+    def build(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).build(spec, prefix)
 
+    @when('+shared')
     def install(self, spec, prefix):
-        # Always build static libraries.
-        self.install_one(spec, prefix, False)
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).install(spec, prefix)
 
-        # Build shared libraries if requested.
-        if '+shared' in spec:
-            self.install_one(spec, prefix, True)
+    @when('+shared')
+    def check(self):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).check()
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/testing.patch b/var/spack/repos/builtin/packages/netlib-lapack/testing.patch
new file mode 100644
index 0000000000..fce18548c4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netlib-lapack/testing.patch
@@ -0,0 +1,13 @@
+diff --git a/TESTING/LIN/alahd.f b/TESTING/LIN/alahd.f
+index 8f4cd58d..6a4946e0 100644
+--- a/TESTING/LIN/alahd.f
++++ b/TESTING/LIN/alahd.f
+@@ -1036,7 +1036,7 @@
+  9929 FORMAT( ' Test ratios (1-3: ', A1, 'TZRZF):' )
+  9920 FORMAT( 3X, ' 7-10: same as 3-6', 3X, ' 11-14: same as 3-6' )
+  9921 FORMAT( ' Test ratios:', / '    (1-2: ', A1, 'GELS, 3-6: ', A1,
+-     $      'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: '
++     $      'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: ',
+      $        A1, 'GETSLS)')
+  9928 FORMAT( 7X, 'where ALPHA = ( 1 + SQRT( 17 ) ) / 8' )
+  9927 FORMAT( 3X, I2, ': ABS( Largest element in L )', / 12X,
diff --git a/var/spack/repos/builtin/packages/netlib-lapack/undefined_declarations.patch b/var/spack/repos/builtin/packages/netlib-lapack/undefined_declarations.patch
new file mode 100644
index 0000000000..9dac2562f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netlib-lapack/undefined_declarations.patch
@@ -0,0 +1,26 @@
+diff --git a/SRC/dsytrf_aa_2stage.f b/SRC/dsytrf_aa_2stage.f
+index 2991305..f5f06cc 100644
+--- a/SRC/dsytrf_aa_2stage.f
++++ b/SRC/dsytrf_aa_2stage.f
+@@ -191,7 +191,7 @@
+       EXTERNAL           LSAME, ILAENV
+ *     ..
+ *     .. External Subroutines ..
+-      EXTERNAL           XERBLA, DCOPY, DLACGV, DLACPY,
++      EXTERNAL           XERBLA, DCOPY, DLACPY,
+      $                   DLASET, DGBTRF, DGEMM,  DGETRF, 
+      $                   DSYGST, DSWAP, DTRSM 
+ *     ..
+diff --git a/SRC/ssytrf_aa_2stage.f b/SRC/ssytrf_aa_2stage.f
+index be6809d..a929749 100644
+--- a/SRC/ssytrf_aa_2stage.f
++++ b/SRC/ssytrf_aa_2stage.f
+@@ -191,7 +191,7 @@
+       EXTERNAL           LSAME, ILAENV
+ *     ..
+ *     .. External Subroutines ..
+-      EXTERNAL           XERBLA, SCOPY, SLACGV, SLACPY,
++      EXTERNAL           XERBLA, SCOPY, SLACPY,
+      $                   SLASET, SGBTRF, SGEMM,  SGETRF, 
+      $                   SSYGST, SSWAP, STRSM 
+ *     ..
diff --git a/var/spack/repos/builtin/packages/netlib-scalapack/package.py b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
index 614cbeea4b..0bc2025ba6 100644
--- a/var/spack/repos/builtin/packages/netlib-scalapack/package.py
+++ b/var/spack/repos/builtin/packages/netlib-scalapack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -59,12 +40,12 @@ class NetlibScalapack(CMakePackage):
     depends_on('cmake', when='@2.0.0:', type='build')
 
     @property
-    def scalapack_libs(self):
+    def libs(self):
         # Note that the default will be to search
         # for 'libnetlib-scalapack.<suffix>'
         shared = True if '+shared' in self.spec else False
         return find_libraries(
-            'libscalapack', root=self.prefix, shared=shared, recurse=True
+            'libscalapack', root=self.prefix, shared=shared, recursive=True
         )
 
     def cmake_args(self):
diff --git a/var/spack/repos/builtin/packages/netlib-xblas/package.py b/var/spack/repos/builtin/packages/netlib-xblas/package.py
new file mode 100644
index 0000000000..6c837f0da8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/netlib-xblas/package.py
@@ -0,0 +1,71 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NetlibXblas(AutotoolsPackage):
+    """XBLAS is a reference implementation for extra precision BLAS.
+
+       XBLAS is a reference implementation for the dense and banded BLAS
+       routines, along with extended and mixed precision version. Extended
+       precision is only used internally; input and output arguments remain
+       the same as in the existing BLAS. Extra precisions is implemented as
+       double-double (i.e., 128-bit total, 106-bit significand). Mixed
+       precision permits some input/output arguments of different types
+       (mixing real and complex) or precisions (mixing single and
+       double). This implementation is proof of concept, and no attempt was
+       made to optimize performance; performance should be as good as
+       straightforward but careful code written by hand."""
+
+    homepage = "http://www.netlib.org/xblas"
+    url      = "http://www.netlib.org/xblas/xblas.tar.gz"
+
+    version('1.0.248', '990c680fb5e446bb86c10936e4cd7f88')
+
+    variant('fortran', default=True,
+            description='Build Fortran interfaces')
+    variant('plain_blas', default=True,
+            description='As part of XBLAS, build plain BLAS routines')
+
+    provides('blas', when='+plain_blas')
+
+    @property
+    def libs(self):
+        return find_libraries(['libxblas'], root=self.prefix,
+                              shared=False, recursive=True)
+
+    def configure_args(self):
+        args = []
+
+        if self.spec.satisfies('~fortran'):
+            args += ['--disable-fortran']
+
+        if self.spec.satisfies('~plain_blas'):
+            args += ['--disable-plain-blas']
+
+        return args
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.lib)
+        install('libxblas.a', prefix.lib)
+
+        if self.spec.satisfies('+plain_blas'):
+            # XBLAS should be a drop-in BLAS replacement
+            install('libxblas.a', join_path(prefix.lib, 'libblas.a'))
+
+        headers = ['f2c-bridge.h',
+                   'blas_dense_proto.h',
+                   'blas_enum.h',
+                   'blas_extended.h',
+                   'blas_extended_private.h',
+                   'blas_extended_proto.h',
+                   'blas_fpu.h',
+                   'blas_malloc.h']
+        mkdirp(prefix.include)
+        for h in headers:
+            install(join_path('src', h), prefix.include)
+
+        return
diff --git a/var/spack/repos/builtin/packages/nettle/package.py b/var/spack/repos/builtin/packages/nettle/package.py
index 591483b2f9..c371327901 100644
--- a/var/spack/repos/builtin/packages/nettle/package.py
+++ b/var/spack/repos/builtin/packages/nettle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Nettle(AutotoolsPackage):
     that is designed to fit easily in many contexts."""
 
     homepage = "https://www.lysator.liu.se/~nisse/nettle/"
-    url      = "http://ftp.gnu.org/gnu/nettle/nettle-3.3.tar.gz"
+    url      = "https://ftpmirror.gnu.org/nettle/nettle-3.3.tar.gz"
 
+    version('3.4',   'dc0f13028264992f58e67b4e8915f53d')
     version('3.3',   '10f969f78a463704ae73529978148dbe')
     version('3.2',   'afb15b4764ebf1b4e6d06c62bd4d29e4')
     version('2.7.1', '003d5147911317931dd453520eb234a5')
diff --git a/var/spack/repos/builtin/packages/neuron/package.py b/var/spack/repos/builtin/packages/neuron/package.py
new file mode 100644
index 0000000000..ade0552c60
--- /dev/null
+++ b/var/spack/repos/builtin/packages/neuron/package.py
@@ -0,0 +1,202 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+from spack import *
+
+
+class Neuron(Package):
+    """NEURON is a simulation environment for single and networks of neurons.
+
+    NEURON is a simulation environment for modeling individual and networks of
+    neurons. NEURON models individual neurons via the use of sections that are
+    automatically subdivided into individual compartments, instead of
+    requiring the user to manually create compartments. The primary scripting
+    language is hoc but a Python interface is also available.
+    """
+
+    homepage = "https://www.neuron.yale.edu/"
+    url      = "http://www.neuron.yale.edu/ftp/neuron/versions/v7.5/nrn-7.5.tar.gz"
+    git      = "https://github.com/nrnhines/nrn.git"
+
+    version('develop', branch='master')
+    version('7.5', 'fb72c841374dfacbb6c2168ff57bfae9')
+    version('7.4', '2c0bbee8a9e55d60fa26336f4ab7acbf')
+    version('7.3', '993e539cb8bf102ca52e9fefd644ab61')
+    version('7.2', '5486709b6366add932e3a6d141c4f7ad')
+
+    variant('mpi',           default=True,  description='Enable MPI parallelism')
+    variant('python',        default=True,  description='Enable python')
+    variant('shared',        default=False, description='Build shared libraries')
+    variant('cross-compile', default=False, description='Build for cross-compile environment')
+    variant('multisend',     default=True,  description="Enable multi-send spike exchange")
+    variant('rx3d',          default=False, description="Enable cython translated 3-d rxd")
+
+    depends_on('flex',       type='build')
+    depends_on('bison',      type='build')
+    depends_on('automake',   type='build')
+    depends_on('automake',   type='build')
+    depends_on('autoconf',   type='build')
+    depends_on('libtool',    type='build')
+    depends_on('pkgconfig',  type='build')
+
+    depends_on('mpi',         when='+mpi')
+    depends_on('python@2.6:', when='+python')
+    depends_on('ncurses',     when='~cross-compile')
+
+    conflicts('~shared', when='+python')
+
+    filter_compiler_wrappers('*/bin/nrniv_makefile')
+
+    def get_neuron_archdir(self):
+        """Determine the architecture-specific neuron base directory.
+
+        Instead of recreating the logic of the neuron's configure
+        we dynamically find the architecture-specific directory by
+        looking for a specific binary.
+        """
+        file_list = find(self.prefix, '*/bin/nrniv_makefile')
+        # check needed as when initially evaluated the prefix is empty
+        if file_list:
+            neuron_archdir = os.path.dirname(os.path.dirname(file_list[0]))
+        else:
+            neuron_archdir = self.prefix
+
+        return neuron_archdir
+
+    def patch(self):
+        # aclocal need complete include path (especially on os x)
+        pkgconf_inc = '-I %s/share/aclocal/' % (self.spec['pkgconfig'].prefix)
+        libtool_inc = '-I %s/share/aclocal/' % (self.spec['libtool'].prefix)
+        newpath = 'aclocal -I m4 %s %s' % (pkgconf_inc, libtool_inc)
+        filter_file(r'aclocal -I m4', r'%s' % newpath, "build.sh")
+
+    def get_arch_options(self, spec):
+        options = []
+
+        if spec.satisfies('+cross-compile'):
+            options.extend(['cross_compiling=yes',
+                            '--without-memacs',
+                            '--without-nmodl'])
+
+        # need to enable bg-q arch
+        if 'bgq' in self.spec.architecture:
+            options.extend(['--enable-bluegeneQ',
+                            '--host=powerpc64'])
+
+        # on os-x disable building carbon 'click' utility
+        if 'darwin' in self.spec.architecture:
+            options.append('macdarwin=no')
+
+        return options
+
+    def get_python_options(self, spec):
+        options = []
+
+        if spec.satisfies('+python'):
+            python_exec = spec['python'].command.path
+            py_inc = spec['python'].headers.directories[0]
+            py_lib = spec['python'].prefix.lib
+
+            if not os.path.isdir(py_lib):
+                py_lib = spec['python'].prefix.lib64
+
+            options.extend(['--with-nrnpython=%s' % python_exec,
+                            '--disable-pysetup',
+                            'PYINCDIR=%s' % py_inc,
+                            'PYLIBDIR=%s' % py_lib])
+
+            if spec.satisfies('~cross-compile'):
+                options.append('PYTHON_BLD=%s' % python_exec)
+
+        else:
+            options.append('--without-nrnpython')
+
+        return options
+
+    def get_compiler_options(self, spec):
+        flags = '-O2 -g'
+
+        if 'bgq' in self.spec.architecture:
+            flags = '-O3 -qtune=qp -qarch=qp -q64 -qstrict -qnohot -g'
+
+        if self.spec.satisfies('%pgi'):
+            flags += ' ' + self.compiler.pic_flag
+
+        return ['CFLAGS=%s' % flags,
+                'CXXFLAGS=%s' % flags]
+
+    def build_nmodl(self, spec, prefix):
+        # build components for front-end arch in cross compiling environment
+        options = ['--prefix=%s' % prefix,
+                   '--with-nmodl-only',
+                   '--without-x']
+
+        if 'bgq' in self.spec.architecture:
+            flags = '-qarch=ppc64'
+            options.extend(['CFLAGS=%s' % flags,
+                            'CXXFLAGS=%s' % flags])
+
+        if 'cray' in self.spec.architecture:
+            flags = '-target-cpu=x86_64 -target-network=none'
+            options.extend(['CFLAGS=%s' % flags,
+                            'CXXFLAGS=%s' % flags])
+
+        configure = Executable(join_path(self.stage.source_path, 'configure'))
+        configure(*options)
+        make()
+        make('install')
+
+    def install(self, spec, prefix):
+
+        options = ['--prefix=%s' % prefix,
+                   '--without-iv',
+                   '--without-x',
+                   '--without-readline']
+
+        if spec.satisfies('+multisend'):
+            options.append('--with-multisend')
+
+        if spec.satisfies('~rx3d'):
+            options.append('--disable-rx3d')
+
+        if spec.satisfies('+mpi'):
+            options.extend(['MPICC=%s' % spec['mpi'].mpicc,
+                            'MPICXX=%s' % spec['mpi'].mpicxx,
+                            '--with-paranrn'])
+        else:
+            options.append('--without-paranrn')
+
+        if spec.satisfies('~shared'):
+            options.extend(['--disable-shared',
+                            'linux_nrnmech=no'])
+
+        options.extend(self.get_arch_options(spec))
+        options.extend(self.get_python_options(spec))
+        options.extend(self.get_compiler_options(spec))
+
+        build = Executable('./build.sh')
+        build()
+
+        with working_dir('build', create=True):
+            if spec.satisfies('+cross-compile'):
+                self.build_nmodl(spec, prefix)
+            srcpath = self.stage.source_path
+            configure = Executable(join_path(srcpath, 'configure'))
+            configure(*options)
+            make('VERBOSE=1')
+            make('install')
+
+    def setup_environment(self, spack_env, run_env):
+        neuron_archdir = self.get_neuron_archdir()
+        run_env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
+        run_env.prepend_path(
+            'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        neuron_archdir = self.get_neuron_archdir()
+        spack_env.prepend_path('PATH', join_path(neuron_archdir, 'bin'))
+        spack_env.prepend_path(
+            'LD_LIBRARY_PATH', join_path(neuron_archdir, 'lib'))
diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py
index 715964bdc1..f1d2718010 100644
--- a/var/spack/repos/builtin/packages/nextflow/package.py
+++ b/var/spack/repos/builtin/packages/nextflow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,6 +18,8 @@ class Nextflow(Package):
             expand=False)
     version('0.23.3', '71fb69275b6788af1c6f1165f40d362e',
             expand=False)
+    version('0.21.0', '38e5e335cb33f05ba358e1f883c8386c',
+             expand=False)
     version('0.20.1', '0e4e0e3eca1c2c97f9b4bffd944b923a',
             expand=False)
     version('0.17.3', '5df00105fb1ce6fd0ba019ae735d9617',
diff --git a/var/spack/repos/builtin/packages/nfft/package.py b/var/spack/repos/builtin/packages/nfft/package.py
index 415ddcf0eb..3e40732f39 100644
--- a/var/spack/repos/builtin/packages/nfft/package.py
+++ b/var/spack/repos/builtin/packages/nfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,10 @@ class Nfft(AutotoolsPackage):
     size, and of complex data."""
 
     homepage = "https://www-user.tu-chemnitz.de/~potts/nfft"
-    url = "https://www-user.tu-chemnitz.de/~potts/nfft/download/nfft-3.3.2.tar.gz"
+    url = "https://github.com/NFFT/nfft/releases/download/3.4.1/nfft-3.4.1.tar.gz"
 
-    version('3.3.2', '550737c06f4d6ea6c156800169d8f0d9')
+    version('3.4.1', '9c2ad6cf86fe4a7bc0de8d2d92b101f4')
+    version('3.3.2', '13e48b923501ed6feb5130c3be115fc8')
 
     depends_on('fftw')
 
diff --git a/var/spack/repos/builtin/packages/nghttp2/package.py b/var/spack/repos/builtin/packages/nghttp2/package.py
index 62b936e054..53d3c6b67f 100644
--- a/var/spack/repos/builtin/packages/nghttp2/package.py
+++ b/var/spack/repos/builtin/packages/nghttp2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nginx/package.py b/var/spack/repos/builtin/packages/nginx/package.py
index a9b5e93bfb..0db0e581c8 100644
--- a/var/spack/repos/builtin/packages/nginx/package.py
+++ b/var/spack/repos/builtin/packages/nginx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class Nginx(AutotoolsPackage):
     homepage = "https://nginx.org/en/"
     url      = "https://nginx.org/download/nginx-1.12.0.tar.gz"
 
+    version('1.13.8', 'df4be9294365782dc1349ca33ce8c4ac')
     version('1.12.0', '995eb0a140455cf0cfc497e5bd7f94b3')
 
     depends_on('openssl')
diff --git a/var/spack/repos/builtin/packages/ngmlr/package.py b/var/spack/repos/builtin/packages/ngmlr/package.py
index e1dbbe709e..1c38c9cd1a 100644
--- a/var/spack/repos/builtin/packages/ngmlr/package.py
+++ b/var/spack/repos/builtin/packages/ngmlr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ninja-fortran/package.py b/var/spack/repos/builtin/packages/ninja-fortran/package.py
index 57903928be..5aaa5039ed 100644
--- a/var/spack/repos/builtin/packages/ninja-fortran/package.py
+++ b/var/spack/repos/builtin/packages/ninja-fortran/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ninja/package.py b/var/spack/repos/builtin/packages/ninja/package.py
index 11c46cb81e..e6283fbff3 100644
--- a/var/spack/repos/builtin/packages/ninja/package.py
+++ b/var/spack/repos/builtin/packages/ninja/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nlohmann-json/package.py b/var/spack/repos/builtin/packages/nlohmann-json/package.py
new file mode 100644
index 0000000000..3cfcd936a9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nlohmann-json/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NlohmannJson(CMakePackage):
+    """JSON for Modern C++"""
+
+    homepage = "https://nlohmann.github.io/json/"
+    url      = "https://github.com/nlohmann/json/archive/v3.1.2.tar.gz"
+    maintainers = ['ax3l']
+
+    version('3.3.0', sha256='2fd1d207b4669a7843296c41d3b6ac5b23d00dec48dba507ba051d14564aa801')
+    version('3.2.0', sha256='2de558ff3b3b32eebfb51cf2ceb835a0fa5170e6b8712b02be9c2c07fcfe52a1')
+    version('3.1.2', sha256='e8fffa6cbdb3c15ecdff32eebf958b6c686bc188da8ad5c6489462d16f83ae54')
+    version('3.1.1', sha256='9f3549824af3ca7e9707a2503959886362801fb4926b869789d6929098a79e47')
+
+    variant('single_header', default=True,
+        description='Use amalgamated single-header')
+    variant('test', default=True,
+        description='Build the tests')
+
+    depends_on('cmake@3.8:', type='build')
+
+    # requires mature C++11 implementations
+    conflicts('%gcc@:4.7')
+    # v3.3.0 adds support for gcc 4.8
+    # https://github.com/nlohmann/json/releases/tag/v3.3.0
+    conflicts('%gcc@:4.8', when='@:3.2.9')
+    conflicts('%intel@:16')
+    conflicts('%pgi@:14')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            '-DJSON_MultipleHeaders:BOOL={0}'.format(
+                'ON' if '~single_header' in spec else 'OFF'),
+            '-DBUILD_TESTING:BOOL={0}'.format(
+                'ON' if '+test' in spec else 'OFF')
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/nlopt/package.py b/var/spack/repos/builtin/packages/nlopt/package.py
new file mode 100644
index 0000000000..c1c69cba01
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nlopt/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Nlopt(CMakePackage):
+    """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."""
+
+    homepage = "https://nlopt.readthedocs.io"
+    url      = "https://github.com/stevengj/nlopt/archive/v2.5.0.tar.gz"
+    git      = "https://github.com/stevengj/nlopt.git"
+
+    version('develop', branch='master')
+    version('2.5.0', 'ada08c648bf9b52faf8729412ff6dd6d')
+
+    variant('shared', default=True, description='Enables the build of shared libraries')
+    variant('python', default=True, description='Build python wrappers')
+    variant('guile',  default=False, description='Enable Guile support')
+    variant('octave', default=False, description='Enable GNU Octave support')
+    variant('cxx',    default=False,  description='Build the C++ routines')
+
+    # Note: matlab is licenced - spack does not download automatically
+    variant("matlab", default=False, description="Build the Matlab bindings.")
+
+    depends_on('cmake@3.0:', type='build', when='@develop')
+    depends_on('python', when='+python')
+    depends_on('py-numpy', when='+python', type=('build', 'run'))
+    depends_on('swig', when='+python')
+    depends_on('guile', when='+guile')
+    depends_on('octave', when='+octave')
+    depends_on('matlab', when='+matlab')
+
+    def cmake_args(self):
+        # Add arguments other than
+        # CMAKE_INSTALL_PREFIX and CMAKE_BUILD_TYPE
+        spec = self.spec
+        args = []
+
+        # Specify on command line to alter defaults:
+        # eg: spack install nlopt@develop +guile -octave +cxx
+
+        # Spack should locate python by default - but to point to a build
+        if '+python' in spec:
+            args.append("-DPYTHON_EXECUTABLE=%s" % spec['python'].command.path)
+
+        # On is default
+        if '-shared' in spec:
+            args.append('-DBUILD_SHARED_LIBS:Bool=OFF')
+
+        if '+cxx' in spec:
+            args.append('-DNLOPT_CXX:BOOL=ON')
+
+        if '+matlab' in spec:
+            args.append("-DMatlab_ROOT_DIR=%s" % spec['matlab'].command.path)
+
+        return args
diff --git a/var/spack/repos/builtin/packages/nmap/package.py b/var/spack/repos/builtin/packages/nmap/package.py
index e4da0fbdcf..43b3aeefac 100644
--- a/var/spack/repos/builtin/packages/nmap/package.py
+++ b/var/spack/repos/builtin/packages/nmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,7 +12,8 @@ class Nmap(AutotoolsPackage):
        It also provides ncat an updated nc"""
 
     homepage = "https://nmap.org"
-    url      = "https://nmap.org/dist/nmap-7.31.tar.bz2"
+    url      = "https://nmap.org/dist/nmap-7.70.tar.bz2"
 
+    version('7.70', '84eb6fbe788e0d4918c2b1e39421bf79')
     version('7.31', 'f2f6660142a777862342a58cc54258ea')
     version('7.30', '8d86797d5c9e56de571f9630c0e6b5f8')
diff --git a/var/spack/repos/builtin/packages/nnvm/package.py b/var/spack/repos/builtin/packages/nnvm/package.py
index 0650df273d..542daa50af 100644
--- a/var/spack/repos/builtin/packages/nnvm/package.py
+++ b/var/spack/repos/builtin/packages/nnvm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,10 @@ class Nnvm(CMakePackage):
     part to help build deep learning libraries."""
 
     homepage = "https://github.com/dmlc/nnvm"
-    url      = "https://github.com/dmlc/nnvm.git"
+    git      = "https://github.com/dmlc/nnvm.git"
 
-    version('master', git='https://github.com/dmlc/nnvm.git', branch='master')
-    version('20170418', git='https://github.com/dmlc/nnvm.git',
-            commit='b279286304ac954098d94a2695bca599e832effb')
+    version('master', branch='master')
+    version('20170418', commit='b279286304ac954098d94a2695bca599e832effb')
 
     variant('shared', default=True, description='Build a shared NNVM lib.')
 
diff --git a/var/spack/repos/builtin/packages/node-js/package.py b/var/spack/repos/builtin/packages/node-js/package.py
index 0b7e942400..ad19340c53 100644
--- a/var/spack/repos/builtin/packages/node-js/package.py
+++ b/var/spack/repos/builtin/packages/node-js/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 import subprocess
@@ -34,6 +15,7 @@ class NodeJs(Package):
     homepage = "https://nodejs.org/"
     url      = "https://nodejs.org/download/release/v6.3.0/node-v6.3.0.tar.gz"
 
+    version('8.9.1', '7482b2523f72000d1b6060c38945026b')
     version('7.1.0', '1db5df2cb025f9c70e83d9cf21c4266a')
     version('6.3.0', '8c14e5c89d66d4d060c91b3ba15dfd31')
     version('6.2.2', '1120e8bf191fdaee42206d031935210d')
@@ -46,7 +28,7 @@ class NodeJs(Package):
     variant('zlib', default=True,  description='Build with Spacks zlib instead of the bundled version')
 
     depends_on('libtool', type='build', when=sys.platform != 'darwin')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('python@2.7:2.8', type='build')
     # depends_on('bash-completion', when="+bash-completion")
     depends_on('icu4c', when='+icu4c')
diff --git a/var/spack/repos/builtin/packages/notmuch/package.py b/var/spack/repos/builtin/packages/notmuch/package.py
index 11ff488d77..9245c76d12 100644
--- a/var/spack/repos/builtin/packages/notmuch/package.py
+++ b/var/spack/repos/builtin/packages/notmuch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/npb/package.py b/var/spack/repos/builtin/packages/npb/package.py
index 65e5294524..0840be9b8c 100644
--- a/var/spack/repos/builtin/packages/npb/package.py
+++ b/var/spack/repos/builtin/packages/npb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import numbers
 
 from spack import *
diff --git a/var/spack/repos/builtin/packages/npm/package.py b/var/spack/repos/builtin/packages/npm/package.py
index 89a46bc19b..5f797165c3 100644
--- a/var/spack/repos/builtin/packages/npm/package.py
+++ b/var/spack/repos/builtin/packages/npm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/npth/package.py b/var/spack/repos/builtin/packages/npth/package.py
index c99c01ebb2..d99da26799 100644
--- a/var/spack/repos/builtin/packages/npth/package.py
+++ b/var/spack/repos/builtin/packages/npth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Npth(AutotoolsPackage):
        non-preemptive threads implementation."""
 
     homepage = "https://gnupg.org/software/npth/index.html"
-    url = "https://gnupg.org/ftp/gcrypt/npth/npth-1.4.tar.bz2"
+    url = "https://gnupg.org/ftp/gcrypt/npth/npth-1.5.tar.bz2"
 
+    version('1.5', '9ba2dc4302d2f32c66737c43ed191b1b')
     version('1.4', '76cef5542e0db6a339cf960641ed86f8')
diff --git a/var/spack/repos/builtin/packages/nspr/package.py b/var/spack/repos/builtin/packages/nspr/package.py
index cddcdb16a0..5ad1d51973 100644
--- a/var/spack/repos/builtin/packages/nspr/package.py
+++ b/var/spack/repos/builtin/packages/nspr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/numactl/numactl-2.0.11-sysmacros.patch b/var/spack/repos/builtin/packages/numactl/numactl-2.0.11-sysmacros.patch
new file mode 100644
index 0000000000..3f95367573
--- /dev/null
+++ b/var/spack/repos/builtin/packages/numactl/numactl-2.0.11-sysmacros.patch
@@ -0,0 +1,41 @@
+https://bugs.gentoo.org/580098
+
+From c1644f92e340d797e490c41a9ef9961125d202b9 Mon Sep 17 00:00:00 2001
+From: Mike Frysinger <vapier@gentoo.org>
+Date: Mon, 18 Apr 2016 18:49:51 -0400
+Subject: [PATCH] include sys/sysmacros.h for major/minor
+
+These functions are not part of any official spec, and glibc has always
+kept them in sys/sysmacros.h.  As glibc moves to conform to POSIX, and
+more alternative C libraries come up, we need to include this header
+explicitly to get the prototypes.  Otherwise we fail to build like:
+
+affinity.c: In function 'affinity_file':
+affinity.c:177:7: warning: implicit declaration of function 'major' [-Wimplicit-function-declaration]
+   if (major(d) != maj || minor(d) != min)
+       ^
+affinity.c:177:26: warning: implicit declaration of function 'minor' [-Wimplicit-function-declaration]
+   if (major(d) != maj || minor(d) != min)
+                          ^
+./.libs/libnuma.so: undefined reference to 'minor'
+./.libs/libnuma.so: undefined reference to 'major'
+collect2: error: ld returned 1 exit status
+---
+ affinity.c | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/affinity.c b/affinity.c
+index 9fbd6af..984291c 100644
+--- a/affinity.c
++++ b/affinity.c
+@@ -40,6 +40,7 @@
+ #include <linux/rtnetlink.h>
+ #include <linux/netlink.h>
+ #include <sys/types.h>
++#include <sys/sysmacros.h>
+ #include <ctype.h>
+ #include <assert.h>
+ #include <regex.h>
+-- 
+2.7.4
+
diff --git a/var/spack/repos/builtin/packages/numactl/package.py b/var/spack/repos/builtin/packages/numactl/package.py
index 26df59c85a..e17a279d21 100644
--- a/var/spack/repos/builtin/packages/numactl/package.py
+++ b/var/spack/repos/builtin/packages/numactl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,8 @@ class Numactl(AutotoolsPackage):
 
     version('2.0.11',     'b56d2367217cde390b4d8087e00773b8')
 
+    patch('numactl-2.0.11-sysmacros.patch', when="@2.0.11")
+
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
     depends_on('libtool',  type='build')
diff --git a/var/spack/repos/builtin/packages/numdiff/package.py b/var/spack/repos/builtin/packages/numdiff/package.py
index b584d1156c..8c7490482a 100644
--- a/var/spack/repos/builtin/packages/numdiff/package.py
+++ b/var/spack/repos/builtin/packages/numdiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/nut/package.py b/var/spack/repos/builtin/packages/nut/package.py
index 2ff9f77c9c..6450d72adf 100644
--- a/var/spack/repos/builtin/packages/nut/package.py
+++ b/var/spack/repos/builtin/packages/nut/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,20 +13,16 @@ class Nut(CMakePackage):
     and performance issues."""
 
     homepage = "https://github.com/lanl/NuT"
-    url      = "https://github.com/lanl/NuT.git"
-    tags     = ['proxy-app']
+    git      = "https://github.com/lanl/NuT.git"
+
+    tags = ['proxy-app']
 
-    version(
-        'serial', git='https://github.com/lanl/NuT.git',
-        branch='master')
-    version(
-        'openmp', git='https://github.com/lanl/NuT.git',
-        branch='openmp')
+    version('serial', branch='master')
+    version('openmp', branch='openmp')
 
+    depends_on('cmake@3.0:')
     depends_on('random123')
 
-    # serial must be built with clang
-    conflicts('%gcc', when='@serial')
     conflicts('%intel', when='@serial')
     conflicts('%pgi', when='@serial')
     conflicts('%xl', when='@serial')
@@ -59,4 +36,9 @@ class Nut(CMakePackage):
     def install(self, spec, prefix):
         install('README.md', prefix)
         mkdirp(prefix.bin)
+        mkdirp(prefix.lib)
         install('spack-build/test/nut_unittests', prefix.bin)
+        install('spack-build/apps/bh-3', prefix.bin)
+        install('spack-build/lib/libnut.a', prefix.lib)
+        install_tree('test/data', prefix.data)
+        install_tree('lib', prefix.include)
diff --git a/var/spack/repos/builtin/packages/nvptx-tools/package.py b/var/spack/repos/builtin/packages/nvptx-tools/package.py
new file mode 100644
index 0000000000..244cd6936c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nvptx-tools/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NvptxTools(AutotoolsPackage):
+    """nvptx-tools: A collection of tools for use with nvptx-none GCC
+    toolchains. These tools are necessary when building a version
+    of GCC that enables offloading of OpenMP/OpenACC code to NVIDIA
+    GPUs."""
+
+    homepage = "https://github.com/MentorEmbedded/nvptx-tools"
+    git      = "https://github.com/MentorEmbedded/nvptx-tools"
+
+    version('2018-03-01', commit='5f6f343a302d620b0868edab376c00b15741e39e')
+
+    depends_on('binutils')
+    depends_on('cuda')
+
+    def configure_args(self):
+        cuda_dir = self.spec['cuda'].prefix
+
+        config_args = [
+            "--with-cuda-driver-include={0}".format(cuda_dir.include),
+            "--with-cuda-driver-lib={0}".format(cuda_dir.lib64)
+        ]
+
+        return config_args
diff --git a/var/spack/repos/builtin/packages/nwchem/package.py b/var/spack/repos/builtin/packages/nwchem/package.py
index 10262be6a8..908740ba4d 100644
--- a/var/spack/repos/builtin/packages/nwchem/package.py
+++ b/var/spack/repos/builtin/packages/nwchem/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 import os
@@ -33,6 +14,12 @@ class Nwchem(Package):
     homepage = "http://www.nwchem-sw.org"
     url      = "http://www.nwchem-sw.org/images/Nwchem-6.6.revision27746-src.2015-10-20.tar.gz"
 
+    tags = ['ecp', 'ecp-apps']
+
+    version('6.8.1', '6eccddc6db11886aa6f152626efc600c',
+            url='https://github.com/nwchemgit/nwchem/releases/download/6.8.1-release/nwchem-6.8.1-release.revision-v6.8-133-ge032219-srconly.2018-06-14.tar.bz2')
+    version('6.8', '50b18116319f4c15d1cb7eaa1b433006',
+            url='https://github.com/nwchemgit/nwchem/archive/v6.8-release.tar.gz')
     version('6.6', 'c581001c004ea5e5dfacb783385825e3',
             url='http://www.nwchem-sw.org/images/Nwchem-6.6.revision27746-src.2015-10-20.tar.gz')
 
@@ -41,7 +28,7 @@ class Nwchem(Package):
     depends_on('mpi')
     depends_on('scalapack')
 
-    depends_on('python@2.7:2.8', type=('build', 'run'))
+    depends_on('python@2.7:2.8', type=('build', 'link', 'run'))
 
     # first hash is sha256 of the patch (required for URL patches),
     # second is sha256 for the archive.
@@ -70,9 +57,9 @@ class Nwchem(Package):
         ]
     }
     # Iterate over patches
-    for condition, urls in urls_for_patches.items():
-        for url, sha256, archive_sha256 in urls:
-            patch(url, when=condition, level=0, sha256=sha256, archive_sha256=archive_sha256)
+    for __condition, __urls in urls_for_patches.items():
+        for __url, __sha256, __archive_sha256 in __urls:
+            patch(__url, when=__condition, level=0, sha256=__sha256, archive_sha256=__archive_sha256)
 
     def install(self, spec, prefix):
         scalapack = spec['scalapack'].libs
@@ -103,9 +90,9 @@ class Nwchem(Package):
         # TODO: query if blas/lapack/scalapack uses 64bit Ints
         # A flag to distinguish between 32bit and 64bit integers in linear
         # algebra (Blas, Lapack, Scalapack)
-        use32bitLinAlg = True
+        use_32_bit_lin_alg = True
 
-        if use32bitLinAlg:
+        if use_32_bit_lin_alg:
             args.extend([
                 'USE_64TO32=y',
                 'BLAS_SIZE=4',
@@ -131,7 +118,7 @@ class Nwchem(Package):
 
         with working_dir('src'):
             make('nwchem_config', *args)
-            if use32bitLinAlg:
+            if use_32_bit_lin_alg:
                 make('64_to_32', *args)
             make(*args)
 
diff --git a/var/spack/repos/builtin/packages/ocaml/package.py b/var/spack/repos/builtin/packages/ocaml/package.py
index e93d811f06..cd88782775 100644
--- a/var/spack/repos/builtin/packages/ocaml/package.py
+++ b/var/spack/repos/builtin/packages/ocaml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,17 @@ class Ocaml(Package):
     homepage = "http://ocaml.org/"
     url      = "http://caml.inria.fr/pub/distrib/ocaml-4.03/ocaml-4.03.0.tar.gz"
 
+    version('4.06.0', '66e5439eb63dbb8b8224cba5d1b20947')
     version('4.03.0', '43812739ea1b4641cf480f57f977c149')
 
     depends_on('ncurses')
 
+    def url_for_version(self, version):
+        url = "http://caml.inria.fr/pub/distrib/ocaml-{0}/ocaml-{1}.tar.gz"
+        return url.format(version.up_to(2), version)
+
     def install(self, spec, prefix):
         configure('-prefix', '{0}'.format(prefix))
 
         make('world.opt')
-        make('install')
+        make('install', 'PREFIX={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/occa/package.py b/var/spack/repos/builtin/packages/occa/package.py
new file mode 100644
index 0000000000..f9276fede9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/occa/package.py
@@ -0,0 +1,111 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Occa(Package):
+    """OCCA is an open-source (MIT license) library used to program current
+       multi-core/many-core architectures. Devices (such as CPUs, GPUs,
+       Intel's Xeon Phi, FPGAs, etc) are abstracted using an offload-model
+       for application development and programming for the devices is done
+       through a C-based (OKL) or Fortran-based kernel language (OFL).
+       OCCA gives developers the ability to target devices at run-time by
+       using run-time compilation for device kernels.
+    """
+
+    homepage = "http://libocca.org"
+    git      = 'https://github.com/libocca/occa.git'
+
+    version('develop')
+    version('v1.0.0-alpha.5', tag='v1.0.0-alpha.5')
+    version('v0.2.0', tag='v0.2.0')
+    version('v0.1.0', tag='v0.1.0')
+
+    variant('cuda',
+            default=True,
+            description='Activates support for CUDA')
+    variant('openmp',
+            default=True,
+            description='Activates support for OpenMP')
+    variant('opencl',
+            default=True,
+            description='Activates support for OpenCL')
+
+    depends_on('cuda', when='+cuda')
+
+    conflicts('%gcc@6:', when='^cuda@:8')
+    conflicts('%gcc@7:', when='^cuda@:9')
+
+    def install(self, spec, prefix):
+        # The build environment is set by the 'setup_environment' method.
+        # Copy the source to the installation directory and build OCCA there.
+        install_tree('.', prefix)
+        make('-C', prefix)
+
+        if self.run_tests:
+            make('-C', prefix, 'test', parallel=False)
+
+    def _setup_runtime_flags(self, s_env):
+        spec = self.spec
+        s_env.set('OCCA_DIR', self.prefix)
+        s_env.set('OCCA_CXX', self.compiler.cxx)
+
+        cxxflags = spec.compiler_flags['cxxflags']
+        if cxxflags:
+            # Run-time compiler flags:
+            s_env.set('OCCA_CXXFLAGS', ' '.join(cxxflags))
+
+        if '+cuda' in spec:
+            cuda_dir = spec['cuda'].prefix
+            # Run-time CUDA compiler:
+            s_env.set('OCCA_CUDA_COMPILER',
+                      join_path(cuda_dir, 'bin', 'nvcc'))
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+        # The environment variable CXX is automatically set to the Spack
+        # compiler wrapper.
+
+        # The cxxflags, if specified, will be set by the Spack compiler wrapper
+        # while the environment variable CXXFLAGS will remain undefined.
+        # We define CXXFLAGS in the environment to tell OCCA to use the user
+        # specified flags instead of its defaults. This way the compiler will
+        # get the cxxflags twice - once from the Spack compiler wrapper and
+        # second time from OCCA - however, only the second one will be seen in
+        # the verbose output, so we keep both.
+        cxxflags = spec.compiler_flags['cxxflags']
+        if cxxflags:
+            spack_env.set('CXXFLAGS', ' '.join(cxxflags))
+
+        # For the cuda, openmp, and opencl variants, set the environment
+        # variable OCCA_{CUDA,OPENMP,OPENCL}_ENABLED only if the variant is
+        # disabled. Otherwise, let OCCA autodetect what is available.
+
+        if '+cuda' in spec:
+            cuda_dir = spec['cuda'].prefix
+            cuda_libs_list = ['libcuda', 'libcudart', 'libOpenCL']
+            cuda_libs = find_libraries(cuda_libs_list,
+                                       cuda_dir,
+                                       shared=True,
+                                       recursive=True)
+            spack_env.set('OCCA_INCLUDE_PATH', cuda_dir.include)
+            spack_env.set('OCCA_LIBRARY_PATH', ':'.join(cuda_libs.directories))
+        else:
+            spack_env.set('OCCA_CUDA_ENABLED', '0')
+
+        if '~opencl' in spec:
+            spack_env.set('OCCA_OPENCL_ENABLED', '0')
+
+        # Setup run-time environment for testing.
+        spack_env.set('OCCA_VERBOSE', '1')
+        self._setup_runtime_flags(spack_env)
+        # The 'run_env' is included in the Spack generated module files.
+        self._setup_runtime_flags(run_env)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # Export OCCA_* variables for everyone using this package from within
+        # Spack.
+        self._setup_runtime_flags(spack_env)
diff --git a/var/spack/repos/builtin/packages/oce/package.py b/var/spack/repos/builtin/packages/oce/package.py
index 6fc6183e40..04af4466e4 100644
--- a/var/spack/repos/builtin/packages/oce/package.py
+++ b/var/spack/repos/builtin/packages/oce/package.py
@@ -1,29 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from spack.operating_systems.mac_os import macOS_version
+from spack.operating_systems.mac_os import macos_version
 import platform
 
 
@@ -35,6 +16,7 @@ class Oce(Package):
     homepage = "https://github.com/tpaviot/oce"
     url = "https://github.com/tpaviot/oce/archive/OCE-0.18.tar.gz"
 
+    version('0.18.3', '1686393c8493bbbb2f3f242330b33cba')
     version('0.18.2', '6dfd68e459e2c62387579888a867281f')
     version('0.18.1', '2a7597f4243ee1f03245aeeb02d00956')
     version('0.18',   '226e45e77c16a4a6e127c71fefcd171410703960ae75c7ecc7eb68895446a993')
@@ -62,12 +44,12 @@ class Oce(Package):
 
     # OCE depends on xlocale.h from glibc-headers but it was removed in 2.26,
     # see https://github.com/tpaviot/oce/issues/675
-    patch('xlocale.patch', level=0, when='@0.18.1:')
+    patch('xlocale.patch', level=0, when='@0.18.1:0.18.2')
 
     # fix build with Xcode 8 "previous definition of CLOCK_REALTIME"
     # reported 27 Sep 2016 https://github.com/tpaviot/oce/issues/643
     if (platform.system() == "Darwin") and (
-       macOS_version() == Version('10.12')):
+       macos_version() == Version('10.12')):
         patch('sierra.patch', when='@0.17.2:0.18.0')
 
     def install(self, spec, prefix):
@@ -98,7 +80,7 @@ class Oce(Package):
             ])
 
         if platform.system() == 'Darwin' and (
-           macOS_version() >= Version('10.12')):
+           macos_version() >= Version('10.12')):
             # use @rpath on Sierra due to limit of dynamic loader
             options.append('-DCMAKE_MACOSX_RPATH=ON')
         else:
diff --git a/var/spack/repos/builtin/packages/oclint/bundle.patch b/var/spack/repos/builtin/packages/oclint/bundle.patch
new file mode 100644
index 0000000000..f40e72bfae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/oclint/bundle.patch
@@ -0,0 +1,16 @@
+--- oclint-scripts/bundle	2017-09-29 10:27:37.000000000 -0700
++++ oclint-scripts/bundle	2018-01-26 03:49:31.000000000 -0800
+@@ -92,7 +92,7 @@
+ 
+ def install_cpp_headers():
+     if environment.is_darwin():
+-        install_dir = path.build.clang_install_dir
++        install_dir = (path.build.clang_install_dir if not args.llvm_root else args.llvm_root)
+         clang_cpp_headers_dir = os.path.join(install_dir, 'include', 'c++')
+         oclint_cpp_headers_dir = os.path.join(bundle_include_dir, 'c++')
+         path.mkdir_p(bundle_include_dir)
+@@ -141,4 +141,3 @@
+ 
+ if args.archive:
+     archive(args.release)
+-
diff --git a/var/spack/repos/builtin/packages/oclint/package.py b/var/spack/repos/builtin/packages/oclint/package.py
new file mode 100644
index 0000000000..a0810739be
--- /dev/null
+++ b/var/spack/repos/builtin/packages/oclint/package.py
@@ -0,0 +1,64 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Oclint(Package):
+    """OClint: a static analysis tool for C, C++, and Objective-C code
+
+       OCLint is a static code analysis tool for improving quality and
+       reducing defects by inspecting C, C++ and Objective-C code and
+       looking for potential problems"""
+
+    homepage = "http://oclint.org/"
+    url      = "https://github.com/oclint/oclint/archive/v0.13.tar.gz"
+
+    version('0.13', '1d0e605eb7815ac15e6a2a82327d2dd8')
+
+    depends_on('python', type=('build'))
+    depends_on('py-argparse', type=('build'))
+    depends_on('git', type=('build'))
+    depends_on('subversion', type=('build'))
+    depends_on('cmake', type=('build'))
+    depends_on('ninja', type=('build'))
+    depends_on('llvm@5.0.0:')
+
+    # Needed to fix a bug in oclint-scripts/bundle script, which
+    # attempts to install c++ headers in the wrong location
+    # contributed upstream as
+    # https://github.com/oclint/oclint/pull/492
+    patch('bundle.patch', level=0)
+
+    def install(self, spec, prefix):
+        # Build from source via directions from
+        # http://docs.oclint.org/en/stable/intro/build.html,
+        cd('oclint-scripts')
+
+        # ...but instead of using oclint-scripts/make, execute the
+        # commands in oclint-scripts/makeWithSystemLLVM so that
+        # oclint links to spack-installed LLVM
+        build_script = Executable(join_path('.', 'build'))
+        bundle_script = Executable(join_path('.', 'bundle'))
+
+        # Add the '-no-analytics' argument to the build script because
+        # 1) it doesn't detect properly a spack install of OpenSSL,
+        #    and throws an error due to missing OpenSSL headers
+        # 2) the bespoke build system is a pain to patch as it is
+        # 3) many sites don't allow software that communicates analytics data
+        build_script('-release',
+                     '-clean',
+                     '-llvm-root={0}'.format(spec['llvm'].prefix),
+                     '-use-system-compiler',
+                     '-no-analytics',
+                     'all')
+        bundle_script('-release', '-llvm-root={0}'.format(spec['llvm'].prefix))
+
+        # Copy install tree into the correct locations using the
+        # directory layout described in
+        cd(join_path('..', 'build'))
+        install_tree(join_path('oclint-release', 'include'), prefix.include)
+        install_tree(join_path('oclint-release', 'lib'), prefix.lib)
+        install_tree(join_path('oclint-release', 'bin'), prefix.bin)
diff --git a/var/spack/repos/builtin/packages/oclock/package.py b/var/spack/repos/builtin/packages/oclock/package.py
index 2d3a40457f..0108623080 100644
--- a/var/spack/repos/builtin/packages/oclock/package.py
+++ b/var/spack/repos/builtin/packages/oclock/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Oclock(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxkbfile')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/octave-optim/package.py b/var/spack/repos/builtin/packages/octave-optim/package.py
new file mode 100644
index 0000000000..5bcb323bbe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/octave-optim/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OctaveOptim(OctavePackage):
+    """Non-linear optimization toolkit for Octave."""
+
+    homepage = "https://octave.sourceforge.io/optim/"
+    url      = "https://downloads.sourceforge.net/octave/optim-1.5.2.tar.gz"
+
+    version('1.5.2', 'd3d77982869ea7c1807b13b24e044d44')
+
+    depends_on('octave-struct@1.0.12:')
+    extends('octave@3.6.0:')
diff --git a/var/spack/repos/builtin/packages/octave-splines/package.py b/var/spack/repos/builtin/packages/octave-splines/package.py
index c9a5f7b01d..857fc48d9c 100644
--- a/var/spack/repos/builtin/packages/octave-splines/package.py
+++ b/var/spack/repos/builtin/packages/octave-splines/package.py
@@ -1,44 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class OctaveSplines(Package):
+class OctaveSplines(OctavePackage):
     """Additional spline functions."""
 
     homepage = "http://octave.sourceforge.net/splines/index.html"
     url      = "http://downloads.sourceforge.net/octave/splines-1.3.1.tar.gz"
 
     version('1.3.1', 'f9665d780c37aa6a6e17d1f424c49bdeedb89d1192319a4e39c08784122d18f9')
-
     extends('octave@3.6.0:')
-
-    def install(self, spec, prefix):
-        octave('--quiet',
-               '--norc',
-               '--built-in-docstrings-file=/dev/null',
-               '--texi-macros-file=/dev/null',
-               '--eval', 'pkg prefix %s; pkg install %s' %
-               (prefix, self.stage.archive_file))
diff --git a/var/spack/repos/builtin/packages/octave-struct/package.py b/var/spack/repos/builtin/packages/octave-struct/package.py
new file mode 100644
index 0000000000..2f08729106
--- /dev/null
+++ b/var/spack/repos/builtin/packages/octave-struct/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OctaveStruct(OctavePackage):
+    """Additional structure manipulation functions for Octave."""
+
+    homepage = "https://octave.sourceforge.io/struct/"
+    url      = "https://downloads.sourceforge.net/octave/struct-1.0.14.tar.gz"
+
+    version('1.0.14', '3589d5eb8000f18426e2178587eb82f4')
+    extends('octave@2.9.7:')
diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py
index 79dc74b518..62f8ea7783 100644
--- a/var/spack/repos/builtin/packages/octave/package.py
+++ b/var/spack/repos/builtin/packages/octave/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -34,10 +15,13 @@ class Octave(AutotoolsPackage):
     Matlab. It may also be used as a batch-oriented language."""
 
     homepage = "https://www.gnu.org/software/octave/"
-    url      = "https://ftp.gnu.org/gnu/octave/octave-4.0.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/octave/octave-4.0.0.tar.gz"
 
     extendable = True
 
+    version('4.4.1', '09fbd0f212f4ef21e53f1d9c41cf30ce3d7f9450fb44911601e21ed64c67ae97')
+    version('4.4.0', '72f846379fcec7e813d46adcbacd069d72c4f4d8f6003bcd92c3513aafcd6e96')
+    version('4.2.2', '77b84395d8e7728a1ab223058fe5e92dc38c03bc13f7358e6533aab36f76726e')
     version('4.2.1', '80c28f6398576b50faca0e602defb9598d6f7308b0903724442c2a35a605333b')
     version('4.2.0', '443ba73782f3531c94bcf016f2f0362a58e186ddb8269af7dcce973562795567')
     version('4.0.2', 'c2a5cacc6e4c52f924739cdf22c2c687')
@@ -76,7 +60,7 @@ class Octave(AutotoolsPackage):
     # Octave does not configure with sed from darwin:
     depends_on('sed', when=sys.platform == 'darwin', type='build')
     depends_on('pcre')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
     # Strongly recommended dependencies
     depends_on('readline',     when='+readline')
@@ -99,7 +83,7 @@ class Octave(AutotoolsPackage):
     depends_on('qhull',        when='+qhull')
     depends_on('qrupdate',     when='+qrupdate')
     # depends_on('qscintilla',  when='+qscintilla) # TODO: add package
-    depends_on('qt',           when='+qt')
+    depends_on('qt+opengl',    when='+qt')
     depends_on('suite-sparse', when='+suitesparse')
     depends_on('zlib',         when='+zlib')
 
@@ -186,9 +170,9 @@ class Octave(AutotoolsPackage):
 
         if '+jdk' in spec:
             config_args.extend([
-                "--with-java-homedir=%s"    % spec['java'].prefix,
-                "--with-java-includedir=%s" % spec['java'].prefix.include,
-                "--with-java-libdir=%s"     % spec['java'].prefix.lib
+                "--with-java-homedir=%s"    % spec['java'].home,
+                "--with-java-includedir=%s" % spec['java'].home.include,
+                "--with-java-libdir=%s"     % spec['java'].libs.directories[0]
             ])
         else:
             config_args.append("--disable-java")
diff --git a/var/spack/repos/builtin/packages/octopus/package.py b/var/spack/repos/builtin/packages/octopus/package.py
index c450cf6020..315beb57b5 100644
--- a/var/spack/repos/builtin/packages/octopus/package.py
+++ b/var/spack/repos/builtin/packages/octopus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,13 @@ class Octopus(Package):
     homepage = "http://www.tddft.org/programs/octopus/"
     url      = "http://www.tddft.org/programs/octopus/down.php?file=6.0/octopus-6.0.tar.gz"
 
+    version('7.3', '87e51fa4a3a999706ea4ea5e9136996f')
     version('6.0', '5d1168c2a8d7fd9cb9492eaebaa7182e')
     version('5.0.1', '2b6392ab67b843f9d4ca7413fc07e822')
 
     variant('scalapack', default=False,
             description='Compile with Scalapack')
-    variant('metis', default=True,
+    variant('metis', default=False,
             description='Compile with METIS')
     variant('parmetis', default=False,
             description='Compile with ParMETIS')
@@ -47,11 +29,11 @@ class Octopus(Package):
             description='Compile with ARPACK')
 
     depends_on('blas')
-    depends_on('gsl')
+    depends_on('gsl@1.9:')
     depends_on('lapack')
     depends_on('libxc')
     depends_on('mpi')
-    depends_on('fftw+mpi')
+    depends_on('fftw@3:+mpi+openmp')
     depends_on('metis@5:', when='+metis')
     depends_on('parmetis', when='+parmetis')
     depends_on('scalapack', when='+scalapack')
@@ -59,7 +41,7 @@ class Octopus(Package):
     depends_on('arpack-ng', when='+arpack')
 
     # optional dependencies:
-    # TODO: parmetis, etsf-io, sparskit,
+    # TODO: etsf-io, sparskit,
     # feast, libfm, pfft, isf, pnfft
 
     def install(self, spec, prefix):
@@ -75,7 +57,7 @@ class Octopus(Package):
             'CC=%s' % spec['mpi'].mpicc,
             'FC=%s' % spec['mpi'].mpifc,
             '--enable-mpi',
-            '--with-fft-lib=-L%s -lfftw3' % spec['fftw'].prefix.lib,
+            '--with-fftw-prefix==%s' % spec['fftw'].prefix,
         ])
         if '+metis' in spec:
             args.extend([
diff --git a/var/spack/repos/builtin/packages/of-adios-write/package.py b/var/spack/repos/builtin/packages/of-adios-write/package.py
index 0c56f0286c..98a293c1d9 100644
--- a/var/spack/repos/builtin/packages/of-adios-write/package.py
+++ b/var/spack/repos/builtin/packages/of-adios-write/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# Copyright (c) 2017 Mark Olesen, OpenCFD Ltd.
-#
-# This file was authored by Mark Olesen <mark.olesen@esi-group.com>
-# and is released as part of spack under the LGPL license.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for the LLNL notice and LGPL.
-#
-# License
-# -------
-# 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
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Legal Notice
 # ------------
 # OPENFOAM is a trademark owned by OpenCFD Ltd
@@ -56,11 +36,11 @@ class OfAdiosWrite(Package):
     # Currently only via git, but with some branches corresponding to main
     # OpenFOAM releases.
     homepage = "https://develop.openfoam.com/Community/feature-adiosWrite/"
-    gitrepo  = "https://develop.openfoam.com/Community/feature-adiosWrite.git"
+    git      = "https://develop.openfoam.com/Community/feature-adiosWrite.git"
 
-    version('develop', branch='develop', git=gitrepo)
-    version('1706', branch='v1706', git=gitrepo)
-    version('1612', branch='v1612', git=gitrepo)
+    version('develop', branch='develop')
+    version('1706', branch='v1706')
+    version('1612', branch='v1612')
 
     variant('source', default=True, description='Install library source')
 
diff --git a/var/spack/repos/builtin/packages/of-precice/package.py b/var/spack/repos/builtin/packages/of-precice/package.py
new file mode 100644
index 0000000000..31cd530002
--- /dev/null
+++ b/var/spack/repos/builtin/packages/of-precice/package.py
@@ -0,0 +1,86 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+import llnl.util.tty as tty
+
+from spack import *
+from spack.pkg.builtin.openfoam_com import add_extra_files
+
+
+class OfPrecice(Package):
+    """preCICE adapter for OpenFOAM"""
+
+    homepage = 'https://www.precice.org'
+    git      = 'https://github.com/precice/openfoam-adapter.git'
+
+    # Currently develop only
+    version('develop', branch='master')
+
+    depends_on('openfoam+source')
+    depends_on('precice')
+    depends_on('yaml-cpp')
+
+    # General patches
+    common = ['change-userdir.sh', 'spack-derived-Allwmake']
+    assets = []
+
+    build_script  = './spack-derived-Allwmake'
+    build_userdir = 'spack-userdir'  # Build user APPBIN, LIBBIN into here
+
+    phases = ['configure', 'build', 'install']
+
+    #
+    # - End of definitions / setup -
+    #
+
+    def patch(self):
+        """Copy additional files or other patching."""
+        add_extra_files(self, self.common, self.assets)
+        # Emit openfoam version immediately, if we resolved the wrong version
+        # it takes a very long time to rebuild!
+        tty.info('Build for ' + self.spec['openfoam'].format('$_$@$%@+$+'))
+
+    def configure(self, spec, prefix):
+        """Generate spack-config.sh file."""
+        # Local tweaks
+        # This is ugly, but otherwise it only looks for src/precice,
+        # not the installed include files
+        config = join_path(self.stage.source_path, 'spack-config.sh')
+        with open(config, 'w') as out:
+            out.write(
+                """# Local tweaks for building
+CPLUS_INCLUDE_PATH="{precice_dir}/include/precice${{CPLUS_INCLUDE_PATH:+:}}$CPLUS_INCLUDE_PATH"  ## noqa: E501
+export CPLUS_INCLUDE_PATH
+# Local build (for user appbin, libbin)
+. ./change-userdir.sh $PWD/{user_dir}
+#
+"""
+                .format(
+                    precice_dir=spec['precice'].prefix,
+                    user_dir=self.build_userdir))
+
+    def build(self, spec, prefix):
+        """Build with Allwmake script, wrapped to source environment first."""
+        args = []
+        if self.parallel:  # Parallel build? - pass via environment
+            os.environ['WM_NCOMPPROCS'] = str(make_jobs)
+        builder = Executable(self.build_script)
+        builder(*args)
+
+    def install(self, spec, prefix):
+        """Install under the prefix directory"""
+
+        for f in ['README.md', 'LICENSE']:
+            if os.path.isfile(f):
+                install(f, join_path(self.prefix, f))
+
+        install_tree('tutorials', join_path(self.prefix, 'tutorials'))
+
+        # Place directly under 'lib' (no bin)
+        install_tree(
+            join_path(self.build_userdir, 'lib'),
+            join_path(self.prefix, 'lib'))
diff --git a/var/spack/repos/builtin/packages/omega-h/package.py b/var/spack/repos/builtin/packages/omega-h/package.py
new file mode 100644
index 0000000000..18f5563cb4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/omega-h/package.py
@@ -0,0 +1,91 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OmegaH(CMakePackage):
+    """Omega_h is a C++11 library providing data structures and algorithms
+    for adaptive discretizations. Its specialty is anisotropic triangle and
+    tetrahedral mesh adaptation. It runs efficiently on most modern HPC
+    hardware including GPUs.
+    """
+
+    homepage = "https://github.com/ibaned/omega_h"
+    url      = "https://github.com/ibaned/omega_h/archive/v9.13.4.tar.gz"
+    git      = "https://github.com/ibaned/omega_h.git"
+
+    version('develop', branch='master')
+    version('9.19.1', sha256='60ef65c2957ce03ef9d1b995d842fb65c32c5659d064de002c071effe66b1b1f')
+    version('9.19.0', sha256='4a1606c4e7287a1b67359cf6ef1c2d7e24b7dc379065566a1d2e0b0330c0abbd')
+    version('9.15.0', sha256='342a506a0ff22f6cac759862efdcf34e360110f7901eb9b4c5de8afe38741522')
+    version('9.14.0', sha256='035d0f47142f965a57818d1cb6c5c00b5ae6b5a0178b67b0bc9177fa99ba083d')
+    version('9.13.14', sha256='f617dfd024c9cc323e56800ca23df3386bfa37e1b9bd378847d1f5d32d2b8e5d')
+    version('9.13.13', sha256='753702edf4bda9ae57ea21f09ca071e341604a468d8c86468c9aebba049f581c')
+
+    variant('shared', default=True, description='Build shared libraries')
+    variant('mpi', default=True, description='Activates MPI support')
+    variant('zlib', default=True, description='Activates ZLib support')
+    variant('trilinos', default=False, description='Use Teuchos and Kokkos')
+    variant('build_type', default='')
+    variant('throw', default=False, description='Errors throw exceptions instead of abort')
+    variant('examples', default=False, description='Compile examples')
+    variant('optimize', default=True, description='Compile C++ with optimization')
+    variant('symbols', default=True, description='Compile C++ with debug symbols')
+    variant('warnings', default=False, description='Compile C++ with warnings')
+
+    depends_on('gmsh', when='+examples', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('trilinos +kokkos +teuchos', when='+trilinos')
+    depends_on('zlib', when='+zlib')
+
+    # https://gcc.gnu.org/bugzilla/show_bug.cgi?id=86610
+    conflicts('%gcc@8:')
+
+    def _bob_options(self):
+        cmake_var_prefix = 'Omega_h_CXX_'
+        for variant in ['optimize', 'symbols', 'warnings']:
+            cmake_var = cmake_var_prefix + variant.upper()
+            if '+' + variant in self.spec:
+                yield '-D' + cmake_var + ':BOOL=ON'
+            else:
+                yield '-D' + cmake_var + ':BOOL=FALSE'
+
+    def cmake_args(self):
+        args = ['-DUSE_XSDK_DEFAULTS:BOOL=OFF']
+        if '+shared' in self.spec:
+            args.append('-DBUILD_SHARED_LIBS:BOOL=ON')
+        else:
+            args.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
+        if '+mpi' in self.spec:
+            args.append('-DOmega_h_USE_MPI:BOOL=ON')
+            args.append('-DCMAKE_CXX_COMPILER:FILEPATH={0}'.format(
+                self.spec['mpi'].mpicxx))
+        else:
+            args.append('-DOmega_h_USE_MPI:BOOL=OFF')
+        if '+trilinos' in self.spec:
+            args.append('-DOmega_h_USE_Trilinos:BOOL=ON')
+        if '+zlib' in self.spec:
+            args.append('-DOmega_h_USE_ZLIB:BOOL=ON')
+            args.append('-DZLIB_ROOT:PATH={0}'.format(
+                self.spec['zlib'].prefix))
+        else:
+            args.append('-DOmega_h_USE_ZLIB:BOOL=OFF')
+        if '+examples' in self.spec:
+            args.append('-DOmega_h_EXAMPLES:BOOL=ON')
+        else:
+            args.append('-DOmega_h_EXAMPLES:BOOL=OFF')
+        if '+throw' in self.spec:
+            args.append('-DOmega_h_THROW:BOOL=ON')
+        else:
+            args.append('-DOmega_h_THROW:BOOL=OFF')
+        args += list(self._bob_options())
+        return args
+
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if name == 'cxxflags':
+            flags.append(self.compiler.cxx11_flag)
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/ompss/package.py b/var/spack/repos/builtin/packages/ompss/package.py
index f3cea1597d..e9f4f4a757 100644
--- a/var/spack/repos/builtin/packages/ompss/package.py
+++ b/var/spack/repos/builtin/packages/ompss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import glob
diff --git a/var/spack/repos/builtin/packages/ompt-openmp/package.py b/var/spack/repos/builtin/packages/ompt-openmp/package.py
index 803f70c7c2..50641146c1 100644
--- a/var/spack/repos/builtin/packages/ompt-openmp/package.py
+++ b/var/spack/repos/builtin/packages/ompt-openmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/oniguruma/package.py b/var/spack/repos/builtin/packages/oniguruma/package.py
index 28fb33590c..7dda866f16 100644
--- a/var/spack/repos/builtin/packages/oniguruma/package.py
+++ b/var/spack/repos/builtin/packages/oniguruma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ont-albacore/package.py b/var/spack/repos/builtin/packages/ont-albacore/package.py
index 882b6f6925..79da108daf 100644
--- a/var/spack/repos/builtin/packages/ont-albacore/package.py
+++ b/var/spack/repos/builtin/packages/ont-albacore/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,8 +14,10 @@ class OntAlbacore(Package):
     kits and Flow Cells."""
 
     homepage = "https://nanoporetech.com"
-    url = "https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-1.2.4-cp35-cp35m-manylinux1_x86_64.whl"
+    url = "https://mirror.oxfordnanoportal.com/software/analysis/ont_albacore-2.3.1-cp35-cp35m-manylinux1_x86_64.whl"
 
+    version('2.3.1', '0e85ad176e691252344c4c4b673c4b68', expand=False)
+    version('2.1.2', '1e60cfb95628829f2a61a85247f1b6af', expand=False)
     version('1.2.4', '559640bec4693af12e4d923e8d77adf6', expand=False)
     version('1.1.0', 'fab4502ea1bad99d813aa2629e03e83d', expand=False)
     extends('python')
diff --git a/var/spack/repos/builtin/packages/opa-psm2/package.py b/var/spack/repos/builtin/packages/opa-psm2/package.py
new file mode 100644
index 0000000000..c10130ba55
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opa-psm2/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OpaPsm2(MakefilePackage):
+    """ Intel Omni-Path Performance Scaled Messaging 2 (PSM2) library"""
+
+    homepage = "http://github.com/01org/opa-psm2"
+    url      = "https://github.com/01org/opa-psm2/archive/PSM2_10.3-8.tar.gz"
+
+    version('10.3-37',  '9bfca04f29b937b3856f893e1f8b1b60')
+    version('10.3-17',  'e7263eb449939cb87612e2c7623ca21c')
+    version('10.3-10',  '59d36b49eb126f980f3272a9d66a8e98')
+    version('10.3-8',   '07bc5cb2a6bf1189a29cbea836843db2')
+    version('10.2-260', '71df31b5776be64ff243417ac88eec66')
+    version('10.2-235', '23539f725a597bf2d35aac47a793a37b')
+    version('10.2-175', 'c542b8641ad573f08f61d0a6a70f4013')
+
+    depends_on('numactl')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('DESTDIR', self.prefix)
+        run_env.prepend_path('CPATH',
+                             join_path(self.prefix, 'usr', 'include'))
+        run_env.prepend_path('LIBRARY_PATH',
+                             join_path(self.prefix, 'usr', 'lib64'))
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'usr', 'lib64'))
+
+    def install(self, spec, prefix):
+        make('--environment-overrides', 'install')
diff --git a/var/spack/repos/builtin/packages/opam/package.py b/var/spack/repos/builtin/packages/opam/package.py
new file mode 100644
index 0000000000..0ff0af9157
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opam/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Opam(AutotoolsPackage):
+    """OPAM: OCaml Package Manager
+
+       OPAM is a source-based package manager for OCaml. It supports
+       multiple simultaneous compiler installations, flexible package
+       constraints, and a Git-friendly development workflow."""
+
+    homepage = "https://opam.ocaml.org/"
+    url      = "https://github.com/ocaml/opam/releases/download/1.2.2/opam-full-1.2.2.tar.gz"
+
+    version('1.2.2', '7d348c2898795e9f325fb80eaaf5eae8')
+    version('1.2.1', '04e8823a099ab631943952e4c2ab18fc')
+
+    depends_on('ocaml')  # Not a strict dependency, but recommended
+
+    parallel = False
+
+    def setup_environment(self, spack_env, run_env):
+        # Environment variable setting taken from
+        # https://github.com/Homebrew/homebrew-core/blob/master/Formula/opam.rb
+        spack_env.set('OCAMLPARAM', 'safe-string=0,_')  # OCaml 4.06.0 compat
+
+    def build(self, spec, prefix):
+        make('lib-ext')
+        make()
+        make('man')
diff --git a/var/spack/repos/builtin/packages/opari2/package.py b/var/spack/repos/builtin/packages/opari2/package.py
index 9b0a4e9c47..e48d64be5e 100644
--- a/var/spack/repos/builtin/packages/opari2/package.py
+++ b/var/spack/repos/builtin/packages/opari2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,6 +20,8 @@ class Opari2(AutotoolsPackage):
     homepage = "http://www.vi-hps.org/projects/score-p"
     url      = "http://www.vi-hps.org/upload/packages/opari2/opari2-1.1.2.tar.gz"
 
+    version('2.0.4', 'f69e324792f66780b473daf2b3c81f58ee8188adc72b6fe0dacf43d4c1a0a131')
+    version('2.0.3', 'f34674718ffdb098a48732a1eb9c1aa2')
     version('2.0.1', '74af78f1f27b8caaa4271e0b97fb0fba')
     version('2.0',   '72350dbdb6139f2e68a5055a4f0ba16c')
     version('1.1.4', '245d3d11147a06de77909b0805f530c0')
diff --git a/var/spack/repos/builtin/packages/openbabel/package.py b/var/spack/repos/builtin/packages/openbabel/package.py
index b88693d531..c7d6a68ec3 100644
--- a/var/spack/repos/builtin/packages/openbabel/package.py
+++ b/var/spack/repos/builtin/packages/openbabel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,7 +23,7 @@ class Openbabel(CMakePackage):
 
     depends_on('python', type=('build', 'run'), when='+python')
     depends_on('cmake@2.4.8:', type='build')
-    depends_on('pkg-config',   type='build')
+    depends_on('pkgconfig',   type='build')
     depends_on('cairo')       # required to support PNG depiction
     depends_on('eigen@3.0:')  # required if using the language bindings
     depends_on('libxml2')     # required to read/write CML files, XML formats
diff --git a/var/spack/repos/builtin/packages/openblas/openblas-0.3.2-cmake.patch b/var/spack/repos/builtin/packages/openblas/openblas-0.3.2-cmake.patch
new file mode 100644
index 0000000000..50df19805f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openblas/openblas-0.3.2-cmake.patch
@@ -0,0 +1,43 @@
+From 8ebf541e97e7c0573cde6a51353a47e3c509ca00 Mon Sep 17 00:00:00 2001
+From: Scott Thornton <wsttiger@gmail.com>
+Date: Mon, 30 Jul 2018 15:18:29 -0500
+Subject: [PATCH 1/2] Set EXPORT_NAME to match OpenBLASConfig.cmake
+
+---
+ CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 97f8adeda..4dc18da99 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -169,6 +169,7 @@ endif()
+ # Set output for libopenblas
+ set_target_properties( ${OpenBLAS_LIBNAME} PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
+ set_target_properties( ${OpenBLAS_LIBNAME} PROPERTIES LIBRARY_OUTPUT_NAME_DEBUG "${OpenBLAS_LIBNAME}_d")
++set_target_properties( ${OpenBLAS_LIBNAME} PROPERTIES EXPORT_NAME "OpenBLAS")
+ 
+ foreach (OUTPUTCONFIG ${CMAKE_CONFIGURATION_TYPES})
+   string( TOUPPER ${OUTPUTCONFIG} OUTPUTCONFIG )
+
+From 2a9a9389ef6c3da56fda859c9586becc41a2e780 Mon Sep 17 00:00:00 2001
+From: Scott Thornton <wsttiger@gmail.com>
+Date: Thu, 2 Aug 2018 14:58:52 -0500
+Subject: [PATCH 2/2] Added target_include_directories()
+
+---
+ CMakeLists.txt | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 4dc18da99..20ce02e87 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -150,6 +150,7 @@ endif()
+ 
+ # add objects to the openblas lib
+ add_library(${OpenBLAS_LIBNAME} ${LA_SOURCES} ${LAPACKE_SOURCES} ${RELA_SOURCES} ${TARGET_OBJS} ${OpenBLAS_DEF_FILE})
++target_include_directories(${OpenBLAS_LIBNAME} INTERFACE $<INSTALL_INTERFACE:include>)
+ 
+ # Android needs to explicitly link against libm
+ if(ANDROID)
diff --git a/var/spack/repos/builtin/packages/openblas/openblas_icc_fortran2.patch b/var/spack/repos/builtin/packages/openblas/openblas_icc_fortran2.patch
new file mode 100644
index 0000000000..64785d4f45
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openblas/openblas_icc_fortran2.patch
@@ -0,0 +1,14 @@
+diff --git a/f_check b/f_check
+index 79febfb..c9da6ed 100644
+--- a/f_check
++++ b/f_check
+@@ -359,9 +359,6 @@ print MAKEFILE "NOFORTRAN=1\n" if $nofortran == 1;
+ 
+ print CONFFILE "#define BUNDERSCORE\t$bu\n" if $bu ne "";
+ print CONFFILE "#define NEEDBUNDERSCORE\t1\n" if $bu ne "";
+-print CONFFILE "#define NEED2UNDERSCORES\t1\n" if $need2bu ne "";
+-
+-print MAKEFILE "NEED2UNDERSCORES=1\n" if $need2bu ne "";
+ 
+ if (($linker_l ne "") || ($linker_a ne "")) {
+     print MAKEFILE "FEXTRALIB=$linker_L $linker_l $linker_a\n";
diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py
index f85d0e2a02..ffa02c23e6 100644
--- a/var/spack/repos/builtin/packages/openblas/package.py
+++ b/var/spack/repos/builtin/packages/openblas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 from spack import *
@@ -31,16 +12,22 @@ import spack.architecture
 
 class Openblas(MakefilePackage):
     """OpenBLAS: An optimized BLAS library"""
-    homepage = 'http://www.openblas.net'
-    url = 'http://github.com/xianyi/OpenBLAS/archive/v0.2.19.tar.gz'
 
+    homepage = 'http://www.openblas.net'
+    url      = 'http://github.com/xianyi/OpenBLAS/archive/v0.2.19.tar.gz'
+    git      = 'https://github.com/xianyi/OpenBLAS.git'
+
+    version('develop', branch='develop')
+    version('0.3.3', sha256='49d88f4494ae780e3d7fa51769c00d982d7cdb73e696054ac3baa81d42f13bab')
+    version('0.3.2', sha256='e8ba64f6b103c511ae13736100347deb7121ba9b41ba82052b1a018a65c0cb15')
+    version('0.3.1', sha256='1f5e956f35f3acdd3c74516e955d797a320c2e0135e31d838cbdb3ea94d0eb33')
+    version('0.3.0',  '42cde2c1059a8a12227f1e6551c8dbd2')
     version('0.2.20', '48637eb29f5b492b91459175dcc574b1')
     version('0.2.19', '28c998054fd377279741c6f0b9ea7941')
     version('0.2.18', '805e7f660877d588ea7e3792cda2ee65')
     version('0.2.17', '664a12807f2a2a7cda4781e3ab2ae0e1')
     version('0.2.16', 'fef46ab92463bdbb1479dcec594ef6dc')
     version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9')
-    version('develop', git='https://github.com/xianyi/OpenBLAS.git', branch='develop')
 
     variant(
         'shared',
@@ -61,6 +48,12 @@ class Openblas(MakefilePackage):
         multi=False
     )
 
+    variant(
+        'virtual_machine',
+        default=False,
+        description="Adding options to build openblas on Linux virtual machine"
+    )
+
     # virtual dependency
     provides('blas')
     provides('lapack')
@@ -70,8 +63,9 @@ class Openblas(MakefilePackage):
     #  https://github.com/xianyi/OpenBLAS/pull/915
     #  UPD: the patch has been merged starting version 0.2.20
     patch('openblas_icc.patch', when='@:0.2.19%intel')
-    patch('openblas_icc_openmp.patch', when='%intel@16.0:')
+    patch('openblas_icc_openmp.patch', when='@:0.2.20%intel@16.0:')
     patch('openblas_icc_fortran.patch', when='%intel@16.0:')
+    patch('openblas_icc_fortran2.patch', when='%intel@18.0:')
 
     # Fixes compilation error on POWER8 with GCC 7
     # https://github.com/xianyi/OpenBLAS/pull/1098
@@ -81,6 +75,18 @@ class Openblas(MakefilePackage):
     # https://github.com/xianyi/OpenBLAS/pull/982
     patch('openblas0.2.19.diff', when='@0.2.19')
 
+    # Fix CMake export symbol error
+    # https://github.com/xianyi/OpenBLAS/pull/1703
+    patch('openblas-0.3.2-cmake.patch', when='@0.3.1:0.3.2')
+
+    # Disable experimental TLS code that lead to many threading issues
+    # https://github.com/xianyi/OpenBLAS/issues/1735#issuecomment-422954465
+    # https://github.com/xianyi/OpenBLAS/issues/1761#issuecomment-421039174
+    # https://github.com/xianyi/OpenBLAS/pull/1765
+    patch('https://github.com/xianyi/OpenBLAS/commit/4d183e5567346f80f2ef97eb98f8601c47f8cb56.patch',
+          sha256='714aea33692304a50bd0ccde42590c176c82ded4a8ac7f06e573dc8071929c33',
+          when='@0.3.3')
+
     parallel = False
 
     conflicts('%intel@16', when='@0.2.15:0.2.19')
@@ -90,10 +96,11 @@ class Openblas(MakefilePackage):
         # As of 06/2016 there is no mechanism to specify that packages which
         # depends on Blas/Lapack need C or/and Fortran symbols. For now
         # require both.
-        if self.compiler.f77 is None:
+        if self.compiler.fc is None:
             raise InstallError(
                 'OpenBLAS requires both C and Fortran compilers!'
             )
+
         # Add support for OpenMP
         if (self.spec.satisfies('threads=openmp') and
             self.spec.satisfies('%clang')):
@@ -108,7 +115,7 @@ class Openblas(MakefilePackage):
 
     @property
     def make_defs(self):
-        # Configure fails to pick up fortran from FC=/abs/path/to/f77, but
+        # Configure fails to pick up fortran from FC=/abs/path/to/fc, but
         # works fine with FC=/abs/path/to/gfortran.
         # When mixing compilers make sure that
         # $SPACK_ROOT/lib/spack/env/<compiler> have symlinks with reasonable
@@ -116,9 +123,16 @@ class Openblas(MakefilePackage):
 
         make_defs = [
             'CC={0}'.format(spack_cc),
-            'FC={0}'.format(spack_f77),
+            'FC={0}'.format(spack_fc),
             'MAKE_NO_J=1'
         ]
+
+        if self.spec.variants['virtual_machine'].value:
+            make_defs += [
+                'DYNAMIC_ARCH=1',
+                'NO_AVX2=1'
+            ]
+
         if self.spec.variants['cpu_target'].value:
             make_defs += [
                 'TARGET={0}'.format(self.spec.variants['cpu_target'].value)
diff --git a/var/spack/repos/builtin/packages/opencoarrays/CMakeLists.patch b/var/spack/repos/builtin/packages/opencoarrays/CMakeLists.patch
new file mode 100644
index 0000000000..7ce5a60479
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencoarrays/CMakeLists.patch
@@ -0,0 +1,27 @@
+diff --git a/src/mpi/CMakeLists.txt b/src/mpi/CMakeLists.txt
+index 590d646..3f2bded 100644
+--- a/src/mpi/CMakeLists.txt
++++ b/src/mpi/CMakeLists.txt
+@@ -8,22 +8,6 @@ if (NOT MPI_C_FOUND)
+   include_directories(BEFORE ${MPI_C_INCLUDE_PATH} ${MPI_Fortran_INCLUDE_PATH})
+    endif()
+
+    -#----------------------------------
+    -# Determine if we're using Open MPI
+    -#----------------------------------
+    -cmake_host_system_information(RESULT N_CPU QUERY NUMBER_OF_LOGICAL_CORES)
+    -set(N_CPU ${N_CPU} PARENT_SCOPE)
+    -cmake_host_system_information(RESULT HOST_NAME QUERY HOSTNAME)
+    -set(HOSTNAME ${HOSTNAME} PARENT_SCOPE)
+    -execute_process(COMMAND ${MPIEXEC} --version
+    -  OUTPUT_VARIABLE mpi_version_out)
+    -if (mpi_version_out MATCHES "[Oo]pen[ -][Mm][Pp][Ii]")
+    -  message( STATUS "OpenMPI detected")
+    -  set ( openmpi true PARENT_SCOPE)
+    -  # Write out a host file because OMPI's mpiexec is dumb
+    -  file(WRITE ${CMAKE_BINARY_DIR}/hostfile "${HOST_NAME} slots=${N_CPU}\n")
+    -endif ()
+    -
+     if("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "GNU")
+           set(gfortran_compiler true)
+            elseif("${CMAKE_Fortran_COMPILER_ID}" STREQUAL "Cray")
diff --git a/var/spack/repos/builtin/packages/opencoarrays/package.py b/var/spack/repos/builtin/packages/opencoarrays/package.py
index cba5651fc7..e3da9753ae 100644
--- a/var/spack/repos/builtin/packages/opencoarrays/package.py
+++ b/var/spack/repos/builtin/packages/opencoarrays/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,8 +15,9 @@ class Opencoarrays(CMakePackage):
     """
 
     homepage = "http://www.opencoarrays.org/"
-    url      = "https://github.com/sourceryinstitute/OpenCoarrays/releases/download/1.8.4/OpenCoarrays-1.8.4.tar.gz"
+    url      = "https://github.com/sourceryinstitute/OpenCoarrays/releases/download/2.2.0/OpenCoarrays-2.2.0.tar.gz"
 
+    version('2.2.0', '9311547a85a21853111f1e8555ceab4593731c6fd9edb64cfb9588805f9d1a0d')
     version('1.8.10', '9ba1670647db4d986634abf743abfd6a')
     version('1.8.4', '7c9eaffc3a0b5748d0d840e52ec9d4ad')
     version('1.8.0', 'ca78d1507b2a118c75128c6c2e093e27')
@@ -48,6 +30,9 @@ class Opencoarrays(CMakePackage):
                     'MinSizeRel', 'CodeCoverage'))
 
     depends_on('mpi')
+    # This patch removes a bunch of checks for the version of MPI available on
+    # the system. They make the Crays hang.
+    patch('CMakeLists.patch', when='platform=cray')
 
     def cmake_args(self):
         args = []
diff --git a/var/spack/repos/builtin/packages/opencv/dnn_cuda.patch b/var/spack/repos/builtin/packages/opencv/dnn_cuda.patch
new file mode 100644
index 0000000000..66ab59ba26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opencv/dnn_cuda.patch
@@ -0,0 +1,44 @@
+--- opencv-3.4.1/modules/dnn/src/layers/mvn_layer.cpp.orig	2018-06-14 10:46:28.025703093 +0200
++++ opencv-3.4.1/modules/dnn/src/layers/mvn_layer.cpp	2018-06-14 10:40:56.266069123 +0200
+@@ -43,7 +43,7 @@
+ #include "../precomp.hpp"
+ #include "layers_common.hpp"
+ #include <opencv2/dnn/shape_utils.hpp>
+-#include "math_functions.hpp"
++#include "../ocl4dnn/include/math_functions.hpp"
+ #include "opencl_kernels_dnn.hpp"
+ 
+ namespace cv
+--- opencv-3.4.1/modules/dnn/src/ocl4dnn/src/math_functions.cpp.orig	2018-06-14 10:45:23.565162940 +0200
++++ opencv-3.4.1/modules/dnn/src/ocl4dnn/src/math_functions.cpp	2018-06-14 10:44:48.513412965 +0200
+@@ -42,7 +42,7 @@
+ 
+ #include "../../precomp.hpp"
+ #include "common.hpp"
+-#include "math_functions.hpp"
++#include "../include/math_functions.hpp"
+ #include <vector>
+ #include "opencl_kernels_dnn.hpp"
+ 
+--- opencv-3.4.1/modules/dnn/src/ocl4dnn/src/ocl4dnn_conv_spatial.cpp.orig	2018-06-14 10:42:11.319534007 +0200
++++ opencv-3.4.1/modules/dnn/src/ocl4dnn/src/ocl4dnn_conv_spatial.cpp	2018-06-14 10:42:52.988236879 +0200
+@@ -52,7 +52,7 @@
+ #include "common.hpp"
+ #include "ocl4dnn.hpp"
+ #include "opencl_kernels_dnn.hpp"
+-#include "math_functions.hpp"
++#include "../include/math_functions.hpp"
+ #include "default_kernel_config.hpp"
+ 
+ #if defined WIN32 || defined _WIN32
+--- opencv-3.4.1/modules/dnn/src/ocl4dnn/src/ocl4dnn_inner_product.cpp.orig	2018-06-14 10:45:41.245036822 +0200
++++ opencv-3.4.1/modules/dnn/src/ocl4dnn/src/ocl4dnn_inner_product.cpp	2018-06-14 10:45:55.543934818 +0200
+@@ -43,7 +43,7 @@
+ #include "../../precomp.hpp"
+ #include "common.hpp"
+ #include "ocl4dnn.hpp"
+-#include "math_functions.hpp"
++#include "../include/math_functions.hpp"
+ 
+ #ifdef HAVE_OPENCL
+ namespace cv { namespace dnn { namespace ocl4dnn {
diff --git a/var/spack/repos/builtin/packages/opencv/package.py b/var/spack/repos/builtin/packages/opencv/package.py
index e76f763ffb..96a643f3a4 100644
--- a/var/spack/repos/builtin/packages/opencv/package.py
+++ b/var/spack/repos/builtin/packages/opencv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,12 +21,17 @@ class Opencv(CMakePackage):
     """
 
     homepage = 'http://opencv.org/'
-    url = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz'
+    url      = 'https://github.com/Itseez/opencv/archive/3.1.0.tar.gz'
+    git      = 'https://github.com/opencv/opencv.git'
 
-    version('master', git="https://github.com/opencv/opencv.git", branch="master")
+    version('master', branch='master')
+    version('3.4.3',    '712896f5815938c014c199dde142d508')
+    version('3.4.1',    'a0b7a47899e67b3490ea31edc4f6e8e6')
+    version('3.4.0',    '170732dc760e5f7ddeccbe53ba5d16a6')
+    version('3.3.1',    'b1ed9aea030bb5bd9df28524d97de84c')
     version('3.3.0',    '98a4e4c6f23ec725e808a891dc11eec4')
-    version('3.2.0',    'a43b65488124ba33dde195fea9041b70')
-    version('3.1.0',    '70e1dd07f0aa06606f1bc0e3fa15abd3')
+    version('3.2.0',    '1ea44a1d98c126ad40079d8eb914a72e')
+    version('3.1.0',    'a0669e22172dfc3225835b180744c9f0')
     version('2.4.13.2', 'fe52791ce523681a67036def4c25261b')
     version('2.4.13.1', 'f6d354500d5013e60dc0fc44b07a63d1')
     version('2.4.13',   '8feb45a71adad89b8017a777477c3eff')
@@ -53,29 +39,59 @@ class Opencv(CMakePackage):
     version('2.4.12.2', 'bc0c60c2ea1cf4078deef99569912fc7')
     version('2.4.12.1', '7192f51434710904b5e3594872b897c3')
 
+    # Standard variants
     variant('shared', default=True,
             description='Enables the build of shared libraries')
+    variant('lapack', default=True, description='Include Lapack library support')
+    variant('powerpc', default=False, description='Enable PowerPC for GCC')
+    variant('vsx', default=False, description='Enable POWER8 and above VSX (64-bit little-endian)')
+    variant('fast-math', default=False,
+            description='Enable -ffast-math (not recommended for GCC 4.6.x)')
+
+    # OpenCV modules
+    variant('calib3d', default=True, description='calib3d module')
+    variant('core', default=True, description='Include opencv_core module into the OpenCV build')
+    variant('dnn', default=True, description='Build DNN support')
+    variant('features2d', default=True, description='features2d module')
+    variant('flann', default=True, description='flann module')
+    variant('highgui', default=True, description='Include opencv_highgui module into the OpenCV build')
+    variant('imgproc', default=True, description='Include opencv_imgproc module into the OpenCV build')
+    variant('java', default=True,
+            description='Activates support for Java')
+    variant('ml', default=True, description='Build ML support')
+    variant('python', default=True,
+            description='Enables the build of Python extensions')
+    variant('stitching', default=True, description='stitching module')
+    variant('superres', default=True, description='superres module')
+    variant('ts', default=True, description='Include opencv_ts module into the OpenCV build')
+    variant('video', default=True, description='video module')
+    variant('videostab', default=True, description='videostab module')
+    variant('videoio', default=True, description='videoio module')
 
+    # Optional 3rd party components
+    variant('cuda', default=True, description='Activates support for CUDA')
     variant('eigen', default=True, description='Activates support for eigen')
     variant('ipp', default=True, description='Activates support for IPP')
+    variant('ipp_iw', default=True, description='Build IPP IW from source')
     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('jpeg', default=True, description='Include JPEG support')
+    variant('opencl', default=True, description='Include OpenCL Runtime support')
+    variant('opencl_svm', default=True, description='Include OpenCL Shared Virtual Memory support')
+    variant('openclamdfft', default=True, description='Include OpenCL AMD OpenCL FFT library support')
+    variant('openclamdblas', default=True, description='Include OpenCL AMD OpenCL BLAS library support')
+    variant('openmp', default=True, description='Activates support for OpenMP threads')
+    variant('pthreads_pf', default=True, description='Use pthreads-based parallel_for')
+    variant('png', default=True, description='Include PNG support')
     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')
-    variant('openmp', default=False, description='Activates support for OpenMP threads')
-    variant('core', default=True, description='Include opencv_core module into the OpenCV build')
-    variant('highgui', default=False, description='Include opencv_highgui module into the OpenCV build')
-    variant('imgproc', default=False, description='Include opencv_imgproc module into the OpenCV build')
-    variant('jpeg', default=False, description='Include JPEG support')
-    variant('png', default=False, description='Include PNG support')
-    variant('tiff', default=False, description='Include TIFF support')
-    variant('zlib', default=False, description='Build zlib from source')
-    variant('dnn', default=False, description='Build DNN support')
+    variant('gtk', default=True, description='Activates support for GTK')
+    variant('tiff', default=True, description='Include TIFF support')
+    variant('vtk', default=True, description='Activates support for VTK')
+    variant('zlib', default=True, description='Build zlib from source')
+
+    # Patch to fix conflict between CUDA and OpenCV (reproduced with 3.3.0
+    # and 3.4.1) header file that have the same name.Problem is fixed in
+    # the current development branch of OpenCV. See #8461 for more information.
+    patch('dnn_cuda.patch', when='@3.3.0:3.4.1+cuda+dnn')
 
     depends_on('eigen~mpfr', when='+eigen', type='build')
 
@@ -93,94 +109,147 @@ class Opencv(CMakePackage):
     depends_on('py-numpy', when='+python', type=('build', 'run'))
     depends_on('protobuf@3.1.0', when='@3.3.0: +dnn')
 
+    depends_on('ffmpeg', when='+videoio')
+    depends_on('mpi', when='+videoio')
+
     extends('python', when='+python')
 
     def cmake_args(self):
         spec = self.spec
 
+        # Standard variants
         args = [
             '-DBUILD_SHARED_LIBS:BOOL={0}'.format((
                 'ON' if '+shared' in spec else 'OFF')),
             '-DENABLE_PRECOMPILED_HEADERS:BOOL=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')),
+            '-DWITH_LAPACK={0}'.format((
+                'ON' if '+lapack' in spec else 'OFF')),
+            '-DENABLE_POWERPC={0}'.format((
+                'ON' if '+powerpc' in spec else 'OFF')),
+            '-DENABLE_VSX={0}'.format((
+                'ON' if '+vsx' in spec else 'OFF')),
+            '-DENABLE_FAST_MATH={0}'.format((
+                'ON' if '+fast-math' in spec else 'OFF')),
+        ]
+
+        # modules
+        args.extend([
+            '-DBUILD_opencv_calib3d={0}'.format((
+                'ON' if '+calib3d' in spec else 'OFF')),
             '-DBUILD_opencv_core:BOOL={0}'.format((
                 'ON' if '+core' in spec else 'OFF')),
+            '-DBUILD_opencv_dnn:BOOL={0}'.format((
+                'ON' if '+dnn' in spec else 'OFF')),
+            '-DBUILD_opencv_features2d={0}'.format((
+                'ON' if '+features2d' in spec else 'OFF')),
+            '-DBUILD_opencv_flann={0}'.format((
+                'ON' if '+flann' in spec else 'OFF')),
             '-DBUILD_opencv_highgui:BOOL={0}'.format((
                 'ON' if '+highgui' in spec else 'OFF')),
             '-DBUILD_opencv_imgproc:BOOL={0}'.format((
                 'ON' if '+imgproc' in spec else 'OFF')),
+            '-DBUILD_opencv_java:BOOL={0}'.format((
+                'ON' if '+java' in spec else 'OFF')),
+            '-DBUILD_opencv_ml={0}'.format((
+                'ON' if '+ml' in spec else 'OFF')),
+            '-DBUILD_opencv_stitching={0}'.format((
+                'ON' if '+stitching' in spec else 'OFF')),
+            '-DBUILD_opencv_superres={0}'.format((
+                'ON' if '+superres' in spec else 'OFF')),
+            '-DBUILD_opencv_ts={0}'.format((
+                'ON' if '+ts' in spec else 'OFF')),
+            '-DBUILD_opencv_video={0}'.format((
+                'ON' if '+video' in spec else 'OFF')),
+            '-DBUILD_opencv_videostab={0}'.format((
+                'ON' if '+videostab' in spec else 'OFF')),
+            '-DBUILD_opencv_videoio={0}'.format((
+                'ON' if '+videoio' in spec else 'OFF')),
+        ])
+
+        # 3rd party components
+        args.extend([
+            '-DBUILD_IPP_IW:BOOL={0}'.format((
+                'ON' if '+ipp_iw' in spec else 'OFF')),
+            '-DWITH_CUDA:BOOL={0}'.format((
+                'ON' if '+cuda' in spec else 'OFF')),
+            '-DWITH_EIGEN:BOOL={0}'.format((
+                'ON' if '+eigen' in spec else 'OFF')),
+            '-DWITH_IPP:BOOL={0}'.format((
+                'ON' if '+ipp' in spec else 'OFF')),
+            '-DWITH_JASPER:BOOL={0}'.format((
+                'ON' if '+jasper' in spec else 'OFF')),
             '-DWITH_JPEG:BOOL={0}'.format((
                 'ON' if '+jpeg' in spec else 'OFF')),
+            '-DWITH_OPENCL:BOOL={0}'.format((
+                'ON' if '+opencl' in spec else 'OFF')),
+            '-DWITH_OPENCL_SVM:BOOL={0}'.format((
+                'ON' if '+opencl_svm' in spec else 'OFF')),
+            '-DWITH_OPENCLAMDFFT:BOOL={0}'.format((
+                'ON' if '+openclamdfft' in spec else 'OFF')),
+            '-DWITH_OPENCLAMDBLAS:BOOL={0}'.format((
+                'ON' if '+openclamdblas' in spec else 'OFF')),
+            '-DWITH_OPENMP:BOOL={0}'.format((
+                'ON' if '+openmp' in spec else 'OFF')),
+            '-DWITH_PTHREADS_PF:BOOL={0}'.format((
+                'ON' if '+pthreads_pf' in spec else 'OFF')),
             '-DWITH_PNG:BOOL={0}'.format((
                 'ON' if '+png' in spec else 'OFF')),
+            '-DWITH_QT:BOOL={0}'.format((
+                'ON' if '+qt' in spec else 'OFF')),
             '-DWITH_TIFF:BOOL={0}'.format((
                 'ON' if '+tiff' in spec else 'OFF')),
-            '-DWITH_ZLIB:BOOL={0}'.format((
-                'ON' if '+zlib' in spec else 'OFF')),
-            '-DWITH_OPENMP:BOOL={0}'.format((
-                'ON' if '+openmp' in spec else 'OFF')),
-            '-DBUILD_opencv_dnn:BOOL={0}'.format((
-                'ON' if '+dnn' in spec else 'OFF')),
-        ]
+            '-DWITH_VTK:BOOL={0}'.format((
+                'ON' if '+vtk' in spec else 'OFF')),
+        ])
 
         # Media I/O
         if '+zlib' in spec:
             zlib = spec['zlib']
             args.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)
+                    'DEBUG' if 'build_type=Debug' in spec else 'RELEASE'),
+                    zlib.libs[0]),
+                '-DZLIB_INCLUDE_DIR:PATH={0}'.format(
+                    zlib.headers.directories[0])
             ])
 
         if '+png' in spec:
             libpng = spec['libpng']
             args.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)
+                    'DEBUG' if 'build_type=Debug' in spec else 'RELEASE'),
+                    libpng.libs[0]),
+                '-DPNG_INCLUDE_DIR:PATH={0}'.format(
+                    libpng.headers.directories[0])
             ])
 
         if '+jpeg' in spec:
             libjpeg = spec['jpeg']
             args.extend([
                 '-DBUILD_JPEG:BOOL=OFF',
-                '-DJPEG_LIBRARY:FILEPATH={0}'.format(
-                    join_path(libjpeg.prefix.lib,
-                              'libjpeg.{0}'.format(dso_suffix))),
-                '-DJPEG_INCLUDE_DIR:PATH={0}'.format(libjpeg.prefix.include)
+                '-DJPEG_LIBRARY:FILEPATH={0}'.format(libjpeg.libs[0]),
+                '-DJPEG_INCLUDE_DIR:PATH={0}'.format(
+                    libjpeg.headers.directories[0])
             ])
 
         if '+tiff' in spec:
             libtiff = spec['libtiff']
             args.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)
+                    'DEBUG' if 'build_type=Debug' in spec else 'RELEASE'),
+                    libtiff.libs[0]),
+                '-DTIFF_INCLUDE_DIR:PATH={0}'.format(
+                    libtiff.headers.directories[0])
             ])
 
         if '+jasper' in spec:
             jasper = spec['jasper']
             args.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)
+                    'DEBUG' if 'build_type=Debug' in spec else 'RELEASE'),
+                    jasper.libs[0]),
+                '-DJASPER_INCLUDE_DIR:PATH={0}'.format(
+                    jasper.headers.directories[0])
             ])
 
         # GUI
@@ -229,3 +298,10 @@ class Opencv(CMakePackage):
             ])
 
         return args
+
+    @property
+    def libs(self):
+        shared = "+shared" in self.spec
+        return find_libraries(
+            "libopencv_*", root=self.prefix, shared=shared, recursive=True
+        )
diff --git a/var/spack/repos/builtin/packages/openexr/package.py b/var/spack/repos/builtin/packages/openexr/package.py
index ad463bc792..6cb17ee9ce 100644
--- a/var/spack/repos/builtin/packages/openexr/package.py
+++ b/var/spack/repos/builtin/packages/openexr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,7 +24,7 @@ class Openexr(Package):
     variant('debug', default=False,
             description='Builds a debug version of the libraries')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('ilmbase')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/openfast/package.py b/var/spack/repos/builtin/packages/openfast/package.py
index 74d1881de9..14824588db 100644
--- a/var/spack/repos/builtin/packages/openfast/package.py
+++ b/var/spack/repos/builtin/packages/openfast/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,18 +10,14 @@ class Openfast(CMakePackage):
     """Wind turbine simulation package from NREL"""
 
     homepage = "http://openfast.readthedocs.io/en/latest/"
-    url      = "https://github.com/OpenFAST/openfast.git"
+    git      = "https://github.com/OpenFAST/openfast.git"
 
     maintainers = ['jrood-nrel']
 
-    version('develop',
-            git='https://github.com/OpenFAST/openfast.git',
-            branch='dev')
-    version('master',
-            git='https://github.com/OpenFAST/openfast.git',
-            branch='master')
+    version('develop', branch='dev')
+    version('master', branch='master')
 
-    variant('shared', default=False,
+    variant('shared', default=True,
             description="Build shared libraries")
     variant('double-precision', default=True,
             description="Treat REAL as double precision")
@@ -48,6 +25,8 @@ class Openfast(CMakePackage):
             description="Enable dynamic library loading interface")
     variant('cxx', default=False,
             description="Enable C++ bindings")
+    variant('pic', default=True,
+            description="Position independent code")
 
     # Dependencies for OpenFAST Fortran
     depends_on('blas')
@@ -56,7 +35,7 @@ class Openfast(CMakePackage):
     # Additional dependencies when compiling C++ library
     depends_on('mpi', when='+cxx')
     depends_on('yaml-cpp', when='+cxx')
-    depends_on('hdf5+mpi+cxx', when='+cxx')
+    depends_on('hdf5+mpi+cxx+hl', when='+cxx')
     depends_on('zlib', when='+cxx')
     depends_on('libxml2', when='+cxx')
 
@@ -77,10 +56,22 @@ class Openfast(CMakePackage):
                 'ON' if '+dll-interface' in spec else 'OFF'),
             '-DBUILD_FAST_CPP_API:BOOL=%s' % (
                 'ON' if '+cxx' in spec else 'OFF'),
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % (
+                'ON' if '+pic' in spec else 'OFF'),
+        ])
+
+        # Make sure we use Spack's blas/lapack:
+        blas_libs = spec['lapack'].libs + spec['blas'].libs
+        options.extend([
+            '-DBLAS_LIBRARIES=%s' % blas_libs.joined(';'),
+            '-DLAPACK_LIBRARIES=%s' % blas_libs.joined(';')
         ])
 
         if '+cxx' in spec:
             options.extend([
+                '-DMPI_CXX_COMPILER:PATH=%s' % spec['mpi'].mpicxx,
+                '-DMPI_C_COMPILER:PATH=%s' % spec['mpi'].mpicc,
+                '-DMPI_Fortran_COMPILER:PATH=%s' % spec['mpi'].mpifc,
                 '-DHDF5_ROOT:PATH=%s' % spec['hdf5'].prefix,
                 '-DYAML_ROOT:PATH=%s' % spec['yaml-cpp'].prefix,
             ])
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-bin.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-bin.patch
deleted file mode 100644
index b9e87a7ec8..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-bin.patch
+++ /dev/null
@@ -1,503 +0,0 @@
---- OpenFOAM-v1612+.orig/bin/foamEtcFile	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/bin/foamEtcFile	2017-03-23 10:08:37.296887070 +0100
-@@ -4,7 +4,7 @@
- # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
- #  \\    /   O peration     |
- #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
--#    \\/     M anipulation  |
-+#    \\/     M anipulation  | Copyright (C) 2017 OpenCFD Ltd.
- #-------------------------------------------------------------------------------
- # License
- #     This file is part of OpenFOAM.
-@@ -26,7 +26,7 @@
- #     foamEtcFile
- #
- # Description
--#     Locate user/group/shipped file with semantics similar to the
-+#     Locate user/group/other files with semantics similar to the
- #     ~OpenFOAM/fileName expansion.
- #
- #     The -mode option can be used to allow chaining from
-@@ -34,40 +34,53 @@
- #
- #     For example, within the user ~/.OpenFOAM/<VER>/prefs.sh:
- #     \code
--#        foamPrefs=`$WM_PROJECT_DIR/bin/foamEtcFile -m go prefs.sh` \
--#            && _foamSource $foamPrefs
-+#        eval $(foamEtcFile -sh -mode=go prefs.sh)
- #     \endcode
- #
-+# Environment
-+#     - WM_PROJECT:         (unset defaults to OpenFOAM)
-+#     - WM_PROJECT_SITE:    (unset defaults to PREFIX/site)
-+#     - WM_PROJECT_VERSION: (unset defaults to detect from path)
-+#
- # Note
--#     This script must exist in $FOAM_INST_DIR/OpenFOAM-<VERSION>/bin/
--#     or $FOAM_INST_DIR/openfoam<VERSION>/bin/ (for the debian version)
-+#     This script must exist in one of these locations:
-+#     - $WM_PROJECT_INST_DIR/OpenFOAM-<VERSION>/bin
-+#     - $WM_PROJECT_INST_DIR/openfoam-<VERSION>/bin
-+#     - $WM_PROJECT_INST_DIR/OpenFOAM+<VERSION>/bin
-+#     - $WM_PROJECT_INST_DIR/openfoam+<VERSION>/bin
-+#     - $WM_PROJECT_INST_DIR/openfoam<VERSION>/bin  (debian version)
- #
- #-------------------------------------------------------------------------------
-+unset optQuiet optSilent
- usage() {
-     [ "${optQuiet:-$optSilent}" = true ] && exit 1
--
-     exec 1>&2
-     while [ "$#" -ge 1 ]; do echo "$1"; shift; done
-     cat<<USAGE
- 
--Usage: ${0##*/} [OPTION] fileName
--       ${0##*/} [OPTION] -list
-+Usage: foamEtcFile [OPTION] fileName
-+       foamEtcFile [OPTION] [-list|-list-test] [fileName]
- options:
--  -all              return all files (otherwise stop after the first match)
--  -list             list the directories to be searched
--  -mode <mode>      any combination of u(user), g(group), o(other)
--  -prefix <dir>     specify an alternative installation prefix
--  -quiet            suppress all normal output
--  -silent           suppress all stderr output
--  -version <ver>    specify an alternative OpenFOAM version
--                    in the form Maj.Min.Rev (eg, 1.7.0)
--  -help             print the usage
-+  -a, -all          Return all files (otherwise stop after the first match)
-+  -l, -list         List directories or files to be checked
-+  -list-test        List (existing) directories or files to be checked
-+  -mode=MODE        Any combination of u(user), g(group), o(other)
-+  -prefix=DIR       Specify an alternative installation prefix
-+  -version=VER      Specify alternative OpenFOAM version (eg, 3.0, 1612, ...)
-+  -csh | -sh        Produce output suitable for a csh or sh 'eval'
-+  -csh-verbose | -sh-verbose
-+                    As per -csh | -sh, with additional verbosity
-+  -q, -quiet        Suppress all normal output
-+  -s, -silent       Suppress stderr, except -csh-verbose, -sh-verbose output
-+  -help             Print the usage
- 
--  Locate user/group/shipped file with semantics similar to the
-+  Locate user/group/other file with semantics similar to the
-   ~OpenFOAM/fileName expansion.
- 
--  The options can also be specified as a single character
--  (eg, '-q' instead of '-quiet'), but must not be grouped.
-+  Single character options must not be grouped. Equivalent options:
-+      -mode=MODE,   -mode MODE,   -m MODE
-+      -prefix=DIR,  -prefix DIR,  -p DIR
-+      -version=VER, -version VER, -v VER
- 
-   Exit status
-       0  when the file is found. Print resolved path to stdout.
-@@ -78,61 +91,117 @@
-     exit 1
- }
- 
--#-------------------------------------------------------------------------------
-+# Report error and exit
-+die()
-+{
-+    [ "${optQuiet:-$optSilent}" = true ] && exit 1
-+    exec 1>&2
-+    echo
-+    echo "Error encountered:"
-+    while [ "$#" -ge 1 ]; do echo "    $1"; shift; done
-+    echo
-+    echo "See 'foamEtcFile -help' for usage"
-+    echo
-+    exit 1
-+}
- 
--# the bin dir:
--binDir="${0%/*}"
-+#-------------------------------------------------------------------------------
-+binDir="${0%/*}"                # The bin dir
-+projectDir="${binDir%/bin}"     # The project dir
-+prefixDir="${projectDir%/*}"    # The prefix dir (same as $WM_PROJECT_INST_DIR)
- 
--# the project dir:
-+# Could not resolve projectDir, prefixDir? (eg, called as ./bin/foamEtcFile)
-+if [ "$prefixDir" = "$projectDir" ]
-+then
-+    binDir="$(cd $binDir && pwd -L)"
- projectDir="${binDir%/bin}"
--
--# the prefix dir (same as $FOAM_INST_DIR):
- prefixDir="${projectDir%/*}"
-+fi
-+projectDirName="${projectDir##*/}"      # The project directory name
- 
--# the name used for the project directory
--projectDirName="${projectDir##*/}"
-+projectName="${WM_PROJECT:-OpenFOAM}"   # The project name
-+projectVersion="$WM_PROJECT_VERSION"    # Empty? - will be treated later
- 
--# version number used for debian packaging
--unset versionNum
- 
-+#-------------------------------------------------------------------------------
-+
-+# Guess project version or simply get the stem part of the projectDirName.
-+# Handle standard and debian naming conventions.
- #
--# handle standard and debian naming convention
-+# - projectVersion: update unless already set
- #
--case "$projectDirName" in
--OpenFOAM-*)         # standard naming convention OpenFOAM-<VERSION>
--    version="${projectDirName##OpenFOAM-}"
--    ;;
-+# Helper variables:
-+# - dirBase (for reassembling name) == projectDirName without the version
-+# - versionNum (debian packaging)
-+unset dirBase versionNum
-+guessVersion()
-+{
-+    local version
- 
--openfoam[0-9]* | openfoam-dev)     # debian naming convention 'openfoam<VERSION>'
--    versionNum="${projectDirName##openfoam}"
--    case "$versionNum" in
--    ??)         # convert 2 digit version number to decimal delineated
--        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)@\1.\2@')
--        ;;
--    ???)        # convert 3 digit version number to decimal delineated
--        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)\(.\)@\1.\2.\3@')
--        ;;
--    ????)       # convert 4 digit version number to decimal delineated
--        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)\(.\)\(.\)@\1.\2.\3.\4@')
--        ;;
--    *)          # failback - use current environment setting
--        version="$WM_PROJECT_VERSION"
-+    case "$projectDirName" in
-+    (OpenFOAM-* | openfoam-*)
-+        # Standard naming: OpenFOAM-<VERSION> or openfoam-<VERSION>
-+        dirBase="${projectDirName%%-*}-"
-+        version="${projectDirName#*-}"
-+        version="${version%%*-}" # Extra safety, eg openfoam-version-packager
-+        ;;
-+
-+    (OpenFOAM+* | openfoam+*)
-+        # Alternative naming: OpenFOAM+<VERSION> or openfoam+<VERSION>
-+        dirBase="${projectDirName%%+*}+"
-+        version="${projectDirName#*+}"
-+        version="${version%%*-}" # Extra safety, eg openfoam-version-packager
-+        ;;
-+
-+    (openfoam[0-9]*)
-+        # Debian naming: openfoam<VERSION>
-+        dirBase="openfoam"
-+        version="${projectDirName#openfoam}"
-+        versionNum="$version"
-+
-+        # Convert digits version number to decimal delineated
-+        case "${#versionNum}" in (2|3|4)
-+            version=$(echo "$versionNum" | sed -e 's@\([0-9]\)@\1.@g')
-+            version="${version%.}"
-         ;;
-     esac
-+
-+        # Ignore special treatment if no decimals were inserted.
-+        [ "${#version}" -gt "${#versionNum}" ] || unset versionNum
-     ;;
- 
--*)
--    echo "Error : unknown/unsupported naming convention"
--    exit 1
-+    (*)
-+        die "unknown/unsupported naming convention for '$projectDirName'"
-     ;;
- esac
- 
-+    # Set projectVersion if required
-+    : ${projectVersion:=$version}
-+}
-+
-+
-+# Set projectVersion and update versionNum, projectDirName accordingly
-+setVersion()
-+{
-+    projectVersion="$1"
-+
-+    # Need dirBase when reassembling projectDirName
-+    [ -n "$dirBase" ] || guessVersion
-+
-+    # Debian: update x.y.z -> xyz version
-+    if [ -n "$versionNum" ]
-+    then
-+        versionNum=$(echo "$projectVersion" | sed -e 's@\.@@g')
-+    fi
-+
-+    projectDirName="$dirBase${versionNum:-$projectVersion}"
-+}
-+
- 
--# default mode is 'ugo'
--mode=ugo
--unset optAll optList optQuiet optSilent
-+optMode=ugo         # Default mode is always 'ugo'
-+unset optAll optList optShell optVersion
- 
--# parse options
-+# Parse options
- while [ "$#" -gt 0 ]
- do
-     case "$1" in
-@@ -141,27 +210,45 @@
-         ;;
-     -a | -all)
-         optAll=true
-+        unset optShell
-         ;;
-     -l | -list)
-         optList=true
-+        unset optShell
-+        ;;
-+    -list-test)
-+        optList='test'
-+        unset optShell
-+        ;;
-+    -csh | -sh | -csh-verbose | -sh-verbose)
-+        optShell="${1#-}"
-+        unset optAll
-+        ;;
-+    -mode=[ugo]*)
-+        optMode="${1#*=}"
-+        ;;
-+    -prefix=/*)
-+        prefixDir="${1#*=}"
-+        prefixDir="${prefixDir%/}"
-+        ;;
-+    -version=*)
-+        optVersion="${1#*=}"
-         ;;
-     -m | -mode)
--        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
--        mode="$2"
--
--        # sanity check:
--        case "$mode" in
--        *u* | *g* | *o* )
-+        optMode="$2"
-+        shift
-+        # Sanity check. Handles missing argument too.
-+        case "$optMode" in
-+        ([ugo]*)
-            ;;
--        *)
--           usage "'$1' option with invalid mode '$mode'"
-+        (*)
-+            die "invalid mode '$optMode'"
-            ;;
-         esac
--        shift
-         ;;
-     -p | -prefix)
--        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
--        prefixDir="$2"
-+        [ "$#" -ge 2 ] || die "'$1' option requires an argument"
-+        prefixDir="${2%/}"
-         shift
-         ;;
-     -q | -quiet)
-@@ -171,13 +258,8 @@
-         optSilent=true
-         ;;
-     -v | -version)
--        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
--        version="$2"
--        # convert x.y.z -> xyz version (if installation looked like debian)
--        if [ -n "$versionNum" ]
--        then
--            versionNum=$(echo "$version" | sed -e 's@\.@@g')
--        fi
-+        [ "$#" -ge 2 ] || die "'$1' option requires an argument"
-+        optVersion="$2"
-         shift
-         ;;
-     --)
-@@ -185,7 +267,7 @@
-         break
-         ;;
-     -*)
--        usage "unknown option: '$*'"
-+        die "unknown option: '$1'"
-         ;;
-     *)
-         break
-@@ -195,11 +277,28 @@
- done
- 
- 
--# debugging:
--# echo "Installed locations:"
--# for i in projectDir prefixDir projectDirName version versionNum
-+#-------------------------------------------------------------------------------
-+
-+if [ -n "$optVersion" ]
-+then
-+    setVersion $optVersion
-+elif [ -z "$projectVersion" ]
-+then
-+    guessVersion
-+fi
-+
-+# Updates:
-+# - projectDir  for changes via -prefix or -version
-+# - projectSite for changes via -prefix
-+projectDir="$prefixDir/$projectDirName"
-+projectSite="${WM_PROJECT_SITE:-$prefixDir/site}"
-+
-+
-+# Debugging:
-+# echo "Installed locations:" 1>&2
-+# for i in projectDir prefixDir projectDirName projectVersion
- # do
--#     eval echo "$i=\$$i"
-+#     eval echo "$i=\$$i" 1>&2
- # done
- 
- 
-@@ -210,30 +309,18 @@
- 
- # Define the various places to be searched:
- unset dirList
--case "$mode" in
--*u*)  # user
--    userDir="$HOME/.${WM_PROJECT:-OpenFOAM}"
--    dirList="$dirList $userDir/$version $userDir"
-+case "$optMode" in (*u*) # (U)ser
-+    dirList="$dirList $HOME/.$projectName/$projectVersion $HOME/.$projectName"
-     ;;
- esac
- 
--case "$mode" in
--*g*)  # group (site)
--    siteDir="${WM_PROJECT_SITE:-$prefixDir/site}"
--    dirList="$dirList $siteDir/$version $siteDir"
-+case "$optMode" in (*g*) # (G)roup == site
-+    dirList="$dirList $projectSite/$projectVersion $projectSite"
-     ;;
- esac
- 
--case "$mode" in
--*o*)  # other (shipped)
--    if [ -n "$versionNum" ]
--    then
--        # debian packaging
--        dirList="$dirList $prefixDir/openfoam$versionNum/etc"
--    else
--        # standard packaging
--        dirList="$dirList $prefixDir/${WM_PROJECT:-OpenFOAM}-$version/etc"
--    fi
-+case "$optMode" in (*o*) # (O)ther == shipped
-+    dirList="$dirList $projectDir/etc"
-     ;;
- esac
- set -- $dirList
-@@ -244,50 +331,87 @@
- #
- 
- exitCode=0
--if [ "$optList" = true ]
-+if [ -n "$optList" ]
- then
- 
--    # list directories, or potential file locations
--    [ "$nArgs" -le 1 ] || usage
-+    # List directories, or potential file locations
-+    [ "$nArgs" -le 1 ] || \
-+    die "-list expects 0 or 1 filename, but $nArgs provided"
-+
-+    # A silly combination, but -quiet does have precedence
-+    [ -n "$optQuiet" ] && exit 0
- 
--    # a silly combination, but -quiet does have precedence
--    [ "$optQuiet" = true ] && exit 0
-+    # Test for directory or file too?
-+    if [ "$optList" = "test" ]
-+    then
-+        exitCode=2  # Fallback to a general error (file not found)
- 
-+        if [ "$nArgs" -eq 1 ]
-+        then
-     for dir
-     do
--        if [ "$nArgs" -eq 1 ]
-+                resolved="$dir/$fileName"
-+                if [ -f "$resolved" ]
-         then
--            echo "$dir/$fileName"
-+                    echo "$resolved"
-+                    exitCode=0  # OK
-+                fi
-+            done
-         else
-+            for dir
-+            do
-+                if [ -d "$dir" ]
-+                then
-             echo "$dir"
-+                    exitCode=0  # OK
-         fi
-     done
-+        fi
-+    else
-+        for dir
-+        do
-+            echo "$dir${fileName:+/}$fileName"
-+        done
-+    fi
- 
- else
- 
--    [ "$nArgs" -eq 1 ] || usage
-+    [ "$nArgs" -eq 1 ] || die "One filename expected - $nArgs provided"
- 
--    # general error, eg file not found
--    exitCode=2
-+    exitCode=2  # Fallback to a general error (file not found)
- 
-     for dir
-     do
-         if [ -f "$dir/$fileName" ]
-         then
-             exitCode=0
--            if [ "$optQuiet" = true ]
--            then
-+            [ -n "$optQuiet" ] && break
-+
-+            case "$optShell" in
-+            (*verbose)
-+                echo "Using: $dir/$fileName" 1>&2
-+                ;;
-+            esac
-+
-+            case "$optShell" in
-+            csh*)
-+                echo "source $dir/$fileName"
-                 break
--            else
-+                ;;
-+            sh*)
-+                echo ". $dir/$fileName"
-+                break
-+                ;;
-+            *)
-                 echo "$dir/$fileName"
--                [ "$optAll" = true ] || break
--            fi
-+                [ -n "$optAll" ] || break
-+                ;;
-+            esac
-         fi
-     done
- 
- fi
- 
--
- exit $exitCode
- 
- #------------------------------------------------------------------------------
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-build.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-build.patch
deleted file mode 100644
index 26e2d8f085..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-build.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- OpenFOAM-v1612+.orig/Allwmake	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/Allwmake	2017-03-29 09:08:15.503865203 +0200
-@@ -17,6 +17,14 @@
-     exit 1
- }
- 
-+#------------------------------------------------------------------------------
-+echo "========================================"
-+date "+%Y-%m-%d %H:%M:%S %z" 2>/dev/null || echo "date is unknown"
-+echo "Starting ${WM_PROJECT_DIR##*/} ${0##*}"
-+echo "  $WM_COMPILER $WM_COMPILER_TYPE compiler"
-+echo "  ${WM_OPTIONS}, with ${WM_MPLIB} ${FOAM_MPI}"
-+echo
-+
- # Compile wmake support applications
- (cd wmake/src && make)
- 
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-etc.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-etc.patch
deleted file mode 100644
index dd8146e953..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-etc.patch
+++ /dev/null
@@ -1,41 +0,0 @@
---- OpenFOAM-v1612+.orig/etc/bashrc	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/bashrc	2017-03-22 16:05:05.751237072 +0100
-@@ -42,7 +42,8 @@
- #
- # Please set to the appropriate path if the default is not correct.
- #
--[ $BASH_SOURCE ] && FOAM_INST_DIR=$(\cd ${BASH_SOURCE%/*/*/*} && \pwd -P) || \
-+rc="${BASH_SOURCE:-${ZSH_NAME:+$0}}"
-+[ -n "$rc" ] && FOAM_INST_DIR=$(\cd $(dirname $rc)/../.. && \pwd -L) || \
- FOAM_INST_DIR=$HOME/$WM_PROJECT
- # FOAM_INST_DIR=~$WM_PROJECT
- # FOAM_INST_DIR=/opt/$WM_PROJECT
-@@ -135,8 +136,10 @@
- # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- . $WM_PROJECT_DIR/etc/config.sh/functions
- 
--# Add in preset user or site preferences:
--_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.sh`
-+# Override definitions via prefs, with 'other' first so the sys-admin
-+# can provide base values independent of WM_PROJECT_SITE
-+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode o  prefs.sh`
-+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode ug prefs.sh`
- 
- # Evaluate command-line parameters and record settings for later
- # these can be used to set/unset values, or specify alternative pref files
-diff -uw OpenFOAM-v1612+.orig/etc/cshrc OpenFOAM-v1612+/etc/cshrc
---- OpenFOAM-v1612+.orig/etc/cshrc	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/cshrc	2017-03-22 16:04:51.839291067 +0100
-@@ -148,8 +148,10 @@
- # Source files, possibly with some verbosity
- alias _foamSource 'if ($?FOAM_VERBOSE && $?prompt) echo "Sourcing: \!*"; if (\!* != "") source \!*'
- 
--# Add in preset user or site preferences:
--_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.csh`
-+# Override definitions via prefs, with 'other' first so the sys-admin
-+# can provide base values independent of WM_PROJECT_SITE
-+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode o  prefs.csh`
-+_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode ug prefs.csh`
- 
- # Evaluate command-line parameters and record settings for later
- # these can be used to set/unset values, or specify alternative pref files
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-mgridgen-lib.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-mgridgen-lib.patch
deleted file mode 100644
index 8dc0b995ff..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-mgridgen-lib.patch
+++ /dev/null
@@ -1,41 +0,0 @@
---- OpenFOAM-v1612+.orig/src/fvAgglomerationMethods/Allwmake	2017-01-02 09:56:17.578558265 +0100
-+++ OpenFOAM-v1612+/src/fvAgglomerationMethods/Allwmake	2017-04-18 18:58:38.236795902 +0200
-@@ -4,9 +4,13 @@
- # Parse arguments for library compilation
- . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
- 
--export ParMGridGen=$WM_THIRD_PARTY_DIR/ParMGridGen-1.0
-+unset MGRIDGEN_ARCH_PATH
-+if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/mgridgen)
-+then
-+    . $settings
-+fi
- 
--if [ -e "$FOAM_LIBBIN/libMGridGen.so" ]
-+if [ -e "$MGRIDGEN_ARCH_PATH/include/mgridgen.h" ]
- then
-     wmake $targetType MGridGenGamgAgglomeration
- fi
---- OpenFOAM-v1612+.orig/src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options	2017-01-02 09:56:17.578558265 +0100
-+++ OpenFOAM-v1612+/src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options	2017-04-18 18:59:16.860662811 +0200
-@@ -1,15 +1,9 @@
--/* Needs ParMGridGen environment variable set. (see Allwmake script) */
--
--TYPE_REAL=
--#if defined(WM_SP)
--TYPE_REAL=-DTYPE_REAL
--#endif
--
- EXE_INC = \
-     -I$(LIB_SRC)/finiteVolume/lnInclude \
--    -I$(ParMGridGen)/MGridGen/Lib/lnInclude \
--    -I$(ParMGridGen)/MGridGen/IMlib/lnInclude \
--    $(TYPE_REAL)
-+    -I$(MGRIDGEN_ARCH_PATH)/include
- 
- LIB_LIBS = \
--    -L$(FOAM_EXT_LIBBIN) -lMGridGen
-+    -L$(FOAM_EXT_LIBBIN) \
-+    -L$(MGRIDGEN_ARCH_PATH)/lib \
-+    -L$(MGRIDGEN_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-+    -lmgrid
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-mpi.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-mpi.patch
deleted file mode 100644
index b3663b0a49..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-mpi.patch
+++ /dev/null
@@ -1,36 +0,0 @@
---- OpenFOAM-v1612+.orig/etc/config.sh/mpi	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/config.sh/mpi	2017-03-29 13:55:57.507980699 +0200
-@@ -75,8 +75,15 @@
-     _foamAddMan     $MPI_ARCH_PATH/share/man
-     ;;
- 
-+USERMPI)
-+    # Use an arbitrary, user-specified mpi implementation
-+    export FOAM_MPI=mpi-user
-+    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi-user`
-+    ;;
-+
- SYSTEMMPI)
-     export FOAM_MPI=mpi-system
-+    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi-system`
- 
-     if [ -z "$MPI_ROOT" ]
-     then
---- OpenFOAM-v1612+.orig/etc/config.csh/mpi	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/config.csh/mpi	2017-03-29 13:56:36.347835938 +0200
-@@ -71,8 +71,15 @@
-     _foamAddMan     $MPI_ARCH_PATH/share/man
-     breaksw
- 
-+case USERMPI:
-+    # Use an arbitrary, user-specified mpi implementation
-+    setenv FOAM_MPI mpi-user
-+    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/mpi-user`
-+    breaksw
-+
- case SYSTEMMPI:
-     setenv FOAM_MPI mpi-system
-+    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/mpi-system`
- 
-     if ( ! ($?MPI_ROOT) ) then
-         echo
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-scotch-metis-lib.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-scotch-metis-lib.patch
deleted file mode 100644
index b7530e6320..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-scotch-metis-lib.patch
+++ /dev/null
@@ -1,48 +0,0 @@
---- OpenFOAM-v1612+.orig/src/parallel/decompose/Allwmake	2017-03-21 16:34:44.599021283 +0100
-+++ OpenFOAM-v1612+/src/parallel/decompose/Allwmake	2017-03-21 16:28:57.243969660 +0100
-@@ -36,6 +36,7 @@
- 
-     # Library
-     [ -r $FOAM_EXT_LIBBIN/libmetis.so ] || \
-+    [ -r $METIS_ARCH_PATH/lib/libmetis.so ] || \
-     [ -r $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libmetis.so ] || \
-     [ "${METIS_ARCH_PATH##*-}" = system ] || {
-         echo "$warning (missing library)"
-@@ -90,6 +91,7 @@
- 
-     # Library
-     [ -r $FOAM_EXT_LIBBIN/libscotch.so ] || \
-+    [ -r $SCOTCH_ARCH_PATH/lib/libscotch.so ] || \
-     [ -r $SCOTCH_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libscotch.so ] || \
-     [ "${SCOTCH_ARCH_PATH##*-}" = system ] || {
-         echo "$warning (missing library)"
---- OpenFOAM-v1612+.orig/src/parallel/decompose/metisDecomp/Make/options	2017-03-21 16:34:25.383075328 +0100
-+++ OpenFOAM-v1612+/src/parallel/decompose/metisDecomp/Make/options	2017-03-21 16:30:15.727758338 +0100
-@@ -8,6 +8,7 @@
-  * to support central, non-thirdparty installations
-  */
- LIB_LIBS = \
-+    -L$(METIS_ARCH_PATH)/lib \
-     -L$(METIS_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-     -L$(FOAM_EXT_LIBBIN) \
-     -lmetis
---- OpenFOAM-v1612+.orig/src/parallel/decompose/ptscotchDecomp/Make/options	2017-03-21 16:34:34.607049385 +0100
-+++ OpenFOAM-v1612+/src/parallel/decompose/ptscotchDecomp/Make/options	2017-03-21 16:30:00.479799399 +0100
-@@ -16,6 +16,7 @@
-  * to support central, non-thirdparty installations
-  */
- LIB_LIBS = \
-+    -L$(SCOTCH_ARCH_PATH)/lib \
-     -L$(SCOTCH_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-     -L$(FOAM_EXT_LIBBIN) \
-     -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \
---- OpenFOAM-v1612+.orig/src/parallel/decompose/scotchDecomp/Make/options	2017-03-21 16:34:39.159036582 +0100
-+++ OpenFOAM-v1612+/src/parallel/decompose/scotchDecomp/Make/options	2017-03-21 16:29:46.719836452 +0100
-@@ -16,6 +16,7 @@
-  * to support central, non-thirdparty installations
-  */
- LIB_LIBS = \
-+    -L$(SCOTCH_ARCH_PATH)/lib \
-     -L$(SCOTCH_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-     -L$(FOAM_EXT_LIBBIN) \
-     -lscotch \
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-site.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-site.patch
deleted file mode 100644
index d988c2f9b8..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-site.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-diff -uw OpenFOAM-v1612+.orig/etc/config.sh/settings OpenFOAM-v1612+/etc/config.sh/settings
---- OpenFOAM-v1612+.orig/etc/config.sh/settings	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/config.sh/settings	2017-03-23 12:22:52.002101020 +0100
-@@ -141,7 +141,7 @@
- #------------------------------------------------------------------------------
- 
- # Location of the jobControl directory
--export FOAM_JOB_DIR=$WM_PROJECT_INST_DIR/jobControl
-+export FOAM_JOB_DIR=$HOME/.OpenFOAM/jobControl  #SPACK: non-central location
- 
- # wmake configuration
- export WM_DIR=$WM_PROJECT_DIR/wmake
-@@ -157,7 +157,7 @@
- export FOAM_EXT_LIBBIN=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/lib
- 
- # Site-specific directory
--siteDir="${WM_PROJECT_SITE:-$WM_PROJECT_INST_DIR/site}"
-+siteDir="${WM_PROJECT_SITE:-$WM_PROJECT_DIR/site}"  #SPACK: not in parent directory
- 
- # Shared site executables/libraries
- # Similar naming convention as ~OpenFOAM expansion
-diff -uw OpenFOAM-v1612+.orig/etc/config.csh/settings OpenFOAM-v1612+/etc/config.csh/settings
---- OpenFOAM-v1612+.orig/etc/config.csh/settings	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/etc/config.csh/settings	2017-03-23 12:23:52.737891912 +0100
-@@ -137,7 +137,7 @@
- #------------------------------------------------------------------------------
- 
- # Location of the jobControl directory
--setenv FOAM_JOB_DIR $WM_PROJECT_INST_DIR/jobControl
-+setenv FOAM_JOB_DIR=$HOME/.OpenFOAM/jobControl  #SPACK: non-central location
- 
- # wmake configuration
- setenv WM_DIR $WM_PROJECT_DIR/wmake
-@@ -156,7 +156,7 @@
- if ( $?WM_PROJECT_SITE ) then
-     set siteDir=$WM_PROJECT_SITE
- else
--    set siteDir=$WM_PROJECT_INST_DIR/site
-+    set siteDir=$WM_PROJECT_DIR/site  #SPACK: not in parent directory
- endif
- 
- # Shared site executables/libraries
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-spack-patches.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-spack-patches.patch
new file mode 100644
index 0000000000..00679c4c1d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openfoam-com/1612-spack-patches.patch
@@ -0,0 +1,876 @@
+#############################################################################
+# This patch for OpenFOAM-1612 comprises the following changes:
+#
+# bin/foamEtcFile
+# - Adjust to cope with spack naming (eg, openfoam-com-1612-abcxzy).
+#   Lets us avoid a needless directory layer.
+#
+# etc/bashrc
+# - improved robustness when sourcing.
+# - source top-level prefs.sh first (for sysadmin changes)
+#
+# etc/config.*/settings
+# - write job control information to the user directory
+# - site/ directory under the OpenFOAM project dir, not its parent dir
+#
+# etc/config.*/mpi
+# - added USERMPI as place for spack mpi information
+#
+# mgridgen, zoltan:
+# - make location configurable
+#
+# metis, scotch:
+# - also check lib path (not just lib64)
+#
+# All issues patched here are addressed in OpenFOAM-1706 and later.
+#
+# <Mark.Olesen@esi-group.com>   ESI-OpenCFD   www.openfoam.com
+#
+#############################################################################
+--- OpenFOAM-v1612+.orig/bin/foamEtcFile	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-plus/bin/foamEtcFile	2017-12-18 17:48:35.043291205 +0100
+@@ -4,164 +4,235 @@
+ # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
+ #  \\    /   O peration     |
+ #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
+-#    \\/     M anipulation  |
++#    \\/     M anipulation  | Copyright (C) 2017 OpenCFD Ltd.
+ #-------------------------------------------------------------------------------
+ # License
+-#     This file is part of OpenFOAM.
+-#
+-#     OpenFOAM is free software: you can redistribute it and/or modify it
+-#     under the terms of the GNU General Public License as published by
+-#     the Free Software Foundation, either version 3 of the License, or
+-#     (at your option) any later version.
+-#
+-#     OpenFOAM 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 GNU General Public License
+-#     for more details.
+-#
+-#     You should have received a copy of the GNU General Public License
+-#     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
++#     This file is part of OpenFOAM, licensed under GNU General Public License
++#     <http://www.gnu.org/licenses/>.
+ #
+ # Script
+ #     foamEtcFile
+ #
+ # Description
+-#     Locate user/group/shipped file with semantics similar to the
+-#     ~OpenFOAM/fileName expansion.
++#     Locate user/group/other file as per '#includeEtc'.
++#
++#     The -mode option can be used to allow chaining from personal settings
++#     to site-wide settings.
+ #
+-#     The -mode option can be used to allow chaining from
+-#     personal settings to site-wide settings.
++#     For example, within the user ~/.OpenFOAM/<VER>/config.sh/compiler:
++#     \code
++#        eval $(foamEtcFile -sh -mode=go config.sh/compiler)
++#     \endcode
+ #
+-#     For example, within the user ~/.OpenFOAM/<VER>/prefs.sh:
++#     The -mode option is similarly used within etc/{bashrc,cshrc} to ensure
++#     that system prefs are respected:
+ #     \code
+-#        foamPrefs=`$WM_PROJECT_DIR/bin/foamEtcFile -m go prefs.sh` \
+-#            && _foamSource $foamPrefs
++#        eval $(foamEtcFile -sh -mode=o  prefs.sh)
++#        eval $(foamEtcFile -sh -mode=ug prefs.sh)
+ #     \endcode
+ #
++# Environment
++#     - WM_PROJECT:         (unset defaults to OpenFOAM)
++#     - WM_PROJECT_SITE:    (unset defaults to PREFIX/site)
++#     - WM_PROJECT_VERSION: (unset defaults to detect from path)
++#
+ # Note
+-#     This script must exist in $FOAM_INST_DIR/OpenFOAM-<VERSION>/bin/
+-#     or $FOAM_INST_DIR/openfoam<VERSION>/bin/ (for the debian version)
++#     This script must exist in one of these locations:
++#     - $WM_PROJECT_INST_DIR/OpenFOAM-<VERSION>/bin
++#     - $WM_PROJECT_INST_DIR/openfoam-<VERSION>/bin
++#     - $WM_PROJECT_INST_DIR/openfoam<VERSION>/bin  (debian version)
+ #
+ #-------------------------------------------------------------------------------
+-usage() {
+-    [ "${optQuiet:-$optSilent}" = true ] && exit 1
+-
+-    exec 1>&2
+-    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
++printHelp() {
+     cat<<USAGE
+ 
+-Usage: ${0##*/} [OPTION] fileName
+-       ${0##*/} [OPTION] -list
++Usage: foamEtcFile [OPTION] fileName
++       foamEtcFile [OPTION] [-list|-list-test] [fileName]
++
+ options:
+-  -all              return all files (otherwise stop after the first match)
+-  -list             list the directories to be searched
+-  -mode <mode>      any combination of u(user), g(group), o(other)
+-  -prefix <dir>     specify an alternative installation prefix
+-  -quiet            suppress all normal output
+-  -silent           suppress all stderr output
+-  -version <ver>    specify an alternative OpenFOAM version
+-                    in the form Maj.Min.Rev (eg, 1.7.0)
+-  -help             print the usage
+-
+-  Locate user/group/shipped file with semantics similar to the
+-  ~OpenFOAM/fileName expansion.
+-
+-  The options can also be specified as a single character
+-  (eg, '-q' instead of '-quiet'), but must not be grouped.
+-
+-  Exit status
+-      0  when the file is found. Print resolved path to stdout.
+-      1  for miscellaneous errors.
+-      2  when the file is not found.
++  -all (-a)         Return all files (otherwise stop after the first match)
++  -list (-l)        List directories or files to be checked
++  -list-test        List (existing) directories or files to be checked
++  -mode=MODE        Any combination of u(user), g(group), o(other)
++  -prefix=DIR       Specify an alternative installation prefix
++  -version=VER      Specify alternative OpenFOAM version (eg, 3.0, 1612, ...)
++  -csh              Produce output suitable for a csh or sh 'eval'
++  -csh-verbose      As per -csh with additional verbosity
++  -sh               Produce output suitable for a csh or sh 'eval'
++  -sh-verbose       As per -sh  with additional verbosity
++  -quiet (-q)       Suppress all normal output
++  -silent (-s)      Suppress stderr, except -csh-verbose, -sh-verbose output
++  -help             Print the usage
++
++Locate user/group/other file as per '#includeEtc'
++
++Do not group single character options.
++Equivalent options:
++  |  -mode=MODE     |  -mode MODE     | -m MODE
++  |  -prefix=DIR    |  -prefix DIR    | -p DIR
++  |  -version=VER   |  -version VER   | -v VER
++
++Exit status
++    0  when the file is found. Print resolved path to stdout.
++    1  for miscellaneous errors.
++    2  when the file is not found.
+ 
+ USAGE
+-    exit 1
++    exit 0  # A clean exit
+ }
+ 
+-#-------------------------------------------------------------------------------
+ 
+-# the bin dir:
+-binDir="${0%/*}"
++unset optQuiet optSilent
++# Report error and exit
++die()
++{
++    [ "${optQuiet:-$optSilent}" = true ] && exit 1
++    exec 1>&2
++    echo
++    echo "Error encountered:"
++    while [ "$#" -ge 1 ]; do echo "    $1"; shift; done
++    echo
++    echo "See 'foamEtcFile -help' for usage"
++    echo
++    exit 1
++}
+ 
+-# the project dir:
+-projectDir="${binDir%/bin}"
++#-------------------------------------------------------------------------------
++binDir="${0%/*}"                # The bin dir
++projectDir="${binDir%/bin}"     # The project dir
++prefixDir="${projectDir%/*}"    # The prefix dir (same as $WM_PROJECT_INST_DIR)
+ 
+-# the prefix dir (same as $FOAM_INST_DIR):
+-prefixDir="${projectDir%/*}"
++# Could not resolve projectDir, prefixDir? (eg, called as ./bin/foamEtcFile)
++if [ "$prefixDir" = "$projectDir" ]
++then
++    binDir="$(cd $binDir && pwd -L)"
++    projectDir="${binDir%/bin}"
++    prefixDir="${projectDir%/*}"
++fi
++projectDirName="${projectDir##*/}"      # The project directory name
+ 
+-# the name used for the project directory
+-projectDirName="${projectDir##*/}"
++projectVersion="$WM_PROJECT_VERSION"    # Empty? - will be treated later
++userDir="$HOME/.OpenFOAM"               # Hard-coded as per foamVersion.H
+ 
+-# version number used for debian packaging
+-unset versionNum
++#-------------------------------------------------------------------------------
+ 
++# Guess project version or simply get the stem part of the projectDirName.
++# Handle standard and debian naming conventions.
+ #
+-# handle standard and debian naming convention
++# - projectVersion: update unless already set
+ #
+-case "$projectDirName" in
+-OpenFOAM-*)         # standard naming convention OpenFOAM-<VERSION>
+-    version="${projectDirName##OpenFOAM-}"
+-    ;;
++# Helper variables:
++# - dirBase (for reassembling name) == projectDirName without the version
++# - versionNum (debian packaging)
++unset dirBase versionNum
++guessVersion()
++{
++    local version
++
++    case "$projectDirName" in
++    (OpenFOAM-* | openfoam-*)
++        # Standard naming: OpenFOAM-<VERSION> or openfoam-<VERSION>
++        dirBase="${projectDirName%%-*}-"
++        version="${projectDirName#*-}"
++        version="${version%%*-}" # Extra safety, eg openfoam-version-packager
++        ;;
++
++    (openfoam[0-9]*)
++        # Debian naming: openfoam<VERSION>
++        dirBase="openfoam"
++        version="${projectDirName#openfoam}"
++        versionNum="$version"
++
++        # Convert digits version number to decimal delineated
++        case "${#versionNum}" in (2|3|4)
++            version=$(echo "$versionNum" | sed -e 's@\([0-9]\)@\1.@g')
++            version="${version%.}"
++            ;;
++        esac
+ 
+-openfoam[0-9]* | openfoam-dev)     # debian naming convention 'openfoam<VERSION>'
+-    versionNum="${projectDirName##openfoam}"
+-    case "$versionNum" in
+-    ??)         # convert 2 digit version number to decimal delineated
+-        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)@\1.\2@')
+-        ;;
+-    ???)        # convert 3 digit version number to decimal delineated
+-        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)\(.\)@\1.\2.\3@')
++        # Ignore special treatment if no decimals were inserted.
++        [ "${#version}" -gt "${#versionNum}" ] || unset versionNum
+         ;;
+-    ????)       # convert 4 digit version number to decimal delineated
+-        version=$(echo "$versionNum" | sed -e 's@\(.\)\(.\)\(.\)\(.\)@\1.\2.\3.\4@')
+-        ;;
+-    *)          # failback - use current environment setting
+-        version="$WM_PROJECT_VERSION"
++
++    (*)
++        die "unknown/unsupported naming convention for '$projectDirName'"
+         ;;
+     esac
+-    ;;
+ 
+-*)
+-    echo "Error : unknown/unsupported naming convention"
+-    exit 1
+-    ;;
+-esac
++    # Set projectVersion if required
++    : ${projectVersion:=$version}
++}
+ 
+ 
+-# default mode is 'ugo'
+-mode=ugo
+-unset optAll optList optQuiet optSilent
++# Set projectVersion and update versionNum, projectDirName accordingly
++setVersion()
++{
++    projectVersion="$1"
+ 
+-# parse options
++    # Need dirBase when reassembling projectDirName
++    [ -n "$dirBase" ] || guessVersion
++
++    # Debian: update x.y.z -> xyz version
++    if [ -n "$versionNum" ]
++    then
++        versionNum=$(echo "$projectVersion" | sed -e 's@\.@@g')
++    fi
++
++    projectDirName="$dirBase${versionNum:-$projectVersion}"
++}
++
++
++optMode=ugo         # Default mode is always 'ugo'
++unset optAll optList optShell optVersion
++
++# Parse options
+ while [ "$#" -gt 0 ]
+ do
+     case "$1" in
+-    -h | -help)
+-        usage
++    -h | -help*)
++        printHelp
+         ;;
+     -a | -all)
+         optAll=true
++        unset optShell
+         ;;
+     -l | -list)
+         optList=true
++        unset optShell
++        ;;
++    -list-test)
++        optList='test'
++        unset optShell
++        ;;
++    -csh | -sh | -csh-verbose | -sh-verbose)
++        optShell="${1#-}"
++        unset optAll
++        ;;
++    -mode=[ugo]*)
++        optMode="${1#*=}"
++        ;;
++    -prefix=/*)
++        prefixDir="${1#*=}"
++        prefixDir="${prefixDir%/}"
++        ;;
++    -version=*)
++        optVersion="${1#*=}"
+         ;;
+     -m | -mode)
+-        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+-        mode="$2"
+-
+-        # sanity check:
+-        case "$mode" in
+-        *u* | *g* | *o* )
+-           ;;
+-        *)
+-           usage "'$1' option with invalid mode '$mode'"
+-           ;;
+-        esac
++        optMode="$2"
+         shift
++        # Sanity check. Handles missing argument too.
++        case "$optMode" in
++        ([ugo]*)
++            ;;
++        (*)
++            die "invalid mode '$optMode'"
++            ;;
++        esac
+         ;;
+     -p | -prefix)
+-        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+-        prefixDir="$2"
++        [ "$#" -ge 2 ] || die "'$1' option requires an argument"
++        prefixDir="${2%/}"
+         shift
+         ;;
+     -q | -quiet)
+@@ -171,13 +242,8 @@
+         optSilent=true
+         ;;
+     -v | -version)
+-        [ "$#" -ge 2 ] || usage "'$1' option requires an argument"
+-        version="$2"
+-        # convert x.y.z -> xyz version (if installation looked like debian)
+-        if [ -n "$versionNum" ]
+-        then
+-            versionNum=$(echo "$version" | sed -e 's@\.@@g')
+-        fi
++        [ "$#" -ge 2 ] || die "'$1' option requires an argument"
++        optVersion="$2"
+         shift
+         ;;
+     --)
+@@ -185,7 +251,7 @@
+         break
+         ;;
+     -*)
+-        usage "unknown option: '$*'"
++        die "unknown option: '$1'"
+         ;;
+     *)
+         break
+@@ -195,11 +261,28 @@
+ done
+ 
+ 
+-# debugging:
+-# echo "Installed locations:"
+-# for i in projectDir prefixDir projectDirName version versionNum
++#-------------------------------------------------------------------------------
++
++if [ -n "$optVersion" ]
++then
++    setVersion $optVersion
++elif [ -z "$projectVersion" ]
++then
++    guessVersion
++fi
++
++# Updates:
++# - projectDir  for changes via -prefix or -version
++# - groupDir    for changes via -prefix
++projectDir="$prefixDir/$projectDirName"
++groupDir="${WM_PROJECT_SITE:-$prefixDir/site}"
++
++
++# Debugging:
++# echo "Installed locations:" 1>&2
++# for i in projectDir prefixDir projectDirName projectVersion
+ # do
+-#     eval echo "$i=\$$i"
++#     eval echo "$i=\$$i" 1>&2
+ # done
+ 
+ 
+@@ -210,30 +293,18 @@
+ 
+ # Define the various places to be searched:
+ unset dirList
+-case "$mode" in
+-*u*)  # user
+-    userDir="$HOME/.${WM_PROJECT:-OpenFOAM}"
+-    dirList="$dirList $userDir/$version $userDir"
++case "$optMode" in (*u*) # (U)ser
++    dirList="$dirList $userDir/$projectVersion $userDir"
+     ;;
+ esac
+ 
+-case "$mode" in
+-*g*)  # group (site)
+-    siteDir="${WM_PROJECT_SITE:-$prefixDir/site}"
+-    dirList="$dirList $siteDir/$version $siteDir"
++case "$optMode" in (*g*) # (G)roup == site
++    dirList="$dirList $groupDir/$projectVersion $groupDir"
+     ;;
+ esac
+ 
+-case "$mode" in
+-*o*)  # other (shipped)
+-    if [ -n "$versionNum" ]
+-    then
+-        # debian packaging
+-        dirList="$dirList $prefixDir/openfoam$versionNum/etc"
+-    else
+-        # standard packaging
+-        dirList="$dirList $prefixDir/${WM_PROJECT:-OpenFOAM}-$version/etc"
+-    fi
++case "$optMode" in (*o*) # (O)ther == shipped
++    dirList="$dirList $projectDir/etc"
+     ;;
+ esac
+ set -- $dirList
+@@ -244,50 +315,87 @@
+ #
+ 
+ exitCode=0
+-if [ "$optList" = true ]
++if [ -n "$optList" ]
+ then
+ 
+-    # list directories, or potential file locations
+-    [ "$nArgs" -le 1 ] || usage
++    # List directories, or potential file locations
++    [ "$nArgs" -le 1 ] || \
++    die "-list expects 0 or 1 filename, but $nArgs provided"
+ 
+-    # a silly combination, but -quiet does have precedence
+-    [ "$optQuiet" = true ] && exit 0
++    # A silly combination, but -quiet does have precedence
++    [ -n "$optQuiet" ] && exit 0
++
++    # Test for directory or file too?
++    if [ "$optList" = "test" ]
++    then
++        exitCode=2  # Fallback to a general error (file not found)
+ 
+-    for dir
+-    do
+         if [ "$nArgs" -eq 1 ]
+         then
+-            echo "$dir/$fileName"
++            for dir
++            do
++                resolved="$dir/$fileName"
++                if [ -f "$resolved" ]
++                then
++                    echo "$resolved"
++                    exitCode=0  # OK
++                fi
++            done
+         else
+-            echo "$dir"
++            for dir
++            do
++                if [ -d "$dir" ]
++                then
++                    echo "$dir"
++                    exitCode=0  # OK
++                fi
++            done
+         fi
+-    done
++    else
++        for dir
++        do
++            echo "$dir${fileName:+/}$fileName"
++        done
++    fi
+ 
+ else
+ 
+-    [ "$nArgs" -eq 1 ] || usage
++    [ "$nArgs" -eq 1 ] || die "One filename expected - $nArgs provided"
+ 
+-    # general error, eg file not found
+-    exitCode=2
++    exitCode=2  # Fallback to a general error (file not found)
+ 
+     for dir
+     do
+         if [ -f "$dir/$fileName" ]
+         then
+             exitCode=0
+-            if [ "$optQuiet" = true ]
+-            then
++            [ -n "$optQuiet" ] && break
++
++            case "$optShell" in
++            (*verbose)
++                echo "Using: $dir/$fileName" 1>&2
++                ;;
++            esac
++
++            case "$optShell" in
++            csh*)
++                echo "source $dir/$fileName"
+                 break
+-            else
++                ;;
++            sh*)
++                echo ". $dir/$fileName"
++                break
++                ;;
++            *)
+                 echo "$dir/$fileName"
+-                [ "$optAll" = true ] || break
+-            fi
++                [ -n "$optAll" ] || break
++                ;;
++            esac
+         fi
+     done
+ 
+ fi
+ 
+-
+ exit $exitCode
+ 
+ #------------------------------------------------------------------------------
+--- OpenFOAM-v1612+.orig/etc/bashrc	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/bashrc	2017-03-22 16:05:05.751237072 +0100
+@@ -42,7 +42,8 @@
+ #
+ # Please set to the appropriate path if the default is not correct.
+ #
+-[ $BASH_SOURCE ] && FOAM_INST_DIR=$(\cd ${BASH_SOURCE%/*/*/*} && \pwd -P) || \
++rc="${BASH_SOURCE:-${ZSH_NAME:+$0}}"
++[ -n "$rc" ] && FOAM_INST_DIR=$(\cd $(dirname $rc)/../.. && \pwd -L) || \
+ FOAM_INST_DIR=$HOME/$WM_PROJECT
+ # FOAM_INST_DIR=~$WM_PROJECT
+ # FOAM_INST_DIR=/opt/$WM_PROJECT
+@@ -135,8 +136,10 @@
+ # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ . $WM_PROJECT_DIR/etc/config.sh/functions
+ 
+-# Add in preset user or site preferences:
+-_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.sh`
++# Override definitions via prefs, with 'other' first so the sys-admin
++# can provide base values independent of WM_PROJECT_SITE
++_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode o  prefs.sh`
++_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode ug prefs.sh`
+ 
+ # Evaluate command-line parameters and record settings for later
+ # these can be used to set/unset values, or specify alternative pref files
+diff -uw OpenFOAM-v1612+.orig/etc/cshrc OpenFOAM-v1612+/etc/cshrc
+--- OpenFOAM-v1612+.orig/etc/cshrc	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/cshrc	2017-03-22 16:04:51.839291067 +0100
+@@ -148,8 +148,10 @@
+ # Source files, possibly with some verbosity
+ alias _foamSource 'if ($?FOAM_VERBOSE && $?prompt) echo "Sourcing: \!*"; if (\!* != "") source \!*'
+ 
+-# Add in preset user or site preferences:
+-_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.csh`
++# Override definitions via prefs, with 'other' first so the sys-admin
++# can provide base values independent of WM_PROJECT_SITE
++_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode o  prefs.csh`
++_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -mode ug prefs.csh`
+ 
+ # Evaluate command-line parameters and record settings for later
+ # these can be used to set/unset values, or specify alternative pref files
+--- OpenFOAM-v1612+.orig/etc/config.sh/settings	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/config.sh/settings	2017-12-21 20:40:50.109036445 +0100
+@@ -141,7 +141,7 @@
+ #------------------------------------------------------------------------------
+ 
+ # Location of the jobControl directory
+-export FOAM_JOB_DIR=$WM_PROJECT_INST_DIR/jobControl
++export FOAM_JOB_DIR="$HOME/.OpenFOAM/jobControl"
+ 
+ # wmake configuration
+ export WM_DIR=$WM_PROJECT_DIR/wmake
+@@ -198,8 +198,12 @@
+ unset siteDir
+ 
+ _foamAddPath $FOAM_USER_APPBIN:$FOAM_SITE_APPBIN:$FOAM_APPBIN
+-# Make sure to pick up dummy versions of external libraries last
+-_foamAddLib  $FOAM_USER_LIBBIN:$FOAM_SITE_LIBBIN:$FOAM_LIBBIN:$FOAM_EXT_LIBBIN:$FOAM_LIBBIN/dummy
++_foamAddLib  $FOAM_LIBBIN/dummy     # Dummy versions of external libraries last
++if [ -n "$FOAM_EXT_LIBBIN" ]        # External libraries (allowed to be unset)
++then
++    _foamAddLib $FOAM_EXT_LIBBIN
++fi
++_foamAddLib  $FOAM_USER_LIBBIN:$FOAM_SITE_LIBBIN:$FOAM_LIBBIN
+ 
+ # Compiler settings
+ # ~~~~~~~~~~~~~~~~~
+--- OpenFOAM-v1612+.orig/etc/config.csh/settings	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/config.csh/settings	2017-12-21 20:37:24.301773802 +0100
+@@ -137,7 +137,7 @@
+ #------------------------------------------------------------------------------
+ 
+ # Location of the jobControl directory
+-setenv FOAM_JOB_DIR $WM_PROJECT_INST_DIR/jobControl
++setenv FOAM_JOB_DIR "$HOME/.OpenFOAM/jobControl"
+ 
+ # wmake configuration
+ setenv WM_DIR $WM_PROJECT_DIR/wmake
+@@ -196,8 +196,11 @@
+ unset siteDir
+ 
+ _foamAddPath ${FOAM_USER_APPBIN}:${FOAM_SITE_APPBIN}:${FOAM_APPBIN}
+-# Make sure to pick up dummy versions of external libraries last
+-_foamAddLib  ${FOAM_USER_LIBBIN}:${FOAM_SITE_LIBBIN}:${FOAM_LIBBIN}:${FOAM_EXT_LIBBIN}:${FOAM_LIBBIN}/dummy
++_foamAddLib  $FOAM_LIBBIN/dummy     # Dummy versions of external libraries last
++if ( $?FOAM_EXT_LIBBIN ) then       # External libraries (allowed to be unset)
++    _foamAddLib $FOAM_EXT_LIBBIN
++endif
++_foamAddLib  ${FOAM_USER_LIBBIN}:${FOAM_SITE_LIBBIN}:${FOAM_LIBBIN}
+ 
+ # Compiler settings
+ # ~~~~~~~~~~~~~~~~~
+--- OpenFOAM-v1612+.orig/etc/config.sh/mpi	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/config.sh/mpi	2017-03-29 13:55:57.507980699 +0200
+@@ -75,8 +75,15 @@
+     _foamAddMan     $MPI_ARCH_PATH/share/man
+     ;;
+ 
++USERMPI)
++    # Use an arbitrary, user-specified mpi implementation
++    export FOAM_MPI=mpi-user
++    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi-user`
++    ;;
++
+ SYSTEMMPI)
+     export FOAM_MPI=mpi-system
++    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.sh/mpi-system`
+ 
+     if [ -z "$MPI_ROOT" ]
+     then
+--- OpenFOAM-v1612+.orig/etc/config.csh/mpi	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/etc/config.csh/mpi	2017-03-29 13:56:36.347835938 +0200
+@@ -71,8 +71,15 @@
+     _foamAddMan     $MPI_ARCH_PATH/share/man
+     breaksw
+ 
++case USERMPI:
++    # Use an arbitrary, user-specified mpi implementation
++    setenv FOAM_MPI mpi-user
++    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/mpi-user`
++    breaksw
++
+ case SYSTEMMPI:
+     setenv FOAM_MPI mpi-system
++    _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/mpi-system`
+ 
+     if ( ! ($?MPI_ROOT) ) then
+         echo
+--- OpenFOAM-v1612+.orig/src/fvAgglomerationMethods/Allwmake	2017-01-02 09:56:17.578558265 +0100
++++ OpenFOAM-v1612+/src/fvAgglomerationMethods/Allwmake	2017-04-18 18:58:38.236795902 +0200
+@@ -4,9 +4,13 @@
+ # Parse arguments for library compilation
+ . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
+ 
+-export ParMGridGen=$WM_THIRD_PARTY_DIR/ParMGridGen-1.0
++unset MGRIDGEN_ARCH_PATH
++if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/mgridgen)
++then
++    . $settings
++fi
+ 
+-if [ -e "$FOAM_LIBBIN/libMGridGen.so" ]
++if [ -e "$MGRIDGEN_ARCH_PATH/include/mgridgen.h" ]
+ then
+     wmake $targetType MGridGenGamgAgglomeration
+ fi
+--- OpenFOAM-v1612+.orig/src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options	2017-01-02 09:56:17.578558265 +0100
++++ OpenFOAM-v1612+/src/fvAgglomerationMethods/MGridGenGamgAgglomeration/Make/options	2017-04-18 18:59:16.860662811 +0200
+@@ -1,15 +1,9 @@
+-/* Needs ParMGridGen environment variable set. (see Allwmake script) */
+-
+-TYPE_REAL=
+-#if defined(WM_SP)
+-TYPE_REAL=-DTYPE_REAL
+-#endif
+-
+ EXE_INC = \
+     -I$(LIB_SRC)/finiteVolume/lnInclude \
+-    -I$(ParMGridGen)/MGridGen/Lib/lnInclude \
+-    -I$(ParMGridGen)/MGridGen/IMlib/lnInclude \
+-    $(TYPE_REAL)
++    -I$(MGRIDGEN_ARCH_PATH)/include
+ 
+ LIB_LIBS = \
+-    -L$(FOAM_EXT_LIBBIN) -lMGridGen
++    -L$(FOAM_EXT_LIBBIN) \
++    -L$(MGRIDGEN_ARCH_PATH)/lib \
++    -L$(MGRIDGEN_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
++    -lmgrid
+--- OpenFOAM-v1612+.orig/src/parallel/decompose/Allwmake	2017-03-21 16:34:44.599021283 +0100
++++ OpenFOAM-v1612+/src/parallel/decompose/Allwmake	2017-03-21 16:28:57.243969660 +0100
+@@ -36,6 +36,7 @@
+ 
+     # Library
+     [ -r $FOAM_EXT_LIBBIN/libmetis.so ] || \
++    [ -r $METIS_ARCH_PATH/lib/libmetis.so ] || \
+     [ -r $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libmetis.so ] || \
+     [ "${METIS_ARCH_PATH##*-}" = system ] || {
+         echo "$warning (missing library)"
+@@ -90,6 +91,7 @@
+ 
+     # Library
+     [ -r $FOAM_EXT_LIBBIN/libscotch.so ] || \
++    [ -r $SCOTCH_ARCH_PATH/lib/libscotch.so ] || \
+     [ -r $SCOTCH_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/libscotch.so ] || \
+     [ "${SCOTCH_ARCH_PATH##*-}" = system ] || {
+         echo "$warning (missing library)"
+--- OpenFOAM-v1612+.orig/src/parallel/decompose/metisDecomp/Make/options	2017-03-21 16:34:25.383075328 +0100
++++ OpenFOAM-v1612+/src/parallel/decompose/metisDecomp/Make/options	2017-03-21 16:30:15.727758338 +0100
+@@ -8,6 +8,7 @@
+  * to support central, non-thirdparty installations
+  */
+ LIB_LIBS = \
++    -L$(METIS_ARCH_PATH)/lib \
+     -L$(METIS_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
+     -L$(FOAM_EXT_LIBBIN) \
+     -lmetis
+--- OpenFOAM-v1612+.orig/src/parallel/decompose/ptscotchDecomp/Make/options	2017-03-21 16:34:34.607049385 +0100
++++ OpenFOAM-v1612+/src/parallel/decompose/ptscotchDecomp/Make/options	2017-03-21 16:30:00.479799399 +0100
+@@ -16,6 +16,7 @@
+  * to support central, non-thirdparty installations
+  */
+ LIB_LIBS = \
++    -L$(SCOTCH_ARCH_PATH)/lib \
+     -L$(SCOTCH_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
+     -L$(FOAM_EXT_LIBBIN) \
+     -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \
+--- OpenFOAM-v1612+.orig/src/parallel/decompose/scotchDecomp/Make/options	2017-03-21 16:34:39.159036582 +0100
++++ OpenFOAM-v1612+/src/parallel/decompose/scotchDecomp/Make/options	2017-03-21 16:29:46.719836452 +0100
+@@ -16,6 +16,7 @@
+  * to support central, non-thirdparty installations
+  */
+ LIB_LIBS = \
++    -L$(SCOTCH_ARCH_PATH)/lib \
+     -L$(SCOTCH_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
+     -L$(FOAM_EXT_LIBBIN) \
+     -lscotch \
+--- OpenFOAM-v1612+.orig/applications/utilities/mesh/manipulation/renumberMesh/Allwmake	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/applications/utilities/mesh/manipulation/renumberMesh/Allwmake	2017-03-28 11:13:35.222727218 +0200
+@@ -4,20 +4,35 @@
+ # Parse arguments for compilation (at least for error catching)
+ . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
+ 
+-export COMPILE_FLAGS=''
+-export LINK_FLAGS=''
++unset COMP_FLAGS LINK_FLAGS
+ 
+ if [ -f "${FOAM_LIBBIN}/libSloanRenumber.so" ]
+ then
+-    echo "Found libSloanRenumber.so  --  enabling Sloan renumbering support."
++    echo "    found libSloanRenumber  --  enabling sloan renumbering support."
+     export LINK_FLAGS="${LINK_FLAGS} -lSloanRenumber"
+ fi
+ 
+-if [ -f "${ZOLTAN_ARCH_PATH}/lib/libzoltan.a" -a -f "${FOAM_LIBBIN}/libzoltanRenumber.so" ]
++if [ -f "${FOAM_LIBBIN}/libzoltanRenumber.so" ]
+ then
+-    echo "Found libzoltanRenumber.so  --  enabling zoltan renumbering support."
+-    export COMPILE_FLAGS="-DFOAM_USE_ZOLTAN"
+-    export LINK_FLAGS="${LINK_FLAGS} -lzoltanRenumber -L${ZOLTAN_ARCH_PATH}/lib -lzoltan"
++    if [ -z "$ZOLTAN_ARCH_PATH" ]
++    then
++        # Optional: get ZOLTAN_ARCH_PATH
++        if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
++        then
++            . $settings
++        fi
++    fi
++
++    for libdir in lib "lib${WM_COMPILER_LIB_ARCH}"
++    do
++        if [ -f "$ZOLTAN_ARCH_PATH/$libdir/libzoltan.a" ]
++        then
++            echo "    found libzoltanRenumber  --  enabling zoltan renumbering support."
++            export COMP_FLAGS="-DFOAM_USE_ZOLTAN"
++            export LINK_FLAGS="${LINK_FLAGS} -lzoltanRenumber -L$ZOLTAN_ARCH_PATH/$libdir -lzoltan"
++            break
++        fi
++    done
+ fi
+ 
+ wmake $targetType
+--- OpenFOAM-v1612+.orig/src/renumber/Allwmake	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/src/renumber/Allwmake	2017-03-28 11:10:22.195543610 +0200
+@@ -5,14 +5,11 @@
+ targetType=libso
+ . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
+ 
+-## Get ZOLTAN_ARCH_PATH
+-#if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
+-#then
+-#    . $settings
+-#    echo "using ZOLTAN_ARCH_PATH=$ZOLTAN_ARCH_PATH"
+-#else
+-#    echo "Error: no config.sh/zoltan settings"
+-#fi
++# Optional: get ZOLTAN_ARCH_PATH
++if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
++then
++    . $settings
++fi
+ 
+ wmake $targetType renumberMethods
+ 
+--- OpenFOAM-v1612+.orig/src/renumber/zoltanRenumber/Make/options	2016-12-23 15:22:59.000000000 +0100
++++ OpenFOAM-v1612+/src/renumber/zoltanRenumber/Make/options	2017-03-28 11:50:46.484343848 +0200
+@@ -4,10 +4,13 @@
+ EXE_INC = \
+     /* -DFULLDEBUG -g -O0 */ \
+     $(PFLAGS) $(PINC) \
++    ${c++LESSWARN} \
+     -I$(FOAM_SRC)/renumber/renumberMethods/lnInclude \
+     -I$(ZOLTAN_ARCH_PATH)/include/ \
+     -I$(LIB_SRC)/meshTools/lnInclude
+ 
+ LIB_LIBS = \
+-    /* -L$(ZOLTAN_ARCH_PATH)/lib -lzoltan */ \
++    -L$(ZOLTAN_ARCH_PATH)/lib \
++    -L$(ZOLTAN_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
++    -lzoltan \
+     -lmeshTools
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1612-zoltan-lib.patch b/var/spack/repos/builtin/packages/openfoam-com/1612-zoltan-lib.patch
deleted file mode 100644
index 712e6a7dfd..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/1612-zoltan-lib.patch
+++ /dev/null
@@ -1,84 +0,0 @@
---- OpenFOAM-v1612+.orig/applications/utilities/mesh/manipulation/renumberMesh/Allwmake	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/applications/utilities/mesh/manipulation/renumberMesh/Allwmake	2017-03-28 11:13:35.222727218 +0200
-@@ -4,20 +4,35 @@
- # Parse arguments for compilation (at least for error catching)
- . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
- 
--export COMPILE_FLAGS=''
--export LINK_FLAGS=''
-+unset COMP_FLAGS LINK_FLAGS
- 
- if [ -f "${FOAM_LIBBIN}/libSloanRenumber.so" ]
- then
--    echo "Found libSloanRenumber.so  --  enabling Sloan renumbering support."
-+    echo "    found libSloanRenumber  --  enabling sloan renumbering support."
-     export LINK_FLAGS="${LINK_FLAGS} -lSloanRenumber"
- fi
- 
--if [ -f "${ZOLTAN_ARCH_PATH}/lib/libzoltan.a" -a -f "${FOAM_LIBBIN}/libzoltanRenumber.so" ]
-+if [ -f "${FOAM_LIBBIN}/libzoltanRenumber.so" ]
- then
--    echo "Found libzoltanRenumber.so  --  enabling zoltan renumbering support."
--    export COMPILE_FLAGS="-DFOAM_USE_ZOLTAN"
--    export LINK_FLAGS="${LINK_FLAGS} -lzoltanRenumber -L${ZOLTAN_ARCH_PATH}/lib -lzoltan"
-+    if [ -z "$ZOLTAN_ARCH_PATH" ]
-+    then
-+        # Optional: get ZOLTAN_ARCH_PATH
-+        if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
-+        then
-+            . $settings
-+        fi
-+    fi
-+
-+    for libdir in lib "lib${WM_COMPILER_LIB_ARCH}"
-+    do
-+        if [ -f "$ZOLTAN_ARCH_PATH/$libdir/libzoltan.a" ]
-+        then
-+            echo "    found libzoltanRenumber  --  enabling zoltan renumbering support."
-+            export COMP_FLAGS="-DFOAM_USE_ZOLTAN"
-+            export LINK_FLAGS="${LINK_FLAGS} -lzoltanRenumber -L$ZOLTAN_ARCH_PATH/$libdir -lzoltan"
-+            break
-+        fi
-+    done
- fi
- 
- wmake $targetType
---- OpenFOAM-v1612+.orig/src/renumber/Allwmake	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/src/renumber/Allwmake	2017-03-28 11:10:22.195543610 +0200
-@@ -5,14 +5,11 @@
- targetType=libso
- . $WM_PROJECT_DIR/wmake/scripts/AllwmakeParseArguments
- 
--## Get ZOLTAN_ARCH_PATH
--#if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
--#then
--#    . $settings
--#    echo "using ZOLTAN_ARCH_PATH=$ZOLTAN_ARCH_PATH"
--#else
--#    echo "Error: no config.sh/zoltan settings"
--#fi
-+# Optional: get ZOLTAN_ARCH_PATH
-+if settings=$($WM_PROJECT_DIR/bin/foamEtcFile config.sh/zoltan)
-+then
-+    . $settings
-+fi
- 
- wmake $targetType renumberMethods
- 
---- OpenFOAM-v1612+.orig/src/renumber/zoltanRenumber/Make/options	2016-12-23 15:22:59.000000000 +0100
-+++ OpenFOAM-v1612+/src/renumber/zoltanRenumber/Make/options	2017-03-28 11:50:46.484343848 +0200
-@@ -4,10 +4,13 @@
- EXE_INC = \
-     /* -DFULLDEBUG -g -O0 */ \
-     $(PFLAGS) $(PINC) \
-+    ${c++LESSWARN} \
-     -I$(FOAM_SRC)/renumber/renumberMethods/lnInclude \
-     -I$(ZOLTAN_ARCH_PATH)/include/ \
-     -I$(LIB_SRC)/meshTools/lnInclude
- 
- LIB_LIBS = \
--    /* -L$(ZOLTAN_ARCH_PATH)/lib -lzoltan */ \
-+    -L$(ZOLTAN_ARCH_PATH)/lib \
-+    -L$(ZOLTAN_ARCH_PATH)/lib$(WM_COMPILER_LIB_ARCH) \
-+    -lzoltan \
-     -lmeshTools
diff --git a/var/spack/repos/builtin/packages/openfoam-com/1806-have-kahip.patch b/var/spack/repos/builtin/packages/openfoam-com/1806-have-kahip.patch
new file mode 100644
index 0000000000..3e10a44145
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openfoam-com/1806-have-kahip.patch
@@ -0,0 +1,17 @@
+--- OpenFOAM-v1806/wmake/scripts/have_kahip-ORIG	2018-06-28 16:39:32.000000000 +0200
++++ OpenFOAM-v1806/wmake/scripts/have_kahip	2018-08-11 13:37:18.250219013 +0200
+@@ -83,10 +83,10 @@
+         # FOAM_EXT_LIBBIN is allowed to be unset
+         library=$(findFirstFile \
+             $FOAM_EXT_LIBBIN/$library \
+-            $METIS_ARCH_PATH/lib/$static \
+-            $METIS_ARCH_PATH/lib/$library \
+-            $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$static \
+-            $METIS_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$library \
++            $KAHIP_ARCH_PATH/lib/$static \
++            $KAHIP_ARCH_PATH/lib/$library \
++            $KAHIP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$static \
++            $KAHIP_ARCH_PATH/lib$WM_COMPILER_LIB_ARCH/$library \
+         )
+     elif isSystem "$KAHIP_ARCH_PATH"
+     then
diff --git a/var/spack/repos/builtin/packages/openfoam-com/common/spack-Allwmake b/var/spack/repos/builtin/packages/openfoam-com/common/spack-Allwmake
index cff22daf10..6c53c2fd70 100755
--- a/var/spack/repos/builtin/packages/openfoam-com/common/spack-Allwmake
+++ b/var/spack/repos/builtin/packages/openfoam-com/common/spack-Allwmake
@@ -5,7 +5,15 @@ export FOAM_INST_DIR=$(cd .. && pwd -L)
 mkdir -p $FOAM_APPBIN $FOAM_LIBBIN 2>/dev/null  # Allow interrupt
 echo "Build openfoam with SPACK ($@)"
 echo WM_PROJECT_DIR = $WM_PROJECT_DIR
-./Allwmake $@                                   # Pass arguments
+
+# Prefer spack-specific Allwmake if it exists
+if [ -f Allwmake-spack ]
+then
+    ./Allwmake-spack $@   # Pass arguments
+else
+    ./Allwmake $@         # Pass arguments
+fi
+
 
 # Link non-dummy MPI_FOAM type to parent-dir, where rpath can find it
 if [ "${FOAM_MPI:=dummy}" != dummy -a -d "$FOAM_LIBBIN/$FOAM_MPI" ]
diff --git a/var/spack/repos/builtin/packages/openfoam-com/common/spack-derived-Allwmake b/var/spack/repos/builtin/packages/openfoam-com/common/spack-derived-Allwmake
index 407ad734e8..02741f1d13 100755
--- a/var/spack/repos/builtin/packages/openfoam-com/common/spack-derived-Allwmake
+++ b/var/spack/repos/builtin/packages/openfoam-com/common/spack-derived-Allwmake
@@ -1,6 +1,7 @@
 #!/bin/bash
 # The openfoam providers must export 'FOAM_PROJECT_DIR'
-# The package is expected to supply an appropriate Allwmake file.
+# The derived package is expected to supply an appropriate
+# <Allwmake> or <Allwmake-spack> file.
 
 [ -d "$FOAM_PROJECT_DIR" -a -f "$FOAM_PROJECT_DIR/etc/bashrc" ] || {
     echo "Error: no PROJECT=$FOAM_PROJECT_DIR" 1>&2
@@ -22,5 +23,12 @@ echo "  $WM_COMPILER $WM_COMPILER_TYPE compiler"
 echo "  $WM_OPTIONS - with $WM_MPLIB $FOAM_MPI"
 echo
 
-./Allwmake $@  # Pass arguments
+# Prefer spack-specific Allwmake if it exists
+if [ -f Allwmake-spack ]
+then
+    ./Allwmake-spack $@   # Pass arguments
+else
+    ./Allwmake $@         # Pass arguments
+fi
+
 # -----------------------------------------------------------------------------
diff --git a/var/spack/repos/builtin/packages/openfoam-com/openfoam-site.patch b/var/spack/repos/builtin/packages/openfoam-com/openfoam-site.patch
deleted file mode 100644
index a1f5d8a08a..0000000000
--- a/var/spack/repos/builtin/packages/openfoam-com/openfoam-site.patch
+++ /dev/null
@@ -1,35 +0,0 @@
-diff -uw OpenFOAM-plus.orig/etc/config.sh/settings OpenFOAM-plus/etc/config.sh/settings
---- OpenFOAM-plus.orig/etc/config.sh/settings	2017-04-04 17:34:29.875873400 +0200
-+++ OpenFOAM-plus/etc/config.sh/settings	2017-04-04 17:38:40.174992466 +0200
-@@ -154,10 +154,10 @@
- export FOAM_LIBBIN=$WM_PROJECT_DIR/platforms/$WM_OPTIONS/lib
- 
- # External (ThirdParty) libraries
--export FOAM_EXT_LIBBIN=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/lib
-+unset FOAM_EXT_LIBBIN  #SPACK: none
- 
- # Site-specific directory
--siteDir="${WM_PROJECT_SITE:-$WM_PROJECT_INST_DIR/site}"
-+siteDir="${WM_PROJECT_SITE:-$WM_PROJECT_DIR/site}"  #SPACK: not in parent directory
- 
- # Shared site executables/libraries
- # Similar naming convention as ~OpenFOAM expansion
-diff -uw OpenFOAM-plus.orig/etc/config.csh/settings OpenFOAM-plus/etc/config.csh/settings
---- OpenFOAM-plus.orig/etc/config.csh/settings	2017-04-04 17:34:28.255879107 +0200
-+++ OpenFOAM-plus/etc/config.csh/settings	2017-04-04 17:39:22.214844670 +0200
-@@ -151,13 +151,13 @@
- setenv FOAM_LIBBIN $WM_PROJECT_DIR/platforms/$WM_OPTIONS/lib
- 
- # External (ThirdParty) libraries
--setenv FOAM_EXT_LIBBIN $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/lib
-+unsetenv FOAM_EXT_LIBBIN  #SPACK: none
- 
- # Site-specific directory
- if ( $?WM_PROJECT_SITE ) then
-     set siteDir=$WM_PROJECT_SITE
- else
--    set siteDir=$WM_PROJECT_INST_DIR/site
-+    set siteDir=$WM_PROJECT_DIR/site  #SPACK: not in parent directory
- endif
- 
- # Shared site executables/libraries
diff --git a/var/spack/repos/builtin/packages/openfoam-com/package.py b/var/spack/repos/builtin/packages/openfoam-com/package.py
index d184365720..cdb6ae1dac 100644
--- a/var/spack/repos/builtin/packages/openfoam-com/package.py
+++ b/var/spack/repos/builtin/packages/openfoam-com/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# Copyright (c) 2017 Mark Olesen, OpenCFD Ltd.
-#
-# This file was authored by Mark Olesen <mark.olesen@esi-group.com>
-# and is released as part of spack under the LGPL license.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for the LLNL notice and LGPL.
-#
-# License
-# -------
-# 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
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Legal Notice
 # ------------
 # OPENFOAM is a trademark owned by OpenCFD Ltd
@@ -60,10 +40,10 @@
 ##############################################################################
 import glob
 import re
-import shutil
 import os
 
 from spack import *
+from spack.util.environment import EnvironmentModifications
 import llnl.util.tty as tty
 
 
@@ -73,8 +53,8 @@ __all__ = [
     'write_environ',
     'rewrite_environ_files',
     'mplib_content',
-    'foamAddPath',
-    'foamAddLib',
+    'foam_add_path',
+    'foam_add_lib',
     'OpenfoamArch',
 ]
 
@@ -150,8 +130,9 @@ def _write_environ_file(output, environ, formatter):
     Also descends into sub-dict and sub-list, but drops the key.
     """
     with open(output, 'w') as outfile:
-        outfile.write('# SPACK settings\n\n')
+        outfile.write('# spack generated\n')
         _write_environ_entries(outfile, environ, formatter)
+        outfile.write('# spack\n')
 
 
 def write_environ(environ, **kwargs):
@@ -163,12 +144,12 @@ def write_environ(environ, **kwargs):
          posix[=None]    If set, the name of the POSIX file to rewrite.
          cshell[=None]   If set, the name of the C-shell file to rewrite.
     """
-    posix = kwargs.get('posix', None)
-    if posix:
-        _write_environ_file(posix, environ, format_export)
-    cshell = kwargs.get('cshell', None)
-    if cshell:
-        _write_environ_file(cshell, environ, format_setenv)
+    rcfile = kwargs.get('posix', None)
+    if rcfile:
+        _write_environ_file(rcfile, environ, format_export)
+    rcfile = kwargs.get('cshell', None)
+    if rcfile:
+        _write_environ_file(rcfile, environ, format_setenv)
 
 
 def rewrite_environ_files(environ, **kwargs):
@@ -177,30 +158,37 @@ def rewrite_environ_files(environ, **kwargs):
          posix[=None]    If set, the name of the POSIX file to rewrite.
          cshell[=None]   If set, the name of the C-shell file to rewrite.
     """
-    posix = kwargs.get('posix', None)
-    if posix and os.path.isfile(posix):
+    rcfile = kwargs.get('posix', None)
+    if rcfile and os.path.isfile(rcfile):
         for k, v in environ.items():
-            filter_file(
-                r'^(\s*export\s+%s)=.*$' % k,
-                r'\1=%s' % v,
-                posix,
-                backup=False)
-    cshell = kwargs.get('cshell', None)
-    if cshell and os.path.isfile(cshell):
+            regex = r'^(\s*export\s+{0})=.*$'.format(k)
+            if not v:
+                replace = r'unset {0}  #SPACK: unset'.format(k)
+            elif v.startswith('#'):
+                replace = r'unset {0}  {1}'.format(k, v)
+            else:
+                replace = r'\1={0}'.format(v)
+            filter_file(regex, replace, rcfile, backup=False)
+
+    rcfile = kwargs.get('cshell', None)
+    if rcfile and os.path.isfile(rcfile):
         for k, v in environ.items():
-            filter_file(
-                r'^(\s*setenv\s+%s)\s+.*$' % k,
-                r'\1 %s' % v,
-                cshell,
-                backup=False)
+            regex = r'^(\s*setenv\s+{0})\s+.*$'.format(k)
+            if not v:
+                replace = r'unsetenv {0}  #SPACK: unset'.format(k)
+            elif v.startswith('#'):
+                replace = r'unsetenv {0}  {1}'.format(k, v)
+            else:
+                replace = r'\1 {0}'.format(v)
+            filter_file(regex, replace, rcfile, backup=False)
 
 
-def foamAddPath(*args):
+def foam_add_path(*args):
     """A string with args prepended to 'PATH'"""
     return '"' + ':'.join(args) + ':${PATH}"'
 
 
-def foamAddLib(*args):
+def foam_add_lib(*args):
     """A string with args prepended to 'LD_LIBRARY_PATH'"""
     return '"' + ':'.join(args) + ':${LD_LIBRARY_PATH}"'
 
@@ -220,8 +208,8 @@ def pkglib(package, pre=None):
 
 
 def mplib_content(spec, pre=None):
-    """The mpi settings to have wmake
-    use spack information with minimum modifications to OpenFOAM.
+    """The mpi settings (from spack) for the OpenFOAM wmake includes, which
+    allows later reuse within OpenFOAM.
 
     Optional parameter 'pre' to provide alternative prefix
     """
@@ -229,6 +217,11 @@ def mplib_content(spec, pre=None):
     bin = mpi_spec.prefix.bin
     inc = mpi_spec.prefix.include
     lib = pkglib(mpi_spec)
+
+    libname = 'mpi'
+    if 'mpich' in mpi_spec.name:
+        libname = 'mpich'
+
     if pre:
         bin = join_path(pre, os.path.basename(bin))
         inc = join_path(pre, os.path.basename(inc))
@@ -242,9 +235,9 @@ def mplib_content(spec, pre=None):
         'include': inc,
         'bindir':  bin,
         'libdir':  lib,
-        'FLAGS':  '-DOMPI_SKIP_MPICXX -DMPICH_IGNORE_CXX_SEEK',
+        'FLAGS':  '-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX',
         'PINC':   '-I{0}'.format(inc),
-        'PLIBS':  '-L{0} -lmpi'.format(lib),
+        'PLIBS':  '-L{0} -l{1}'.format(lib, libname),
     }
     return info
 
@@ -260,57 +253,70 @@ class OpenfoamCom(Package):
     in 2004.
     """
 
+    maintainers = ['olesenm']
     homepage = "http://www.openfoam.com/"
-    baseurl  = "https://sourceforge.net/projects/openfoamplus/files/"
-    gitrepo  = "https://develop.openfoam.com/Development/OpenFOAM-plus.git"
+    url      = "https://sourceforge.net/projects/openfoamplus/files/v1706/OpenFOAM-v1706.tgz"
+    git      = "https://develop.openfoam.com/Development/OpenFOAM-plus.git"
+    list_url = "https://sourceforge.net/projects/openfoamplus/files/"
+    list_depth = 2
 
-    version('1706', '630d30770f7b54d6809efbf94b7d7c8f',
-            url=baseurl + 'v1706/OpenFOAM-v1706.tgz')
-    version('1612', 'ca02c491369150ab127cbb88ec60fbdf',
-            url=baseurl + 'v1612+/OpenFOAM-v1612+.tgz')
-    version('develop', branch='develop', git=gitrepo)  # Needs credentials
+    version('develop', branch='develop', submodules='True')  # Needs credentials
+    version('1806', 'bb244a3bde7048a03edfccffc46c763f')
+    version('1712', '6ad92df051f4d52c7d0ec34f4b8eb3bc')
+    version('1706', '630d30770f7b54d6809efbf94b7d7c8f')
+    version('1612', 'ca02c491369150ab127cbb88ec60fbdf')
 
-    variant('int64', default=False,
-            description='Compile with 64-bit label')
     variant('float32', default=False,
-            description='Compile with 32-bit scalar (single-precision)')
+            description='Use single-precision')
+    variant('int64', default=False,
+            description='With 64-bit labels')
     variant('knl', default=False,
             description='Use KNL compiler settings')
-    variant('scotch', default=True,
-            description='With scotch/ptscotch for decomposition')
+    variant('kahip', default=True,
+            description='With kahip decomposition')
     variant('metis', default=False,
-            description='With metis for decomposition')
+            description='With metis decomposition')
+    variant('scotch', default=True,
+            description='With scotch/ptscotch decomposition')
     variant('zoltan', default=False,
             description='With zoltan renumbering')
     # TODO?# variant('scalasca', default=False,
     # TODO?#         description='With scalasca profiling')
     variant('mgridgen', default=False, description='With mgridgen support')
-    variant('paraview', default=True,
+    variant('paraview', default=False,
             description='Build paraview plugins and runtime post-processing')
+    variant('vtk', default=False,
+            description='With VTK runTimePostProcessing')
     variant('source', default=True,
             description='Install library/application sources and tutorials')
 
     provides('openfoam')
     depends_on('mpi')
 
-    # After 1712 require openmpi+thread_multiple for collated output
-    conflicts('^openmpi~thread_multiple', when='@1712:')
+    # After 1712, could suggest openmpi+thread_multiple for collated output
+    # but particular mixes of mpi versions and InfiniBand may not work so well
+    # conflicts('^openmpi~thread_multiple', when='@1712:')
 
     depends_on('zlib')
     depends_on('fftw')
     depends_on('boost')
     depends_on('cgal')
-    depends_on('flex',  type='build')
+    # The flex restriction is ONLY to deal with a spec resolution clash
+    # introduced by the restriction within scotch!
+    depends_on('flex@:2.6.1,2.6.4:', type='build')
     depends_on('cmake', type='build')
 
     # Require scotch with ptscotch - corresponds to standard OpenFOAM setup
     depends_on('scotch~metis+mpi~int64', when='+scotch~int64')
     depends_on('scotch~metis+mpi+int64', when='+scotch+int64')
+    depends_on('kahip',        when='+kahip')
     depends_on('metis@5:',     when='+metis')
     depends_on('metis+int64',  when='+metis+int64')
     # mgridgen is statically linked
     depends_on('parmgridgen',  when='+mgridgen', type='build')
     depends_on('zoltan',       when='+zoltan')
+    depends_on('vtk',          when='+vtk')
+
     # TODO?# depends_on('scalasca',     when='+scalasca')
 
     # For OpenFOAM plugins and run-time post-processing this should just be
@@ -328,19 +334,8 @@ class OpenfoamCom(Package):
     assets = []
 
     # Version-specific patches
-    patch('1612-bin.patch', when='@1612')
-    patch('1612-build.patch', when='@1612')
-    patch('1612-etc.patch', when='@1612')
-    patch('1612-site.patch', when='@1612')
-    patch('1612-mpi.patch', when='@1612')
-    patch('1612-mgridgen-lib.patch', when='@1612')
-    patch('1612-scotch-metis-lib.patch', when='@1612')
-    patch('1612-zoltan-lib.patch', when='@1612')
-
-    # This patch is reasonably version-invariant
-    # 1) default site directly under WM_PROJECT_DIR
-    # 2) no FOAM_EXT_LIBBIN required
-    patch('openfoam-site.patch', when='@1706:')
+    patch('1612-spack-patches.patch', when='@1612')
+    patch('1806-have-kahip.patch', when='@1806')
 
     # Some user config settings
     # default: 'compile-option': 'RpathOpt',
@@ -366,14 +361,82 @@ class OpenfoamCom(Package):
     # - End of definitions / setup -
     #
 
+    def url_for_version(self, version):
+        # Prior to 'v1706' and additional '+' in the naming
+        fmt = self.list_url
+        if version <= Version('1612'):
+            fmt += 'v{0}+/OpenFOAM-v{0}+.tgz'
+        else:
+            fmt += 'v{0}/OpenFOAM-v{0}.tgz'
+        return fmt.format(version, version)
+
     def setup_environment(self, spack_env, run_env):
-        run_env.set('FOAM_PROJECT_DIR', self.projectdir)
-        run_env.set('WM_PROJECT_DIR', self.projectdir)
-        for d in ['wmake', self.archbin]:  # bin already added automatically
-            run_env.prepend_path('PATH', join_path(self.projectdir, d))
+        """Add environment variables to the generated module file.
+        These environment variables come from running:
+
+        .. code-block:: console
+
+           $ . $WM_PROJECT_DIR/etc/bashrc
+        """
+
+        # NOTE: Spack runs setup_environment twice.
+        # 1) pre-build to set up the build environment
+        # 2) post-install to determine runtime environment variables
+        # The etc/bashrc is only available (with corrrect content)
+        # post-installation.
+
+        bashrc = join_path(self.projectdir, 'etc', 'bashrc')
+        minimal = True
+        if os.path.isfile(bashrc):
+            # post-install: source the installed bashrc
+            try:
+                mods = EnvironmentModifications.from_sourcing_file(
+                    bashrc,
+                    clean=True,  # Remove duplicate entries
+                    blacklist=[  # Blacklist these
+                        # Inadvertent changes
+                        # -------------------
+                        'PS1',            # Leave unaffected
+                        'MANPATH',        # Leave unaffected
+
+                        # Unneeded bits
+                        # -------------
+                        'FOAM_SETTINGS',  # Do not use with modules
+                        'FOAM_INST_DIR',  # Old
+                        'FOAM_(APP|ETC|SRC|SOLVERS|UTILITIES)',
+                        # 'FOAM_TUTORIALS',  # can be useful
+                        'WM_OSTYPE',      # Purely optional value
+
+                        # Third-party cruft - only used for orig compilation
+                        # -----------------
+                        '[A-Z].*_ARCH_PATH',
+                        '(KAHIP|METIS|SCOTCH)_VERSION',
+
+                        # User-specific
+                        # -------------
+                        'FOAM_RUN',
+                        '(FOAM|WM)_.*USER_.*',
+                    ],
+                    whitelist=[  # Whitelist these
+                        'MPI_ARCH_PATH',  # Can be needed for compilation
+                    ])
+
+                run_env.extend(mods)
+                minimal = False
+                tty.info('OpenFOAM bashrc env: {0}'.format(bashrc))
+            except Exception:
+                minimal = True
+
+        if minimal:
+            # pre-build or minimal environment
+            tty.info('OpenFOAM minimal env {0}'.format(self.prefix))
+            run_env.set('FOAM_PROJECT_DIR', self.projectdir)
+            run_env.set('WM_PROJECT_DIR', self.projectdir)
+            for d in ['wmake', self.archbin]:  # bin added automatically
+                run_env.prepend_path('PATH', join_path(self.projectdir, d))
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        """Provide location of the OpenFOAM project.
+        """Location of the OpenFOAM project directory.
         This is identical to the WM_PROJECT_DIR value, but we avoid that
         variable since it would mask the normal OpenFOAM cleanup of
         previous versions.
@@ -407,18 +470,38 @@ class OpenfoamCom(Package):
         add_extra_files(self, self.common, self.assets)
 
         # Avoid WM_PROJECT_INST_DIR for ThirdParty, site or jobControl.
-        # Use openfoam-site.patch to handle jobControl, site.
         #
         # Filtering: bashrc,cshrc (using a patch is less flexible)
         edits = {
             'WM_THIRD_PARTY_DIR':
-            r'$WM_PROJECT_DIR/ThirdParty #SPACK: No separate third-party',
+            r'$WM_PROJECT_DIR/ThirdParty  #SPACK: No separate third-party',
         }
-        rewrite_environ_files(  # Adjust etc/bashrc and etc/cshrc
+        rewrite_environ_files(  # etc/{bashrc,cshrc}
             edits,
             posix=join_path('etc', 'bashrc'),
             cshell=join_path('etc', 'cshrc'))
 
+        # Filtering: settings
+        edits = {
+            'FOAM_EXT_LIBBIN': '#SPACK: No separate third-party',  # ie, unset
+        }
+        rewrite_environ_files(  # etc/config.{csh,sh}/settings
+            edits,
+            posix=join_path('etc', 'config.sh', 'settings'),
+            cshell=join_path('etc', 'config.csh', 'settings'))
+
+        # The following filtering is non-vital. It simply prevents 'site' dirs
+        # from the the wrong level (likely non-existent anyhow) from being
+        # added to PATH, LD_LIBRARY_PATH.
+        for rcdir in ['config.sh', 'config.csh']:
+            rcfile = join_path('etc', rcdir, 'settings')
+            if os.path.isfile(rcfile):
+                filter_file(
+                    'WM_PROJECT_INST_DIR/',
+                    'WM_PROJECT_DIR/',
+                    rcfile,
+                    backup=False)
+
     def configure(self, spec, prefix):
         """Make adjustments to the OpenFOAM configuration files in their various
         locations: etc/bashrc, etc/config.sh/FEATURE and customizations that
@@ -428,7 +511,7 @@ class OpenfoamCom(Package):
         # Filtering bashrc, cshrc
         edits = {}
         edits.update(self.foam_arch.foam_dict())
-        rewrite_environ_files(  # Adjust etc/bashrc and etc/cshrc
+        rewrite_environ_files(  # etc/{bashrc,cshrc}
             edits,
             posix=join_path('etc', 'bashrc'),
             cshell=join_path('etc', 'cshrc'))
@@ -450,26 +533,29 @@ class OpenfoamCom(Package):
                 ('BOOST_ARCH_PATH', spec['boost'].prefix),
                 ('CGAL_ARCH_PATH',  spec['cgal'].prefix),
                 ('LD_LIBRARY_PATH',
-                 foamAddLib(
+                 foam_add_lib(
                      pkglib(spec['boost'], '${BOOST_ARCH_PATH}'),
                      pkglib(spec['cgal'], '${CGAL_ARCH_PATH}'))),
             ],
             'FFTW': [
                 ('FFTW_ARCH_PATH', spec['fftw'].prefix),  # Absolute
                 ('LD_LIBRARY_PATH',
-                 foamAddLib(
+                 foam_add_lib(
                      pkglib(spec['fftw'], '${BOOST_ARCH_PATH}'))),
             ],
             # User-defined MPI
             'mpi-user': [
                 ('MPI_ARCH_PATH', spec['mpi'].prefix),  # Absolute
-                ('LD_LIBRARY_PATH', foamAddLib(user_mpi['libdir'])),
-                ('PATH', foamAddPath(user_mpi['bindir'])),
+                ('LD_LIBRARY_PATH', foam_add_lib(user_mpi['libdir'])),
+                ('PATH', foam_add_path(user_mpi['bindir'])),
             ],
             'scotch': {},
+            'kahip': {},
             'metis': {},
+            'ensight': {},     # Disable settings
             'paraview': [],
             'gperftools': [],  # Currently unused
+            'vtk': [],
         }
 
         if '+scotch' in spec:
@@ -479,18 +565,30 @@ class OpenfoamCom(Package):
                 'SCOTCH_VERSION': 'scotch-{0}'.format(spec['scotch'].version),
             }
 
+        if '+kahip' in spec:
+            self.etc_config['kahip'] = {
+                'KAHIP_ARCH_PATH': spec['kahip'].prefix,
+            }
+
         if '+metis' in spec:
             self.etc_config['metis'] = {
                 'METIS_ARCH_PATH': spec['metis'].prefix,
             }
 
         if '+paraview' in spec:
-            pvMajor = 'paraview-{0}'.format(spec['paraview'].version.up_to(2))
+            pvmajor = 'paraview-{0}'.format(spec['paraview'].version.up_to(2))
             self.etc_config['paraview'] = [
                 ('ParaView_DIR', spec['paraview'].prefix),
-                ('ParaView_INCLUDE_DIR', '${ParaView_DIR}/include/' + pvMajor),
-                ('PV_PLUGIN_PATH', '$FOAM_LIBBIN/' + pvMajor),
-                ('PATH', foamAddPath('${ParaView_DIR}/bin')),
+                ('ParaView_INCLUDE_DIR', '${ParaView_DIR}/include/' + pvmajor),
+                ('PV_PLUGIN_PATH', '$FOAM_LIBBIN/' + pvmajor),
+                ('PATH', foam_add_path('${ParaView_DIR}/bin')),
+            ]
+
+        if '+vtk' in spec:
+            self.etc_config['vtk'] = [
+                ('VTK_DIR', spec['vtk'].prefix),
+                ('LD_LIBRARY_PATH',
+                 foam_add_lib(pkglib(spec['vtk'], '${VTK_DIR}'))),
             ]
 
         # Optional
@@ -574,12 +672,13 @@ class OpenfoamCom(Package):
             dirs.extend(['doc'])
 
         # Install platforms (and doc) skipping intermediate targets
-        ignored = ['src', 'applications', 'html', 'Guides']
+        relative_ignore_paths = ['src', 'applications', 'html', 'Guides']
+        ignore = lambda p: p in relative_ignore_paths
         for d in dirs:
             install_tree(
                 d,
                 join_path(self.projectdir, d),
-                ignore=shutil.ignore_patterns(*ignored),
+                ignore=ignore,
                 symlinks=True)
 
         etc_dir = join_path(self.projectdir, 'etc')
@@ -613,12 +712,6 @@ class OpenfoamCom(Package):
             ]:
                 os.symlink(f, os.path.basename(f))
 
-    def openfoam_run_environment(self, projdir):
-        # This seems to bomb out with an ImportError 'site'!
-        # mods = EnvironmentModifications.from_sourcing_files(
-        #    join_path(projdir, 'etc/bashrc'))
-        pass
-
 
 # -----------------------------------------------------------------------------
 
@@ -673,6 +766,8 @@ class OpenfoamArch(object):
                 platform += 'ia64'
             elif target == 'armv7l':
                 platform += 'ARM7'
+            elif target == 'aarch64':
+                platform += 'ARM64'
             elif target == 'ppc64':
                 platform += 'PPC64'
             elif target == 'ppc64le':
diff --git a/var/spack/repos/builtin/packages/openfoam-org/240-etc.patch b/var/spack/repos/builtin/packages/openfoam-org/240-etc.patch
new file mode 100644
index 0000000000..cc0c19c78d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openfoam-org/240-etc.patch
@@ -0,0 +1,88 @@
+--- OpenFOAM-2.4.x.orig/etc/bashrc	2016-10-16 16:11:45.000000000 +0200
++++ OpenFOAM-2.4.x/etc/bashrc	2017-03-24 12:41:25.233267894 +0100
+@@ -55,6 +55,8 @@
+ # overridden from the prefs.sh file or from command-line specification
+ #
+ #- note the location for later use (eg, in job scripts)
++rc="${BASH_SOURCE:-${ZSH_NAME:+$0}}"
++[ -n "$rc" ] && FOAM_INST_DIR=$(\cd $(dirname $rc)/../.. && \pwd -L) || \
+ : ${FOAM_INST_DIR:=$foamInstall}; export FOAM_INST_DIR
+ 
+ #- Compiler location:
+--- OpenFOAM-2.4.x.orig/applications/utilities/mesh/conversion/ansysToFoam/ansysToFoam.L	2018-04-05 14:18:12.112228183 +0100
++++ OpenFOAM-2.4.x/applications/utilities/mesh/conversion/ansysToFoam/ansysToFoam.L	2018-04-05 14:19:20.795393577 +0100
+@@ -77,7 +77,7 @@
+ // Dummy yywrap to keep yylex happy at compile time.
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L	2018-04-05 14:18:19.137347383 +0100
++++ OpenFOAM-2.4.x/src/thermophysicalModels/reactionThermo/chemistryReaders/chemkinReader/chemkinLexer.L	2018-04-05 14:19:27.556508297 +0100
+@@ -54,7 +54,7 @@
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+ //! \cond dummy
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/applications/utilities/mesh/conversion/gambitToFoam/gambitToFoam.L	2018-04-05 14:18:45.689797916 +0100
++++ OpenFOAM-2.4.x/applications/utilities/mesh/conversion/gambitToFoam/gambitToFoam.L	2018-04-05 14:19:43.195773659 +0100
+@@ -80,7 +80,7 @@
+ // Dummy yywrap to keep yylex happy at compile time.
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/src/triSurface/triSurface/interfaces/STL/readSTLASCII.L	2018-04-05 14:18:50.432878396 +0100
++++ OpenFOAM-2.4.x/src/triSurface/triSurface/interfaces/STL/readSTLASCII.L	2018-04-05 14:19:46.299826328 +0100
+@@ -55,7 +55,7 @@
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+ //! \cond dummy
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/src/surfMesh/surfaceFormats/stl/STLsurfaceFormatASCII.L	2018-04-05 14:18:57.064990927 +0100
++++ OpenFOAM-2.4.x/src/surfMesh/surfaceFormats/stl/STLsurfaceFormatASCII.L	2018-04-05 14:19:49.258876536 +0100
+@@ -50,7 +50,7 @@
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+ //! \cond dummy
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L	2018-04-05 14:18:27.152483381 +0100
++++ OpenFOAM-2.4.x/applications/utilities/mesh/conversion/fluent3DMeshToFoam/fluent3DMeshToFoam.L	2018-04-05 14:19:32.180586757 +0100
+@@ -123,7 +123,7 @@
+ // Dummy yywrap to keep yylex happy at compile time.
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()
+--- OpenFOAM-2.4.x.orig/applications/utilities/mesh/conversion/fluentMeshToFoam/fluentMeshToFoam.L.	2018-04-05 14:18:35.049617377 +0100
++++ OpenFOAM-2.4.x/applications/utilities/mesh/conversion/fluentMeshToFoam/fluentMeshToFoam.L	2018-04-05 14:19:38.493693876 +0100
+@@ -100,7 +100,7 @@
+ // Dummy yywrap to keep yylex happy at compile time.
+ // It is called by yylex but is not used as the mechanism to change file.
+ // See <<EOF>>
+-#if YY_FLEX_SUBMINOR_VERSION < 34
++#if YY_FLEX_MINOR_VERSION < 6 && YY_FLEX_SUBMINOR_VERSION < 34
+ extern "C" int yywrap()
+ #else
+ int yyFlexLexer::yywrap()int yyFlexLexer::yywrap()
diff --git a/var/spack/repos/builtin/packages/openfoam-org/50-etc.patch b/var/spack/repos/builtin/packages/openfoam-org/50-etc.patch
new file mode 100644
index 0000000000..ee28dfcd1b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openfoam-org/50-etc.patch
@@ -0,0 +1,24 @@
+--- OpenFOAM-5.x.org/etc/bashrc	2017-07-25 18:43:40.000000000 +0200
++++ OpenFOAM-5.x/etc/bashrc	2017-12-11 13:36:09.479818186 +0100
+@@ -42,15 +42,17 @@
+ #
+ # Please set to the appropriate path if the default is not correct.
+ #
+-[ ${BASH_SOURCE:-$0} ] && \
+-export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \
+-export FOAM_INST_DIR=$HOME/$WM_PROJECT
+-# export FOAM_INST_DIR=~$WM_PROJECT
++rc="${BASH_SOURCE:-${ZSH_NAME:+$0}}"
++[ -n "$rc" ] && FOAM_INST_DIR=$(\cd $(dirname $rc)/../.. && \pwd -P) || \
++FOAM_INST_DIR=$HOME/$WM_PROJECT
+ # export FOAM_INST_DIR=/opt/$WM_PROJECT
+ # export FOAM_INST_DIR=/usr/local/$WM_PROJECT
+ #
+ # END OF (NORMAL) USER EDITABLE PART
+ ################################################################################
++: # Extra safety - if the user commented out all fallback values
++export FOAM_INST_DIR
++unset rc
+ 
+ # The default environment variables below can be overridden in a prefs.sh file
+ # located in ~/.OpenFOAM/$WM_PROJECT_VERSION, ~/.OpenFOAM,
diff --git a/var/spack/repos/builtin/packages/openfoam-org/assets/bin/foamEtcFile b/var/spack/repos/builtin/packages/openfoam-org/assets/bin/foamEtcFile
index 294cc26505..195b91bdbe 100755
--- a/var/spack/repos/builtin/packages/openfoam-org/assets/bin/foamEtcFile
+++ b/var/spack/repos/builtin/packages/openfoam-org/assets/bin/foamEtcFile
@@ -4,37 +4,31 @@
 # \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
 #  \\    /   O peration     |
 #   \\  /    A nd           | Copyright (C) 2011-2016 OpenFOAM Foundation
-#    \\/     M anipulation  | Copyright (C) 2017 OpenCFD Ltd.
+#    \\/     M anipulation  | Copyright (C) 2017-2018 OpenCFD Ltd.
 #-------------------------------------------------------------------------------
 # License
-#     This file is part of OpenFOAM.
-#
-#     OpenFOAM is free software: you can redistribute it and/or modify it
-#     under the terms of the GNU General Public License as published by
-#     the Free Software Foundation, either version 3 of the License, or
-#     (at your option) any later version.
-#
-#     OpenFOAM 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 GNU General Public License
-#     for more details.
-#
-#     You should have received a copy of the GNU General Public License
-#     along with OpenFOAM.  If not, see <http://www.gnu.org/licenses/>.
+#     This file is part of OpenFOAM, licensed under GNU General Public License
+#     <http://www.gnu.org/licenses/>.
 #
 # Script
 #     foamEtcFile
 #
 # Description
-#     Locate user/group/other files with semantics similar to the
-#     ~OpenFOAM/fileName expansion.
+#     Locate user/group/other file as per '#includeEtc'.
+#
+#     The -mode option can be used to allow chaining from personal settings
+#     to site-wide settings.
 #
-#     The -mode option can be used to allow chaining from
-#     personal settings to site-wide settings.
+#     For example, within the user ~/.OpenFOAM/<VER>/config.sh/compiler:
+#     \code
+#        eval $(foamEtcFile -sh -mode=go config.sh/compiler)
+#     \endcode
 #
-#     For example, within the user ~/.OpenFOAM/<VER>/prefs.sh:
+#     The -mode option is similarly used within etc/{bashrc,cshrc} to ensure
+#     that system prefs are respected:
 #     \code
-#        eval $(foamEtcFile -sh -mode=go prefs.sh)
+#        eval $(foamEtcFile -sh -mode=o  prefs.sh)
+#        eval $(foamEtcFile -sh -mode=ug prefs.sh)
 #     \endcode
 #
 # Environment
@@ -46,42 +40,40 @@
 #     This script must exist in one of these locations:
 #     - $WM_PROJECT_INST_DIR/OpenFOAM-<VERSION>/bin
 #     - $WM_PROJECT_INST_DIR/openfoam-<VERSION>/bin
-#     - $WM_PROJECT_INST_DIR/OpenFOAM+<VERSION>/bin
-#     - $WM_PROJECT_INST_DIR/openfoam+<VERSION>/bin
 #     - $WM_PROJECT_INST_DIR/openfoam<VERSION>/bin  (debian version)
 #
 #-------------------------------------------------------------------------------
-unset optQuiet optSilent
-usage() {
-    [ "${optQuiet:-$optSilent}" = true ] && exit 1
-    exec 1>&2
-    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
+printHelp() {
     cat<<USAGE
 
-Usage: foamEtcFile [OPTION] fileName
+Usage: foamEtcFile [OPTION] fileName [-- args]
        foamEtcFile [OPTION] [-list|-list-test] [fileName]
 
 options:
-  -a, -all          Return all files (otherwise stop after the first match)
-  -l, -list         List directories or files to be checked
+  -all (-a)         Return all files (otherwise stop after the first match)
+  -list (-l)        List directories or files to be checked
   -list-test        List (existing) directories or files to be checked
   -mode=MODE        Any combination of u(user), g(group), o(other)
   -prefix=DIR       Specify an alternative installation prefix
   -version=VER      Specify alternative OpenFOAM version (eg, 3.0, 1612, ...)
-  -csh | -sh        Produce output suitable for a csh or sh 'eval'
-  -csh-verbose | -sh-verbose
-                    As per -csh | -sh, with additional verbosity
-  -q, -quiet        Suppress all normal output
-  -s, -silent       Suppress stderr, except -csh-verbose, -sh-verbose output
+  -csh              Produce 'source FILE' output for a csh eval
+  -sh               Produce '. FILE' output for a sh eval
+  -csh-verbose      As per -csh, with additional verbosity
+  -sh-verbose       As per -sh,  with additional verbosity
+  -config           Add config directory prefix for shell type:
+                        with -csh* for a config.csh/ prefix
+                        with -sh*  for a config.sh/ prefix
+  -quiet (-q)       Suppress all normal output
+  -silent (-s)      Suppress stderr, except -csh-verbose, -sh-verbose output
   -help             Print the usage
 
-Locate user/group/other file with semantics similar to the
-~OpenFOAM/fileName expansion.
+Locate user/group/other file as per '#includeEtc'
 
-Single character options must not be grouped. Equivalent options:
-    -mode=MODE,   -mode MODE,   -m MODE
-    -prefix=DIR,  -prefix DIR,  -p DIR
-    -version=VER, -version VER, -v VER
+Do not group single character options.
+Equivalent options:
+  |  -mode=MODE     |  -mode MODE     | -m MODE
+  |  -prefix=DIR    |  -prefix DIR    | -p DIR
+  |  -version=VER   |  -version VER   | -v VER
 
 Exit status
     0  when the file is found. Print resolved path to stdout.
@@ -89,9 +81,10 @@ Exit status
     2  when the file is not found.
 
 USAGE
-    exit 1
+    exit 0  # A clean exit
 }
 
+unset optQuiet optSilent
 # Report error and exit
 die()
 {
@@ -146,13 +139,6 @@ guessVersion()
         version="${version%%*-}" # Extra safety, eg openfoam-version-packager
         ;;
 
-    (OpenFOAM+* | openfoam+*)
-        # Alternative naming: OpenFOAM+<VERSION> or openfoam+<VERSION>
-        dirBase="${projectDirName%%+*}+"
-        version="${projectDirName#*+}"
-        version="${version%%*-}" # Extra safety, eg openfoam-version-packager
-        ;;
-
     (openfoam[0-9]*)
         # Debian naming: openfoam<VERSION>
         dirBase="openfoam"
@@ -199,30 +185,36 @@ setVersion()
 
 
 optMode=ugo         # Default mode is always 'ugo'
-unset optAll optList optShell optVersion
+unset shellOutput verboseOutput
+unset optAll optConfig optList optVersion
 
 # Parse options
 while [ "$#" -gt 0 ]
 do
     case "$1" in
-    -h | -help)
-        usage
+    -h | -help*)
+        printHelp
         ;;
     -a | -all)
         optAll=true
-        unset optShell
+        unset shellOutput verboseOutput
         ;;
     -l | -list)
         optList=true
-        unset optShell
         ;;
     -list-test)
         optList='test'
-        unset optShell
         ;;
-    -csh | -sh | -csh-verbose | -sh-verbose)
-        optShell="${1#-}"
-        unset optAll
+    -csh | -sh)
+        shellOutput="${1#-}"
+        unset verboseOutput
+        ;;
+    -csh-verbose | -sh-verbose)
+        shellOutput="${1#-}"
+        verboseOutput="source "         # Report: "source FILE"
+        ;;
+    -config)
+        optConfig=true
         ;;
     -mode=[ugo]*)
         optMode="${1#*=}"
@@ -276,9 +268,33 @@ do
     shift
 done
 
-
 #-------------------------------------------------------------------------------
 
+# Split arguments into filename (for searching) and trailing bits for shell eval
+# Silently remove leading ~OpenFOAM/ (as per Foam::findEtcFile)
+nArgs=$#
+fileName="${1#~OpenFOAM/}"
+unset evalArgs
+
+if [ "$nArgs" -eq 1 ]
+then
+    if [ "$1" = "--" ]
+    then
+        nArgs=0
+        unset fileName
+    fi
+elif [ "$nArgs" -ge 2 ]
+then
+    if [ "$2" = "--" ]
+    then
+        nArgs=1
+        shift 2
+        evalArgs="$@"
+    fi
+fi
+
+
+# Get version information
 if [ -n "$optVersion" ]
 then
     setVersion $optVersion
@@ -301,12 +317,6 @@ groupDir="${WM_PROJECT_SITE:-$prefixDir/site}"
 #     eval echo "$i=\$$i" 1>&2
 # done
 
-
-# Save the essential bits of information
-# silently remove leading ~OpenFOAM/ (used in Foam::findEtcFile)
-nArgs=$#
-fileName="${1#~OpenFOAM/}"
-
 # Define the various places to be searched:
 unset dirList
 case "$optMode" in (*u*) # (U)ser
@@ -325,27 +335,61 @@ case "$optMode" in (*o*) # (O)ther == shipped
 esac
 set -- $dirList
 
+[ "$#" -ge 1 ] || die "No directories to scan. Programming error?"
+exitCode=2  # Fallback is a FileNotFound error
+
+
+#
+# Preliminaries
+#
+
+# Special handling of config.sh/ , config.csh/ directories
+if [ -n "$optConfig" -a -n "$shellOutput" -a -n "$fileName" ]
+then
+    case "$shellOutput" in
+    csh*)
+        optConfig="config.csh/"
+        ;;
+    sh*)
+        optConfig="config.sh/"
+        ;;
+    *)
+        unset optConfig
+        ;;
+    esac
+
+    if [ -n "$optConfig" ]
+    then
+        case "$fileName" in
+        /* | config.csh* | config.sh*)
+            # Does not need or cannot add a prefix
+            unset optConfig
+            ;;
+        *)
+            fileName="$optConfig$fileName"
+            ;;
+        esac
+    fi
+fi
+
 
 #
 # The main routine
 #
 
-exitCode=0
 if [ -n "$optList" ]
 then
 
     # List directories, or potential file locations
     [ "$nArgs" -le 1 ] || \
-    die "-list expects 0 or 1 filename, but $nArgs provided"
+        die "-list options expect 0 or 1 filename, but $nArgs provided"
 
-    # A silly combination, but -quiet does have precedence
+    # A silly combination, but -quiet has absolute precedence
     [ -n "$optQuiet" ] && exit 0
 
     # Test for directory or file too?
     if [ "$optList" = "test" ]
     then
-        exitCode=2  # Fallback to a general error (file not found)
-
         if [ "$nArgs" -eq 1 ]
         then
             for dir
@@ -368,6 +412,7 @@ then
             done
         fi
     else
+        exitCode=0  # OK, already verified that $# != 0
         for dir
         do
             echo "$dir${fileName:+/}$fileName"
@@ -378,35 +423,44 @@ else
 
     [ "$nArgs" -eq 1 ] || die "One filename expected - $nArgs provided"
 
-    exitCode=2  # Fallback to a general error (file not found)
+    # Output for sourcing files ("source" for csh, "." for POSIX shell)
+    # Only allow sourcing a single file (disallow combination with -all)
+    case "$shellOutput" in
+    csh*)
+        shellOutput="source "   # eg, "source FILE"
+        ;;
+    sh*)
+        shellOutput=". "        # eg, ". FILE"
+        ;;
+    esac
+
+    # Anti-pattern: -all disables shell commands
+    if [ -n "$optAll" ]
+    then
+        unset shellOutput verboseOutput
+    fi
 
     for dir
     do
-        if [ -f "$dir/$fileName" ]
+        resolved="$dir/$fileName"
+        if [ -f "$resolved" ]
         then
-            exitCode=0
-            [ -n "$optQuiet" ] && break
-
-            case "$optShell" in
-            (*verbose)
-                echo "Using: $dir/$fileName" 1>&2
-                ;;
-            esac
-
-            case "$optShell" in
-            csh*)
-                echo "source $dir/$fileName"
-                break
-                ;;
-            sh*)
-                echo ". $dir/$fileName"
+            exitCode=0  # OK
+            if [ -n "$optQuiet" ]
+            then
                 break
-                ;;
-            *)
-                echo "$dir/$fileName"
-                [ -n "$optAll" ] || break
-                ;;
-            esac
+            elif [ -n "$verboseOutput" ]
+            then
+                echo "$verboseOutput$resolved" 1>&2
+            fi
+
+            if [ -n "$shellOutput" ]
+            then
+                echo "$shellOutput$resolved $evalArgs"
+            else
+                echo "$resolved"
+            fi
+            [ -n "$optAll" ] || break
         fi
     done
 
diff --git a/var/spack/repos/builtin/packages/openfoam-org/package.py b/var/spack/repos/builtin/packages/openfoam-org/package.py
index c176adcbe5..8857257878 100644
--- a/var/spack/repos/builtin/packages/openfoam-org/package.py
+++ b/var/spack/repos/builtin/packages/openfoam-org/package.py
@@ -1,28 +1,8 @@
-##############################################################################
-# Copyright (c) 2017 Mark Olesen, OpenCFD Ltd.
-#
-# This file was authored by Mark Olesen <mark.olesen@esi-group.com>
-# and is released as part of spack under the LGPL license.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files for the LLNL notice and LGPL.
-#
-# License
-# -------
-# 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
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # Legal Notice
 # ------------
 # OPENFOAM is a trademark owned by OpenCFD Ltd
@@ -55,7 +35,6 @@
 ##############################################################################
 import glob
 import re
-import shutil
 import os
 
 import llnl.util.tty as tty
@@ -80,10 +59,15 @@ class OpenfoamOrg(Package):
     homepage = "http://www.openfoam.org/"
     baseurl  = "https://github.com/OpenFOAM"
     url      = "https://github.com/OpenFOAM/OpenFOAM-4.x/archive/version-4.1.tar.gz"
+    git      = "https://github.com/OpenFOAM/OpenFOAM-dev.git"
 
-    version('4.1', '318a446c4ae6366c7296b61184acd37c',
+    version('develop', branch='master')
+    version('5.0', 'cd8c5bdd3ff39c34f61747c8e55f59d1',
+            url=baseurl + '/OpenFOAM-5.x/archive/version-5.0.tar.gz')
+    version('4.1', 'afd7d8e66e7db0ffaf519b14f1a8e1d4',
             url=baseurl + '/OpenFOAM-4.x/archive/version-4.1.tar.gz')
-    version('develop', git='https://github.com/OpenFOAM/OpenFOAM-dev.git')
+    version('2.4.0', 'ad7d8b7b0753655b2b6fd9e92eefa92a',
+            url=baseurl + '/OpenFOAM-2.4.x/archive/version-2.4.0.tar.gz')
 
     variant('int64', default=False,
             description='Compile with 64-bit label')
@@ -107,15 +91,10 @@ class OpenfoamOrg(Package):
     assets = ['bin/foamEtcFile']
 
     # Version-specific patches
+    patch('50-etc.patch', when='@5.0:')
     patch('41-etc.patch', when='@4.1')
-    patch('41-site.patch', when='@4.1')
-
-    # Some user config settings
-    config = {
-        'mplib': 'SYSTEMMPI',   # Use system mpi for spack
-        # Add links into bin/, lib/ (eg, for other applications)
-        'link': False
-    }
+    patch('41-site.patch', when='@4.1:')
+    patch('240-etc.patch', when='@2.4.0')
 
     # The openfoam architecture, compiler information etc
     _foam_arch = None
@@ -133,14 +112,34 @@ class OpenfoamOrg(Package):
     # - End of definitions / setup -
     #
 
+    # Some user config settings
+    @property
+    def config(self):
+        settings = {
+            # Use system mpi for spack
+            'mplib': 'SYSTEMMPI',
+
+            # Add links into bin/, lib/ (eg, for other applications)
+            'link': False,
+        }
+        # OpenFOAM v2.4 and earlier lacks WM_LABEL_OPTION
+        if self.spec.satisfies('@:2.4'):
+            settings['label-size'] = False
+        return settings
+
     def setup_environment(self, spack_env, run_env):
+        # This should be similar to the openfoam-com package,
+        # but sourcing the etc/bashrc here seems to exit with an error.
+        # ... this needs to be examined in more detail.
+        #
+        # Minimal environment only.
         run_env.set('FOAM_PROJECT_DIR', self.projectdir)
         run_env.set('WM_PROJECT_DIR', self.projectdir)
         for d in ['wmake', self.archbin]:  # bin already added automatically
             run_env.prepend_path('PATH', join_path(self.projectdir, d))
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        """Provide location of the OpenFOAM project.
+        """Location of the OpenFOAM project directory.
         This is identical to the WM_PROJECT_DIR value, but we avoid that
         variable since it would mask the normal OpenFOAM cleanup of
         previous versions.
@@ -199,8 +198,8 @@ class OpenfoamOrg(Package):
         edits = {
             'WM_THIRD_PARTY_DIR':
             r'$WM_PROJECT_DIR/ThirdParty #SPACK: No separate third-party',
-            'WM_VERSION': self.version,    # consistency
-            'FOAMY_HEX_MESH': '',          # This is horrible (unset variable?)
+            'WM_VERSION': str(self.version),  # consistency
+            'FOAMY_HEX_MESH': '',  # This is horrible (unset variable?)
         }
         rewrite_environ_files(  # Adjust etc/bashrc and etc/cshrc
             edits,
@@ -258,10 +257,18 @@ class OpenfoamOrg(Package):
 
         # Adjust components to use SPACK variants
         for component, subdict in self.etc_config.items():
-            write_environ(
-                subdict,
-                posix=join_path('etc', 'config.sh',  component),
-                cshell=join_path('etc', 'config.csh', component))
+            # Versions up to 3.0 used an etc/config/component.sh naming
+            # convention instead of etc/config.sh/component
+            if spec.satisfies('@:3.0'):
+                write_environ(
+                    subdict,
+                    posix=join_path('etc', 'config',  component) + '.sh',
+                    cshell=join_path('etc', 'config', component) + '.csh')
+            else:
+                write_environ(
+                    subdict,
+                    posix=join_path('etc', 'config.sh',  component),
+                    cshell=join_path('etc', 'config.csh', component))
 
     def build(self, spec, prefix):
         """Build using the OpenFOAM Allwmake script, with a wrapper to source
@@ -317,12 +324,13 @@ class OpenfoamOrg(Package):
             dirs.extend(['doc'])
 
         # Install platforms (and doc) skipping intermediate targets
-        ignored = ['src', 'applications', 'html', 'Guides']
+        relative_ignore_paths = ['src', 'applications', 'html', 'Guides']
+        ignore = lambda p: p in relative_ignore_paths
         for d in dirs:
             install_tree(
                 d,
                 join_path(self.projectdir, d),
-                ignore=shutil.ignore_patterns(*ignored),
+                ignore=ignore,
                 symlinks=True)
 
         etc_dir = join_path(self.projectdir, 'etc')
diff --git a/var/spack/repos/builtin/packages/openfst/package.py b/var/spack/repos/builtin/packages/openfst/package.py
index 29b5eca02d..4187ddd258 100644
--- a/var/spack/repos/builtin/packages/openfst/package.py
+++ b/var/spack/repos/builtin/packages/openfst/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,7 +31,18 @@ class Openfst(AutotoolsPackage):
     conflicts('%intel@16:')
     conflicts('%gcc@6:')
 
+    variant('far', default=False, description="Enable FAR support")
+
     # Patch openfst-1.4.1 for kaldi@c024e8
     # See https://github.com/kaldi-asr/kaldi/blob/c024e8aa0a727bf76c91a318f76a1f8b0b59249e/tools/Makefile#L82-L88
     patch('openfst-1.4.1.patch', when='@1.4.1-patch')
     patch('openfst_gcc41up.patch', when='@1.4.1-patch')
+
+    def configure_args(self):
+        args = []
+        spec = self.spec
+        if '+far' in spec:
+            args.append('--enable-far')
+        else:
+            args.append('--disable-far')
+        return args
diff --git a/var/spack/repos/builtin/packages/opengl/package.py b/var/spack/repos/builtin/packages/opengl/package.py
new file mode 100644
index 0000000000..577e22dbf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opengl/package.py
@@ -0,0 +1,70 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Opengl(Package):
+    """Placeholder for external OpenGL libraries from hardware vendors"""
+
+    homepage = "https://www.opengl.org/"
+
+    provides('gl@:4.5', when='@4.5:')
+    provides('gl@:4.4', when='@4.4:')
+    provides('gl@:4.3', when='@4.3:')
+    provides('gl@:4.2', when='@4.2:')
+    provides('gl@:4.1', when='@4.1:')
+    provides('gl@:3.3', when='@3.3:')
+
+    # Override the fetcher method to throw a useful error message;
+    # fixes GitHub issue (#7061) in which this package threw a
+    # generic, uninformative error during the `fetch` step,
+    @property
+    def fetcher(self):
+        msg = """This package is intended to be a placeholder for
+        system-provided OpenGL libraries from hardware vendors.  Please
+        download and install OpenGL drivers/libraries for your graphics
+        hardware separately, and then set that up as an external package.
+        An example of a working packages.yaml:
+
+        packages:
+          opengl:
+            paths:
+              opengl@4.5.0: /opt/opengl
+            buildable: False
+
+        In that case, /opt/opengl/ should contain these two folders:
+
+        include/GL/       (opengl headers, including "gl.h")
+        lib               (opengl libraries, including "libGL.so")
+
+        On Apple Darwin (e.g., OS X, macOS) systems, this package is
+        normally installed as part of the XCode Command Line Tools in
+        /usr/X11R6, so a working packages.yaml would be
+
+        packages:
+          opengl:
+            paths:
+              opengl@4.1: /usr/X11R6
+            buildable: False
+
+        In that case, /usr/X11R6 should contain
+
+        include/GL/      (OpenGL headers, including "gl.h")
+        lib              (OpenGL libraries, including "libGL.dylib")
+
+        On OS X/macOS, note that the version of OpenGL provided
+        depends on your hardware. Look at
+        https://support.apple.com/en-us/HT202823 to see what version
+        of OpenGL your Mac uses."""
+        raise InstallError(msg)
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libGL', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
diff --git a/var/spack/repos/builtin/packages/openglu/package.py b/var/spack/repos/builtin/packages/openglu/package.py
new file mode 100644
index 0000000000..c6468c95b4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openglu/package.py
@@ -0,0 +1,66 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Openglu(Package):
+    """Placeholder for external OpenGL utility library (GLU) from hardware
+       vendors"""
+
+    homepage = "https://www.opengl.org/resources/libraries"
+
+    provides('glu@:1.3', when='@1.3:')
+    provides('glu@:1.2', when='@1.2:')
+    provides('glu@:1.1', when='@1.1:')
+    provides('glu@:1.0', when='@1.0:')
+
+    # Override the fetcher method to throw a useful error message;
+    # fixes an issue similar to Github issue (#7061), in which the
+    # opengl package threw a generic, uninformative error message
+    # during the `fetch` step
+    @property
+    def fetcher(self):
+        msg = """This package is intended to be a placeholder for
+        system-provided OpenGL utility (GLU) libraries from hardware vendors.
+        Please download and install the GLU drivers/libraries for your
+        graphics hardware separately, and then set that up as an external
+        package.  An example of a working packages.yaml:
+
+        packages:
+          openglu:
+            paths:
+              openglu@1.3: /opt/opengl
+            buildable: False
+
+        In that case, /opt/opengl/ should contain these two folders:
+
+        include/GL/       (opengl headers, including "glu.h")
+        lib               (opengl libraries, including "libGLU.so")
+
+        On Apple Darwin (OS X, macOS) systems, this package is
+        normally installed as part of the XCode Command Line Tools in
+        /usr/X11R6, so a working packages.yaml would be
+
+        packages:
+          openglu:
+            paths:
+              openglu@1.3: /usr/X11R6
+            buildable: False
+
+        In that case, /usr/X11R6 should contain
+
+        include/GL       (GLU headers, including "glu.h")
+        lib              (GLU libraries, including "libGLU.dylib")"""
+
+        raise InstallError(msg)
+
+    @property
+    def libs(self):
+        for dir in ['lib64', 'lib']:
+            libs = find_libraries('libGLU', join_path(self.prefix, dir),
+                                  shared=True, recursive=False)
+            if libs:
+                return libs
diff --git a/var/spack/repos/builtin/packages/openjpeg/macos.patch b/var/spack/repos/builtin/packages/openjpeg/macos.patch
new file mode 100644
index 0000000000..f736b92b47
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openjpeg/macos.patch
@@ -0,0 +1,13 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -151,6 +151,10 @@ IF(NOT OPENJPEG_INSTALL_PACKAGE_DIR)
+   SET(OPENJPEG_INSTALL_PACKAGE_DIR "${OPENJPEG_INSTALL_LIB_DIR}/${OPENJPEG_INSTALL_SUBDIR}")
+ ENDIF(NOT OPENJPEG_INSTALL_PACKAGE_DIR)
+ 
++IF(APPLE)
++    LIST(APPEND OPENJPEG_LIBRARY_PROPERTIES INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${OPENJPEG_INSTALL_LIB_DIR}")
++ENDIF()
++
+ #-----------------------------------------------------------------------------
+ # Big endian test:
+ INCLUDE (${CMAKE_ROOT}/Modules/TestBigEndian.cmake)
diff --git a/var/spack/repos/builtin/packages/openjpeg/package.py b/var/spack/repos/builtin/packages/openjpeg/package.py
index 1998885502..34b300371b 100644
--- a/var/spack/repos/builtin/packages/openjpeg/package.py
+++ b/var/spack/repos/builtin/packages/openjpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,11 +16,35 @@ class Openjpeg(CMakePackage):
     ITU-T as a JPEG 2000 Reference Software.
     """
 
-    homepage = "https://github.com/uclouvain/openjpeg"
-    url = "https://github.com/uclouvain/openjpeg/archive/version.2.1.tar.gz"
+    homepage = 'https://github.com/uclouvain/openjpeg'
+    url = 'https://github.com/uclouvain/openjpeg/archive/v2.3.0.tar.gz'
+    list_url = 'https://github.com/uclouvain/openjpeg/releases'
 
-    version('2.1',   '3e1c451c087f8462955426da38aa3b3d')
+    version('2.3.0', '6a1f8aaa1fe55d2088e3a9c942e0f698')
+    version('2.2.0', '269bb0b175476f3addcc0d03bd9a97b6')
+    version('2.1.2', '40a7bfdcc66280b3c1402a0eb1a27624')
+    version('2.1.1', '0cc4b2aee0a9b6e9e21b7abcd201a3ec')
+    version('2.1.0', '3e1c451c087f8462955426da38aa3b3d')
     version('2.0.1', '105876ed43ff7dbb2f90b41b5a43cfa5')
-    version('2.0',   'cdf266530fee8af87454f15feb619609')
+    version('2.0.0', 'cdf266530fee8af87454f15feb619609')
     version('1.5.2', '545f98923430369a6b046ef3632ef95c')
     version('1.5.1', 'd774e4b5a0db5f0f171c4fc0aabfa14e')
+
+    # The problem with install name of the library on MacOs was fixed starting
+    # version 2.1.1: https://github.com/uclouvain/openjpeg/commit/b9a247b559e62e55f5561624cf4a19aee3c8afdc
+    # The solution works for the older versions (at least starting 1.5.1) too.
+    patch('macos.patch', when='@:2.1.0 platform=darwin')
+
+    def url_for_version(self, version):
+        if version >= Version('2.1.1'):
+            return super(Openjpeg, self).url_for_version(version)
+
+        # Before version 2.2.0, release tarballs of the versions like x.y.0
+        # did not have the ".0" in their names:
+        if version[2] == 0:
+            version = version.up_to(2)
+
+        url_fmt = \
+            'https://github.com/uclouvain/openjpeg/archive/version.{0}.tar.gz'
+
+        return url_fmt.format(version)
diff --git a/var/spack/repos/builtin/packages/openmc/package.py b/var/spack/repos/builtin/packages/openmc/package.py
index b48928c02c..8d3175c029 100644
--- a/var/spack/repos/builtin/packages/openmc/package.py
+++ b/var/spack/repos/builtin/packages/openmc/package.py
@@ -1,91 +1,29 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
-class Openmc(MakefilePackage):
+class Openmc(CMakePackage):
     """The OpenMC project aims to provide a fully-featured Monte Carlo particle
        transport code based on modern methods. It is a constructive solid
        geometry, continuous-energy transport code that uses ACE format cross
        sections. The project started under the Computational Reactor Physics
        Group at MIT."""
 
-    homepage = "https://github.com/ANL-CESAR/"
-    url = "https://github.com/ANL-CESAR/openmc.git"
-
-    tags = ['proxy-app']
-
-    version('develop', git='https://github.com/ANL-CESAR/openmc.git')
-
-    build_directory = 'src'
-
-    parallel = False
-
-    @property
-    def build_targets(self):
-
-        targets = []
+    homepage = "http://openmc.readthedocs.io/"
+    url = "https://github.com/openmc-dev/openmc/tarball/v0.10.0"
+    git = "https://github.com/openmc-dev/openmc.git"
 
-        if self.compiler.name == 'gcc':
-            targets.append('COMPILER=gnu')
-            targets.append('MACHINE=UNKNOWN')
-        if self.compiler.name == 'intel':
-            targets.append('COMPILER=intel')
-        if self.compiler.name == 'pgi':
-            targets.append('COMPILER=pgi')
-        if self.compiler.name == 'xl':
-            targets.append('COMPILER=ibm')
-        if self.compiler.name == 'cce':
-            targets.append('COMPILER=cray')
+    version('0.10.0', 'abb57bd1b226eb96909dafeec31369b0')
+    version('develop')
 
-        return targets
+    depends_on("hdf5+hl")
 
-    def install(self, spec, prefix):
-        with working_dir('src'):
-            pth_st_cmp = join_path(prefix.bin, 'statepoint_cmp')
-            pth_st_histogram = join_path(prefix.bin, 'statepoint_histogram')
-            pth_st_meshpoint = join_path(prefix.bin, 'statepoint_meshpoint')
-            pth_openmc = join_path(prefix, 'share/man/man1/openmc.1')
-            pth_copyright = join_path(prefix, 'share/doc/openmc/copyright')
-            mkdir(prefix.bin)
-            mkdirp(pth_st_cmp)
-            mkdirp(pth_st_histogram)
-            mkdirp(pth_st_meshpoint)
-            mkdirp(pth_openmc)
-            mkdirp(pth_copyright)
+    def cmake_args(self):
+        options = ['-DHDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix]
 
-            install('openmc', prefix.bin)
-            install('utils/statepoint_cmp.py', pth_st_cmp)
-            install('utils/statepoint_histogram.py',
-                    pth_st_histogram)
-            install('utils/statepoint_meshplot.py',
-                    pth_st_meshpoint)
-        install('man/man1/openmc.1', pth_openmc)
-        install('LICENSE', pth_copyright)
-        install_tree('docs/', prefix.docs)
-        install_tree('examples/', prefix.examples)
-        install_tree('data/', prefix.data)
-        install_tree('tests/', prefix.tests)
+        return options
diff --git a/var/spack/repos/builtin/packages/openmpi/btl_vader.patch b/var/spack/repos/builtin/packages/openmpi/btl_vader.patch
new file mode 100644
index 0000000000..005537d732
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openmpi/btl_vader.patch
@@ -0,0 +1,24 @@
+diff --git a/opal/mca/btl/vader/btl_vader_fbox.h b/opal/mca/btl/vader/btl_vader_fbox.h
+index 17239ce8ef..ee5c913551 100644
+--- a/opal/mca/btl/vader/btl_vader_fbox.h
++++ b/opal/mca/btl/vader/btl_vader_fbox.h
+@@ -138,9 +138,6 @@ static inline bool mca_btl_vader_fbox_sendi (mca_btl_base_endpoint_t *ep, unsign
+         memcpy (data + header_size, payload, payload_size);
+     }
+ 
+-    /* write out part of the header now. the tag will be written when the data is available */
+-    mca_btl_vader_fbox_set_header (MCA_BTL_VADER_FBOX_HDR(dst), tag, ep->fbox_out.seq++, data_size);
+-
+     end += size;
+ 
+     if (OPAL_UNLIKELY(fbox_size == end)) {
+@@ -152,6 +149,9 @@ static inline bool mca_btl_vader_fbox_sendi (mca_btl_base_endpoint_t *ep, unsign
+         MCA_BTL_VADER_FBOX_HDR(ep->fbox_out.buffer + end)->ival = 0;
+     }
+ 
++    /* write out part of the header now. the tag will be written when the data is available */
++    mca_btl_vader_fbox_set_header (MCA_BTL_VADER_FBOX_HDR(dst), tag, ep->fbox_out.seq++, data_size);
++
+     /* align the buffer */
+     ep->fbox_out.end = ((uint32_t) hbs << 31) | end;
+     opal_atomic_wmb ();
diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py
index 5563198649..40ac79a2e8 100644
--- a/var/spack/repos/builtin/packages/openmpi/package.py
+++ b/var/spack/repos/builtin/packages/openmpi/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
+import sys
 
 from spack import *
 
@@ -65,27 +47,39 @@ def _mxm_dir():
 
 
 class Openmpi(AutotoolsPackage):
-    """The Open MPI Project is an open source Message Passing Interface
-       implementation that is developed and maintained by a consortium
-       of academic, research, and industry partners. Open MPI is
-       therefore able to combine the expertise, technologies, and
-       resources from all across the High Performance Computing
-       community in order to build the best MPI library available.
-       Open MPI offers advantages for system and software vendors,
-       application developers and computer science researchers.
+    """An open source Message Passing Interface implementation.
+
+    The Open MPI Project is an open source Message Passing Interface
+    implementation that is developed and maintained by a consortium
+    of academic, research, and industry partners. Open MPI is
+    therefore able to combine the expertise, technologies, and
+    resources from all across the High Performance Computing
+    community in order to build the best MPI library available.
+    Open MPI offers advantages for system and software vendors,
+    application developers and computer science researchers.
     """
 
     homepage = "http://www.open-mpi.org"
-    url = "https://www.open-mpi.org/software/ompi/v3.0/downloads/openmpi-3.0.0.tar.bz2"
+    url = "https://www.open-mpi.org/software/ompi/v3.1/downloads/openmpi-3.1.2.tar.bz2"
     list_url = "http://www.open-mpi.org/software/ompi/"
 
     # Current
-    version('3.0.0', '757d51719efec08f9f1a7f32d58b3305')  # libmpi.so.40.00.0
+    version('3.1.3', sha256='8be04307c00f51401d3fb9d837321781ea7c79f2a5a4a2e5d4eaedc874087ab6')
+    version('3.1.2', '210df69fafd964158527e7f37e333239')  # libmpi.so.40.10.2
+    version('3.1.1', '493f1db2f75afaab1c8ecba78d2f5aab')  # libmpi.so.40.10.1
+    version('3.1.0', '0895e268ca27735d7654bf64cee6c256')  # libmpi.so.40.10.0
 
     # Still supported
+    version('3.0.2', '098fa89646f5b4438d9d8534bc960cd6')  # libmpi.so.40.00.2
+    version('3.0.1', '565f5060e080b0871a64b295c3d4426a')  # libmpi.so.40.00.1
+    version('3.0.0', '757d51719efec08f9f1a7f32d58b3305')  # libmpi.so.40.00.0
+    version('2.1.5', '6019c8b67d4975d833801e72ba290918')  # libmpi.so.20.10.3 
+    version('2.1.4', '003b356a24a5b7bd1705a23ddc69d9a0')  # libmpi.so.20.10.3
+    version('2.1.3', '46079b6f898a412240a0bf523e6cd24b')  # libmpi.so.20.10.2
     version('2.1.2', 'ff2e55cc529802e7b0738cf87acd3ee4')  # libmpi.so.20.10.2
     version('2.1.1', 'ae542f5cf013943ffbbeb93df883731b')  # libmpi.so.20.10.1
     version('2.1.0', '4838a5973115c44e14442c01d3f21d52')  # libmpi.so.20.10.0
+    version('2.0.4', '7e3c71563787a67dce9acc4d639ef3f8')  # libmpi.so.20.0.4
     version('2.0.3', '6c09e56ac2230c4f9abd8ba029f03edd')  # libmpi.so.20.0.3
     version('2.0.2', 'ecd99aa436a1ca69ce936a96d6a3fa48')  # libmpi.so.20.0.2
     version('2.0.1', '6f78155bd7203039d2448390f3b51c96')  # libmpi.so.20.0.1
@@ -173,11 +167,21 @@ class Openmpi(AutotoolsPackage):
     patch('configure.patch', when="@1.10.1")
     patch('fix_multidef_pmi_class.patch', when="@2.0.0:2.0.1")
 
+    # Vader Bug: https://github.com/open-mpi/ompi/issues/5375
+    # Haven't release fix for 2.1.x
+    patch('btl_vader.patch', when='@2.1.3:2.1.5')
+
+    # Fixed in 3.0.3 and 3.1.3
+    patch('btl_vader.patch', when='@3.0.1:3.0.2')
+    patch('btl_vader.patch', when='@3.1.0:3.1.2')
+
+    fabrics = ('psm', 'psm2', 'verbs', 'mxm', 'ucx', 'libfabric')
+
     variant(
         'fabrics',
         default=None if _verbs_dir() is None else 'verbs',
-        description='List of fabrics that are enabled',
-        values=('psm', 'psm2', 'pmi', 'verbs', 'mxm'),
+        description="List of fabrics that are enabled",
+        values=fabrics,
         multi=True
     )
 
@@ -195,27 +199,74 @@ class Openmpi(AutotoolsPackage):
     variant('thread_multiple', default=False,
             description='Enable MPI_THREAD_MULTIPLE support')
     variant('cuda', default=False, description='Enable CUDA support')
+    variant('pmi', default=False, description='Enable PMI support')
+    variant('cxx_exceptions', default=True, description='Enable C++ Exception support')
+    # Adding support to build a debug version of OpenMPI that activates
+    # Memchecker, as described here:
+    #
+    # https://www.open-mpi.org/faq/?category=debugging#memchecker_what
+    #
+    # This option degrades run-time support, and thus is disabled by default
+    variant(
+        'memchecker',
+        default=False,
+        description='Memchecker support for debugging [degrades performance]'
+    )
+
+    variant(
+        'legacylaunchers',
+        default=False,
+        description='Do not remove mpirun/mpiexec when building with slurm'
+    )
 
     provides('mpi')
     provides('mpi@:2.2', when='@1.6.5')
     provides('mpi@:3.0', when='@1.7.5:')
     provides('mpi@:3.1', when='@2.0.0:')
 
+    if sys.platform != 'darwin':
+        depends_on('numactl')
+
     depends_on('hwloc')
+    # ompi@:3.0.0 doesn't support newer hwloc releases:
+    # "configure: error: OMPI does not currently support hwloc v2 API"
+    # Future ompi releases may support it, needs to be verified.
+    # See #7483 for context.
+    depends_on('hwloc@:1.999')
+
     depends_on('hwloc +cuda', when='+cuda')
     depends_on('java', when='+java')
     depends_on('sqlite', when='+sqlite3@:1.11')
+    depends_on('zlib', when='@3.0.0:')
+    depends_on('valgrind~mpi', when='+memchecker')
+    depends_on('ucx', when='fabrics=ucx')
+    depends_on('libfabric', when='fabrics=libfabric')
+    depends_on('slurm', when='schedulers=slurm')
+    depends_on('binutils+libiberty', when='fabrics=mxm')
 
     conflicts('+cuda', when='@:1.6')  # CUDA support was added in 1.7
     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
+    conflicts('+pmi', when='@:1.5.4')  # PMI support was added in 1.5.5
+    conflicts('schedulers=slurm ~pmi', when='@1.5.4:',
+              msg='+pmi is required for openmpi(>=1.5.5) to work with SLURM.')
+
+    filter_compiler_wrappers('openmpi/*-wrapper-data*', relative_root='share')
+    conflicts('fabrics=libfabric', when='@:1.8')  # libfabric support was added in 1.10.0
+    # It may be worth considering making libfabric an exclusive fabrics choice
 
     def url_for_version(self, version):
         url = "http://www.open-mpi.org/software/ompi/v{0}/downloads/openmpi-{1}.tar.bz2"
         return url.format(version.up_to(2), version)
 
     @property
+    def headers(self):
+        hdrs = HeaderList(find(self.prefix.include, 'mpi.h', recursive=False))
+        if not hdrs:
+            hdrs = HeaderList(find(self.prefix, 'mpi.h', recursive=True))
+        return hdrs or None
+
+    @property
     def libs(self):
         query_parameters = self.spec.last_query.extra_parameters
         libraries = ['libmpi']
@@ -224,7 +275,7 @@ class Openmpi(AutotoolsPackage):
             libraries = ['libmpi_cxx'] + libraries
 
         return find_libraries(
-            libraries, root=self.prefix, shared=True, recurse=True
+            libraries, root=self.prefix, shared=True, recursive=True
         )
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
@@ -290,16 +341,45 @@ class Openmpi(AutotoolsPackage):
         spec = self.spec
         config_args = [
             '--enable-shared',
-            '--enable-static'
         ]
-        if self.spec.satisfies('@2.0:'):
+
+        # Add extra_rpaths dirs from compilers.yaml into link wrapper
+        rpaths = [self.compiler.cc_rpath_arg + path
+                  for path in self.compiler.extra_rpaths]
+        config_args.extend([
+            '--with-wrapper-ldflags={0}'.format(' '.join(rpaths))
+        ])
+
+        # According to this comment on github:
+        #
+        # https://github.com/open-mpi/ompi/issues/4338#issuecomment-383982008
+        #
+        # adding --enable-static silently disables slurm support via pmi/pmi2
+        if spec.satisfies('schedulers=slurm'):
+            config_args.append('--with-pmi={0}'.format(spec['slurm'].prefix))
+        else:
+            config_args.append('--enable-static')
+            config_args.extend(self.with_or_without('pmi'))
+
+        if spec.satisfies('@2.0:'):
             # for Open-MPI 2.0:, C++ bindings are disabled by default.
             config_args.extend(['--enable-mpi-cxx'])
 
-        # Fabrics and schedulers
+        if spec.satisfies('@3.0.0:', strict=True):
+            config_args.append('--with-zlib={0}'.format(spec['zlib'].prefix))
+
+        # Fabrics
         config_args.extend(self.with_or_without('fabrics'))
+        # Schedulers
         config_args.extend(self.with_or_without('schedulers'))
 
+        config_args.extend(self.enable_or_disable('memchecker'))
+        if spec.satisfies('+memchecker', strict=True):
+            config_args.extend([
+                '--enable-debug',
+                '--with-valgrind={0}'.format(spec['valgrind'].prefix),
+            ])
+
         # Hwloc support
         if spec.satisfies('@1.5.2:'):
             config_args.append('--with-hwloc={0}'.format(spec['hwloc'].prefix))
@@ -310,7 +390,7 @@ class Openmpi(AutotoolsPackage):
                 config_args.extend([
                     '--enable-java',
                     '--enable-mpi-java',
-                    '--with-jdk-dir={0}'.format(spec['java'].prefix)
+                    '--with-jdk-dir={0}'.format(spec['java'].home)
                 ])
             else:
                 config_args.extend([
@@ -331,7 +411,7 @@ class Openmpi(AutotoolsPackage):
                 config_args.append('--enable-contrib-no-build=vt')
 
         # Multithreading support
-        if spec.satisfies('@1.5.4:'):
+        if spec.satisfies('@1.5.4:2.999'):
             if '+thread_multiple' in spec:
                 config_args.append('--enable-mpi-thread-multiple')
             else:
@@ -364,45 +444,23 @@ class Openmpi(AutotoolsPackage):
             else:
                 config_args.append('--without-cuda')
 
+        if '+cxx_exceptions' in spec:
+            config_args.append('--enable-cxx-exceptions')
+        else:
+            config_args.append('--disable-cxx-exceptions')
         return config_args
 
     @run_after('install')
-    def filter_compilers(self):
-        """Run after install to make the MPI compilers use the
-        compilers that Spack built the package with.
-
-        If this isn't done, they'll have CC, CXX and FC set
-        to Spack's generic cc, c++ and f90.  We want them to
-        be bound to whatever compiler they were built with.
-        """
-        kwargs = {'ignore_absent': True, 'backup': False, 'string': False}
-        wrapper_basepath = join_path(self.prefix, 'share', 'openmpi')
-
-        wrappers = [
-            ('mpicc-vt-wrapper-data.txt', self.compiler.cc),
-            ('mpicc-wrapper-data.txt', self.compiler.cc),
-            ('ortecc-wrapper-data.txt', self.compiler.cc),
-            ('shmemcc-wrapper-data.txt', self.compiler.cc),
-            ('mpic++-vt-wrapper-data.txt', self.compiler.cxx),
-            ('mpic++-wrapper-data.txt', self.compiler.cxx),
-            ('ortec++-wrapper-data.txt', self.compiler.cxx),
-            ('mpifort-vt-wrapper-data.txt', self.compiler.fc),
-            ('mpifort-wrapper-data.txt', self.compiler.fc),
-            ('shmemfort-wrapper-data.txt', self.compiler.fc),
-            ('mpif90-vt-wrapper-data.txt', self.compiler.fc),
-            ('mpif90-wrapper-data.txt', self.compiler.fc),
-            ('mpif77-vt-wrapper-data.txt',  self.compiler.f77),
-            ('mpif77-wrapper-data.txt',  self.compiler.f77)
-        ]
-
-        for wrapper_name, compiler in wrappers:
-            wrapper = join_path(wrapper_basepath, wrapper_name)
-            if not os.path.islink(wrapper):
-                # Substitute Spack compile wrappers for the real
-                # underlying compiler
-                match = 'compiler=.*'
-                substitute = 'compiler={compiler}'.format(compiler=compiler)
-                filter_file(match, substitute, wrapper, **kwargs)
-                # Remove this linking flag if present
-                # (it turns RPATH into RUNPATH)
-                filter_file('-Wl,--enable-new-dtags', '', wrapper, **kwargs)
+    def delete_mpirun_mpiexec(self):
+        # The preferred way to run an application when Slurm is the
+        # scheduler is to let Slurm manage process spawning via PMI.
+        #
+        # Deleting the links to orterun avoids users running their
+        # applications via mpirun or mpiexec, and leaves srun as the
+        # only sensible choice (orterun is still present, but normal
+        # users don't know about that).
+        if '@1.6: ~legacylaunchers schedulers=slurm' in self.spec:
+            os.remove(self.prefix.bin.mpirun)
+            os.remove(self.prefix.bin.mpiexec)
+            os.remove(self.prefix.bin.shmemrun)
+            os.remove(self.prefix.bin.oshrun)
diff --git a/var/spack/repos/builtin/packages/opennurbs/package.py b/var/spack/repos/builtin/packages/opennurbs/package.py
new file mode 100644
index 0000000000..388633f841
--- /dev/null
+++ b/var/spack/repos/builtin/packages/opennurbs/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Opennurbs(Package):
+    """OpenNURBS is an open-source NURBS-based geometric modeling library
+    and toolset, with meshing and display / output functions.
+    """
+
+    homepage = "https://github.com/OpenNURBS/OpenNURBS"
+    git      = "https://github.com/OpenNURBS/OpenNURBS.git"
+
+    maintainers = ['jrood-nrel']
+
+    version('develop', branch='develop')
+
+    version('percept', '59163fd085a24c7a4c2170c70bb60fea',
+            url='https://github.com/PerceptTools/percept/raw/master/build-cmake/opennurbs-percept.tar.gz')
+
+    variant('shared', default=True,
+            description="Build shared libraries")
+
+    # CMake installation method
+    def install(self, spec, prefix):
+        cmake_args = [
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in spec else 'OFF')
+        ]
+
+        cmake_args.extend(std_cmake_args)
+
+        with working_dir('spack-build', create=True):
+            cmake('..', *cmake_args)
+            make()
+            make('install')
+
+    # Pre-cmake installation method
+    @when('@percept')
+    def install(self, spec, prefix):
+        make(parallel=False)
+
+        # Install manually
+        mkdir(prefix.lib)
+        mkdir(prefix.include)
+        install('libopenNURBS.a', prefix.lib)
+        install_tree('zlib', join_path(prefix.include, 'zlib'))
+        headers = glob.glob(join_path('.', '*.h'))
+        for h in headers:
+            install(h, prefix.include)
diff --git a/var/spack/repos/builtin/packages/openpmd-api/package.py b/var/spack/repos/builtin/packages/openpmd-api/package.py
new file mode 100644
index 0000000000..93082d3b85
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openpmd-api/package.py
@@ -0,0 +1,85 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OpenpmdApi(CMakePackage):
+    """API for easy reading and writing of openPMD files"""
+
+    homepage = "http://www.openPMD.org"
+    git      = "https://github.com/openPMD/openPMD-api.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='dev')
+
+    variant('mpi', default=True,
+            description='Enable parallel I/O')
+    variant('hdf5', default=True,
+            description='Enable HDF5 support')
+    variant('adios1', default=False,
+            description='Enable ADIOS1 support')
+    variant('adios2', default=False,
+            description='Enable ADIOS2 support')
+    # variant('json', default=True,
+    #         description='Enable JSON support')
+    variant('python', default=True,
+            description='Enable Python bindings')
+
+    depends_on('cmake@3.10.0:', type='build')
+    depends_on('mpark-variant@1.3.0:')
+    depends_on('catch@2.3.0: ~single_header', type='test')
+    depends_on('mpi@2.3:', when='+mpi')  # might become MPI 3.0+
+    depends_on('hdf5@1.8.13:', when='+hdf5')
+    depends_on('hdf5@1.8.13: ~mpi', when='~mpi +hdf5')
+    depends_on('hdf5@1.8.13: +mpi', when='+mpi +hdf5')
+    depends_on('adios@1.10.0:', when='+adios1')
+    depends_on('adios@1.10.0: ~mpi', when='~mpi +adios1')
+    depends_on('adios@1.10.0: +mpi', when='+mpi +adios1')
+    depends_on('adios2@2.1.0:', when='+adios2')
+    depends_on('adios2@2.1.0: ~mpi', when='~mpi +adios2')
+    depends_on('adios2@2.1.0: +mpi', when='+mpi +adios2')
+    # ideally we want 2.3.0+ for full C++11 CT function signature support
+    depends_on('py-pybind11@2.2.3:', when='+python')
+    depends_on('py-numpy@1.15.1:', when='+python', type=['test', 'run'])
+
+    extends('python', when='+python')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            # variants
+            '-DopenPMD_USE_MPI:BOOL={0}'.format(
+                'ON' if '+mpi' in spec else 'OFF'),
+            '-DopenPMD_USE_HDF5:BOOL={0}'.format(
+                'ON' if '+hdf5' in spec else 'OFF'),
+            '-DopenPMD_USE_ADIOS1:BOOL={0}'.format(
+                'ON' if '+adios1' in spec else 'OFF'),
+            '-DopenPMD_USE_ADIOS2:BOOL={0}'.format(
+                'ON' if '+adios2' in spec else 'OFF'),
+            # '-DopenPMD_USE_JSON:BOOL={0}'.format(
+            #     'ON' if '+json' in spec else 'OFF'),
+            '-DopenPMD_USE_PYTHON:BOOL={0}'.format(
+                'ON' if '+python' in spec else 'OFF'),
+            # tests and examples
+            '-DBUILD_TESTING:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+            '-DBUILD_EXAMPLES:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF'),
+        ]
+
+        if spec.satisfies('+python'):
+            args.append('-DopenPMD_USE_INTERNAL_PYBIND11:BOOL=OFF')
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH={0}'.format(
+                        self.spec['python'].command.path))
+
+        # switch internally shipped third-party libraries for spack
+        args.append('-DopenPMD_USE_INTERNAL_VARIANT:BOOL=OFF')
+        if self.run_tests:
+            args.append('-DopenPMD_USE_INTERNAL_CATCH:BOOL=OFF')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/openscenegraph/package.py b/var/spack/repos/builtin/packages/openscenegraph/package.py
index 915848fc23..d8adf24bf7 100644
--- a/var/spack/repos/builtin/packages/openscenegraph/package.py
+++ b/var/spack/repos/builtin/packages/openscenegraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/openslide/package.py b/var/spack/repos/builtin/packages/openslide/package.py
new file mode 100644
index 0000000000..2018a7e33b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openslide/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Openslide(AutotoolsPackage):
+    """OpenSlide reads whole slide image files."""
+
+    homepage = "http://openslide.org/"
+    url      = "https://github.com/openslide/openslide/releases/download/v3.4.1/openslide-3.4.1.tar.xz"
+
+    version('3.4.1', 'ad9fa84775ed6b505d6f50bf6420c6bf')
+
+    depends_on('openjpeg')
+    depends_on('jpeg')
+    depends_on('libtiff')
+    depends_on('libxml2')
+    depends_on('sqlite@3.6:')
diff --git a/var/spack/repos/builtin/packages/openspeedshop-utils/package.py b/var/spack/repos/builtin/packages/openspeedshop-utils/package.py
new file mode 100644
index 0000000000..c70013562c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/openspeedshop-utils/package.py
@@ -0,0 +1,304 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+import spack
+import spack.store
+
+import os
+import os.path
+
+
+class OpenspeedshopUtils(CMakePackage):
+    """OpenSpeedShop is a community effort by The Krell Institute with
+       current direct funding from DOEs NNSA.  It builds on top of a
+       broad list of community infrastructures, most notably Dyninst
+       and MRNet from UW, libmonitor from Rice, and PAPI from UTK.
+       OpenSpeedShop is an open source multi platform Linux performance
+       tool which is targeted to support performance analysis of
+       applications running on both single node and large scale IA64,
+       IA32, EM64T, AMD64, PPC, ARM, Power8, Intel Phi, Blue Gene and
+       Cray platforms.  OpenSpeedShop development is hosted by the Krell
+       Institute. The infrastructure and base components of OpenSpeedShop
+       are released as open source code primarily under LGPL.
+       openspeedshop-utils is a package that does not have the
+       qt3 gui.  It was created to avoid a conflict between
+       openspeedshop and cbtf-argonavis-gui based on the fact
+       that spack will not allow a qt3 and qt4/qt5 dependency in a packages
+       dependency tree.
+    """
+
+    homepage = "http://www.openspeedshop.org"
+    git      = "https://github.com/OpenSpeedShop/openspeedshop.git"
+
+    version('develop', branch='master')
+    version('2.4.0', branch='2.4.0')
+    version('2.3.1.5', branch='2.3.1.5')
+    version('2.3.1.4', branch='2.3.1.4')
+    version('2.3.1.3', branch='2.3.1.3')
+
+    variant('runtime', default=False,
+            description="build only the runtime libraries and collectors.")
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+    variant('crayfe', default=False,
+            description="build only the FE tool using the runtime_dir \
+                         to point to target build.")
+    variant('cuda', default=False,
+            description="build with cuda packages included.")
+
+    variant('build_type', default='None', values=('None'),
+            description='CMake build type')
+
+    # MPI variants
+    variant('openmpi', default=False,
+            description="Build mpi collector for openmpi \
+                         MPI when variant is enabled.")
+    variant('mpt', default=False,
+            description="Build mpi collector for SGI \
+                         MPT MPI when variant is enabled.")
+    variant('mvapich2', default=False,
+            description="Build mpi collector for mvapich2\
+                         MPI when variant is enabled.")
+    variant('mvapich', default=False,
+            description="Build mpi collector for mvapich\
+                         MPI when variant is enabled.")
+    variant('mpich2', default=False,
+            description="Build mpi collector for mpich2\
+                         MPI when variant is enabled.")
+    variant('mpich', default=False,
+            description="Build mpi collector for mpich\
+                         MPI when variant is enabled.")
+
+    depends_on("cmake@3.0.2:", type='build')
+
+    # Dependencies for openspeedshop that are common to all
+    # the variants of the OpenSpeedShop build
+    depends_on("libtool", type='build')
+    depends_on("bison", type='build')
+    depends_on("flex@2.6.1", type='build')
+
+    # For binutils
+    depends_on("binutils", type='build')
+
+    depends_on("elf", type="link")
+    depends_on("libdwarf")
+
+    depends_on("sqlite")
+
+    # For boost
+    depends_on("boost@1.66.0:")
+
+    depends_on("dyninst@develop", when='@develop')
+    depends_on("dyninst@10:", when='@2.3.1.3:9999')
+
+    depends_on("python", when='@develop', type=('build', 'run'))
+    depends_on("python@2.7.14:2.7.15", when='@2.3.1.3:9999', type=('build', 'run'))
+
+    depends_on("libxml2")
+
+    # Dependencies for the openspeedshop cbtf packages.
+    depends_on("cbtf@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    depends_on("cbtf-krell@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+crayfe', when='@develop+crayfe', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+crayfe', when='@2.3.1.3:9999+crayfe', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+cti', when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@2.3.1.3:9999+cti', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpich', when='@develop+mpich', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpich', when='@2.3.1.3:9999+mpich', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpich2', when='@develop+mpich2', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpich2', when='@2.3.1.3:9999+mpich2', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpt', when='@develop+mpt', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpt', when='@2.3.1.3:9999+mpt', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mvapich', when='@develop+mvapich', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mvapich', when='@2.3.1.3:9999+mvapich', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mvapich2', when='@develop+mvapich2', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mvapich2', when='@2.3.1.3:9999+mvapich2', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+openmpi', when='@develop+openmpi', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+openmpi', when='@2.3.1.3:9999+openmpi', type=('build', 'link', 'run'))
+
+    depends_on("cbtf-argonavis@develop", when='@develop+cuda', type=('build', 'link', 'run'))
+    depends_on("cbtf-argonavis@1.9.1.0:9999", when='@2.3.1.3:9999+cuda', type=('build', 'link', 'run'))
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop', type=('build', 'link', 'run'))
+
+    depends_on("mrnet@5.0.1-3:+cti", when='@2.3.1.3:9999+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    parallel = False
+
+    build_directory = 'build_openspeedshop'
+
+    def set_cray_login_node_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
+        # Cray login node libraries
+
+        cray_login_node_options = []
+        rt_platform = "cray"
+
+        # How do we get the compute node (CNL) cbtf package install
+        # directory path?
+        # spec['cbtf'].prefix is the login node value for this build, as
+        # we only get here when building the login node components and
+        # that is all that is known to spack.
+        be_ck = spack.store.db.query_one('cbtf-krell arch=cray-CNL-haswell')
+
+        # Equivalent to install-tool cmake arg:
+        # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+        #               % <base dir>/cbtf_v2.3.1.release/compute)
+        cray_login_node_options.append('-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+                                       % be_ck.prefix)
+        cray_login_node_options.append('-DRUNTIME_PLATFORM=%s'
+                                       % rt_platform)
+
+        cmake_options.extend(cray_login_node_options)
+
+    def cmake_args(self):
+        # Appends base options to cmake_args
+        spec = self.spec
+
+        compile_flags = "-O2 -g"
+
+        cmake_args = []
+
+        # Indicate building cbtf vers (transfer rawdata files)
+        instrumentor_setting = "cbtf"
+
+        if spec.satisfies('+runtime'):
+            self.set_defaultbase_cmake_options(spec, cmake_args)
+
+            cmake_args.extend(
+                ['-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
+                 '-DCMAKE_C_FLAGS=%s'    % compile_flags,
+                 '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                 '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                 '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                 '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
+
+        else:
+
+            # Appends base options to cmake_args
+            self.set_defaultbase_cmake_options(spec, cmake_args)
+            cmake_args.extend(
+                ['-DCMAKE_CXX_FLAGS=%s' % compile_flags,
+                 '-DCMAKE_C_FLAGS=%s' % compile_flags,
+                 '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                 '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
+                 '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                 '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                 '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
+
+            if spec.satisfies('+crayfe'):
+                # We need to build target/compute node
+                # components/libraries first then pass
+                # those libraries to the openspeedshop
+                # login node build
+                self.set_cray_login_node_cmake_options(spec, cmake_args)
+
+        cmake_args.extend(['-DBUILD_QT3_GUI=FALSE'])
+
+        return cmake_args
+
+    def set_defaultbase_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
+        # the appropriate base level options to the openspeedshop
+        # cmake build.
+        python_exe = spec['python'].command.path
+        python_library = spec['python'].libs[0]
+        python_include = spec['python'].headers.directories[0]
+
+        base_options = []
+
+        base_options.append('-DBINUTILS_DIR=%s' % spec['binutils'].prefix)
+        base_options.append('-DLIBELF_DIR=%s' % spec['elf'].prefix)
+        base_options.append('-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix)
+        base_options.append('-DPYTHON_EXECUTABLE=%s' % python_exe)
+        base_options.append('-DPYTHON_INCLUDE_DIR=%s' % python_include)
+        base_options.append('-DPYTHON_LIBRARY=%s' % python_library)
+        base_options.append('-DBoost_NO_SYSTEM_PATHS=TRUE')
+        base_options.append('-DBoost_NO_BOOST_CMAKE=TRUE')
+        base_options.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
+        base_options.append('-DBoost_DIR=%s' % spec['boost'].prefix)
+        base_options.append('-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib)
+        base_options.append('-DDYNINST_DIR=%s' % spec['dyninst'].prefix)
+
+        cmake_options.extend(base_options)
+
+    def set_mpi_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
+        # the appropriate MPI implementations
+
+        mpi_options = []
+
+        # openmpi
+        if spec.satisfies('+openmpi'):
+            mpi_options.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
+        # mpich
+        if spec.satisfies('+mpich'):
+            mpi_options.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
+        # mpich2
+        if spec.satisfies('+mpich2'):
+            mpi_options.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
+        # mvapich
+        if spec.satisfies('+mvapich'):
+            mpi_options.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
+        # mvapich2
+        if spec.satisfies('+mvapich2'):
+            mpi_options.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
+        # mpt
+        if spec.satisfies('+mpt'):
+            mpi_options.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
+
+        cmake_options.extend(mpi_options)
+
+    def setup_environment(self, spack_env, run_env):
+        """Set up the compile and runtime environments for a package."""
+
+        # Find Dyninst library path, this is needed to
+        # set the DYNINSTAPI_RT_LIB library which is
+        # required for OpenSpeedShop to find loop level
+        # performance information
+        dyninst_libdir = find_libraries('libdyninstAPI_RT',
+                                        root=self.spec['dyninst'].prefix,
+                                        shared=True, recursive=True)
+
+        # Set Dyninst RT library path to support OSS loop resolution code
+        run_env.set('DYNINSTAPI_RT_LIB', dyninst_libdir)
+
+        # Find openspeedshop library path
+        oss_libdir = find_libraries(
+            'libopenss-framework',
+            root=self.spec['openspeedshop-utils'].prefix,
+            shared=True, recursive=True)
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             os.path.dirname(oss_libdir.joined()))
+
+        run_env.set('OPENSS_RAWDATA_DIR', '.')
+
+        cbtf_mc = '/sbin/cbtf_mrnet_commnode'
+        cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend'
+        run_env.set('XPLAT_RSH', 'ssh')
+        run_env.set('MRNET_COMM_PATH',
+                    join_path(self.spec['cbtf-krell'].prefix + cbtf_mc))
+        run_env.set('CBTF_MRNET_BACKEND_PATH',
+                    join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb))
+        run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin)
+        run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin)
+        run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin)
+        run_env.prepend_path('PATH', self.spec['python'].prefix.bin)
diff --git a/var/spack/repos/builtin/packages/openspeedshop/package.py b/var/spack/repos/builtin/packages/openspeedshop/package.py
index 36e9fb06e4..0d8957f0ac 100644
--- a/var/spack/repos/builtin/packages/openspeedshop/package.py
+++ b/var/spack/repos/builtin/packages/openspeedshop/package.py
@@ -1,48 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-##############################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the Free
-# Software Foundation; either version 2 of the License, or (at your option)
-# any later version.
-#
-# 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 GNU General Public License for
-# more details.
-#
-# You should have received a copy of the GNU 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
-import os
-import os.path
+
+import spack.store
 
 
 class Openspeedshop(CMakePackage):
@@ -60,19 +23,19 @@ class Openspeedshop(CMakePackage):
     """
 
     homepage = "http://www.openspeedshop.org"
-    url = "https://github.com/OpenSpeedShop"
+    git      = "https://github.com/OpenSpeedShop/openspeedshop.git"
 
-    # Use when the git repository is available
-    version('2.3', branch='master',
-            git='https://github.com/OpenSpeedShop/openspeedshop.git')
+    version('develop', branch='master')
+    version('2.4.0', branch='2.4.0')
+    version('2.3.1.5', branch='2.3.1.5')
+    version('2.3.1.4', branch='2.3.1.4')
+    version('2.3.1.3', branch='2.3.1.3')
 
-    variant('offline', default=False,
-            description="build with offline instrumentor enabled.")
-    variant('cbtf', default=True,
-            description="build with cbtf instrumentor enabled.")
     variant('runtime', default=False,
             description="build only the runtime libraries and collectors.")
-    variant('frontend', default=False,
+    variant('cti', default=False,
+            description="Build MRNet with the CTI startup option")
+    variant('crayfe', default=False,
             description="build only the FE tool using the runtime_dir \
                          to point to target build.")
     variant('cuda', default=False,
@@ -106,238 +69,256 @@ class Openspeedshop(CMakePackage):
                          MPI when variant is enabled.")
 
     depends_on("cmake@3.0.2:", type='build')
+
     # Dependencies for openspeedshop that are common to all
     # the variants of the OpenSpeedShop build
     depends_on("libtool", type='build')
     depends_on("bison", type='build')
-    depends_on("flex", type='build')
-    depends_on("binutils", type='build')
+    depends_on("flex@2.6.1", type='build')
+
+    # For binutils
+    depends_on("binutils")
+
     depends_on("elf", type="link")
     depends_on("libdwarf")
+
     depends_on("sqlite")
-    depends_on("boost@1.50.0:1.59.0")
-    depends_on("dyninst@9.3.2")
-    depends_on("libxml2+python")
+
+    # For boost
+    depends_on("boost@1.66.0:")
+
+    depends_on("dyninst@develop", when='@develop')
+    depends_on("dyninst@10:", when='@2.3.1.3:9999')
+
+    depends_on("python", when='@develop', type=('build', 'run'))
+    depends_on("python@2.7.14:2.7.15", when='@2.3.1.3:9999', type=('build', 'run'))
+
+    depends_on("libxml2")
+
     depends_on("qt@3.3.8b+krellpatch", when='gui=qt3')
-    # Actively working on adding this gui package
-    # depends_on("cbtf-argonavis-gui", when='gui=qt4')
-
-    # Dependencies only for the openspeedshop offline package.
-    depends_on("libunwind", when='+offline')
-    depends_on("papi", when='+offline')
-    depends_on("libmonitor+krellpatch", when='+offline')
-    depends_on("openmpi", when='+offline+openmpi')
-    depends_on("mpich", when='+offline+mpich')
-    depends_on("mpich2", when='+offline+mpich2')
-    depends_on("mvapich2", when='+offline+mvapich2')
-    depends_on("mvapich", when='+offline+mvapich')
-    depends_on("mpt", when='+offline+mpt')
-
-    # Dependencies only for the openspeedshop cbtf package.
-    depends_on("cbtf", when='+cbtf')
-    depends_on('cbtf-krell', when='+cbtf')
-    depends_on('cbtf-krell+mpich', when='+cbtf+mpich')
-    depends_on('cbtf-krell+mpich2', when='+cbtf+mpich2')
-    depends_on('cbtf-krell+mpt', when='+cbtf+mpt')
-    depends_on('cbtf-krell+mvapich', when='+cbtf+mvapich')
-    depends_on('cbtf-krell+mvapich2', when='+cbtf+mvapich2')
-    depends_on('cbtf-krell+openmpi', when='+cbtf+openmpi')
-    depends_on("cbtf-argonavis", when='+cbtf+cuda')
-    depends_on("mrnet@5.0.1:+lwthreads", when='+cbtf')
+
+    # Dependencies for the openspeedshop cbtf packages.
+    depends_on("cbtf@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf@1.9.1.0:9999", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    depends_on("cbtf-krell@develop", when='@develop', type=('build', 'link', 'run'))
+    depends_on("cbtf-krell@1.9.1.0:9999", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+crayfe', when='@develop+crayfe', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+crayfe', when='@2.3.1.3:9999+crayfe', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+cti', when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+cti', when='@2.3.1.3:9999+cti', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpich', when='@develop+mpich', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpich', when='@2.3.1.3:9999+mpich', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpich2', when='@develop+mpich2', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpich2', when='@2.3.1.3:9999+mpich2', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mpt', when='@develop+mpt', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mpt', when='@2.3.1.3:9999+mpt', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mvapich', when='@develop+mvapich', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mvapich', when='@2.3.1.3:9999+mvapich', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+mvapich2', when='@develop+mvapich2', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+mvapich2', when='@2.3.1.3:9999+mvapich2', type=('build', 'link', 'run'))
+
+    depends_on('cbtf-krell@develop+openmpi', when='@develop+openmpi', type=('build', 'link', 'run'))
+    depends_on('cbtf-krell@1.9.1.0:9999+openmpi', when='@2.3.1.3:9999+openmpi', type=('build', 'link', 'run'))
+
+    depends_on("cbtf-argonavis@develop", when='@develop+cuda', type=('build', 'link', 'run'))
+    depends_on("cbtf-argonavis@1.9.1.0:9999", when='@2.3.1.3:9999+cuda', type=('build', 'link', 'run'))
+
+    # For MRNet
+    depends_on("mrnet@5.0.1-3:+cti", when='@develop+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@develop', type=('build', 'link', 'run'))
+
+    depends_on("mrnet@5.0.1-3:+cti", when='@2.3.1.3:9999+cti', type=('build', 'link', 'run'))
+    depends_on("mrnet@5.0.1-3:+lwthreads", when='@2.3.1.3:9999', type=('build', 'link', 'run'))
 
     parallel = False
 
     build_directory = 'build_openspeedshop'
 
-    def cmake_args(self):
-        spec = self.spec
-        compile_flags = "-O2 -g"
+    def set_cray_login_node_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable the appropriate
+        # Cray login node libraries
 
-        if '+offline' in spec:
-            # Indicate building offline vers (writes rawdata files)
-            instrumentor_setting = "offline"
-            if '+runtime' in spec:
-                cmake_args = [
-                    '-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
-                    '-DCMAKE_C_FLAGS=%s'    % compile_flags,
-                    '-DINSTRUMENTOR=%s'     % instrumentor_setting,
-                    '-DLIBMONITOR_DIR=%s'   % spec['libmonitor'].prefix,
-                    '-DLIBUNWIND_DIR=%s'    % spec['libunwind'].prefix,
-                    '-DPAPI_DIR=%s'         % spec['papi'].prefix]
+        cray_login_node_options = []
+        rt_platform = "cray"
 
-                # Add any MPI implementations coming from variant settings
-                self.set_mpi_cmakeOptions(spec, cmake_args)
+        # How do we get the compute node (CNL) cbtf package install
+        # directory path?
+        # spec['cbtf'].prefix is the login node value for this build, as
+        # we only get here when building the login node components and
+        # that is all that is known to spack.
+        store = spack.store
+        be_ck = store.db.query_one('cbtf-krell arch=cray-CNL-haswell')
 
-            else:
-                cmake_args = []
+        # Equivalent to install-tool cmake arg:
+        # '-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+        #               % <base dir>/cbtf_v2.3.1.release/compute)
+        cray_login_node_options.append('-DCBTF_KRELL_CN_RUNTIME_DIR=%s'
+                                       % be_ck.prefix)
+        cray_login_node_options.append('-DRUNTIME_PLATFORM=%s'
+                                       % rt_platform)
 
-                # Appends base options to cmake_args
-                self.set_defaultbase_cmakeOptions(spec, cmake_args)
+        cmake_options.extend(cray_login_node_options)
 
-                cmake_args.extend(
-                    ['-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
-                     '-DCMAKE_C_FLAGS=%s'    % compile_flags,
-                     '-DINSTRUMENTOR=%s' % instrumentor_setting,
-                     '-DLIBMONITOR_DIR=%s' % spec['libmonitor'].prefix,
-                     '-DLIBUNWIND_DIR=%s' % spec['libunwind'].prefix,
-                     '-DPAPI_DIR=%s' % spec['papi'].prefix,
-                     '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
-                     '-DQTLIB_DIR=%s' % spec['qt'].prefix])
-
-                # Add any MPI implementations coming from variant settings
-                self.set_mpi_cmakeOptions(spec, cmake_args)
-
-        elif '+cbtf' in spec:
-            # Indicate building cbtf vers (transfer rawdata files)
-            instrumentor_setting = "cbtf"
-
-            if '+runtime' in spec:
-                # Appends base options to cmake_args
-                self.set_defaultbase_cmakeOptions(spec, cmake_args)
+    def cmake_args(self):
+
+        spec = self.spec
 
+        compile_flags = "-O2 -g"
+
+        cmake_args = []
+
+        # Indicate building cbtf vers (transfer rawdata files)
+        instrumentor_setting = "cbtf"
+
+        if spec.satisfies('+runtime'):
+            # Appends base options to cmake_args
+            self.set_defaultbase_cmake_options(spec, cmake_args)
+            cmake_args.extend(
+                ['-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
+                 '-DCMAKE_C_FLAGS=%s'    % compile_flags,
+                 '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                 '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                 '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                 '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
+
+        else:
+
+            # Appends base options to cmake_args
+            self.set_defaultbase_cmake_options(spec, cmake_args)
+            guitype = self.spec.variants['gui'].value
+            cmake_args.extend(
+                ['-DCMAKE_CXX_FLAGS=%s' % compile_flags,
+                 '-DCMAKE_C_FLAGS=%s' % compile_flags,
+                 '-DINSTRUMENTOR=%s' % instrumentor_setting,
+                 '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
+                 '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
+                 '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
+                 '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
+
+            if guitype == 'none':
+                cmake_args.extend(
+                    ['-DBUILD_QT3_GUI=FALSE'])
+            elif guitype == 'qt4':
                 cmake_args.extend(
-                    ['-DCMAKE_CXX_FLAGS=%s'  % compile_flags,
-                     '-DCMAKE_C_FLAGS=%s'    % compile_flags,
-                     '-DINSTRUMENTOR=%s' % instrumentor_setting,
-                     '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
-                     '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
-                     '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
-
-            else:
-                cmake_args = []
-
-                # Appends base options to cmake_args
-                self.set_defaultbase_cmakeOptions(spec, cmake_args)
-                guitype = self.spec.variants['gui'].value
+                    ['-DBUILD_QT3_GUI=FALSE'])
+            elif guitype == 'qt3':
                 cmake_args.extend(
-                    ['-DCMAKE_CXX_FLAGS=%s' % compile_flags,
-                     '-DCMAKE_C_FLAGS=%s' % compile_flags,
-                     '-DINSTRUMENTOR=%s' % instrumentor_setting,
-                     '-DSQLITE3_DIR=%s' % spec['sqlite'].prefix,
-                     '-DCBTF_DIR=%s' % spec['cbtf'].prefix,
-                     '-DCBTF_KRELL_DIR=%s' % spec['cbtf-krell'].prefix,
-                     '-DMRNET_DIR=%s' % spec['mrnet'].prefix])
-
-                if guitype == 'none':
-                    cmake_args.extend(
-                        ['-DBUILD_QT3_GUI=FALSE'])
-                elif guitype == 'qt4':
-                    cmake_args.extend(
-                        ['-DBUILD_QT3_GUI=FALSE'])
-                elif guitype == 'qt3':
-                    cmake_args.extend(
-                        ['-DQTLIB_DIR=%s'
-                            % spec['qt'].prefix])
+                    ['-DQTLIB_DIR=%s'
+                        % spec['qt'].prefix])
+
+            if spec.satisfies('+crayfe'):
+                # We need to build target/compute node
+                # components/libraries first then pass
+                # those libraries to the openspeedshop
+                # login node build
+                self.set_cray_login_node_cmake_options(spec, cmake_args)
 
         return cmake_args
 
-    def set_defaultbase_cmakeOptions(self, spec, cmakeOptions):
-        # Appends to cmakeOptions the options that will enable
+    def set_defaultbase_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
         # the appropriate base level options to the openspeedshop
         # cmake build.
         python_exe = spec['python'].command.path
         python_library = spec['python'].libs[0]
         python_include = spec['python'].headers.directories[0]
 
-        BaseOptions = []
-
-        BaseOptions.append('-DBINUTILS_DIR=%s' % spec['binutils'].prefix)
-        BaseOptions.append('-DLIBELF_DIR=%s' % spec['elf'].prefix)
-        BaseOptions.append('-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix)
-        BaseOptions.append('-DPYTHON_EXECUTABLE=%s' % python_exe)
-        BaseOptions.append('-DPYTHON_INCLUDE_DIR=%s' % python_include)
-        BaseOptions.append('-DPYTHON_LIBRARY=%s' % python_library)
-        BaseOptions.append('-DBoost_NO_SYSTEM_PATHS=TRUE')
-        BaseOptions.append('-DBoost_NO_BOOST_CMAKE=TRUE')
-        BaseOptions.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
-        BaseOptions.append('-DBoost_DIR=%s' % spec['boost'].prefix)
-        BaseOptions.append('-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib)
-        BaseOptions.append('-DDYNINST_DIR=%s' % spec['dyninst'].prefix)
-
-        cmakeOptions.extend(BaseOptions)
-
-    def set_mpi_cmakeOptions(self, spec, cmakeOptions):
-        # Appends to cmakeOptions the options that will enable
+        base_options = []
+
+        base_options.append('-DBINUTILS_DIR=%s' % spec['binutils'].prefix)
+        base_options.append('-DLIBELF_DIR=%s' % spec['elf'].prefix)
+        base_options.append('-DLIBDWARF_DIR=%s' % spec['libdwarf'].prefix)
+        base_options.append('-DPYTHON_EXECUTABLE=%s' % python_exe)
+        base_options.append('-DPYTHON_INCLUDE_DIR=%s' % python_include)
+        base_options.append('-DPYTHON_LIBRARY=%s' % python_library)
+        base_options.append('-DBoost_NO_SYSTEM_PATHS=TRUE')
+        base_options.append('-DBoost_NO_BOOST_CMAKE=TRUE')
+        base_options.append('-DBOOST_ROOT=%s' % spec['boost'].prefix)
+        base_options.append('-DBoost_DIR=%s' % spec['boost'].prefix)
+        base_options.append('-DBOOST_LIBRARYDIR=%s' % spec['boost'].prefix.lib)
+        base_options.append('-DDYNINST_DIR=%s' % spec['dyninst'].prefix)
+
+        cmake_options.extend(base_options)
+
+    def set_mpi_cmake_options(self, spec, cmake_options):
+        # Appends to cmake_options the options that will enable
         # the appropriate MPI implementations
 
-        MPIOptions = []
+        mpi_options = []
 
         # openmpi
-        if '+openmpi' in spec:
-            MPIOptions.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
+        if spec.satisfies('+openmpi'):
+            mpi_options.append('-DOPENMPI_DIR=%s' % spec['openmpi'].prefix)
         # mpich
-        if '+mpich' in spec:
-            MPIOptions.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
+        if spec.satisfies('+mpich'):
+            mpi_options.append('-DMPICH_DIR=%s' % spec['mpich'].prefix)
         # mpich2
-        if '+mpich2' in spec:
-            MPIOptions.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
+        if spec.satisfies('+mpich2'):
+            mpi_options.append('-DMPICH2_DIR=%s' % spec['mpich2'].prefix)
         # mvapich
-        if '+mvapich' in spec:
-            MPIOptions.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
+        if spec.satisfies('+mvapich'):
+            mpi_options.append('-DMVAPICH_DIR=%s' % spec['mvapich'].prefix)
         # mvapich2
-        if '+mvapich2' in spec:
-            MPIOptions.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
+        if spec.satisfies('+mvapich2'):
+            mpi_options.append('-DMVAPICH2_DIR=%s' % spec['mvapich2'].prefix)
         # mpt
-        if '+mpt' in spec:
-            MPIOptions.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
+        if spec.satisfies('+mpt'):
+            mpi_options.append('-DMPT_DIR=%s' % spec['mpt'].prefix)
 
-        cmakeOptions.extend(MPIOptions)
+        cmake_options.extend(mpi_options)
 
     def setup_environment(self, spack_env, run_env):
         """Set up the compile and runtime environments for a package."""
 
-        # Common settings to both offline and cbtf versions
-        # of OpenSpeedShop
-        run_env.prepend_path('PATH', self.prefix.bin)
-
         # Find Dyninst library path, this is needed to
         # set the DYNINSTAPI_RT_LIB library which is
         # required for OpenSpeedShop to find loop level
         # performance information
         dyninst_libdir = find_libraries('libdyninstAPI_RT',
                                         root=self.spec['dyninst'].prefix,
-                                        shared=True, recurse=True)
+                                        shared=True, recursive=True)
 
         # Set Dyninst RT library path to support OSS loop resolution code
         run_env.set('DYNINSTAPI_RT_LIB', dyninst_libdir)
 
-        # Find openspeedshop library path
-        oss_libdir = find_libraries('libopenss-framework',
-                                    root=self.spec['openspeedshop'].prefix,
-                                    shared=True, recurse=True)
-        run_env.prepend_path('LD_LIBRARY_PATH',
-                             os.path.dirname(oss_libdir.joined()))
-
-        # Settings specific to the version, checking here
-        # for the cbtf instrumentor
-        if '+cbtf' in self.spec:
-            cbtf_mc = '/sbin/cbtf_mrnet_commnode'
-            cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend'
-            run_env.set('XPLAT_RSH', 'ssh')
-            run_env.set('MRNET_COMM_PATH',
-                        join_path(self.spec['cbtf-krell'].prefix + cbtf_mc))
-
-            run_env.set('CBTF_MRNET_BACKEND_PATH',
-                        join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb))
-
-            run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin)
-            run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin)
-            run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin)
-
-        elif '+offline' in self.spec:
-            # Had to use this form of syntax self.prefix.lib and
-            # self.prefix.lib64 returned None all the time
-            run_env.set('OPENSS_RAWDATA_DIR', '.')
-            run_env.set('OPENSS_PLUGIN_PATH',
-                        join_path(oss_libdir + '/openspeedshop'))
-            run_env.prepend_path('PATH', self.spec['papi'].prefix.bin)
-            run_env.prepend_path('PATH', self.spec['libdwarf'].prefix.bin)
-
-            if '+mpich' in self.spec:
-                run_env.set('OPENSS_MPI_IMPLEMENTATION', 'mpich')
-            if '+mpich2' in self.spec:
-                run_env.set('OPENSS_MPI_IMPLEMENTATION', 'mpich2')
-            if '+mvapich2' in self.spec:
-                run_env.set('OPENSS_MPI_IMPLEMENTATION', 'mvapich2')
-            if '+openmpi' in self.spec:
-                run_env.set('OPENSS_MPI_IMPLEMENTATION', 'openmpi')
+        run_env.set('OPENSS_RAWDATA_DIR', '.')
+        cbtf_mc = '/sbin/cbtf_mrnet_commnode'
+        cbtf_lmb = '/sbin/cbtf_libcbtf_mrnet_backend'
+        run_env.set('XPLAT_RSH', 'ssh')
+        run_env.set('MRNET_COMM_PATH',
+                    join_path(self.spec['cbtf-krell'].prefix + cbtf_mc))
+
+        # Set CBTF_MPI_IMPLEMENTATON to the appropriate mpi implementation
+        # This is needed by O|SS and CBTF tools to deploy the correct
+        # mpi runtimes for ossmpi, ossmpit, ossmpip, and cbtfsummary
+        # Users may have to set the CBTF_MPI_IMPLEMENTATION variable
+        # manually if multiple mpi's are specified in the build
+        if self.spec.satisfies('+mpich'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mpich")
+
+        if self.spec.satisfies('+mvapich'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich")
+
+        if self.spec.satisfies('+mvapich2'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mvapich2")
+
+        if self.spec.satisfies('+mpt'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "mpt")
+
+        if self.spec.satisfies('+openmpi'):
+            run_env.set('CBTF_MPI_IMPLEMENTATION', "openmpi")
+
+        run_env.set('CBTF_MRNET_BACKEND_PATH',
+                    join_path(self.spec['cbtf-krell'].prefix + cbtf_lmb))
+        run_env.prepend_path('PATH', self.spec['mrnet'].prefix.bin)
+        run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.bin)
+        run_env.prepend_path('PATH', self.spec['cbtf-krell'].prefix.sbin)
+        run_env.prepend_path('PATH', self.spec['python'].prefix.bin)
diff --git a/var/spack/repos/builtin/packages/openssh/package.py b/var/spack/repos/builtin/packages/openssh/package.py
index aab102efbd..45540989b7 100644
--- a/var/spack/repos/builtin/packages/openssh/package.py
+++ b/var/spack/repos/builtin/packages/openssh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,8 +16,9 @@ class Openssh(AutotoolsPackage):
     """
 
     homepage = "https://www.openssh.com/"
-    url      = "https://mirrors.sonic.net/pub/OpenBSD/OpenSSH/portable/openssh-7.5p1.tar.gz"
+    url      = "https://mirrors.sonic.net/pub/OpenBSD/OpenSSH/portable/openssh-7.6p1.tar.gz"
 
+    version('7.6p1',   '06a88699018e5fef13d4655abfed1f63')
     version('7.5p1',   '652fdc7d8392f112bef11cacf7e69e23')
     version('7.4p1',   'b2db2a83caf66a208bb78d6d287cdaa3')
     version('7.3p1',   'dfadd9f035d38ce5d58a3bf130b86d08')
diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py
index 72f35ac4d5..41f73d3d53 100644
--- a/var/spack/repos/builtin/packages/openssl/package.py
+++ b/var/spack/repos/builtin/packages/openssl/package.py
@@ -1,32 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import llnl.util.tty as tty
 
 from spack import *
 import spack.architecture
 
+import os
+
 
 class Openssl(Package):
     """OpenSSL is an open source project that provides a robust,
@@ -36,16 +19,20 @@ class Openssl(Package):
     homepage = "http://www.openssl.org"
 
     # URL must remain http:// so Spack can bootstrap curl
-    url = "http://www.openssl.org/source/openssl-1.0.1h.tar.gz"
+    url = "http://www.openssl.org/source/openssl-1.0.2m.tar.gz"
     list_url = "https://www.openssl.org/source/old/"
     list_depth = 1
 
+    version('1.1.0g', 'ba5f1b8b835b88cadbce9b35ed9531a6')
     version('1.1.0e', '51c42d152122e474754aea96f66928c6')
     version('1.1.0d', '711ce3cd5f53a99c0e12a7d5804f0f63')
     version('1.1.0c', '601e8191f72b18192a937ecf1a800f3f')
     # Note: Version 1.0.2 is the "long-term support" version that will
     # remain supported until 2019.
-    version('1.0.2k', 'f965fc0bf01bf882b31314b61391ae65', preferred=True)
+    version('1.0.2o', '44279b8557c3247cbe324e2322ecd114', preferred=True)
+    version('1.0.2n', '13bdc1b1d1ff39b6fd42a255e74676a4')
+    version('1.0.2m', '10e9e37f492094b9ef296f68f24a7666')
+    version('1.0.2k', 'f965fc0bf01bf882b31314b61391ae65')
     version('1.0.2j', '96322138f0b69e61b7212bc53d5e912b')
     version('1.0.2i', '678374e63f8df456a697d3e5e5a931fb')
     version('1.0.2h', '9392e65072ce4b614c1392eefc1f23d0')
@@ -58,15 +45,18 @@ class Openssl(Package):
     version('1.0.1r', '1abd905e079542ccae948af37e393d28')
     version('1.0.1h', '8d6d684a9430d5cc98a62a5d8fbda8cf')
 
+    variant('systemcerts', default=True, description='Use system certificates')
+
     depends_on('zlib')
 
-    # TODO: 'make test' requires Perl module Test::More version 0.96
-    # TODO: uncomment when test dependency types are supported.
-    # TODO: This is commented in the meantime to avoid dependnecy bloat.
-    # depends_on('perl@5.14.0:', type='build', when='+tests')
+    depends_on('perl@5.14.0:', type=('build', 'test'))
 
     parallel = False
 
+    @property
+    def libs(self):
+        return find_libraries(['libssl', 'libcrypto'], root=self.prefix.lib)
+
     def handle_fetch_error(self, error):
         tty.warn("Fetching OpenSSL failed. This may indicate that OpenSSL has "
                  "been updated, and the version in your instance of Spack is "
@@ -104,7 +94,37 @@ class Openssl(Package):
         filter_file(r'-arch x86_64', '', 'Makefile')
 
         make()
-        # TODO: add this back when we have a 'test' dependency type. See above.
-        # if self.run_tests:
-        #     make('test')            # 'VERBOSE=1'
+        if self.run_tests:
+            make('test')            # 'VERBOSE=1'
         make('install')
+
+    @run_after('install')
+    def link_system_certs(self):
+        if '+systemcerts' not in self.spec:
+            return
+
+        system_dirs = [
+            # CentOS, Fedora, RHEL
+            '/etc/pki/tls',
+            # Ubuntu
+            '/usr/lib/ssl'
+        ]
+
+        pkg_dir = join_path(self.prefix, 'etc', 'openssl')
+
+        for directory in system_dirs:
+            sys_cert = join_path(directory, 'cert.pem')
+            pkg_cert = join_path(pkg_dir, 'cert.pem')
+            # If a bundle exists, use it. This is the preferred way on Fedora,
+            # where the certs directory does not work.
+            if os.path.exists(sys_cert) and not os.path.exists(pkg_cert):
+                os.symlink(sys_cert, pkg_cert)
+
+            sys_certs = join_path(directory, 'certs')
+            pkg_certs = join_path(pkg_dir, 'certs')
+            # If the certs directory exists, symlink it into the package.
+            # We symlink the whole directory instead of all files because
+            # the directory contents might change without Spack noticing.
+            if os.path.isdir(sys_certs) and not os.path.islink(pkg_certs):
+                os.rmdir(pkg_certs)
+                os.symlink(sys_certs, pkg_certs)
diff --git a/var/spack/repos/builtin/packages/opium/package.py b/var/spack/repos/builtin/packages/opium/package.py
index 5ce1d8b332..c0f907c80a 100644
--- a/var/spack/repos/builtin/packages/opium/package.py
+++ b/var/spack/repos/builtin/packages/opium/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/optional-lite/package.py b/var/spack/repos/builtin/packages/optional-lite/package.py
new file mode 100644
index 0000000000..bddb490354
--- /dev/null
+++ b/var/spack/repos/builtin/packages/optional-lite/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from shutil import copytree
+
+
+class OptionalLite(Package):
+    """
+    A single-file header-only version of a C++17-like optional, a nullable
+    object for C++98, C++11 and later.
+    """
+
+    homepage = "https://github.com/martinmoene/optional-lite"
+    url      = "https://github.com/martinmoene/optional-lite/archive/v3.0.0.tar.gz"
+
+    version('3.0.0', sha256='36ae58512c478610647978811f0f4dbe105880372bd7ed39417314d50a27254e')
+    version('2.3.0', sha256='8fe46216147234b172c6a5b182726834afc44dfdca1e976a264d6f96eb183916')
+    version('2.2.0', sha256='9ce1bb021de42f804f8d17ed30b79fc98296122bec8db60492104978cd282fa2')
+    version('2.0.0', sha256='e8d803cbc7be241df41a9ab267b525b7941df09747cd5a7deb55f863bd8a4e8d')
+    version('1.0.3', sha256='7a2fb0fe20d61d091f6730237add9bab58bc0df1288cb96f3e8a61b859539067')
+
+    def install(self, spec, prefix):
+        copytree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/opus/package.py b/var/spack/repos/builtin/packages/opus/package.py
index 03d434926d..0300847923 100644
--- a/var/spack/repos/builtin/packages/opus/package.py
+++ b/var/spack/repos/builtin/packages/opus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/orca/package.py b/var/spack/repos/builtin/packages/orca/package.py
new file mode 100644
index 0000000000..c137589e42
--- /dev/null
+++ b/var/spack/repos/builtin/packages/orca/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Orca(Package):
+    """An ab initio, DFT and semiempirical SCF-MO package
+
+       Note: Orca is licensed software. You will need to create an account
+       on the Orca homepage and download Orca yourself. Spack will search
+       your current directory for the download file. Alternatively, add this
+       file to a mirror so that Spack can find it. For instructions on how to
+       set up a mirror, see http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://cec.mpg.de"
+    url      = "file://{0}/orca_4_0_1_2_linux_x86-64_openmpi202.tar.zst".format(os.getcwd())
+
+    version('4.0.1.2', sha256='cea442aa99ec0d7ffde65014932196b62343f7a6191b4bfc438bfb38c03942f7',
+            expand=False)
+
+    depends_on('zstd', type='build')
+    depends_on('openmpi@2.0.0:2.1.5', type='run')
+
+    def url_for_version(self, version):
+        out = "file://{0}/orca_{1}_linux_x86-64_openmpi202.tar.zst"
+        return out.format(os.getcwd(), version.underscored)
+
+    def install(self, spec, prefix):
+        # we have to extract the archive ourself
+        # fortunately it's just full of a bunch of binaries
+
+        vername = os.path.basename(self.stage.archive_file).split('.')[0]
+
+        zstd = which('zstd')
+        zstd('-d', self.stage.archive_file, '-o', vername + '.tar')
+
+        tar = which('tar')
+        tar('-xvf', vername + '.tar')
+
+        # there are READMEs in there but they don't hurt anyone
+        mkdirp(prefix.bin)
+        install_tree(vername, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/orfm/package.py b/var/spack/repos/builtin/packages/orfm/package.py
index 4b59bca7b6..092a0cb319 100644
--- a/var/spack/repos/builtin/packages/orfm/package.py
+++ b/var/spack/repos/builtin/packages/orfm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,3 +16,5 @@ class Orfm(AutotoolsPackage):
     url      = "https://github.com/wwood/OrfM/releases/download/v0.7.1/orfm-0.7.1.tar.gz"
 
     version('0.7.1', 'fcf18283a028cea2af90663a76a73a2a')
+
+    depends_on('zlib', type='link')
diff --git a/var/spack/repos/builtin/packages/orthofinder/package.py b/var/spack/repos/builtin/packages/orthofinder/package.py
new file mode 100644
index 0000000000..f89eddf6c8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/orthofinder/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Orthofinder(Package):
+    """OrthoFinder is a fast, accurate and comprehensive analysis tool for
+    comparative genomics.
+
+    It finds orthologues and orthogroups infers rooted  gene trees for all
+    orthogroups and infers a rooted species tree for the species being
+    analysed. OrthoFinder also provides comprehensive statistics for
+    comparative genomic analyses. OrthoFinder is simple to use and all you
+    need to run it is a set of protein sequence files (one per species)
+    in FASTA format."""
+
+    homepage = "https://github.com/davidemms/OrthoFinder"
+    url      = "https://github.com/davidemms/OrthoFinder/releases/download/2.2.0/OrthoFinder-2.2.0.tar.gz"
+
+    version('2.2.0', '4ff585e1eb148fc694a219296fbdd431')
+
+    depends_on('blast-plus', type='run')
+    depends_on('mcl', type='run')
+    depends_on('fastme', type='run')
+    depends_on('py-dlcpar', type='run')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(prefix.bin, 'orthofinder'))
diff --git a/var/spack/repos/builtin/packages/orthomcl/package.py b/var/spack/repos/builtin/packages/orthomcl/package.py
index 98bef74726..41badd0f3b 100644
--- a/var/spack/repos/builtin/packages/orthomcl/package.py
+++ b/var/spack/repos/builtin/packages/orthomcl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
index 8e5c7be65a..0797824c3b 100644
--- a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
+++ b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -36,6 +17,7 @@ class OsuMicroBenchmarks(AutotoolsPackage):
     homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/"
     url      = "http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.3.tar.gz"
 
+    version('5.4', '7e7551879b944d71b7cc60d476d5403b')
     version('5.3', '42e22b931d451e8bec31a7424e4adfc2')
 
     variant('cuda', default=False, description="Enable CUDA support")
diff --git a/var/spack/repos/builtin/packages/otf/package.py b/var/spack/repos/builtin/packages/otf/package.py
index 4df0a12bdf..ee94aa20c4 100644
--- a/var/spack/repos/builtin/packages/otf/package.py
+++ b/var/spack/repos/builtin/packages/otf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/otf2/package.py b/var/spack/repos/builtin/packages/otf2/package.py
index ee08a44328..5999a816fa 100644
--- a/var/spack/repos/builtin/packages/otf2/package.py
+++ b/var/spack/repos/builtin/packages/otf2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,6 +15,7 @@ class Otf2(AutotoolsPackage):
     homepage = "http://www.vi-hps.org/projects/score-p"
     url      = "http://www.vi-hps.org/upload/packages/otf2/otf2-1.4.tar.gz"
 
+    version('2.1.1', 'e51ad0d8ca374d25f47426746ca629e7')
     version('2.1',   'e2994e53d9b7c2cbd0c4f564d638751e')
     version('2.0',   '5b546188b25bc1c4e285e06dddf75dfc')
     version('1.5.1', '16a9df46e0da78e374f5d12c8cdc1109')
diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py
index 56c1ffbc93..ea26ee54f9 100644
--- a/var/spack/repos/builtin/packages/p4est/package.py
+++ b/var/spack/repos/builtin/packages/p4est/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,8 @@ class P4est(AutotoolsPackage):
     version('2.0', 'c522c5b69896aab39aa5a81399372a19a6b03fc6200d2d5d677d9a22fe31029a')
     version('1.1', '37ba7f4410958cfb38a2140339dbf64f')
 
+    variant('openmp', default=False, description='Enable OpenMP')
+
     # build dependencies
     depends_on('automake', type='build')
     depends_on('autoconf', type='build')
@@ -45,8 +28,20 @@ class P4est(AutotoolsPackage):
     depends_on('mpi')
     depends_on('zlib')
 
+    # from sc upstream, correct the default libraries
+    patch('https://github.com/cburstedde/libsc/commit/b506aab224b988fec210cc212469f2c4f58b2d04.patch',
+          sha256='e9418b1a9347a409be241cd185519b31950e42a7f55b6fb80ce53097657098ee',
+          working_dir='sc')
+    patch('https://github.com/cburstedde/libsc/commit/b45a51a7ef97883a3d4dcbd05cb2c77890a76f75.patch',
+          sha256='8fb829e34e3a1e28afdd6e56e0bdc1d377af569b7ccb9e9d8da0eeb5829ed27e',
+          working_dir='sc')
+
+    def autoreconf(self, spec, prefix):
+        bootstrap = Executable('./bootstrap')
+        bootstrap()
+
     def configure_args(self):
-        return [
+        args = [
             '--enable-mpi',
             '--enable-shared',
             '--disable-vtk-binary',
@@ -58,3 +53,14 @@ class P4est(AutotoolsPackage):
             'FC=%s'  % self.spec['mpi'].mpifc,
             'F77=%s' % self.spec['mpi'].mpif77
         ]
+
+        if '+openmp' in self.spec:
+            try:
+                args.append(
+                    '--enable-openmp={0}'.format(self.compiler.openmp_flag))
+            except UnsupportedCompilerFlag:
+                args.append('--enable-openmp')
+        else:
+            args.append('--disable-openmp')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/p7zip/package.py b/var/spack/repos/builtin/packages/p7zip/package.py
index 90b7479d80..72665ddc4b 100644
--- a/var/spack/repos/builtin/packages/p7zip/package.py
+++ b/var/spack/repos/builtin/packages/p7zip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pacbio-daligner/package.py b/var/spack/repos/builtin/packages/pacbio-daligner/package.py
index e568c7170e..9703eedc93 100644
--- a/var/spack/repos/builtin/packages/pacbio-daligner/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-daligner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,9 @@ class PacbioDaligner(MakefilePackage):
        required for some pacbio utilities."""
 
     homepage = "https://github.com/PacificBiosciences/DALIGNER"
-    url      = "https://github.com/PacificBiosciences/DALIGNER"
+    git      = "https://github.com/PacificBiosciences/DALIGNER.git"
 
-    version('2017-08-05',
-            git='https://github.com/PacificBiosciences/DALIGNER.git',
-            commit='0fe5240d2cc6b55bf9e04465b700b76110749c9d')
+    version('2017-08-05', commit='0fe5240d2cc6b55bf9e04465b700b76110749c9d')
 
     depends_on('gmake', type='build')
     depends_on('pacbio-dazz-db')
diff --git a/var/spack/repos/builtin/packages/pacbio-damasker/package.py b/var/spack/repos/builtin/packages/pacbio-damasker/package.py
index cc32df052b..92ed8fad12 100644
--- a/var/spack/repos/builtin/packages/pacbio-damasker/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-damasker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,9 @@ class PacbioDamasker(MakefilePackage):
        required for some pacbio utilities."""
 
     homepage = "https://github.com/PacificBiosciences/DAMASKER"
-    url      = "https://github.com/PacificBiosciences/DAMASKER"
+    git      = "https://github.com/PacificBiosciences/DAMASKER.git"
 
-    version('2017-02-11',
-            git='https://github.com/PacificBiosciences/DAMASKER.git',
-            commit='144244b77d52cb785cb1b3b8ae3ab6f3f0c63264')
+    version('2017-02-11', commit='144244b77d52cb785cb1b3b8ae3ab6f3f0c63264')
 
     depends_on('gmake', type='build')
 
diff --git a/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
index 595ab4cd15..8d79eb9e3c 100644
--- a/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-dazz-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,11 +12,9 @@ class PacbioDazzDb(MakefilePackage):
        required for some pacbio utilities."""
 
     homepage = "https://github.com/PacificBiosciences/DAZZ_DB"
-    url      = "https://github.com/PacificBiosciences/DAZZ_DB"
+    git      = "https://github.com/PacificBiosciences/DAZZ_DB.git"
 
-    version('2017-04-10',
-            git='https://github.com/PacificBiosciences/DAZZ_DB.git',
-            commit='f29d27d51f460563481cd227d17f4bdc5e288365')
+    version('2017-04-10', commit='f29d27d51f460563481cd227d17f4bdc5e288365')
 
     depends_on('gmake', type='build')
 
diff --git a/var/spack/repos/builtin/packages/pacbio-dextractor/package.py b/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
index 75bc553733..43630ecc5e 100644
--- a/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
+++ b/var/spack/repos/builtin/packages/pacbio-dextractor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,9 @@ class PacbioDextractor(MakefilePackage):
        fork required by some pacbio utilities."""
 
     homepage = "https://github.com/PacificBiosciences/DEXTRACTOR"
-    url      = "https://github.com/PacificBiosciences/DEXTRACTOR"
+    git      = "https://github.com/PacificBiosciences/DEXTRACTOR.git"
 
-    version('2016-08-09',
-            git='https://github.com/PacificBiosciences/DEXTRACTOR.git',
-            commit='89726800346d0bed15d98dcc577f4c7733aab4b1')
+    version('2016-08-09', commit='89726800346d0bed15d98dcc577f4c7733aab4b1')
 
     depends_on('hdf5')
     depends_on('gmake', type='build')
diff --git a/var/spack/repos/builtin/packages/packmol/package.py b/var/spack/repos/builtin/packages/packmol/package.py
new file mode 100644
index 0000000000..873e354f13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/packmol/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Packmol(CMakePackage):
+    """Packmol creates an initial point for molecular dynamics simulations
+    by packing molecules in defined regions of space."""
+
+    homepage = "http://m3g.iqm.unicamp.br/packmol/home.shtml"
+    url      = "https://github.com/mcubeg/packmol/archive/18.169.tar.gz"
+
+    version('18.169', sha256='8acf2cbc742a609e763eb00cae55aecd09af2edb4cc4e931706e2f06ac380de9')
diff --git a/var/spack/repos/builtin/packages/pacvim/package.py b/var/spack/repos/builtin/packages/pacvim/package.py
new file mode 100644
index 0000000000..1a2fa45637
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pacvim/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pacvim(MakefilePackage):
+    """Pacvim is a command-line-based game based off of Pacman.
+       The main purpose of this software is to familiarize individuals
+       with Vim."""
+
+    homepage = "https://github.com/jmoon018/PacVim"
+    url      = "https://github.com/jmoon018/PacVim/archive/v1.1.1.tar.gz"
+
+    version('1.1.1', sha256='c869c5450fbafdfe8ba8a8a9bba3718775926f276f0552052dcfa090d21acb28')
+
+    depends_on('ncurses')
+
+    def edit(self, stage, prefix):
+        makefile = FileFilter('Makefile')
+
+        makefile.filter(r'PREFIX = /usr/local',
+                        'PREFIX={0}'.format(self.prefix))
diff --git a/var/spack/repos/builtin/packages/pagit/package.py b/var/spack/repos/builtin/packages/pagit/package.py
index 7c40da934b..b45154befd 100644
--- a/var/spack/repos/builtin/packages/pagit/package.py
+++ b/var/spack/repos/builtin/packages/pagit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pagmo/package.py b/var/spack/repos/builtin/packages/pagmo/package.py
index 0d30d847f0..4367500442 100644
--- a/var/spack/repos/builtin/packages/pagmo/package.py
+++ b/var/spack/repos/builtin/packages/pagmo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/paml/package.py b/var/spack/repos/builtin/packages/paml/package.py
index 81d9e7c25b..9805e6bccd 100644
--- a/var/spack/repos/builtin/packages/paml/package.py
+++ b/var/spack/repos/builtin/packages/paml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Paml(MakefilePackage):
        protein sewuences using maximum likelihood."""
 
     homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html"
-    url      = "http://abacus.gene.ucl.ac.uk/software/paml4.9e.tgz"
+    url      = "http://abacus.gene.ucl.ac.uk/software/paml4.9h.tgz"
 
-    version('4.9e', 'ac5a062bfea1f4eaac79008434030acf')
+    version('4.9h', sha256='623bf6cf4a018a4e7b4dbba189c41d6c0c25fdca3a0ae24703b82965c772edb3')
 
     build_directory = 'src'
 
diff --git a/var/spack/repos/builtin/packages/panda/package.py b/var/spack/repos/builtin/packages/panda/package.py
index 30323fa65a..72bac89f33 100644
--- a/var/spack/repos/builtin/packages/panda/package.py
+++ b/var/spack/repos/builtin/packages/panda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pandaseq/package.py b/var/spack/repos/builtin/packages/pandaseq/package.py
new file mode 100644
index 0000000000..877a55dd6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pandaseq/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pandaseq(AutotoolsPackage):
+    """PANDASEQ is a program to align Illumina reads, optionally with PCR
+    primers embedded in the sequence, and reconstruct an overlapping
+    sequence."""
+
+    homepage = "https://github.com/neufeld/pandaseq"
+    url      = "https://github.com/neufeld/pandaseq/archive/v2.11.tar.gz"
+
+    version('2.11', 'a8ae0e938bac592fc07dfa668147d80b')
+    version('2.10', '5b5b04c9b693a999f10a9c9bd643f068')
+
+    depends_on('autoconf',    type='build')
+    depends_on('automake',    type='build')
+    depends_on('libtool',     type=('build', 'link'))
+    depends_on('m4',          type='build')
+    depends_on('zlib',        type='build')
+    depends_on('pkgconfig',   type='build')
+    depends_on('bzip2',       type='link')
+
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen.sh')
diff --git a/var/spack/repos/builtin/packages/pango/package.py b/var/spack/repos/builtin/packages/pango/package.py
index 26ba05df6a..ced2c63065 100644
--- a/var/spack/repos/builtin/packages/pango/package.py
+++ b/var/spack/repos/builtin/packages/pango/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,13 +16,14 @@ class Pango(AutotoolsPackage):
     list_url = "http://ftp.gnome.org/pub/gnome/sources/pango/"
     list_depth = 1
 
+    version('1.41.0', '1f76ef95953dc58ee5d6a53e5f1cb6db913f3e0eb489713ee9266695cae580ba')
     version('1.40.3', 'abba8b5ce728520c3a0f1535eab19eac3c14aeef7faa5aded90017ceac2711d3')
     version('1.40.1', 'e27af54172c72b3ac6be53c9a4c67053e16c905e02addcf3a603ceb2005c1a40')
     version('1.36.8', '18dbb51b8ae12bae0ab7a958e7cf3317c9acfc8a1e1103ec2f147164a0fc2d07')
 
     variant('X', default=False, description="Enable an X toolkit")
 
-    depends_on("pkg-config", type="build")
+    depends_on("pkgconfig", type="build")
     depends_on("harfbuzz")
     depends_on("cairo")
     depends_on("cairo~X", when='~X')
@@ -50,6 +32,10 @@ class Pango(AutotoolsPackage):
     depends_on("glib")
     depends_on('gobject-introspection')
 
+    def url_for_version(self, version):
+        url = "http://ftp.gnome.org/pub/GNOME/sources/pango/{0}/pango-{1}.tar.xz"
+        return url.format(version.up_to(2), version)
+
     def configure_args(self):
         args = []
         if self.spec.satisfies('+X'):
diff --git a/var/spack/repos/builtin/packages/pangomm/package.py b/var/spack/repos/builtin/packages/pangomm/package.py
new file mode 100644
index 0000000000..e4275eef8d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pangomm/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pangomm(AutotoolsPackage):
+    """Pangomm is a C++ interface to Pango."""
+
+    homepage = "http://www.pango.org/"
+    url      = "https://ftp.gnome.org/pub/GNOME/sources/pangomm/2.14/pangomm-2.14.1.tar.gz"
+
+    version('2.14.1', '607a404291d9eeb895f1df3d08f531d7')
+    version('2.14.0', '897d8c56cec4a9c297a426eb0fc2af91')
+
+    depends_on('pango')
+    depends_on('glibmm')
+    depends_on('cairomm')
+
+    def url_for_version(self, version):
+        """Handle version-based custom URLs."""
+        url = "https://ftp.acc.umu.se/pub/GNOME/sources/pangomm"
+        ext = '.tar.gz' if version < Version('2.28.3') else '.tar.xz'
+        return url + "/%s/pangomm-%s%s" % (version.up_to(2), version, ext)
diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py
index 4809295bb6..57de47f4d9 100644
--- a/var/spack/repos/builtin/packages/papi/package.py
+++ b/var/spack/repos/builtin/packages/papi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
@@ -41,12 +22,17 @@ class Papi(Package):
     homepage = "http://icl.cs.utk.edu/papi/index.html"
 
     url      = "http://icl.cs.utk.edu/projects/papi/downloads/papi-5.4.1.tar.gz"
+    version('5.6.0', 'fdd075860b2bc4b8de8b8b5c3abf594a')
     version('5.5.1', '86a8a6f3d0f34cd83251da3514aae15d')
     version('5.5.0', '5e1244a04ca031d4cc29b46ce3dd05b5')
     version('5.4.3', '3211b5a5bb389fe692370f5cf4cc2412')
     version('5.4.1', '9134a99219c79767a11463a76b0b01a2')
     version('5.3.0', '367961dd0ab426e5ae367c2713924ffb')
 
+    # Does not build with newer versions of gcc, see
+    # https://bitbucket.org/icl/papi/issues/46/cannot-compile-on-arch-linux
+    patch('https://bitbucket.org/icl/papi/commits/53de184a162b8a7edff48fed01a15980664e15b1/raw', sha256='64c57b3ad4026255238cc495df6abfacc41de391a0af497c27d0ac819444a1f8', when='@5.4.0:5.6.99%gcc@8')
+
     def install(self, spec, prefix):
         with working_dir("src"):
 
diff --git a/var/spack/repos/builtin/packages/papyrus/package.py b/var/spack/repos/builtin/packages/papyrus/package.py
new file mode 100644
index 0000000000..c3a1f8e52c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/papyrus/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Papyrus(CMakePackage):
+    """Parallel Aggregate Persistent Storage"""
+
+    homepage = "https://code.ornl.gov/eck/papyrus"
+    url      = "https://code.ornl.gov/eck/papyrus/repository/archive.tar.bz2?ref=v1.0.0"
+    git      = "https://code.ornl.gov/eck/papyrus.git"
+
+    version('develop', branch='master')
+    version('1.0.0', 'fe0fca073c3604110f0507f375d71e64')
+
+    depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py
index 036d7cdb4f..c559f6cf59 100644
--- a/var/spack/repos/builtin/packages/paradiseo/package.py
+++ b/var/spack/repos/builtin/packages/paradiseo/package.py
@@ -1,46 +1,27 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Paradiseo(CMakePackage):
     """A C++ white-box object-oriented framework dedicated to the reusable
        design of metaheuristics."""
+
     homepage = "http://paradiseo.gforge.inria.fr/"
+    git      = "https://gforge.inria.fr/git/paradiseo/paradiseo.git"
 
     # Installing from the development version is a better option at this
     # point than using the very old supplied packages
-    version('head', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git')
+    version('head')
 
     # This is a version that the package formula author has tested
     # successfully.  However, the clone is very large (~1Gb git
     # history). The history in the head version has been trimmed
     # significantly.
-    version(
-        'dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git',
-        commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6')
+    version('dev-safe', commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6')
 
     variant('mpi',      default=True,
             description='Compile with parallel and distributed '
diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
index 4d49ae6f8b..c1bde21108 100644
--- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py
+++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -53,6 +34,10 @@ class ParallelNetcdf(AutotoolsPackage):
         spec = self.spec
 
         args = ['--with-mpi={0}'.format(spec['mpi'].prefix)]
+        args.append('MPICC={0}'.format(spec['mpi'].mpicc))
+        args.append('MPICXX={0}'.format(spec['mpi'].mpicxx))
+        args.append('MPIF77={0}'.format(spec['mpi'].mpifc))
+        args.append('MPIF90={0}'.format(spec['mpi'].mpifc))
         args.append('SEQ_CC={0}'.format(spack_cc))
 
         if '+pic' in spec:
@@ -69,3 +54,7 @@ class ParallelNetcdf(AutotoolsPackage):
             args.append('--disable-fortran')
 
         return args
+
+    def install(self, spec, prefix):
+        # Installation fails in parallel
+        make('install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/parallel/package.py b/var/spack/repos/builtin/packages/parallel/package.py
index 407eb4af09..dbc7c8085e 100644
--- a/var/spack/repos/builtin/packages/parallel/package.py
+++ b/var/spack/repos/builtin/packages/parallel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Parallel(AutotoolsPackage):
     """
 
     homepage = "http://www.gnu.org/software/parallel/"
-    url      = "http://ftp.gnu.org/gnu/parallel/parallel-20170122.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/parallel/parallel-20170122.tar.bz2"
 
     version('20170322', '4fe1b8d2e3974d26c77f0b514988214d')
     version('20170122', 'c9f0ec01463dc75dbbf292fd8be5f1eb')
diff --git a/var/spack/repos/builtin/packages/paraver/package.py b/var/spack/repos/builtin/packages/paraver/package.py
index 3a015d4b63..5945e06d69 100644
--- a/var/spack/repos/builtin/packages/paraver/package.py
+++ b/var/spack/repos/builtin/packages/paraver/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py
index 8bf43b6132..32fdf3746a 100644
--- a/var/spack/repos/builtin/packages/paraview/package.py
+++ b/var/spack/repos/builtin/packages/paraview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -34,6 +15,9 @@ class Paraview(CMakePackage):
     url      = "http://www.paraview.org/files/v5.3/ParaView-v5.3.0.tar.gz"
     _urlfmt  = 'http://www.paraview.org/files/v{0}/ParaView-v{1}{2}.tar.gz'
 
+    version('5.5.2', '7eb93c31a1e5deb7098c3b4275e53a4a')
+    version('5.5.1', 'a7d92a45837b67c3371006cc45163277')
+    version('5.5.0', 'a8f2f41edadffdcc89b37fdc9aa7f005')
     version('5.4.1', '4030c70477ec5a85aa72d6fc86a30753')
     version('5.4.0', 'b92847605bac9036414b644f33cb7163')
     version('5.3.0', '68fbbbe733aa607ec13d1db1ab5eba71')
@@ -49,21 +33,27 @@ class Paraview(CMakePackage):
     variant('osmesa', default=False, description='Enable OSMesa support')
     variant('qt', default=False, description='Enable Qt (gui) support')
     variant('opengl2', default=True, description='Enable OpenGL2 backend')
+    variant('examples', default=False, description="Build examples")
+    variant('hdf5', default=False, description="Use external HDF5")
 
     depends_on('python@2:2.8', when='+python')
     depends_on('py-numpy', when='+python', type='run')
     depends_on('py-matplotlib', when='+python', type='run')
     depends_on('mpi', when='+mpi')
-    depends_on('qt', when='@5.3.0:+qt')
+    depends_on('qt+opengl', when='@5.3.0:+qt+opengl2')
+    depends_on('qt~opengl', when='@5.3.0:+qt~opengl2')
     depends_on('qt@:4', when='@:5.2.0+qt')
 
     depends_on('mesa+swrender', when='+osmesa')
+    depends_on('libxt', when='+qt')
     conflicts('+qt', when='+osmesa')
 
     depends_on('bzip2')
     depends_on('freetype')
     # depends_on('hdf5+mpi', when='+mpi')
     # depends_on('hdf5~mpi', when='~mpi')
+    depends_on('hdf5+hl+mpi', when='+hdf5+mpi')
+    depends_on('hdf5+hl~mpi', when='+hdf5~mpi')
     depends_on('jpeg')
     depends_on('libpng')
     depends_on('libtiff')
@@ -90,6 +80,15 @@ class Paraview(CMakePackage):
         else:
             return self._urlfmt.format(version.up_to(2), version, '')
 
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        if os.path.isdir(self.prefix.lib64):
+            lib_dir = self.prefix.lib64
+        else:
+            lib_dir = self.prefix.lib
+        paraview_version = 'paraview-%s' % self.spec.version.up_to(2)
+        spack_env.set('PARAVIEW_VTK_DIR',
+                      join_path(lib_dir, 'cmake', paraview_version))
+
     def setup_environment(self, spack_env, run_env):
         if os.path.isdir(self.prefix.lib64):
             lib_dir = self.prefix.lib64
@@ -100,6 +99,15 @@ class Paraview(CMakePackage):
                              paraview_version))
         run_env.prepend_path('LD_LIBRARY_PATH', join_path(lib_dir,
                              paraview_version))
+        run_env.set('PARAVIEW_VTK_DIR',
+                    join_path(lib_dir, 'cmake', paraview_version))
+        if '+python' in self.spec:
+            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
+                                 paraview_version))
+            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
+                                 paraview_version, 'site-packages'))
+            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
+                                 paraview_version, 'site-packages', 'vtk'))
 
     def cmake_args(self):
         """Populate cmake arguments for ParaView."""
@@ -125,8 +133,9 @@ class Paraview(CMakePackage):
             '-DVTK_RENDERING_BACKEND:STRING=%s' % rendering,
             '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES:BOOL=%s' % includes,
             '-DBUILD_TESTING:BOOL=OFF',
+            '-DBUILD_EXAMPLES:BOOL=%s' % variant_bool('+examples'),
             '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON',
-            '-DVTK_USE_SYSTEM_HDF5:BOOL=OFF',
+            '-DVTK_USE_SYSTEM_HDF5:BOOL=%s' % variant_bool('+hdf5'),
             '-DVTK_USE_SYSTEM_JPEG:BOOL=ON',
             '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON',
             '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF',
@@ -150,7 +159,10 @@ class Paraview(CMakePackage):
         if '+mpi' in spec:
             cmake_args.extend([
                 '-DPARAVIEW_USE_MPI:BOOL=ON',
-                '-DMPIEXEC:FILEPATH=%s/bin/mpiexec' % spec['mpi'].prefix
+                '-DMPIEXEC:FILEPATH=%s/bin/mpiexec' % spec['mpi'].prefix,
+                '-DMPI_CXX_COMPILER:PATH=%s' % spec['mpi'].mpicxx,
+                '-DMPI_C_COMPILER:PATH=%s' % spec['mpi'].mpicc,
+                '-DMPI_Fortran_COMPILER:PATH=%s' % spec['mpi'].mpifc
             ])
 
         if 'darwin' in spec.architecture:
diff --git a/var/spack/repos/builtin/packages/parmetis/package.py b/var/spack/repos/builtin/packages/parmetis/package.py
index 565c06686c..dad8a7cb1e 100644
--- a/var/spack/repos/builtin/packages/parmetis/package.py
+++ b/var/spack/repos/builtin/packages/parmetis/package.py
@@ -1,33 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import sys
 
 
-class Parmetis(Package):
+class Parmetis(CMakePackage):
     """ParMETIS is an MPI-based parallel library that implements a variety of
        algorithms for partitioning unstructured graphs, meshes, and for
        computing fill-reducing orderings of sparse matrices."""
@@ -40,7 +21,6 @@ class Parmetis(Package):
     version('4.0.2', '0912a953da5bb9b5e5e10542298ffdce')
 
     variant('shared', default=True, description='Enables the build of shared libraries.')
-    variant('debug', default=False, description='Builds the library in debug mode.')
     variant('gdb', default=False, description='Enables gdb support.')
 
     depends_on('cmake@2.8:', type='build')
@@ -68,11 +48,10 @@ class Parmetis(Package):
         url += '/parmetis-{0}.tar.gz'.format(version)
         return url
 
-    def install(self, spec, prefix):
-        source_directory = self.stage.source_path
-        build_directory = join_path(source_directory, 'build')
+    def cmake_args(self):
+        spec = self.spec
 
-        options = std_cmake_args[:]
+        options = []
         options.extend([
             '-DGKLIB_PATH:PATH=%s/GKlib' % spec['metis'].prefix.include,
             '-DMETIS_PATH:PATH=%s' % spec['metis'].prefix,
@@ -92,17 +71,13 @@ class Parmetis(Package):
             for o in rpath_options:
                 options.remove(o)
 
-        if '+debug' in spec:
-            options.extend(['-DDEBUG:BOOL=ON',
-                            '-DCMAKE_BUILD_TYPE:STRING=Debug'])
         if '+gdb' in spec:
             options.append('-DGDB:BOOL=ON')
 
-        with working_dir(build_directory, create=True):
-            cmake(source_directory, *options)
-            make()
-            make('install')
+        return options
 
-            # The shared library is not installed correctly on Darwin; fix this
-            if (sys.platform == 'darwin') and ('+shared' in spec):
-                fix_darwin_install_name(prefix.lib)
+    @run_after('install')
+    def darwin_fix(self):
+        # The shared library is not installed correctly on Darwin; fix this
+        if (sys.platform == 'darwin') and ('+shared' in self.spec):
+            fix_darwin_install_name(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/parmgridgen/package.py b/var/spack/repos/builtin/packages/parmgridgen/package.py
index bbacf519fa..58960caaf2 100644
--- a/var/spack/repos/builtin/packages/parmgridgen/package.py
+++ b/var/spack/repos/builtin/packages/parmgridgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/parquet/package.py b/var/spack/repos/builtin/packages/parquet/package.py
new file mode 100644
index 0000000000..ce683895f6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/parquet/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Parquet(CMakePackage):
+    """C++ bindings for the Apache Parquet columnar data format.
+    """
+
+    homepage = "https://github.com/apache/parquet-cpp"
+    url = "https://github.com/apache/parquet-cpp/archive/apache-parquet-cpp-1.4.0.tar.gz"
+
+    version('1.4.0', '3a3659e65052ef5a76fb88e4922283b9')
+
+    depends_on('arrow')
+    depends_on('boost')
+    depends_on('cmake@3.2.0:', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('thrift+pic')
+
+    variant('pic', default=True,
+            description='Build position independent code')
+    variant('build_type', default='Release',
+            description='CMake build type',
+            values=('Debug', 'FastDebug', 'Release'))
+
+    def cmake_args(self):
+        args = ['-DPARQUET_USE_SSE=OFF', '-DPARQUET_BUILD_TESTS=OFF']
+        for dep in ('arrow', 'thrift'):
+            args.append("-D{0}_HOME={1}".format(dep.upper(),
+                                                self.spec[dep].prefix))
+        return args
+
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if '+pic' in self.spec and name in ('cflags', 'cxxflags'):
+            flags.append(self.compiler.pic_flag)
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/parsimonator/package.py b/var/spack/repos/builtin/packages/parsimonator/package.py
index 462f81e6cf..70ac718ae9 100644
--- a/var/spack/repos/builtin/packages/parsimonator/package.py
+++ b/var/spack/repos/builtin/packages/parsimonator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Parsimonator(MakefilePackage):
        starting trees under parsimony for RAxML"""
 
     homepage = "http://www.exelixis-lab.org/"
-    url      = "https://github.com/stamatak/Parsimonator-1.0.2"
+    git      = "https://github.com/stamatak/Parsimonator-1.0.2.git"
 
-    version('1.0.2', git='https://github.com/stamatak/Parsimonator-1.0.2.git', commit='78368c6ab1e9adc7e9c6ec9256dd7ff2a5bb1b0a')
+    version('1.0.2', commit='78368c6ab1e9adc7e9c6ec9256dd7ff2a5bb1b0a')
 
     variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
     variant('avx', default=False, description='Enable AVX in order to substantially speed up execution')
diff --git a/var/spack/repos/builtin/packages/parsplice/package.py b/var/spack/repos/builtin/packages/parsplice/package.py
index 24b950548f..e07a704eb8 100644
--- a/var/spack/repos/builtin/packages/parsplice/package.py
+++ b/var/spack/repos/builtin/packages/parsplice/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,10 +11,13 @@ class Parsplice(CMakePackage):
     """ParSplice code implements the Parallel Trajectory Splicing algorithm"""
 
     homepage = "https://gitlab.com/exaalt/parsplice"
-    url      = "https://gitlab.com/exaalt/parsplice/repository/archive.tar.gz?ref=v1.1"
+    url      = "https://gitlab.com/api/v4/projects/exaalt%2Fparsplice/repository/archive.tar.gz?sha=v1.1"
+    git      = "https://gitlab.com/exaalt/parsplice.git"
+
+    tags = ['ecp', 'ecp-apps']
 
+    version('develop', branch='master')
     version('1.1', '3a72340d49d731a076e8942f2ae2f4e9')
-    version('develop', git='https://gitlab.com/exaalt/parsplice', branch='master')
 
     depends_on("cmake@3.1:", type='build')
     depends_on("berkeley-db")
diff --git a/var/spack/repos/builtin/packages/partitionfinder/package.py b/var/spack/repos/builtin/packages/partitionfinder/package.py
index 3089eca783..6c36c33c5c 100644
--- a/var/spack/repos/builtin/packages/partitionfinder/package.py
+++ b/var/spack/repos/builtin/packages/partitionfinder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/patch/package.py b/var/spack/repos/builtin/packages/patch/package.py
index 6c69b7994f..78868feacf 100644
--- a/var/spack/repos/builtin/packages/patch/package.py
+++ b/var/spack/repos/builtin/packages/patch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Patch(AutotoolsPackage):
     """
 
     homepage = "http://savannah.gnu.org/projects/patch/"
-    url      = "http://ftp.gnu.org/gnu/patch/patch-2.7.5.tar.xz"
+    url      = "https://ftpmirror.gnu.org/patch/patch-2.7.6.tar.xz"
 
+    version('2.7.6', '78ad9937e4caadcba1526ef1853730d5')
     version('2.7.5', 'e3da7940431633fb65a01b91d3b7a27a')
 
     build_directory = 'spack-build'
diff --git a/var/spack/repos/builtin/packages/patchelf/package.py b/var/spack/repos/builtin/packages/patchelf/package.py
index 273d10486c..793991cb3e 100644
--- a/var/spack/repos/builtin/packages/patchelf/package.py
+++ b/var/spack/repos/builtin/packages/patchelf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pathfinder/package.py b/var/spack/repos/builtin/packages/pathfinder/package.py
index 79bba915d0..ec17859780 100644
--- a/var/spack/repos/builtin/packages/pathfinder/package.py
+++ b/var/spack/repos/builtin/packages/pathfinder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pax-utils/package.py b/var/spack/repos/builtin/packages/pax-utils/package.py
index 0230419ac0..58a77568b7 100644
--- a/var/spack/repos/builtin/packages/pax-utils/package.py
+++ b/var/spack/repos/builtin/packages/pax-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pbbam/package.py b/var/spack/repos/builtin/packages/pbbam/package.py
new file mode 100644
index 0000000000..67e2e8c585
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pbbam/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pbbam(CMakePackage):
+    """The pbbam software package provides components to create, query,
+    & edit PacBio BAM files and associated indices.
+    These components include a core C++ library,
+    bindings for additional languages, and command-line utilities."""
+
+    homepage = "https://github.com/PacificBiosciences/pbbam"
+    url      = "https://github.com/PacificBiosciences/pbbam/archive/0.18.0.tar.gz"
+
+    version('0.18.0', 'abbb687b1e7ea08916c26da828e11384')
+
+    depends_on('zlib')
+    depends_on('boost@1.55.0:')
+    depends_on('htslib@1.3.1:')
+    depends_on('doxygen+graphviz')
+
+    conflicts('%gcc@:5.2.0')
+
+    def cmake_args(self):
+        options = []
+        if self.run_tests:
+            options.append('-DPacBioBAM_build_tests:BOOL=ON')
+        else:
+            options.append('-DPacBioBAM_build_tests:BOOL=OFF')
+
+        return options
+
+    def install(self, spec, prefix):
+        install_tree('spack-build/bin', prefix.bin)
+        install_tree('spack-build/lib', prefix.lib)
+        install_tree('include/pbbam', prefix.include.pbbam)
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('PacBioBAM_LIBRARIES', self.prefix.lib)
+        spack_env.set('PacBioBAM_INCLUDE_DIRS', self.prefix.include)
diff --git a/var/spack/repos/builtin/packages/pbmpi/package.py b/var/spack/repos/builtin/packages/pbmpi/package.py
index a8bbece03d..f0432453ed 100644
--- a/var/spack/repos/builtin/packages/pbmpi/package.py
+++ b/var/spack/repos/builtin/packages/pbmpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Pbmpi(MakefilePackage):
     """
 
     homepage = "http://megasun.bch.umontreal.ca/People/lartillot/www/index.htm"
-    url      = "https://github.com/bayesiancook/pbmpi"
+    git      = "https://github.com/bayesiancook/pbmpi.git"
 
-    version('partition', git='https://github.com/bayesiancook/pbmpi.git', branch='partition')
+    version('partition', branch='partition')
 
     depends_on('mpi')
     depends_on('libfabric')
diff --git a/var/spack/repos/builtin/packages/pcma/package.py b/var/spack/repos/builtin/packages/pcma/package.py
index d4f998d104..7d4f084402 100644
--- a/var/spack/repos/builtin/packages/pcma/package.py
+++ b/var/spack/repos/builtin/packages/pcma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pcre/package.py b/var/spack/repos/builtin/packages/pcre/package.py
index 213a49f731..32d61f10af 100644
--- a/var/spack/repos/builtin/packages/pcre/package.py
+++ b/var/spack/repos/builtin/packages/pcre/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,10 @@ class Pcre(AutotoolsPackage):
     pattern matching using the same syntax and semantics as Perl 5."""
 
     homepage = "http://www.pcre.org"
-    url      = "https://ftp.pcre.org/pub/pcre/pcre-8.40.tar.bz2"
+    url      = "https://ftp.pcre.org/pub/pcre/pcre-8.42.tar.bz2"
 
+    version('8.42', '085b6aa253e0f91cae70b3cdbe8c1ac2')
+    version('8.41', 'c160d22723b1670447341b08c58981c1')
     version('8.40', '41a842bf7dcecd6634219336e2167d1d')
     version('8.39', 'e3fca7650a0556a2647821679d81f585')
     version('8.38', '00aabbfe56d5a48b270f999b508c5ad2')
diff --git a/var/spack/repos/builtin/packages/pcre2/package.py b/var/spack/repos/builtin/packages/pcre2/package.py
index 531a175ef7..855696dbf3 100644
--- a/var/spack/repos/builtin/packages/pcre2/package.py
+++ b/var/spack/repos/builtin/packages/pcre2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,9 @@ class Pcre2(AutotoolsPackage):
     """The PCRE2 package contains Perl Compatible Regular Expression
        libraries. These are useful for implementing regular expression
        pattern matching using the same syntax and semantics as Perl 5."""
+
     homepage = "http://www.pcre.org"""
-    url      = "https://ftp.pcre.org/pub/pcre/pcre2-10.20.tar.bz2"
+    url      = "https://ftp.pcre.org/pub/pcre/pcre2-10.31.tar.bz2"
 
+    version('10.31', 'e0b91c891a3c49050f7fd15de33d0ba4')
     version('10.20', 'dcd027c57ecfdc8a6c3af9d0acf5e3f7')
diff --git a/var/spack/repos/builtin/packages/pdf2svg/package.py b/var/spack/repos/builtin/packages/pdf2svg/package.py
new file mode 100644
index 0000000000..7253d498c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pdf2svg/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pdf2svg(AutotoolsPackage):
+    """A simple PDF to SVG converter using the Poppler and Cairo libraries."""
+
+    homepage = "http://www.cityinthesky.co.uk/opensource/pdf2svg"
+    url      = "https://github.com/dawbarton/pdf2svg/archive/v0.2.3.tar.gz"
+
+    version('0.2.3', 'd398b3b1c1979f554596238a44f12123')
+    version('0.2.2', 'f7e0d2213f9e1422cee9421e18f72553')
+
+    depends_on('cairo', type='run')
+    depends_on('poppler', type='run')
diff --git a/var/spack/repos/builtin/packages/pdftk/package.py b/var/spack/repos/builtin/packages/pdftk/package.py
new file mode 100644
index 0000000000..10179873c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pdftk/package.py
@@ -0,0 +1,83 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Pdftk(MakefilePackage):
+    """PDFtk Server is a command-line tool for working with PDFs. It is
+    commonly used for client-side scripting or server-side processing
+    of PDFs."""
+
+    homepage = "https://www.pdflabs.com/tools/pdftk-server"
+    url      = "https://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/pdftk-2.02-src.zip"
+    # Alternative download locations:
+    # https://sources.debian.org/src/pdftk/
+    # http://archive.ubuntu.com/ubuntu/pool/universe/p/pdftk/pdftk_2.02.orig.tar.gz
+
+    maintainers = ['citibeth']
+
+    version('2.02', '6534365fd6727724f288a556ede33faa')
+
+    depends_on('eclipse-gcj-parser', type='build')
+
+    # Only takes effect in phases not overridden here
+    build_directory = 'pdftk'
+
+    # https://www.pdflabs.com/docs/install-pdftk-on-redhat-or-centos/
+    def edit(self, spec, prefix):
+
+        # ------ Fix install directory in main Makefile
+        makefile = FileFilter(join_path('pdftk', 'Makefile.Base'))
+        makefile.filter('/usr/local/bin', spec.prefix.bin)
+
+        # ------ Create new config file
+        compiler = self.compiler
+        gcc_base = os.path.split(os.path.split(compiler.cxx)[0])[0]
+        gcc_version = compiler.version
+
+        cppflags = (
+            '-DPATH_DELIM=0x2f',
+            '-DASK_ABOUT_WARNINGS=false',
+            '-DUNBLOCK_SIGNALS',
+            '-fdollars-in-identifiers')
+        cxxflags = ('-Wall', '-Wextra', '-Weffc++', '-O2')
+        gcjflags = ('-Wall', '-Wextra', '-O2')
+        vars = [
+            ('VERSUFF', '-%s' % gcc_version),
+            ('CXX', compiler.cxx),
+            ('GCJ', spec['eclipse-gcj-parser'].package.gcj),
+            ('GCJH', join_path(gcc_base, 'bin', 'gcjh')),
+            ('GJAR', join_path(gcc_base, 'bin', 'gjar')),
+            ('LIBGCJ', join_path(
+                gcc_base, 'share', 'java',
+                'libgcj-{0}.jar'.format(gcc_version))),
+            ('AR', 'ar'),
+            ('RM', 'rm'),
+            ('ARFLAGS', 'rs'),
+            ('RMFLAGS', '-vf'),
+            ('CPPFLAGS', ' '.join(cppflags)),
+            ('CXXFLAGS', ' '.join(cxxflags)),
+            ('GCJFLAGS', ' '.join(gcjflags)),
+            ('GCJHFLAGS', '-force'),
+            ('LDLIBS', '-lgcj')
+        ]
+        with open(join_path('pdftk', 'Makefile.Spack'), 'w') as mk:
+            for var, val in vars:
+                mk.write("export {0}={1}\n".format(var, str(val)))
+            mk.write('include Makefile.Base\n')
+
+    def build(self, spec, prefix):
+        compiler = self.compiler
+        gcc_base = os.path.split(os.path.split(compiler.cxx)[0])[0]
+        env['PATH'] = join_path(gcc_base, 'bin') + ':' + env['PATH']
+        with working_dir(self.build_directory):
+            make('-f', 'Makefile.Spack', parallel=False)
+
+    def install(self, spec, prefix):
+        mkdirp(self.spec.prefix.bin)
+        with working_dir(self.build_directory):
+            make('-f', 'Makefile.Spack', 'install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/pdsh/package.py b/var/spack/repos/builtin/packages/pdsh/package.py
index 708dea108c..353ea081a1 100644
--- a/var/spack/repos/builtin/packages/pdsh/package.py
+++ b/var/spack/repos/builtin/packages/pdsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pdt/package.py b/var/spack/repos/builtin/packages/pdt/package.py
index ef8592e44d..503957a6c7 100644
--- a/var/spack/repos/builtin/packages/pdt/package.py
+++ b/var/spack/repos/builtin/packages/pdt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
@@ -38,6 +19,9 @@ class Pdt(AutotoolsPackage):
     homepage = "https://www.cs.uoregon.edu/research/pdt/home.php"
     url      = "http://www.cs.uoregon.edu/research/paracomp/pdtoolkit/Download/pdtoolkit-3.22.1.tar.gz"
 
+    version('3.25', '2cad41fcabf4c79cab8780d3b87f7bb4')
+    version('3.24', 'b8fa5189e5602276ce225ba497b617e4')
+    version('3.23', 'd61e7a631a27b00e58def52950230a2c')
     version('3.22.1', 'b56b9b3e621161c7fd9e4908b944840d')
     version('3.22',   '982d667617802962a1f7fe6c4c31184f')
     version('3.21',   '3092ca0d8833b69992c17e63ae66c263')
diff --git a/var/spack/repos/builtin/packages/pegtl/package.py b/var/spack/repos/builtin/packages/pegtl/package.py
index c297854797..b04d65fba2 100644
--- a/var/spack/repos/builtin/packages/pegtl/package.py
+++ b/var/spack/repos/builtin/packages/pegtl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,8 +15,9 @@ class Pegtl(CMakePackage):
     """
 
     homepage = "https://github.com/taocpp/PEGTL"
-    url      = "https://github.com/taocpp/PEGTL/tarball/1.3.1"
+    url      = "https://github.com/taocpp/PEGTL/tarball/2.1.4"
+    git      = "https://github.com/taocpp/PEGTL.git"
 
-    version('develop', git='https://github.com/taocpp/PEGTL', branch='master')
+    version('develop', branch='master')
     version('2.1.4', 'e5288b6968e6e910287fce93dc5557bf')
     version('2.0.0', 'c772828e7188459338a920c21f9896db')
diff --git a/var/spack/repos/builtin/packages/pennant/package.py b/var/spack/repos/builtin/packages/pennant/package.py
index e318cd991d..f8b6c22815 100644
--- a/var/spack/repos/builtin/packages/pennant/package.py
+++ b/var/spack/repos/builtin/packages/pennant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/percept/fix_cmakelists.patch b/var/spack/repos/builtin/packages/percept/fix_cmakelists.patch
new file mode 100644
index 0000000000..a3ce6b1d95
--- /dev/null
+++ b/var/spack/repos/builtin/packages/percept/fix_cmakelists.patch
@@ -0,0 +1,54 @@
+--- percept.orig/CMakeLists.txt	2017-12-08 09:16:41.572819000 -0700
++++ percept/CMakeLists.txt	2017-12-08 09:17:25.028818000 -0700
+@@ -97,13 +97,6 @@
+     SET (INSTALL_PERCEPT TRUE)
+ ENDIF()
+ 
+-IF (INSTALL_PERCEPT)
+-  set(BINARY_INSTALL_DIR bin)
+-  set(INCLUDE_INSTALL_DIR include)
+-  set(LIB_INSTALL_DIR lib)
+-  INCLUDE(CMakePackageConfigHelpers)
+-ENDIF ()
+-
+ MESSAGE("Setting and checking of compilers:")
+ SET(CMAKE_CXX_COMPILER ${Trilinos_CXX_COMPILER} )
+ SET(CMAKE_C_COMPILER ${Trilinos_C_COMPILER} )
+@@ -269,6 +262,8 @@
+ FILE (GLOB ADAPT_SOURCE src/adapt/main/*.cpp)
+ MESSAGE("-- ADAPT_SOURCE = ${ADAPT_SOURCE}")
+ 
++file(GLOB TRANSFER_SOURCE src/percept/mesh_transfer/*.cpp)
++
+ FILE (GLOB PERCEPT_UTEST_SOURCE test/unit_tests/*.cpp)
+ MESSAGE("-- PERCEPT_UTEST_SOURCE = ${PERCEPT_UTEST_SOURCE}")
+ 
+@@ -330,8 +325,11 @@
+   TARGET_LINK_LIBRARIES(${percept_lib_name} ${Trilinos_LIBRARIES} ${YAML_LIBRARY} ${OPENNURBS_LIBRARY} ${BOOST_LIBRARIES})
+ #  TARGET_LINK_LIBRARIES(${percept_lib_name} ${GTEST_LIBRARY})
+ 
++  add_executable(mesh_transfer ${TRANSFER_SOURCE})
++  target_link_libraries(mesh_transfer ${percept_lib_name})
++
+   SET_PROPERTY(
+-    TARGET ${percept_lib_name} ${adapt_ex_name} ${percept_utest_name} ${percept_rtest_name}
++    TARGET ${percept_lib_name} mesh_transfer ${adapt_ex_name} ${percept_utest_name} ${percept_rtest_name}
+     PROPERTY COMPILE_DEFINITIONS STK_PERCEPT_LITE=0 STK_PERCEPT_HAS_GEOMETRY STK_PERCEPT_USE_INTREPID
+   )
+ 
+@@ -342,5 +340,15 @@
+ 
+ ENDIF()
+ 
++IF (INSTALL_PERCEPT)
++  install(TARGETS ${percept_ex_name} ${adapt_ex_name}
++          ${percept_htest_name} ${percept_rtest_name} ${percept_utest_name}
++          mesh_transfer percept
++          RUNTIME DESTINATION bin
++          ARCHIVE DESTINATION lib
++          LIBRARY DESTINATION lib)
++  #install(DIRECTORY include/ DESTINATION include)
++  include(CMakePackageConfigHelpers)
++ENDIF ()
+ 
+ MESSAGE("\nAnd CMake says...:")
diff --git a/var/spack/repos/builtin/packages/percept/fix_header.patch b/var/spack/repos/builtin/packages/percept/fix_header.patch
new file mode 100644
index 0000000000..feca6d022c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/percept/fix_header.patch
@@ -0,0 +1,19 @@
+--- percept.orig/src/percept/MeshType.hpp	2017-12-08 09:16:42.080818000 -0700
++++ percept/src/percept/MeshType.hpp	2017-12-08 09:17:25.568819000 -0700
+@@ -11,6 +11,7 @@
+ #include <percept/Percept.hpp>
+ 
+ #include <array>
++#include <memory>
+ #include <stk_mesh/base/Field.hpp>
+ #include <stk_mesh/base/Entity.hpp>
+ #include <stk_mesh/base/Bucket.hpp>
+@@ -62,7 +63,7 @@
+       typedef Kokkos::LayoutRight   SecondaryDataLayout;
+ #endif
+ 
+-	#elif KOKKOS_HAVE_OPENMP
++	#elif defined(KOKKOS_HAVE_OPENMP)
+   	  typedef Kokkos::OpenMP     ExecSpace;
+   	  typedef Kokkos::OpenMP     MemSpace;
+   	  typedef Kokkos::LayoutLeft DataLayout;
diff --git a/var/spack/repos/builtin/packages/percept/package.py b/var/spack/repos/builtin/packages/percept/package.py
new file mode 100644
index 0000000000..40a1d04fc9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/percept/package.py
@@ -0,0 +1,55 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Percept(CMakePackage):
+    """Parallel mesh refinement and adaptivity tools for the finite
+    element method.
+    """
+
+    homepage = "https://github.com/PerceptTools/percept"
+    git      = "https://github.com/PerceptTools/percept.git"
+
+    # This package file was created at percept
+    # commit dc1c8ec0175213146ac139946beca185a84c22e8
+    version('develop', branch='master')
+
+    depends_on('googletest~shared')
+    depends_on('opennurbs@percept')
+    depends_on('boost+graph+mpi')
+    depends_on('yaml-cpp+pic~shared@0.5.3:')
+    # Percept was initially tested against Trilinos 12.12.1
+    depends_on('trilinos~shared+exodus+tpetra+epetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf+aztec+sacado~openmp+shards+intrepid+cgns@master,12.12.1:')
+
+    patch('fix_cmakelists.patch')
+    patch('fix_header.patch')
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        options.extend([
+            '-DSTK_PERCEPT_LITE:BOOL=OFF',
+            '-DSTK_ADAPT_HAVE_YAML_CPP:BOOL=ON',
+            '-DTrilinos_DIR:PATH=%s' %
+            spec['trilinos'].prefix,
+            '-DYAML_DIR:PATH=%s' %
+            spec['yaml-cpp'].prefix,
+            '-DBOOST_DIR:PATH=%s' %
+            spec['boost'].prefix,
+            '-DOPENNURBS_DIR:PATH=%s' %
+            spec['opennurbs'].prefix,
+            '-DOPENNURBS_INCLUDE_DIR:PATH=%s' %
+            spec['opennurbs'].prefix.include,
+            '-DOPENNURBS_LIBRARY_DIR:PATH=%s' %
+            spec['opennurbs'].prefix.lib,
+            '-DPERCEPT_TPLS_INSTALL_DIR:PATH=%s' %
+            spec['googletest'].prefix,
+            '-DENABLE_INSTALL:BOOL=ON'
+        ])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py
index 79f4076da5..707651baea 100644
--- a/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py
+++ b/var/spack/repos/builtin/packages/perl-algorithm-diff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-app-cmd/package.py b/var/spack/repos/builtin/packages/perl-app-cmd/package.py
new file mode 100644
index 0000000000..3240f053c0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-app-cmd/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlAppCmd(PerlPackage):
+    """Write command line apps with less suffering"""
+
+    homepage = "http://search.cpan.org/~rjbs/App-Cmd/lib/App/Cmd.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/App-Cmd-0.331.tar.gz"
+
+    version('0.331', 'b43c07d7b4d4e2a6baf32aa92cd00b93')
diff --git a/var/spack/repos/builtin/packages/perl-array-utils/package.py b/var/spack/repos/builtin/packages/perl-array-utils/package.py
new file mode 100644
index 0000000000..157cf5c77e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-array-utils/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlArrayUtils(PerlPackage):
+    """Small utils for array manipulation"""
+
+    homepage = "http://search.cpan.org/~zmij/Array-Utils/Utils.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/Z/ZM/ZMIJ/Array/Array-Utils-0.5.tar.gz"
+
+    version('0.5', 'ac15e6dce2c7c9d1855ecab9eb00aee6')
diff --git a/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py b/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py
index eecd0b69cc..39a48c4ea9 100644
--- a/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py
+++ b/var/spack/repos/builtin/packages/perl-b-hooks-endofscope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-bio-perl/package.py b/var/spack/repos/builtin/packages/perl-bio-perl/package.py
index afbef8001c..6f16117b40 100644
--- a/var/spack/repos/builtin/packages/perl-bio-perl/package.py
+++ b/var/spack/repos/builtin/packages/perl-bio-perl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import inspect
 
diff --git a/var/spack/repos/builtin/packages/perl-bit-vector/package.py b/var/spack/repos/builtin/packages/perl-bit-vector/package.py
new file mode 100644
index 0000000000..1e4360a6c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-bit-vector/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlBitVector(PerlPackage):
+    """Efficient bit vector, set of integers and "big int" math library"""
+
+    homepage = "http://search.cpan.org/~stbey/Bit-Vector-7.4/Vector.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/ST/STBEY/Bit-Vector-7.4.tar.gz"
+
+    version('7.4', 'bf67f144e5be5327ed79d4c69e6e0086')
+
+    depends_on('perl-carp-clan', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-cairo/package.py b/var/spack/repos/builtin/packages/perl-cairo/package.py
new file mode 100644
index 0000000000..bda7297118
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-cairo/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCairo(PerlPackage):
+    """Perl interface to the cairo 2d vector graphics library"""
+
+    homepage = "http://search.cpan.org/~xaoc/Cairo/lib/Cairo.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/Cairo-1.106.tar.gz"
+
+    version('1.106', '47ca0ae0f5b9bc4c16a27627ff48bd8b')
+
+    depends_on('cairo')
+    depends_on('perl-extutils-depends')
+    depends_on('perl-extutils-pkgconfig')
diff --git a/var/spack/repos/builtin/packages/perl-capture-tiny/package.py b/var/spack/repos/builtin/packages/perl-capture-tiny/package.py
index 952ff2999c..6b60946ca5 100644
--- a/var/spack/repos/builtin/packages/perl-capture-tiny/package.py
+++ b/var/spack/repos/builtin/packages/perl-capture-tiny/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-carp-clan/package.py b/var/spack/repos/builtin/packages/perl-carp-clan/package.py
new file mode 100644
index 0000000000..d55ac04be5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-carp-clan/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCarpClan(PerlPackage):
+    """Report errors from perspective of caller of a "clan" of modules"""
+
+    homepage = "http://search.cpan.org/~kentnl/Carp-Clan-6.06/lib/Carp/Clan.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/K/KE/KENTNL/Carp-Clan-6.06.tar.gz"
+
+    version('6.06', 'c562a35c48f43665fab735cdc7fe3cb2')
+
+    depends_on('perl-test-exception', type=('build', 'run'))
+    depends_on('perl-sub-uplevel', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-cgi/package.py b/var/spack/repos/builtin/packages/perl-cgi/package.py
new file mode 100644
index 0000000000..4d0294293f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-cgi/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCgi(PerlPackage):
+    """CGI - Handle Common Gateway Interface requests and responses
+
+       CGI was included in the Perl distribution from 5.4 to 5.20 but
+       has since been removed."""
+
+    homepage = "https://metacpan.org/pod/CGI"
+    url      = "https://cpan.metacpan.org/authors/id/L/LE/LEEJO/CGI-4.40.tar.gz"
+
+    version('4.40', sha256='10efff3061b3c31a33b3cc59f955aef9c88d57d12dbac46389758cef92f24f56')
+    version('4.39', sha256='7e73417072445f24e03d63802ed3a9e368c9b103ddc96e2a9bcb6a251215fb76')
+    version('4.38', sha256='8c58f4a529bb92a914b22b7e64c5e31185c9854a4070a6dfad44fe5cc248e7d4')
+    version('4.37', sha256='7a14eee5df640f7141848f653cf48d99bfc9b5c68e18167338ee01b91cdfb883')
+
+    depends_on('perl-html-parser', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py
index 2fd349b077..951d254395 100644
--- a/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py
+++ b/var/spack/repos/builtin/packages/perl-class-data-inheritable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-class-inspector/package.py b/var/spack/repos/builtin/packages/perl-class-inspector/package.py
new file mode 100644
index 0000000000..7bbd3cbbe3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-class-inspector/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlClassInspector(PerlPackage):
+    """Get information about a class and its structure"""
+
+    homepage = "http://search.cpan.org/~plicease/Class-Inspector-1.32/lib/Class/Inspector.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/Class-Inspector-1.32.tar.gz"
+
+    version('1.32', 'db471d6ecf47fa054726553319b7c34f')
diff --git a/var/spack/repos/builtin/packages/perl-class-load-xs/package.py b/var/spack/repos/builtin/packages/perl-class-load-xs/package.py
index 11130afd97..a6a21821e8 100644
--- a/var/spack/repos/builtin/packages/perl-class-load-xs/package.py
+++ b/var/spack/repos/builtin/packages/perl-class-load-xs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-class-load/package.py b/var/spack/repos/builtin/packages/perl-class-load/package.py
index 0d10f82813..2c5b91ebf9 100644
--- a/var/spack/repos/builtin/packages/perl-class-load/package.py
+++ b/var/spack/repos/builtin/packages/perl-class-load/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py b/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py
new file mode 100644
index 0000000000..fe7e47f2f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-compress-raw-bzip2/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCompressRawBzip2(PerlPackage):
+    """A low-Level Interface to bzip2 compression library."""
+
+    homepage = "http://search.cpan.org/~pmqs/Compress-Raw-Bzip2-2.081/lib/Compress/Raw/Bzip2.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PM/PMQS/Compress-Raw-Bzip2-2.081.tar.gz"
+
+    version('2.081', '25fa9c9cc4fd3250b65b91694f9eac2e')
+
+    depends_on('bzip2')
+    depends_on('perl-extutils-makemaker', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py b/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py
new file mode 100644
index 0000000000..215554ef97
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-compress-raw-zlib/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlCompressRawZlib(PerlPackage):
+    "A low-Level Interface to zlib compression library"
+
+    homepage = "http://search.cpan.org/~pmqs/Compress-Raw-Zlib-2.081/lib/Compress/Raw/Zlib.pm"
+    url      = "https://cpan.metacpan.org/authors/id/P/PM/PMQS/Compress-Raw-Zlib-2.081.tar.gz"
+
+    version('2.081', 'a22d23bb4f8ce92a41ace1dff29f2bd1')
+
+    depends_on('zlib')
+    depends_on('perl-extutils-makemaker', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-contextual-return/package.py b/var/spack/repos/builtin/packages/perl-contextual-return/package.py
new file mode 100644
index 0000000000..752e807eab
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-contextual-return/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlContextualReturn(PerlPackage):
+    """Create context-sensitive return values"""
+
+    homepage = "http://search.cpan.org/~dconway/Contextual-Return/lib/Contextual/Return.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/Contextual-Return-0.004014.tar.gz"
+
+    version('0.004014', '5cb31f1637c17af6a8e5b852d820af79')
+
+    depends_on('perl-want')
diff --git a/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py b/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py
index 7fe16bb2a0..b1743bcd2a 100644
--- a/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py
+++ b/var/spack/repos/builtin/packages/perl-cpan-meta-check/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-data-optlist/package.py b/var/spack/repos/builtin/packages/perl-data-optlist/package.py
index 4eaeaca1a4..acc3b0cc94 100644
--- a/var/spack/repos/builtin/packages/perl-data-optlist/package.py
+++ b/var/spack/repos/builtin/packages/perl-data-optlist/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-data-stag/package.py b/var/spack/repos/builtin/packages/perl-data-stag/package.py
index fd1bff285f..0af9e0f25f 100644
--- a/var/spack/repos/builtin/packages/perl-data-stag/package.py
+++ b/var/spack/repos/builtin/packages/perl-data-stag/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py b/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py
new file mode 100644
index 0000000000..81f6134814
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-dbd-mysql/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlDbdMysql(PerlPackage):
+    """MySQL driver for the Perl5 Database Interface (DBI)"""
+
+    homepage = "http://search.cpan.org/~michielb/DBD-mysql-4.043/lib/DBD/mysql.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MI/MICHIELB/DBD-mysql-4.043.tar.gz"
+
+    version('4.043', '4a00dd7f1c057931147c65dfc4901c36')
+
+    depends_on('perl-test-deep', type=('build', 'run'))
+    depends_on('perl-dbi', type=('build', 'run'))
+    depends_on('mariadb@:10.1.23')
diff --git a/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py b/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py
new file mode 100644
index 0000000000..6c8bd95ad7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-dbd-sqlite/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlDbdSqlite(PerlPackage):
+    """DBD::SQLite - Self-contained RDBMS in a DBI Driver"""
+
+    homepage = "https://metacpan.org/pod/DBD::SQLite"
+    url      = "https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI/DBD-SQLite-1.58.tar.gz"
+
+    version('1.59_01', sha256='b6f331e4054688572c2010e72c355f7ba3f30d86051e50d9925d34d9df1001e2')
+    version('1.58',    sha256='7120dd99d0338dea2802fda8bfe3fbf10077d5af559f6c67ae35e9270d1a1d3b')
+    version('1.57_01', sha256='fa7fb111fa8bfc257c3208f8980ac802a9cac4531ab98afc1988b88929672184')
+    version('1.56',    sha256='c5f831a67a94f9bb2fb3c44051f309fc7994b2725d1896c018ad5d4cd865e991')
+
+    depends_on('perl-dbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-dbfile/package.py b/var/spack/repos/builtin/packages/perl-dbfile/package.py
index 3a5d8fea94..e1c5ba0df7 100644
--- a/var/spack/repos/builtin/packages/perl-dbfile/package.py
+++ b/var/spack/repos/builtin/packages/perl-dbfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-dbi/package.py b/var/spack/repos/builtin/packages/perl-dbi/package.py
index a6e5e76cc5..694aee138a 100644
--- a/var/spack/repos/builtin/packages/perl-dbi/package.py
+++ b/var/spack/repos/builtin/packages/perl-dbi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-devel-cycle/package.py b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py
index ad4c575025..061b71350c 100644
--- a/var/spack/repos/builtin/packages/perl-devel-cycle/package.py
+++ b/var/spack/repos/builtin/packages/perl-devel-cycle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py b/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py
index aca5245611..297a770dd1 100644
--- a/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py
+++ b/var/spack/repos/builtin/packages/perl-devel-globaldestruction/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py b/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py
index 60a80aed90..3499660c94 100644
--- a/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py
+++ b/var/spack/repos/builtin/packages/perl-devel-overloadinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PerlDevelOverloadinfo(PerlPackage):
     homepage = "http://search.cpan.org/~ilmari/Devel-OverloadInfo-0.004/lib/Devel/OverloadInfo.pm"
     url      = "http://search.cpan.org/CPAN/authors/id/I/IL/ILMARI/Devel-OverloadInfo-0.004.tar.gz"
 
+    version('0.005', '607b65dfe9fdb47df780f3b22dcb7917')
     version('0.004', '97a27e31858b073daba54121d57be705')
 
     depends_on('perl-mro-compat', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py b/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py
index d6b7b8f484..2e366a2c1a 100644
--- a/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py
+++ b/var/spack/repos/builtin/packages/perl-devel-stacktrace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-digest-md5/package.py b/var/spack/repos/builtin/packages/perl-digest-md5/package.py
new file mode 100644
index 0000000000..5466bd2078
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-digest-md5/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlDigestMd5(PerlPackage):
+    """Perl interface to the MD5 Algorithm"""
+
+    homepage = "http://search.cpan.org/dist/Digest-MD5/MD5.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Digest-MD5-2.55.tar.gz"
+
+    version('2.55', '601519b826ca14c233f13a4578b967ef')
diff --git a/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py b/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py
index f09ebd4a31..f545b9845e 100644
--- a/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py
+++ b/var/spack/repos/builtin/packages/perl-dist-checkconflicts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-encode-locale/package.py b/var/spack/repos/builtin/packages/perl-encode-locale/package.py
new file mode 100644
index 0000000000..f052970435
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-encode-locale/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlEncodeLocale(PerlPackage):
+    """Determine the locale encoding"""
+
+    homepage = "http://search.cpan.org/~gaas/Encode-Locale-1.05/lib/Encode/Locale.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/Encode-Locale-1.05.tar.gz"
+
+    version('1.05', 'fcfdb8e4ee34bcf62aed429b4a23db27')
diff --git a/var/spack/repos/builtin/packages/perl-eval-closure/package.py b/var/spack/repos/builtin/packages/perl-eval-closure/package.py
index d79d119140..5134ddaea6 100644
--- a/var/spack/repos/builtin/packages/perl-eval-closure/package.py
+++ b/var/spack/repos/builtin/packages/perl-eval-closure/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-exception-class/package.py b/var/spack/repos/builtin/packages/perl-exception-class/package.py
index 715830432d..2877352b3e 100644
--- a/var/spack/repos/builtin/packages/perl-exception-class/package.py
+++ b/var/spack/repos/builtin/packages/perl-exception-class/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py b/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py
new file mode 100644
index 0000000000..cea49dbba3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-exporter-tiny/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlExporterTiny(PerlPackage):
+    """An exporter with the features of Sub::Exporter but only core
+    dependencies"""
+
+    homepage = "http://search.cpan.org/~tobyink/Exporter-Tiny/lib/Exporter/Tiny.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/T/TO/TOBYINK/Exporter-Tiny-1.000000.tar.gz"
+
+    version('1.000000', '0d413747bdcf880f9ec62de8801ccf5e')
diff --git a/var/spack/repos/builtin/packages/perl-extutils-depends/package.py b/var/spack/repos/builtin/packages/perl-extutils-depends/package.py
new file mode 100644
index 0000000000..d837ca9386
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-extutils-depends/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlExtutilsDepends(PerlPackage):
+    """Easily build XS extensions that depend on XS extensions"""
+
+    homepage = "http://search.cpan.org/~xaoc/ExtUtils-Depends/lib/ExtUtils/Depends.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/ExtUtils-Depends-0.405.tar.gz"
+
+    version('0.405', 'caefbca2f173d0cea3f5ac26b6c08a2c')
diff --git a/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py b/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py
index c346cead50..248056bc18 100644
--- a/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py
+++ b/var/spack/repos/builtin/packages/perl-extutils-makemaker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py
index 547d2d2866..1d1e4427cc 100644
--- a/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py
+++ b/var/spack/repos/builtin/packages/perl-extutils-pkgconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,3 +13,5 @@ class PerlExtutilsPkgconfig(PerlPackage):
     url      = "http://search.cpan.org/CPAN/authors/id/X/XA/XAOC/ExtUtils-PkgConfig-1.16.tar.gz"
 
     version('1.16', 'b86318f2b6ac6af3ee985299e1e38fe5')
+
+    depends_on('pkgconfig', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py b/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py
new file mode 100644
index 0000000000..4a39f17318
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-copy-recursive/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileCopyRecursive(PerlPackage):
+    """Perl extension for recursively copying files and directories"""
+
+    homepage = "http://search.cpan.org/~dmuey/File-Copy-Recursive-0.38/Recursive.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DM/DMUEY/File-Copy-Recursive-0.38.tar.gz"
+
+    version('0.40', '659c634f248885c4b3876b15baf56c79')
+    version('0.38', 'e76dc75ab456510d67c6c3a95183f72f')
diff --git a/var/spack/repos/builtin/packages/perl-file-listing/package.py b/var/spack/repos/builtin/packages/perl-file-listing/package.py
new file mode 100644
index 0000000000..7907b8df1f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-listing/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileListing(PerlPackage):
+    """Parse directory listing"""
+
+    homepage = "http://search.cpan.org/~gaas/File-Listing-6.04/lib/File/Listing.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/File-Listing-6.04.tar.gz"
+
+    version('6.04', '83f636b477741f3a014585bb9cc079a6')
+
+    depends_on('perl-http-date', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-file-pushd/package.py b/var/spack/repos/builtin/packages/perl-file-pushd/package.py
index fea45e0f9e..5cea0aed7b 100644
--- a/var/spack/repos/builtin/packages/perl-file-pushd/package.py
+++ b/var/spack/repos/builtin/packages/perl-file-pushd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py b/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py
new file mode 100644
index 0000000000..294342c1ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-sharedir-install/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileSharedirInstall(PerlPackage):
+    """Install shared files"""
+
+    homepage = "http://search.cpan.org/~ether/File-ShareDir-Install-0.11/lib/File/ShareDir/Install.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/File-ShareDir-Install-0.11.tar.gz"
+
+    version('0.11', '61107e6ce6eee42bf29525b1a4d029e0')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py b/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py
new file mode 100644
index 0000000000..dd37eb5cb8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-slurp-tiny/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileSlurpTiny(PerlPackage):
+    """A simple, sane and efficient file slurper"""
+
+    homepage = "http://search.cpan.org/~leont/File-Slurp-Tiny-0.004/lib/File/Slurp/Tiny.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/File-Slurp-Tiny-0.004.tar.gz"
+
+    version('0.004', '7575b81543281ea57cdb7e5eb3f73264')
diff --git a/var/spack/repos/builtin/packages/perl-file-slurper/package.py b/var/spack/repos/builtin/packages/perl-file-slurper/package.py
new file mode 100644
index 0000000000..45a5fac76a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-slurper/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileSlurper(PerlPackage):
+    """A simple, sane and efficient module to slurp a file"""
+
+    homepage = "http://search.cpan.org/~leont/File-Slurper/lib/File/Slurper.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/File-Slurper-0.011.tar.gz"
+
+    version('0.011', 'e0482d3d5a0522e39132ba54af9f1ce3')
diff --git a/var/spack/repos/builtin/packages/perl-file-which/package.py b/var/spack/repos/builtin/packages/perl-file-which/package.py
new file mode 100644
index 0000000000..bda5f58262
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-file-which/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlFileWhich(PerlPackage):
+    """Perl implementation of the which utility as an API"""
+
+    homepage = "http://cpansearch.perl.org/src/PLICEASE/File-Which-1.22/lib/File/Which.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PL/PLICEASE/File-Which-1.22.tar.gz"
+
+    version('1.22', 'face60fafd220dc83fa581ef6f96d480')
diff --git a/var/spack/repos/builtin/packages/perl-font-ttf/package.py b/var/spack/repos/builtin/packages/perl-font-ttf/package.py
index 81ddbf20b5..aa40f10abf 100644
--- a/var/spack/repos/builtin/packages/perl-font-ttf/package.py
+++ b/var/spack/repos/builtin/packages/perl-font-ttf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-gd-graph/package.py b/var/spack/repos/builtin/packages/perl-gd-graph/package.py
index 9e68fb208a..15b8a765ce 100644
--- a/var/spack/repos/builtin/packages/perl-gd-graph/package.py
+++ b/var/spack/repos/builtin/packages/perl-gd-graph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class PerlGdGraph(PerlPackage):
     """Graph Plotting Module for Perl 5"""
 
     homepage = "http://search.cpan.org/~bwarfield/GDGraph/Graph.pm"
-    url      = "http://search.cpan.org/CPAN/authors/id/B/BW/BWARFIELD/GDGraph-1.44.tar.gz"
+    url      = "http://search.cpan.org/CPAN/authors/id/B/BW/BWARFIELD/GDGraph-1.4308.tar.gz"
 
     version('1.4308', 'fcdd34d5e09ae917b5d264887734b3b1')
 
diff --git a/var/spack/repos/builtin/packages/perl-gd-text/package.py b/var/spack/repos/builtin/packages/perl-gd-text/package.py
index a0a512352a..71c4d053e0 100644
--- a/var/spack/repos/builtin/packages/perl-gd-text/package.py
+++ b/var/spack/repos/builtin/packages/perl-gd-text/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-gd/package.py b/var/spack/repos/builtin/packages/perl-gd/package.py
index 77e5c01aee..8b2367d439 100644
--- a/var/spack/repos/builtin/packages/perl-gd/package.py
+++ b/var/spack/repos/builtin/packages/perl-gd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py b/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py
new file mode 100644
index 0000000000..ec632bceb9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-gdgraph-histogram/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlGdgraphHistogram(PerlPackage):
+    """GD::Graph::histogram extends the GD::Graph module to create histograms.
+       The module allow creation of count or percentage histograms."""
+
+    homepage = "https://metacpan.org/pod/GD::Graph::histogram"
+    url      = "https://cpan.metacpan.org/authors/id/W/WH/WHIZDOG/GDGraph-histogram-1.1.tar.gz"
+
+    version('1.1', sha256='20f752d0e6deb59b29aa2ec3496b5883476d00280b6e83f5b47c33fac4097f8a')
diff --git a/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py b/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py
new file mode 100644
index 0000000000..cb4ffe7251
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-graph-readwrite/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlGraphReadwrite(PerlPackage):
+    """Write out directed graph in Dot format"""
+
+    homepage = "http://search.cpan.org/~neilb/Graph-ReadWrite/lib/Graph/Writer/Dot.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/N/NE/NEILB/Graph-ReadWrite-2.09.tar.gz"
+
+    version('2.09', '5cd9191eadd2fe8fe8bb431575434f67')
diff --git a/var/spack/repos/builtin/packages/perl-graph/package.py b/var/spack/repos/builtin/packages/perl-graph/package.py
new file mode 100644
index 0000000000..0bb59195c7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-graph/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlGraph(PerlPackage):
+    """Graph data structures and algorithms"""
+
+    homepage = "http://search.cpan.org/~jhi/Graph/lib/Graph.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/J/JH/JHI/Graph-0.9704.tar.gz"
+
+    version('0.9704', '1ab4e49420e56eeb1bc81d842aa8f3af')
+
+    depends_on('perl@5.6.0:')
diff --git a/var/spack/repos/builtin/packages/perl-html-parser/package.py b/var/spack/repos/builtin/packages/perl-html-parser/package.py
new file mode 100644
index 0000000000..bdf2418437
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-html-parser/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHtmlParser(PerlPackage):
+    """HTML parser class"""
+
+    homepage = "http://search.cpan.org/~gaas/HTML-Parser-3.72/Parser.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTML-Parser-3.72.tar.gz"
+
+    version('3.72', 'eb7505e5f626913350df9dd4a03d54a8')
+
+    depends_on('perl-html-tagset', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-html-tagset/package.py b/var/spack/repos/builtin/packages/perl-html-tagset/package.py
new file mode 100644
index 0000000000..ef838d9369
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-html-tagset/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHtmlTagset(PerlPackage):
+    """Data tables useful in parsing HTML"""
+
+    homepage = "http://search.cpan.org/~petdance/HTML-Tagset-3.20/Tagset.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PE/PETDANCE/HTML-Tagset-3.20.tar.gz"
+
+    version('3.20', 'd2bfa18fe1904df7f683e96611e87437')
diff --git a/var/spack/repos/builtin/packages/perl-http-cookies/package.py b/var/spack/repos/builtin/packages/perl-http-cookies/package.py
new file mode 100644
index 0000000000..41d5857f6b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-cookies/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpCookies(PerlPackage):
+    """HTTP cookie jars"""
+
+    homepage = "http://search.cpan.org/~oalders/HTTP-Cookies-6.04/lib/HTTP/Cookies.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/HTTP-Cookies-6.04.tar.gz"
+
+    version('6.04', '7bf1e277bd5c886bc18d21eb8423b65f')
+
+    depends_on('perl-uri', type=('build', 'run'))
+    depends_on('perl-http-message', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-http-daemon/package.py b/var/spack/repos/builtin/packages/perl-http-daemon/package.py
new file mode 100644
index 0000000000..7d07ad3637
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-daemon/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpDaemon(PerlPackage):
+    """A simple http server class"""
+
+    homepage = "http://search.cpan.org/~gaas/HTTP-Daemon-6.01/lib/HTTP/Daemon.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Daemon-6.01.tar.gz"
+
+    version('6.01', 'ed0ae02d25d7f1e89456d4d69732adc2')
+
+    depends_on('perl-lwp-mediatypes', type=('build', 'run'))
+    depends_on('perl-http-message', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-http-date/package.py b/var/spack/repos/builtin/packages/perl-http-date/package.py
new file mode 100644
index 0000000000..a8a0f53b8a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-date/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpDate(PerlPackage):
+    """Date conversion routines"""
+
+    homepage = "http://search.cpan.org/~gaas/HTTP-Date-6.02/lib/HTTP/Date.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Date-6.02.tar.gz"
+
+    version('6.02', '52b7a0d5982d61be1edb217751d7daba')
diff --git a/var/spack/repos/builtin/packages/perl-http-message/package.py b/var/spack/repos/builtin/packages/perl-http-message/package.py
new file mode 100644
index 0000000000..4068241c75
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-message/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpMessage(PerlPackage):
+    """HTTP style message (base class)"""
+
+    homepage = "http://search.cpan.org/~oalders/HTTP-Message-6.13/lib/HTTP/Status.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/HTTP-Message-6.13.tar.gz"
+
+    version('6.13', '4c1b7c6ee114c1cff69379ec9651d9ac')
+
+    depends_on('perl-lwp-mediatypes', type=('build', 'run'))
+    depends_on('perl-encode-locale', type=('build', 'run'))
+    depends_on('perl-io-html', type=('build', 'run'))
+    depends_on('perl-try-tiny', type=('build', 'run'))
+    depends_on('perl-uri', type=('build', 'run'))
+    depends_on('perl-http-date', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-http-negotiate/package.py b/var/spack/repos/builtin/packages/perl-http-negotiate/package.py
new file mode 100644
index 0000000000..cca1ddc47a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-http-negotiate/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlHttpNegotiate(PerlPackage):
+    """Choose a variant to serve"""
+
+    homepage = "http://search.cpan.org/~gaas/HTTP-Negotiate-6.01/lib/HTTP/Negotiate.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/HTTP-Negotiate-6.01.tar.gz"
+
+    version('6.01', '1236195250e264d7436e7bb02031671b')
+
+    depends_on('perl-http-message', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-inline-c/package.py b/var/spack/repos/builtin/packages/perl-inline-c/package.py
new file mode 100644
index 0000000000..c5af6af4b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-inline-c/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlInlineC(PerlPackage):
+    """C Language Support for Inline"""
+
+    homepage = "http://search.cpan.org/~tinita/Inline-C-0.78/lib/Inline/C.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/T/TI/TINITA/Inline-C-0.78.tar.gz"
+
+    version('0.78', '710a454b5337b1cbf3f2ae5c8c45b413')
+
+    depends_on('perl-yaml-libyaml', type=('build', 'run'))
+    depends_on('perl-parse-recdescent', type=('build', 'run'))
+    depends_on('perl-inline', type=('build', 'run'))
+    depends_on('perl-pegex', type=('build', 'run'))
+    depends_on('perl-file-copy-recursive', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-inline/package.py b/var/spack/repos/builtin/packages/perl-inline/package.py
new file mode 100644
index 0000000000..00ee8c3d9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-inline/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlInline(PerlPackage):
+    """Write Perl Subroutines in Other Programming Languages"""
+
+    homepage = "http://search.cpan.org/~ingy/Inline-0.80/lib/Inline.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/I/IN/INGY/Inline-0.80.tar.gz"
+
+    version('0.80', '510bbac46e727bcaf240b7feac2646c9')
+
+    depends_on('perl-test-warn', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-intervaltree/package.py b/var/spack/repos/builtin/packages/perl-intervaltree/package.py
index 1a3a31f9d7..76b7c4b469 100644
--- a/var/spack/repos/builtin/packages/perl-intervaltree/package.py
+++ b/var/spack/repos/builtin/packages/perl-intervaltree/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-io-compress/package.py b/var/spack/repos/builtin/packages/perl-io-compress/package.py
new file mode 100644
index 0000000000..ed8af2cbbf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-io-compress/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlIoCompress(PerlPackage):
+    """A perl library for uncompressing gzip, zip, bzip2
+    or lzop file/buffer."""
+
+    homepage = "http://search.cpan.org/~pmqs/IO-Compress-2.070/lib/IO/Uncompress/AnyUncompress.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PM/PMQS/IO-Compress-2.081.tar.gz"
+
+    version('2.081', '379932c1b9428b873ed7ad3c1db15872')
+
+    depends_on('perl-compress-raw-zlib', type='run')
+    depends_on('perl-compress-raw-bzip2', type='run')
diff --git a/var/spack/repos/builtin/packages/perl-io-html/package.py b/var/spack/repos/builtin/packages/perl-io-html/package.py
new file mode 100644
index 0000000000..4fed8539bb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-io-html/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlIoHtml(PerlPackage):
+    """Open an HTML file with automatic charset detection."""
+
+    homepage = "http://search.cpan.org/~cjm/IO-HTML-1.001/lib/IO/HTML.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/C/CJ/CJM/IO-HTML-1.001.tar.gz"
+
+    version('1.001', '3f8958718844dc96b9f6946f21d70d22')
diff --git a/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py b/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py
new file mode 100644
index 0000000000..426a0afed5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-io-sessiondata/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlIoSessiondata(PerlPackage):
+    """A wrapper around a single IO::Socket object"""
+
+    homepage = "http://search.cpan.org/~phred/IO-SessionData-1.03/"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/IO-SessionData-1.03.tar.gz"
+
+    version('1.03', '790f9e05465c774cf9a6299500463104')
diff --git a/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py b/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py
new file mode 100644
index 0000000000..25df82bf0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-io-socket-ssl/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import inspect
+
+
+class PerlIoSocketSsl(PerlPackage):
+    """SSL sockets with IO::Socket interface"""
+
+    homepage = "http://search.cpan.org/~sullr/IO-Socket-SSL-2.052/lib/IO/Socket/SSL.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/SU/SULLR/IO-Socket-SSL-2.052.tar.gz"
+
+    version('2.052', '26c9bcdfb4ba8763ef89264f21326a48')
+
+    depends_on('perl-net-ssleay', type=('build', 'run'))
+
+    def configure(self, spec, prefix):
+        self.build_method = 'Makefile.PL'
+        self.build_executable = inspect.getmodule(self).make
+        # Should I do external tests?
+        config_answers = ['n\n']
+        config_answers_filename = 'spack-config.in'
+
+        with open(config_answers_filename, 'w') as f:
+            f.writelines(config_answers)
+
+        with open(config_answers_filename, 'r') as f:
+            inspect.getmodule(self).perl('Makefile.PL', 'INSTALL_BASE={0}'.
+                                         format(prefix), input=f)
diff --git a/var/spack/repos/builtin/packages/perl-io-string/package.py b/var/spack/repos/builtin/packages/perl-io-string/package.py
index ec08ac3078..2ce98e7627 100644
--- a/var/spack/repos/builtin/packages/perl-io-string/package.py
+++ b/var/spack/repos/builtin/packages/perl-io-string/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-json/package.py b/var/spack/repos/builtin/packages/perl-json/package.py
new file mode 100644
index 0000000000..2c0b41dcad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-json/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlJson(PerlPackage):
+    """JSON (JavaScript Object Notation) encoder/decoder"""
+
+    homepage = "http://search.cpan.org/~ishigaki/JSON/lib/JSON.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/JSON-2.97001.tar.gz"
+
+    version('2.97001', '693d6ff167496362f8ec6c3c5b8ba5ee')
diff --git a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py
new file mode 100644
index 0000000000..93344cc710
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLibwwwPerl(PerlPackage):
+    """The libwww-perl collection is a set of Perl modules which provides
+    a simple and consistent application programming interface to the
+    World-Wide Web. The main focus of the library is to provide classes and
+    functions that allow you to write WWW clients."""
+
+    homepage = "https://github.com/libwww-perl/libwww-perl"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz"
+
+    version('6.33', '2e15c1c789ac9036c99d094e47e3da23')
diff --git a/var/spack/repos/builtin/packages/perl-list-moreutils/package.py b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py
new file mode 100644
index 0000000000..6a23032fd1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-list-moreutils/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlListMoreutils(PerlPackage):
+    """Provide the stuff missing in List::Util"""
+
+    homepage = "http://search.cpan.org/~rehsack/List-MoreUtils/lib/List/MoreUtils.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RE/REHSACK/List-MoreUtils-0.428.tar.gz"
+
+    version('0.428', '493032a211cdff1fcf45f59ebd680407')
diff --git a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py
new file mode 100644
index 0000000000..dabb293e13
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLogLog4perl(PerlPackage):
+    """Log4j implementation for Perl"""
+
+    homepage = "http://search.cpan.org/~mschilli/Log-Log4perl-1.44/lib/Log/Log4perl.pm"
+    url      = "https://github.com/mschilli/log4perl/archive/rel_146.tar.gz"
+
+    version('146', '500abbd978ed326cfe5367dc4f9f3be2')
diff --git a/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py b/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py
new file mode 100644
index 0000000000..6955add7fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-lwp-mediatypes/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLwpMediatypes(PerlPackage):
+    """Guess media type for a file or a URL"""
+
+    homepage = "http://search.cpan.org/~gaas/LWP-MediaTypes-6.02/lib/LWP/MediaTypes.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/LWP-MediaTypes-6.02.tar.gz"
+
+    version('6.02', '8c5f25fb64b974d22aff424476ba13c9')
diff --git a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py
new file mode 100644
index 0000000000..200bd7700c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLwpProtocolHttps(PerlPackage):
+    """ Provide https support for LWP::UserAgent"""
+
+    homepage = "http://search.cpan.org/~gaas/LWP-Protocol-https-6.04/lib/LWP/Protocol/https.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/LWP-Protocol-https-6.04.tar.gz"
+
+    version('6.04', '1b422a7d3b5fed1eb4d748fdc9fd79a4')
+
+    depends_on('perl-test-requiresinternet', type=('build', 'run'))
+    depends_on('perl-io-socket-ssl', type=('build', 'run'))
+    depends_on('perl-net-http', type=('build', 'run'))
+    depends_on('perl-mozilla-ca', type=('build', 'run'))
+    depends_on('perl-lwp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-lwp/package.py b/var/spack/repos/builtin/packages/perl-lwp/package.py
new file mode 100644
index 0000000000..7d00186250
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-lwp/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlLwp(PerlPackage):
+    """The World-Wide Web library for Perl"""
+
+    homepage = "http://search.cpan.org/~oalders/libwww-perl-6.29/lib/LWP.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.29.tar.gz"
+
+    version('6.29', 'efec8d563ffd3652333356aa722c2b56')
+
+    depends_on('perl-test-requiresinternet', type=('build', 'run'))
+    depends_on('perl-http-message', type=('build', 'run'))
+    depends_on('perl-file-listing', type=('build', 'run'))
+    depends_on('perl-http-daemon', type=('build', 'run'))
+    depends_on('perl-html-parser', type=('build', 'run'))
+    depends_on('perl-http-cookies', type=('build', 'run'))
+    depends_on('perl-www-robotrules', type=('build', 'run'))
+    depends_on('perl-test-fatal', type=('build', 'run'))
+    depends_on('perl-http-negotiate', type=('build', 'run'))
+    depends_on('perl-net-http', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-math-cdf/package.py b/var/spack/repos/builtin/packages/perl-math-cdf/package.py
index 094b08dd1d..509b916868 100644
--- a/var/spack/repos/builtin/packages/perl-math-cdf/package.py
+++ b/var/spack/repos/builtin/packages/perl-math-cdf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-math-cephes/package.py b/var/spack/repos/builtin/packages/perl-math-cephes/package.py
new file mode 100644
index 0000000000..4b5899271e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-math-cephes/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlMathCephes(PerlPackage):
+    """This module provides an interface to over 150 functions of the
+       cephes math library of Stephen Moshier."""
+
+    homepage = "http://search.cpan.org/~shlomif/Math-Cephes/lib/Math/Cephes.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Math-Cephes-0.5305.tar.gz"
+
+    version('0.5305', '30922dd213783aaaf91a47626f6a1853')
diff --git a/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py b/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py
new file mode 100644
index 0000000000..54d57d564e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-math-matrixreal/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlMathMatrixreal(PerlPackage):
+    """Implements the data type "matrix of real numbers" (and consequently
+    also "vector of real numbers")."""
+
+    homepage = "http://search.cpan.org/~leto/Math-MatrixReal/lib/Math/MatrixReal.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LETO/Math-MatrixReal-2.13.tar.gz"
+
+    version('2.13', 'cf9d6ff71f2df075559ea752104ca199')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-module-build/package.py b/var/spack/repos/builtin/packages/perl-module-build/package.py
index 53bc80a062..cfe492c9e0 100644
--- a/var/spack/repos/builtin/packages/perl-module-build/package.py
+++ b/var/spack/repos/builtin/packages/perl-module-build/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
@@ -36,6 +17,7 @@ class PerlModuleBuild(PerlPackage):
     """
 
     homepage = "http://search.cpan.org/perldoc/Module::Build"
-    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/Module-Build-0.4220.tar.gz"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/Module-Build-0.4224.tar.gz"
 
+    version('0.4224', sha256='a6ca15d78244a7b50fdbf27f85c85f4035aa799ce7dd018a0d98b358ef7bc782')
     version('0.4220', '9df204e188462a4410d496f316c2c531')
diff --git a/var/spack/repos/builtin/packages/perl-module-implementation/package.py b/var/spack/repos/builtin/packages/perl-module-implementation/package.py
new file mode 100644
index 0000000000..ca8c2be284
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-module-implementation/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlModuleImplementation(PerlPackage):
+    """Loads one of several alternate underlying implementations for a
+    module"""
+
+    homepage = "http://search.cpan.org/~drolsky/Module-Implementation/lib/Module/Implementation.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DR/DROLSKY/Module-Implementation-0.09.tar.gz"
+
+    version('0.09', '52e3fe0ca6b1eff0488d59b7aacc0667')
+
+    depends_on('perl-module-runtime', type=('build', 'run'))
+    depends_on('perl-test-fatal', type=('build', 'run'))
+    depends_on('perl-test-requires', type=('build', 'run'))
+    depends_on('perl-try-tiny', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py b/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py
index 1b499ce7f9..d3e8c6757f 100644
--- a/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py
+++ b/var/spack/repos/builtin/packages/perl-module-runtime-conflicts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-module-runtime/package.py b/var/spack/repos/builtin/packages/perl-module-runtime/package.py
new file mode 100644
index 0000000000..b694f2eeed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-module-runtime/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlModuleRuntime(PerlPackage):
+    """Runtime module handling"""
+
+    homepage = "http://search.cpan.org/~zefram/Module-Runtime/lib/Module/Runtime.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/Z/ZE/ZEFRAM/Module-Runtime-0.016.tar.gz"
+
+    version('0.016', 'd3d47222fa2e3dfcb4526f6cc8437b20')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-moose/package.py b/var/spack/repos/builtin/packages/perl-moose/package.py
index 2a0261599f..25c5402691 100644
--- a/var/spack/repos/builtin/packages/perl-moose/package.py
+++ b/var/spack/repos/builtin/packages/perl-moose/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,9 @@ class PerlMoose(PerlPackage):
     homepage = "http://search.cpan.org/~ether/Moose-2.2006/lib/Moose.pm"
     url      = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Moose-2.2006.tar.gz"
 
+    version('2.2010', '636238ac384818ee1e92eff6b9ecc50a')
+    version('2.2009', '5527b1a5abc29b5c57fc488447e76ccd')
+    version('2.2007', 'de487ae226003f7e7f22c0fd8f0074e6')
     version('2.2006', '929c6b3877a6054ef617cf7ef1e220b5')
 
     depends_on('perl-cpan-meta-check', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py b/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py
new file mode 100644
index 0000000000..6ab7f85ade
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-mozilla-ca/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlMozillaCa(PerlPackage):
+    """Mozilla's CA cert bundle in PEM format"""
+
+    homepage = "http://search.cpan.org/~abh/Mozilla-CA-20160104/lib/Mozilla/CA.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/A/AB/ABH/Mozilla-CA-20160104.tar.gz"
+
+    version('20160104', '1b91edb15953a8188f011ab5ff433300')
diff --git a/var/spack/repos/builtin/packages/perl-mro-compat/package.py b/var/spack/repos/builtin/packages/perl-mro-compat/package.py
index 81b6f19ffa..be1b7ec3a5 100644
--- a/var/spack/repos/builtin/packages/perl-mro-compat/package.py
+++ b/var/spack/repos/builtin/packages/perl-mro-compat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-namespace-clean/package.py b/var/spack/repos/builtin/packages/perl-namespace-clean/package.py
index 8dc2492430..fec8be732e 100644
--- a/var/spack/repos/builtin/packages/perl-namespace-clean/package.py
+++ b/var/spack/repos/builtin/packages/perl-namespace-clean/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-net-http/package.py b/var/spack/repos/builtin/packages/perl-net-http/package.py
new file mode 100644
index 0000000000..272ce07bb0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-net-http/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlNetHttp(PerlPackage):
+    """Low-level HTTP connection (client)"""
+
+    homepage = "http://search.cpan.org/~oalders/Net-HTTP-6.17/lib/Net/HTTP.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/Net-HTTP-6.17.tar.gz"
+
+    version('6.17', '068fa02fd3c8a5b63316025b5a24844c')
+
+    depends_on('perl-uri', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py b/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py
new file mode 100644
index 0000000000..5969f63a4b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-net-scp-expect/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlNetScpExpect(PerlPackage):
+    """Wrapper for scp that allows passwords via Expect."""
+
+    homepage = "http://search.cpan.org/~rybskej/Net-SCP-Expect/Expect.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RY/RYBSKEJ/Net-SCP-Expect-0.16.tar.gz"
+
+    version('0.16', 'a3d8f5e6a34ba3df8527aea098f64a58')
diff --git a/var/spack/repos/builtin/packages/perl-net-ssleay/package.py b/var/spack/repos/builtin/packages/perl-net-ssleay/package.py
new file mode 100644
index 0000000000..5f84ceebfb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-net-ssleay/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import inspect
+
+
+class PerlNetSsleay(PerlPackage):
+    """Perl extension for using OpenSSL"""
+
+    homepage = "http://search.cpan.org/~mikem/Net-SSLeay-1.82/lib/Net/SSLeay.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MI/MIKEM/Net-SSLeay-1.82.tar.gz"
+
+    version('1.82', '2170469d929d5173bacffd0cb2d7fafa')
+
+    depends_on('openssl')
+
+    def configure(self, spec, prefix):
+        self.build_method = 'Makefile.PL'
+        self.build_executable = inspect.getmodule(self).make
+        # Do you want to run external tests?
+        config_answers = ['\n']
+        config_answers_filename = 'spack-config.in'
+
+        with open(config_answers_filename, 'w') as f:
+            f.writelines(config_answers)
+
+        with open(config_answers_filename, 'r') as f:
+            inspect.getmodule(self).perl('Makefile.PL', 'INSTALL_BASE={0}'.
+                                         format(prefix), 'OPENSSL_PREFIX=%s' %
+                                         self.spec['openssl'].prefix, input=f)
diff --git a/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py b/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py
index 89e1690fdd..ba07697509 100644
--- a/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py
+++ b/var/spack/repos/builtin/packages/perl-package-deprecationmanager/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py b/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py
index 7d627ffb65..9dd65c9fb3 100644
--- a/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py
+++ b/var/spack/repos/builtin/packages/perl-package-stash-xs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-package-stash/package.py b/var/spack/repos/builtin/packages/perl-package-stash/package.py
index abc8a5ccfe..9f772e5196 100644
--- a/var/spack/repos/builtin/packages/perl-package-stash/package.py
+++ b/var/spack/repos/builtin/packages/perl-package-stash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-padwalker/package.py b/var/spack/repos/builtin/packages/perl-padwalker/package.py
index 0ffef9cf18..f9e028e35d 100644
--- a/var/spack/repos/builtin/packages/perl-padwalker/package.py
+++ b/var/spack/repos/builtin/packages/perl-padwalker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py b/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py
new file mode 100644
index 0000000000..46cb34f99f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-parallel-forkmanager/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlParallelForkmanager(PerlPackage):
+    """A simple parallel processing fork manager"""
+
+    homepage = "http://search.cpan.org/~yanick/Parallel-ForkManager/lib/Parallel/ForkManager.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz"
+
+    version('1.19', '0e7137dd4b6948e1633b3b9ebe3b87e1')
diff --git a/var/spack/repos/builtin/packages/perl-params-util/package.py b/var/spack/repos/builtin/packages/perl-params-util/package.py
index 834601512b..503b276a6c 100644
--- a/var/spack/repos/builtin/packages/perl-params-util/package.py
+++ b/var/spack/repos/builtin/packages/perl-params-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py b/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py
new file mode 100644
index 0000000000..a9623c453a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-parse-recdescent/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlParseRecdescent(PerlPackage):
+    """Generate Recursive-Descent Parsers"""
+
+    homepage = "http://search.cpan.org/~jtbraun/Parse-RecDescent-1.967015/lib/Parse/RecDescent.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/J/JT/JTBRAUN/Parse-RecDescent-1.967015.tar.gz"
+
+    version('1.967015', '7a36d45d62a9b68603edcdbd276006cc')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-pdf-api2/package.py b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py
index 216971529c..6322e13558 100644
--- a/var/spack/repos/builtin/packages/perl-pdf-api2/package.py
+++ b/var/spack/repos/builtin/packages/perl-pdf-api2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-pegex/package.py b/var/spack/repos/builtin/packages/perl-pegex/package.py
new file mode 100644
index 0000000000..62015d2682
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-pegex/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPegex(PerlPackage):
+    """Acmeist PEG Parser Framework"""
+
+    homepage = "http://search.cpan.org/~ingy/Pegex-0.64/lib/Pegex.pod"
+    url      = "http://search.cpan.org/CPAN/authors/id/I/IN/INGY/Pegex-0.64.tar.gz"
+
+    version('0.64', 'db86d4f1ddc36c4c7860ce060e77976f')
+
+    depends_on('perl-file-sharedir-install', type=('build', 'run'))
+    depends_on('perl-yaml-libyaml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py b/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py
new file mode 100644
index 0000000000..cd4f4d1d4e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-perl4-corelibs/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPerl4Corelibs(PerlPackage):
+    """Perl4::CoreLibs - libraries historically supplied with Perl 4"""
+
+    # doesn't look like a homepage but it is
+    homepage = "https://metacpan.org/pod/release/ZEFRAM/Perl4-CoreLibs-0.003/lib/Perl4/CoreLibs.pm"
+    url      = "https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/Perl4-CoreLibs-0.003.tar.gz"
+
+    version('0.004', sha256='78887e3365f8935ab00d528832e9b7a426fb684ffc5c03c20e67a217ca4ac64a')
+    version('0.003', sha256='55c9b2b032944406dbaa2fd97aa3692a1ebce558effc457b4e800dabfaad9ade')
+    version('0.002', sha256='c68272e8b0e37268d9fbb93f5ef5708e12e0a13bbb5a6123af3f493ea8852521')
+    version('0.001', sha256='f7479f63e8b0cc344752a59f66fd084a14ee87bcc2a1f67c1a413afab8d0ad37')
+    version('0.000', sha256='d8f2310ad0b0f48c8fc258a75042ebeedf47bcefb231be427761dba77e734875')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py b/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py
new file mode 100644
index 0000000000..69721a7d04
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-perl6-slurp/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPerl6Slurp(PerlPackage):
+    """Perl6::Slurp - Implements the Perl 6 'slurp' built-in"""
+
+    homepage = "http://search.cpan.org/~dconway/Perl6-Slurp-0.051005/lib/Perl6/Slurp.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DC/DCONWAY/Perl6-Slurp-0.051005.tar.gz"
+
+    version('0.051005', '6095c8df495c7983f36996ed78c5ead7')
+
+    depends_on('perl@5.8:5.999', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py
new file mode 100644
index 0000000000..44996865bc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-perlio-gzip/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPerlioGzip(PerlPackage):
+    """Perl extension to provide a PerlIO layer to gzip/gunzip"""
+
+    homepage = "http://search.cpan.org/~nwclark/PerlIO-gzip/gzip.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/N/NW/NWCLARK/PerlIO-gzip-0.19.tar.gz"
+
+    version('0.20', '0393eae5d0b23df6cf40ed44af7d711c')
+    version('0.19', 'dbcfc1450f6b593b65048b8ced061c98')
diff --git a/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py b/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py
new file mode 100644
index 0000000000..5bd83c8fdc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-perlio-utf8-strict/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlPerlioUtf8Strict(PerlPackage):
+    """This module provides a fast and correct UTF-8 PerlIO layer."""
+
+    homepage = "http://search.cpan.org/~leont/PerlIO-utf8_strict/lib/PerlIO/utf8_strict.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/PerlIO-utf8_strict-0.002.tar.gz"
+
+    version('0.002', '2e5b13efe6dfd7748e44e47f6dedb1da')
diff --git a/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py b/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py
new file mode 100644
index 0000000000..dbc3e96388
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-scalar-util-numeric/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlScalarUtilNumeric(PerlPackage):
+    """This module exports a number of wrappers around perl's builtin grok_number
+       function, which returns the numeric type of its argument, or 0 if it
+       isn't numeric."""
+
+    homepage = "https://metacpan.org/pod/Scalar::Util::Numeric"
+    url      = "https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE/Scalar-Util-Numeric-0.40.tar.gz"
+
+    version('0.40', sha256='d7501b6d410703db5b1c1942fbfc41af8964a35525d7f766058acf5ca2cc4440')
diff --git a/var/spack/repos/builtin/packages/perl-soap-lite/package.py b/var/spack/repos/builtin/packages/perl-soap-lite/package.py
new file mode 100644
index 0000000000..f6e357a65b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-soap-lite/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlSoapLite(PerlPackage):
+    """Perl's Web Services Toolkit"""
+
+    homepage = "http://search.cpan.org/~phred/SOAP-Lite-1.20/lib/SOAP/Lite.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/SOAP-Lite-1.22.tar.gz"
+
+    version('1.22', '86c31341311498a08c6309e62168f655')
+
+    depends_on('perl-io-sessiondata', type=('build', 'run'))
+    depends_on('perl-lwp-protocol-https', type=('build', 'run'))
+    depends_on('perl-task-weaken', type=('build', 'run'))
+    depends_on('perl-xml-parser-lite', type=('build', 'run'))
+    depends_on('perl-xml-parser', type=('build', 'run'))
+    depends_on('perl-test-warn', type=('build', 'run'))
+    depends_on('perl-class-inspector', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-star-fusion/package.py b/var/spack/repos/builtin/packages/perl-star-fusion/package.py
index 5985bd7fd3..4c137739d5 100644
--- a/var/spack/repos/builtin/packages/perl-star-fusion/package.py
+++ b/var/spack/repos/builtin/packages/perl-star-fusion/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from glob import glob
 
@@ -34,9 +15,9 @@ class PerlStarFusion(Package):
     and spanning reads to a reference annotation set."""
 
     homepage = "https://github.com/STAR-Fusion/STAR-Fusion"
-    url      = "https://github.com/STAR-Fusion/STAR-Fusion.git"
+    git      = "https://github.com/STAR-Fusion/STAR-Fusion.git"
 
-    version('master', git='https://github.com/STAR-Fusion/STAR-Fusion.git', commit='a16a0a8')
+    version('master', commit='8c5a541')
 
     extends('perl')
 
diff --git a/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py b/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py
new file mode 100644
index 0000000000..e35bca37c0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-statistics-descriptive/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlStatisticsDescriptive(PerlPackage):
+    """Module of basic descriptive statistical functions."""
+
+    homepage = "http://search.cpan.org/~shlomif/Statistics-Descriptive-3.0612/lib/Statistics/Descriptive.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0612.tar.gz"
+
+    version('3.0612', 'e38cfbc1e3962d099b62a14a57a175f1')
diff --git a/var/spack/repos/builtin/packages/perl-statistics-pca/package.py b/var/spack/repos/builtin/packages/perl-statistics-pca/package.py
new file mode 100644
index 0000000000..cd2e6844a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-statistics-pca/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlStatisticsPca(PerlPackage):
+    """A simple Perl implementation of Principal Component Analysis."""
+
+    homepage = "http://search.cpan.org/~dsth/Statistics-PCA/lib/Statistics/PCA.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/D/DS/DSTH/Statistics-PCA-0.0.1.tar.gz"
+
+    version('0.0.1', '6e0e05fe13f6becea525b973a0c29001')
+
+    depends_on('perl-module-build', type='build')
+    depends_on('perl-contextual-return', type=('build', 'run'))
+    depends_on('perl-text-simpletable', type=('build', 'run'))
+    depends_on('perl-math-matrixreal', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py b/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py
index a6642fce2c..88930215ef 100644
--- a/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-exporter-progressive/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-exporter/package.py b/var/spack/repos/builtin/packages/perl-sub-exporter/package.py
index 0b13cb870e..184af5ccda 100644
--- a/var/spack/repos/builtin/packages/perl-sub-exporter/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-exporter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-identify/package.py b/var/spack/repos/builtin/packages/perl-sub-identify/package.py
index e173ebfeae..6970774946 100644
--- a/var/spack/repos/builtin/packages/perl-sub-identify/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-identify/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-install/package.py b/var/spack/repos/builtin/packages/perl-sub-install/package.py
index 8354eb5be7..ee0088d3c0 100644
--- a/var/spack/repos/builtin/packages/perl-sub-install/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-install/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-name/package.py b/var/spack/repos/builtin/packages/perl-sub-name/package.py
index 74df14dbd1..82d4606fff 100644
--- a/var/spack/repos/builtin/packages/perl-sub-name/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-name/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py
index 049c844e1d..46f4b4f68b 100644
--- a/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py
+++ b/var/spack/repos/builtin/packages/perl-sub-uplevel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-svg/package.py b/var/spack/repos/builtin/packages/perl-svg/package.py
new file mode 100644
index 0000000000..6152c8395e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-svg/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlSvg(PerlPackage):
+    """Perl extension for generating Scalable Vector Graphics (SVG) documents.
+    """
+
+    homepage = "http://search.cpan.org/~manwar/SVG-2.78/lib/SVG.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MA/MANWAR/SVG-2.78.tar.gz"
+
+    version('2.78', 'b247c216ab11fae24533d0ce556e2e75')
diff --git a/var/spack/repos/builtin/packages/perl-swissknife/package.py b/var/spack/repos/builtin/packages/perl-swissknife/package.py
new file mode 100644
index 0000000000..6f0a105b4c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-swissknife/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlSwissknife(PerlPackage):
+    """An object-oriented Perl library to handle Swiss-Prot entries"""
+
+    homepage = "http://swissknife.sourceforge.net"
+    url      = "https://downloads.sourceforge.net/project/swissknife/swissknife/1.75/Swissknife_1.75.tar.gz"
+
+    version('1.75', '09d008cb1d1d211ae4eb9f087c213edf')
+
+    depends_on('perl-module-build', type='build')
diff --git a/var/spack/repos/builtin/packages/perl-task-weaken/package.py b/var/spack/repos/builtin/packages/perl-task-weaken/package.py
new file mode 100644
index 0000000000..810ce1dae8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-task-weaken/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTaskWeaken(PerlPackage):
+    """Ensure that a platform has weaken support"""
+
+    homepage = "http://search.cpan.org/~adamk/Task-Weaken-1.04/lib/Task/Weaken.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/A/AD/ADAMK/Task-Weaken-1.04.tar.gz"
+
+    version('1.04', 'affd0c395515bb95d29968404d7fe6de')
diff --git a/var/spack/repos/builtin/packages/perl-term-readkey/package.py b/var/spack/repos/builtin/packages/perl-term-readkey/package.py
index b25e34c04d..fa812f1bf5 100644
--- a/var/spack/repos/builtin/packages/perl-term-readkey/package.py
+++ b/var/spack/repos/builtin/packages/perl-term-readkey/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py b/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py
index 86e8bfae4a..a80ec687ab 100644
--- a/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-cleannamespaces/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-deep/package.py b/var/spack/repos/builtin/packages/perl-test-deep/package.py
index d1a6d248f5..94b6edc5cb 100644
--- a/var/spack/repos/builtin/packages/perl-test-deep/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-deep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-differences/package.py b/var/spack/repos/builtin/packages/perl-test-differences/package.py
index b37442fc28..10a738737c 100644
--- a/var/spack/repos/builtin/packages/perl-test-differences/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-differences/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-exception/package.py b/var/spack/repos/builtin/packages/perl-test-exception/package.py
index 32b902221e..05ffa21c9e 100644
--- a/var/spack/repos/builtin/packages/perl-test-exception/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-exception/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-fatal/package.py b/var/spack/repos/builtin/packages/perl-test-fatal/package.py
index 314fee9df6..6e7833f291 100644
--- a/var/spack/repos/builtin/packages/perl-test-fatal/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-fatal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py
index b9132952b2..e8c42e3839 100644
--- a/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-memory-cycle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-most/package.py b/var/spack/repos/builtin/packages/perl-test-most/package.py
index a6a3650c42..90aa5cf79c 100644
--- a/var/spack/repos/builtin/packages/perl-test-most/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-most/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-needs/package.py b/var/spack/repos/builtin/packages/perl-test-needs/package.py
index 9006067309..8d07133156 100644
--- a/var/spack/repos/builtin/packages/perl-test-needs/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-needs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-requires/package.py b/var/spack/repos/builtin/packages/perl-test-requires/package.py
index 79bfb211a0..bd4c395c68 100644
--- a/var/spack/repos/builtin/packages/perl-test-requires/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-requires/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py b/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py
new file mode 100644
index 0000000000..e8f412a74f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-test-requiresinternet/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTestRequiresinternet(PerlPackage):
+    """Easily test network connectivity"""
+
+    homepage = "http://search.cpan.org/~mallen/Test-RequiresInternet-0.05/lib/Test/RequiresInternet.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MA/MALLEN/Test-RequiresInternet-0.05.tar.gz"
+
+    version('0.05', '0ba9f1cff4cf90ed2618c2eddfd525d8')
diff --git a/var/spack/repos/builtin/packages/perl-test-warn/package.py b/var/spack/repos/builtin/packages/perl-test-warn/package.py
index e1e9a873a6..d72aea1349 100644
--- a/var/spack/repos/builtin/packages/perl-test-warn/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-warn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-test-warnings/package.py b/var/spack/repos/builtin/packages/perl-test-warnings/package.py
index dc3640fe33..5d36d5d20f 100644
--- a/var/spack/repos/builtin/packages/perl-test-warnings/package.py
+++ b/var/spack/repos/builtin/packages/perl-test-warnings/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-text-csv/package.py b/var/spack/repos/builtin/packages/perl-text-csv/package.py
new file mode 100644
index 0000000000..4f57470fb4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-text-csv/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTextCsv(PerlPackage):
+    """Comma-separated values manipulator (using XS or PurePerl)"""
+
+    homepage = "http://search.cpan.org/~ishigaki/Text-CSV/lib/Text/CSV.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI/Text-CSV-1.95.tar.gz"
+
+    version('1.95', '1e076b4b1f8ba6a5003bf93f3c437a9e')
diff --git a/var/spack/repos/builtin/packages/perl-text-diff/package.py b/var/spack/repos/builtin/packages/perl-text-diff/package.py
index 4c61b3cbb1..2213365571 100644
--- a/var/spack/repos/builtin/packages/perl-text-diff/package.py
+++ b/var/spack/repos/builtin/packages/perl-text-diff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-text-simpletable/package.py b/var/spack/repos/builtin/packages/perl-text-simpletable/package.py
new file mode 100644
index 0000000000..175d707fc8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-text-simpletable/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTextSimpletable(PerlPackage):
+    """Simple Eyecandy ASCII Tables"""
+
+    homepage = "http://search.cpan.org/~mramberg/Text-SimpleTable/lib/Text/SimpleTable.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/M/MR/MRAMBERG/Text-SimpleTable-2.04.tar.gz"
+
+    version('2.04', '550136523c8da37b616988f9a5f58d59')
diff --git a/var/spack/repos/builtin/packages/perl-text-soundex/package.py b/var/spack/repos/builtin/packages/perl-text-soundex/package.py
new file mode 100644
index 0000000000..69ca76f262
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-text-soundex/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTextSoundex(PerlPackage):
+    """Soundex is a phonetic algorithm for indexing names by sound, as
+       pronounced in English. The goal is for names with the same
+       pronunciation to be encoded to the same representation so
+       that they can be matched despite minor differences in spelling"""
+
+    homepage = "http://search.cpan.org/~rjbs/Text-Soundex-3.05/Soundex.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RJ/RJBS/Text-Soundex-3.05.tar.gz"
+
+    version('3.05', 'cb40ded7a5d27aa3a411d274d6ec18ae')
diff --git a/var/spack/repos/builtin/packages/perl-text-unidecode/package.py b/var/spack/repos/builtin/packages/perl-text-unidecode/package.py
new file mode 100644
index 0000000000..792f8e8e74
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-text-unidecode/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTextUnidecode(PerlPackage):
+    """plain ASCII transliterations of Unicode text"""
+
+    homepage = "http://search.cpan.org/~sburke/Text-Unidecode/lib/Text/Unidecode.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/S/SB/SBURKE/Text-Unidecode-1.30.tar.gz"
+
+    version('1.30', '31cca8505bd74ed9d8036cdc84c808ca')
diff --git a/var/spack/repos/builtin/packages/perl-time-hires/package.py b/var/spack/repos/builtin/packages/perl-time-hires/package.py
new file mode 100644
index 0000000000..5250614010
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-time-hires/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTimeHires(PerlPackage):
+    """High resolution alarm, sleep, gettimeofday, interval timers"""
+
+    homepage = "http://search.cpan.org/~jhi/Time-HiRes-1.9746/HiRes.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/J/JH/JHI/Time-HiRes-1.9746.tar.gz"
+
+    version('1.9746', '728dc2c2715313a056792191d7d0726c')
diff --git a/var/spack/repos/builtin/packages/perl-time-piece/package.py b/var/spack/repos/builtin/packages/perl-time-piece/package.py
new file mode 100644
index 0000000000..fe24c198ac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-time-piece/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTimePiece(PerlPackage):
+    """Object Oriented time objects"""
+
+    homepage = "http://search.cpan.org/~esaym/Time-Piece/Piece.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/E/ES/ESAYM/Time-Piece-1.3203.tar.gz"
+
+    version('1.3203', '515c1306f123a00116a95335cf543501')
diff --git a/var/spack/repos/builtin/packages/perl-try-tiny/package.py b/var/spack/repos/builtin/packages/perl-try-tiny/package.py
new file mode 100644
index 0000000000..a985b7e7fb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-try-tiny/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlTryTiny(PerlPackage):
+    """Minimal try/catch with proper preservation of $@"""
+
+    homepage = "http://search.cpan.org/~ether/Try-Tiny-0.28/lib/Try/Tiny.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/Try-Tiny-0.28.tar.gz"
+
+    version('0.28', 'e2f8af601a62981aab30df15a6f47475')
diff --git a/var/spack/repos/builtin/packages/perl-uri-escape/package.py b/var/spack/repos/builtin/packages/perl-uri-escape/package.py
index 29f96003e3..64d7ba40fc 100644
--- a/var/spack/repos/builtin/packages/perl-uri-escape/package.py
+++ b/var/spack/repos/builtin/packages/perl-uri-escape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/perl-uri/package.py b/var/spack/repos/builtin/packages/perl-uri/package.py
new file mode 100644
index 0000000000..af5fb9a980
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-uri/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlUri(PerlPackage):
+    """Uniform Resource Identifiers (absolute and relative)"""
+
+    homepage = "http://search.cpan.org/~ether/URI-1.72/lib/URI.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/URI-1.72.tar.gz"
+
+    version('1.72', 'cd56d81ed429efaa97e7f3ff08851b48')
+
+    depends_on('perl-test-needs', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-version/package.py b/var/spack/repos/builtin/packages/perl-version/package.py
new file mode 100644
index 0000000000..e9a40018c8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-version/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlVersion(PerlPackage):
+    """Parse and manipulate Perl version strings"""
+
+    homepage = "http://search.cpan.org/~bdfoy/Perl-Version-1.013/lib/Perl/Version.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/B/BD/BDFOY/Perl-Version-1.013_03.tar.gz"
+
+    version('1.013_03', 'b2c94c8b33ccfa1635c760fcfa1c5358')
+
+    depends_on('perl-file-slurp-tiny', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-want/package.py b/var/spack/repos/builtin/packages/perl-want/package.py
new file mode 100644
index 0000000000..acd9e31da2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-want/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlWant(PerlPackage):
+    """A generalisation of wantarray."""
+
+    homepage = "search.cpan.org/~robin/Want/Want.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/R/RO/ROBIN/Want-0.29.tar.gz"
+
+    version('0.29', '33b2dae5db59781b9a0434fa1db04aab')
diff --git a/var/spack/repos/builtin/packages/perl-www-robotrules/package.py b/var/spack/repos/builtin/packages/perl-www-robotrules/package.py
new file mode 100644
index 0000000000..5f54470821
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-www-robotrules/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlWwwRobotrules(PerlPackage):
+    """Database of robots.txt-derived permissions"""
+
+    homepage = "http://deps.cpantesters.org/?module=WWW%3A%3ARobotRules;perl=latest"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GA/GAAS/WWW-RobotRules-6.02.tar.gz"
+
+    version('6.02', 'b7186e8b8b3701e70c22abf430742403')
+
+    depends_on('perl-uri', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py b/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py
new file mode 100644
index 0000000000..f4b7773e21
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-xml-parser-lite/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlXmlParserLite(PerlPackage):
+    """Lightweight pure-perl XML Parser (based on regexps)"""
+
+    homepage = "http://search.cpan.org/~phred/XML-Parser-Lite-0.721/lib/XML/Parser/Lite.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/P/PH/PHRED/XML-Parser-Lite-0.721.tar.gz"
+
+    version('0.721', 'ad8a87b9bf413aa540c7cb724d650808')
+
+    depends_on('perl-test-requires', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-xml-parser/package.py b/var/spack/repos/builtin/packages/perl-xml-parser/package.py
index baa337319d..9b04cdd1b3 100644
--- a/var/spack/repos/builtin/packages/perl-xml-parser/package.py
+++ b/var/spack/repos/builtin/packages/perl-xml-parser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/perl-xml-simple/package.py b/var/spack/repos/builtin/packages/perl-xml-simple/package.py
new file mode 100644
index 0000000000..fa7aed9723
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-xml-simple/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlXmlSimple(PerlPackage):
+    """An API for simple XML files"""
+
+    homepage = "http://search.cpan.org/~grantm/XML-Simple/lib/XML/Simple.pm"
+    url      = "http://search.cpan.org/CPAN/authors/id/G/GR/GRANTM/XML-Simple-2.24.tar.gz"
+
+    version('2.24', '1cd2e8e3421160c42277523d5b2f4dd2')
+
+    depends_on('perl-xml-parser', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py b/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py
new file mode 100644
index 0000000000..6893e7ac81
--- /dev/null
+++ b/var/spack/repos/builtin/packages/perl-yaml-libyaml/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PerlYamlLibyaml(PerlPackage):
+    """Perl YAML Serialization using XS and libyaml  """
+
+    homepage = "http://search.cpan.org/~tinita/YAML-LibYAML/"
+    url      = "http://search.cpan.org/CPAN/authors/id/T/TI/TINITA/YAML-LibYAML-0.67.tar.gz"
+
+    version('0.67', '5a787150db680e3ab3f753f2e54640ab')
diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py
index fbf788d106..fd0c4aef17 100644
--- a/var/spack/repos/builtin/packages/perl/package.py
+++ b/var/spack/repos/builtin/packages/perl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # Author: Milton Woods <milton.woods@bom.gov.au>
 # Date: March 22, 2017
@@ -30,12 +11,13 @@
 # Author: Justin Too <justin@doubleotoo.com>
 # Date: September 6, 2015
 #
-from spack import *
 import os
 from contextlib import contextmanager
-import spack
+
 from llnl.util.lang import match_predicate
 
+from spack import *
+
 
 class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     """Perl 5 is a highly capable, feature-rich programming language with over
@@ -45,19 +27,23 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     # URL must remain http:// so Spack can bootstrap curl
     url = "http://www.cpan.org/src/5.0/perl-5.24.1.tar.gz"
 
-    # Development releases
+    # see http://www.cpan.org/src/README.html for
+    # explanation of version numbering scheme
+
+    # Development releases (odd numbers)
     version('5.25.11', '37a398682c36cd85992b34b5c1c25dc1')
 
-    # Maintenance releases (recommended)
-    version('5.24.1', '765ef511b5b87a164e2531403ee16b3c', preferred=True)
-    version('5.22.3', 'aa4f236dc2fc6f88b871436b8d0fda95')
+    # Maintenance releases (even numbers, recommended)
+    version('5.28.0', sha256='7e929f64d4cb0e9d1159d4a59fc89394e27fa1f7004d0836ca0d514685406ea8')
+    version('5.26.2', 'dc0fea097f3992a8cd53f8ac0810d523', preferred=True)
+    version('5.24.1', '765ef511b5b87a164e2531403ee16b3c')
 
-    # Misc releases that people need
+    # End of life releases
+    version('5.22.4', '31a71821682e02378fcdadeed85688b8')
+    version('5.22.3', 'aa4f236dc2fc6f88b871436b8d0fda95')
     version('5.22.2', '5767e2a10dd62a46d7b57f74a90d952b')
     version('5.22.1', '19295bbb775a3c36123161b9bf4892f1')
     version('5.22.0', 'e32cb6a8dda0084f2a43dac76318d68d')
-
-    # End of life releases
     version('5.20.3', 'd647d0ea5a7a8194c34759ab9f2610cd')
     version('5.18.4', '1f9334ff730adc05acd3dd7130d295db')
     version('5.16.3', 'eb5c40f2575df6c155bc99e3fe0a9d82')
@@ -71,6 +57,10 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     # https://rt.perl.org/Public/Bug/Display.html?id=126468
     patch('protect-quotes-in-ccflags.patch', when='@5.22.0')
 
+    # Fix build on Fedora 28
+    # https://bugzilla.redhat.com/show_bug.cgi?id=1536752
+    patch('https://src.fedoraproject.org/rpms/perl/raw/004cea3a67df42e92ffdf4e9ac36d47a3c6a05a4/f/perl-5.26.1-guard_old_libcrypt_fix.patch', level=1, sha256='0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac', when='@:5.26.2')
+
     # Installing cpanm alongside the core makes it safe and simple for
     # people/projects to install their own sets of perl modules.  Not
     # having it in core increases the "energy of activation" for doing
@@ -81,6 +71,9 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
     variant('shared', default=True,
             description='Build a shared libperl.so library')
 
+    variant('threads', default=True,
+            description='Build perl with threads support')
+
     resource(
         name="cpanm",
         url="http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7042.tar.gz",
@@ -91,6 +84,18 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
 
     phases = ['configure', 'build', 'install']
 
+    # On a lustre filesystem, patch may fail when files
+    # aren't writeable so make pp.c user writeable
+    # before patching. This should probably walk the
+    # source and make everything writeable in the future.
+    def do_stage(self, mirror_only=False):
+        # Do Spack's regular stage
+        super(Perl, self).do_stage(mirror_only)
+        # Add write permissions on file to be patched
+        filename = join_path(self.stage.source_path, 'pp.c')
+        perm = os.stat(filename).st_mode
+        os.chmod(filename, perm | 0o200)
+
     def configure_args(self):
         spec = self.spec
         prefix = self.prefix
@@ -128,6 +133,9 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
         if '+shared' in spec:
             config_args.append('-Duseshrplib')
 
+        if '+threads' in spec:
+            config_args.append('-Dusethreads')
+
         return config_args
 
     def configure(self, spec, prefix):
@@ -252,27 +260,23 @@ class Perl(Package):  # Perl doesn't use Autotools, it should subclass Package
 
         return match_predicate(ignore_arg, patterns)
 
-    def activate(self, ext_pkg, **args):
+    def activate(self, ext_pkg, view, **args):
         ignore = self.perl_ignore(ext_pkg, args)
         args.update(ignore=ignore)
 
-        super(Perl, self).activate(ext_pkg, **args)
-
-        extensions_layout = args.get("extensions_layout",
-                                     spack.store.extensions)
+        super(Perl, self).activate(ext_pkg, view, **args)
 
+        extensions_layout = view.extensions_layout
         exts = extensions_layout.extension_map(self.spec)
         exts[ext_pkg.name] = ext_pkg.spec
 
-    def deactivate(self, ext_pkg, **args):
+    def deactivate(self, ext_pkg, view, **args):
         ignore = self.perl_ignore(ext_pkg, args)
         args.update(ignore=ignore)
 
-        super(Perl, self).deactivate(ext_pkg, **args)
-
-        extensions_layout = args.get("extensions_layout",
-                                     spack.store.extensions)
+        super(Perl, self).deactivate(ext_pkg, view, **args)
 
+        extensions_layout = view.extensions_layout
         exts = extensions_layout.extension_map(self.spec)
         # Make deactivate idempotent
         if ext_pkg.name in exts:
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 838369f4e4..8be5d8cce5 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
 import sys
@@ -35,13 +16,24 @@ class Petsc(Package):
     """
 
     homepage = "http://www.mcs.anl.gov/petsc/index.html"
-    url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
+    url      = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
+    git      = "https://bitbucket.org/petsc/petsc.git"
 
-    maintainers = ['balay', 'barrysmith']
+    maintainers = ['balay', 'barrysmith', 'jedbrown']
 
-    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('develop', branch='master')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
 
+    version('3.10.2', '63ed950653ae9b8d19daea47e24c0338')
+    version('3.10.1', '2d0d5a9bd8112a4147a2a23f7f62a906')
+    version('3.10.0', '0240c2ce8c54e47b3531a743ee844d41')
+    version('3.9.4', 'c98eb67573efb2f91c6f239368259e44')
+    version('3.9.3', '7b71d705f66f9961cb0e2da3f9da79a1')
+    version('3.9.2', '8bedc0cd8c8603d54bfd99a6e8f77b3d')
+    version('3.9.1', 'd3a229a188dbeef9b3f29b9a63622fad')
+    version('3.9.0', '34b8a81814ca050a96d58e53a2f0ac7a')
+    version('3.8.4', 'd7767fe2919536aa393eb22841899306')
+    version('3.8.3', '322cbcf2a0f7b7bad562643b05d66f11')
     version('3.8.2', '00666e1c4cbfa8dd6eebf91ff8180f79')
     version('3.8.1', '3ed75c1147800fc156fe1f1e515a68a7')
     version('3.8.0', '02680f1f78a0d4c5a9de80a366793eb8')
@@ -69,7 +61,6 @@ class Petsc(Package):
             description='Activates support for metis and parmetis')
     variant('hdf5',    default=True,
             description='Activates support for HDF5 (only parallel)')
-    variant('boost',   default=True,  description='Activates support for Boost')
     variant('hypre',   default=True,
             description='Activates support for Hypre (only parallel)')
     # Mumps is disabled by default, because it depends on Scalapack
@@ -83,6 +74,11 @@ class Petsc(Package):
             description='Activates support for Trilinos (only parallel)')
     variant('int64', default=False,
             description='Compile with 64bit indices')
+    variant('clanguage', default='C', values=('C', 'C++'),
+            description='Specify C (recommended) or C++ to compile PETSc',
+            multi=False)
+    variant('suite-sparse', default=False,
+            description='Activates support for SuiteSparse')
 
     # 3.8.0 has a build issue with MKL - so list this conflict explicitly
     conflicts('^intel-mkl', when='@3.8.0')
@@ -93,6 +89,7 @@ class Petsc(Package):
     if sys.platform == "darwin":
         patch('macos-clang-8.1.0.diff',
               when='@3.7.5%clang@8.1.0:')
+    patch('pkg-config-3.7.6-3.8.4.diff', when='@3.7.6:3.8.4')
 
     # Virtual dependencies
     # Git repository needs sowing to build Fortran interface
@@ -108,11 +105,13 @@ class Petsc(Package):
     depends_on('python@2.6:2.8', type='build')
 
     # Other dependencies
-    depends_on('boost', when='@:3.5+boost')
-    depends_on('metis@5:~int64+real64', when='+metis~int64+double')
-    depends_on('metis@5:+int64', when='+metis+int64~double')
-    depends_on('metis@5:~int64+real64', when='+metis~int64+double')
-    depends_on('metis@5:+int64', when='+metis+int64~double')
+    depends_on('metis@5:~int64+real64', when='@:3.7.99+metis~int64+double')
+    depends_on('metis@5:~int64', when='@:3.7.99+metis~int64~double')
+    depends_on('metis@5:+int64+real64', when='@:3.7.99+metis+int64+double')
+    depends_on('metis@5:+int64', when='@:3.7.99+metis+int64~double')
+    # petsc-3.8+ uses default (float) metis with any (petsc) precision
+    depends_on('metis@5:~int64', when='@3.8:+metis~int64')
+    depends_on('metis@5:+int64', when='@3.8:+metis+int64')
 
     depends_on('hdf5+mpi+hl', when='+hdf5+mpi')
     depends_on('zlib', when='+hdf5')
@@ -121,18 +120,22 @@ class Petsc(Package):
     # Also PETSc prefer to build it without internal superlu, likely due to
     # conflict in headers see
     # https://bitbucket.org/petsc/petsc/src/90564b43f6b05485163c147b464b5d6d28cde3ef/config/BuildSystem/config/packages/hypre.py
-    depends_on('hypre~internal-superlu~int64', when='+hypre+mpi~complex~int64')
+    depends_on('hypre@:2.13.99~internal-superlu~int64', when='@:3.8.99+hypre+mpi~complex~int64')
+    depends_on('hypre@:2.13.99~internal-superlu+int64', when='@:3.8.99+hypre+mpi~complex+int64')
+    depends_on('hypre@2.14:~internal-superlu~int64', when='@3.9:+hypre+mpi~complex~int64')
+    depends_on('hypre@2.14:~internal-superlu+int64', when='@3.9+hypre+mpi~complex+int64')
     depends_on('hypre@xsdk-0.2.0~internal-superlu+int64', when='@xsdk-0.2.0+hypre+mpi~complex+int64')
     depends_on('hypre@xsdk-0.2.0~internal-superlu~int64', when='@xsdk-0.2.0+hypre+mpi~complex~int64')
     depends_on('hypre@develop~internal-superlu+int64', when='@develop+hypre+mpi~complex+int64')
     depends_on('hypre@develop~internal-superlu~int64', when='@develop+hypre+mpi~complex~int64')
-    depends_on('hypre~internal-superlu+int64', when='+hypre+mpi~complex+int64')
     depends_on('superlu-dist@:4.3~int64', when='@3.4.4:3.6.4+superlu-dist+mpi~int64')
     depends_on('superlu-dist@:4.3+int64', when='@3.4.4:3.6.4+superlu-dist+mpi+int64')
     depends_on('superlu-dist@5.0.0:~int64', when='@3.7:3.7.99+superlu-dist+mpi~int64')
     depends_on('superlu-dist@5.0.0:+int64', when='@3.7:3.7.99+superlu-dist+mpi+int64')
-    depends_on('superlu-dist@5.2:5.2.99~int64', when='@3.8:3.8.99+superlu-dist+mpi~int64')
-    depends_on('superlu-dist@5.2:5.2.99+int64', when='@3.8:3.8.99+superlu-dist+mpi+int64')
+    depends_on('superlu-dist@5.2:5.2.99~int64', when='@3.8:3.9.99+superlu-dist+mpi~int64')
+    depends_on('superlu-dist@5.2:5.2.99+int64', when='@3.8:3.9.99+superlu-dist+mpi+int64')
+    depends_on('superlu-dist@5.4:5.4.99~int64', when='@3.10:3.10.99+superlu-dist+mpi~int64')
+    depends_on('superlu-dist@5.4:5.4.99+int64', when='@3.10:3.10.99+superlu-dist+mpi+int64')
     depends_on('superlu-dist@xsdk-0.2.0~int64', when='@xsdk-0.2.0+superlu-dist+mpi~int64')
     depends_on('superlu-dist@xsdk-0.2.0+int64', when='@xsdk-0.2.0+superlu-dist+mpi+int64')
     depends_on('superlu-dist@develop~int64', when='@develop+superlu-dist+mpi~int64')
@@ -142,6 +145,7 @@ class Petsc(Package):
     depends_on('trilinos@12.6.2:', when='@3.7.0:+trilinos+mpi')
     depends_on('trilinos@xsdk-0.2.0', when='@xsdk-0.2.0+trilinos+mpi')
     depends_on('trilinos@develop', when='@xdevelop+trilinos+mpi')
+    depends_on('suite-sparse', when='+suite-sparse')
 
     def mpi_dependent_options(self):
         if '~mpi' in self.spec:
@@ -169,8 +173,12 @@ class Petsc(Package):
             compiler_opts = [
                 '--with-cc=%s' % self.spec['mpi'].mpicc,
                 '--with-cxx=%s' % self.spec['mpi'].mpicxx,
-                '--with-fc=%s' % self.spec['mpi'].mpifc
+                '--with-fc=%s' % self.spec['mpi'].mpifc,
             ]
+            if self.spec.satisfies('%intel'):
+                # mpiifort needs some help to automatically link
+                # all necessary run-time libraries
+                compiler_opts.append('--FC_LINKER_FLAGS=-lintlc')
         return compiler_opts
 
     def install(self, spec, prefix):
@@ -178,7 +186,13 @@ class Petsc(Package):
                    '--with-x=0',
                    '--download-c2html=0',
                    '--download-sowing=0',
-                   '--download-hwloc=0']
+                   '--download-hwloc=0',
+                   'CFLAGS=%s' % ' '.join(spec.compiler_flags['cflags']),
+                   'FFLAGS=%s' % ' '.join(spec.compiler_flags['fflags']),
+                   'CXXFLAGS=%s' % ' '.join(spec.compiler_flags['cxxflags']),
+                   'COPTFLAGS=',
+                   'FOPTFLAGS=',
+                   'CXXOPTFLAGS=']
         options.extend(self.mpi_dependent_options())
         options.extend([
             '--with-precision=%s' % (
@@ -198,9 +212,17 @@ class Petsc(Package):
 
         if 'trilinos' in spec:
             options.append('--with-cxx-dialect=C++11')
+            if spec.satisfies('^trilinos+boost'):
+                options.append('--with-boost=1')
+
+        if self.spec.satisfies('clanguage=C++'):
+            options.append('--with-clanguage=C++')
+        else:
+            options.append('--with-clanguage=C')
 
-        # Help PETSc pick up Scalapack from MKL:
-        if 'scalapack' in spec:
+        # PETSc depends on scalapack when '+mumps+mpi~int64' (see depends())
+        # help PETSc pick up Scalapack from MKL
+        if spec.satisfies('+mumps+mpi~int64'):
             scalapack = spec['scalapack'].libs
             options.extend([
                 '--with-scalapack-lib=%s' % scalapack.joined(),
@@ -212,8 +234,8 @@ class Petsc(Package):
             ])
 
         # Activates library support if needed
-        for library in ('metis', 'boost', 'hdf5', 'hypre', 'parmetis',
-                        'mumps', 'trilinos', 'zlib'):
+        for library in ('metis', 'hdf5', 'hypre', 'parmetis',
+                        'mumps', 'trilinos'):
             options.append(
                 '--with-{library}={value}'.format(
                     library=library, value=('1' if library in spec else '0'))
@@ -238,8 +260,31 @@ class Petsc(Package):
             options.append(
                 '--with-superlu_dist=0'
             )
+        # SuiteSparse: configuring using '--with-suitesparse-dir=...' has some
+        # issues, so specify directly the include path and the libraries.
+        if '+suite-sparse' in spec:
+            ss_spec = 'suite-sparse:umfpack,klu,cholmod,btf,ccolamd,colamd,' \
+                'camd,amd,suitesparseconfig'
+            options.extend([
+                '--with-suitesparse-include=%s' % spec[ss_spec].prefix.include,
+                '--with-suitesparse-lib=%s' % spec[ss_spec].libs.ld_flags,
+                '--with-suitesparse=1'
+            ])
+        else:
+            options.append('--with-suitesparse=0')
+
+        # zlib: configuring using '--with-zlib-dir=...' has some issues with
+        # SuiteSparse so specify directly the include path and the libraries.
+        if 'zlib' in spec:
+            options.extend([
+                '--with-zlib-include=%s' % spec['zlib'].prefix.include,
+                '--with-zlib-lib=%s'     % spec['zlib'].libs.ld_flags,
+                '--with-zlib=1'
+            ])
+        else:
+            options.append('--with-zlib=0')
 
-        configure('--prefix=%s' % prefix, *options)
+        python('configure', '--prefix=%s' % prefix, *options)
 
         # PETSc has its own way of doing parallel make.
         make('MAKE_NP=%s' % make_jobs, parallel=False)
@@ -253,6 +298,18 @@ class Petsc(Package):
                 cc('ex50.c', '-I%s' % prefix.include, '-L%s' % prefix.lib,
                    '-lpetsc', '-lm', '-o', 'ex50')
                 run = Executable(join_path(spec['mpi'].prefix.bin, 'mpirun'))
+                # For Spectrum MPI, if -np is omitted, the default behavior is
+                # to assign one process per process slot, where the default
+                # process slot allocation is one per core. On systems with
+                # many cores, the number of processes can exceed the size of
+                # the grid specified when the testcase is run and the test case
+                # fails. Specify a small number of processes to prevent
+                # failure.
+                # For more information about Spectrum MPI invocation, see URL
+                # https://www.ibm.com/support/knowledgecenter/en/SSZTET_10.1.0/smpi02/smpi02_mpirun_options.html
+                if ('spectrum-mpi' in spec):
+                    run.add_default_arg('-np')
+                    run.add_default_arg('4')
                 run('ex50', '-da_grid_x', '4', '-da_grid_y', '4')
                 if 'superlu-dist' in spec:
                     run('ex50',
@@ -288,3 +345,10 @@ class Petsc(Package):
         # Set up PETSC_DIR for everyone using PETSc package
         spack_env.set('PETSC_DIR', self.prefix)
         spack_env.unset('PETSC_ARCH')
+
+    @property
+    def headers(self):
+        return find_headers('petsc', self.prefix.include, recursive=False) \
+            or None  # return None to indicate failure
+
+    # For the 'libs' property - use the default handler.
diff --git a/var/spack/repos/builtin/packages/petsc/pkg-config-3.7.6-3.8.4.diff b/var/spack/repos/builtin/packages/petsc/pkg-config-3.7.6-3.8.4.diff
new file mode 100644
index 0000000000..a0c960dcae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/petsc/pkg-config-3.7.6-3.8.4.diff
@@ -0,0 +1,29 @@
+diff --git c/config/PETSc/Configure.py w/config/PETSc/Configure.py
+index ca65368e54..995afd0799 100644
+--- c/config/PETSc/Configure.py
++++ w/config/PETSc/Configure.py
+@@ -174,19 +174,19 @@ class Configure(config.base.Configure):
+ 
+     self.setCompilers.pushLanguage('C')
+     fd.write('ccompiler='+self.setCompilers.getCompiler()+'\n')
+-    fd.write('cflags_extra="'+self.setCompilers.getCompilerFlags().strip()+'"\n')
+-    fd.write('cflags_dep="'+self.compilers.dependenciesGenerationFlag.get('C','')+'"\n')
+-    fd.write('ldflag_rpath="'+self.setCompilers.CSharedLinkerFlag+'"\n')
++    fd.write('cflags_extra='+self.setCompilers.getCompilerFlags().strip()+'\n')
++    fd.write('cflags_dep='+self.compilers.dependenciesGenerationFlag.get('C','')+'\n')
++    fd.write('ldflag_rpath='+self.setCompilers.CSharedLinkerFlag+'\n')
+     self.setCompilers.popLanguage()
+     if hasattr(self.compilers, 'C++'):
+       self.setCompilers.pushLanguage('C++')
+       fd.write('cxxcompiler='+self.setCompilers.getCompiler()+'\n')
+-      fd.write('cxxflags_extra="'+self.setCompilers.getCompilerFlags().strip()+'"\n')
++      fd.write('cxxflags_extra='+self.setCompilers.getCompilerFlags().strip()+'\n')
+       self.setCompilers.popLanguage()
+     if hasattr(self.compilers, 'FC'):
+       self.setCompilers.pushLanguage('FC')
+       fd.write('fcompiler='+self.setCompilers.getCompiler()+'\n')
+-      fd.write('fflags_extra="'+self.setCompilers.getCompilerFlags().strip()+'"\n')
++      fd.write('fflags_extra='+self.setCompilers.getCompilerFlags().strip()+'\n')
+       self.setCompilers.popLanguage()
+ 
+     fd.write('\n')
diff --git a/var/spack/repos/builtin/packages/petsc/xlc-test-3.10.1.diff b/var/spack/repos/builtin/packages/petsc/xlc-test-3.10.1.diff
new file mode 100644
index 0000000000..7009ea450d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/petsc/xlc-test-3.10.1.diff
@@ -0,0 +1,19 @@
+--- a/gmakefile.test
++++ b/gmakefile.test
+@@ -127,11 +127,14 @@
+ endif
+ 	-@$(GFORTRAN_DEP_CLEANUP)
+ 
++#add xlf2003 flags
++XLF2003FLAGS = "-qxlf2003=polymorphic:bozlitargs:stopexcept:volatile:autorealloc"
++
+ $(TESTDIR)/%.o : $(EXAMPLESDIR)/%.F90 | $$(@D)/.DIR
+ ifeq ($(FC_MODULE_OUTPUT_FLAG),)
+ 	$(call quiet,FCMOD) $(MODDIR) && $(FC) -c $(FC_FLAGS) $(FFLAGS) $(FCPPFLAGS) $(FC_DEPFLAGS) -I$(dir $<) $(abspath $<) -o $(abspath $@)
+ else
+-	$(PETSC_COMPILE.F) -I$(dir $<) $(abspath $<) -o $@ $(FC_MODULE_OUTPUT_FLAG)$(MODDIR) $(FC_MODULE_FLAG)$(MODDIR)
++	$(PETSC_COMPILE.F) ${XLF2003FLAGS} -I$(dir $<) $(abspath $<) -o $@ $(FC_MODULE_OUTPUT_FLAG)$(MODDIR) $(FC_MODULE_FLAG)$(MODDIR)
+ endif
+ 	-@$(GFORTRAN_DEP_CLEANUP)
+ 
+
diff --git a/var/spack/repos/builtin/packages/pexsi/package.py b/var/spack/repos/builtin/packages/pexsi/package.py
index 63819923af..fa93fac715 100644
--- a/var/spack/repos/builtin/packages/pexsi/package.py
+++ b/var/spack/repos/builtin/packages/pexsi/package.py
@@ -1,31 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import inspect
 import os.path
-import shutil
 
 from spack import *
 
@@ -54,7 +34,7 @@ class Pexsi(MakefilePackage):
     depends_on('parmetis')
     depends_on('superlu-dist@3.3:3.999', when='@:0.9.0')
     depends_on('superlu-dist@4.3:4.999', when='@0.9.2')
-    depends_on('superlu-dist@5.1.2:', when='@0.10.2:')
+    depends_on('superlu-dist@5.1.2:5.3.999', when='@0.10.2:')
 
     variant(
         'fortran', default=False, description='Builds the Fortran interface'
@@ -64,27 +44,32 @@ class Pexsi(MakefilePackage):
 
     def edit(self, spec, prefix):
 
-        substitutions = {
-            '@MPICC': self.spec['mpi'].mpicc,
-            '@MPICXX': self.spec['mpi'].mpicxx,
-            '@MPIFC': self.spec['mpi'].mpifc,
-            '@MPICXX_LIB': self.spec['mpi:cxx'].libs.joined(),
-            '@RANLIB': 'ranlib',
-            '@PEXSI_STAGE': self.stage.source_path,
-            '@SUPERLU_PREFIX': self.spec['superlu-dist'].prefix,
-            '@METIS_PREFIX': self.spec['metis'].prefix,
-            '@PARMETIS_PREFIX': self.spec['parmetis'].prefix,
-            '@LAPACK_PREFIX': self.spec['lapack'].prefix,
-            '@BLAS_PREFIX': self.spec['blas'].prefix,
-            '@LAPACK_LIBS': self.spec['lapack'].libs.joined(),
-            '@BLAS_LIBS': self.spec['blas'].libs.joined(),
+        substitutions = [
+            ('@MPICC', self.spec['mpi'].mpicc),
+            ('@MPICXX_LIB', self.spec['mpi:cxx'].libs.joined()),
+            ('@MPICXX', self.spec['mpi'].mpicxx),
+            ('@MPIFC', self.spec['mpi'].mpifc),
+            ('@RANLIB', 'ranlib'),
+            ('@PEXSI_STAGE', self.stage.source_path),
+            ('@SUPERLU_PREFIX', self.spec['superlu-dist'].prefix),
+            ('@METIS_PREFIX', self.spec['metis'].prefix),
+            ('@PARMETIS_PREFIX', self.spec['parmetis'].prefix),
+            ('@LAPACK_PREFIX', self.spec['lapack'].prefix),
+            ('@BLAS_PREFIX', self.spec['blas'].prefix),
+            ('@LAPACK_LIBS', self.spec['lapack'].libs.joined()),
+            ('@BLAS_LIBS', self.spec['blas'].libs.joined()),
             # FIXME : what to do with compiler provided libraries ?
-            '@STDCXX_LIB': ' '.join(self.compiler.stdcxx_libs),
-            '@FLDFLAGS': ''
-        }
+            ('@STDCXX_LIB', ' '.join(self.compiler.stdcxx_libs))
+        ]
 
         if '@0.9.2' in self.spec:
-            substitutions['@FLDFLAGS'] = '-Wl,--allow-multiple-definition'
+            substitutions.append(
+                ('@FLDFLAGS', '-Wl,--allow-multiple-definition')
+            )
+        else:
+            substitutions.append(
+                ('@FLDFLAGS', '')
+            )
 
         template = join_path(
             os.path.dirname(inspect.getmodule(self).__file__),
@@ -94,8 +79,8 @@ class Pexsi(MakefilePackage):
             self.stage.source_path,
             'make.inc'
         )
-        shutil.copy(template, makefile)
-        for key, value in substitutions.items():
+        copy(template, makefile)
+        for key, value in substitutions:
             filter_file(key, value, makefile)
 
     def build(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/pfft/package.py b/var/spack/repos/builtin/packages/pfft/package.py
index 93f0222a48..4121d90caa 100644
--- a/var/spack/repos/builtin/packages/pfft/package.py
+++ b/var/spack/repos/builtin/packages/pfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pflotran/package.py b/var/spack/repos/builtin/packages/pflotran/package.py
index e04e33a1db..73f95f75f7 100644
--- a/var/spack/repos/builtin/packages/pflotran/package.py
+++ b/var/spack/repos/builtin/packages/pflotran/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,13 +13,18 @@ class Pflotran(AutotoolsPackage):
     """
 
     homepage = "http://www.pflotran.org"
+    git      = "https://bitbucket.org/pflotran/pflotran.git"
 
-    version('develop', git='https://bitbucket.org/pflotran/pflotran')
-    version('xsdk-0.2.0', git='https://bitbucket.org/pflotran/pflotran', tag='master')
+    version('develop')
+    version('xsdk-0.2.0', tag='master')
+    version('xsdk-0.3.0', branch='release/xsdk-0.3.0')
 
     depends_on('mpi')
     depends_on('hdf5@1.8.12:+mpi+fortran')
     depends_on('petsc@develop+hdf5+metis', when='@develop')
-    depends_on('petsc@xsdk-0.2.0+hdf5+metis', when='@xsdk-0.2.0')    
+    depends_on('petsc@xsdk-0.2.0+hdf5+metis', when='@xsdk-0.2.0')
+    depends_on('petsc@3.8.0:+hdf5+metis', when='@xsdk-0.3.0')
 
-    parallel = False
+    @property
+    def parallel(self):
+        return self.spec.satisfies('@develop')
diff --git a/var/spack/repos/builtin/packages/pfunit/package.py b/var/spack/repos/builtin/packages/pfunit/package.py
new file mode 100644
index 0000000000..e9faaaebbf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pfunit/package.py
@@ -0,0 +1,81 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+import glob
+
+
+class Pfunit(CMakePackage):
+    """pFUnit is a unit testing framework enabling JUnit-like testing of
+    serial and MPI-parallel software written in Fortran."""
+
+    homepage = "http://pfunit.sourceforge.net/"
+    url      = "https://github.com/Goddard-Fortran-Ecosystem/pFUnit/archive/3.2.9.tar.gz"
+
+    maintainers = ['citibeth']
+
+    version('3.2.9', 'e13d8362284b13b7c863e2fe769a9d5c')
+
+    variant('shared', default=True,
+            description='Build shared library in addition to static')
+    variant('mpi', default=False, description='Enable MPI')
+    variant('openmp', default=False, description='Enable OpenMP')
+    variant('docs', default=False, description='Build docs')
+
+    depends_on('python@2.7:', type=('build', 'run'))  # python3 too!
+    depends_on('mpi', when='+mpi')
+
+    def patch(self):
+        # The package tries to put .mod files in directory ./mod;
+        # spack needs to put them in a standard location:
+        for file in glob.glob('*/CMakeLists.txt'):
+            filter_file(r'.*/mod($|[^\w].*)', '', file)
+
+    def cmake_args(self):
+        spec = self.spec
+        args = [
+            '-DPYTHON_EXECUTABLE=%s' % spec['python'].command,
+            '-DBUILD_SHARED=%s' % ('YES' if '+shared' in spec else 'NO'),
+            '-DCMAKE_Fortran_MODULE_DIRECTORY=%s' % spec.prefix.include,
+            '-DBUILD_DOCS=%s' % ('YES' if '+docs' in spec else 'NO'),
+            '-DOPENMP=%s' % ('YES' if '+openmp' in spec else 'NO')]
+
+        if spec.satisfies('+mpi'):
+            args.extend(['-DMPI=YES', '-DMPI_USE_MPIEXEC=YES',
+                         '-DMPI_Fortran_COMPILER=%s' % spec['mpi'].mpifc])
+        else:
+            args.append('-DMPI=NO')
+        return args
+
+    def check(self):
+        """Searches the CMake-generated Makefile for the target ``test``
+        and runs it if found.
+        """
+        args = ['tests']
+        if self.spec.satisfies('+mpi'):
+            args.append('MPI=YES')
+        if self.spec.satisfies('+openmp'):
+            args.append('OPENMP=YES')
+        with working_dir(self.build_directory):
+            make(*args)
+
+    def compiler_vendor(self):
+        vendors = {'%gcc': 'GNU', '%clang': 'GNU', '%intel': 'Intel',
+                   '%pgi': 'PGI', '%nag': 'NAG'}
+        for key, value in vendors.items():
+            if self.spec.satisfies(key):
+                return value
+        raise InstallError('Unsupported compiler.')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('PFUNIT', self.spec.prefix)
+        run_env.set('PFUNIT', self.spec.prefix)
+        spack_env.set('F90_VENDOR', self.compiler_vendor())
+        run_env.set('F90_VENDOR', self.compiler_vendor())
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('PFUNIT', self.spec.prefix)
+        spack_env.set('F90_VENDOR', self.compiler_vendor())
diff --git a/var/spack/repos/builtin/packages/pgdspider/package.py b/var/spack/repos/builtin/packages/pgdspider/package.py
index 39a518113f..5a4dab9516 100644
--- a/var/spack/repos/builtin/packages/pgdspider/package.py
+++ b/var/spack/repos/builtin/packages/pgdspider/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin/packages/pgi/package.py b/var/spack/repos/builtin/packages/pgi/package.py
index 63592d6cc6..47242e4ecd 100644
--- a/var/spack/repos/builtin/packages/pgi/package.py
+++ b/var/spack/repos/builtin/packages/pgi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from spack.util.prefix import Prefix
 import os
@@ -39,6 +20,8 @@ class Pgi(Package):
 
     homepage = "http://www.pgroup.com/"
 
+    version('18.4',  'b55461f9f0986acbd51902c51c2074b9')
+    version('17.10', '85ad6506e7ada610ab11ddb35d697efa')
     version('17.4',  'a311d2756ddda657860bad8e5725597b')
     version('17.3',  '6eefc42f85e756cbaba76467ed640902')
     version('16.10', '9bb6bfb7b1052f9e6a45829ba7a24e47')
diff --git a/var/spack/repos/builtin/packages/pgmath/package.py b/var/spack/repos/builtin/packages/pgmath/package.py
new file mode 100644
index 0000000000..7b4f98be5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pgmath/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Pgmath(CMakePackage):
+    """Flang's math library"""
+
+    homepage = "https://github.com/flang-compiler/flang"
+    url      = "https://github.com/flang-compiler/flang/archive/flang_20180612.tar.gz"
+    git      = "https://github.com/flang-compiler/flang.git"
+
+    version('develop', branch='master')
+    version('20180612', '62284e26214eaaff261a922c67f6878c')
+
+    conflicts("%gcc@:7.1.9999")
+
+    root_cmakelists_dir = 'runtime/libpgmath'
diff --git a/var/spack/repos/builtin/packages/phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py
new file mode 100644
index 0000000000..118d7032c9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phantompeakqualtools/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Phantompeakqualtools(RPackage):
+    """This package computes informative enrichment and quality measures for
+       ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data."""
+
+    homepage = "https://github.com/kundajelab/phantompeakqualtools"
+    url      = "https://github.com/kundajelab/phantompeakqualtools/archive/1.2.tar.gz"
+
+    version('1.2', 'e94943a42132b9ff2886f006ab34c121')
+
+    depends_on('awk')
+    depends_on('samtools')
+    depends_on('r', type=('build', 'run'))
+    depends_on('r-phantompeakqualtools', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('run_spp.R', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/phast/package.py b/var/spack/repos/builtin/packages/phast/package.py
new file mode 100644
index 0000000000..503246614c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phast/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Phast(MakefilePackage):
+    """PHAST is a freely available software package for comparative and
+       evolutionary genomics."""
+
+    homepage = "http://compgen.cshl.edu/phast/index.php"
+    url      = "https://github.com/CshlSiepelLab/phast/archive/v1.4.tar.gz"
+
+    version('1.4', '2bc0412ba58ea1f08ba5e12fad43b4c7')
+
+    # phast cannot build with clapack using external blas
+    depends_on('clapack~external-blas')
+
+    build_directory = 'src'
+
+    @property
+    def build_targets(self):
+        targets = ['CLAPACKPATH={0}'.format(self.spec['clapack'].prefix)]
+        return targets
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            filter_file(r'\$\{PWD\}',
+                        '$(dir $(realpath $(firstword $(MAKEFILE_LIST))))',
+                        'make-include.mk')
+            filter_file(r'\$\{PWD\}',
+                        '$(dir $(realpath $(firstword $(MAKEFILE_LIST))))',
+                        'Makefile')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/phasta/package.py b/var/spack/repos/builtin/packages/phasta/package.py
index a73c90848b..2243281b5a 100644
--- a/var/spack/repos/builtin/packages/phasta/package.py
+++ b/var/spack/repos/builtin/packages/phasta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,10 @@ class Phasta(CMakePackage):
        (PHASTA) of compressible and incompressible Navier Stokes equations."""
 
     homepage = "https://www.scorec.rpi.edu/software.php"
-    url      = "https://github.com/PHASTA/phasta.git"
+    git      = "https://github.com/PHASTA/phasta.git"
 
-    version('0.0.1', git='https://github.com/PHASTA/phasta.git',
-        commit='11f431f2d1a53a529dab4b0f079ab8aab7ca1109')
-    version('develop', git='https://github.com/PHASTA/phasta.git',
-        branch='master')
+    version('develop', branch='master')
+    version('0.0.1', commit='11f431f2d1a53a529dab4b0f079ab8aab7ca1109')
 
     depends_on('mpi')
 
diff --git a/var/spack/repos/builtin/packages/phist/package.py b/var/spack/repos/builtin/packages/phist/package.py
new file mode 100644
index 0000000000..aa593157b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phist/package.py
@@ -0,0 +1,144 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Phist(CMakePackage):
+    """The Pipelined, Hybrid-parallel Iterative Solver Toolkit provides
+    implementations of and interfaces to block iterative solvers for sparse
+    linear and eigenvalue problems. In contrast to other libraries we support
+    multiple backends (e.g. Trilinos, PETSc and our own optimized kernels),
+    and interfaces in multiple languages such as C, C++, Fortran 2003 and
+    Python. PHIST has a clear focus on portability and hardware performance:
+    in particular support row-major storage of block vectors and using GPUs
+    (via the ghost library or Trilinos/Tpetra).
+    """
+
+    homepage = "https://bitbucket.org/essex/phist/"
+    url      = "https://bitbucket.org/essex/phist/get/phist-1.4.3.tar.gz"
+    git      = "https://bitbucket.org/essex/phist/phist.git"
+
+    version('develop', branch='devel')
+    version('master', branch='master')
+    version('1.7.3', sha256='ab2d853c9ba13bcd3069fcc61c359cb412466a2e4b22ebbd2f5263cffa685126')
+    version('1.7.2', sha256='29b504d78b5efd57b87d2ca6e20bc8a32b1ba55b40f5a5b7189cc0d28e43bcc0')
+    version('1.6.1', sha256='4ed4869f24f920a494aeae0f7d1d94fe9efce55ebe0d298a5948c9603e07994d')
+    version('1.6.0', '751f855230d6227b972b5ab7bce2c65f')
+    version('1.4.3', 'af3300378d4282366d148e38c3a3199a')
+
+    variant(name='kernel_lib', default='builtin',
+            description='select the kernel library (backend) for phist',
+            values=['builtin',
+                    'epetra',
+                    'tpetra',
+                    'petsc',
+                    'eigen',
+                    'ghost'])
+
+    variant(name='outlev', default='2', values=['0', '1', '2', '3', '4', '5'],
+            description='verbosity. 0: errors 1: +warnings 2: +info '
+                        '3: +verbose 4: +extreme 5; +debug')
+
+    variant('shared',  default=True,
+            description='Enables the build of shared libraries')
+
+    variant('mpi', default=True,
+            description='enable/disable MPI (note that the kernel library may '
+            'not support this choice)')
+
+    variant('openmp', default=True,
+            description='enable/disable OpenMP')
+
+    variant('parmetis', default=False,
+            description='enable/disable ParMETIS partitioning (only actually '
+                        'used with kernel_lib=builtin)')
+
+    variant('scamac', default=True,
+            description='enable/disable building the "SCAlable MAtrix '
+                        'Collection" matrix generators.')
+
+    variant('trilinos', default=False,
+            description='enable/disable Trilinos third-party libraries. '
+                        'For all kernel_libs, we can use Belos and Anasazi '
+                        'iterative solvers. For the Trilinos backends '
+                        '(kernel_lib=epetra|tpetra) we can use preconditioner '
+                        'packages such as Ifpack, Ifpack2 and ML.')
+
+    variant('fortran', default=True,
+            description='generate Fortran 2003 bindings (requires Python3 and '
+                        'a Fortran compiler)')
+
+    # ###################### Dependencies ##########################
+
+    depends_on('cmake@3.8:', type='build')
+    depends_on('blas')
+    depends_on('lapack')
+    # Python 3 or later is required for generating the Fortran 2003 bindings
+    # since version 1.7, you can get rid of the dependency by switching off
+    # the feature (e.g. use the '~fortran' variant)
+    depends_on('python@3:', when='@1.7: +fortran', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('trilinos+anasazi+belos+teuchos', when='+trilinos')
+    depends_on('trilinos@12:+tpetra', when='kernel_lib=tpetra')
+    # Epetra backend also works with older Trilinos versions
+    depends_on('trilinos+epetra', when='kernel_lib=epetra')
+    depends_on('petsc', when='kernel_lib=petsc')
+    depends_on('eigen', when='kernel_lib=eigen')
+    depends_on('ghost', when='kernel_lib=ghost')
+
+    depends_on('trilinos', when='+trilinos')
+    depends_on('parmetis ^metis+int64', when='+parmetis')
+
+    # Fortran 2003 bindings were included in version 1.7, previously they
+    # required a separate package
+    conflicts('+fortran', when='@:1.6.99')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        kernel_lib = spec.variants['kernel_lib'].value
+        outlev = spec.variants['outlev'].value
+
+        lapacke_libs = (spec['lapack:c'].libs + spec['blas:c'].libs +
+                        find_system_libraries(['libm'])).joined(';')
+        lapacke_include_dir = spec['lapack:c'].headers.directories[0]
+
+        args = ['-DPHIST_KERNEL_LIB=%s' % kernel_lib,
+                '-DPHIST_OUTLEV=%s' % outlev,
+                '-DTPL_LAPACKE_LIBRARIES=%s' % lapacke_libs,
+                '-DTPL_LAPACKE_INCLUDE_DIRS=%s' % lapacke_include_dir,
+                '-DPHIST_ENABLE_MPI:BOOL=%s'
+                % ('ON' if '+mpi' in spec else 'OFF'),
+                '-DPHIST_ENABLE_OPENMP=%s'
+                % ('ON' if '+openmp' in spec else 'OFF'),
+                '-DBUILD_SHARED_LIBS:BOOL=%s'
+                % ('ON' if '+shared' in spec else 'OFF'),
+                '-DPHIST_ENABLE_SCAMAC:BOOL=%s'
+                % ('ON' if '+scamac' in spec else 'OFF'),
+                '-DPHIST_USE_TRILINOS_TPLS:BOOL=%s'
+                % ('ON' if '+trilinos' in spec else 'OFF'),
+                '-DPHIST_USE_SOLVER_TPLS:BOOL=%s'
+                % ('ON' if '+trilinos' in spec else 'OFF'),
+                '-DPHIST_USE_PRECON_TPLS:BOOL=%s'
+                % ('ON' if '+trilinos' in spec else 'OFF'),
+                '-DXSDK_ENABLE_Fortran:BOOL=%s'
+                % ('ON' if '+fortran' in spec else 'OFF'),
+                ]
+
+        return args
+
+    @run_after('build')
+    @on_package_attributes(run_tests=True)
+    def check(self):
+        with working_dir(self.build_directory):
+            make("check")
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def test_install(self):
+        with working_dir(self.build_directory):
+            make("test_install")
diff --git a/var/spack/repos/builtin/packages/phylip/package.py b/var/spack/repos/builtin/packages/phylip/package.py
index 1ebe04f4ca..8869f75390 100644
--- a/var/spack/repos/builtin/packages/phylip/package.py
+++ b/var/spack/repos/builtin/packages/phylip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Phylip(Package):
        inferring phylogenies (evolutionary trees)."""
 
     homepage = "http://evolution.genetics.washington.edu/phylip/"
-    url      = "http://evolution.gs.washington.edu/phylip/download/phylip-3.696.tar.gz"
+    url      = "http://evolution.gs.washington.edu/phylip/download/phylip-3.697.tar.gz"
 
+    version('3.697', '0e83d17fb4d668213603c86bc21d9012')
     version('3.696', 'dbe5abc26f6089ead3dba41c2db526ee')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/phyluce/package.py b/var/spack/repos/builtin/packages/phyluce/package.py
new file mode 100644
index 0000000000..3a28108ace
--- /dev/null
+++ b/var/spack/repos/builtin/packages/phyluce/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Phyluce(PythonPackage):
+    """phyluce (phy-loo-chee) is a software package that was initially
+       developed for analyzing data collected from ultraconserved
+       elements in organismal genomes"""
+
+    homepage = "https://github.com/faircloth-lab/phyluce"
+    url      = "https://github.com/faircloth-lab/phyluce/archive/v1.6.7.tar.gz"
+
+    version('1.6.7', sha256='98c213ab1610506722ad1440ffc93f9cbc78d8b3aaf3d9a47837e1231452cdb6')
+
+    extends('python')
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-biopython', type='run')
+
+    # runtime binary dependencies
+    depends_on('abyss', type='run')
+    depends_on('bcftools', type='run')
+    depends_on('bwa', type='run')
+    depends_on('gatk', type='run')
+    depends_on('gblocks', type='run')
+    depends_on('lastz', type='run')
+    depends_on('mafft', type='run')
+    depends_on('muscle', type='run')
+    depends_on('picard', type='run')
+    depends_on('raxml+pthreads+sse', type='run')
+    depends_on('samtools', type='run')
+    depends_on('seqtk', type='run')
+    depends_on('spades', type='run')
+    depends_on('trimal', type='run')
+    depends_on('trinity', type='run')
+    depends_on('velvet', type='run')
+
+    def install(self, spec, prefix):
+        python = which('python')
+        python('setup.py', 'install', '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/picard/package.py b/var/spack/repos/builtin/packages/picard/package.py
index 744479a7f3..86c6cd6e90 100644
--- a/var/spack/repos/builtin/packages/picard/package.py
+++ b/var/spack/repos/builtin/packages/picard/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
 import glob
 import os.path
 import re
@@ -36,13 +16,25 @@ class Picard(Package):
 
     homepage = "http://broadinstitute.github.io/picard/"
     url      = "https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar"
+    _urlfmt  = "https://github.com/broadinstitute/picard/releases/download/{0}/picard.jar"
+    _oldurlfmt = 'https://github.com/broadinstitute/picard/releases/download/{0}/picard-tools-{0}.zip'
 
     # They started distributing a single jar file at v2.6.0, prior to
     # that it was a .zip file with multiple .jar and .so files
-    version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False,
-            url="https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar")
-    version('1.140', '308f95516d94c1f3273a4e7e2b315ec2',
-            url='https://github.com/broadinstitute/picard/releases/download/1.140/picard-tools-1.140.zip')
+    version('2.18.3', '181b1b0731fd35f0d8bd44677d8787e9', expand=False)
+    version('2.18.0', '20045ff141e4a67512365f0b6bbd8229', expand=False)
+    version('2.17.0', '72cc527f1e4ca6a799ae0117af60b54e', expand=False)
+    version('2.16.0', 'fed8928b03bb36e355656f349e579083', expand=False)
+    version('2.15.0', '3f5751630b1a3449edda47a0712a64e4', expand=False)
+    version('2.13.2', '3d7b33fd1f43ad2129e6ec7883af56f5', expand=False)
+    version('2.10.0', '96f3c11b1c9be9fc8088bc1b7b9f7538', expand=False)
+    version('2.9.4', '5ce72af4d5efd02fba7084dcfbb3c7b3', expand=False)
+    version('2.9.3', '3a33c231bcf3a61870c3d44b3b183924', expand=False)
+    version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False)
+    version('2.9.0', 'b711d492f16dfe0084d33e684dca2202', expand=False)
+    version('2.8.3', '4a181f55d378cd61d0b127a40dfd5016', expand=False)
+    version('2.6.0', '91f35f22977d9692ce2718270077dc50', expand=False)
+    version('1.140', '308f95516d94c1f3273a4e7e2b315ec2')
 
     depends_on('java@8:', type='run')
 
@@ -57,13 +49,13 @@ class Picard(Package):
         # Set up a helper script to call java on the jar file,
         # explicitly codes the path for java and the jar file.
         script_sh = join_path(os.path.dirname(__file__), "picard.sh")
-        script = join_path(prefix.bin, "picard")
-        copyfile(script_sh, script)
+        script = prefix.bin.picard
+        install(script_sh, script)
         set_executable(script)
 
         # Munge the helper script to explicitly point to java and the
         # jar file.
-        java = join_path(self.spec['java'].prefix, 'bin', 'java')
+        java = self.spec['java'].prefix.bin.java
         kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
         filter_file('^java', java, script, **kwargs)
         filter_file('picard.jar', join_path(prefix.bin, 'picard.jar'),
@@ -73,3 +65,9 @@ class Picard(Package):
         """The Picard docs suggest setting this as a convenience."""
         run_env.prepend_path('PICARD',
                              join_path(self.prefix, 'bin', 'picard.jar'))
+
+    def url_for_version(self, version):
+        if version < Version('2.6.0'):
+            return self._oldurlfmt.format(version)
+        else:
+            return self._urlfmt.format(version)
diff --git a/var/spack/repos/builtin/packages/picsar/package.py b/var/spack/repos/builtin/packages/picsar/package.py
new file mode 100644
index 0000000000..234b5ee856
--- /dev/null
+++ b/var/spack/repos/builtin/packages/picsar/package.py
@@ -0,0 +1,75 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Picsar(MakefilePackage):
+    """PICSAR is a high performance library of optimized versions of the key
+       functionalities of the PIC loop.
+    """
+
+    homepage = "https://picsar.net"
+    git      = "https://bitbucket.org/berkeleylab/picsar.git"
+
+    version('develop', branch='master')
+
+    variant('prod', default=True, description='Production mode (without FFTW)')
+    variant('prod_spectral', default=False,
+            description='Production mode with spectral solver and FFTW')
+    variant('debug', default=False, description='Debug mode')
+    variant('vtune', default=False, description='Vtune profiling')
+    variant('sde', default=False, description='sde profiling')
+    variant('map', default=False, description='Allinea Map profiling')
+    variant('library', default=False, 
+            description='Create static and dynamic library')
+
+    depends_on('mpi')
+    depends_on('fftw@3.0: +mpi', when='+prod_spectral')
+
+    parallel = False
+
+    @property
+    def build_targets(self):
+        targets = []
+        targets.append('FC={0}'.format(self.spec['mpi'].mpifc))
+        targets.append('CC={0}'.format(self.spec['mpi'].mpicc))
+
+        comp = 'user'
+        vendors = {'%gcc': 'gnu', '%intel': 'intel'}
+        for key, value in vendors.items():
+            if self.spec.satisfies(key):
+                comp = value
+        targets.append('COMP={0}'.format(comp))
+        if comp is 'user':
+            targets.append('FARGS={0}{1}'.format('-g -O3 ',
+                           self.compiler.openmp_flag))
+
+        if '+prod' in self.spec:
+            mode = 'prod'
+        elif '+prod_spectral' in self.spec:
+            mode = 'prod_spectral'
+        elif '+debug' in self.spec:
+            mode = 'debug'
+        elif '+vtune' in self.spec:
+            mode = 'vtune'
+        elif '+sde' in self.spec:
+            mode = 'sde'
+        elif '+map' in self.spec:
+            mode = 'map'
+        elif '+library' in self.spec:
+            mode = 'library'
+        targets.append('MODE = {0}'.format(mode))
+
+        targets.append('SYS = default')
+
+        return targets
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.docs)
+        install('README.md', prefix.docs)
+
+        mkdirp(prefix.bin)
+        install('fortran_bin/picsar', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/picsarlite/package.py b/var/spack/repos/builtin/packages/picsarlite/package.py
new file mode 100644
index 0000000000..5a5b5b58b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/picsarlite/package.py
@@ -0,0 +1,80 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Picsarlite(MakefilePackage):
+    """PICSARlite is a self-contained proxy that adequately portrays the
+       computational loads and dataflow of more complex PIC codes.
+    """
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "https://picsar.net"
+    git      = "https://bitbucket.org/berkeleylab/picsar.git"
+
+    version('develop', branch='PICSARlite')
+    version('0.1', tag='PICSARlite-0.1')
+
+    variant('prod', default=True, description='Production mode (without FFTW)')
+    variant('prod_spectral', default=False,
+            description='Production mode with spectral solver and FFTW')
+    variant('debug', default=False, description='Debug mode')
+    variant('vtune', default=False, description='Vtune profiling')
+    variant('sde', default=False, description='sde profiling')
+    variant('map', default=False, description='Allinea Map profiling')
+    variant('library', default=False, 
+            description='Create static and dynamic library')
+
+    depends_on('mpi')
+    depends_on('fftw@3.0: +mpi', when='+prod_spectral')
+
+    @property
+    def build_targets(self):
+        targets = []
+        targets.append('FC={0}'.format(self.spec['mpi'].mpifc))
+        targets.append('CC={0}'.format(self.spec['mpi'].mpicc))
+
+        comp = 'user'
+        vendors = {'%gcc': 'gnu', '%intel': 'intel'}
+        for key, value in vendors.items():
+            if self.spec.satisfies(key):
+                comp = value
+        targets.append('COMP={0}'.format(comp))
+        if comp is 'user':
+            targets.append('FARGS={0}{1}'.format('-g -O3 ',
+                           self.compiler.openmp_flag))
+
+        if '+prod' in self.spec:
+            mode = 'prod'
+        elif '+prod_spectral' in self.spec:
+            mode = 'prod_spectral'
+        elif '+debug' in self.spec:
+            mode = 'debug'
+        elif '+vtune' in self.spec:
+            mode = 'vtune'
+        elif '+sde' in self.spec:
+            mode = 'sde'
+        elif '+map' in self.spec:
+            mode = 'map'
+        elif '+library' in self.spec:
+            mode = 'library'
+        targets.append('MODE = {0}'.format(mode))
+
+        targets.append('SYS = default')
+
+        return targets
+
+    def build(self, spec, prefix):
+        with working_dir('PICSARlite'):
+            make(parallel=False)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.docs)
+        install('PICSARlite/README.md', prefix.docs)
+
+        mkdirp(prefix.bin)
+        install('PICSARlite/bin/picsar', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/pidx/package.py b/var/spack/repos/builtin/packages/pidx/package.py
index bc3977d733..9aaf021de5 100644
--- a/var/spack/repos/builtin/packages/pidx/package.py
+++ b/var/spack/repos/builtin/packages/pidx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class Pidx(CMakePackage):
     """
 
     homepage = "http://www.cedmav.com/pidx"
+    git      = "https://github.com/sci-visus/PIDX.git"
 
-    version('1.0', git='https://github.com/sci-visus/PIDX.git',
-            commit='6afa1cf71d1c41263296dc049c8fabaf73c296da')
+    version('1.0', commit='6afa1cf71d1c41263296dc049c8fabaf73c296da')
 
     depends_on('cmake@2.8.4:', type='build')
     depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/pigz/package.py b/var/spack/repos/builtin/packages/pigz/package.py
index fe933c4f54..4b8eae6936 100644
--- a/var/spack/repos/builtin/packages/pigz/package.py
+++ b/var/spack/repos/builtin/packages/pigz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,10 @@ class Pigz(MakefilePackage):
        multi-core machines."""
 
     homepage = "http://zlib.net/pigz/"
-    url      = "http://zlib.net/pigz/pigz-2.3.4.tar.gz"
+    url      = "https://github.com/madler/pigz/archive/v2.3.4.tar.gz"
 
-    version('2.3.4', '08e6b2e682bbf65ccf12c8966d633fc6')
+    version('2.4', '3c8a601db141d3013ef9fe5f2daaf73f')
+    version('2.3.4', 'c109057050b15edf3eb9bb4d0805235e')
 
     depends_on('zlib')
 
diff --git a/var/spack/repos/builtin/packages/pilon/package.py b/var/spack/repos/builtin/packages/pilon/package.py
new file mode 100644
index 0000000000..afcdfd4a44
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pilon/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class Pilon(Package):
+    """Pilon is an automated genome assembly improvement and variant
+    detection tool."""
+
+    homepage = "https://github.com/broadinstitute/pilon"
+    url      = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar"
+
+    version('1.22', '3c45568dc1b878a9a0316410ec62ab04', expand=False)
+    version('1.13', '9e96b4cf4ea595b1996c7e9ca76498b5', expand=False)
+
+    depends_on('java@1.7:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'pilon-{0}.jar'.format(self.version.dotted)
+        install(jar_file, prefix.bin)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "pilon.sh")
+        script = prefix.bin.pilon
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = self.spec['java'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('pilon-{0}.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/pilon/pilon.sh b/var/spack/repos/builtin/packages/pilon/pilon.sh
new file mode 100644
index 0000000000..41a31b3407
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pilon/pilon.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the pilon jar file
+java -jar pilon.jar "$@"
diff --git a/var/spack/repos/builtin/packages/pindel/package.py b/var/spack/repos/builtin/packages/pindel/package.py
new file mode 100644
index 0000000000..7755fdd8aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pindel/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pindel(MakefilePackage):
+    """Pindel can detect breakpoints from next-gen sequence data."""
+
+    homepage = "http://gmt.genome.wustl.edu/packages/pindel/"
+    url      = "https://github.com/genome/pindel/archive/v0.2.5.tar.gz"
+
+    version('0.2.5b8', 'e6de2ffb38ba1cb89351cdccabe78cde')
+    version('0.2.5b6', 'dc2febb18c203f0ef1ba02b7b882e94b')
+    version('0.2.5b5', '73e964bc19de9ab9e6e8a316353e3184')
+    version('0.2.5b4', 'b4aefd538d9f62578f46440c4bce497e')
+    version('0.2.5b1', 'a8e53e8919aa29093db13fad5ede93a5')
+    version('0.2.5a7', '5fb2bac6108547b5d60c38fc66abdfc4')
+    version('0.2.5',   'd4568cbb83ec25ef9f9f6f058b30053e')
+
+    depends_on('htslib@1.7:')
+    #
+    # This Makefile2 stuff is due to the original installer,
+    # The author wants to run make twice, the first
+    # time generates a Makefile.local then returns "false"
+    # User is then suppose to run make again and the
+    # package will compile. This is an attempt to
+    # stay as close to the original installer as possible
+    #
+
+    def edit(self, spec, prefix):
+        copy('Makefile', 'Makefile2')
+        myedit = FileFilter('Makefile2')
+        myedit.filter('-include Makefile.local', '#removed include')
+        myedit.filter('@false', '#removed autofailure')
+
+    def build(self, spec, prefix):
+        make("Makefile.local", "-f",
+             "Makefile2",
+             "HTSLIB=%s" % spec['htslib'].prefix)
+        make("HTSLIB=%s" % spec['htslib'].prefix)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('src/pindel', prefix.bin)
+        install('src/pindel2vcf', prefix.bin)
+        install('src/sam2pindel', prefix.bin)
+        install('src/pindel2vcf4tcga', prefix.bin)
+        install_tree('demo', prefix.doc)
diff --git a/var/spack/repos/builtin/packages/piranha/package.py b/var/spack/repos/builtin/packages/piranha/package.py
index 9f4b26d050..8488e826a4 100644
--- a/var/spack/repos/builtin/packages/piranha/package.py
+++ b/var/spack/repos/builtin/packages/piranha/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,10 @@ class Piranha(CMakePackage):
 
     homepage = "https://bluescarni.github.io/piranha/sphinx/"
     url      = "https://github.com/bluescarni/piranha/archive/v0.5.tar.gz"
+    git      = "https://github.com/bluescarni/piranha.git"
 
+    version('develop', branch='master')
     version('0.5', '99546bae2be115737b6316751eb0b84d')
-    version('develop', git='https://github.com/bluescarni/piranha.git')
 
     variant('python',   default=True,
             description='Build the Python bindings')
diff --git a/var/spack/repos/builtin/packages/pism/package.py b/var/spack/repos/builtin/packages/pism/package.py
new file mode 100644
index 0000000000..6eedcbced3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pism/package.py
@@ -0,0 +1,147 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pism(CMakePackage):
+    """Parallel Ice Sheet Model"""
+
+    homepage = "http://pism-docs.org/wiki/doku.php:="
+    url      = "https://github.com/pism/pism/archive/v0.7.3.tar.gz"
+    git      = "https://github.com/pism/pism.git"
+
+    maintainers = ['citibeth']
+
+    version('develop', branch='dev')
+    version('0.7.3', '7cfb034100d99d5c313c4ac06b7f17b6')
+    version('0.7.x', branch='stable0.7')
+    version('icebin', branch='efischer/dev')
+
+    variant('extra', default=False,
+            description='Build extra executables (testing/verification)')
+    variant('shared', default=True,
+            description='Build shared Pism libraries')
+    variant('python', default=False,
+            description='Build python bindings')
+    variant('icebin', default=False,
+            description='Build classes needed by IceBin')
+    variant('proj', default=True,
+            description='Use Proj.4 to compute cell areas, '
+            'longitudes, and latitudes.')
+    variant('parallel-netcdf4', default=False,
+            description='Enables parallel NetCDF-4 I/O.')
+    variant('parallel-netcdf3', default=False,
+            description='Enables parallel NetCDF-3 I/O using PnetCDF.')
+    variant('parallel-hdf5', default=False,
+            description='Enables parallel HDF5 I/O.')
+    # variant('tao', default=False,
+    #         description='Use TAO in inverse solvers.')
+
+    description = 'Build PISM documentation (requires LaTeX and Doxygen)'
+    variant('doc', default=False, description=description)
+
+    variant('examples', default=False,
+            description='Install examples directory')
+
+    description = 'Report errors through Everytrace (requires Everytrace)'
+    variant('everytrace', default=False, description=description)
+
+    # CMake build options not transferred to Spack variants
+    # (except from CMakeLists.txt)
+    #
+    # option (Pism_TEST_USING_VALGRIND "Add extra regression tests
+    #         using valgrind" OFF)
+    # mark_as_advanced (Pism_TEST_USING_VALGRIND)
+    #
+    # option (Pism_ADD_FPIC "Add -fPIC to C++ compiler flags
+    #         (CMAKE_CXX_FLAGS). Try turning it off if it does not work." ON)
+    # option (Pism_LINK_STATICALLY
+    #         "Set CMake flags to try to ensure that everything is
+    #         linked statically")
+    # option (Pism_LOOK_FOR_LIBRARIES
+    #         "Specifies whether PISM should look for libraries. (Disable
+    #         this on Crays.)" ON)
+    # option (Pism_USE_TR1
+    #        "Use the std::tr1 namespace to access shared pointer
+    #        definitions. Disable to get shared pointers from the std
+    #        namespace (might be needed with some compilers)." ON)
+    # option (Pism_USE_TAO "Use TAO in inverse solvers." OFF)
+
+    depends_on('fftw')
+    depends_on('gsl')
+    depends_on('mpi')
+    depends_on('netcdf')    # Only the C interface is used, no netcdf-cxx4
+    depends_on('petsc')
+    depends_on('udunits2')
+    depends_on('proj')
+    depends_on('everytrace', when='+everytrace')
+
+    extends('python', when='+python')
+    depends_on('python@2.7:2.8', when='+python')
+    depends_on('py-matplotlib', when='+python')
+    depends_on('py-numpy', when='+python')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        return [
+            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            # Fortran not needed for PISM...
+            # '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DPism_BUILD_EXTRA_EXECS=%s' %
+            ('YES' if '+extra' in spec else 'NO'),
+            '-DBUILD_SHARED_LIBS=%s' %
+            ('YES' if '+shared' in spec else 'NO'),
+            '-DPism_BUILD_PYTHON_BINDINGS=%s' %
+            ('YES' if '+python' in spec else 'NO'),
+            '-DPism_BUILD_ICEBIN=%s' %
+            ('YES' if '+icebin' in spec else 'NO'),
+            '-DPism_USE_PROJ4=%s' %
+            ('YES' if '+proj' in spec else 'NO'),
+            '-DPism_USE_PARALLEL_NETCDF4=%s' %
+            ('YES' if '+parallel-netcdf4' in spec else 'NO'),
+            '-DPism_USE_PNETCDF=%s' %
+            ('YES' if '+parallel-netcdf3' in spec else 'NO'),
+            '-DPism_USE_PARALLEL_HDF5=%s' %
+            ('YES' if '+parallel-hdf5' in spec else 'NO'),
+            '-DPism_BUILD_PDFS=%s' %
+            ('YES' if '+doc' in spec else 'NO'),
+            '-DPism_INSTALL_EXAMPLES=%s' %
+            ('YES' if '+examples' in spec else 'NO'),
+            '-DPism_USE_EVERYTRACE=%s' %
+            ('YES' if '+everytrace' in spec else 'NO')]
+
+    def setup_environment(self, spack_env, env):
+        env.set('PISM_PREFIX', self.prefix)
+        env.set('PISM_BIN', self.prefix.bin)
+
+
+# From email correspondence with Constantine Khroulev:
+#
+# > Do you have handy a table of which versions of PETSc are required
+# > for which versions of PISM?
+#
+# We don't. The installation manual [1] specifies the minimum PETSc
+# version for the latest "stable" release (currently PETSc 3.3). The
+# stable PISM version should support all PETSc versions starting from the
+# one specified in the manual and up to the latest PETSc release.
+#
+# The current development PISM version should be built with the latest
+# PETSc release at the time (the "maint" branch of PETSc).
+#
+# Thanks to Git it is relatively easy to find this info, though:
+#
+# | PISM version | PETSc version |
+# |--------------+---------------|
+# |          0.7 | 3.3 and later |
+# |          0.6 | 3.3           |
+# |       new_bc | 3.4.4         |
+# |          0.5 | 3.2           |
+# |          0.4 | 3.1           |
+# |          0.3 | 2.3.3 to 3.1  |
+# |          0.2 | 2.3.3 to 3.0  |
+# |          0.1 | 2.3.3-p2      |
diff --git a/var/spack/repos/builtin/packages/pixman/clang.patch b/var/spack/repos/builtin/packages/pixman/clang.patch
new file mode 100644
index 0000000000..9de9c1be60
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pixman/clang.patch
@@ -0,0 +1,28 @@
+--- pixman-0.34.0/test/utils-prng.c.bak	2018-02-01 00:34:15.757691302 +0100
++++ pixman-0.34.0/test/utils-prng.c	2018-02-01 00:36:38.285690995 +0100
+@@ -199,12 +199,24 @@
+         }
+         else
+         {
++
++#ifndef __has_builtin
++#define __has_builtin(x) 0
++#endif
++
+ #ifdef HAVE_GCC_VECTOR_EXTENSIONS
++# if !defined(__clang__) || __has_builtin(__builtin_shuffle)
+             const uint8x16 bswap_shufflemask =
+             {
+                 3, 2, 1, 0, 7, 6, 5, 4, 11, 10, 9, 8, 15, 14, 13, 12
+             };
+             randdata.vb = __builtin_shuffle (randdata.vb, bswap_shufflemask);
++# elif __has_builtin(__builtin_shufflevector)
++            randdata.vb = __builtin_shufflevector(randdata.vb, randdata.vb, 3, 2, 1, 0, 7, 6, 5, 4, 11, 10, 9, 8, 15, 14, 13, 12);
++# else
++#  error "GCC_VECTOR_EXTENSION is defined, but neither __builtin_shuffle nor __builtin_shufflevector is supported!"
++# endif
++
+             store_rand_128_data (buf, &randdata, aligned);
+             buf += 16;
+ #else
+
diff --git a/var/spack/repos/builtin/packages/pixman/package.py b/var/spack/repos/builtin/packages/pixman/package.py
index 4191550803..d3e8661dd2 100644
--- a/var/spack/repos/builtin/packages/pixman/package.py
+++ b/var/spack/repos/builtin/packages/pixman/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -37,9 +18,35 @@ class Pixman(AutotoolsPackage):
     version('0.34.0', 'e80ebae4da01e77f68744319f01d52a3')
     version('0.32.6', '3a30859719a41bd0f5cccffbfefdd4c2')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('libpng')
 
+    # As discussed here:
+    # https://bugs.freedesktop.org/show_bug.cgi?id=104886
+    # __builtin_shuffle was removed in clang 5.0.
+    # From version 9.1 apple-clang is based on clang 5.0.
+    # Patch is obtained from above link.
+    patch('clang.patch', when='%clang@9.1.0-apple:')
+
+    @run_before('build')
+    def patch_config_h_for_intel(self):
+        config_h = join_path(self.stage.source_path, 'config.h')
+
+        # Intel disguises itself as GNU, but doesn't implement
+        # the same builtin functions. This causes in this case
+        # a positive detection of GCC vector extensions, which
+        # is bound to fail at compile time because Intel has no
+        # __builtin_shuffle. See also:
+        #
+        # https://software.intel.com/en-us/forums/intel-c-compiler/topic/758013
+        #
+        if '%intel' in self.spec:
+            filter_file(
+                '#define HAVE_GCC_VECTOR_EXTENSIONS /\*\*/',
+                '/* #undef HAVE_GCC_VECTOR_EXTENSIONS */',
+                config_h
+            )
+
     def configure_args(self):
         args = [
             '--enable-libpng',
diff --git a/var/spack/repos/builtin/packages/pkg-config/package.py b/var/spack/repos/builtin/packages/pkg-config/package.py
index 22a8833a11..a27df03b40 100644
--- a/var/spack/repos/builtin/packages/pkg-config/package.py
+++ b/var/spack/repos/builtin/packages/pkg-config/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,8 @@ class PkgConfig(AutotoolsPackage):
     version('0.29.1', 'f739a28cae4e0ca291f82d1d41ef107d')
     version('0.28',   'aa3c86e67551adc3ac865160e34a2a0d')
 
+    provides('pkgconfig')
+
     variant('internal_glib', default=True,
             description='Builds with internal glib')
 
@@ -45,17 +28,9 @@ class PkgConfig(AutotoolsPackage):
     parallel = False
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
-        """spack built pkg-config on cray's requires adding /usr/local/
-        and /usr/lib64/  to PKG_CONFIG_PATH in order to access cray '.pc'
-        files.
-        Adds the ACLOCAL path for autotools."""
+        """Adds the ACLOCAL path for autotools."""
         spack_env.append_path('ACLOCAL_PATH',
                               join_path(self.prefix.share, 'aclocal'))
-        if 'platform=cray' in self.spec:
-            spack_env.append_path('PKG_CONFIG_PATH',
-                                  '/usr/lib64/pkgconfig')
-            spack_env.append_path('PKG_CONFIG_PATH',
-                                  '/usr/local/lib64/pkgconfig')
 
     def configure_args(self):
         config_args = ['--enable-shared']
diff --git a/var/spack/repos/builtin/packages/pkgconf/package.py b/var/spack/repos/builtin/packages/pkgconf/package.py
index 7b4b570945..742713c0ff 100644
--- a/var/spack/repos/builtin/packages/pkgconf/package.py
+++ b/var/spack/repos/builtin/packages/pkgconf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,22 @@ class Pkgconf(AutotoolsPackage):
     maintaining compatibility."""
 
     homepage = "http://pkgconf.org/"
-    url      = "https://distfiles.dereferenced.org/pkgconf/pkgconf-1.3.8.tar.xz"
+    url      = "http://distfiles.alpinelinux.org/distfiles/pkgconf-1.4.2.tar.xz"
+
+    version('1.4.2',  '678d242b4eef1754bba6a58642af10bb')
+    version('1.4.0',  'c509c0dad5a70aa4bc3210557b7eafce')
+    version('1.3.10', '9b63707bf6f8da6efb3868101d7525fe')
+    version('1.3.8',  '484ba3360d983ce07416843d5bc916a8')
+
+    provides('pkgconfig')
+
+    # TODO: Add a package for the kyua testing framework
+    # depends_on('kyua', type='test')
 
-    version('1.3.8', '484ba3360d983ce07416843d5bc916a8')
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        """Adds the ACLOCAL path for autotools."""
+        spack_env.append_path('ACLOCAL_PATH',
+                              join_path(self.prefix.share, 'aclocal'))
 
     @run_after('install')
     def link_pkg_config(self):
diff --git a/var/spack/repos/builtin/packages/planck-likelihood/package.py b/var/spack/repos/builtin/packages/planck-likelihood/package.py
index a92fc328db..0b04aec89f 100644
--- a/var/spack/repos/builtin/packages/planck-likelihood/package.py
+++ b/var/spack/repos/builtin/packages/planck-likelihood/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -141,8 +122,8 @@ class PlanckLikelihood(Package):
     @on_package_attributes(run_tests=True)
     def check_install(self):
         prefix = self.prefix
-        clik_example_C = Executable(join_path(prefix.bin, 'clik_example_C'))
+        clik_example_c = Executable(join_path(prefix.bin, 'clik_example_C'))
         with working_dir('spack-check', create=True):
-            clik_example_C(join_path(prefix, 'share', 'clik',
+            clik_example_c(join_path(prefix, 'share', 'clik',
                                      'plc_2.0', 'hi_l', 'plik',
                                      'plik_dx11dr2_HM_v18_TT.clik'))
diff --git a/var/spack/repos/builtin/packages/plasma/package.py b/var/spack/repos/builtin/packages/plasma/package.py
index 46b662d63d..54ef75c207 100644
--- a/var/spack/repos/builtin/packages/plasma/package.py
+++ b/var/spack/repos/builtin/packages/plasma/package.py
@@ -1,17 +1,12 @@
-##############################################################################
-# Copyright (c) 2017, Innovative Computing Laboratory
-# Produced at the Innovative Computing Laboratory.
-#
-# Created by Piotr Luszczek, luszczek@icl.utk.edu, All rights reserved.
-#
-# For details, see https://github.com/spack/spack
-#
-##############################################################################
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Plasma(MakefilePackage):
+class Plasma(CMakePackage):
     """Parallel Linear Algebra Software for Multicore Architectures, PLASMA is
     a software package for solving problems in dense linear algebra using
     multicore processors and Xeon Phi coprocessors. PLASMA provides
@@ -21,24 +16,38 @@ class Plasma(MakefilePackage):
     problems, and singular value problems."""
 
     homepage = "https://bitbucket.org/icl/plasma/"
-    url      = "https://bitbucket.org/icl/plasma/downloads/plasma-17.1.tar.gz"
+    url = "https://bitbucket.org/icl/plasma/downloads/plasma-18.10.0.tar.gz"
+    hg = "https://luszczek@bitbucket.org/icl/plasma"
 
-    version("17.1", "64b410b76023a41b3f07a5f0dca554e1")
+    version("develop", hg=hg)
+    version("18.10.0", sha256="93dceae93f57a2fbd79b85d2fbf7907d1d32e158b8d1d93892d9ff3df9963210")
+    version("18.9.0", sha256="753eae28ea48986a2cc7b8204d6eef646584541e59d42c3c94fa9879116b0774")
+    version("17.1",
+            sha256="d4b89f7c3d240a69dfe986284a14471eec4830b9e352ae902ea8861f15573dee",
+            url="https://bitbucket.org/icl/plasma/downloads/plasma-17.1.tar.gz")
 
-    version("develop", hg="https://luszczek@bitbucket.org/icl/plasma")
+    variant("shared", default=True,
+            description="Build shared library (disables static library)")
 
     depends_on("blas")
     depends_on("lapack")
 
     conflicts("atlas")  # does not have LAPACKE interface
-    conflicts("netlib-lapack@:2.999")  # missing LAPACKE features
+
+    # missing LAPACKE features and/or CBLAS headers
+    conflicts("netlib-lapack@:3.5.999")
+
     # clashes with OpenBLAS declarations and has a problem compiling on its own
     conflicts("cblas")
+
     conflicts("openblas-with-lapack")  # incomplete LAPACK implementation
     conflicts("veclibfort")
 
-    # only GCC 7+ and higher have sufficient support for OpenMP 4+ tasks+deps
-    conflicts("%gcc@:6.999")
+    # only GCC 4.9+ and higher have sufficient support for OpenMP 4+ tasks+deps
+    conflicts("%gcc@:4.8.99", when='@:17.1')
+    # only GCC 6.0+ and higher have for OpenMP 4+ Clause "priority"
+    conflicts("%gcc@:5.99", when='@17.2:')
+
     conflicts("%cce")
     conflicts("%clang")
     conflicts("%intel")
@@ -49,14 +58,52 @@ class Plasma(MakefilePackage):
 
     patch("remove_absolute_mkl_include.patch", when="@17.1")
 
+    @when("@18.9.0:")
+    def cmake_args(self):
+        options = list()
+
+        options.extend([
+            "-DCMAKE_INSTALL_PREFIX=%s" % prefix,
+            "-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib" % prefix,
+            "-DBLAS_LIBRARIES=%s" % self.spec["blas"].libs.joined(";"),
+            "-DLAPACK_LIBRARIES=%s" % self.spec["lapack"].libs.joined(";")
+        ])
+
+        options += [
+            "-DBUILD_SHARED_LIBS=%s" %
+            ('ON' if ('+shared' in self.spec) else 'OFF')
+        ]
+
+        return options
+
+    # Before 18.9.0 it was an Makefile package
+    @when("@:17.1")
+    def cmake(self, spec, prefix):
+        pass
+
+    # Before 18.9.0 it was an Makefile package
+    @when("@:17.1")
+    def build(self, spec, prefix):
+        pass
+
+    # Before 18.9.0 it was an Makefile package
+    @when("@:17.1")
+    def install(self, spec, prefix):
+        self.edit(spec, prefix)
+        make()
+        make("install")
+
+    @when("@:17.1")
     def edit(self, spec, prefix):
         # copy "make.inc.mkl-gcc" provided by default into "make.inc"
         open("make.inc", "w").write(open("make.inc.mkl-gcc").read())
 
         make_inc = FileFilter("make.inc")
 
-        if not spec.satisfies("^mkl"):
+        if not spec.satisfies("^intel-mkl"):
             make_inc.filter("-DPLASMA_WITH_MKL", "")  # not using MKL
+            make_inc.filter("LIBS *= *.*", "LIBS = " +
+                            self.spec["blas"].libs.ld_flags + " -lm")
 
         header_flags = ""
         # accumulate CPP flags for headers: <cblas.h> and <lapacke.h>
@@ -73,18 +120,3 @@ class Plasma(MakefilePackage):
 
         # make sure CC variable comes from build environment
         make_inc.filter("CC *[?]*= * .*cc", "")
-
-    @property
-    def build_targets(self):
-        targets = list()
-
-        # use $CC set by Spack
-        targets.append("CC = {0}".format(self.compiler.cc))
-
-        if self.spec.satisfies("^mkl"):
-            targets.append("MKLROOT = {0}/mkl".format(env["MKLROOT"]))
-
-        # pass BLAS library flags
-        targets.append("LIBS = {0}".format(self.spec["blas"].libs.ld_flags))
-
-        return targets
diff --git a/var/spack/repos/builtin/packages/platypus/package.py b/var/spack/repos/builtin/packages/platypus/package.py
new file mode 100644
index 0000000000..7ef22abc74
--- /dev/null
+++ b/var/spack/repos/builtin/packages/platypus/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Platypus(Package):
+    """A Haplotype-Based Variant Caller For Next Generation Sequence Data"""
+
+    homepage = "http://www.well.ox.ac.uk/platypus"
+    url      = "http://www.well.ox.ac.uk/bioinformatics/Software/Platypus-latest.tgz"
+
+    version('0.8.1', 'edf3fb5bf080241ddb75a413c8529d57')
+
+    depends_on('python@2.6:', type=('build', 'run'))
+    depends_on('py-cython', type='build')
+    depends_on('htslib')
+
+    def install(self, spec, prefix):
+        build_platypus = Executable('./buildPlatypus.sh')
+        build_platypus()
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/plink/package.py b/var/spack/repos/builtin/packages/plink/package.py
index b6df013978..2f571e25e4 100644
--- a/var/spack/repos/builtin/packages/plink/package.py
+++ b/var/spack/repos/builtin/packages/plink/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,22 @@ class Plink(Package):
 
     homepage = "https://www.cog-genomics.org/plink/1.9/"
 
-    version('1.9', 'a2325881594856c0f1b7523290d1e04f',
-            url='https://www.cog-genomics.org/static/bin/plink170815/plink_linux_x86_64.zip')
+    version('1.9-beta5', '737545504ae19348a44a05fa69b75c28',
+            url='https://github.com/chrchang/plink-ng/archive/b15c19f.tar.gz')
+    version('1.07', 'fd0bafeda42151b20534e4f97b0d97df',
+            url='http://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip',
+            preferred=True)
+
+    depends_on('atlas', when='@1.9-beta5')
+    depends_on('netlib-lapack', when='@1.9-beta5')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
-        install('plink', prefix.bin)
-        install('prettify', prefix.bin)
+        if spec.version == Version('1.07'):
+            install('plink', prefix.bin)
+            install('gPLINK.jar', prefix.bin)
+        if spec.version == Version('1.9-beta5'):
+            with working_dir('1.9'):
+                first_compile = Executable('./plink_first_compile')
+                first_compile()
+                install('plink', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/plplot/package.py b/var/spack/repos/builtin/packages/plplot/package.py
new file mode 100644
index 0000000000..5e0d23b930
--- /dev/null
+++ b/var/spack/repos/builtin/packages/plplot/package.py
@@ -0,0 +1,104 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Plplot(CMakePackage):
+    """PLplot is a cross-platform package for creating scientific plots."""
+
+    homepage = "http://plplot.sourceforge.net/"
+    url      = "https://sourceforge.net/projects/plplot/files/plplot/5.13.0%20Source/plplot-5.13.0.tar.gz/download"
+
+    version('5.13.0', 'bfefeae7fb9a23377c6dc37b44a7da8a')
+    version('5.12.0', '998a05be218e5de8f2faf988b8dbdc51')
+    version('5.11.0', '632c9e13b09f4e2b2517b3567bc3cece')
+
+    variant('java', default=False, description='Enable Java binding')
+    variant('lua', default=False, description='Enable Lua binding')
+    variant('pango', default=False, description='Enable Pango')
+    variant('python', default=False, description='Enable Python binding')
+    variant('qt', default=False, description='Enable QT binding')
+    variant('tcl', default=True, description='Enable TCL binding')
+    variant('wx', default=False, description='Enable WxWidgets')
+    variant('wxold', default=False, description='Use WxWidgets old interface')
+
+    conflicts('~wx', when='+wxold')
+    conflicts('+wxold', when='@:5.11')
+
+    depends_on('java', when='+java')
+    depends_on('lua', when='+lua')
+    depends_on('pango', when='+pango')
+    depends_on('py-numpy', type=('build', 'run'), when='+python')
+    depends_on('python@2.7:2.8', type=('build', 'run'), when='+python')
+    depends_on('qt', when='+qt')
+    depends_on('tcl', when='+tcl')
+    depends_on('wx', when='+wx')
+
+    depends_on('freetype')
+    depends_on('gtkplus')
+    depends_on('libx11')
+    depends_on('qhull')
+    depends_on('swig')
+
+    def cmake_args(self):
+        args = []
+        # needs 'tk with wish'
+        args += ['-DENABLE_tk=OFF']
+
+        if '+java' in self.spec:
+            args += ['-DENABLE_java=ON']
+        else:
+            args += ['-DENABLE_java=OFF']
+
+        if '+lua' in self.spec:
+            args += ['-DENABLE_lua=ON']
+        else:
+            args += ['-DENABLE_lua=OFF']
+
+        if '+python' in self.spec:
+            args += ['-DENABLE_python=ON']
+        else:
+            args += ['-DENABLE_python=OFF']
+
+        if '+qt' in self.spec:
+            args += ['-DENABLE_qt=ON']
+        else:
+            args += ['-DENABLE_qt=OFF']
+
+        if '+tcl' in self.spec:
+            args += ['-DENABLE_tcl=ON']
+            # could also be addressed by creating the links within tcl
+            # as is done for the tclsh executable
+            args += [
+                '-DTCL_INCLUDE_PATH={0}/include'.format(
+                    self.spec['tcl'].prefix.include
+                ),
+                '-DTCL_LIBRARY={0}'.format(
+                    LibraryList(find_libraries(
+                        'libtcl*',
+                        self.spec['tcl'].prefix.lib,
+                        shared=True,
+                    )),
+                ),
+                '-DTCL_STUB_LIBRARY={0}'.format(
+                    LibraryList(find_libraries(
+                        'libtclstub*',
+                        self.spec['tcl'].prefix.lib,
+                        shared=False,
+                    )),
+                )
+            ]
+        else:
+            args += ['-DENABLE_tcl=OFF']
+
+        if '+wx' in self.spec:
+            args += ['-DENABLE_wxwidgets=ON']
+            if '+wxold' in self.spec:
+                args += ['-DOLD_WXWIDGETS=ON']
+        else:
+            args += ['-DENABLE_wxwidgets=OFF']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/plumed/package.py b/var/spack/repos/builtin/packages/plumed/package.py
index cac4f4254f..35cad3d0b7 100644
--- a/var/spack/repos/builtin/packages/plumed/package.py
+++ b/var/spack/repos/builtin/packages/plumed/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import collections
 
 from spack import *
@@ -43,6 +24,9 @@ class Plumed(AutotoolsPackage):
     homepage = 'http://www.plumed.org/'
     url = 'https://github.com/plumed/plumed2/archive/v2.2.3.tar.gz'
 
+    version('2.4.2', '0f66f24b4c763ae8b2f39574113e9935')
+    version('2.4.1', '6558e1fd02fc46e847ab6a3fb5ed5411')
+    version('2.3.5', '3cc5f025cb6f5d963f3c778f15c77d44')
     version('2.3.3', '9f5729e406e79a06a16976fcb020e024')
     version('2.3.0', 'a9b5728f115dca8f0519111f1f5a6fa5')
     version('2.2.4', 'afb00da25a3fbd47acf377e53342059d')
@@ -66,6 +50,9 @@ class Plumed(AutotoolsPackage):
     depends_on('zlib')
     depends_on('blas')
     depends_on('lapack')
+    # For libmatheval support through the 'function' module
+    # which is enabled by default (or when optional_modules=all)
+    depends_on('libmatheval')
 
     depends_on('mpi', when='+mpi')
     depends_on('gsl', when='+gsl')
diff --git a/var/spack/repos/builtin/packages/pmgr-collective/package.py b/var/spack/repos/builtin/packages/pmgr-collective/package.py
index c96e777e5b..ff08d784b1 100644
--- a/var/spack/repos/builtin/packages/pmgr-collective/package.py
+++ b/var/spack/repos/builtin/packages/pmgr-collective/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pmix/package.py b/var/spack/repos/builtin/packages/pmix/package.py
index 0763dfbaed..0f09c4df66 100644
--- a/var/spack/repos/builtin/packages/pmix/package.py
+++ b/var/spack/repos/builtin/packages/pmix/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
+import spack.architecture
 
 
 class Pmix(AutotoolsPackage):
@@ -48,8 +30,16 @@ class Pmix(AutotoolsPackage):
     homepage = "https://pmix.github.io/pmix"
     url      = "https://github.com/pmix/pmix/releases/download/v2.0.1/pmix-2.0.1.tar.bz2"
 
+    version('3.0.2',    sha256='df68f35a3ed9517eeade80b13855cebad8fde2772b36a3f6be87559b6d430670')
+    version('3.0.1',    sha256='b81055d2c0d61ef5a451b63debc39c820bcd530490e2e4dcb4cdbacb618c157c')
+    version('3.0.0',    sha256='ee8f68107c24b706237a53333d832445315ae37de6773c5413d7fda415a6e2ee')
+    version('2.1.4',    sha256='eb72d292e76e200f02cf162a477eecea2559ef3ac2edf50ee95b3fe3983d033e')
+    version('2.1.3',    sha256='281283133498e7e5999ed5c6557542c22408bc9eb51ecbcf7696160616782a41')
+    version('2.1.2',    sha256='94bb9c801c51a6caa1b8cef2b85ecf67703a5dfa4d79262e6668c37c744bb643')
     version('2.0.1',    'ba3193b485843516e6b4e8641e443b1e')
     version('2.0.0',    '3e047c2ea0ba8ee9925ed92b205fd92e')
+    version('1.2.5',    'c3d20cd9d365a813dc367afdf0f41c37')
+    version('1.2.4',    '242a812e206e7c5948f1f5c9688eb2a7')
     version('1.2.3',    '102b1cc650018b62348b45d572b158e9')
     version('1.2.2',    'd85c8fd437bd88f984549425ad369e9f')
     version('1.2.1',    'f090f524681c52001ea2db3b0285596f')
@@ -58,6 +48,7 @@ class Pmix(AutotoolsPackage):
     depends_on('libevent')
 
     def configure_args(self):
+
         spec = self.spec
         config_args = [
             '--enable-shared',
@@ -68,4 +59,11 @@ class Pmix(AutotoolsPackage):
         config_args.append(
             '--with-libevent={0}'.format(spec['libevent'].prefix))
 
+        # Versions < 2.1.1 have a bug in the test code that *sometimes*
+        # causes problems on strict alignment architectures such as
+        # aarch64.  Work-around is to just not build the test code.
+        if 'aarch64' in spack.architecture.sys_type() and \
+           self.spec.version < Version('2.1.1'):
+            config_args.append('--without-tests-examples')
+
         return config_args
diff --git a/var/spack/repos/builtin/packages/pnfft/package.py b/var/spack/repos/builtin/packages/pnfft/package.py
index fbb6b636b1..d34104669d 100644
--- a/var/spack/repos/builtin/packages/pnfft/package.py
+++ b/var/spack/repos/builtin/packages/pnfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class Pnfft(AutotoolsPackage):
     version('1.0.7-alpha', '5caa7f214eed99de2281043ca2367e9e')
 
     depends_on('pfft')
+    depends_on('gsl')
 
     def configure(self, spec, prefix):
         options = ['--prefix={0}'.format(prefix)]
diff --git a/var/spack/repos/builtin/packages/pngwriter/package.py b/var/spack/repos/builtin/packages/pngwriter/package.py
index 896b660ac6..76f4553826 100644
--- a/var/spack/repos/builtin/packages/pngwriter/package.py
+++ b/var/spack/repos/builtin/packages/pngwriter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,14 +18,25 @@ class Pngwriter(CMakePackage):
 
     homepage = "http://pngwriter.sourceforge.net/"
     url      = "https://github.com/pngwriter/pngwriter/archive/0.5.6.tar.gz"
+    git      = "https://github.com/pngwriter/pngwriter.git"
 
-    version('develop', branch='dev',
-            git='https://github.com/pngwriter/pngwriter.git')
-    version('master', branch='master',
-            git='https://github.com/pngwriter/pngwriter.git')
+    maintainers = ['ax3l']
+
+    version('develop', branch='dev')
+    version('master', branch='master')
+    version('0.7.0', 'a68aa0889f120f5bb07848afce278a95')
     version('0.6.0', '0a19bc55c5f6379fea7343752fd3ffae')
     version('0.5.6', 'c13bd1fdc0e331a246e6127b5f262136')
 
     depends_on('libpng')
     depends_on('zlib')
     depends_on('freetype')
+
+    def cmake_args(self):
+        spec = self.spec
+        args = []
+
+        if spec.satisfies('@0.7.0:'):
+            args += ['-DPNGwriter_USE_FREETYPE:BOOL=ON']
+
+        return args
diff --git a/var/spack/repos/builtin/packages/pnmpi/package.py b/var/spack/repos/builtin/packages/pnmpi/package.py
new file mode 100644
index 0000000000..0d483724ba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pnmpi/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pnmpi(CMakePackage):
+    """PnMPI is a dynamic MPI tool infrastructure that builds on top of
+       the standardized PMPI interface. """
+
+    homepage = "https://github.com/LLNL/PnMPI"
+    url      = "https://github.com/LLNL/PnMPI/releases/download/v1.7/PnMPI-v1.7-full.tar.gz"
+
+    version('1.7', '8040c1558c0deaa3d964c35d1760f3a8')
+
+    variant('fortran', default=False,
+            description='Configure PnMPI with Fortran support')
+    variant('tests', default=False,
+            description='Build test cases and enable "test" makefile target')
+
+    depends_on('cmake', type='build')
+    depends_on('argp-standalone', when='platform=darwin')
+    depends_on('binutils')
+    depends_on('help2man')
+    depends_on('doxygen')
+    depends_on('mpi')
+
+    @run_before('cmake')
+    def check_fortran(self):
+        is_no_fortran_compiler = not self.compiler.f77 and not self.compiler.fc
+        if self.spec.satisfies('+fortran'):
+            if is_no_fortran_compiler:
+                raise InstallError('pnmpi+fortran requires Fortran compiler '
+                                   'but no Fortran compiler found!')
+
+    def cmake_args(self):
+        args = []
+        spec = self.spec
+        on_off = {True: 'ON', False: 'OFF'}
+
+        has_fortran = spec.satisfies('+fortran')
+        has_tests = spec.satisfies('+tests')
+
+        args.append('-DENABLE_FORTRAN:BOOL={0}'.format(on_off[has_fortran]))
+        args.append('-DENABLE_TESTING:BOOL={0}'.format(on_off[has_tests]))
+        return args
diff --git a/var/spack/repos/builtin/packages/poamsa/package.py b/var/spack/repos/builtin/packages/poamsa/package.py
index dba8a03546..e109e39423 100644
--- a/var/spack/repos/builtin/packages/poamsa/package.py
+++ b/var/spack/repos/builtin/packages/poamsa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pocl/package.py b/var/spack/repos/builtin/packages/pocl/package.py
index ec4ef09bbe..c020dd9cf6 100644
--- a/var/spack/repos/builtin/packages/pocl/package.py
+++ b/var/spack/repos/builtin/packages/pocl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 from spack import *
@@ -35,16 +16,17 @@ class Pocl(CMakePackage):
     GPUs/accelerators."""
 
     homepage = "http://portablecl.org"
-    url = "http://portablecl.org/downloads/pocl-0.13.tar.gz"
+    url      = "https://github.com/pocl/pocl/archive/v1.1.tar.gz"
+    git      = "https://github.com/pocl/pocl.git"
 
-    version("master", git="https://github.com/pocl/pocl.git")
-    version('0.14', '1d35f09299e76b9e3918c42826555194')
-    # version("0.14-rc",
-    #         git="https://github.com/pocl/pocl.git", branch="release_0_14")
-    version("0.13", "344480864d4269f2f63f1509395898bd")
-    version("0.12", "e197ba3aa01a35f40581c48e053330dd")
-    version("0.11", "9be0640cde2983062c47393d9e8e8fe7")
-    version("0.10", "0096be4f595c7b5cbfa42430c8b3af6a")
+    version("master", branch="master")
+    version('1.1', sha256='1e8dd0693a88c84937754df947b202871a40545b1b0a97ebefa370b0281c3c53')
+    version('1.0', sha256='94bd86a2f9847c03e6c3bf8dca12af3734f8b272ffeacbc3fa8fcca58844b1d4')
+    version('0.14', sha256='2127bf925a91fbbe3daf2f1bac0da5c8aceb16e2a9434977a3057eade974106a')
+    version('0.13', sha256='a17f37d8f26819c0c8efc6de2b57f67a0c8a81514fc9cd5005434e49d67499f9')
+    version('0.12', sha256='5160d7a59721e6a7d0fc85868381c0afceaa7c07b9956c9be1e3b51e80c29f76')
+    version('0.11', sha256='24bb801fb87d104b66faaa95d1890776fdeabb37ad1b12fb977281737c7f29bb')
+    version('0.10', sha256='e9c38f774a77e61f66d850b705a5ba42d49356c40e75733db4c4811e091e5088')
 
     # This is Github's pocl/pocl#373
     patch("uint.patch", when="@:0.13")
@@ -57,20 +39,22 @@ class Pocl(CMakePackage):
 
     depends_on("cmake @2.8.12:", type="build")
     depends_on("hwloc")
-    depends_on("libtool", type=("build", "run"))
+    depends_on("hwloc@:1.99.99", when="@:1.1.99")
+    depends_on("libtool", type=("build", "link", "run"))
+    depends_on("pkgconfig", type="build")
+
     # We don't request LLVM's shared libraries because these are not
     # enabled by default, and also because they fail to build for us
     # (see #1616)
-    depends_on("llvm +clang")
-    depends_on("pkg-config", type="build")
-
     # These are the supported LLVM versions
-    depends_on("llvm @3.7:3.9", when="@master")
-    depends_on("llvm @3.7:4.0", when="@0.14")
-    depends_on("llvm @3.7:3.8", when="@0.13")
-    depends_on("llvm @3.2:3.7", when="@0.12")
-    depends_on("llvm @3.2:3.6", when="@0.11")
-    depends_on("llvm @3.2:3.5", when="@0.10")
+    depends_on("llvm +clang @6.0:7.0", when="@master")
+    depends_on("llvm +clang @5.0:6.0", when="@1.1")
+    depends_on("llvm +clang @4.0:5.0", when="@1.0")
+    depends_on("llvm +clang @3.7:4.0", when="@0.14")
+    depends_on("llvm +clang @3.7:3.8", when="@0.13")
+    depends_on("llvm +clang @3.2:3.7", when="@0.12")
+    depends_on("llvm +clang @3.2:3.6", when="@0.11")
+    depends_on("llvm +clang @3.2:3.5", when="@0.10")
 
     variant("distro", default=False,
             description=("Support several CPU architectures, "
@@ -79,6 +63,14 @@ class Pocl(CMakePackage):
     variant("icd", default=False,
             description="Support a system-wide ICD loader")
 
+    def url_for_version(self, version):
+        if version >= Version('1.0'):
+            url = "https://github.com/pocl/pocl/archive/v{0}.tar.gz"
+        else:
+            url = "http://portablecl.org/downloads/pocl-{0}.tar.gz"
+
+        return url.format(version.up_to(2))
+
     def cmake_args(self):
         spec = self.spec
         args = ["-DINSTALL_OPENCL_HEADERS=ON"]
@@ -91,8 +83,7 @@ class Pocl(CMakePackage):
 
     @run_after('install')
     def symlink_opencl(self):
-        with working_dir(self.build_directory):
-            os.symlink("OpenCL", join_path(self.prefix.include, "CL"))
+        os.symlink("CL", self.prefix.include.OpenCL)
 
     @run_after('install')
     @on_package_attributes(run_tests=True)
diff --git a/var/spack/repos/builtin/packages/polymake/package.py b/var/spack/repos/builtin/packages/polymake/package.py
index 0fbfe52640..62e7013e5a 100644
--- a/var/spack/repos/builtin/packages/polymake/package.py
+++ b/var/spack/repos/builtin/packages/polymake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/poppler-data/package.py b/var/spack/repos/builtin/packages/poppler-data/package.py
new file mode 100644
index 0000000000..3bb5ba3e34
--- /dev/null
+++ b/var/spack/repos/builtin/packages/poppler-data/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PopplerData(CMakePackage):
+    """This package consists of encoding files for use with poppler. The
+    encoding files are optional and poppler will automatically read them if
+    they are present.  When installed, the encoding files enables poppler to
+    correctly render CJK and Cyrrilic properly.  While poppler is licensed
+    under the GPL, these encoding files have different license, and thus
+    distributed separately."""
+
+    homepage = "https://poppler.freedesktop.org/"
+    url      = "https://poppler.freedesktop.org/poppler-data-0.4.9.tar.gz"
+
+    version('0.4.9', '35cc7beba00aa174631466f06732be40')
+
+    depends_on('cmake@2.6:', type='build')
diff --git a/var/spack/repos/builtin/packages/poppler/package.py b/var/spack/repos/builtin/packages/poppler/package.py
new file mode 100644
index 0000000000..653dd2e96d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/poppler/package.py
@@ -0,0 +1,135 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Poppler(CMakePackage):
+    """Poppler is a PDF rendering library based on the xpdf-3.0 code base."""
+
+    homepage = "https://poppler.freedesktop.org"
+    url      = "https://poppler.freedesktop.org/poppler-0.65.0.tar.xz"
+    list_url = "https://poppler.freedesktop.org/releases.html"
+
+    version('0.65.0', 'b9a0af02e43deb26265f130343e90d78')
+    version('0.64.0', 'f7f687ebb60004f8ad61994575018044')
+
+    variant('cms',      default=False, description='Use color management system')
+    variant('glib',     default=False, description='Compile poppler glib wrapper')
+    variant('gobject',  default=False, description='Generate GObject introspection')
+    variant('libcurl',  default=False, description='Build libcurl based HTTP support')
+    variant('openjpeg', default=False, description='Use libopenjpeg for JPX streams')
+    variant('qt5',      default=False, description='Compile poppler qt5 wrapper')
+    variant('zlib',     default=False, description='Build with zlib')
+    variant('cairo',    default=False, description='Search for Cairo package')
+    variant('iconv',    default=False, description='Search for Iconv package')
+    variant('jpeg',     default=False, description='Search for JPEG package')
+    variant('png',      default=False, description='Search for PNG package')
+    variant('tiff',     default=False, description='Search for TIFF package')
+
+    depends_on('cmake@3.1.0:', type='build')
+    depends_on('pkgconfig', type='build')
+    depends_on('poppler-data', type=('build', 'run'))
+    depends_on('fontconfig')
+    depends_on('freetype')
+
+    depends_on('lcms', when='+cms')
+    depends_on('glib', when='+glib')
+    depends_on('gobject-introspection', when='+gobject')
+    depends_on('curl', when='+libcurl')
+    depends_on('openjpeg', when='+openjpeg')
+    depends_on('qt@5.0:5.999', when='+qt5')
+    depends_on('zlib', when='+zlib')
+    depends_on('cairo', when='+cairo')
+    depends_on('libiconv', when='+iconv')
+    depends_on('jpeg', when='+jpeg')
+    depends_on('libpng', when='+png')
+    depends_on('libtiff', when='+tiff')
+
+    # Only needed to run `make test`
+    resource(
+        name='test',
+        git='https://anongit.freedesktop.org/git/poppler/test.git',
+        placement='testdata'
+    )
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            '-DTESTDATADIR={0}'.format(
+                join_path(self.stage.source_path, 'testdata')),
+            # TODO: Add packages for these missing dependencies
+            '-DENABLE_SPLASH=OFF',
+            '-DWITH_NSS3=OFF',
+        ]
+
+        if '+cms' in spec:
+            args.append('-DENABLE_CMS=lcms2')
+        else:
+            args.append('-DENABLE_CMS=none')
+
+        if '+glib' in spec:
+            args.append('-DENABLE_GLIB=ON')
+        else:
+            args.append('-DENABLE_GLIB=OFF')
+
+        if '+gobject' in spec:
+            args.append('-DENABLE_GOBJECT_INTROSPECTION=ON')
+        else:
+            args.append('-DENABLE_GOBJECT_INTROSPECTION=OFF')
+
+        if '+libcurl' in spec:
+            args.append('-DENABLE_LIBCURL=ON')
+        else:
+            args.append('-DENABLE_LIBCURL=OFF')
+
+        if '+openjpeg' in spec:
+            args.append('-DENABLE_LIBOPENJPEG=openjpeg2')
+        else:
+            args.append('-DENABLE_LIBOPENJPEG=none')
+
+        if '+qt5' in spec:
+            args.append('-DENABLE_QT5=ON')
+        else:
+            args.append('-DENABLE_QT5=OFF')
+
+        if '+zlib' in spec:
+            args.append('-DENABLE_ZLIB=ON')
+        else:
+            args.append('-DENABLE_ZLIB=OFF')
+
+        if '+cairo' in spec:
+            args.append('-DWITH_Cairo=ON')
+        else:
+            args.append('-DWITH_Cairo=OFF')
+
+        if '+iconv' in spec:
+            args.append('-DWITH_Iconv=ON')
+        else:
+            args.append('-DWITH_Iconv=OFF')
+
+        if '+jpeg' in spec:
+            args.extend([
+                '-DENABLE_DCTDECODER=libjpeg',
+                '-DWITH_JPEG=ON'
+            ])
+        else:
+            args.extend([
+                '-DENABLE_DCTDECODER=none',
+                '-DWITH_JPEG=OFF'
+            ])
+
+        if '+png' in spec:
+            args.append('-DWITH_PNG=ON')
+        else:
+            args.append('-DWITH_PNG=OFF')
+
+        if '+tiff' in spec:
+            args.append('-DWITH_TIFF=ON')
+        else:
+            args.append('-DWITH_TIFF=OFF')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/porta/package.py b/var/spack/repos/builtin/packages/porta/package.py
index e54187188f..e43374933d 100644
--- a/var/spack/repos/builtin/packages/porta/package.py
+++ b/var/spack/repos/builtin/packages/porta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/portage/package.py b/var/spack/repos/builtin/packages/portage/package.py
index b70139c3ed..f423551243 100644
--- a/var/spack/repos/builtin/packages/portage/package.py
+++ b/var/spack/repos/builtin/packages/portage/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,12 +13,12 @@ class Portage(CMakePackage):
        remapping library for transfer of field data between meshes.
     """
     homepage = "http://portage.lanl.gov/"
-    url      = "https://github.com/laristra/portage/tarball/v1.0"
+    git      = "https://github.com/laristra/portage.git"
 
     # tarballs don't have submodules, so use git tags
-    version('1.1.1', git='https://github.com/laristra/portage', tag='v1.1.1', submodules=True)
-    version('1.1.0', git='https://github.com/laristra/portage', tag='v1.1.0', submodules=True)
-    version('develop', git='https://github.com/laristra/portage', branch='master', submodules=True)
+    version('develop', branch='master', submodules=True)
+    version('1.1.1', tag='v1.1.1', submodules=True)
+    version('1.1.0', tag='v1.1.0', submodules=True)
 
     variant('mpi', default=True, description='Support MPI')
 
diff --git a/var/spack/repos/builtin/packages/portcullis/package.py b/var/spack/repos/builtin/packages/portcullis/package.py
new file mode 100644
index 0000000000..6a3c334ce5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/portcullis/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Portcullis(AutotoolsPackage):
+    """PORTable CULLing of Invalid Splice junctions"""
+
+    homepage = "https://github.com/maplesond/portcullis"
+    url      = "https://github.com/maplesond/portcullis/archive/Release-1.1.2.tar.gz"
+
+    version('1.1.2', '5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749')
+
+    depends_on('autoconf@2.53:', type='build')
+    depends_on('automake@1.11:', type='build')
+    depends_on('libtool@2.4.2:',  type='build')
+    depends_on('m4', type='build')
+
+    depends_on('zlib', type='build')
+    depends_on('samtools', type='build')
+
+    depends_on('python@3.4:', type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-pandas', type=('build', 'run'))
+
+    # later versions of py-sphinx don't get detected by the configure script
+    depends_on('py-sphinx@1.3:1.4')
+
+    def patch(self):
+        # remove static linking to libstdc++
+        filter_file(
+            'AM_LDFLAGS="-static-libstdc++"',
+            'AM_LDFLAGS=""',
+            'configure.ac', string=True
+        )
+
+        # prevent install scripts from ruining our PYTHONPATH
+        filter_file(
+            'export PYTHONPATH=$(DESTDIR)$(pythondir)',
+            'export PYTHONPATH="$(PYTHONPATH):$(DESTDIR)$(pythondir)"',
+            'scripts/Makefile.am', string=True
+        )
+
+    def build(self, spec, prefix):
+        # build manpages
+        make('man')
+
+        # run boost build script
+        sh = which('sh')
+        sh('build_boost.sh')
diff --git a/var/spack/repos/builtin/packages/postgresql/package.py b/var/spack/repos/builtin/packages/postgresql/package.py
index 1323405b1f..ee33e5c55f 100644
--- a/var/spack/repos/builtin/packages/postgresql/package.py
+++ b/var/spack/repos/builtin/packages/postgresql/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,8 @@ class Postgresql(AutotoolsPackage):
     homepage = "http://www.postgresql.org/"
     url      = "http://ftp.postgresql.org/pub/source/v9.3.4/postgresql-9.3.4.tar.bz2"
 
+    version('10.3', '506498796a314c549388cafb3d5c717a')
+    version('10.2', 'e97c3cc72bdf661441f29069299b260a')
     version('9.3.4', 'd0a41f54c377b2d2fab4a003b0dac762')
     version('9.5.3', '3f0c388566c688c82b01a0edf1e6b7a0')
 
diff --git a/var/spack/repos/builtin/packages/ppl/package.py b/var/spack/repos/builtin/packages/ppl/package.py
index 0a5636d457..d2f4eafb7b 100644
--- a/var/spack/repos/builtin/packages/ppl/package.py
+++ b/var/spack/repos/builtin/packages/ppl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/pplacer/package.py b/var/spack/repos/builtin/packages/pplacer/package.py
new file mode 100644
index 0000000000..bfcd2f2d7f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pplacer/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pplacer(Package):
+    """Pplacer places query sequences on a fixed reference phylogenetic tree
+       to maximize phylogenetic likelihood or posterior probability according
+       to a reference alignment. Pplacer is designed to be fast, to give
+       useful information about uncertainty, and to offer advanced
+       visualization and downstream analysis.
+    """
+
+    homepage = "http://matsen.fhcrc.org/pplacer/"
+    url      = "https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip"
+
+    version('1.1.alpha19', 'e6b78604882d41d4bf13592c7edebfa2')
+
+    def install(self, spec, prefix):
+        install_tree('scripts', prefix.bin)
+        force_remove(join_path(prefix.bin, 'setup.py'))
+        install('guppy', prefix.bin)
+        install('pplacer', prefix.bin)
+        install('rppr', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py
index 740cb63b85..1dc78db621 100644
--- a/var/spack/repos/builtin/packages/prank/package.py
+++ b/var/spack/repos/builtin/packages/prank/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,13 @@ class Prank(Package):
     homepage = "http://wasabiapp.org/software/prank/"
     url      = "http://wasabiapp.org/download/prank/prank.source.150803.tgz"
 
+    version('170427', 'a5cda14dc4e5efe1f14b84eb7a7caabd')
     version('150803', '71ac2659e91c385c96473712c0a23e8a')
 
     depends_on('mafft')
     depends_on('exonerate')
     depends_on('bpp-suite')      # for bppancestor
+    conflicts('%gcc@7.2.0', when='@:150803')
 
     def install(self, spec, prefix):
         with working_dir('src'):
diff --git a/var/spack/repos/builtin/packages/precice/package.py b/var/spack/repos/builtin/packages/precice/package.py
new file mode 100644
index 0000000000..74f78d67aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/precice/package.py
@@ -0,0 +1,59 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Precice(CMakePackage):
+    """preCICE (Precise Code Interaction Coupling Environment) is a
+    coupling library for partitioned multi-physics simulations.
+    Partitioned means that preCICE couples existing programs (solvers)
+    capable of simulating a subpart of the complete physics involved in
+    a simulation."""
+
+    homepage = 'https://www.precice.org'
+    git      = 'https://github.com/precice/precice.git'
+
+    # Skip version 1.1.1 entirely, the cmake was lacking install.
+    version('develop', branch='develop')
+
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('petsc', default=False, description='Enable PETSc support')
+    variant('python', default=False, description='Enable Python support')
+    variant('shared', default=True, description='Build shared libraries')
+
+    # Not yet
+#    variant(
+#        'float', default=False,
+#        description='Use single precision for field data exchange')
+#    variant(
+#        'int64',
+#        default=False, description='Use 64-bit integers for indices')
+
+    depends_on('cmake@3.5:', type='build')
+    depends_on('boost@1.60.0:')
+    depends_on('eigen@3.2:')
+    # Implicit via eigen, don't over-constrain: depends_on('libxml2')
+    depends_on('mpi', when='+mpi')
+    depends_on('petsc', when='+petsc')
+    depends_on('python@2.7', when='+python', type=('build', 'run'))
+
+    def cmake_args(self):
+        """Populate cmake arguments for precice."""
+        spec = self.spec
+
+        def variant_bool(feature, on='ON', off='OFF'):
+            """Ternary for spec variant to ON/OFF string"""
+            if feature in spec:
+                return on
+            return off
+
+        cmake_args = [
+            '-DMPI:BOOL=%s' % variant_bool('+mpi'),
+            '-DPETSC:BOOL=%s' % variant_bool('+petsc'),
+            '-DPYTHON:BOOL=%s' % variant_bool('+python'),
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % variant_bool('+shared'),
+        ]
+        return cmake_args
diff --git a/var/spack/repos/builtin/packages/presentproto/package.py b/var/spack/repos/builtin/packages/presentproto/package.py
index e31490a07c..991db65217 100644
--- a/var/spack/repos/builtin/packages/presentproto/package.py
+++ b/var/spack/repos/builtin/packages/presentproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,5 +14,5 @@ class Presentproto(AutotoolsPackage):
 
     version('1.0', '57eaf4bb58e86476ec89cfb42d675961')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/preseq/package.py b/var/spack/repos/builtin/packages/preseq/package.py
index 136bbb62b9..cbd72ce317 100644
--- a/var/spack/repos/builtin/packages/preseq/package.py
+++ b/var/spack/repos/builtin/packages/preseq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/price/package.py b/var/spack/repos/builtin/packages/price/package.py
index ee47d600b8..8f6f1a1ef6 100644
--- a/var/spack/repos/builtin/packages/price/package.py
+++ b/var/spack/repos/builtin/packages/price/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/primer3/package.py b/var/spack/repos/builtin/packages/primer3/package.py
index 5a747d8dec..cdf17a5677 100644
--- a/var/spack/repos/builtin/packages/primer3/package.py
+++ b/var/spack/repos/builtin/packages/primer3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/prinseq-lite/package.py b/var/spack/repos/builtin/packages/prinseq-lite/package.py
new file mode 100644
index 0000000000..764a390343
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prinseq-lite/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PrinseqLite(Package):
+    """PRINSEQ will help you to preprocess your genomic or metagenomic
+    sequence data in FASTA or FASTQ format."""
+
+    homepage = "http://prinseq.sourceforge.net"
+    url      = "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-0.20.4.tar.gz"
+
+    version('0.20.4', '3be1a572073ebbbecfeba42a42853ff5')
+
+    variant('nopca', default=True, description="Graphs version without PCA")
+
+    depends_on('perl', type='run')
+    depends_on('perl-cairo', type='run')
+    depends_on('perl-digest-md5', type='run')
+    depends_on('perl-json', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'prinseq-graphs-noPCA.pl')
+
+        filter_file(r'#!/usr/bin/perl',
+                    '#!/usr/bin/env perl',
+                    'prinseq-lite.pl')
+
+        install('prinseq-graphs-noPCA.pl', prefix.bin)
+        install('prinseq-lite.pl', prefix.bin)
+
+        chmod = which('chmod')
+        chmod('+x', join_path(self.prefix.bin, 'prinseq-graphs-noPCA.pl'))
+        chmod('+x', join_path(self.prefix.bin, 'prinseq-lite.pl'))
diff --git a/var/spack/repos/builtin/packages/printproto/package.py b/var/spack/repos/builtin/packages/printproto/package.py
index c3d0e28e8f..8eb55fabeb 100644
--- a/var/spack/repos/builtin/packages/printproto/package.py
+++ b/var/spack/repos/builtin/packages/printproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,5 +15,5 @@ class Printproto(AutotoolsPackage):
 
     version('1.0.5', '5afeb3a7de8a14b417239a14ea724268')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/prng/package.py b/var/spack/repos/builtin/packages/prng/package.py
new file mode 100644
index 0000000000..3db827fd03
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prng/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Prng(AutotoolsPackage):
+    """Pseudo-Random Number Generator library."""
+
+    homepage = "http://statmath.wu.ac.at/prng/"
+    url      = "http://statmath.wu.ac.at/prng/prng-3.0.2.tar.gz"
+
+    version('3.0.2', '80cb0870f2d18618bd2772f9e1dc1a70')
+
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+
+    patch('prng-3.0.2-shared.patch', when="@3.0.2")
+    patch('prng-3.0.2-fix-c99-inline-semantics.patch', when="@3.0.2")
+
+    # Force the autoreconf step
+    force_autoreconf = True
diff --git a/var/spack/repos/builtin/packages/prng/prng-3.0.2-fix-c99-inline-semantics.patch b/var/spack/repos/builtin/packages/prng/prng-3.0.2-fix-c99-inline-semantics.patch
new file mode 100644
index 0000000000..c84a288d47
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prng/prng-3.0.2-fix-c99-inline-semantics.patch
@@ -0,0 +1,146 @@
+Use portable 'static inline' semantics that work in GNU89 and C99
+See also: http://www.greenend.org.uk/rjk/tech/inline.html
+
+--- a/src/dicg.c
++++ b/src/dicg.c
+@@ -441,7 +441,7 @@
+  * Algorithm by Karin Schaber and Otmar Lendl.
+  *
+  */                                                  
+-inline prng_num prng_dicg_multiply(int k,prng_num c, prng_num d)
++prng_num prng_dicg_multiply(int k,prng_num c, prng_num d)
+ {
+   int i;
+   struct mtable *t;
+--- a/src/external.c
++++ b/src/external.c
+@@ -139,7 +139,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_tt800_get_next_int(struct prng *gen)
++prng_num prng_tt800_get_next_int(struct prng *gen)
+ {
+ unsigned int y;
+ struct tt800_state *g;
+--- a/src/icg.c
++++ b/src/icg.c
+@@ -110,7 +110,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_icg_get_next_int(struct prng *gen)
++prng_num prng_icg_get_next_int(struct prng *gen)
+ {
+   s_prng_num inv, current, prod;
+   
+--- a/src/lcg.c
++++ b/src/lcg.c
+@@ -111,7 +111,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_lcg_get_next_int(struct prng *gen)
++prng_num prng_lcg_get_next_int(struct prng *gen)
+ {
+   s_prng_num ax, current;
+ 
+--- a/src/meicg.c
++++ b/src/meicg.c
+@@ -106,7 +106,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_meicg_get_next_int(struct prng *gen)
++prng_num prng_meicg_get_next_int(struct prng *gen)
+ {
+   s_prng_num an, sum, inv, n;
+ 
+--- a/src/mt19937.c
++++ b/src/mt19937.c
+@@ -172,7 +172,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_mt19937_get_next_int(struct prng *gen)
++prng_num prng_mt19937_get_next_int(struct prng *gen)
+ {
+ #define MT  gen->data.mt19937_data.mt
+ #define MTI gen->data.mt19937_data.mti
+--- a/src/prng.h
++++ b/src/prng.h
+@@ -406,7 +406,7 @@
+ /* INLINE fnk def. for mult_mod, I don't know if this works for non-GCC */
+ 
+ #ifdef __GNUC__
+-extern __inline__ prng_num mult_mod(prng_num s,struct mult_mod_struct *mm)
++static inline prng_num mult_mod(prng_num s,struct mult_mod_struct *mm)
+ {
+ s_prng_num s_tmp;
+ 
+--- a/src/qcg.c
++++ b/src/qcg.c
+@@ -107,7 +107,7 @@
+  *      gen:  Pointer to a struct prng.
+  *
+  */
+-inline prng_num prng_qcg_get_next_int(struct prng *gen)
++prng_num prng_qcg_get_next_int(struct prng *gen)
+ {
+   s_prng_num current, sum, square, q_term, l_term;
+ 
+--- a/src/support.c
++++ b/src/support.c
+@@ -449,52 +449,6 @@
+ 		}
+ }
+ 
+-#ifndef __cplusplus
+-/* 
+- * Modular Multiplication. Uses the precalculated values from mult_mod_setup.
+- *
+- *
+- * Input: 
+- *	s	An prng_num. 
+- *	mm	pointer to a struct mult_mod_struct initialized 
+- *		by mult_mod_setup.
+- *
+- * Output:
+- *      (mm->a*s) mod mm->p
+- *
+- */
+-prng_num mult_mod(prng_num s,struct mult_mod_struct *mm)
+-{
+-s_prng_num s_tmp;
+-
+-switch(mm->algorithm)
+-	{
+-	case PRNG_MM_ZERO:	return(0);
+-			break;
+-	case PRNG_MM_ONE:	return(s);
+-			break;
+-	case PRNG_MM_SIMPLE: return((s * mm->a) % mm->p );
+-			break;
+-	case PRNG_MM_SCHRAGE:
+-			s_tmp = mm->a * ( s % mm->q ) - 
+-				mm->r * ( s / mm->q );
+-			if (s_tmp < 0) s_tmp += mm->p;
+-			return(s_tmp);
+-			break;
+-	case PRNG_MM_DECOMP: return(mult_mod_generic(s,mm->a,mm->p)); 
+-			break;
+-#ifdef HAVE_LONGLONG
+-	case PRNG_MM_LL:	return(mult_mod_ll(s,mm->a,mm->p));
+-			break;
+-#endif
+-	case PRNG_MM_POW2:	return((s*mm->a) & mm->mask);
+-			break;
+-	}
+-/* not reached */
+-return(0);
+-}
+-#endif
+-
+ 
+ /* 
+  * Modular Multiplication: Decomposition method (from L'Ecuyer & Cote)
diff --git a/var/spack/repos/builtin/packages/prng/prng-3.0.2-shared.patch b/var/spack/repos/builtin/packages/prng/prng-3.0.2-shared.patch
new file mode 100644
index 0000000000..cee8de060f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prng/prng-3.0.2-shared.patch
@@ -0,0 +1,52 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -23,6 +23,7 @@
+ AC_PROG_RANLIB
+ AC_PROG_INSTALL
+ AC_PROG_LN_S
++AC_PROG_LIBTOOL
+ 
+ dnl Checks for typedefs, structures, and compiler characteristics.
+ AC_C_CONST
+@@ -39,10 +40,7 @@
+ dnl Checks for library functions.
+ AC_CHECK_FUNCS(strtoul)
+ 
+-dnl Set flags for compiler
+-if test X"$GCC" = Xyes ; then
+-	AC_SUBST(AM_CFLAGS,"-Wall -fomit-frame-pointer")
+-fi
++AC_CHECK_LIB([m], [pow])
+ 
+ AC_CONFIG_FILES([\
+         Makefile \
+--- a/examples/Makefile.am
++++ b/examples/Makefile.am
+@@ -1,11 +1,11 @@
+ ## Process this file with automake to produce Makefile.in
+ # $Id$
+ 
+-LDADD = $(top_builddir)/src/libprng.a -lm
++LDADD = $(top_builddir)/src/libprng.la -lm
+ 
+ INCLUDES = -I$(top_srcdir)/src
+ 
+-noinst_PROGRAMS = pairs tuples
++check_PROGRAMS = pairs tuples
+ 
+ # clean backup files
+ CLEANFILES = *~
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -3,9 +3,9 @@
+ 
+ INCLUDES = 
+ 
+-lib_LIBRARIES = libprng.a
++lib_LTLIBRARIES = libprng.la
+ 
+-libprng_a_SOURCES = \
++libprng_la_SOURCES = \
+  prng.c \
+  dicg.c \
+  eicg.c \
diff --git a/var/spack/repos/builtin/packages/probconsrna/package.py b/var/spack/repos/builtin/packages/probconsrna/package.py
index 56abd8b59e..31ef7e8b28 100644
--- a/var/spack/repos/builtin/packages/probconsrna/package.py
+++ b/var/spack/repos/builtin/packages/probconsrna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/prodigal/package.py b/var/spack/repos/builtin/packages/prodigal/package.py
new file mode 100644
index 0000000000..75ce486f50
--- /dev/null
+++ b/var/spack/repos/builtin/packages/prodigal/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Prodigal(MakefilePackage):
+    """Fast, reliable protein-coding gene prediction for prokaryotic
+    genomes."""
+
+    homepage = "https://github.com/hyattpd/Prodigal"
+    url      = "https://github.com/hyattpd/Prodigal/archive/v2.6.3.tar.gz"
+
+    version('2.6.3', '5181809fdb740e9a675cfdbb6c038466')
+
+    def install(self, spec, prefix):
+        make('INSTALLDIR={0}'.format(self.prefix), 'install')
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', prefix)
diff --git a/var/spack/repos/builtin/packages/proj/package.py b/var/spack/repos/builtin/packages/proj/package.py
index efddcb876c..fe20f4e58a 100644
--- a/var/spack/repos/builtin/packages/proj/package.py
+++ b/var/spack/repos/builtin/packages/proj/package.py
@@ -1,37 +1,37 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Proj(AutotoolsPackage):
-    """Cartographic Projections"""
-    homepage = "https://github.com/OSGeo/proj.4/wiki"
-    url      = "http://download.osgeo.org/proj/proj-4.9.2.tar.gz"
+    """PROJ is a generic coordinate transformation software, that transforms
+    geospatial coordinates from one coordinate reference system (CRS) to
+    another. This includes cartographic projections as well as geodetic
+    transformations."""
+
+    homepage = "https://proj4.org/"
+    url      = "http://download.osgeo.org/proj/proj-5.0.1.tar.gz"
 
+    version('5.0.1', '15c8d7d6a8cb945c7878d0ff322a232c')
     version('4.9.2', '9843131676e31bbd903d60ae7dc76cf9')
     version('4.9.1', '3cbb2a964fd19a496f5f4265a717d31c')
     version('4.8.0', 'd815838c92a29179298c126effbb1537')
     version('4.7.0', '927d34623b52e0209ba2bfcca18fe8cd')
     version('4.6.1', '7dbaab8431ad50c25669fd3fb28dc493')
+
+    # https://github.com/OSGeo/proj.4#distribution-files-and-format
+    # https://github.com/OSGeo/proj-datumgrid
+    resource(
+        name='proj-datumgrid',
+        url='https://download.osgeo.org/proj/proj-datumgrid-1.7.tar.gz',
+        md5='6799bd8ac411b8a78724e34850c206c4',
+        placement='nad'
+    )
+
+    def configure_args(self):
+        return [
+            'PROJ_LIB={0}'.format(join_path(self.stage.source_path, 'nad'))
+        ]
diff --git a/var/spack/repos/builtin/packages/protobuf/intel_inline.patch b/var/spack/repos/builtin/packages/protobuf/intel_inline.patch
new file mode 100644
index 0000000000..61f1334293
--- /dev/null
+++ b/var/spack/repos/builtin/packages/protobuf/intel_inline.patch
@@ -0,0 +1,25 @@
+diff -Naur src_a/google/protobuf/stubs/port.h src_b/google/protobuf/stubs/port.h
+--- a/src/google/protobuf/stubs/port.h	2017-08-24 18:17:47.149533997 -0700
++++ b/src/google/protobuf/stubs/port.h	2017-08-24 22:13:12.907241538 -0700
+@@ -167,7 +167,9 @@
+ //   is not right for you.
+ 
+ #ifndef GOOGLE_ATTRIBUTE_ALWAYS_INLINE
+-#if defined(__GNUC__) && (__GNUC__ > 3 ||(__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
++#if defined(__INTEL_COMPILER) && (__INTEL_COMPILER > 1700)
++#define GOOGLE_ATTRIBUTE_ALWAYS_INLINE __attribute__ ((always_inline))
++#elif defined(__GNUC__) && (__GNUC__ > 3 ||(__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
+ // For functions we want to force inline.
+ // Introduced in gcc 3.1.
+ #define GOOGLE_ATTRIBUTE_ALWAYS_INLINE __attribute__ ((always_inline))
+@@ -178,7 +180,9 @@
+ #endif
+ 
+ #ifndef GOOGLE_ATTRIBUTE_NOINLINE
+-#if defined(__GNUC__) && (__GNUC__ > 3 ||(__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
++#if defined(__INTEL_COMPILER) && (__INTEL_COMPILER > 1700)
++#define GOOGLE_ATTRIBUTE_NOINLINE
++#elif defined(__GNUC__) && (__GNUC__ > 3 ||(__GNUC__ == 3 && __GNUC_MINOR__ >= 1))
+ // For functions we want to force not inline.
+ // Introduced in gcc 3.1.
+ #define GOOGLE_ATTRIBUTE_NOINLINE __attribute__ ((noinline))
diff --git a/var/spack/repos/builtin/packages/protobuf/package.py b/var/spack/repos/builtin/packages/protobuf/package.py
index 038c208864..62486aeb58 100644
--- a/var/spack/repos/builtin/packages/protobuf/package.py
+++ b/var/spack/repos/builtin/packages/protobuf/package.py
@@ -1,27 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import sys
 from spack import *
 import spack.util.web
 
@@ -33,6 +15,12 @@ class Protobuf(CMakePackage):
     url      = "https://github.com/google/protobuf/archive/v3.2.0.tar.gz"
     root_cmakelists_dir = "cmake"
 
+    version('3.5.2', 'ff6742018c172c66ecc627029ad54280')
+    version('3.5.1.1', '5005003ae6b94773c4bbca87a644b131')
+    version('3.5.1',   '710f1a75983092c9b45ecef207236104')
+    version('3.5.0.1', 'b3ed2401acf167207277b254fd7f9638')
+    version('3.5.0',   'd95db321e1a9901fffc51ed8994afd36')
+    version('3.4.1',   '31b19dcfd6567095fdb66a8c07347222')
     version('3.4.0', '1d077a7d4db3d75681f5c333f2de9b1a')
     version('3.3.0', 'f0f712e98de3db0c65c0c417f5e7aca8')
     version('3.2.0', 'efaa08ae635664fb5e7f31421a41a995')
@@ -41,6 +29,9 @@ class Protobuf(CMakePackage):
     # does not build with CMake:
     # version('2.5.0', '9c21577a03adc1879aba5b52d06e25cf')
 
+    variant('shared', default=True,
+            description='Enables the build of shared libraries')
+
     depends_on('zlib')
 
     conflicts('%gcc@:4.6')  # Requires c++11
@@ -48,6 +39,8 @@ class Protobuf(CMakePackage):
     # first fixed in 3.4.0: https://github.com/google/protobuf/pull/3406
     patch('pkgconfig.patch', when='@:3.3.2')
 
+    patch('intel_inline.patch', when='@3.2.0: %intel')
+
     def fetch_remote_versions(self):
         """Ignore additional source artifacts uploaded with releases,
            only keep known versions
@@ -60,7 +53,10 @@ class Protobuf(CMakePackage):
 
     def cmake_args(self):
         args = [
+            '-DBUILD_SHARED_LIBS=%s' % int('+shared' in self.spec),
             '-Dprotobuf_BUILD_TESTS:BOOL=OFF',
             '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON'
         ]
+        if sys.platform == 'darwin':
+            args.extend(['-DCMAKE_MACOSX_RPATH=ON'])
         return args
diff --git a/var/spack/repos/builtin/packages/proxymngr/package.py b/var/spack/repos/builtin/packages/proxymngr/package.py
index cc38d6ae55..6f6e118e22 100644
--- a/var/spack/repos/builtin/packages/proxymngr/package.py
+++ b/var/spack/repos/builtin/packages/proxymngr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Proxymngr(AutotoolsPackage):
 
     depends_on('xproto@7.0.17:', type='build')
     depends_on('xproxymanagementprotocol', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/pruners-ninja/package.py b/var/spack/repos/builtin/packages/pruners-ninja/package.py
index c8e93ad997..0c86c9e2bc 100644
--- a/var/spack/repos/builtin/packages/pruners-ninja/package.py
+++ b/var/spack/repos/builtin/packages/pruners-ninja/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ps-lite/package.py b/var/spack/repos/builtin/packages/ps-lite/package.py
index b78315c060..887e126814 100644
--- a/var/spack/repos/builtin/packages/ps-lite/package.py
+++ b/var/spack/repos/builtin/packages/ps-lite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,10 @@ class PsLite(CMakePackage):
     of the parameter server framework."""
 
     homepage = "https://github.com/dmlc/ps-lite"
-    url      = "https://github.com/dmlc/ps-lite.git"
+    git      = "https://github.com/dmlc/ps-lite.git"
 
-    version('master', git='https://github.com/dmlc/ps-lite.git', branch='master')
-    version('20170328', git='https://github.com/dmlc/ps-lite.git',
-            commit='acdb698fa3bb80929ef83bb37c705f025e119b82')
+    version('master', branch='master')
+    version('20170328', commit='acdb698fa3bb80929ef83bb37c705f025e119b82')
 
     depends_on('protobuf@3:')
     depends_on('zeromq')
diff --git a/var/spack/repos/builtin/packages/psi4/package.py b/var/spack/repos/builtin/packages/psi4/package.py
index f322e6c1ca..eb3e7863fe 100644
--- a/var/spack/repos/builtin/packages/psi4/package.py
+++ b/var/spack/repos/builtin/packages/psi4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/pslib/package.py b/var/spack/repos/builtin/packages/pslib/package.py
new file mode 100644
index 0000000000..c15a7f8b83
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pslib/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pslib(AutotoolsPackage):
+    """C-library to create PostScript files on the fly."""
+
+    homepage = "http://pslib.sourceforge.net/"
+    url      = "https://kent.dl.sourceforge.net/project/pslib/pslib/0.4.5/pslib-0.4.5.tar.gz"
+
+    version('0.4.5', '03f39393628a6d758799b9f845047e27')
+
+    depends_on('jpeg')
+    depends_on('libpng')
diff --git a/var/spack/repos/builtin/packages/psm/package.py b/var/spack/repos/builtin/packages/psm/package.py
new file mode 100644
index 0000000000..ba661394f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/psm/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Psm(MakefilePackage):
+    """Intel Performance scaled messaging library"""
+
+    homepage = "https://github.com/intel/psm"
+    url      = "https://github.com/intel/psm/archive/v3.3.tar.gz"
+    git      = "https://github.com/intel/psm.git"
+
+    version('3.3', '031eb27688c932867d55054e76d00875', preferred=True)
+    version('2017-04-28', commit='604758e')
+
+    conflicts('%gcc@6:', when='@3.3')
+
+    depends_on('libuuid')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('{DESTDIR}/usr/', '{LOCAL_PREFIX}/')
+
+    def install(self, spec, prefix):
+        make('LOCAL_PREFIX=%s' % prefix, 'install')
diff --git a/var/spack/repos/builtin/packages/psmc/package.py b/var/spack/repos/builtin/packages/psmc/package.py
new file mode 100644
index 0000000000..019d664e39
--- /dev/null
+++ b/var/spack/repos/builtin/packages/psmc/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Psmc(MakefilePackage):
+    """mplementation of the Pairwise Sequentially Markovian Coalescent
+    (PSMC) model"""
+
+    homepage = "https://github.com/lh3/psmc"
+    git      = "https://github.com/lh3/psmc.git"
+
+    version('2016-1-21', commit='e5f7df5d00bb75ec603ae0beff62c0d7e37640b9')
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', prefix.bin.utils)
+
+    def build(self, spec, prefix):
+        make()
+        with working_dir('utils'):
+            make()
+
+    def install(self, spec, prefix):
+        install_tree(self.build_directory, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/pstreams/package.py b/var/spack/repos/builtin/packages/pstreams/package.py
index 2bf7fa63c9..8c4ebc5377 100644
--- a/var/spack/repos/builtin/packages/pstreams/package.py
+++ b/var/spack/repos/builtin/packages/pstreams/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pugixml/package.py b/var/spack/repos/builtin/packages/pugixml/package.py
index 5cab25c3b3..9418cae3e2 100644
--- a/var/spack/repos/builtin/packages/pugixml/package.py
+++ b/var/spack/repos/builtin/packages/pugixml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/pumi/package.py b/var/spack/repos/builtin/packages/pumi/package.py
index f4f65a33d3..02cef568e4 100644
--- a/var/spack/repos/builtin/packages/pumi/package.py
+++ b/var/spack/repos/builtin/packages/pumi/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import sys
 
 
 class Pumi(CMakePackage):
@@ -37,19 +17,23 @@ class Pumi(CMakePackage):
        and dynamic load balancing."""
 
     homepage = "https://www.scorec.rpi.edu/pumi"
-    url      = "https://github.com/SCOREC/core.git"
-
-    version('0.0.1', git='https://github.com/SCOREC/core.git',
-        commit='0c315e82b3f2478dc18bdd6cfa89f1cddb85cd6a')
-    version('develop', git='https://github.com/SCOREC/core.git',
-        branch='master')
-
-    if sys.platform == 'darwin':
-        patch('phiotimer.cc.darwin.patch', level=0)  # !clock_gettime
+    git      = "https://github.com/SCOREC/core.git"
+
+    # We will use the scorec/core master branch as the 'nightly' version
+    # of pumi in spack.  The master branch is more stable than the
+    # scorec/core develop branch and we perfer not to expose spack users
+    # to the added instability. The spack version string is 'develop' since
+    # it compares greater than a numbered version (e.g., 2.1.0). The spack
+    # version string 'master' compares less than a numbered version.
+    version('develop', branch='master')
+    version('2.2.0', commit='8c7e6f13943893b2bc1ece15003e4869a0e9634f')  # tag 2.2.0
+    version('2.1.0', commit='840fbf6ec49a63aeaa3945f11ddb224f6055ac9f')
 
     variant('zoltan', default=False, description='Enable Zoltan Features')
+    variant('fortran', default=False, description='Enable FORTRAN interface')
 
     depends_on('mpi')
+    depends_on('cmake@3:', type='build')
     depends_on('zoltan', when='+zoltan')
 
     def cmake_args(self):
@@ -60,6 +44,9 @@ class Pumi(CMakePackage):
             '-DENABLE_ZOLTAN=%s' % ('ON' if '+zoltan' in spec else 'OFF'),
             '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
             '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DPUMI_FORTRAN_INTERFACE=%s' %
+            ('ON' if '+fortran' in spec else 'OFF')
         ]
 
         return args
diff --git a/var/spack/repos/builtin/packages/pumi/phiotimer.cc.darwin.patch b/var/spack/repos/builtin/packages/pumi/phiotimer.cc.darwin.patch
deleted file mode 100644
index 52c6e63fca..0000000000
--- a/var/spack/repos/builtin/packages/pumi/phiotimer.cc.darwin.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-*** ./phasta/phiotimer.cc	2017-05-03 12:26:25.000000000 -0700
---- ./phasta/phiotimer.cc.patched	2017-05-03 12:26:11.000000000 -0700
-***************
-*** 56,63 ****
-  }
-  #else
-  void phastaio_time(phastaioTime* t) {
-!   int err;
-!   err = clock_gettime(CLOCK_MONOTONIC,t);
-    PCU_ALWAYS_ASSERT(!err);
-  }
-  /*return elapsed time in micro seconds*/
---- 56,63 ----
-  }
-  #else
-  void phastaio_time(phastaioTime* t) {
-!   int err=0;
-!   /*err = clock_gettime(CLOCK_MONOTONIC,t);*/
-    PCU_ALWAYS_ASSERT(!err);
-  }
-  /*return elapsed time in micro seconds*/
diff --git a/var/spack/repos/builtin/packages/pv/package.py b/var/spack/repos/builtin/packages/pv/package.py
new file mode 100644
index 0000000000..8a1e63a735
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pv/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pv(AutotoolsPackage):
+    """ Pipe Viewer - is a terminal-based tool for monitoring the progress
+        of data through a pipeline
+    """
+
+    homepage = "http://www.ivarch.com/programs/pv.shtml"
+    url      = "http://www.ivarch.com/programs/sources/pv-1.6.6.tar.bz2"
+
+    version('1.6.6', 'ff3564fddcc2b9bd4a9c1d143aba4b4c')
diff --git a/var/spack/repos/builtin/packages/pvm/package.py b/var/spack/repos/builtin/packages/pvm/package.py
index de4848413d..4cb797f52d 100644
--- a/var/spack/repos/builtin/packages/pvm/package.py
+++ b/var/spack/repos/builtin/packages/pvm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import subprocess
 
diff --git a/var/spack/repos/builtin/packages/pxz/package.py b/var/spack/repos/builtin/packages/pxz/package.py
new file mode 100644
index 0000000000..8cfced300b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pxz/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Pxz(MakefilePackage):
+    """Pxz is a parallel LZMA compressor using liblzma."""
+
+    homepage = "https://jnovy.fedorapeople.org/pxz/pxz.html"
+    url      = "http://jnovy.fedorapeople.org/pxz/pxz-4.999.9beta.20091201git.tar.xz"
+    git      = "https://github.com/jnovy/pxz.git"
+
+    version('develop', branch='master')
+    version('4.999.9beta.20091201git', '4ae3926185978f5c95c9414dc4634451')
+
+    depends_on('lzma')
+
+    conflicts('platform=darwin', msg='Pxz runs only on Linux.')
+
+    def install(self, spec, prefix):
+        make('install', "DESTDIR=%s" % prefix,
+             "BINDIR=/bin", "MANDIR=/share/man")
diff --git a/var/spack/repos/builtin/packages/py-3to2/package.py b/var/spack/repos/builtin/packages/py-3to2/package.py
index 1a1a6f8805..12a3a9fef3 100644
--- a/var/spack/repos/builtin/packages/py-3to2/package.py
+++ b/var/spack/repos/builtin/packages/py-3to2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-4suite-xml/package.py b/var/spack/repos/builtin/packages/py-4suite-xml/package.py
index e0fa713fd8..872d5e75d0 100644
--- a/var/spack/repos/builtin/packages/py-4suite-xml/package.py
+++ b/var/spack/repos/builtin/packages/py-4suite-xml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-abipy/package.py b/var/spack/repos/builtin/packages/py-abipy/package.py
index dc07aaebd2..1ab1b316ef 100644
--- a/var/spack/repos/builtin/packages/py-abipy/package.py
+++ b/var/spack/repos/builtin/packages/py-abipy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-adios/package.py b/var/spack/repos/builtin/packages/py-adios/package.py
new file mode 100644
index 0000000000..ff59a71afb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-adios/package.py
@@ -0,0 +1,60 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAdios(PythonPackage):
+    """NumPy bindings of ADIOS1"""
+
+    homepage = "https://www.olcf.ornl.gov/center-projects/adios/"
+    url      = "https://github.com/ornladios/ADIOS/archive/v1.12.0.tar.gz"
+    git      = "https://github.com/ornladios/ADIOS.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('1.13.0', '68af36b821debbdf4748b20320a990ce')
+    version('1.12.0', '84a1c71b6698009224f6f748c5257fc9')
+    version('1.11.1', '5639bfc235e50bf17ba9dafb14ea4185')
+    version('1.11.0', '5eead5b2ccf962f5e6d5f254d29d5238')
+    version('1.10.0', 'eff450a4c0130479417cfd63186957f3')
+    version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
+
+    variant('mpi', default=True,
+            description='Enable MPI support')
+
+    for v in ['1.9.0', '1.10.0', '1.11.0', '1.11.1', '1.12.0', '1.13.0',
+              'develop']:
+        depends_on('adios@{0} ~mpi'.format(v),
+                   when='@{0} ~mpi'.format(v),
+                   type=['build', 'link', 'run'])
+        depends_on('adios@{0} +mpi'.format(v),
+                   when='@{0} +mpi'.format(v),
+                   type=['build', 'link', 'run'])
+
+    depends_on('py-numpy', type=['build', 'run'])
+    depends_on('mpi', when='+mpi')
+    depends_on('py-mpi4py', type=['run'], when='+mpi')
+    depends_on('py-cython', type=['build'])
+
+    phases = ['build_clib', 'install']
+    build_directory = 'wrappers/numpy'
+
+    def setup_file(self):
+        """Returns the name of the setup file to use."""
+        if '+mpi' in self.spec:
+            return 'setup_mpi.py'
+        else:
+            return 'setup.py'
+
+    def build_clib(self, spec, prefix):
+        # calls: make [MPI=y] python
+        args = ''
+        if '+mpi' in self.spec:
+            args = 'MPI=y '
+        args += 'python'
+        with working_dir(self.build_directory):
+            make(args)
diff --git a/var/spack/repos/builtin/packages/py-affine/package.py b/var/spack/repos/builtin/packages/py-affine/package.py
new file mode 100644
index 0000000000..f421d60ae5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-affine/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAffine(PythonPackage):
+    """Matrices describing affine transformation of the plane."""
+
+    homepage = "https://github.com/sgillies/affine"
+    url      = "https://github.com/sgillies/affine/archive/2.1.0.zip"
+
+    depends_on('py-setuptools', type='build')
+
+    version('2.1.0', '99cf61c3ef484f93da9dc062dfbce4b5')
diff --git a/var/spack/repos/builtin/packages/py-alabaster/package.py b/var/spack/repos/builtin/packages/py-alabaster/package.py
index 2f718ca9e8..f4268171b6 100644
--- a/var/spack/repos/builtin/packages/py-alabaster/package.py
+++ b/var/spack/repos/builtin/packages/py-alabaster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-apache-libcloud/package.py b/var/spack/repos/builtin/packages/py-apache-libcloud/package.py
index c46987f2ce..157c15d592 100644
--- a/var/spack/repos/builtin/packages/py-apache-libcloud/package.py
+++ b/var/spack/repos/builtin/packages/py-apache-libcloud/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-apipkg/package.py b/var/spack/repos/builtin/packages/py-apipkg/package.py
index ee0f979b63..c2425c334e 100644
--- a/var/spack/repos/builtin/packages/py-apipkg/package.py
+++ b/var/spack/repos/builtin/packages/py-apipkg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-appdirs/package.py b/var/spack/repos/builtin/packages/py-appdirs/package.py
index 4fd412bb39..998b71d6ba 100644
--- a/var/spack/repos/builtin/packages/py-appdirs/package.py
+++ b/var/spack/repos/builtin/packages/py-appdirs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-appnope/package.py b/var/spack/repos/builtin/packages/py-appnope/package.py
index 98d3e44032..e17db899f8 100644
--- a/var/spack/repos/builtin/packages/py-appnope/package.py
+++ b/var/spack/repos/builtin/packages/py-appnope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-apscheduler/package.py b/var/spack/repos/builtin/packages/py-apscheduler/package.py
index 47404f9944..ae5424f81c 100644
--- a/var/spack/repos/builtin/packages/py-apscheduler/package.py
+++ b/var/spack/repos/builtin/packages/py-apscheduler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-argcomplete/package.py b/var/spack/repos/builtin/packages/py-argcomplete/package.py
index 9c08f46b19..057ee6c16c 100644
--- a/var/spack/repos/builtin/packages/py-argcomplete/package.py
+++ b/var/spack/repos/builtin/packages/py-argcomplete/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-argparse/package.py b/var/spack/repos/builtin/packages/py-argparse/package.py
index c89e30fdb2..14071cc026 100644
--- a/var/spack/repos/builtin/packages/py-argparse/package.py
+++ b/var/spack/repos/builtin/packages/py-argparse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ase/package.py b/var/spack/repos/builtin/packages/py-ase/package.py
index 0030615861..2a58740045 100644
--- a/var/spack/repos/builtin/packages/py-ase/package.py
+++ b/var/spack/repos/builtin/packages/py-ase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class PyAse(PythonPackage):
     homepage = "https://wiki.fysik.dtu.dk/ase/"
     url      = "https://pypi.io/packages/source/a/ase/ase-3.13.0.tar.gz"
 
+    version('3.15.0', '65a0143753517c2df157e53bd29a18e3')
     version('3.13.0', 'e946a0addc5b61e5e2e75857e0f99b89')
 
     depends_on('python@2.6:')
diff --git a/var/spack/repos/builtin/packages/py-asn1crypto/package.py b/var/spack/repos/builtin/packages/py-asn1crypto/package.py
index 1e1e408b4a..ed12054d7e 100644
--- a/var/spack/repos/builtin/packages/py-asn1crypto/package.py
+++ b/var/spack/repos/builtin/packages/py-asn1crypto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-astroid/package.py b/var/spack/repos/builtin/packages/py-astroid/package.py
index 63be8ae470..ea55f30939 100644
--- a/var/spack/repos/builtin/packages/py-astroid/package.py
+++ b/var/spack/repos/builtin/packages/py-astroid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,17 @@ class PyAstroid(PythonPackage):
     homepage = "https://www.astroid.org/"
     url      = "https://github.com/PyCQA/astroid/archive/astroid-1.4.5.tar.gz"
 
+    # version('1.5.3', '6f65e4ea8290ec032320460905afb828') # has broken unit tests
     version('1.4.5', '7adfc55809908297ef430efe4ea20ac3')
     version('1.4.4', '8ae6f63f6a2b260bb7f647dafccbc796')
     version('1.4.3', '4647159de7d4d0c4b1de23ecbfb8e246')
     version('1.4.2', '677f7965840f375af51b0e86403bee6a')
     version('1.4.1', 'ed70bfed5e4b25be4292e7fe72da2c02')
 
-    depends_on('py-logilab-common', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
-    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-lazy-object-proxy')
+    depends_on('py-six')
+    depends_on('py-wrapt')
+    depends_on('py-enum34@1.1.3:', when='^python@:3.3.99')
+    depends_on('py-singledispatch', when='^python@:3.3.99')
+    depends_on('py-backports-functools-lru-cache', when='^python@:3.2.99')
+    depends_on('py-setuptools@17.1:')
diff --git a/var/spack/repos/builtin/packages/py-astropy/package.py b/var/spack/repos/builtin/packages/py-astropy/package.py
index e40fee11c6..1009b2e15b 100644
--- a/var/spack/repos/builtin/packages/py-astropy/package.py
+++ b/var/spack/repos/builtin/packages/py-astropy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -50,6 +31,7 @@ class PyAstropy(PythonPackage):
     depends_on('py-pytz', type=('build', 'run'))
     depends_on('py-scikit-image', type=('build', 'run'))
     depends_on('py-pandas', type=('build', 'run'))
+    depends_on('py-markupsafe', type=('build', 'run'))
 
     # System dependencies
     depends_on('cfitsio')
diff --git a/var/spack/repos/builtin/packages/py-atomicwrites/package.py b/var/spack/repos/builtin/packages/py-atomicwrites/package.py
new file mode 100644
index 0000000000..6cd224087e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-atomicwrites/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAtomicwrites(PythonPackage):
+    """Atomic file writes."""
+
+    homepage = "https://github.com/untitaker/python-atomicwrites"
+    url      = "https://pypi.io/packages/source/a/atomicwrites/atomicwrites-1.1.5.tar.gz"
+
+    import_modules = ['atomicwrites']
+
+    version('1.1.5', sha256='240831ea22da9ab882b551b31d4225591e5e447a68c5e188db5b89ca1d487585')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-attrs/package.py b/var/spack/repos/builtin/packages/py-attrs/package.py
index 04daf75da4..eb63525b86 100644
--- a/var/spack/repos/builtin/packages/py-attrs/package.py
+++ b/var/spack/repos/builtin/packages/py-attrs/package.py
@@ -1,36 +1,27 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyAttrs(PythonPackage):
-    """Python Attributes Without Boilerplate"""
+    """Classes Without Boilerplate"""
 
     homepage = "http://attrs.org/"
-    url = "https://pypi.io/packages/source/a/attrs/attrs-16.3.0.tar.gz"
+    url      = "https://pypi.io/packages/source/a/attrs/attrs-18.1.0.tar.gz"
+
+    import_modules = ['attr']
 
+    version('18.1.0', '3f3f3e0750dab74cfa1dc8b0fd7a5f86')
     version('16.3.0', '4ec003c49360853cf935113d1ae56151')
 
-    depends_on('py-setuptools',         type='build')
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-coverage', type='test')
+    depends_on('py-hypothesis', type='test')
+    depends_on('py-pympler', type='test')
+    depends_on('py-pytest', type='test')
+    depends_on('py-six', type='test')
+    depends_on('py-zope-interface', type='test')
diff --git a/var/spack/repos/builtin/packages/py-autopep8/package.py b/var/spack/repos/builtin/packages/py-autopep8/package.py
index 3dff029a8a..c882e2506f 100644
--- a/var/spack/repos/builtin/packages/py-autopep8/package.py
+++ b/var/spack/repos/builtin/packages/py-autopep8/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,14 @@ class PyAutopep8(PythonPackage):
     homepage = "https://github.com/hhatto/autopep8"
     url      = "https://pypi.io/packages/source/a/autopep8/autopep8-1.2.4.tar.gz"
 
+    version('1.3.3', '8951f43748406015b663a54ab05d891a')
     version('1.2.4', 'fcea19c0c5e505b425e2a78afb771f5c')
     version('1.2.2', '3d97f9c89d14a0975bffd32a2c61c36c')
 
     extends('python', ignore='bin/pep8')
     depends_on('python@2.6:2.8,3.2:')
 
-    depends_on('py-pycodestyle@1.5.7:1.7.0', type=('build', 'run'))
+    depends_on('py-pycodestyle@1.5.7:1.7.0', type=('build', 'run'), when='@:1.2.4')
+    depends_on('py-pycodestyle@2.3.0:', type=('build', 'run'), when='@1.3:')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py
new file mode 100644
index 0000000000..52f98286e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAvroJsonSerializer(PythonPackage):
+    """Serializes data into a JSON format using AVRO schema."""
+
+    homepage = "https://github.com/linkedin/python-avro-json-serializer"
+    url      = "https://github.com/linkedin/python-avro-json-serializer/archive/0.4.tar.gz"
+
+    version('0.4',  'ee32f415e03820653cf8477bf5bfc779')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-simplejson', type=('build', 'run'))
+    depends_on('py-avro', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-avro/package.py b/var/spack/repos/builtin/packages/py-avro/package.py
new file mode 100644
index 0000000000..13e8670b56
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-avro/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyAvro(PythonPackage):
+    """Avro is a serialization and RPC framework."""
+
+    homepage = "http://avro.apache.org/docs/current/"
+    url      = "https://pypi.io/packages/source/a/avro/avro-1.8.2.tar.gz"
+
+    version('1.8.2', '44ec007d432a2f3c35f87eee01f1e9ec')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-babel/package.py b/var/spack/repos/builtin/packages/py-babel/package.py
index 8b20318c20..e502b2e7c2 100644
--- a/var/spack/repos/builtin/packages/py-babel/package.py
+++ b/var/spack/repos/builtin/packages/py-babel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-backcall/package.py b/var/spack/repos/builtin/packages/py-backcall/package.py
new file mode 100644
index 0000000000..f255945211
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-backcall/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBackcall(PythonPackage):
+    """Specifications for callback functions passed in to an API"""
+
+    homepage = "https://github.com/takluyver/backcall"
+    url = "https://pypi.io/packages/source/b/backcall/backcall-0.1.0.tar.gz"
+
+    version('0.1.0', '87ce0c7839808e6a3427d57df6a792e7')
diff --git a/var/spack/repos/builtin/packages/py-backports-abc/package.py b/var/spack/repos/builtin/packages/py-backports-abc/package.py
index 69cd6165b5..a287daaa83 100644
--- a/var/spack/repos/builtin/packages/py-backports-abc/package.py
+++ b/var/spack/repos/builtin/packages/py-backports-abc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py b/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py
new file mode 100644
index 0000000000..f573a05594
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-backports-functools-lru-cache/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBackportsFunctoolsLruCache(PythonPackage):
+    """Backport of functools.lru_cache from Python 3.3"""
+
+    homepage = "https://github.com/jaraco/backports.functools_lru_cache"
+    url = "https://pypi.io/packages/source/b/backports.functools_lru_cache/backports.functools_lru_cache-1.4.tar.gz"
+
+    py_namespace = 'backports'
+
+    version('1.5', '20f53f54cd3f04b3346ce75a54959754')
+    version('1.4', 'b954e7d5e2ca0f0f66ad2ed12ba800e5')
+    version('1.0.1', 'c789ef439d189330b99872746a6d9e85',
+            url="https://pypi.io/packages/source/b/backports.functools_lru_cache/backports.functools_lru_cache-1.0.1.zip")
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools-scm@1.15.0:', type='build')
+    depends_on('python@2.6.0:3.3.99',        type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py b/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py
index daa019daef..40c9d88c26 100644
--- a/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py
+++ b/var/spack/repos/builtin/packages/py-backports-shutil-get-terminal-size/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,8 @@ class PyBackportsShutilGetTerminalSize(PythonPackage):
     homepage = "https://pypi.python.org/pypi/backports.shutil_get_terminal_size"
     url      = "https://pypi.io/packages/source/b/backports.shutil_get_terminal_size/backports.shutil_get_terminal_size-1.0.0.tar.gz"
 
+    py_namespace = 'backports'
+
     version('1.0.0', '03267762480bd86b50580dc19dff3c66')
 
     # newer setuptools version mess with "namespace" packages in an
diff --git a/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py b/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py
index 88edc5b571..a1e3871b54 100644
--- a/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py
+++ b/var/spack/repos/builtin/packages/py-backports-ssl-match-hostname/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,4 +12,6 @@ class PyBackportsSslMatchHostname(PythonPackage):
     homepage = "https://pypi.python.org/pypi/backports.ssl_match_hostname"
     url      = "https://pypi.io/packages/source/b/backports.ssl_match_hostname/backports.ssl_match_hostname-3.5.0.1.tar.gz"
 
+    py_namespace = 'backports'
+
     version('3.5.0.1', 'c03fc5e2c7b3da46b81acf5cbacfe1e6')
diff --git a/var/spack/repos/builtin/packages/py-basemap/package.py b/var/spack/repos/builtin/packages/py-basemap/package.py
index 4e127f9626..1b531c1cf3 100644
--- a/var/spack/repos/builtin/packages/py-basemap/package.py
+++ b/var/spack/repos/builtin/packages/py-basemap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class PyBasemap(PythonPackage):
     # Per Github issue #3813, setuptools is required at runtime in order
     # to make mpl_toolkits a namespace package that can span multiple
     # directories (i.e., matplotlib and basemap)
-    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-setuptools', type=('run'))
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-matplotlib', type=('build', 'run'))
     depends_on('pil', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-bcbio-gff/package.py b/var/spack/repos/builtin/packages/py-bcbio-gff/package.py
new file mode 100644
index 0000000000..4bdd1a27a5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bcbio-gff/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBcbioGff(PythonPackage):
+    """Read and write Generic Feature Format (GFF) with Biopython
+    integration."""
+
+    homepage = "https://pypi.python.org/pypi/bcbio-gff/0.6.2"
+    url      = "https://pypi.io/packages/source/b/bcbio-gff/bcbio-gff-0.6.2.tar.gz"
+
+    version('0.6.2', 'd5aae8b125cdad4291f15bec20cfb0ef')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six',        type=('build', 'run'))
+    depends_on('py-biopython',  type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
index 4874f1cba5..8fd8ea3d0c 100644
--- a/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
+++ b/var/spack/repos/builtin/packages/py-beautifulsoup4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-binwalk/package.py b/var/spack/repos/builtin/packages/py-binwalk/package.py
index 25f9eb5dd0..01bc360580 100644
--- a/var/spack/repos/builtin/packages/py-binwalk/package.py
+++ b/var/spack/repos/builtin/packages/py-binwalk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-biom-format/package.py b/var/spack/repos/builtin/packages/py-biom-format/package.py
index 1323ddee3b..cc317aeb96 100644
--- a/var/spack/repos/builtin/packages/py-biom-format/package.py
+++ b/var/spack/repos/builtin/packages/py-biom-format/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class PyBiomFormat(PythonPackage):
 
     variant('h5py', default=True, description='For use with BIOM 2.0+ files')
 
-    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-cython', type='build')
     depends_on('py-h5py', type=('build', 'run'), when='+h5py')
     depends_on('py-click', type=('build', 'run'))
@@ -46,3 +27,4 @@ class PyBiomFormat(PythonPackage):
     depends_on('py-scipy@0.13.0:', type=('build', 'run'))
     depends_on('py-pandas@0.19.2:', type=('build', 'run'))
     depends_on('py-six@1.10.0:', type=('build', 'run'))
+    depends_on('py-pyqi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-biopython/package.py b/var/spack/repos/builtin/packages/py-biopython/package.py
index 4fcfeaf81d..a833fd8b66 100644
--- a/var/spack/repos/builtin/packages/py-biopython/package.py
+++ b/var/spack/repos/builtin/packages/py-biopython/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class PyBiopython(PythonPackage):
     homepage = "http://biopython.org/wiki/Main_Page"
     url      = "http://biopython.org/DIST/biopython-1.65.tar.gz"
 
+    version('1.70', 'feff7a3e2777e43f9b13039b344e06ff')
     version('1.65', '143e7861ade85c0a8b5e2bbdd1da1f67')
 
-    depends_on('py-mx', type=('build', 'run'))
     depends_on('py-numpy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-bitarray/package.py b/var/spack/repos/builtin/packages/py-bitarray/package.py
new file mode 100644
index 0000000000..3f653892a3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bitarray/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBitarray(PythonPackage):
+    """Efficient array of booleans - C extension"""
+
+    homepage = "https://pypi.python.org/pypi/bitarray"
+    url      = "https://pypi.io/packages/source/b/bitarray/bitarray-0.8.1.tar.gz"
+
+    version('0.8.1', '3825184f54f4d93508a28031b4c65d3b')
+
+    depends_on('python')
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-bitstring/package.py b/var/spack/repos/builtin/packages/py-bitstring/package.py
new file mode 100644
index 0000000000..ac8e8da41b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bitstring/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBitstring(PythonPackage):
+    """Simple construction, analysis and modification of binary data."""
+
+    homepage = "http://pythonhosted.org/bitstring"
+    url      = "https://pypi.io/packages/source/b/bitstring/bitstring-3.1.5.zip"
+
+    version('3.1.5', '70689a282f66625d0c7c3579a13e66db')
diff --git a/var/spack/repos/builtin/packages/py-bleach/package.py b/var/spack/repos/builtin/packages/py-bleach/package.py
index aa7866c3c3..728ac4ff9e 100644
--- a/var/spack/repos/builtin/packages/py-bleach/package.py
+++ b/var/spack/repos/builtin/packages/py-bleach/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-blessings/package.py b/var/spack/repos/builtin/packages/py-blessings/package.py
index 9f5b57c469..932426cf0b 100644
--- a/var/spack/repos/builtin/packages/py-blessings/package.py
+++ b/var/spack/repos/builtin/packages/py-blessings/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-bokeh/package.py b/var/spack/repos/builtin/packages/py-bokeh/package.py
index 00850c51aa..c06ad86625 100644
--- a/var/spack/repos/builtin/packages/py-bokeh/package.py
+++ b/var/spack/repos/builtin/packages/py-bokeh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-boltons/package.py b/var/spack/repos/builtin/packages/py-boltons/package.py
index 54355ad7f1..be60d629a9 100644
--- a/var/spack/repos/builtin/packages/py-boltons/package.py
+++ b/var/spack/repos/builtin/packages/py-boltons/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py
index 4fe32139b6..1a4ccddc3e 100644
--- a/var/spack/repos/builtin/packages/py-bottleneck/package.py
+++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class PyBottleneck(PythonPackage):
     homepage = "https://pypi.python.org/pypi/Bottleneck/1.0.0"
     url      = "https://pypi.io/packages/source/B/Bottleneck/Bottleneck-1.0.0.tar.gz"
 
+    version('1.2.1', sha256='6efcde5f830aed64feafca0359b51db0e184c72af8ba6675b4a99f263922eb36')
     version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-breakseq2/package.py b/var/spack/repos/builtin/packages/py-breakseq2/package.py
new file mode 100644
index 0000000000..91d519e795
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-breakseq2/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBreakseq2(PythonPackage):
+    """nucleotide-resolution analysis of structural variants"""
+
+    homepage = "http://bioinform.github.io/breakseq2/"
+    url      = "https://github.com/bioinform/breakseq2/archive/2.2.tar.gz"
+
+    version('2.2', '6fd5a103c2781717b0b1d0efcbdc17e7')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-biopython@1.65', type=('build', 'run'))
+    depends_on('py-cython', type='build')
+    depends_on('py-pysam@0.7.7', type=('build', 'run'))
+    depends_on('bwa', type='run')
+    depends_on('samtools', type='run')
diff --git a/var/spack/repos/builtin/packages/py-brian/package.py b/var/spack/repos/builtin/packages/py-brian/package.py
index 68ed005b4a..49b5d9ed1d 100644
--- a/var/spack/repos/builtin/packages/py-brian/package.py
+++ b/var/spack/repos/builtin/packages/py-brian/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-brian2/package.py b/var/spack/repos/builtin/packages/py-brian2/package.py
index bf28c5cda2..9e374e293a 100644
--- a/var/spack/repos/builtin/packages/py-brian2/package.py
+++ b/var/spack/repos/builtin/packages/py-brian2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class PyBrian2(PythonPackage):
     version('2.0.1', 'df5990e9a71f7344887bc02f54dfd0f0')
     version('2.0rc3', '3100c5e4eb9eb83a06ff0413a7d43152')
 
-    variant('docs', default=False, description='Build the documentation')
+    variant('doc', default=False, description='Build the documentation')
 
     # depends on py-setuptools@6: for windows, if spack targets windows,
     # this will need to be added here
@@ -44,7 +25,5 @@ class PyBrian2(PythonPackage):
     depends_on('py-pyparsing',      type=('build', 'run'))
     depends_on('py-jinja2@2.7:',    type=('build', 'run'))
     depends_on('py-cpuinfo@0.1.6:', type=('build', 'run'))
-
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nosetests@1.0:', type='test')
     depends_on('py-sphinx@1.4.2:',  type=('build', 'run'), when='+docs')
+    depends_on('py-nosetests@1.0:', type='test')
\ No newline at end of file
diff --git a/var/spack/repos/builtin/packages/py-bsddb3/package.py b/var/spack/repos/builtin/packages/py-bsddb3/package.py
index 91b8d72665..81d9d2e203 100644
--- a/var/spack/repos/builtin/packages/py-bsddb3/package.py
+++ b/var/spack/repos/builtin/packages/py-bsddb3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,14 @@ class PyBsddb3(PythonPackage):
        Sequence and Transaction objects, and each of these is exposed
        as a Python type in the bsddb3.db module."""
 
-    homepage = "://pypi.python.org/pypi/bsddb3/6.2.5"
-    url      = "https://pypi.python.org/packages/ba/a7/131dfd4e3a5002ef30e20bee679d5e6bcb2fcc6af21bd5079dc1707a132c/bsddb3-6.2.5.tar.gz#md5=610267c189964c905a931990e1ba438c"
+    homepage = "https://pypi.python.org/pypi/bsddb3/6.2.5"
+    url      = "https://pypi.io/packages/source/b/bsddb3/bsddb3-6.2.5.tar.gz"
 
     version('6.2.5', '610267c189964c905a931990e1ba438c')
 
     depends_on('python@2.6:')
-    depends_on('py-setuptools')
+    depends_on('py-setuptools', type='build')
+    depends_on('berkeley-db')
+
+    # For testing... see here for an example that uses BerkeleyDB
+    # http://code.activestate.com/recipes/189060-using-berkeley-db-database/
diff --git a/var/spack/repos/builtin/packages/py-bx-python/package.py b/var/spack/repos/builtin/packages/py-bx-python/package.py
new file mode 100644
index 0000000000..b562ad0308
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bx-python/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyBxPython(PythonPackage):
+    """The bx-python project is a python library and associated set of scripts
+    to allow for rapid implementation of genome scale analyses."""
+
+    homepage = "https://github.com/bxlab/bx-python"
+    url      = "https://github.com/bxlab/bx-python/archive/v0.7.4.tar.gz"
+
+    version('0.7.4', 'a47b8cc55c104ac97440c6cc62be8697')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy',      type=('build', 'run'))
+    depends_on('py-six',        type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cartopy/package.py b/var/spack/repos/builtin/packages/py-cartopy/package.py
new file mode 100644
index 0000000000..f347652f26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cartopy/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCartopy(PythonPackage):
+    """Cartopy - a cartographic python library with matplotlib support."""
+
+    homepage = "http://scitools.org.uk/cartopy/"
+    url      = "https://github.com/SciTools/cartopy/archive/v0.16.0.tar.gz"
+
+    version('0.16.0', 'f9e2e528d7758da7c64f824548a53f32')
+
+    depends_on('py-setuptools@0.7.2:', type='build')
+    depends_on('py-cython@0.15.1:',    type='build')
+    depends_on('py-numpy@1.10.0:',  type=('build', 'run'))
+    depends_on('py-shapely@1.5.6:', type=('build', 'run'))
+    depends_on('py-pyshp@1.1.4:',   type=('build', 'run'))
+    depends_on('py-six@1.3.0:',     type=('build', 'run'))
+    depends_on('geos@3.3.3:')
+    depends_on('proj@4.9.0:')
+
+    # optional dependecies
+    depends_on('py-matplotlib@1.5.1:', type=('build', 'run'))
+    depends_on('gdal@1.10.0:+python',  type=('build', 'run'))
+    depends_on('py-pillow@1.7.8:',     type=('build', 'run'))
+    depends_on('py-pyepsg@0.2.0:',     type=('build', 'run'))
+    depends_on('py-scipy@0.10:',       type=('build', 'run'))
+    depends_on('py-owslib@0.8.11:',    type=('build', 'run'))
+
+    # testing dependencies
+    depends_on('py-mock@1.0.1',    type='test')
+    depends_on('py-pytest@3.0.0:', type='test')
+
+    phases = ['build_ext', 'install']
+
+    def build_ext_args(self, spec, prefix):
+        args = ['-I{0}'.format(spec['proj'].prefix.include),
+                '-L{0}'.format(spec['proj'].prefix.lib)
+                ]
+        return args
diff --git a/var/spack/repos/builtin/packages/py-cclib/package.py b/var/spack/repos/builtin/packages/py-cclib/package.py
index 7d47dcf3fb..32d55b0269 100644
--- a/var/spack/repos/builtin/packages/py-cclib/package.py
+++ b/var/spack/repos/builtin/packages/py-cclib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cdat-lite/package.py b/var/spack/repos/builtin/packages/py-cdat-lite/package.py
index a7bf68d50f..33ce8dce3e 100644
--- a/var/spack/repos/builtin/packages/py-cdat-lite/package.py
+++ b/var/spack/repos/builtin/packages/py-cdat-lite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-cdo/package.py b/var/spack/repos/builtin/packages/py-cdo/package.py
index c5b6d39982..f2628d5e7f 100644
--- a/var/spack/repos/builtin/packages/py-cdo/package.py
+++ b/var/spack/repos/builtin/packages/py-cdo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-certifi/package.py b/var/spack/repos/builtin/packages/py-certifi/package.py
index 8a5df53a27..c13112d182 100644
--- a/var/spack/repos/builtin/packages/py-certifi/package.py
+++ b/var/spack/repos/builtin/packages/py-certifi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cffi/package.py b/var/spack/repos/builtin/packages/py-cffi/package.py
index d75c9a4f38..2b32e8d60f 100644
--- a/var/spack/repos/builtin/packages/py-cffi/package.py
+++ b/var/spack/repos/builtin/packages/py-cffi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -33,6 +14,7 @@ class PyCffi(PythonPackage):
 
     import_modules = ['cffi']
 
+    version('1.11.5', 'ac8492f4ad952360737413e82d661908')
     version('1.10.0', '2b5fa41182ed0edaf929a789e602a070')
     version('1.1.2',  'ca6e6c45b45caa87aee9adc7c796eaea')
 
diff --git a/var/spack/repos/builtin/packages/py-chardet/package.py b/var/spack/repos/builtin/packages/py-chardet/package.py
index c62bd1bef3..ab4b79982d 100644
--- a/var/spack/repos/builtin/packages/py-chardet/package.py
+++ b/var/spack/repos/builtin/packages/py-chardet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-checkm-genome/package.py b/var/spack/repos/builtin/packages/py-checkm-genome/package.py
new file mode 100644
index 0000000000..fa4fe7c3f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-checkm-genome/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCheckmGenome(PythonPackage):
+    """Assess the quality of microbial genomes recovered from isolates, single
+    cells, and metagenomes"""
+
+    homepage = "https://ecogenomics.github.io/CheckM"
+    url      = "https://pypi.io/packages/source/c/checkm-genome/checkm-genome-1.0.11.tar.gz"
+
+    version('1.0.11', '3058546ec324e2420cf72f0d2576114b')
+
+    depends_on('hmmer@3.1b1:')
+    depends_on('prodigal@2.6.1:')
+    depends_on('py-numpy@1.8.0:',        type=('build', 'run'))
+    depends_on('py-scipy@0.9.0:',        type=('build', 'run'))
+    depends_on('py-matplotlib@1.3.1:',   type=('build', 'run'))
+    depends_on('py-pysam@0.8.3:',        type=('build', 'run'))
+    depends_on('py-dendropy@4.0.0:',     type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cheetah/package.py b/var/spack/repos/builtin/packages/py-cheetah/package.py
new file mode 100644
index 0000000000..da75917d12
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cheetah/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCheetah(PythonPackage):
+    """Cheetah is a template engine and code generation tool."""
+
+    homepage = "https://pypi.python.org/pypi/Cheetah/2.4.4"
+    url      = "https://pypi.io/packages/source/C/Cheetah/Cheetah-2.3.0.tar.gz"
+
+    version('2.3.0', 'e28ffef7f5c1660d66196639f162d9ce')
diff --git a/var/spack/repos/builtin/packages/py-click/package.py b/var/spack/repos/builtin/packages/py-click/package.py
index dd2b1b3e5e..5bebd2d2ae 100644
--- a/var/spack/repos/builtin/packages/py-click/package.py
+++ b/var/spack/repos/builtin/packages/py-click/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cligj/package.py b/var/spack/repos/builtin/packages/py-cligj/package.py
new file mode 100644
index 0000000000..fed854065c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cligj/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCligj(PythonPackage):
+    """Click-based argument and option decorators for Python GIS command
+    line programs"""
+
+    homepage = "https://github.com/mapbox/cligj"
+    url      = "https://github.com/mapbox/cligj/archive/0.4.0.zip"
+
+    version('0.4.0', 'fe5376068b84c5ed01e2d3adf553e226')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-click', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cloudpickle/package.py b/var/spack/repos/builtin/packages/py-cloudpickle/package.py
new file mode 100644
index 0000000000..de87e1c8bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cloudpickle/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCloudpickle(PythonPackage):
+    """Extended pickling support for Python objects."""
+
+    homepage = "https://github.com/cloudpipe/cloudpickle"
+    url      = "https://pypi.io/packages/source/c/cloudpickle/cloudpickle-0.5.2.tar.gz"
+
+    import_modules = ['cloudpickle']
+
+    version('0.5.2', 'd0f6fc27882f865f2eb185fb0a32c84b')
+
+    depends_on('py-setuptools', type='build')
+
+    def test(self):
+        # PyPI tarball does not come with unit tests
+        pass
diff --git a/var/spack/repos/builtin/packages/py-cogent/package.py b/var/spack/repos/builtin/packages/py-cogent/package.py
new file mode 100644
index 0000000000..00111650a3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cogent/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCogent(PythonPackage):
+    """A toolkit for statistical analysis of biological sequences."""
+
+    homepage = "http://pycogent.org"
+    url      = "https://pypi.io/packages/source/c/cogent/cogent-1.9.tar.gz"
+
+    version('1.9', sha256='57d8c58e0273ffe4f2b907874f9b49dadfd0600f5507b7666369f4e44d56ce14')
+    version('1.5.3', url="https://pypi.io/packages/source/c/cogent/cogent-1.5.3.tgz", 
+        sha256='1215ac219070b7b2207b0b47b4388510f3e30ccd88160aa9f02f25d24bcbcd95')
+
+    variant('matplotlib', default=False, description="graphs related to codon usage")
+    variant('mpi', default=False, description='MPI required for parallel computation.')
+    variant('mysql', default=False, description='Required for the Ensembl querying code.')
+
+    depends_on('py-setuptools', type=('build'), when='@1.9')
+    depends_on('python@2.6:2.999', type=('build', 'run'))
+    depends_on('py-numpy@1.3:', type=('build', 'run'))
+    depends_on('zlib')
+    depends_on('py-matplotlib', when='+matplotlib', type=('build', 'run'))
+    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
+    depends_on('py-sqlalchemy', when='+mysql', type=('build', 'run'))
+    depends_on('py-pymysql', when='+mysql', type=('build', 'run'))
+    depends_on('py-cython@0.17.1:', type='build')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('DONT_USE_PYREX', '1')
diff --git a/var/spack/repos/builtin/packages/py-colorama/package.py b/var/spack/repos/builtin/packages/py-colorama/package.py
index d9e2678e6e..154ff3f449 100644
--- a/var/spack/repos/builtin/packages/py-colorama/package.py
+++ b/var/spack/repos/builtin/packages/py-colorama/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-colormath/package.py b/var/spack/repos/builtin/packages/py-colormath/package.py
index 374dcd3c8e..234b60abbd 100644
--- a/var/spack/repos/builtin/packages/py-colormath/package.py
+++ b/var/spack/repos/builtin/packages/py-colormath/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,10 @@ class PyColormath(PythonPackage):
     homepage = "https://pypi.python.org/pypi/colormath/2.1.1"
     url      = "https://pypi.io/packages/source/c/colormath/colormath-2.1.1.tar.gz"
 
+    version('3.0.0', '3d4605af344527da0e4f9f504fad7ddbebda35322c566a6c72e28edb1ff31217')
     version('2.1.1', '10a0fb17e3c24363d0e1a3f2dccaa33b')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-networkx', type=('build', 'run'))
+    depends_on('py-networkx@2.0:', type=('build', 'run'), when='@3.0.0:')
diff --git a/var/spack/repos/builtin/packages/py-configparser/package.py b/var/spack/repos/builtin/packages/py-configparser/package.py
index 2d463b3ef3..6652dc449e 100644
--- a/var/spack/repos/builtin/packages/py-configparser/package.py
+++ b/var/spack/repos/builtin/packages/py-configparser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-counter/package.py b/var/spack/repos/builtin/packages/py-counter/package.py
index 37f1d62203..8bea3d5f9d 100644
--- a/var/spack/repos/builtin/packages/py-counter/package.py
+++ b/var/spack/repos/builtin/packages/py-counter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-coverage/package.py b/var/spack/repos/builtin/packages/py-coverage/package.py
index 6912c7e898..fe95770ccf 100644
--- a/var/spack/repos/builtin/packages/py-coverage/package.py
+++ b/var/spack/repos/builtin/packages/py-coverage/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cpuinfo/package.py b/var/spack/repos/builtin/packages/py-cpuinfo/package.py
index ae75451311..8cc74a09b9 100644
--- a/var/spack/repos/builtin/packages/py-cpuinfo/package.py
+++ b/var/spack/repos/builtin/packages/py-cpuinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-crispresso/package.py b/var/spack/repos/builtin/packages/py-crispresso/package.py
new file mode 100644
index 0000000000..c2b0ec85ae
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-crispresso/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCrispresso(PythonPackage):
+    """Software pipeline for the analysis of CRISPR-Cas9 genome editing
+    outcomes from deep sequencing data."""
+
+    homepage = "https://github.com/lucapinello/CRISPResso"
+    url      = "https://pypi.io/packages/source/C/CRISPResso/CRISPResso-1.0.8.tar.gz"
+
+    version('1.0.8', '2f9b52fe62cf49012a9525845f4aea45')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@2.7.0:2.7.999', type=('build', 'run'))
+    depends_on('py-biopython@1.6.5:', type=('build', 'run'))
+    depends_on('py-matplotlib@1.3.1:', type=('build', 'run'))
+    depends_on('py-numpy@1.9:', type=('build', 'run'))
+    depends_on('py-pandas@0.15:', type=('build', 'run'))
+    depends_on('py-seaborn@0.7.1:', type=('build', 'run'))
+    depends_on('emboss@6:', type=('build', 'run'))
+    depends_on('flash', type=('build', 'run'))
+    depends_on('java', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cryptography/package.py b/var/spack/repos/builtin/packages/py-cryptography/package.py
index 9ecf7015fc..d03bf4fb43 100644
--- a/var/spack/repos/builtin/packages/py-cryptography/package.py
+++ b/var/spack/repos/builtin/packages/py-cryptography/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py
index 05682652c0..93248613b1 100644
--- a/var/spack/repos/builtin/packages/py-csvkit/package.py
+++ b/var/spack/repos/builtin/packages/py-csvkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-current/package.py b/var/spack/repos/builtin/packages/py-current/package.py
index f4cd082492..08093894e0 100644
--- a/var/spack/repos/builtin/packages/py-current/package.py
+++ b/var/spack/repos/builtin/packages/py-current/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cutadapt/package.py b/var/spack/repos/builtin/packages/py-cutadapt/package.py
index 5f029375e7..84bca9c3ad 100644
--- a/var/spack/repos/builtin/packages/py-cutadapt/package.py
+++ b/var/spack/repos/builtin/packages/py-cutadapt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class PyCutadapt(PythonPackage):
     version('1.13', '2d2d14e0c20ad53d7d84b57bc3e63b4c')
 
     depends_on('python@2.6:', type=('build', 'run'))
-    depends_on('py-setuptools',        type=('build'))
+    depends_on('py-setuptools', type=('build', 'run'))
     depends_on('py-xopen@0.1.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-cvxopt/package.py b/var/spack/repos/builtin/packages/py-cvxopt/package.py
new file mode 100644
index 0000000000..7da5f6bed6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-cvxopt/package.py
@@ -0,0 +1,124 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyCvxopt(PythonPackage):
+    """CVXOPT is a free software package for convex optimization based on the
+    Python programming language."""
+
+    homepage = "http://cvxopt.org/"
+    url      = "https://pypi.io/packages/source/c/cvxopt/cvxopt-1.1.9.tar.gz"
+
+    import_modules = ['cvxopt']
+
+    version('1.1.9', 'a56e7b23d76c2b5aaf3bea2a7c245ea7')
+
+    variant('gsl',   default=False, description='Use GSL random number generators for constructing random matrices')
+    variant('fftw',  default=False, description='Install the cvxopt.fftw interface to FFTW')
+    variant('glpk',  default=False, description='Enable support for the linear programming solver GLPK')
+    # variant('mosek', default=False, description='Enable support for the linear, second-order cone, and quadratic programming solvers in MOSEK')  # noqa: flake8
+    variant('dsdp',  default=False, description='Enable support for the semidefinite programming solver DSDP')
+
+    # Required dependencies
+    depends_on('python@2.7:')
+    depends_on('py-setuptools', type='build')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('suite-sparse')
+
+    # Optional dependencies
+    depends_on('gsl',       when='+gsl')
+    depends_on('fftw',      when='+fftw')
+    depends_on('glpk',      when='+glpk')
+    # depends_on('mosek@8:',  when='+mosek')
+    depends_on('dsdp@5.8:', when='+dsdp')
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+
+        # BLAS/LAPACK Libraries
+
+        # Default names of BLAS and LAPACK libraries
+        spack_env.set('CVXOPT_BLAS_LIB', ';'.join(spec['blas'].libs.names))
+        spack_env.set('CVXOPT_LAPACK_LIB', ';'.join(spec['lapack'].libs.names))
+
+        # Directory containing BLAS and LAPACK libraries
+        spack_env.set('CVXOPT_BLAS_LIB_DIR', spec['blas'].libs.directories[0])
+
+        # SuiteSparse Libraries
+
+        # Directory containing SuiteSparse libraries
+        spack_env.set('CVXOPT_SUITESPARSE_LIB_DIR',
+                      spec['suite-sparse'].libs.directories[0])
+
+        # Directory containing SuiteSparse header files
+        spack_env.set('CVXOPT_SUITESPARSE_INC_DIR',
+                      spec['suite-sparse'].headers.directories[0])
+
+        # GSL Libraries
+
+        if '+gsl' in spec:
+            spack_env.set('CVXOPT_BUILD_GSL', 1)
+
+            # Directory containing libgsl
+            spack_env.set('CVXOPT_GSL_LIB_DIR',
+                          spec['gsl'].libs.directories[0])
+
+            # Directory containing the GSL header files
+            spack_env.set('CVXOPT_GSL_INC_DIR',
+                          spec['gsl'].headers.directories[0])
+        else:
+            spack_env.set('CVXOPT_BUILD_GSL', 0)
+
+        # FFTW Libraries
+
+        if '+fftw' in spec:
+            spack_env.set('CVXOPT_BUILD_FFTW', 1)
+
+            # Directory containing libfftw3
+            spack_env.set('CVXOPT_FFTW_LIB_DIR',
+                          spec['fftw'].libs.directories[0])
+
+            # Directory containing fftw.h
+            spack_env.set('CVXOPT_FFTW_INC_DIR',
+                          spec['fftw'].headers.directories[0])
+        else:
+            spack_env.set('CVXOPT_BUILD_FFTW', 0)
+
+        # GLPK Libraries
+
+        if '+glpk' in spec:
+            spack_env.set('CVXOPT_BUILD_GLPK', 1)
+
+            # Directory containing libglpk
+            spack_env.set('CVXOPT_GLPK_LIB_DIR',
+                          spec['glpk'].libs.directories[0])
+
+            # Directory containing glpk.h
+            spack_env.set('CVXOPT_GLPK_INC_DIR',
+                          spec['glpk'].headers.directories[0])
+        else:
+            spack_env.set('CVXOPT_BUILD_GLPK', 0)
+
+        # DSDP Libraries
+
+        if '+dsdp' in spec:
+            spack_env.set('CVXOPT_BUILD_DSDP', 1)
+
+            # Directory containing libdsdp
+            spack_env.set('CVXOPT_DSDP_LIB_DIR',
+                          spec['dsdp'].libs.directories[0])
+
+            # Directory containing dsdp5.h
+            spack_env.set('CVXOPT_DSDP_INC_DIR',
+                          spec['dsdp'].headers.directories[0])
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+        """Test that the installation was successful."""
+        python('-m', 'unittest', 'discover', '-s', 'tests')
diff --git a/var/spack/repos/builtin/packages/py-cycler/package.py b/var/spack/repos/builtin/packages/py-cycler/package.py
index de0be6903f..2e2c52811e 100644
--- a/var/spack/repos/builtin/packages/py-cycler/package.py
+++ b/var/spack/repos/builtin/packages/py-cycler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-cython/package.py b/var/spack/repos/builtin/packages/py-cython/package.py
index 33b980d87b..610a6aa3b7 100644
--- a/var/spack/repos/builtin/packages/py-cython/package.py
+++ b/var/spack/repos/builtin/packages/py-cython/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,17 @@ class PyCython(PythonPackage):
     homepage = "https://pypi.python.org/pypi/cython"
     url      = "https://pypi.io/packages/source/c/cython/Cython-0.25.2.tar.gz"
 
+    version('0.28.3', '586f0eb70ba1fcc34334e9e10c5e68c0')
+    version('0.28.1', 'c549effadb52d90bdcb1affc1e5dbb97')
     version('0.25.2', '642c81285e1bb833b14ab3f439964086')
-
     version('0.23.5', '66b62989a67c55af016c916da36e7514')
     version('0.23.4', '157df1f69bcec6b56fd97e0f2e057f6e')
 
     # These versions contain illegal Python3 code...
     version('0.22', '1ae25add4ef7b63ee9b4af697300d6b6')
     version('0.21.2', 'd21adb870c75680dc857cd05d41046a4')
+
+    @property
+    def command(self):
+        """Returns the Cython command"""
+        return Executable(self.prefix.bin.cython)
diff --git a/var/spack/repos/builtin/packages/py-dask/package.py b/var/spack/repos/builtin/packages/py-dask/package.py
index 7534e7ae7e..72f4667b61 100644
--- a/var/spack/repos/builtin/packages/py-dask/package.py
+++ b/var/spack/repos/builtin/packages/py-dask/package.py
@@ -1,35 +1,63 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyDask(PythonPackage):
-    """Minimal task scheduling abstraction"""
+    """Dask is a flexible parallel computing library for analytics."""
+
     homepage = "https://github.com/dask/dask/"
-    url      = "https://pypi.io/packages/source/d/dask/dask-0.8.1.tar.gz"
+    url      = "https://pypi.io/packages/source/d/dask/dask-0.17.4.tar.gz"
+
+    version('0.17.4', '4a7b9c5d7ddf52639b1c6b9e8a68d146')
+    version('0.8.1',  '5dd8e3a3823b3bc62c9a6d192e2cb5b4')
+
+    variant('array',       default=True, description='Install requirements for dask.array')
+    variant('bag',         default=True, description='Install requirements for dask.bag')
+    variant('dataframe',   default=True, description='Install requirements for dask.dataframe')
+    variant('delayed',     default=True, description='Install requirements for dask.delayed')
+
+    depends_on('py-setuptools',         type='build')
+    depends_on('py-pytest@3.1.0:',      type='test')
+    depends_on('py-requests',           type='test')
+
+    # Requirements for dask.array
+    depends_on('py-numpy@1.11.0:',      type=('build', 'run'), when='+array')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+array')
+
+    # Requirements for dask.bag
+    depends_on('py-cloudpickle@0.2.1:', type=('build', 'run'), when='+bag')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+bag')
+    depends_on('py-partd@0.3.8:',       type=('build', 'run'), when='+bag')
+
+    # Requirements for dask.dataframe
+    depends_on('py-numpy@1.11.0:',      type=('build', 'run'), when='+dataframe')
+    depends_on('py-pandas@0.19.0:',     type=('build', 'run'), when='+dataframe')
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+dataframe')
+    depends_on('py-partd@0.3.8:',       type=('build', 'run'), when='+dataframe')
+    depends_on('py-cloudpickle@0.2.1:', type=('build', 'run'), when='+dataframe')
+
+    # Requirements for dask.delayed
+    depends_on('py-toolz@0.7.3:',       type=('build', 'run'), when='+delayed')
+
+    @property
+    def import_modules(self):
+        modules = [
+            'dask', 'dask.bytes', 'dask.diagnostics', 'dask.store'
+        ]
+
+        if '+array' in self.spec:
+            modules.append('dask.array')
+
+        if '+bag' in self.spec:
+            modules.append('dask.bag')
 
-    version('0.8.1', '5dd8e3a3823b3bc62c9a6d192e2cb5b4')
+        if '+dataframe' in self.spec:
+            modules.extend([
+                'dask.dataframe', 'dask.dataframe.io', 'dask.dataframe.tseries'
+            ])
 
-    depends_on('py-setuptools', type='build')
+        return modules
diff --git a/var/spack/repos/builtin/packages/py-dateutil/package.py b/var/spack/repos/builtin/packages/py-dateutil/package.py
index f2b8b29429..34922f3c40 100644
--- a/var/spack/repos/builtin/packages/py-dateutil/package.py
+++ b/var/spack/repos/builtin/packages/py-dateutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py
index 2dfc9cd3ec..071472321d 100644
--- a/var/spack/repos/builtin/packages/py-dbf/package.py
+++ b/var/spack/repos/builtin/packages/py-dbf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-decorator/package.py b/var/spack/repos/builtin/packages/py-decorator/package.py
index b33bcbc6ee..0ebe02a893 100644
--- a/var/spack/repos/builtin/packages/py-decorator/package.py
+++ b/var/spack/repos/builtin/packages/py-decorator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class PyDecorator(PythonPackage):
     homepage = "https://github.com/micheles/decorator"
     url      = "https://pypi.io/packages/source/d/decorator/decorator-4.0.9.tar.gz"
 
+    version('4.3.0', sha256='c39efa13fbdeb4506c476c9b3babf6a718da943dab7811c206005a4a956c080c')
     version('4.0.9', 'f12c5651ccd707e12a0abaa4f76cd69a')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-deeptools/package.py b/var/spack/repos/builtin/packages/py-deeptools/package.py
index 68f77628ea..270da83b93 100644
--- a/var/spack/repos/builtin/packages/py-deeptools/package.py
+++ b/var/spack/repos/builtin/packages/py-deeptools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-dendropy/package.py b/var/spack/repos/builtin/packages/py-dendropy/package.py
new file mode 100644
index 0000000000..4434d1eb40
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-dendropy/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyDendropy(PythonPackage):
+    """DendroPy is a Python library for phylogenetic computing. It provides
+    classes and functions for the simulation, processing, and manipulation of
+    phylogenetic trees and character matrices, and supports the reading and
+    writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK,
+    NeXML, Phylip, FASTA, etc."""
+
+    homepage = "https://www.dendropy.org"
+    url      = "https://pypi.io/packages/source/d/dendropy/DendroPy-4.3.0.tar.gz"
+
+    version('4.3.0',  '56c37eb7db69686c8ef3467562f4e7c5')
+    version('3.12.0', '6971ac9a8508b4198fd357fab0affc84')
+
+    depends_on('python@2.7:,3.4:')
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-dev/__init__.py.patch b/var/spack/repos/builtin/packages/py-dev/__init__.py.patch
deleted file mode 100644
index 1c783b82c8..0000000000
--- a/var/spack/repos/builtin/packages/py-dev/__init__.py.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- a/dev/__init__.py	2017-03-24 13:46:56.211385166 +0000
-+++ b/dev/__init__.py	2017-03-24 13:47:01.535332256 +0000
-@@ -1,6 +1,6 @@
- """
- 
--🚧 About
-+About
- --------
- 
- dev is a collection of Python developer tools presented as a
diff --git a/var/spack/repos/builtin/packages/py-dev/package.py b/var/spack/repos/builtin/packages/py-dev/package.py
deleted file mode 100644
index 49b0e9b2c3..0000000000
--- a/var/spack/repos/builtin/packages/py-dev/package.py
+++ /dev/null
@@ -1,38 +0,0 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 PyDev(PythonPackage):
-    """libraries and tools for Python development"""
-
-    homepage = "https://pypi.python.org/pypi/dev"
-    url      = "https://pypi.io/packages/source/d/dev/dev-0.4.0.tar.gz"
-
-    version('0.4.0', '00449cf0b347c32da9c840adcb4cf24b')
-
-    patch('__init__.py.patch')
-
-    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-dill/package.py b/var/spack/repos/builtin/packages/py-dill/package.py
index f5be93cdd7..c2980db0f4 100644
--- a/var/spack/repos/builtin/packages/py-dill/package.py
+++ b/var/spack/repos/builtin/packages/py-dill/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-discover/package.py b/var/spack/repos/builtin/packages/py-discover/package.py
new file mode 100644
index 0000000000..ee9231c23d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-discover/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyDiscover(PythonPackage):
+    """Test discovery for unittest."""
+
+    homepage = "https://pypi.python.org/pypi/discover"
+    url      = "https://pypi.io/packages/source/d/discover/discover-0.4.0.tar.gz"
+
+    version('0.4.0', '30bb643af4f5ea47fff572b5c346207d')
diff --git a/var/spack/repos/builtin/packages/py-dlcpar/package.py b/var/spack/repos/builtin/packages/py-dlcpar/package.py
index 22e1ccd5a6..d71c0e7bc8 100644
--- a/var/spack/repos/builtin/packages/py-dlcpar/package.py
+++ b/var/spack/repos/builtin/packages/py-dlcpar/package.py
@@ -1,32 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyDlcpar(PythonPackage):
-    """FIXME: Put a proper description of your package here."""
+    """DLCpar is a reconciliation method for inferring gene duplications,
+    losses, and coalescence (accounting for incomplete lineage sorting)."""
 
     homepage = "https://www.cs.hmc.edu/~yjw/software/dlcpar/"
     url      = "https://www.cs.hmc.edu/~yjw/software/dlcpar/pub/sw/dlcpar-1.0.tar.gz"
diff --git a/var/spack/repos/builtin/packages/py-docopt/package.py b/var/spack/repos/builtin/packages/py-docopt/package.py
new file mode 100644
index 0000000000..25b4c85653
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-docopt/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyDocopt(PythonPackage):
+    """Command-line interface description language."""
+
+    homepage = "http://docopt.org/"
+    url      = "https://pypi.io/packages/source/d/docopt/docopt-0.6.2.tar.gz"
+
+    import_modules = ['docopt']
+
+    version('0.6.2', '4bc74561b37fad5d3e7d037f82a4c3b1')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-docutils/package.py b/var/spack/repos/builtin/packages/py-docutils/package.py
index 25881c9e77..732440a2a6 100644
--- a/var/spack/repos/builtin/packages/py-docutils/package.py
+++ b/var/spack/repos/builtin/packages/py-docutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-doxypy/package.py b/var/spack/repos/builtin/packages/py-doxypy/package.py
index eb81b080c0..d1530b40fa 100644
--- a/var/spack/repos/builtin/packages/py-doxypy/package.py
+++ b/var/spack/repos/builtin/packages/py-doxypy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,3 +13,5 @@ class PyDoxypy(PythonPackage):
     url      = "https://pypi.io/packages/source/d/doxypy/doxypy-0.3.tar.gz"
 
     version('0.3', '3b52289e0962d31b92af8be0eef8cbb2')
+
+    depends_on('python@:2.8')
diff --git a/var/spack/repos/builtin/packages/py-doxypypy/package.py b/var/spack/repos/builtin/packages/py-doxypypy/package.py
index 243909dffc..55f4e846f9 100644
--- a/var/spack/repos/builtin/packages/py-doxypypy/package.py
+++ b/var/spack/repos/builtin/packages/py-doxypypy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-dryscrape/package.py b/var/spack/repos/builtin/packages/py-dryscrape/package.py
index 675b8f87e5..2036804d88 100644
--- a/var/spack/repos/builtin/packages/py-dryscrape/package.py
+++ b/var/spack/repos/builtin/packages/py-dryscrape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class PyDryscrape(PythonPackage):
 
     homepage = "https://github.com/niklasb/dryscrape"
     url      = "https://pypi.io/packages/source/d/dryscrape/dryscrape-1.0.tar.gz"
+    git      = "https://github.com/niklasb/dryscrape.git"
 
-    version('develop', git="https://github.com/niklasb/dryscrape",
-            branch="master")
+    version('develop', branch='master')
     version('1.0', '267e380a8efaf9cd8fd94de1639d3198')
 
     depends_on('py-lxml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-dxchange/package.py b/var/spack/repos/builtin/packages/py-dxchange/package.py
index 6c04f119ae..d70bbd3ec3 100644
--- a/var/spack/repos/builtin/packages/py-dxchange/package.py
+++ b/var/spack/repos/builtin/packages/py-dxchange/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-dxfile/package.py b/var/spack/repos/builtin/packages/py-dxfile/package.py
index f131b51f85..f5ca0d5764 100644
--- a/var/spack/repos/builtin/packages/py-dxfile/package.py
+++ b/var/spack/repos/builtin/packages/py-dxfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py
index 1a116c5a15..7e8d92ae4c 100644
--- a/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py
+++ b/var/spack/repos/builtin/packages/py-easybuild-easyblocks/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py
index 2acb09213b..6ab9fa9409 100644
--- a/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py
+++ b/var/spack/repos/builtin/packages/py-easybuild-easyconfigs/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py
index 61e4ee1c70..04dbe5e068 100644
--- a/var/spack/repos/builtin/packages/py-easybuild-framework/package.py
+++ b/var/spack/repos/builtin/packages/py-easybuild-framework/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-edffile/package.py b/var/spack/repos/builtin/packages/py-edffile/package.py
index 460840e708..69e2927e6b 100644
--- a/var/spack/repos/builtin/packages/py-edffile/package.py
+++ b/var/spack/repos/builtin/packages/py-edffile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,11 @@ class PyEdffile(PythonPackage):
     """Generic class for Edf files manipulation."""
 
     homepage = "https://github.com/vasole/pymca/blob/master/PyMca5/PyMcaIO/EdfFile.py"
-    url      = "https://github.com/conda-forge/edffile-feedstock.git"
+    git      = "https://github.com/conda-forge/edffile-feedstock.git"
 
     import_modules = ['EdfFile']
 
-    version('5.0.0', git='https://github.com/conda-forge/edffile-feedstock.git',
-            commit='be5ab4199db9f8209c59e31874934b8536b52301')
+    version('5.0.0', commit='be5ab4199db9f8209c59e31874934b8536b52301')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-editdistance/package.py b/var/spack/repos/builtin/packages/py-editdistance/package.py
new file mode 100644
index 0000000000..c3f79c1782
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-editdistance/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyEditdistance(PythonPackage):
+    """Fast implementation of the edit distance (Levenshtein distance)."""
+
+    homepage = "https://github.com/aflc/editdistance"
+    url      = "https://pypi.io/packages/source/e/editdistance/editdistance-0.4.tar.gz"
+
+    version('0.4', '27434720ca0930a9b6974b182b6237bc')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-elasticsearch/package.py b/var/spack/repos/builtin/packages/py-elasticsearch/package.py
index 8b324b29e2..287d2b84a1 100644
--- a/var/spack/repos/builtin/packages/py-elasticsearch/package.py
+++ b/var/spack/repos/builtin/packages/py-elasticsearch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-elephant/package.py b/var/spack/repos/builtin/packages/py-elephant/package.py
index 3cc36b8769..c54797b073 100644
--- a/var/spack/repos/builtin/packages/py-elephant/package.py
+++ b/var/spack/repos/builtin/packages/py-elephant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,10 @@ class PyElephant(PythonPackage):
     homepage = "http://neuralensemble.org/elephant"
     url      = "https://pypi.io/packages/source/e/elephant/elephant-0.3.0.tar.gz"
 
+    version('0.4.1', '0e6214c96cae6ce777e4b3cf29bbdaa9')
     version('0.3.0', '84e69e6628fd617af469780c30d2da6c')
 
-    variant('docs', default=False, description='Build the documentation')
+    variant('doc', default=False, description='Build the documentation')
     variant('pandas', default=True, description='Build with pandas')
 
     depends_on('py-setuptools',         type='build')
@@ -45,4 +27,4 @@ class PyElephant(PythonPackage):
     depends_on('py-pandas@0.14.1:',     type=('build', 'run'), when='+pandas')
     depends_on('py-numpydoc@0.5:',      type=('build', 'run'), when='+docs')
     depends_on('py-sphinx@1.2.2:',      type=('build', 'run'), when='+docs')
-    # depends_on('py-nose@1.3.3:',        type=('build', 'run')) # tests
+    depends_on('py-nose@1.3.3:',        type='test')
diff --git a/var/spack/repos/builtin/packages/py-emcee/package.py b/var/spack/repos/builtin/packages/py-emcee/package.py
index 1fc6d0ac27..6077af7b01 100644
--- a/var/spack/repos/builtin/packages/py-emcee/package.py
+++ b/var/spack/repos/builtin/packages/py-emcee/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-entrypoints/package.py b/var/spack/repos/builtin/packages/py-entrypoints/package.py
index 335c04267c..6e43570832 100644
--- a/var/spack/repos/builtin/packages/py-entrypoints/package.py
+++ b/var/spack/repos/builtin/packages/py-entrypoints/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-enum34/package.py b/var/spack/repos/builtin/packages/py-enum34/package.py
index 35808b0094..eb28715f24 100644
--- a/var/spack/repos/builtin/packages/py-enum34/package.py
+++ b/var/spack/repos/builtin/packages/py-enum34/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,7 @@ class PyEnum34(PythonPackage):
     version('1.1.6', '5f13a0841a61f7fc295c514490d120d0')
 
     depends_on('python')
+    conflicts('python@3.4:')
 
     # This dependency breaks concretization
     # See https://github.com/spack/spack/issues/2793
diff --git a/var/spack/repos/builtin/packages/py-epydoc/package.py b/var/spack/repos/builtin/packages/py-epydoc/package.py
index e6eed4c94c..03fabe3d49 100644
--- a/var/spack/repos/builtin/packages/py-epydoc/package.py
+++ b/var/spack/repos/builtin/packages/py-epydoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-espresso/2244.patch b/var/spack/repos/builtin/packages/py-espresso/2244.patch
new file mode 100644
index 0000000000..9a6b95a573
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-espresso/2244.patch
@@ -0,0 +1,25 @@
+From 8c1b77e48f2984f7a11434959e37d08514521595 Mon Sep 17 00:00:00 2001
+From: Christoph Junghans <junghans@votca.org>
+Date: Sun, 9 Sep 2018 07:04:09 -0600
+Subject: [PATCH] cmake: workaround for cmake bug#18349
+
+---
+ CMakeLists.txt | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 8f384f423b..f84095b5f4 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -286,7 +286,10 @@ endif(WITH_VALGRIND_INSTRUMENTATION)
+ #######################################################################
+ 
+ find_package(MPI REQUIRED)
+-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_COMPILE_FLAGS}")
++# Workaround for https://gitlab.kitware.com/cmake/cmake/issues/18349
++foreach(_MPI_FLAG ${MPI_COMPILE_FLAGS})
++  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_MPI_FLAG}")
++endforeach()
+ set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MPI_LINK_FLAGS}")
+ include_directories(SYSTEM ${MPI_INCLUDE_PATH})
+ list(APPEND LIBRARIES ${MPI_LIBRARIES})
diff --git a/var/spack/repos/builtin/packages/py-espresso/package.py b/var/spack/repos/builtin/packages/py-espresso/package.py
index 768fae16ee..235b622cac 100644
--- a/var/spack/repos/builtin/packages/py-espresso/package.py
+++ b/var/spack/repos/builtin/packages/py-espresso/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -38,15 +19,20 @@ class PyEspresso(CMakePackage):
        particle couplings to the LB fluid.
     """
     homepage = "http://espressomd.org/"
-    url      = "https://github.com/espressomd/espresso/tarball/v4.0"
+    git      = "https://github.com/espressomd/espresso.git"
+    url      = "https://github.com/espressomd/espresso/releases/download/4.0.0/espresso-4.0.0.tar.gz"
+
+    version('develop', branch='python')
+    version('4.0.0', sha256='8e128847447eebd843de24be9b4ad14aa19c028ae48879a5a4535a9683836e6b')
 
-    version('develop', git='https://github.com/espressomd/espresso.git', branch='python')
+    # espressomd/espresso#2244 merge upstream
+    patch('2244.patch', when="@4.0.0")
 
     depends_on("cmake@3.0:", type='build')
     depends_on("mpi")
     depends_on("boost+serialization+filesystem+system+python+mpi")
     extends("python")
-    depends_on("python")
-    depends_on("py-cython@0.23:")
-    depends_on("py-numpy")
+    depends_on("py-cython@0.23:", type="build")
+    depends_on("py-numpy", type=("build", "run"))
     depends_on("fftw")
+    depends_on("hdf5+hl+mpi")
diff --git a/var/spack/repos/builtin/packages/py-espressopp/package.py b/var/spack/repos/builtin/packages/py-espressopp/package.py
index 53d1cc4f50..c9ffea486b 100644
--- a/var/spack/repos/builtin/packages/py-espressopp/package.py
+++ b/var/spack/repos/builtin/packages/py-espressopp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,11 +15,12 @@ class PyEspressopp(CMakePackage):
     """
     homepage = "https://espressopp.github.io"
     url      = "https://github.com/espressopp/espressopp/tarball/v1.9.4.1"
+    git      = "https://github.com/espressopp/espressopp.git"
 
-    version('develop', git='https://github.com/espressopp/espressopp.git', branch='master')
-    version('1.9.5', '13a93c30b07132b5e5fa0d828aa17d79')
+    version('develop', branch='master')
+    version('1.9.5',   '13a93c30b07132b5e5fa0d828aa17d79')
     version('1.9.4.1', '0da74a6d4e1bfa6a2a24fca354245a4f')
-    version('1.9.4', 'f2a27993a83547ad014335006eea74ea')
+    version('1.9.4',   'f2a27993a83547ad014335006eea74ea')
 
     variant('ug', default=False, description='Build user guide')
     variant('pdf', default=False, description='Build user guide in pdf format')
diff --git a/var/spack/repos/builtin/packages/py-et-xmlfile/package.py b/var/spack/repos/builtin/packages/py-et-xmlfile/package.py
index bbe649f042..ffd88933fa 100644
--- a/var/spack/repos/builtin/packages/py-et-xmlfile/package.py
+++ b/var/spack/repos/builtin/packages/py-et-xmlfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-eventlet/package.py b/var/spack/repos/builtin/packages/py-eventlet/package.py
new file mode 100644
index 0000000000..af69911130
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-eventlet/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyEventlet(PythonPackage):
+    """Concurrent networking library for Python"""
+
+    homepage = "https://github.com/eventlet/eventlet"
+    url      = "https://github.com/eventlet/eventlet/releases/download/v0.22.0/eventlet-0.22.0.tar.gz"
+
+    version('0.22.0', 'a1199cecd44d7ce2ea624ac6c21db877')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-greenlet@0.3:')
+    depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3.99')
diff --git a/var/spack/repos/builtin/packages/py-execnet/package.py b/var/spack/repos/builtin/packages/py-execnet/package.py
index c2b3d38b6b..c14e8823a0 100644
--- a/var/spack/repos/builtin/packages/py-execnet/package.py
+++ b/var/spack/repos/builtin/packages/py-execnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,4 +17,5 @@ class PyExecnet(PythonPackage):
     version('1.4.1', '0ff84b6c79d0dafb7e2971629c4d127a')
 
     depends_on('py-setuptools',  type='build')
+    depends_on('py-setuptools-scm',  type='build')
     depends_on('py-apipkg@1.4:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-fastaindex/package.py b/var/spack/repos/builtin/packages/py-fastaindex/package.py
index e22ff80326..1ddd16d4e8 100644
--- a/var/spack/repos/builtin/packages/py-fastaindex/package.py
+++ b/var/spack/repos/builtin/packages/py-fastaindex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-fasteners/package.py b/var/spack/repos/builtin/packages/py-fasteners/package.py
index 54a21ceae4..557e3505bc 100644
--- a/var/spack/repos/builtin/packages/py-fasteners/package.py
+++ b/var/spack/repos/builtin/packages/py-fasteners/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-faststructure/package.py b/var/spack/repos/builtin/packages/py-faststructure/package.py
index ddbf1b5d8c..8d0d7833be 100644
--- a/var/spack/repos/builtin/packages/py-faststructure/package.py
+++ b/var/spack/repos/builtin/packages/py-faststructure/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-filelock/package.py b/var/spack/repos/builtin/packages/py-filelock/package.py
new file mode 100644
index 0000000000..a67d1d7be8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-filelock/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFilelock(PythonPackage):
+    """This package contains a single module, which implements a platform
+    independent file lock in Python, which provides a simple way of
+    inter-process communication"""
+
+    homepage = "https://github.com/benediktschmitt/py-filelock"
+    url = "https://github.com/benediktschmitt/py-filelock/archive/v3.0.4.tar.gz"
+
+    version('3.0.4',  '3cafce82375c3b635f2c872acaf3a00b')
+    version('3.0.3',  'e4bd69f15ebcc6d5a3d684cea3694840')
+    version('3.0.1',  'cbf41ad3d89c89e2b752bc85b501dff6')
+    version('3.0.0',  '29d199e8998ac324d0d7cab7aa814943')
+    version('2.0.13', 'cdd0c4f3e905fbab76d1202ce8e8b454')
+    version('2.0.12', 'fffda24b6cfd459ea5d2d5c335e949e2')
+    version('2.0.11', '9e8cbbe18494d12647050bb32a7e624d')
+    version('2.0.10', '1791e72bb19e503fdd0f365fb8ce2a4d')
+    version('2.0.9',  'b0269e7f77a090cc0d5fc9cf5fbe6ac2')
+    version('2.0.8',  '939ec6d4e2ecdc353a1f27fc452d8e8c')
diff --git a/var/spack/repos/builtin/packages/py-fiscalyear/package.py b/var/spack/repos/builtin/packages/py-fiscalyear/package.py
index e86e2a397d..0f3081653c 100644
--- a/var/spack/repos/builtin/packages/py-fiscalyear/package.py
+++ b/var/spack/repos/builtin/packages/py-fiscalyear/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,16 +14,16 @@ class PyFiscalyear(PythonPackage):
 
     homepage = "https://github.com/adamjstewart/fiscalyear"
     url      = "https://pypi.io/packages/source/f/fiscalyear/fiscalyear-0.1.0.tar.gz"
+    git      = "https://github.com/adamjstewart/fiscalyear.git"
 
+    maintainers = ['adamjstewart']
     import_modules = ['fiscalyear']
 
-    version('master', branch='master',
-            git='https://github.com/adamjstewart/fiscalyear.git')
+    version('master', branch='master')
     version('0.1.0', '30e36b259f3e72e4929abbf259335742')
 
     depends_on('python@2.5:')
     depends_on('py-setuptools', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest', type='test')
-    # depends_on('py-pytest-runner', type='test')
+    depends_on('py-pytest', type='test')
+    depends_on('py-pytest-runner', type='test')
diff --git a/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py
new file mode 100644
index 0000000000..2a23489694
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-flake8-polyfill/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFlake8Polyfill(PythonPackage):
+    """flake8-polyfill is a package that provides some compatibility helpers
+       for Flake8 plugins that intend to support Flake8 2.x and 3.x
+       simultaneously.
+    """
+    homepage = "https://pypi.org/project/flake8-polyfill/"
+    url      = "https://files.pythonhosted.org/packages/e6/67/1c26634a770db5c442e361311bee73cb3a177adb2eb3f7af8953cfd9f553/flake8-polyfill-1.0.2.tar.gz"
+
+    version('1.0.2', 'e44b087597f6da52ec6393a709e7108b2905317d0c0b744cdca6208e670d8eda')
+
+    extends('python', ignore='bin/(flake8|pyflakes|pycodestyle)')
+    depends_on('py-flake8', type='run')
diff --git a/var/spack/repos/builtin/packages/py-flake8/package.py b/var/spack/repos/builtin/packages/py-flake8/package.py
index c4926ae64f..75a8e999f4 100644
--- a/var/spack/repos/builtin/packages/py-flake8/package.py
+++ b/var/spack/repos/builtin/packages/py-flake8/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class PyFlake8(PythonPackage):
     homepage = "https://github.com/PyCQA/flake8"
     url      = "https://github.com/PyCQA/flake8/archive/3.0.4.tar.gz"
 
+    version('3.5.0', '4e312803bbd8e4a1e566ffac887ae647')
     version('3.0.4', 'cf2a7d8c92070f7b62253404ffb54df7')
     version('2.5.4', '366dd1de6c300254c830b81e66979f06')
 
@@ -40,18 +22,24 @@ class PyFlake8(PythonPackage):
 
     # Most Python packages only require py-setuptools as a build dependency.
     # However, py-flake8 requires py-setuptools during runtime as well.
-    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-setuptools@30:', type=('build', 'run'))
 
+    # pyflakes >= 1.5.0, < 1.7.0
+    depends_on('py-pyflakes@1.5.0:1.6.999', when='@3.5.0', type=('build', 'run'))
     # pyflakes >= 0.8.1, != 1.2.0, != 1.2.1, != 1.2.2, < 1.3.0
     depends_on('py-pyflakes@0.8.1:1.1.0,1.2.3:1.2.3', when='@3.0.4', type=('build', 'run'))
     # pyflakes >= 0.8.1, < 1.1
     depends_on('py-pyflakes@0.8.1:1.0.0', when='@2.5.4', type=('build', 'run'))
 
+    # pycodestyle >= 2.3.0, < 2.4.0
+    depends_on('py-pycodestyle@2.3.0:2.3.999', when='@3.5.0', type=('build', 'run'))
     # pycodestyle >= 2.0.0, < 2.1.0
     depends_on('py-pycodestyle@2.0.0:2.0.999', when='@3.0.4', type=('build', 'run'))
     # pep8 >= 1.5.7, != 1.6.0, != 1.6.1, != 1.6.2
     depends_on('py-pycodestyle@1.5.7,1.7.0:', when='@2.5.4', type=('build', 'run'))
 
+    # mccabe >= 0.6.0, < 0.7.0
+    depends_on('py-mccabe@0.6.0:0.6.999', when='@3.5.0', type=('build', 'run'))
     # mccabe >= 0.5.0, < 0.6.0
     depends_on('py-mccabe@0.5.0:0.5.999', when='@3.0.4', type=('build', 'run'))
     # mccabe >= 0.2.1, < 0.5
@@ -62,10 +50,14 @@ class PyFlake8(PythonPackage):
     # depends_on('py-configparser', when='^python@:3.3', type=('build', 'run'))
     # depends_on('py-enum34', when='^python@:3.1', type=('build', 'run'))
     depends_on('py-configparser', type=('build', 'run'))
-    depends_on('py-enum34', type=('build', 'run'))
 
-    # TODO: Add test dependencies
-    # depends_on('py-nose', type='test')
+    # py-enum34 provides enum module from Python 3.4 for Python
+    # versions 2.4, 2.5, 2.6, 2.7, 3.1, 3.2, and 3.3; use built-in enum
+    # module for Python versions 3.4 and later
+    depends_on('py-enum34', when='^python@2.4:2.7.999,3.1:3.3.999',
+               type=('build', 'run'))
+
+    depends_on('py-nose', type='test')
 
     def patch(self):
         """Filter pytest-runner requirement out of setup.py."""
diff --git a/var/spack/repos/builtin/packages/py-flask-compress/package.py b/var/spack/repos/builtin/packages/py-flask-compress/package.py
new file mode 100644
index 0000000000..56565a20e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-flask-compress/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFlaskCompress(PythonPackage):
+    """Flask-Compress allows you to easily compress your Flask application's
+    responses with gzip."""
+
+    homepage = "https://github.com/libwilliam/flask-compress"
+    url      = "https://pypi.io/packages/source/F/Flask-Compress/Flask-Compress-1.4.0.tar.gz"
+
+    version('1.4.0', 'd997f73e4ed5793ec526c135aa765e15')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-flask@0.9:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-flask-socketio/package.py b/var/spack/repos/builtin/packages/py-flask-socketio/package.py
new file mode 100644
index 0000000000..5b016f1d5f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-flask-socketio/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFlaskSocketio(PythonPackage):
+    """Flask-SocketIO gives Flask applications access to low latency
+    bi-directional communications between the clients and the server.
+    The client-side application can use any of the SocketIO official clients
+    libraries in Javascript, C++, Java and Swift, or any compatible client to
+    establish a permanent connection to the server.
+    """
+
+    homepage = "https://flask-socketio.readthedocs.io"
+    url      = "https://pypi.io/packages/source/F/Flask-SocketIO/Flask-SocketIO-2.9.6.tar.gz"
+
+    version('2.9.6', 'bca83faf38355bd91911f2f140f9b50f')
+
+    depends_on('py-setuptools',             type='build')
+    depends_on('py-flask@0.9:',             type=('build', 'run'))
+    depends_on('py-python-socketio@1.6.1:', type=('build', 'run'))
+    depends_on('py-werkzeug',               type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-flask/package.py b/var/spack/repos/builtin/packages/py-flask/package.py
index fb59c93a4e..50f45b2788 100644
--- a/var/spack/repos/builtin/packages/py-flask/package.py
+++ b/var/spack/repos/builtin/packages/py-flask/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PyFlask(PythonPackage):
     homepage = "http://github.com/pallets/flask"
     url      = "https://pypi.io/packages/source/F/Flask/Flask-0.11.1.tar.gz"
 
+    version('0.12.2', '97278dfdafda98ba7902e890b0289177')
     version('0.12.1', '76e9fee5c3afcf4634b9baf96c578207')
     version('0.11.1', 'd2af95d8fe79cf7da099f062dd122a08')
 
diff --git a/var/spack/repos/builtin/packages/py-flexx/package.py b/var/spack/repos/builtin/packages/py-flexx/package.py
index 30485eafa7..bf949e62bd 100644
--- a/var/spack/repos/builtin/packages/py-flexx/package.py
+++ b/var/spack/repos/builtin/packages/py-flexx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-fn/package.py b/var/spack/repos/builtin/packages/py-fn/package.py
new file mode 100644
index 0000000000..adf6a474dc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fn/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFn(PythonPackage):
+    """Functional programming in Python: implementation of missing features
+    to enjoy FP."""
+
+    homepage = "https://github.com/fnpy/fn.py"
+    url      = "https://github.com/fnpy/fn.py/archive/v0.5.2.tar.gz"
+
+    version('0.5.2', '48c168fe335e31fc6152ea0944741be2')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-fparser/package.py b/var/spack/repos/builtin/packages/py-fparser/package.py
new file mode 100644
index 0000000000..a1eccda121
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fparser/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+
+
+class PyFparser(PythonPackage):
+    """Parser for Fortran 77..2003 code."""
+
+    homepage = "https://github.com/stfc/fparser"
+    url      = "https://github.com/stfc/fparser/archive/0.0.5.tar.gz"
+    git      = "https://github.com/stfc/fparser.git"
+
+    version('develop', branch='master')
+    version('0.0.6', '15553fde76b4685fa8edb0a5472b1b53d308c3b8')
+    version('0.0.5', '14630afdb8c8bd025e5504c5ab19d133aa8cf8c7')
+
+    depends_on('py-setuptools', type='build')
+
+    depends_on('py-numpy', type=('build', 'run'), when='@:0.0.5')
+    depends_on('py-nose', type='build')
+    depends_on('py-six', type='build', when='@0.0.6:')
+
+    depends_on('py-pytest', type='test')
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_build(self):
+        # Ensure that pytest.ini exists inside the source tree,
+        # otherwise an external pytest.ini can cause havoc:
+        touch('pytest.ini')
+        with working_dir('src'):
+            Executable('py.test')()
diff --git a/var/spack/repos/builtin/packages/py-funcsigs/package.py b/var/spack/repos/builtin/packages/py-funcsigs/package.py
index d2d8ff2de5..c39c95ac8b 100644
--- a/var/spack/repos/builtin/packages/py-funcsigs/package.py
+++ b/var/spack/repos/builtin/packages/py-funcsigs/package.py
@@ -1,35 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyFuncsigs(PythonPackage):
     """Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2."""
+
     homepage = "https://pypi.python.org/pypi/funcsigs"
-    url      = "https://pypi.io/packages/source/f/funcsigs/funcsigs-0.4.tar.gz"
+    url      = "https://pypi.io/packages/source/f/funcsigs/funcsigs-1.0.2.tar.gz"
+
+    import_modules = ['funcsigs']
 
-    version('0.4', 'fb1d031f284233e09701f6db1281c2a5')
+    version('1.0.2', '7e583285b1fb8a76305d6d68f4ccc14e')
+    version('0.4',   'fb1d031f284233e09701f6db1281c2a5')
 
-    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools@17.1:', type='build')
+    depends_on('py-unittest2', type='test')
diff --git a/var/spack/repos/builtin/packages/py-functools32/package.py b/var/spack/repos/builtin/packages/py-functools32/package.py
index aebf170e46..e33afafdfe 100644
--- a/var/spack/repos/builtin/packages/py-functools32/package.py
+++ b/var/spack/repos/builtin/packages/py-functools32/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-future/package.py b/var/spack/repos/builtin/packages/py-future/package.py
index 1ebce3c7d1..862abd8e64 100644
--- a/var/spack/repos/builtin/packages/py-future/package.py
+++ b/var/spack/repos/builtin/packages/py-future/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-futures/package.py b/var/spack/repos/builtin/packages/py-futures/package.py
index c3370cbeaa..8db11089f5 100644
--- a/var/spack/repos/builtin/packages/py-futures/package.py
+++ b/var/spack/repos/builtin/packages/py-futures/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-fypp/package.py b/var/spack/repos/builtin/packages/py-fypp/package.py
new file mode 100644
index 0000000000..e2a92453d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-fypp/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyFypp(PythonPackage):
+    """Python powered Fortran preprocessor."""
+
+    homepage = "https://github.com/aradi/fypp"
+    url      = "https://github.com/aradi/fypp/archive/2.1.1.zip"
+
+    version('2.1.1', sha256='3744ad17045e91466bbb75a33ce0cab0f65bc2c377127067a932cdf15655e049')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-gdbgui/package.py b/var/spack/repos/builtin/packages/py-gdbgui/package.py
new file mode 100644
index 0000000000..3f32218ef4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gdbgui/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGdbgui(PythonPackage):
+    """gdbgui is a modern, free, browser-based frontend to gdb"""
+
+    homepage = "https://gdbgui.com"
+    url      = "https://pypi.io/packages/source/g/gdbgui/gdbgui-0.11.2.1.tar.gz"
+
+    version('0.11.2.1', 'c15dd3f60fe372b2e93f705c7ee75f51')
+
+    depends_on('py-setuptools',             type=('build', 'run'))
+    depends_on('py-flask@0.12.2:',          type=('build', 'run'))
+    depends_on('py-flask-compress@1.4.0:',  type=('build', 'run'))
+    depends_on('py-flask-socketio@2.9.3:',  type=('build', 'run'))
+    depends_on('py-gevent@1.2.2:',          type=('build', 'run'))
+    depends_on('py-pygdbmi@0.8.2.0:',       type=('build', 'run'))
+    depends_on('py-pygments@2.2.0:',        type=('build', 'run'))
+    depends_on('gdb',                       type='run')
diff --git a/var/spack/repos/builtin/packages/py-genders/package.py b/var/spack/repos/builtin/packages/py-genders/package.py
index 248e4764cc..c3a210361d 100644
--- a/var/spack/repos/builtin/packages/py-genders/package.py
+++ b/var/spack/repos/builtin/packages/py-genders/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-genshi/package.py b/var/spack/repos/builtin/packages/py-genshi/package.py
index a9296ab6ed..0b2405d6e4 100644
--- a/var/spack/repos/builtin/packages/py-genshi/package.py
+++ b/var/spack/repos/builtin/packages/py-genshi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-gevent/package.py b/var/spack/repos/builtin/packages/py-gevent/package.py
new file mode 100644
index 0000000000..a69a3e5bf8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gevent/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGevent(PythonPackage):
+    """gevent is a coroutine-based Python networking library."""
+
+    homepage = "http://www.gevent.org"
+    url      = "https://pypi.io/packages/source/g/gevent/gevent-1.3a2.tar.gz"
+
+    version('1.3a2', '8d73a7b0ceb0ca791b22e6f7b7061e9e')
+
+    depends_on('py-setuptools@24.2:',   type='build')
+    depends_on('py-cython@0.27:',       type='build')
+    depends_on('py-cffi@1.4.0:',        type=('build', 'run'))
+    depends_on('py-greenlet@0.4.13:',   type=('build', 'run'))
+    depends_on('python@2.7:2.8,3.4:',   type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-git-review/package.py b/var/spack/repos/builtin/packages/py-git-review/package.py
index 596f8016aa..60291f5b1a 100644
--- a/var/spack/repos/builtin/packages/py-git-review/package.py
+++ b/var/spack/repos/builtin/packages/py-git-review/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PyGitReview(PythonPackage):
     homepage = "http://docs.openstack.org/infra/git-review"
     url = "https://pypi.io/packages/source/g/git-review/git-review-1.25.0.tar.gz"
 
+    version('1.26.0', 'dec20e8a259c03fe19c9dd2362c4ec3f')
     version('1.25.0', '0a061d0e23ee9b93c6212a3fe68fb7ab')
     version('1.24',   '145116fe58a3487c3ad1bf55538fd741')
     version('1.23',   'b0023ad8c037ab710da81412194c6a3a')
@@ -46,4 +28,4 @@ class PyGitReview(PythonPackage):
     depends_on('tk',               type=('run'))
 
     def setup_environment(self, spack_env, run_env):
-        run_env.set('PBR_VERSION', self.spec.version)
+        run_env.set('PBR_VERSION', str(self.spec.version))
diff --git a/var/spack/repos/builtin/packages/py-git2/package.py b/var/spack/repos/builtin/packages/py-git2/package.py
index 9e601aa3a2..ce6be1164e 100644
--- a/var/spack/repos/builtin/packages/py-git2/package.py
+++ b/var/spack/repos/builtin/packages/py-git2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-gnuplot/package.py b/var/spack/repos/builtin/packages/py-gnuplot/package.py
index e6972d280f..782c3cbe32 100644
--- a/var/spack/repos/builtin/packages/py-gnuplot/package.py
+++ b/var/spack/repos/builtin/packages/py-gnuplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-goatools/package.py b/var/spack/repos/builtin/packages/py-goatools/package.py
new file mode 100644
index 0000000000..4e97681f78
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-goatools/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGoatools(PythonPackage):
+    """Python scripts to find enrichment of GO terms"""
+
+    homepage = "https://github.com/tanghaibao/goatools"
+    url      = "https://pypi.io/packages/source/g/goatools/goatools-0.7.11.tar.gz"
+
+    version('0.7.11', 'f2ab989ec9c4acdd80504b263c3b3188')
+
+    depends_on('py-nose',        type=('build', 'run'))
+    depends_on('py-numpy',       type=('build', 'run'))
+    depends_on('py-pandas',      type=('build', 'run'))
+    depends_on('py-pydot',       type=('build', 'run'))
+    depends_on('py-pyparsing',   type=('build', 'run'))
+    depends_on('py-pytest',      type=('build', 'run'))
+    depends_on('py-scipy',       type=('build', 'run'))
+    depends_on('py-statsmodels', type=('build', 'run'))
+    depends_on('py-xlrd',        type=('build', 'run'))
+    depends_on('py-xlsxwriter',  type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-gpaw/package.py b/var/spack/repos/builtin/packages/py-gpaw/package.py
new file mode 100644
index 0000000000..6761ca97e2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gpaw/package.py
@@ -0,0 +1,88 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGpaw(PythonPackage):
+    """GPAW is a density-functional theory (DFT) Python code based on the
+    projector-augmented wave (PAW) method and the atomic simulation environment
+    (ASE)."""
+
+    homepage = "https://wiki.fysik.dtu.dk/gpaw/index.html"
+    url      = "https://pypi.io/packages/source/g/gpaw/gpaw-1.3.0.tar.gz"
+
+    version('1.3.0', '82e8c80e637696248db00b5713cdffd1')
+
+    variant('mpi', default=True, description='Build with MPI support')
+    variant('scalapack', default=False,
+            description='Build with ScaLAPACK support')
+    variant('fftw', default=True, description='Build with FFTW support')
+
+    depends_on('mpi', when='+mpi', type=('build', 'link', 'run'))
+    depends_on('python@2.6:')
+    depends_on('py-ase@3.13.0:', type=('build', 'run'))
+    depends_on('py-numpy +blas +lapack', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('libxc')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('fftw+mpi', when='+fftw +mpi')
+    depends_on('fftw~mpi', when='+fftw ~mpi')
+    depends_on('scalapack', when='+scalapack')
+
+    def patch(self):
+        spec = self.spec
+        # For build notes see https://wiki.fysik.dtu.dk/gpaw/install.html
+
+        libxc = spec['libxc']
+        blas = spec['blas']
+        lapack = spec['lapack']
+
+        libs = blas.libs + lapack.libs + libxc.libs
+        include_dirs = [
+            blas.prefix.include,
+            lapack.prefix.include,
+            libxc.prefix.include
+        ]
+        if '+mpi' in spec:
+            libs += spec['mpi'].libs
+            mpi_include_dirs = repr([spec['mpi'].prefix.include])
+            mpi_library_dirs = repr(list(spec['mpi'].libs.directories))
+            include_dirs.append(spec['mpi'].prefix.include)
+        if '+scalapack' in spec:
+            libs += spec['scalapack'].libs
+            include_dirs.append(spec['scalapack'].prefix.include)
+            scalapack_macros = repr([
+                ('GPAW_NO_UNDERSCORE_CBLACS', '1'),
+                ('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')
+            ])
+        if '+fftw' in spec:
+            libs += spec['fftw'].libs
+            include_dirs.append(spec['fftw'].prefix.include)
+
+        lib_dirs = list(libs.directories)
+        libs = list(libs.names)
+        rpath_str = ':'.join(self.rpath)
+
+        with open('customize.py', 'w') as f:
+            f.write("libraries = {0}\n".format(repr(libs)))
+            f.write("include_dirs = {0}\n".format(repr(include_dirs)))
+            f.write("library_dirs = {0}\n".format(repr(lib_dirs)))
+            f.write(
+                "extra_link_args += ['-Wl,-rpath={0}']\n".format(rpath_str)
+            )
+            if '+mpi' in spec:
+                f.write("define_macros += [('PARALLEL', '1')]\n")
+                f.write("compiler='{0}'\n".format(spec['mpi'].mpicc))
+                f.write("mpicompiler = '{0}'\n".format(spec['mpi'].mpicc))
+                f.write("mpi_include_dirs = {0}\n".format(mpi_include_dirs))
+                f.write("mpi_library_dirs = {0}\n".format(mpi_library_dirs))
+            else:
+                f.write("compiler='{0}'\n".format(self.compiler.cc))
+                f.write("mpicompiler = None\n")
+            if '+scalapack' in spec:
+                f.write("scalapack = True\n")
+                f.write("define_macros += {0}\n".format(scalapack_macros))
diff --git a/var/spack/repos/builtin/packages/py-greenlet/package.py b/var/spack/repos/builtin/packages/py-greenlet/package.py
new file mode 100644
index 0000000000..7e62859eea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-greenlet/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyGreenlet(PythonPackage):
+    """Lightweight in-process concurrent programming"""
+
+    homepage = "https://github.com/python-greenlet/greenlet"
+    url      = "https://pypi.io/packages/source/g/greenlet/greenlet-0.4.13.tar.gz"
+
+    version('0.4.13', '6e0b9dd5385f81d478451ec8ed1d62b3')
diff --git a/var/spack/repos/builtin/packages/py-griddataformats/package.py b/var/spack/repos/builtin/packages/py-griddataformats/package.py
index 0880d860eb..70b71323b2 100644
--- a/var/spack/repos/builtin/packages/py-griddataformats/package.py
+++ b/var/spack/repos/builtin/packages/py-griddataformats/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-guidata/package.py b/var/spack/repos/builtin/packages/py-guidata/package.py
index cf0e8447ff..328e8d36a7 100644
--- a/var/spack/repos/builtin/packages/py-guidata/package.py
+++ b/var/spack/repos/builtin/packages/py-guidata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-guiqwt/package.py b/var/spack/repos/builtin/packages/py-guiqwt/package.py
index f135b24c57..98716625cd 100644
--- a/var/spack/repos/builtin/packages/py-guiqwt/package.py
+++ b/var/spack/repos/builtin/packages/py-guiqwt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py
index 94dd8d6986..7a6b61c269 100644
--- a/var/spack/repos/builtin/packages/py-h5py/package.py
+++ b/var/spack/repos/builtin/packages/py-h5py/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,14 @@ class PyH5py(PythonPackage):
     """The h5py package provides both a high- and low-level interface to the
     HDF5 library from Python."""
 
-    homepage = "https://pypi.python.org/pypi/h5py"
-    url      = "https://pypi.io/packages/source/h/h5py/h5py-2.4.0.tar.gz"
+    homepage = "http://www.h5py.org/"
+    url      = "https://pypi.io/packages/source/h/h5py/h5py-2.8.0.tar.gz"
+
+    import_modules = ['h5py', 'h5py._hl']
 
+    version('2.8.0', 'ece4f358e69fc8a416f95953b91bc373')
+    version('2.7.1', 'da630aebe3ab9fa218ac405a218e95e0')
+    version('2.7.0', 'f62937f40f68d3b128b3941be239dd93')
     version('2.6.0', 'ec476211bd1de3f5ac150544189b0bf4')
     version('2.5.0', '6e4301b5ad5da0d51b0a1e5ac19e3b74')
     version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
@@ -39,20 +25,22 @@ class PyH5py(PythonPackage):
     variant('mpi', default=True, description='Build with MPI support')
 
     # Build dependencies
-    depends_on('py-cython@0.19:', type='build')
+    depends_on('py-cython@0.23:', type='build')
     depends_on('py-pkgconfig', type='build')
     depends_on('py-setuptools', type='build')
-    depends_on('hdf5@1.8.4:')
-    depends_on('hdf5+mpi', when='+mpi')
-    depends_on('mpi', when='+mpi')
-    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
 
     # Build and runtime dependencies
-    depends_on('py-numpy@1.6.1:', type=('build', 'run'))
-
-    # Runtime dependencies
+    depends_on('py-numpy@1.7:', type=('build', 'run'))
     depends_on('py-six', type=('build', 'run'))
 
+    # Link dependencies
+    depends_on('hdf5@1.8.4:+hl')
+
+    # MPI dependencies
+    depends_on('hdf5+mpi', when='+mpi')
+    depends_on('mpi', when='+mpi')
+    depends_on('py-mpi4py', when='+mpi', type=('build', 'run'))
+
     phases = ['configure', 'install']
 
     def configure(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/py-hdfs/package.py b/var/spack/repos/builtin/packages/py-hdfs/package.py
new file mode 100644
index 0000000000..f983ec48a2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-hdfs/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyHdfs(PythonPackage):
+    """API and command line interface for HDFS"""
+    homepage = "https://hdfscli.readthedocs.io/en/latest/"
+    url      = "https://pypi.org/packages/source/h/hdfs/hdfs-2.1.0.tar.gz"
+
+    version('2.1.0', sha256='a40fe99ccb03b5c3247b33a4110eb21b57405dd7c3f1b775e362e66c19b44bc6')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-docopt', type=('build', 'run'))
+    depends_on('py-requests@2.7.0:', type=('build', 'run'))
+    depends_on('py-six@1.9.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-hepdata-validator/package.py b/var/spack/repos/builtin/packages/py-hepdata-validator/package.py
new file mode 100644
index 0000000000..71b79c5dc2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-hepdata-validator/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyHepdataValidator(PythonPackage):
+    """Validation schema and code for HEPdata submissions."""
+
+    homepage = "https://github.com/hepdata/hepdata-validator"
+    url = "https://pypi.io/packages/source/h/hepdata_validator/hepdata_validator-0.1.16.tar.gz"
+
+    version('0.1.16', '62e80db7425a4a48050af29e05295e0d')
+    version('0.1.15', 'e29aa75780b9963997e79f572ca0209f')
+    version('0.1.14', '386a2440f23fda7d877764d120bf61fb')
+    version('0.1.8', '5bf388a507a857afbe0deba0857125c7')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-jsonschema', type=('build', 'run'))
+    depends_on('py-pyyaml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-html2text/package.py b/var/spack/repos/builtin/packages/py-html2text/package.py
index 118b86e2c9..b7509e6e72 100644
--- a/var/spack/repos/builtin/packages/py-html2text/package.py
+++ b/var/spack/repos/builtin/packages/py-html2text/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-html5lib/package.py b/var/spack/repos/builtin/packages/py-html5lib/package.py
index 927614002a..f80d0bea34 100644
--- a/var/spack/repos/builtin/packages/py-html5lib/package.py
+++ b/var/spack/repos/builtin/packages/py-html5lib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-htseq/package.py b/var/spack/repos/builtin/packages/py-htseq/package.py
new file mode 100644
index 0000000000..0e24981d1a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-htseq/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyHtseq(PythonPackage):
+    """HTSeq is a Python package that provides infrastructure to process
+    data from high-throughput sequencing assays."""
+
+    homepage = "http://htseq.readthedocs.io/en/release_0.9.1/overview.html"
+    url      = "https://github.com/simon-anders/htseq/archive/release_0.9.1.tar.gz"
+
+    version('0.9.1', '269e7de5d39fc31f609cccd4a4740e61')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-pysam', type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-cython', type=('build', 'run'))
+    depends_on('swig', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-httpbin/package.py b/var/spack/repos/builtin/packages/py-httpbin/package.py
index f8411112ad..f4a2048b4e 100644
--- a/var/spack/repos/builtin/packages/py-httpbin/package.py
+++ b/var/spack/repos/builtin/packages/py-httpbin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-hypothesis/package.py b/var/spack/repos/builtin/packages/py-hypothesis/package.py
index ffa4e0a54e..3c9abda75c 100644
--- a/var/spack/repos/builtin/packages/py-hypothesis/package.py
+++ b/var/spack/repos/builtin/packages/py-hypothesis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-idna/package.py b/var/spack/repos/builtin/packages/py-idna/package.py
index 74e6c0fd5d..7e37aa6441 100644
--- a/var/spack/repos/builtin/packages/py-idna/package.py
+++ b/var/spack/repos/builtin/packages/py-idna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-igraph/package.py b/var/spack/repos/builtin/packages/py-igraph/package.py
index 11f7c4a990..03fe3a8a8a 100644
--- a/var/spack/repos/builtin/packages/py-igraph/package.py
+++ b/var/spack/repos/builtin/packages/py-igraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-illumina-utils/package.py b/var/spack/repos/builtin/packages/py-illumina-utils/package.py
new file mode 100644
index 0000000000..b970e69797
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-illumina-utils/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyIlluminaUtils(PythonPackage):
+    """A library and collection of scripts to work with Illumina paired-end
+    data (for CASAVA 1.8+)."""
+
+    homepage = "https://github.com/meren/illumina-utils"
+    url      = "https://pypi.io/packages/source/i/illumina-utils/illumina-utils-2.2.tar.gz"
+
+    version('2.3', 'c0af71723e52ab2b14660d2138620e39')
+    version('2.2', '9e19cf112ccc38a903fc41f431804d21')
+
+    depends_on('python@3:', type=('build', 'run'))
+    depends_on('py-pip', type='build')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-python-levenshtein', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-imageio/package.py b/var/spack/repos/builtin/packages/py-imageio/package.py
new file mode 100644
index 0000000000..bff47aa4ee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-imageio/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyImageio(PythonPackage):
+    """ Imageio is a Python library that provides an easy interface
+    to read and write a wide range of image data, including animated
+    images, video, volumetric data, and scientific formats. It is
+    cross-platform, runs on Python 2.7 and 3.4+, and is easy to install."""
+
+    homepage = "http://imageio.github.io/"
+    url      = "https://pypi.io/packages/source/i/imageio/imageio-2.3.0.tar.gz"
+
+    version('2.3.0', '4722c4e1c366748abcb18729881cffb8')
+
+    # TODO: Add variants for plugins, and optional dependencies
+
+    # Fix for python 2 if needed.
+    depends_on('py-numpy',            type=('build', 'run'))
+    depends_on('py-pillow',           type=('build', 'run'))
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+    depends_on('py-setuptools',       type='build')
+    depends_on('ffmpeg',              type='run')
diff --git a/var/spack/repos/builtin/packages/py-imagesize/package.py b/var/spack/repos/builtin/packages/py-imagesize/package.py
index f9aa0334ae..c1fc830a60 100644
--- a/var/spack/repos/builtin/packages/py-imagesize/package.py
+++ b/var/spack/repos/builtin/packages/py-imagesize/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-iminuit/package.py b/var/spack/repos/builtin/packages/py-iminuit/package.py
index cbeafa683c..01dcd9f37d 100644
--- a/var/spack/repos/builtin/packages/py-iminuit/package.py
+++ b/var/spack/repos/builtin/packages/py-iminuit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-importlib/package.py b/var/spack/repos/builtin/packages/py-importlib/package.py
index 27221dc99a..90bd1dd9df 100644
--- a/var/spack/repos/builtin/packages/py-importlib/package.py
+++ b/var/spack/repos/builtin/packages/py-importlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ipaddress/package.py b/var/spack/repos/builtin/packages/py-ipaddress/package.py
index 3a84366225..287a4850ba 100644
--- a/var/spack/repos/builtin/packages/py-ipaddress/package.py
+++ b/var/spack/repos/builtin/packages/py-ipaddress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-ipdb/package.py b/var/spack/repos/builtin/packages/py-ipdb/package.py
index 047a8ce2a7..f60e3b58af 100644
--- a/var/spack/repos/builtin/packages/py-ipdb/package.py
+++ b/var/spack/repos/builtin/packages/py-ipdb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ipykernel/package.py b/var/spack/repos/builtin/packages/py-ipykernel/package.py
index d703f94a25..804bfe88d4 100644
--- a/var/spack/repos/builtin/packages/py-ipykernel/package.py
+++ b/var/spack/repos/builtin/packages/py-ipykernel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ipython-genutils/package.py b/var/spack/repos/builtin/packages/py-ipython-genutils/package.py
index e0e0865238..e09aca3606 100644
--- a/var/spack/repos/builtin/packages/py-ipython-genutils/package.py
+++ b/var/spack/repos/builtin/packages/py-ipython-genutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ipython/package.py b/var/spack/repos/builtin/packages/py-ipython/package.py
index 7f4aafa7a6..d6373ab393 100644
--- a/var/spack/repos/builtin/packages/py-ipython/package.py
+++ b/var/spack/repos/builtin/packages/py-ipython/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 import platform
diff --git a/var/spack/repos/builtin/packages/py-ipywidgets/package.py b/var/spack/repos/builtin/packages/py-ipywidgets/package.py
index b7c67b241c..58ce772216 100644
--- a/var/spack/repos/builtin/packages/py-ipywidgets/package.py
+++ b/var/spack/repos/builtin/packages/py-ipywidgets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-isort/package.py b/var/spack/repos/builtin/packages/py-isort/package.py
new file mode 100644
index 0000000000..b3b9dfdd6d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-isort/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyIsort(PythonPackage):
+    """A Python utility / library to sort Python imports."""
+
+    homepage = "https://github.com/timothycrosley/isort"
+    url      = "https://pypi.io/packages/source/i/isort/isort-4.2.15.tar.gz"
+
+    version('4.2.15', '34915a2ce60e6fe3dbcbf5982deef9b4')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-itsdangerous/package.py b/var/spack/repos/builtin/packages/py-itsdangerous/package.py
index 7bb7671571..9ee5505f93 100644
--- a/var/spack/repos/builtin/packages/py-itsdangerous/package.py
+++ b/var/spack/repos/builtin/packages/py-itsdangerous/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py
index 8b22cd191c..7274df377f 100644
--- a/var/spack/repos/builtin/packages/py-jdcal/package.py
+++ b/var/spack/repos/builtin/packages/py-jdcal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jedi/package.py b/var/spack/repos/builtin/packages/py-jedi/package.py
index fcf4043afa..3bb5b51ed9 100644
--- a/var/spack/repos/builtin/packages/py-jedi/package.py
+++ b/var/spack/repos/builtin/packages/py-jedi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jinja2/package.py b/var/spack/repos/builtin/packages/py-jinja2/package.py
index 1df8c7366f..454ec2691c 100644
--- a/var/spack/repos/builtin/packages/py-jinja2/package.py
+++ b/var/spack/repos/builtin/packages/py-jinja2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-joblib/package.py b/var/spack/repos/builtin/packages/py-joblib/package.py
index 7792a34539..3f0e8c86af 100644
--- a/var/spack/repos/builtin/packages/py-joblib/package.py
+++ b/var/spack/repos/builtin/packages/py-joblib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jprops/package.py b/var/spack/repos/builtin/packages/py-jprops/package.py
new file mode 100644
index 0000000000..ed0cafdc2d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-jprops/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyJprops(PythonPackage):
+    """Java properties file parser for Python"""
+
+    homepage = "https://github.com/mgood/jprops/"
+    url      = "https://pypi.org/packages/source/j/jprops/jprops-2.0.2.tar.gz"
+
+    version('2.0.2', sha256='d297231833b6cd0a3f982a48fe148a7f9817f2895661743d166b267e4d3d5b2c')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-jpype/package.py b/var/spack/repos/builtin/packages/py-jpype/package.py
index 204da5d79e..ba72b9ac91 100644
--- a/var/spack/repos/builtin/packages/py-jpype/package.py
+++ b/var/spack/repos/builtin/packages/py-jpype/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jsonschema/package.py b/var/spack/repos/builtin/packages/py-jsonschema/package.py
index 3c7178a4ab..dacd9cad01 100644
--- a/var/spack/repos/builtin/packages/py-jsonschema/package.py
+++ b/var/spack/repos/builtin/packages/py-jsonschema/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-junit-xml/package.py b/var/spack/repos/builtin/packages/py-junit-xml/package.py
index d256797086..f1e76c409e 100644
--- a/var/spack/repos/builtin/packages/py-junit-xml/package.py
+++ b/var/spack/repos/builtin/packages/py-junit-xml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jupyter-client/package.py b/var/spack/repos/builtin/packages/py-jupyter-client/package.py
index b291fcf448..23d22e2e00 100644
--- a/var/spack/repos/builtin/packages/py-jupyter-client/package.py
+++ b/var/spack/repos/builtin/packages/py-jupyter-client/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jupyter-console/package.py b/var/spack/repos/builtin/packages/py-jupyter-console/package.py
index 7a3098b0e8..6b041bf996 100644
--- a/var/spack/repos/builtin/packages/py-jupyter-console/package.py
+++ b/var/spack/repos/builtin/packages/py-jupyter-console/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jupyter-core/package.py b/var/spack/repos/builtin/packages/py-jupyter-core/package.py
index a07aa3fda9..f9e7af9a70 100644
--- a/var/spack/repos/builtin/packages/py-jupyter-core/package.py
+++ b/var/spack/repos/builtin/packages/py-jupyter-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py b/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py
index 39f65d9ac7..c3cc182200 100644
--- a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py
+++ b/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-keras/package.py b/var/spack/repos/builtin/packages/py-keras/package.py
index d995111ca9..24ee491907 100644
--- a/var/spack/repos/builtin/packages/py-keras/package.py
+++ b/var/spack/repos/builtin/packages/py-keras/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-kiwisolver/package.py b/var/spack/repos/builtin/packages/py-kiwisolver/package.py
new file mode 100644
index 0000000000..09acd58afc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-kiwisolver/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyKiwisolver(PythonPackage):
+    """A fast implementation of the Cassowary constraint solver"""
+
+    homepage = "https://github.com/nucleic/kiwi"
+    url      = "https://pypi.io/packages/source/k/kiwisolver/kiwisolver-1.0.1.tar.gz"
+
+    version('1.0.1', 'e2a1718b837e2cd001f7c06934616fcd')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-lark-parser/package.py b/var/spack/repos/builtin/packages/py-lark-parser/package.py
new file mode 100644
index 0000000000..08dce8163c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lark-parser/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLarkParser(PythonPackage):
+    """Lark is a modern general-purpose parsing library for Python."""
+
+    homepage = "https://github.com/lark-parser/lark/"
+    url      = "https://pypi.io/packages/source/l/lark-parser/lark-parser-0.6.2.tar.gz"
+
+    version('0.6.2', '675058937a7f41e661bcf2b3bfdb7ceb')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-latexcodec/package.py b/var/spack/repos/builtin/packages/py-latexcodec/package.py
index a768eaebf4..6870a4c686 100644
--- a/var/spack/repos/builtin/packages/py-latexcodec/package.py
+++ b/var/spack/repos/builtin/packages/py-latexcodec/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py
new file mode 100644
index 0000000000..c2b420d70f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lazy-object-proxy/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLazyObjectProxy(PythonPackage):
+    """A fast and thorough lazy object proxy."""
+
+    homepage = "https://github.com/ionelmc/python-lazy-object-proxy"
+    url      = "https://pypi.io/packages/source/l/lazy-object-proxy/lazy-object-proxy-1.3.1.tar.gz"
+
+    version('1.3.1', 'e128152b76eb5b9ba759504936139fd0')
+
+    conflicts('^python@3.0:3.2.99')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-lazy-property/package.py b/var/spack/repos/builtin/packages/py-lazy-property/package.py
new file mode 100644
index 0000000000..8e6b0d13c9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lazy-property/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLazyProperty(PythonPackage):
+    """A package for making properties lazy"""
+
+    homepage = "https://github.com/jackmaney/lazy-property"
+    url      = "https://github.com/jackmaney/lazy-property/archive/0.0.1.tar.gz"
+
+    version('0.0.1', '7e046c2441abe1bd272d5360827237b3')
+    version('0.0.0', 'fda622b7f1c46ee72ad25f5e88c928f5')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-lazy/package.py b/var/spack/repos/builtin/packages/py-lazy/package.py
index d976001296..a58bc887df 100644
--- a/var/spack/repos/builtin/packages/py-lazy/package.py
+++ b/var/spack/repos/builtin/packages/py-lazy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-lazyarray/package.py b/var/spack/repos/builtin/packages/py-lazyarray/package.py
index 5b5828182f..0b60b82154 100644
--- a/var/spack/repos/builtin/packages/py-lazyarray/package.py
+++ b/var/spack/repos/builtin/packages/py-lazyarray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-libconf/package.py b/var/spack/repos/builtin/packages/py-libconf/package.py
index 9a9d0d1059..bd7db99d99 100644
--- a/var/spack/repos/builtin/packages/py-libconf/package.py
+++ b/var/spack/repos/builtin/packages/py-libconf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-libensemble/package.py b/var/spack/repos/builtin/packages/py-libensemble/package.py
new file mode 100644
index 0000000000..bb06ab3b3b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-libensemble/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyLibensemble(PythonPackage):
+    """Library for managing ensemble-like collections of computations."""
+
+    homepage = "https://libensemble.readthedocs.io"
+    url      = "https://pypi.io/packages/source/l/libensemble/libensemble-0.3.0.tar.gz"
+    git      = "https://github.com/Libensemble/libensemble.git"
+
+    version('develop', branch='master')
+    version('0.3.0', sha256='c8efdf45d0da0ef6299ee778cea1c285c95972af70d3a729ee6dc855e66f9294')
+    version('0.2.0', 'ee96047594a3f5a1533f24d3b1f365f9')
+    version('0.1.0', '0c3d45dd139429de1a5273e5bd8e46ec')
+
+    depends_on('python@2.7:2.8,3.3:')
+    depends_on('py-setuptools', type='build')
+    depends_on('mpi')
+    depends_on('py-mpi4py@2.0:', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-petsc4py@3.5:', type=('build', 'run'))
+    depends_on('nlopt', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-line-profiler/package.py b/var/spack/repos/builtin/packages/py-line-profiler/package.py
index 809d9e751f..2079945405 100644
--- a/var/spack/repos/builtin/packages/py-line-profiler/package.py
+++ b/var/spack/repos/builtin/packages/py-line-profiler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-linecache2/package.py b/var/spack/repos/builtin/packages/py-linecache2/package.py
new file mode 100644
index 0000000000..1d0595d464
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-linecache2/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLinecache2(PythonPackage):
+    """Backports of the linecache module"""
+
+    homepage = "https://github.com/testing-cabal/linecache2"
+    url      = "https://pypi.io/packages/source/l/linecache2/linecache2-1.0.0.tar.gz"
+
+    version('1.0.0', '7b25d0289ec36bff1f9e63c4329ce65c')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pbr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-lit/package.py b/var/spack/repos/builtin/packages/py-lit/package.py
index aa7d58bc45..0712ccc1c2 100644
--- a/var/spack/repos/builtin/packages/py-lit/package.py
+++ b/var/spack/repos/builtin/packages/py-lit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-llvmlite/package.py b/var/spack/repos/builtin/packages/py-llvmlite/package.py
new file mode 100644
index 0000000000..9a597f7a29
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-llvmlite/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLlvmlite(PythonPackage):
+    """A lightweight LLVM python binding for writing JIT compilers"""
+
+    homepage = "http://llvmlite.readthedocs.io/en/latest/index.html"
+    url = "https://pypi.io/packages/source/l/llvmlite/llvmlite-0.23.0.tar.gz"
+
+    version('0.23.0', '6fc856576a11dbeef71de862f7c419de')
+    version('0.20.0', 'f2aa60d0981842b7930ba001b03679ab')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@2.6:2.8,3.4:', type=('build', 'run'))
+    depends_on('py-enum34', type=('build', 'run'), when='^python@:3.3.99')
+    depends_on('llvm@6.0:6.99', when='@0.23.0:')
+    depends_on('llvm@4.0:4.99', when='@0.17.0:0.20.99')
+    depends_on('binutils', type='build')
diff --git a/var/spack/repos/builtin/packages/py-lmfit/package.py b/var/spack/repos/builtin/packages/py-lmfit/package.py
index f02440c98d..7247c55cdb 100644
--- a/var/spack/repos/builtin/packages/py-lmfit/package.py
+++ b/var/spack/repos/builtin/packages/py-lmfit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-localcider/package.py b/var/spack/repos/builtin/packages/py-localcider/package.py
new file mode 100644
index 0000000000..51fc5c50e0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-localcider/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLocalcider(PythonPackage):
+    """Tools for calculating sequence properties of disordered proteins"""
+
+    homepage = "http://pappulab.github.io/localCIDER"
+    url      = "https://pypi.io/packages/source/l/localcider/localcider-0.1.14.tar.gz"
+
+    version('0.1.14', 'cd3c992595c5cb280374de3750663cfa')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy',        type=('build', 'run'))
+    depends_on('py-matplotlib',   type=('build', 'run'))
+    depends_on('py-scipy',        type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-locket/package.py b/var/spack/repos/builtin/packages/py-locket/package.py
new file mode 100644
index 0000000000..addc225fbb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-locket/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyLocket(PythonPackage):
+    """File-based locks for Python for Linux and Windows."""
+
+    homepage = "http://github.com/mwilliamson/locket.py"
+    url      = "https://pypi.io/packages/source/l/locket/locket-0.2.0.tar.gz"
+
+    import_modules = ['locket']
+
+    version('0.2.0', 'fe870949c513d8f7079ba352463833ca')
diff --git a/var/spack/repos/builtin/packages/py-lockfile/package.py b/var/spack/repos/builtin/packages/py-lockfile/package.py
index c3aec05f45..deb8c08e0d 100644
--- a/var/spack/repos/builtin/packages/py-lockfile/package.py
+++ b/var/spack/repos/builtin/packages/py-lockfile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-logilab-common/package.py b/var/spack/repos/builtin/packages/py-logilab-common/package.py
index 35e5d9aa88..20c1649c7a 100644
--- a/var/spack/repos/builtin/packages/py-logilab-common/package.py
+++ b/var/spack/repos/builtin/packages/py-logilab-common/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-lrudict/package.py b/var/spack/repos/builtin/packages/py-lrudict/package.py
new file mode 100644
index 0000000000..48a94c04e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-lrudict/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyLrudict(PythonPackage):
+    """ A fast LRU cache"""
+
+    homepage = "https://github.com/amitdev/lru-dict"
+    url      = "https://pypi.io/packages/source/l/lru-dict/lru-dict-1.1.6.tar.gz"
+
+    version('1.1.6', 'b33f54f1257ab541f4df4bacc7509f5a')
+
+    depends_on('python@2.7:')
+    depends_on('py-setuptools', type=('build'))
diff --git a/var/spack/repos/builtin/packages/py-lxml/package.py b/var/spack/repos/builtin/packages/py-lxml/package.py
index 10e2435562..63d2024e24 100644
--- a/var/spack/repos/builtin/packages/py-lxml/package.py
+++ b/var/spack/repos/builtin/packages/py-lxml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-lzstring/package.py b/var/spack/repos/builtin/packages/py-lzstring/package.py
index 8ab7658339..0302eab94d 100644
--- a/var/spack/repos/builtin/packages/py-lzstring/package.py
+++ b/var/spack/repos/builtin/packages/py-lzstring/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-macholib/package.py b/var/spack/repos/builtin/packages/py-macholib/package.py
index d6755f20ba..5a82411b16 100644
--- a/var/spack/repos/builtin/packages/py-macholib/package.py
+++ b/var/spack/repos/builtin/packages/py-macholib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-machotools/package.py b/var/spack/repos/builtin/packages/py-machotools/package.py
index d51fa17469..3ad4ca45e5 100644
--- a/var/spack/repos/builtin/packages/py-machotools/package.py
+++ b/var/spack/repos/builtin/packages/py-machotools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-macs2/package.py b/var/spack/repos/builtin/packages/py-macs2/package.py
index 9d66440373..6f0d78e33b 100644
--- a/var/spack/repos/builtin/packages/py-macs2/package.py
+++ b/var/spack/repos/builtin/packages/py-macs2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-maestrowf/package.py b/var/spack/repos/builtin/packages/py-maestrowf/package.py
new file mode 100644
index 0000000000..06857ed21d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-maestrowf/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMaestrowf(PythonPackage):
+    """A general purpose workflow conductor for running multi-step
+       simulation studies."""
+
+    homepage = "https://github.com/LLNL/maestrowf/"
+    url      = "https://github.com/LLNL/maestrowf/archive/v1.1.2.tar.gz"
+
+    version('1.1.2', 'a9e05d82910cd2dd077321fb9b0c8dcd')
+    version('1.1.1', 'd38bbf634de4f29fd01d1864ba2f70e0')
+    version('1.1.0', '3c20bf36fbb85d14c3bfdb865944a409')
+    version('1.0.1', '6838fc8bdc7ca0c1adbb6a0333f005b4')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pyyaml',     type=('build', 'run'))
+    depends_on('py-six',        type=('build', 'run'))
+    depends_on('py-enum34',     type=('build', 'run'))
+    depends_on('py-tabulate',   type=('build', 'run'), when='@1.1.0:')
+    depends_on('py-filelock',   type=('build', 'run'), when='@1.1.0:')
diff --git a/var/spack/repos/builtin/packages/py-mako/package.py b/var/spack/repos/builtin/packages/py-mako/package.py
index b6100d43bf..7bb89b2d39 100644
--- a/var/spack/repos/builtin/packages/py-mako/package.py
+++ b/var/spack/repos/builtin/packages/py-mako/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,6 @@ class PyMako(PythonPackage):
     version('1.0.1', '9f0aafd177b039ef67b90ea350497a54')
 
     depends_on('py-setuptools', type='build')
-    # depends_on('py-mock',   type='test')  # TODO: Add test deptype
-    # depends_on('py-pytest', type='test')  # TODO: Add test deptype
+    depends_on('py-mock',   type='test')
+    depends_on('py-pytest', type='test')
     depends_on('py-markupsafe@0.9.2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-mappy/package.py b/var/spack/repos/builtin/packages/py-mappy/package.py
index 27ca1cbb11..23f975dd8a 100644
--- a/var/spack/repos/builtin/packages/py-mappy/package.py
+++ b/var/spack/repos/builtin/packages/py-mappy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-markdown/package.py b/var/spack/repos/builtin/packages/py-markdown/package.py
index d6356d8a52..80f395dbc8 100644
--- a/var/spack/repos/builtin/packages/py-markdown/package.py
+++ b/var/spack/repos/builtin/packages/py-markdown/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,18 +15,20 @@ class PyMarkdown(PythonPackage):
     """
 
     homepage = "https://pythonhosted.org/Markdown/"
-    url      = "https://github.com/waylan/Python-Markdown/archive/2.6.7-final.tar.gz"
+    url      = "https://pypi.io/packages/source/m/markdown/Markdown-2.6.11.tar.gz"
 
-    version('2.6.7', 'fd27044042e197ad99249b3d60215d97')
-    version('2.6.6', '2b47a0ff7eb19ef34453fe198a0cccc4')
-    version('2.6.5', 'e4b6b65b2d6bcac07176fb209bc55614')
-    version('2.6.4', '5fb3cd9945eb534e71af597f8ee3622b')
-    version('2.6.3', 'ec7a50ce9fd4a5fd0b24555d47e9d7d1')
-    version('2.6.2', '6ce86913e9bf5bb34d9ee394ac71f044')
-    version('2.6.1', '0ae69693c5adb27caf0160941d7dcbdf')
-    version('2.6', '9acdde43d99847d0c4ef03ea56b1d2c5')
-    version('2.5.2', 'ed2a662d22799186c1ef85d173d38b8a')
-    version('2.5.1', 'be6f6ba65a8fb843d2aaf1fcdd68c755')
-    version('2.5', '8393ceab9c6e33357fb8a7be063a4849')
+    version('2.6.11', sha256='a856869c7ff079ad84a3e19cd87a64998350c2b94e9e08e44270faef33400f81')
+    version('2.6.7', sha256='daebf24846efa7ff269cfde8c41a48bb2303920c7b2c7c5e04fa82e6282d05c0')
+    version('2.6.6', sha256='9a292bb40d6d29abac8024887bcfc1159d7a32dc1d6f1f6e8d6d8e293666c504')
+    version('2.6.5', sha256='8d94cf6273606f76753fcb1324623792b3738c7612c2b180c85cc5e88642e560')
+    version('2.6.4', sha256='e436eee7aaf2a230ca3315034dd39e8a0fc27036708acaa3dd70625ec62a94ce')
+    version('2.6.3', sha256='ad75fc03c45492eba3bc63645e1e6465f65523a05fff0abf36910f810465a9af')
+    version('2.6.2', sha256='ee17d0d7dc091e645dd48302a2e21301cc68f188505c2069d8635f94554170bf')
+    version('2.6.1', sha256='b5879b87e8e5c125c92ab8c8f3babce78ad4e840446eed73c5b6e2984648d2b1')
+    version('2.6', sha256='e1c8a489bb7c7154bc5a8c14f0fd1fc356ee36c8b9988f9fd8febff22dd435da')
+    version('2.5.2', sha256='284e97e56db9ada03ede9c0ed2870ca6590ce7869f3119104d53510debf1533d')
+    version('2.5.1', sha256='8f81ed12c18608a502828acb7d318f362c42f4eca97d01e93cadfc52c1e40b73')
+    version('2.5', sha256='6ba74a1e7141c9603750d80711b639a7577bffb785708e6260090239ee5bc76d')
 
     depends_on('python@2.7:2.8,3.2:3.4')
+    depends_on('py-setuptools', type='build', when='@2.6.11:')
diff --git a/var/spack/repos/builtin/packages/py-markupsafe/package.py b/var/spack/repos/builtin/packages/py-markupsafe/package.py
index dc1bf781a0..1d681f2987 100644
--- a/var/spack/repos/builtin/packages/py-markupsafe/package.py
+++ b/var/spack/repos/builtin/packages/py-markupsafe/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-matplotlib/freetype-include-path.patch b/var/spack/repos/builtin/packages/py-matplotlib/freetype-include-path.patch
new file mode 100644
index 0000000000..7007c88d0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-matplotlib/freetype-include-path.patch
@@ -0,0 +1,16 @@
+diff --git a/setupext.py b/setupext.py
+index 6d363012eb4..00ef3fe5a3d 100644
+--- a/setupext.py
++++ b/setupext.py
+@@ -162,8 +162,10 @@ def get_include_dirs():
+     """
+     include_dirs = [os.path.join(d, 'include') for d in get_base_dirs()]
+     if sys.platform != 'win32':
+-        # gcc includes this dir automatically, so also look for headers in
++        # gcc includes these dirs automatically, so also look for headers in
+         # these dirs
++        include_dirs.extend(
++            os.environ.get('CPATH', '').split(os.pathsep))
+         include_dirs.extend(
+             os.environ.get('CPLUS_INCLUDE_PATH', '').split(os.pathsep))
+     return include_dirs
diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py
index cd9abd2bc1..b63a52d9ba 100644
--- a/var/spack/repos/builtin/packages/py-matplotlib/package.py
+++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -34,6 +15,9 @@ class PyMatplotlib(PythonPackage):
     homepage = "https://pypi.python.org/pypi/matplotlib"
     url      = "https://pypi.io/packages/source/m/matplotlib/matplotlib-2.0.2.tar.gz"
 
+    version('3.0.0', '39c7f44c8fa0f24cbf684137371ce4ae')
+    version('2.2.3', '403b0bddd751d71187416f20d4cff100')
+    version('2.2.2', 'dd1e49e041309a7fd4e32be8bf17c3b6')
     version('2.0.2', '061111784278bde89b5d4987014be4ca')
     version('2.0.0', '7aa54b06327f0e1c4f3877fc2f7d6b17')
     version('1.5.3', 'ba993b06113040fee6628d74b80af0fd')
@@ -65,8 +49,10 @@ class PyMatplotlib(PythonPackage):
     # directories (i.e., matplotlib and basemap)
     depends_on('py-setuptools', type=('build', 'run'))
 
+    depends_on('python@3.5:', when='@3:')
     depends_on('libpng@1.2:')
     depends_on('freetype@2.3:')
+    patch('freetype-include-path.patch', when='@2.2.2:2.9.9')  # Patch to pick up correct freetype headers
 
     depends_on('py-numpy@1.6:', type=('build', 'run'))
     depends_on('py-dateutil@1.1:', type=('build', 'run'))
@@ -75,6 +61,7 @@ class PyMatplotlib(PythonPackage):
     depends_on('py-cycler@0.9:', type=('build', 'run'))
     depends_on('py-subprocess32', type=('build', 'run'), when='^python@:2.7')
     depends_on('py-functools32', type=('build', 'run'), when='^python@2.7')
+    depends_on('py-kiwisolver', type=('build', 'run'), when='@2.2.0:')
 
     # ------ Optional GUI frameworks
     depends_on('tk@8.3:', when='+tk')  # not 8.6.0 or 8.6.1
@@ -86,16 +73,15 @@ class PyMatplotlib(PythonPackage):
     depends_on('image-magick', when='+animation')
 
     # --------- Optional dependencies
-    depends_on('pkg-config', type='build')    # why not...
+    depends_on('pkgconfig', type='build')    # why not...
     depends_on('pil', when='+image', type=('build', 'run'))
     depends_on('py-ipython', when='+ipython', type=('build', 'run'))
     depends_on('ghostscript', when='+latex', type='run')
     depends_on('texlive', when='+latex', type='run')
 
     # Testing dependencies
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
-    # depends_on('py-mock', type='test')
+    depends_on('py-nose', type='test')
+    depends_on('py-mock', type='test')
 
     # Required libraries that ship with matplotlib
     # depends_on('agg@2.4:')
diff --git a/var/spack/repos/builtin/packages/py-mccabe/package.py b/var/spack/repos/builtin/packages/py-mccabe/package.py
index 9a8e39f4c4..13dfddc0c4 100644
--- a/var/spack/repos/builtin/packages/py-mccabe/package.py
+++ b/var/spack/repos/builtin/packages/py-mccabe/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,9 @@ class PyMccabe(PythonPackage):
     homepage = "https://github.com/PyCQA/mccabe"
     url      = "https://github.com/PyCQA/mccabe/archive/0.5.2.tar.gz"
 
+    version('0.6.1', '0360af86f0bce7a839bd3cba517edf9c')
+    version('0.6.0', '38f46ff70b5d2c02155f8fd4d96fb791')
+    version('0.5.3', 'a75f57079ce10556fd3c63a5f6b4d706')
     version('0.5.2', '3cdf2d7faa1464b18905fe9a7063a632')
     version('0.5.1', '864b364829156701bec797712be8ece0')
     version('0.5.0', '71c0ce5e5c4676753525154f6c5d3af8')
@@ -44,9 +28,7 @@ class PyMccabe(PythonPackage):
     depends_on('python@2.7:2.8,3.3:')
 
     depends_on('py-setuptools', type='build')
-
-    # TODO: Add test dependencies
-    # depends_on('py-pytest', type='test')
+    depends_on('py-pytest', type='test')
 
     def patch(self):
         """Filter pytest-runner requirement out of setup.py."""
diff --git a/var/spack/repos/builtin/packages/py-mdanalysis/package.py b/var/spack/repos/builtin/packages/py-mdanalysis/package.py
index 437f2445a7..15f40f1861 100644
--- a/var/spack/repos/builtin/packages/py-mdanalysis/package.py
+++ b/var/spack/repos/builtin/packages/py-mdanalysis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-meep/package.py b/var/spack/repos/builtin/packages/py-meep/package.py
index a2252c3b00..0b257a64c6 100644
--- a/var/spack/repos/builtin/packages/py-meep/package.py
+++ b/var/spack/repos/builtin/packages/py-meep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-memory-profiler/package.py b/var/spack/repos/builtin/packages/py-memory-profiler/package.py
index 7bd6b70ca1..92ccc763dc 100644
--- a/var/spack/repos/builtin/packages/py-memory-profiler/package.py
+++ b/var/spack/repos/builtin/packages/py-memory-profiler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-methylcode/package.py b/var/spack/repos/builtin/packages/py-methylcode/package.py
index 00171890f5..b416b27f62 100644
--- a/var/spack/repos/builtin/packages/py-methylcode/package.py
+++ b/var/spack/repos/builtin/packages/py-methylcode/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py b/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py
new file mode 100644
index 0000000000..0d2c084142
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-mg-rast-tools/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMgRastTools(PythonPackage):
+    """Repository of scripts and libraries for using the MG-RAST API and
+    MG-RAST data."""
+
+    homepage = "https://github.com/MG-RAST/MG-RAST-Tools"
+    git      = "https://github.com/MG-RAST/MG-RAST-Tools.git"
+
+    version('2018.04.17', commit='a40c6e6539ad0bc1c08e1b03dfc0a9759755a326')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('py-setuptools@28.0:', type='build')
+    depends_on('py-prettytable@0.7:', type=('build', 'run'))
+    depends_on('py-poster@0.8.1:', type=('build', 'run'))
+    depends_on('py-requests', type=('build', 'run'))
+    depends_on('py-requests-toolbelt@0.8:', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('r-matr', type=('build', 'run'))
+    depends_on('shocklibs@0.1.30:')
+    depends_on('perl-list-moreutils', type=('build', 'run'))
+    depends_on('perl-exporter-tiny', type=('build', 'run'))
+    depends_on('perl-libwww-perl', type=('build', 'run'))
+    depends_on('perl-http-message', type=('build', 'run'))
+    depends_on('perl-json', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-misopy/package.py b/var/spack/repos/builtin/packages/py-misopy/package.py
index 6c274dbfbc..832c8ca605 100644
--- a/var/spack/repos/builtin/packages/py-misopy/package.py
+++ b/var/spack/repos/builtin/packages/py-misopy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-mistune/package.py b/var/spack/repos/builtin/packages/py-mistune/package.py
index 22b7c5e790..71378fb539 100644
--- a/var/spack/repos/builtin/packages/py-mistune/package.py
+++ b/var/spack/repos/builtin/packages/py-mistune/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-mock/package.py b/var/spack/repos/builtin/packages/py-mock/package.py
index 5600072e63..861ca10f9c 100644
--- a/var/spack/repos/builtin/packages/py-mock/package.py
+++ b/var/spack/repos/builtin/packages/py-mock/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,9 @@ class PyMock(PythonPackage):
     version('2.0.0', '0febfafd14330c9dcaa40de2d82d40ad')
     version('1.3.0', '73ee8a4afb3ff4da1b4afa287f39fdeb')
 
-    depends_on('py-pbr', type=('build', 'run'))
+    depends_on('py-pbr@0.11:', type=('build', 'run'))
+    depends_on('py-six@1.7:',  type=('build', 'run'))
+    depends_on('py-six@1.9:',  type=('build', 'run'), when='@2.0.0:')
+    # requirements.txt references @1:, but 0.4 is newest available..
+    depends_on('py-funcsigs',  type=('build', 'run'), when='^python@:3.2.99')
     depends_on('py-setuptools@17.1:', type='build')
diff --git a/var/spack/repos/builtin/packages/py-moltemplate/package.py b/var/spack/repos/builtin/packages/py-moltemplate/package.py
new file mode 100644
index 0000000000..00993fb4de
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-moltemplate/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMoltemplate(PythonPackage):
+    """Moltemplate is a general cross-platform text-based molecule builder for
+    LAMMPS."""
+
+    homepage = "http://moltemplate.org"
+    url      = "https://github.com/jewettaij/moltemplate/archive/v2.5.8.tar.gz"
+
+    version('2.5.8', '9e127a254a206222e8a31684780f8dba')
+
+    depends_on('python@2.7:',   type=('build', 'run'))
+    depends_on('py-setuptools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-mongo/package.py b/var/spack/repos/builtin/packages/py-mongo/package.py
index aa24299d2b..ae364c1a3f 100644
--- a/var/spack/repos/builtin/packages/py-mongo/package.py
+++ b/var/spack/repos/builtin/packages/py-mongo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,11 @@ class PyMongo(PythonPackage):
     """Python driver for MongoDB <http://www.mongodb.org>"""
 
     homepage = "http://github.com/mongodb/mongo-python-driver"
-    url      = "https://pypi.io/packages/source/p/pymongo/pymongo-3.3.0.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pymongo/pymongo-3.6.0.tar.gz"
 
+    version('3.6.0', '2f64fa7691c77535b72050704cc12afb')
     version('3.3.0', '42cd12a5014fb7d3e1987ca04f5c651f')
 
     depends_on('python@2.6:2.8,3.3:')
 
-    depends_on('setuptools', type='build')
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-monotonic/package.py b/var/spack/repos/builtin/packages/py-monotonic/package.py
index 3f8ba05a03..1d32f68c53 100644
--- a/var/spack/repos/builtin/packages/py-monotonic/package.py
+++ b/var/spack/repos/builtin/packages/py-monotonic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-monty/package.py b/var/spack/repos/builtin/packages/py-monty/package.py
index 8b35fb6e19..abe10c6ee7 100644
--- a/var/spack/repos/builtin/packages/py-monty/package.py
+++ b/var/spack/repos/builtin/packages/py-monty/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-more-itertools/package.py b/var/spack/repos/builtin/packages/py-more-itertools/package.py
new file mode 100644
index 0000000000..eda31ded25
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-more-itertools/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyMoreItertools(PythonPackage):
+    """Additions to the standard Python itertools package."""
+
+    homepage = "https://github.com/erikrose/more-itertools"
+    url      = "https://pypi.io/packages/source/m/more-itertools/more-itertools-4.3.0.tar.gz"
+
+    import_modules = ['more_itertools', 'more_itertools.tests']
+
+    version('4.3.0', '42157ef9b677bdf6d3609ed6eadcbd4a')
+    version('4.1.0', '246f46686d95879fbad37855c115dc52')
+    version('2.2',   'b8d328a33f966bf40bb829bcf8da35ce')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six@1.0.0:1.999', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-mpi4py/package.py b/var/spack/repos/builtin/packages/py-mpi4py/package.py
index 7193800506..aad9998201 100644
--- a/var/spack/repos/builtin/packages/py-mpi4py/package.py
+++ b/var/spack/repos/builtin/packages/py-mpi4py/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,16 +11,17 @@ class PyMpi4py(PythonPackage):
        Interface (MPI) standard. It is implemented on top of the
        MPI-1/MPI-2 specification and exposes an API which grounds on the
        standard MPI-2 C++ bindings.
-
     """
     homepage = "https://pypi.python.org/pypi/mpi4py"
-    url      = "https://pypi.io/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz"
+    url      = "https://pypi.io/packages/source/m/mpi4py/mpi4py-3.0.0.tar.gz"
+    git      = "https://github.com/mpi4py/mpi4py.git"
 
-    version('develop', git='https://github.com/mpi4py/mpi4py.git', branch='master')
+    version('develop', branch='master')
+    version('3.0.0', 'bfe19f20cef5e92f6e49e50fb627ee70')
     version('2.0.0', '4f7d8126d7367c239fd67615680990e3')
     version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c')
 
     depends_on('python@2.7:2.8,3.3:')
     depends_on('py-setuptools', type='build')
     depends_on('mpi')
-    depends_on('py-cython', when='@2.0.1:', type='build')
+    depends_on('py-cython', when='@develop', type='build')
diff --git a/var/spack/repos/builtin/packages/py-mpmath/package.py b/var/spack/repos/builtin/packages/py-mpmath/package.py
index d3250b43e5..b7bb79b0b1 100644
--- a/var/spack/repos/builtin/packages/py-mpmath/package.py
+++ b/var/spack/repos/builtin/packages/py-mpmath/package.py
@@ -1,33 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyMpmath(PythonPackage):
     """A Python library for arbitrary-precision floating-point arithmetic."""
     homepage = "http://mpmath.org"
-    url      = "https://pypi.io/packages/source/m/mpmath/mpmath-all-0.19.tar.gz"
+    url      = "https://pypi.io/packages/source/m/mpmath/mpmath-1.0.0.tar.gz"
 
-    version('0.19', 'd1b7e19dd6830d0d7b5e1bc93d46c02c')
+    version('1.0.0', '998f10cb231af62743212ca80693f1b5')
+    version('0.19', 'af5cc956b2673b33a25c3e57299bae7b')
diff --git a/var/spack/repos/builtin/packages/py-multiprocess/package.py b/var/spack/repos/builtin/packages/py-multiprocess/package.py
index 307433e759..e9c6bbc0b5 100644
--- a/var/spack/repos/builtin/packages/py-multiprocess/package.py
+++ b/var/spack/repos/builtin/packages/py-multiprocess/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-multiqc/package.py b/var/spack/repos/builtin/packages/py-multiqc/package.py
index f2b9377b1e..62547b8873 100644
--- a/var/spack/repos/builtin/packages/py-multiqc/package.py
+++ b/var/spack/repos/builtin/packages/py-multiqc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,8 @@ class PyMultiqc(PythonPackage):
     homepage = "https://multiqc.info"
     url      = "https://pypi.io/packages/source/m/multiqc/multiqc-1.0.tar.gz"
 
+    version('1.5', 'c9fc5f54a75b1d0c3e119e0db7f5fe72')
+    version('1.3', '78fef8a89c0bd40d559b10c1f736bbcd')
     version('1.0', '0b7310b3f75595e5be8099fbed2d2515')
 
     depends_on('python@2.7:')
@@ -41,8 +24,11 @@ class PyMultiqc(PythonPackage):
     depends_on('py-jinja2@2.9:', type=('build', 'run'))
     depends_on('py-lzstring', type=('build', 'run'))
     depends_on('py-future@0.14.1:', type=('build', 'run'))
-    depends_on('py-spectra', type=('build', 'run'))
+    depends_on('py-spectra@0.0.10:', type=('build', 'run'))
     depends_on('py-matplotlib', type=('build', 'run'))
     depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-pyyaml', type=('build', 'run'))
     depends_on('py-simplejson', type=('build', 'run'))
+    depends_on('py-requests', type=('build', 'run'), when='@1.5:')
+    depends_on('py-enum34', type=('build', 'run'), when='@1.5:')
+    depends_on('py-markdown', type=('build', 'run'), when='@1.5:')
diff --git a/var/spack/repos/builtin/packages/py-mx/package.py b/var/spack/repos/builtin/packages/py-mx/package.py
index 1902b33c4f..fe4ff8fff1 100644
--- a/var/spack/repos/builtin/packages/py-mx/package.py
+++ b/var/spack/repos/builtin/packages/py-mx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-mxnet/package.py b/var/spack/repos/builtin/packages/py-mxnet/package.py
index 5b7cca85ef..9d11ce9e20 100644
--- a/var/spack/repos/builtin/packages/py-mxnet/package.py
+++ b/var/spack/repos/builtin/packages/py-mxnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-myhdl/package.py b/var/spack/repos/builtin/packages/py-myhdl/package.py
index 69bf8d04b6..38f03691e0 100644
--- a/var/spack/repos/builtin/packages/py-myhdl/package.py
+++ b/var/spack/repos/builtin/packages/py-myhdl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-mysqldb1/package.py b/var/spack/repos/builtin/packages/py-mysqldb1/package.py
index b3d17c543a..989ddc6679 100644
--- a/var/spack/repos/builtin/packages/py-mysqldb1/package.py
+++ b/var/spack/repos/builtin/packages/py-mysqldb1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-natsort/package.py b/var/spack/repos/builtin/packages/py-natsort/package.py
new file mode 100644
index 0000000000..958f0c1d5f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-natsort/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyNatsort(PythonPackage):
+    """Simple yet flexible natural sorting in Python."""
+
+    homepage = "https://pypi.org/project/natsort/"
+    url = "https://github.com/SethMMorton/natsort/archive/5.2.0.zip"
+
+    version('5.2.0', '2ed2826550eef1f9ea3dd04f08b5da8b')
+    version('5.1.1', '0525d4897fc98f40df5cc5a4a05f3c82')
+    version('5.1.0', '518688548936d548775fb00afba999fb')
+    version('5.0.3', '11147d75693995a946656927df7617d0')
+    version('5.0.2', '1eb11a69086a5fb21d03f8189f1afed3')
+    version('5.0.1', 'ca21c728bb3dd5dcfb010fa50b9c5e3c')
+    version('5.0.0', 'fc7800fea50dcccbf8b116e1dff2ebf8')
+    version('4.0.4', '7478ba31ec7fe554fcbfda41bb01f5ef')
+    version('4.0.3', '2dc4fb1eb6ebfe4c9d95a12c2406df33')
+    version('4.0.1', '659cf6ce95951003de0c85fc80b9f135')
+
+    depends_on('py-setuptools', type=('build'))
diff --git a/var/spack/repos/builtin/packages/py-nbconvert/package.py b/var/spack/repos/builtin/packages/py-nbconvert/package.py
index ea93c618c7..e6dc35441f 100644
--- a/var/spack/repos/builtin/packages/py-nbconvert/package.py
+++ b/var/spack/repos/builtin/packages/py-nbconvert/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-nbformat/package.py b/var/spack/repos/builtin/packages/py-nbformat/package.py
index 5f7ca27008..48f20262f2 100644
--- a/var/spack/repos/builtin/packages/py-nbformat/package.py
+++ b/var/spack/repos/builtin/packages/py-nbformat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-neo/package.py b/var/spack/repos/builtin/packages/py-neo/package.py
index 03a060dec4..b1ea797753 100644
--- a/var/spack/repos/builtin/packages/py-neo/package.py
+++ b/var/spack/repos/builtin/packages/py-neo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class PyNeo(PythonPackage):
     homepage = "http://neuralensemble.org/neo"
     url      = "https://pypi.io/packages/source/n/neo/neo-0.4.1.tar.gz"
 
+    version('0.5.2', 'e2b55b112ae245f24cc8ad63cfef986c')
     version('0.4.1', 'f706df3a1bce835cb490b812ac198a6e')
 
     depends_on('py-setuptools',        type='build')
diff --git a/var/spack/repos/builtin/packages/py-nestle/package.py b/var/spack/repos/builtin/packages/py-nestle/package.py
index ff64b08716..2796de3333 100644
--- a/var/spack/repos/builtin/packages/py-nestle/package.py
+++ b/var/spack/repos/builtin/packages/py-nestle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-netcdf4/package.py b/var/spack/repos/builtin/packages/py-netcdf4/package.py
index 73e0d38586..5099183816 100644
--- a/var/spack/repos/builtin/packages/py-netcdf4/package.py
+++ b/var/spack/repos/builtin/packages/py-netcdf4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-netifaces/package.py b/var/spack/repos/builtin/packages/py-netifaces/package.py
index fcdbf80092..3120e2b13f 100644
--- a/var/spack/repos/builtin/packages/py-netifaces/package.py
+++ b/var/spack/repos/builtin/packages/py-netifaces/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py
index 528fe59a01..b499ca9c4e 100644
--- a/var/spack/repos/builtin/packages/py-networkx/package.py
+++ b/var/spack/repos/builtin/packages/py-networkx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,11 @@ class PyNetworkx(PythonPackage):
     homepage = "http://networkx.github.io/"
     url      = "https://pypi.io/packages/source/n/networkx/networkx-1.11.tar.gz"
 
-    version('1.11', '6ef584a879e9163013e9a762e1cf7cd1')
-    version('1.10', 'eb7a065e37250a4cc009919dacfe7a9d')
+    version('2.1', sha256='64272ca418972b70a196cb15d9c85a5a6041f09a2f32e0d30c0255f25d458bb1',
+            url='https://pypi.io/packages/source/n/networkx/networkx-2.1.zip')
+    version('1.11', md5='6ef584a879e9163013e9a762e1cf7cd1')
+    version('1.10', md5='eb7a065e37250a4cc009919dacfe7a9d')
 
     depends_on('py-decorator', type=('build', 'run'))
+    depends_on('py-decorator@4.1.0:', type=('build', 'run'), when='@2.1:')
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-nose/package.py b/var/spack/repos/builtin/packages/py-nose/package.py
index 566808b711..636d1d2195 100644
--- a/var/spack/repos/builtin/packages/py-nose/package.py
+++ b/var/spack/repos/builtin/packages/py-nose/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-nosexcover/package.py b/var/spack/repos/builtin/packages/py-nosexcover/package.py
index 7625a39d99..45da661a20 100644
--- a/var/spack/repos/builtin/packages/py-nosexcover/package.py
+++ b/var/spack/repos/builtin/packages/py-nosexcover/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-numba/package.py b/var/spack/repos/builtin/packages/py-numba/package.py
new file mode 100644
index 0000000000..550ac571a8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-numba/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyNumba(PythonPackage):
+    """NumPy aware dynamic Python compiler using LLVM"""
+
+    homepage = "https://numba.pydata.org/"
+    url      = "https://pypi.io/packages/source/n/numba/numba-0.35.0.tar.gz"
+
+    version('0.35.0', '4f447383406f54aaf18ffaba3a0e79e8')
+
+    depends_on('py-numpy@1.10:',    type=('build', 'run'))
+    depends_on('py-llvmlite@0.20:', type=('build', 'run'))
+    depends_on('py-argparse',       type=('build', 'run'))
+    depends_on('py-funcsigs',       type=('build', 'run'), when='^python@:3.3.99')
+    depends_on('py-singledispatch', type=('build', 'run'), when='^python@:3.3.99')
+
+    # Version 6.0.0 of llvm had a hidden symbol which breaks numba at runtime.
+    # See https://reviews.llvm.org/D44140
+    conflicts('^llvm@6.0.0')
diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py
index 6db50bf00d..9695afb50c 100644
--- a/var/spack/repos/builtin/packages/py-numexpr/package.py
+++ b/var/spack/repos/builtin/packages/py-numexpr/package.py
@@ -1,35 +1,17 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyNumexpr(PythonPackage):
     """Fast numerical expression evaluator for NumPy"""
     homepage = "https://pypi.python.org/pypi/numexpr"
-    url      = "https://pypi.io/packages/source/n/numexpr/numexpr-2.6.1.tar.gz"
+    url      = "https://pypi.io/packages/source/n/numexpr/numexpr-2.6.5.tar.gz"
 
+    version('2.6.5', 'c9b5859c11bd6da092f6c8a84a472e77')
     version('2.6.1', '6365245705b446426df9543ad218dd8e')
     version('2.5',   '84f66cced45ba3e30dcf77a937763aaa')
     version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd')
diff --git a/var/spack/repos/builtin/packages/py-numexpr3/package.py b/var/spack/repos/builtin/packages/py-numexpr3/package.py
new file mode 100644
index 0000000000..9b5f1e7dd5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-numexpr3/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyNumexpr3(PythonPackage):
+    """Numexpr3 is a fast numerical expression evaluator for NumPy. With it,
+    expressions that operate on arrays (like "3*a+4*b") are accelerated and
+    use less memory than doing the same calculation in Python.
+    In addition, its multi-threaded capabilities can make use of all your
+    cores, which may accelerate computations, most specially if they are not
+    memory-bounded (e.g. those using transcendental functions).
+    Compared to NumExpr 2.6, functions have been re-written in a fashion such
+    that gcc can auto-vectorize them with SIMD instruction sets such as
+    SSE2 or AVX2, if your processor supports them. Use of a newer version of
+    gcc such as 5.4 is strongly recommended."""
+    homepage = "https://github.com/pydata/numexpr/tree/numexpr-3.0"
+    url = "https://pypi.io/packages/source/n/numexpr3/numexpr3-3.0.1a1.tar.gz"
+
+    version('3.0.1.a1', '9fa8dc59b149aa1956fc755f982a78ad')
+    # TODO: Add CMake build system for better control of passing flags related
+    # to CPU ISA.
+
+    depends_on('python@2.6:2.8,3.3:', type=('build', 'run'))
+    depends_on('py-numpy@1.7:', type=('build', 'run'))
+    depends_on('py-setuptools@18.2:', type='build')
diff --git a/var/spack/repos/builtin/packages/py-numpy/package.py b/var/spack/repos/builtin/packages/py-numpy/package.py
index f5126e36a0..39fb4f0c4c 100644
--- a/var/spack/repos/builtin/packages/py-numpy/package.py
+++ b/var/spack/repos/builtin/packages/py-numpy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import platform
 
@@ -34,7 +15,7 @@ class PyNumpy(PythonPackage):
     number capabilities"""
 
     homepage = "http://www.numpy.org/"
-    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.13.1.zip"
+    url      = "https://pypi.io/packages/source/n/numpy/numpy-1.15.1.zip"
 
     install_time_test_callbacks = ['install_test', 'import_module_test']
 
@@ -45,9 +26,13 @@ class PyNumpy(PythonPackage):
         'numpy.distutils.command', 'numpy.distutils.fcompiler'
     ]
 
-    # FIXME: numpy._build_utils and numpy.core.code_generators failed to import
-    # FIXME: Is this expected?
-
+    version('1.15.2', sha256='27a0d018f608a3fe34ac5e2b876f4c23c47e38295c47dd0775cc294cd2614bc1')
+    version('1.15.1', '898004d5be091fde59ae353e3008fe9b')
+    version('1.14.3', '97416212c0a172db4bc6b905e9c4634b')
+    version('1.14.2', '080f01a19707cf467393e426382c7619')
+    version('1.14.1', 'b8324ef90ac9064cd0eac46b8b388674')
+    version('1.14.0', 'c12d4bf380ac925fcdc8a59ada6c3298')
+    version('1.13.3', '300a6f0528122128ac07c6deb5c95917')
     version('1.13.1', '2c3c0f4edf720c3a7b525dacc825b9ae')
     version('1.13.0', 'fd044f0b8079abeaf5e6d2e93b2c1d03')
     version('1.12.1', 'c75b072a984028ac746a6a332c209a91')
@@ -62,25 +47,21 @@ class PyNumpy(PythonPackage):
     variant('blas',   default=True, description='Build with BLAS support')
     variant('lapack', default=True, description='Build with LAPACK support')
 
-    depends_on('python@2.7:2.8,3.4:')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
     depends_on('blas',   when='+blas')
     depends_on('lapack', when='+lapack')
 
-    # Tests require:
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose@1.0.0:', type='test')
+    depends_on('py-nose@1.0.0:', when='@:1.14', type='test')
+    depends_on('py-pytest', when='@1.15:', type='test')
 
     def setup_dependent_package(self, module, dependent_spec):
         python_version = self.spec['python'].version.up_to(2)
-        arch = '{0}-{1}'.format(platform.system().lower(), platform.machine())
 
         self.spec.include = join_path(
             self.prefix.lib,
             'python{0}'.format(python_version),
             'site-packages',
-            'numpy-{0}-py{1}-{2}.egg'.format(
-                self.spec.version, python_version, arch),
             'numpy/core/include')
 
     def patch(self):
@@ -145,12 +126,27 @@ class PyNumpy(PythonPackage):
     def build_args(self, spec, prefix):
         args = []
 
-        # From NumPy 1.10.0 on it's possible to do a parallel build
+        # From NumPy 1.10.0 on it's possible to do a parallel build.
         if self.version >= Version('1.10.0'):
-            args = ['-j', str(make_jobs)]
+            # But Parallel build in Python 3.5+ is broken.  See:
+            # https://github.com/spack/spack/issues/7927
+            # https://github.com/scipy/scipy/issues/7112
+            if spec['python'].version < Version('3.5'):
+                args = ['-j', str(make_jobs)]
 
         return args
 
+    def setup_environment(self, spack_env, run_env):
+        python_version = self.spec['python'].version.up_to(2)
+
+        include_path = join_path(
+            self.prefix.lib,
+            'python{0}'.format(python_version),
+            'site-packages',
+            'numpy/core/include')
+
+        run_env.prepend_path('CPATH', include_path)
+
     def test(self):
         # `setup.py test` is not supported.  Use one of the following
         # instead:
@@ -167,5 +163,5 @@ class PyNumpy(PythonPackage):
         # ImportError: Error importing numpy: you should not try to import
         #       numpy from its source directory; please exit the numpy
         #       source tree, and relaunch your python interpreter from there.
-        with working_dir('..'):
+        with working_dir('spack-test', create=True):
             python('-c', 'import numpy; numpy.test("full", verbose=2)')
diff --git a/var/spack/repos/builtin/packages/py-numpydoc/package.py b/var/spack/repos/builtin/packages/py-numpydoc/package.py
index f0ecfbc411..48512b1943 100644
--- a/var/spack/repos/builtin/packages/py-numpydoc/package.py
+++ b/var/spack/repos/builtin/packages/py-numpydoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-olefile/package.py b/var/spack/repos/builtin/packages/py-olefile/package.py
index 0925f67d96..3430f4360a 100644
--- a/var/spack/repos/builtin/packages/py-olefile/package.py
+++ b/var/spack/repos/builtin/packages/py-olefile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py
index d2e868c7c5..e31eeccefc 100644
--- a/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py
+++ b/var/spack/repos/builtin/packages/py-ont-fast5-api/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-openpmd-validator/package.py b/var/spack/repos/builtin/packages/py-openpmd-validator/package.py
new file mode 100644
index 0000000000..64c33b8614
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-openpmd-validator/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyOpenpmdValidator(PythonPackage):
+    """Validator and Example Scripts for the openPMD markup.
+
+    openPMD is an open standard for particle-mesh data files."""
+
+    homepage = "http://www.openPMD.org"
+    url      = "https://github.com/openPMD/openPMD-validator/archive/1.0.0.2.tar.gz"
+    maintainers = ['ax3l']
+
+    version('1.0.0.2', '2b71b786288c1e7a2134bd6818ad1999')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-numpy@1.6.1:', type=('build', 'run'))
+    depends_on('py-dateutil@2.3.0:', type=('build', 'run'))
+    depends_on('py-h5py@2.0.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py
index 6f28526b8e..b61118426e 100644
--- a/var/spack/repos/builtin/packages/py-openpyxl/package.py
+++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-openslide-python/package.py b/var/spack/repos/builtin/packages/py-openslide-python/package.py
new file mode 100644
index 0000000000..5fcefccc7d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-openslide-python/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyOpenslidePython(PythonPackage):
+    """OpenSlide Python is a Python interface to the OpenSlide library."""
+
+    homepage = "https://github.com/openslide/openslide-python"
+    url      = "https://github.com/openslide/openslide-python/archive/v1.1.1.tar.gz"
+
+    version('1.1.1', '8c207e48069887b63ea1c7bc9eb7dfc0')
+
+    import_modules = ['openslide']
+
+    depends_on('openslide@3.4.0:')
+    depends_on('python@2.6:2.8,3.3:')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pillow+jpeg+jpeg2000+tiff', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-opentuner/package.py b/var/spack/repos/builtin/packages/py-opentuner/package.py
new file mode 100644
index 0000000000..77071a7c0d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-opentuner/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyOpentuner(PythonPackage):
+    """An extensible framework for program autotuning."""
+
+    homepage = "http://opentuner.org/"
+    git      = "https://github.com/jansel/opentuner.git"
+
+    version('0.8.0', commit='4cb9135')
+
+    # No support for Python 3 yet
+    depends_on('python@2.7:2.8', type=('build', 'run'))
+
+    depends_on('py-argparse@1.2.1:', type=('build', 'run'))
+    depends_on('py-fn@0.2.12:', type=('build', 'run'))
+    depends_on('py-numpy@1.8.0:', type=('build', 'run'))
+    depends_on('py-pysqlite@2.6.3:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-sqlalchemy@0.8.2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-ordereddict/package.py b/var/spack/repos/builtin/packages/py-ordereddict/package.py
index 16587ba978..6167607cc7 100644
--- a/var/spack/repos/builtin/packages/py-ordereddict/package.py
+++ b/var/spack/repos/builtin/packages/py-ordereddict/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-oset/package.py b/var/spack/repos/builtin/packages/py-oset/package.py
index 10a5007932..808f785eb4 100644
--- a/var/spack/repos/builtin/packages/py-oset/package.py
+++ b/var/spack/repos/builtin/packages/py-oset/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-owslib/package.py b/var/spack/repos/builtin/packages/py-owslib/package.py
new file mode 100644
index 0000000000..dfb2372d8f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-owslib/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyOwslib(PythonPackage):
+    """OWSLib is a Python package for client programming with Open Geospatial
+    Consortium (OGC) web service (hence OWS) interface standards, and their
+    related content models."""
+
+    homepage = "http://http://geopython.github.io/OWSLib/#installation"
+    url      = "https://pypi.io/packages/source/O/OWSLib/OWSLib-0.16.0.tar.gz"
+
+    version('0.16.0', '7ff9c9edde95eadeb27ea8d8fbd1a2cf')
+
+    depends_on('py-setuptools',     type='build')
+    depends_on('py-dateutil@1.5:',  type=('build', 'run'))
+    depends_on('py-pytz',           type=('build', 'run'))
+    depends_on('py-requests@1.0:',  type=('build', 'run'))
+    depends_on('py-proj',           type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-packaging/package.py b/var/spack/repos/builtin/packages/py-packaging/package.py
index 0ee13a5cdf..71253f1689 100644
--- a/var/spack/repos/builtin/packages/py-packaging/package.py
+++ b/var/spack/repos/builtin/packages/py-packaging/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,11 @@ class PyPackaging(PythonPackage):
     """Core utilities for Python packages."""
 
     homepage = "https://github.com/pypa/packaging"
-    url      = "https://pypi.io/packages/source/p/packaging/packaging-16.8.tar.gz"
+    url      = "https://pypi.io/packages/source/p/packaging/packaging-17.1.tar.gz"
 
     import_modules = ['packaging']
 
+    version('17.1', '8baf8241d1b6b0a5fae9b00f359976a8')
     version('16.8', '53895cdca04ecff80b54128e475b5d3b')
 
     # Not needed for the installation, but used at runtime
diff --git a/var/spack/repos/builtin/packages/py-palettable/package.py b/var/spack/repos/builtin/packages/py-palettable/package.py
index 65b7a9a27b..9bef932156 100644
--- a/var/spack/repos/builtin/packages/py-palettable/package.py
+++ b/var/spack/repos/builtin/packages/py-palettable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py
index b6d8403502..3267ec1cd6 100644
--- a/var/spack/repos/builtin/packages/py-pandas/package.py
+++ b/var/spack/repos/builtin/packages/py-pandas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,6 +19,9 @@ class PyPandas(PythonPackage):
     homepage = "http://pandas.pydata.org/"
     url = "https://pypi.io/packages/source/p/pandas/pandas-0.19.0.tar.gz"
 
+    version('0.23.4', sha256='5b24ca47acf69222e82530e89111dd9d14f9b970ab2cd3a1c2c78f0c4fbba4f4')
+    version('0.21.1', '42ae7f81b81a86c3f91f663b66c525f7')
+    version('0.19.2', '26df3ef7cd5686fa284321f4f48b38cd')
     version('0.19.0', 'bc9bb7188e510b5d44fbdd249698a2c3')
     version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6')
     version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8')
diff --git a/var/spack/repos/builtin/packages/py-paramiko/package.py b/var/spack/repos/builtin/packages/py-paramiko/package.py
index 90784be649..e0650560f0 100644
--- a/var/spack/repos/builtin/packages/py-paramiko/package.py
+++ b/var/spack/repos/builtin/packages/py-paramiko/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-partd/package.py b/var/spack/repos/builtin/packages/py-partd/package.py
new file mode 100644
index 0000000000..425b5566d7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-partd/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPartd(PythonPackage):
+    """Key-value byte store with appendable values."""
+
+    homepage = "http://github.com/dask/partd/"
+    url      = "https://pypi.io/packages/source/p/partd/partd-0.3.8.tar.gz"
+
+    import_modules = ['partd']
+
+    version('0.3.8', '554d0e6511c0df4c907f034858be847f')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-locket', type=('build', 'run'))
+    depends_on('py-toolz', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pathlib2/package.py b/var/spack/repos/builtin/packages/py-pathlib2/package.py
index f5cf9cf381..e8dfd995aa 100644
--- a/var/spack/repos/builtin/packages/py-pathlib2/package.py
+++ b/var/spack/repos/builtin/packages/py-pathlib2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,13 @@ class PyPathlib2(PythonPackage):
     """Backport of pathlib from python 3.4"""
 
     homepage = "https://pypi.python.org/pypi/pathlib2"
-    url      = "https://pypi.io/packages/source/p/pathlib2/pathlib2-2.1.0.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pathlib2/pathlib2-2.3.2.tar.gz"
+
+    import_modules = ['pathlib2']
 
+    version('2.3.2', 'fd76fb5d0baa798bfe12fb7965da97f8')
     version('2.1.0', '38e4f58b4d69dfcb9edb49a54a8b28d2')
 
     depends_on('py-setuptools', type='build')
-    depends_on('python@:3.3')
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-scandir', when='^python@:3.4', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pathos/package.py b/var/spack/repos/builtin/packages/py-pathos/package.py
index 1ebbae5cf2..5c713c3e0b 100644
--- a/var/spack/repos/builtin/packages/py-pathos/package.py
+++ b/var/spack/repos/builtin/packages/py-pathos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pathspec/package.py b/var/spack/repos/builtin/packages/py-pathspec/package.py
index 8857ee40f5..8320b653f0 100644
--- a/var/spack/repos/builtin/packages/py-pathspec/package.py
+++ b/var/spack/repos/builtin/packages/py-pathspec/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-patsy/package.py b/var/spack/repos/builtin/packages/py-patsy/package.py
index 1b60b76cd7..44882fed93 100644
--- a/var/spack/repos/builtin/packages/py-patsy/package.py
+++ b/var/spack/repos/builtin/packages/py-patsy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,4 @@ class PyPatsy(PythonPackage):
     depends_on('py-scipy',       type=('build', 'run'), when="+splines")
     depends_on('py-six',         type=('build', 'run'))
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
+    depends_on('py-nose', type='test')
diff --git a/var/spack/repos/builtin/packages/py-pbr/package.py b/var/spack/repos/builtin/packages/py-pbr/package.py
index 4ada322c89..edb79072c3 100644
--- a/var/spack/repos/builtin/packages/py-pbr/package.py
+++ b/var/spack/repos/builtin/packages/py-pbr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,8 @@ class PyPbr(PythonPackage):
     homepage = "https://pypi.python.org/pypi/pbr"
     url      = "https://pypi.io/packages/source/p/pbr/pbr-1.10.0.tar.gz"
 
+    version('3.1.1', '4e82c2e07af544c56a5b71c801525b00')
+    version('2.0.0', 'dfc1c3788eff06acfaade6f1655fa490')
     version('1.10.0', '8e4968c587268f030e38329feb9c8f17')
     version('1.8.1', 'c8f9285e1a4ca6f9654c529b158baa3a')
 
diff --git a/var/spack/repos/builtin/packages/py-pep8-naming/package.py b/var/spack/repos/builtin/packages/py-pep8-naming/package.py
new file mode 100644
index 0000000000..796e18a18f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pep8-naming/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPep8Naming(PythonPackage):
+    """Check PEP-8 naming conventions, plugin for flake8."""
+
+    homepage = "https://pypi.org/project/pep8-naming/"
+    url      = "https://files.pythonhosted.org/packages/3e/4a/125425d6b1e017f48dfc9c961f4bb9510168db7a090618906c750184ed03/pep8-naming-0.7.0.tar.gz"
+
+    extends('python', ignore='bin/(flake8|pyflakes|pycodestyle)')
+    version('0.7.0', '624258e0dd06ef32a9daf3c36cc925ff7314da7233209c5b01f7e5cdd3c34826')
+
+    depends_on('py-flake8-polyfill', type='run')
diff --git a/var/spack/repos/builtin/packages/py-perf/package.py b/var/spack/repos/builtin/packages/py-perf/package.py
new file mode 100644
index 0000000000..4925611f02
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-perf/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPerf(PythonPackage):
+    """The Python perf module is a toolkit to write, run and
+    analyze benchmarks.
+    """
+
+    homepage = "https://pypi.python.org/pypi/perf"
+    url = "https://github.com/vstinner/perf/archive/1.5.1.tar.gz"
+
+    version('1.5.1', 'e3dc532fdbaf44f2d921556164bd74e5')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-performance/package.py b/var/spack/repos/builtin/packages/py-performance/package.py
new file mode 100644
index 0000000000..445c365025
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-performance/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPerformance(PythonPackage):
+    """The performance project is intended to be an authoritative source
+    of benchmarks for all Python implementations.
+
+    The focus is on real-world benchmarks, rather than synthetic benchmarks,
+    using whole applications when possible.
+    """
+
+    homepage = 'http://pyperformance.readthedocs.io/'
+    url = 'https://github.com/python/performance/archive/0.6.1.tar.gz'
+
+    version('0.6.1', '95477b584a284582b66c922a5335b427')
+    version('0.6.0', 'b93661e07668fa0b461236dca164eedf')
+
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-perf', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-periodictable/package.py b/var/spack/repos/builtin/packages/py-periodictable/package.py
index 6b6cd2ecf5..0d51387392 100644
--- a/var/spack/repos/builtin/packages/py-periodictable/package.py
+++ b/var/spack/repos/builtin/packages/py-periodictable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-petsc4py/package.py b/var/spack/repos/builtin/packages/py-petsc4py/package.py
index 383c11fd94..4e4d00f139 100644
--- a/var/spack/repos/builtin/packages/py-petsc4py/package.py
+++ b/var/spack/repos/builtin/packages/py-petsc4py/package.py
@@ -1,38 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyPetsc4py(PythonPackage):
     """This package provides Python bindings for the PETSc package.
     """
+
     homepage = "https://pypi.python.org/pypi/petsc4py"
-    url      = "https://pypi.io/packages/source/p/petsc4py/petsc4py-3.7.0.tar.gz"
+    url      = "https://pypi.io/packages/source/p/petsc4py/petsc4py-3.8.1.tar.gz"
 
+    version('3.8.1', '5157220c2b81765c581d2b17c03259f8')
+    version('3.8.0', '02029be4bdec904854f0e0692005fb06')
     version('3.7.0', '816a20040a6a477bd637f397c9fb5b6d')
 
+    depends_on('python@2.6:2.8,3.3:', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
+    depends_on('py-numpy', type=('build', 'run'))
     depends_on('py-mpi4py', type=('build', 'run'))
     depends_on('petsc+mpi')
diff --git a/var/spack/repos/builtin/packages/py-pexpect/package.py b/var/spack/repos/builtin/packages/py-pexpect/package.py
index 8900698f00..85ed20ac81 100644
--- a/var/spack/repos/builtin/packages/py-pexpect/package.py
+++ b/var/spack/repos/builtin/packages/py-pexpect/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-phonopy/package.py b/var/spack/repos/builtin/packages/py-phonopy/package.py
index fd45d7db28..0e939406a6 100644
--- a/var/spack/repos/builtin/packages/py-phonopy/package.py
+++ b/var/spack/repos/builtin/packages/py-phonopy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pickleshare/package.py b/var/spack/repos/builtin/packages/py-pickleshare/package.py
index da8bdccb5e..c2b61fb28d 100644
--- a/var/spack/repos/builtin/packages/py-pickleshare/package.py
+++ b/var/spack/repos/builtin/packages/py-pickleshare/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-picrust/package.py b/var/spack/repos/builtin/packages/py-picrust/package.py
new file mode 100644
index 0000000000..347f199441
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-picrust/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPicrust(PythonPackage):
+    """bioinformatics software package designed to predict metagenome
+        functional content from marker gene surveys and full genomes."""
+
+    homepage = "http://picrust.github.io/picrust/index.html"
+    url      = "https://github.com/picrust/picrust/releases/download/v1.1.3/picrust-1.1.3.tar.gz"
+
+    version('1.1.3', sha256='7538c8544899b8855deb73a2d7a4ccac4808ff294e161530a8c8762d472d8906')
+
+    depends_on('python@2.7:2.999', type=('build', 'run'))
+    depends_on('py-cogent@1.5.3', type=('build', 'run'))
+    depends_on('py-biom-format@2.1.4:2.1.999', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-future@0.16.0', type=('build', 'run'))
+    depends_on('py-numpy@1.5.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pil/package.py b/var/spack/repos/builtin/packages/py-pil/package.py
index 332a7e91ee..4bbecf9a47 100644
--- a/var/spack/repos/builtin/packages/py-pil/package.py
+++ b/var/spack/repos/builtin/packages/py-pil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pillow/package.py b/var/spack/repos/builtin/packages/py-pillow/package.py
index 3b54ee32ae..2bce199940 100644
--- a/var/spack/repos/builtin/packages/py-pillow/package.py
+++ b/var/spack/repos/builtin/packages/py-pillow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -33,17 +14,10 @@ class PyPillow(PythonPackage):
     capabilities."""
 
     homepage = "https://python-pillow.org/"
-    url = "https://pypi.io/packages/source/P/Pillow/Pillow-3.0.0.tar.gz"
-
-    # TODO: This version should be deleted once the next release comes out.
-    # TODO: It fixes a bug that prevented us from linking to Tk/Tcl.
-    # TODO: Tk/Tcl support is necessary for tkinter bitmap and photo images.
-    # TODO: If you require this support, run the following command:
-    # TODO:     `spack install py-pillow@3.3.0.dev0 ^python+tk`
-    version('3.3.0.dev0', git='https://github.com/python-pillow/Pillow.git',
-            commit='30eced62868141a6c859a4370efd40b9434a7c3f')
+    url = "https://pypi.io/packages/source/P/Pillow/Pillow-5.1.0.tar.gz"
 
-    version('3.2.0', '7cfd093c11205d9e2ebe3c51dfcad510', preferred=True)
+    version('5.1.0', '308f9c13b376abce96ab6ebd6c889cc4')
+    version('3.2.0', '7cfd093c11205d9e2ebe3c51dfcad510')
     version('3.0.0', 'fc8ac44e93da09678eac7e30c9b7377d')
 
     provides('pil')
@@ -54,8 +28,7 @@ class PyPillow(PythonPackage):
     variant('tiff', default=False, description='Access to TIFF files')
     variant('freetype', default=False, description='Font related services')
     variant('lcms', default=False, description='Color management')
-    variant('jpeg2000', default=False,
-            description='Provide JPEG 2000 functionality')
+    variant('jpeg2000', default=False, description='Provide JPEG 2000 functionality')
 
     # Spack does not (yet) support these modes of building
     # variant('webp', default=False, description='Provide the WebP format')
@@ -94,8 +67,8 @@ class PyPillow(PythonPackage):
 
         if '+jpeg' in spec:
             setup.filter('JPEG_ROOT = None',
-                         'JPEG_ROOT = ("{0}", "{1}")'.format(
-                             spec['jpeg'].prefix.lib,
+                         'JPEG_ROOT=("{0}","{1}")'.format(
+                             spec['jpeg'].libs.directories[0],
                              spec['jpeg'].prefix.include))
         if '+zlib' in spec:
             setup.filter('ZLIB_ROOT = None',
diff --git a/var/spack/repos/builtin/packages/py-pip/package.py b/var/spack/repos/builtin/packages/py-pip/package.py
index d0da3dd153..def321c229 100644
--- a/var/spack/repos/builtin/packages/py-pip/package.py
+++ b/var/spack/repos/builtin/packages/py-pip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PyPip(PythonPackage):
     homepage = "https://pypi.python.org/pypi/pip"
     url      = "https://pypi.io/packages/source/p/pip/pip-9.0.1.tar.gz"
 
+    version('10.0.1', '83a177756e2c801d0b3a6f7b0d4f3f7e')
     version('9.0.1', '35f01da33009719497f01a4ba69d63c9')
 
     depends_on('python@2.6:2.8,3.3:')
diff --git a/var/spack/repos/builtin/packages/py-pipits/package.py b/var/spack/repos/builtin/packages/py-pipits/package.py
index e24f4718db..beef939772 100644
--- a/var/spack/repos/builtin/packages/py-pipits/package.py
+++ b/var/spack/repos/builtin/packages/py-pipits/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pkgconfig/package.py b/var/spack/repos/builtin/packages/py-pkgconfig/package.py
index eb3be23871..ccab4d8cad 100644
--- a/var/spack/repos/builtin/packages/py-pkgconfig/package.py
+++ b/var/spack/repos/builtin/packages/py-pkgconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,6 @@ class PyPkgconfig(PythonPackage):
     depends_on('python@2.6:')
     depends_on('py-setuptools', type='build')
 
-    depends_on('pkg-config', type=('build', 'run'))
+    depends_on('pkgconfig', type=('build', 'run'))
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose@1.0:', type='test')
+    depends_on('py-nose@1.0:', type=('build', 'test'))
diff --git a/var/spack/repos/builtin/packages/py-plotly/package.py b/var/spack/repos/builtin/packages/py-plotly/package.py
new file mode 100644
index 0000000000..6ad7a68a7e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-plotly/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPlotly(PythonPackage):
+    """An interactive, browser-based graphing library for Python"""
+
+    homepage = "https://plot.ly/python/"
+    url      = "https://github.com/plotly/plotly.py/archive/v2.2.0.tar.gz"
+
+    version('2.2.0', '835802cdc6743439ff993447dfe47a0e')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-requests@2.3.0', type=('build', 'run'))
+    depends_on('py-six@1.8.0', type=('build', 'run'))
+    depends_on('py-pytz@2014.9', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pluggy/package.py b/var/spack/repos/builtin/packages/py-pluggy/package.py
new file mode 100644
index 0000000000..62e50a6710
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pluggy/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPluggy(PythonPackage):
+    """Plugin and hook calling mechanisms for python."""
+
+    homepage = "https://github.com/pytest-dev/pluggy"
+    url      = "https://pypi.io/packages/source/p/pluggy/pluggy-0.7.1.tar.gz"
+
+    import_modules = ['pluggy']
+
+    version('0.7.1', 'cd5cc1003143f86dd6e2a865a20f8837')
+    version('0.6.0', 'ffdde7c3a5ba9a440404570366ffb6d5')
+
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools-scm', type='build')
diff --git a/var/spack/repos/builtin/packages/py-ply/package.py b/var/spack/repos/builtin/packages/py-ply/package.py
index f1ccd85c3f..38d81ee10d 100644
--- a/var/spack/repos/builtin/packages/py-ply/package.py
+++ b/var/spack/repos/builtin/packages/py-ply/package.py
@@ -1,33 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyPly(PythonPackage):
     """PLY is nothing more than a straightforward lex/yacc implementation."""
     homepage = "http://www.dabeaz.com/ply"
-    url      = "http://www.dabeaz.com/ply/ply-3.8.tar.gz"
+    url      = "https://github.com/dabeaz/ply/archive/3.11.tar.gz"
 
-    version('3.8', '94726411496c52c87c2b9429b12d5c50')
+    version('3.11', '6465f602e656455affcd7c5734c638f8')
+    version('3.8', '94726411496c52c87c2b9429b12d5c50', url='http://www.dabeaz.com/ply/ply-3.8.tar.gz')
diff --git a/var/spack/repos/builtin/packages/py-pmw/package.py b/var/spack/repos/builtin/packages/py-pmw/package.py
index b22499d137..f2f775ced7 100644
--- a/var/spack/repos/builtin/packages/py-pmw/package.py
+++ b/var/spack/repos/builtin/packages/py-pmw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-poster/package.py b/var/spack/repos/builtin/packages/py-poster/package.py
new file mode 100644
index 0000000000..dc1a569dc6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-poster/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPoster(PythonPackage):
+    """Streaming HTTP uploads and multipart/form-data encoding."""
+
+    homepage = "https://pypi.org/project/poster/"
+    url      = "https://atlee.ca/software/poster/dist/0.8.1/poster-0.8.1.tar.gz"
+
+    version('0.8.1', '2db12704538781fbaa7e63f1505d6fc8')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pox/package.py b/var/spack/repos/builtin/packages/py-pox/package.py
index a4fe508ab2..cf4471c461 100644
--- a/var/spack/repos/builtin/packages/py-pox/package.py
+++ b/var/spack/repos/builtin/packages/py-pox/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ppft/package.py b/var/spack/repos/builtin/packages/py-ppft/package.py
index ca14fbb6b0..eff3559e35 100644
--- a/var/spack/repos/builtin/packages/py-ppft/package.py
+++ b/var/spack/repos/builtin/packages/py-ppft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-prettytable/package.py b/var/spack/repos/builtin/packages/py-prettytable/package.py
index 5f8378ca7c..1ebc32887d 100644
--- a/var/spack/repos/builtin/packages/py-prettytable/package.py
+++ b/var/spack/repos/builtin/packages/py-prettytable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-progress/package.py b/var/spack/repos/builtin/packages/py-progress/package.py
new file mode 100644
index 0000000000..bf5697e4d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-progress/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyProgress(PythonPackage):
+    """Easy progress reporting for Python"""
+
+    homepage = "https://github.com/verigak/progress/"
+    url      = "https://pypi.org/packages/source/p/progress/progress-1.4.tar.gz"
+
+    version('1.4', sha256='5e2f9da88ed8236a76fffbee3ceefd259589cf42dfbc2cec2877102189fae58a')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-proj/package.py b/var/spack/repos/builtin/packages/py-proj/package.py
index cea4f0c3ea..554b404742 100644
--- a/var/spack/repos/builtin/packages/py-proj/package.py
+++ b/var/spack/repos/builtin/packages/py-proj/package.py
@@ -1,39 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyProj(PythonPackage):
     """Python interface to the PROJ.4 Library."""
+
     homepage = "http://jswhit.github.io/pyproj/"
     url      = "https://github.com/jswhit/pyproj/tarball/v1.9.5.1rel"
+    git      = "https://www.github.com/jswhit/pyproj.git"
 
     # This is not a tagged release of pyproj.
     # The changes in this "version" fix some bugs, especially with Python3 use.
-    version('1.9.5.1.1', git='https://www.github.com/jswhit/pyproj.git',
-            commit='0be612cc9f972e38b50a90c946a9b353e2ab140f')
+    version('1.9.5.1.1', commit='0be612cc9f972e38b50a90c946a9b353e2ab140f')
     version('1.9.5.1', 'a4b80d7170fc82aee363d7f980279835')
 
     depends_on('py-cython', type='build')
diff --git a/var/spack/repos/builtin/packages/py-projectq/package.py b/var/spack/repos/builtin/packages/py-projectq/package.py
new file mode 100644
index 0000000000..d322bbb4e1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-projectq/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyProjectq(PythonPackage):
+    """
+    ProjectQ is an open-source software framework for quantum computing started
+    at ETH Zurich. It allows users to implement their quantum programs in
+    Python using a powerful and intuitive syntax. ProjectQ can then translate
+    these programs to any type of back-end, be it a simulator run on a
+    classical computer of an actual quantum chip.
+    """
+
+    # Homepage and git repository
+    homepage = "https://projectq.ch"
+    git      = "https://github.com/projectq-framework/projectq.git"
+
+    # Provided python modules
+    import_modules = ['projectq', 'projectq.backends', 'projectq.cengines',
+                      'projectq.libs', 'projectq.meta', 'projectq.ops',
+                      'projectq.setups', 'projectq.types']
+
+    # Versions
+    version('develop', branch='develop')
+    version('0.3.6', commit='fa484fe037a3a1772127bbd00fe4628ddba34611')
+
+    # Dependencies
+    depends_on('py-setuptools', type=('build'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-future', type=('build', 'run'))
+    depends_on('py-pytest@3.1.0:', type=('test'))
+    depends_on('py-requests', type=('build', 'run'))
+    # conflict with pybind11@2.2.0 -> see requirements.txt
+    depends_on('py-pybind11@1.7:2.1,2.2.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py b/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py
index f9b07f30d1..99e32ed782 100644
--- a/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/py-prompt-toolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-protobuf/package.py b/var/spack/repos/builtin/packages/py-protobuf/package.py
index fd3e4a6f09..1b8e99ddfd 100644
--- a/var/spack/repos/builtin/packages/py-protobuf/package.py
+++ b/var/spack/repos/builtin/packages/py-protobuf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,12 @@ class PyProtobuf(PythonPackage):
     homepage = 'https://developers.google.com/protocol-buffers/'
     url      = 'https://pypi.io/packages/source/p/protobuf/protobuf-3.0.0b2.tar.gz'
 
+    variant('cpp', default=False,
+            description='Enable the cpp implementation')
+
+    version('3.5.2.post1', '3b60685732bd0cbdc802dfcb6071efbcf5d927ce3127c13c33ea1a8efae3aa76')
+    version('3.5.2', '09879a295fd7234e523b62066223b128c5a8a88f682e3aff62fb115e4a0d8be0')
+    version('3.5.1', '95b78959572de7d7fafa3acb718ed71f482932ddddddbd29ba8319c10639d863')
     version('3.0.0b2', 'f0d3bd2394345a9af4a277cd0302ae83')
     version('2.6.1', '6bf843912193f70073db7f22e2ea55e2')
     version('2.5.0', '338813f3629d59e9579fed9035ecd457')
@@ -43,3 +30,13 @@ class PyProtobuf(PythonPackage):
     version('2.3.0', 'bb020c962f252fe81bfda8fb433bafdd')
 
     depends_on('py-setuptools', type='build')
+    depends_on('protobuf', when='+cpp')
+
+    @when('+cpp')
+    def build_args(self, spec, prefix):
+        return ['--cpp_implementation']
+
+    @when('+cpp')
+    def install_args(self, spec, prefix):
+        args = super(PyProtobuf, self).install_args(spec, prefix)
+        return args + ['--cpp_implementation']
diff --git a/var/spack/repos/builtin/packages/py-psutil/package.py b/var/spack/repos/builtin/packages/py-psutil/package.py
index 60c3368966..2888c109bd 100644
--- a/var/spack/repos/builtin/packages/py-psutil/package.py
+++ b/var/spack/repos/builtin/packages/py-psutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class PyPsutil(PythonPackage):
     in Python."""
 
     homepage = "https://pypi.python.org/pypi/psutil"
-    url      = "https://pypi.io/packages/source/p/psutil/psutil-5.0.1.tar.gz"
+    url      = "https://pypi.io/packages/source/p/psutil/psutil-5.4.5.tar.gz"
 
+    version('5.4.5', '7d3d7954782bba4a400e106e66f10656')
     version('5.0.1', '153dc8be94badc4072016ceeac7808dc')
 
     depends_on('python@2.6:')
diff --git a/var/spack/repos/builtin/packages/py-psyclone/package.py b/var/spack/repos/builtin/packages/py-psyclone/package.py
new file mode 100644
index 0000000000..218dedf9bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-psyclone/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+
+
+class PyPsyclone(PythonPackage):
+    """Code generation for the PSyKAl framework from the GungHo project,
+       as used by the LFRic model at the UK Met Office."""
+
+    homepage = "https://github.com/stfc/PSyclone"
+    url      = "https://github.com/stfc/PSyclone/archive/1.5.1.tar.gz"
+    git      = "https://github.com/stfc/PSyclone.git"
+
+    version('develop', branch='master')
+    version('1.5.1', commit='eba7a097175b02f75dec70616cf267b7b3170d78')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-pyparsing', type=('build', 'run'))
+
+    # Test cases fail without compatible versions of py-fparser:
+    depends_on('py-fparser@0.0.5', type=('build', 'run'), when='@1.5.1')
+    depends_on('py-fparser', type=('build', 'run'), when='@1.5.2:')
+
+    # Dependencies only required for tests:
+    depends_on('py-numpy',  type='test')
+    depends_on('py-nose',   type='test')
+    depends_on('py-pytest', type='test')
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_build(self):
+        # Limit py.test to search inside the build tree:
+        touch('pytest.ini')
+        with working_dir('src'):
+            Executable('py.test')()
+
+    def setup_environment(self, spack_env, run_env):
+        # Allow testing with installed executables:
+        spack_env.prepend_path('PATH', self.prefix.bin)
diff --git a/var/spack/repos/builtin/packages/py-ptyprocess/package.py b/var/spack/repos/builtin/packages/py-ptyprocess/package.py
index f97ff6e048..cef35e3115 100644
--- a/var/spack/repos/builtin/packages/py-ptyprocess/package.py
+++ b/var/spack/repos/builtin/packages/py-ptyprocess/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pudb/package.py b/var/spack/repos/builtin/packages/py-pudb/package.py
index bbc89251fe..f37904194f 100644
--- a/var/spack/repos/builtin/packages/py-pudb/package.py
+++ b/var/spack/repos/builtin/packages/py-pudb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-py/package.py b/var/spack/repos/builtin/packages/py-py/package.py
index 9706a2659d..51efc6ceae 100644
--- a/var/spack/repos/builtin/packages/py-py/package.py
+++ b/var/spack/repos/builtin/packages/py-py/package.py
@@ -1,41 +1,32 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyPy(PythonPackage):
-    """library with cross-python path, ini-parsing, io, code, log facilities"""
+    """Library with cross-python path, ini-parsing, io, code, log facilities"""
 
     homepage = "http://pylib.readthedocs.io/en/latest/"
-    url      = "https://pypi.io/packages/source/p/py/py-1.4.33.tar.gz"
+    url      = "https://pypi.io/packages/source/p/py/py-1.5.4.tar.gz"
 
     import_modules = [
-        'py', 'py._code', 'py._io', 'py._log', 'py._path', 'py._process',
+        'py', 'py._process', 'py._vendored_packages', 'py._path',
+        'py._log', 'py._code', 'py._io'
     ]
 
+    version('1.5.4',  '7502d66fa68ea4ae5b61c511cd177d6a')
+    version('1.5.3',  '667d37a148ad9fb81266492903f2d880')
     version('1.4.33', '15d7107cbb8b86593bf9afa16e56da65')
     version('1.4.31', '5d2c63c56dc3f2115ec35c066ecd582b')
 
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
     depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools-scm', type='build')
+
+    def test(self):
+        # Tests require pytest, creating a circular dependency
+        pass
diff --git a/var/spack/repos/builtin/packages/py-py2bit/package.py b/var/spack/repos/builtin/packages/py-py2bit/package.py
index 26d1f42a7b..2bb90a37a7 100644
--- a/var/spack/repos/builtin/packages/py-py2bit/package.py
+++ b/var/spack/repos/builtin/packages/py-py2bit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-py2cairo/package.py b/var/spack/repos/builtin/packages/py-py2cairo/package.py
index 30e363885d..13975addd2 100644
--- a/var/spack/repos/builtin/packages/py-py2cairo/package.py
+++ b/var/spack/repos/builtin/packages/py-py2cairo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,10 +19,9 @@ class PyPy2cairo(WafPackage):
     depends_on('python', type=('build', 'run'))
     depends_on('cairo@1.10.0:')
     depends_on('pixman')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest', type='test')
+    depends_on('py-pytest', type='test')
 
     def installtest(self):
         with working_dir('test'):
diff --git a/var/spack/repos/builtin/packages/py-py2neo/package.py b/var/spack/repos/builtin/packages/py-py2neo/package.py
index 27bb043116..9ecc72d3ce 100644
--- a/var/spack/repos/builtin/packages/py-py2neo/package.py
+++ b/var/spack/repos/builtin/packages/py-py2neo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-py4j/package.py b/var/spack/repos/builtin/packages/py-py4j/package.py
index 0c7e41a1d7..c369fd3d98 100644
--- a/var/spack/repos/builtin/packages/py-py4j/package.py
+++ b/var/spack/repos/builtin/packages/py-py4j/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,10 @@ class PyPy4j(PythonPackage):
     objects."""
 
     homepage = "https://www.py4j.org/"
-    url = "https://pypi.io/packages/source/p/py4j/py4j-0.10.4.tar.gz"
+    url = "https://pypi.io/packages/source/p/py4j/py4j-0.10.4.zip"
 
-    version('0.10.4', 'de1ce072fb8d5bff8aba537b1700ace4')
-    version('0.10.3', '6c86aebb4f1cdd4bf192b16c8a8fe8e4')
+    version('0.10.6', sha256='d3e7ac7c2171c290eba87e70aa5095b7eb6d6ad34789c007c88d550d9f575083')
+    version('0.10.4', sha256='406fbfdbcbbb398739f61fafd25724670a405a668eb08c1721d832eadce06aae')
+    version('0.10.3', sha256='f4570108ad014dd52a65c2288418e31cb8227b5ecc39ad7fc7fe98314f7a26f2')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pyani/package.py b/var/spack/repos/builtin/packages/py-pyani/package.py
new file mode 100644
index 0000000000..b17125eddb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyani/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyani(PythonPackage):
+    """pyani is a Python3 module that provides support for calculating
+    average nucleotide identity (ANI) and related measures for whole genome
+    comparisons, and rendering relevant graphical summary output. Where
+    available, it takes advantage of multicore systems, and can integrate
+    with SGE/OGE-type job schedulers for the sequence comparisons."""
+
+    homepage = "http://widdowquinn.github.io/pyani"
+    url      = "https://pypi.io/packages/source/p/pyani/pyani-0.2.7.tar.gz"
+
+    version('0.2.7', '239ba630d375a81c35b7c60fb9bec6fa')
+    version('0.2.6', 'd5524b9a3c62c36063ed474ea95785c9')
+
+    depends_on('python@3.5:')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-seaborn',    type=('build', 'run'))
+
+    # Required for ANI analysis
+    depends_on('py-biopython',  type=('build', 'run'))
+    depends_on('py-pandas',     type=('build', 'run'))
+    depends_on('py-scipy',      type=('build', 'run'))
+
+    # Required for ANIb analysis
+    depends_on('blast-plus~python', type='run')
+
+    # Required for ANIm analysis
+    depends_on('mummer', type='run')
diff --git a/var/spack/repos/builtin/packages/py-pyarrow/package.py b/var/spack/repos/builtin/packages/py-pyarrow/package.py
new file mode 100644
index 0000000000..650e209034
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyarrow/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyarrow(PythonPackage):
+    """A cross-language development platform for in-memory data.
+
+    This package contains the Python bindings.
+    """
+
+    homepage = "http://arrow.apache.org"
+    url      = "https://pypi.org/packages/source/p/pyarrow/pyarrow-0.9.0.tar.gz"
+
+    version('0.11.0', sha256='07a6fd71c5d7440f2c42383dd2c5daa12d7f0a012f1e88288ed08a247032aead')
+    version('0.9.0', sha256='7db8ce2f0eff5a00d6da918ce9f9cfec265e13f8a119b4adb1595e5b19fd6242')
+
+    variant('parquet', default=False, description="Build with Parquet support")
+
+    depends_on('cmake@3.0.0:', type='build')
+    depends_on('pkg-config', type='build')
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython', type='build')
+
+    depends_on('arrow+python')
+    depends_on('arrow+parquet+python', when='+parquet')
+
+    phases = ['build_ext', 'install']
+
+    def build_ext_args(self, spec, prefix):
+        args = []
+        if spec.satisfies('+parquet'):
+            args.append('--with-parquet')
+        return args
diff --git a/var/spack/repos/builtin/packages/py-pyasn1/package.py b/var/spack/repos/builtin/packages/py-pyasn1/package.py
index 3a7fc949c5..e2bdf80d26 100644
--- a/var/spack/repos/builtin/packages/py-pyasn1/package.py
+++ b/var/spack/repos/builtin/packages/py-pyasn1/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-pybigwig/package.py b/var/spack/repos/builtin/packages/py-pybigwig/package.py
index 5c88d111f5..b0b33b76d4 100644
--- a/var/spack/repos/builtin/packages/py-pybigwig/package.py
+++ b/var/spack/repos/builtin/packages/py-pybigwig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pybind11/package.py b/var/spack/repos/builtin/packages/py-pybind11/package.py
index aaa54370bf..b6e3118118 100644
--- a/var/spack/repos/builtin/packages/py-pybind11/package.py
+++ b/var/spack/repos/builtin/packages/py-pybind11/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,17 +17,41 @@ class PyPybind11(CMakePackage):
 
     homepage = "https://pybind11.readthedocs.io"
     url      = "https://github.com/pybind/pybind11/archive/v2.1.0.tar.gz"
+    git      = "https://github.com/pybind/pybind11.git"
 
+    version('develop', branch='master')
+    version('2.2.4', 'b69e83658513215b8d1443544d0549b7d231b9f201f6fc787a2b2218b408181e')
+    version('2.2.3', '55b637945bbf47d99d2c906bf0c13f49')
+    version('2.2.2', 'fc174e1bbfe7ec069af7eea86ec37b5c')
+    version('2.2.1', 'bab1d46bbc465af5af3a4129b12bfa3b')
     version('2.2.0', '978b26aea1c6bfc4f88518ef33771af2')
     version('2.1.1', '5518988698df937ccee53fb6ba91d12a')
     version('2.1.0', '3cf07043d677d200720c928569635e12')
 
-    depends_on('py-pytest', type=('build'))
+    depends_on('py-pytest', type='test')
+    depends_on('py-setuptools', type='build')
 
     extends('python')
 
+    # compiler support
+    conflicts('%gcc@:4.7')
+    conflicts('%clang@:3.2')
+    conflicts('%intel@:16')
+
     def cmake_args(self):
         args = []
         args.append('-DPYTHON_EXECUTABLE:FILEPATH=%s'
                     % self.spec['python'].command.path)
+        args += [
+            '-DPYBIND11_TEST:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF')
+        ]
         return args
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('PYBIND11_USE_CMAKE', 1)
+
+    def install(self, spec, prefix):
+        super(PyPybind11, self).install(spec, prefix)
+        setup_py('install', '--single-version-externally-managed', '--root=/',
+                 '--prefix={0}'.format(prefix))
diff --git a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py
index 45371400a3..fa46889631 100644
--- a/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py
+++ b/var/spack/repos/builtin/packages/py-pybtex-docutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pybtex/package.py b/var/spack/repos/builtin/packages/py-pybtex/package.py
index 606c047232..fd0bac735a 100644
--- a/var/spack/repos/builtin/packages/py-pybtex/package.py
+++ b/var/spack/repos/builtin/packages/py-pybtex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-pycairo/package.py b/var/spack/repos/builtin/packages/py-pycairo/package.py
new file mode 100644
index 0000000000..607981a060
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pycairo/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class PyPycairo(PythonPackage):
+    """Pycairo is a set of Python bindings for the cairo graphics library."""
+
+    homepage = "https://www.cairographics.org/pycairo/"
+    url      = "https://github.com/pygobject/pycairo/releases/download/v1.17.1/pycairo-1.17.1.tar.gz"
+    url      = "https://files.pythonhosted.org/packages/68/76/340ff847897296b2c8174dfa5a5ec3406e3ed783a2abac918cf326abad86/pycairo-1.17.1.tar.gz"
+
+    version('1.17.1', '34c1ee106655b450c4bd57e29371a4a7')
+
+    depends_on('cairo@1.2.0:')
+    depends_on('pkgconfig', type='build')
+    depends_on('py-setuptools', type='build')
+
+    @run_after('install')
+    def post_install(self):
+        src = self.prefix.lib + '/pkgconfig/py3cairo.pc'
+        dst = self.prefix.lib + '/pkgconfig/pycairo.pc'
+        if os.path.exists(src) and not os.path.exists(dst):
+            copy(src, dst)
diff --git a/var/spack/repos/builtin/packages/py-pychecker/package.py b/var/spack/repos/builtin/packages/py-pychecker/package.py
index 2f85fa88ac..49f4b39f86 100644
--- a/var/spack/repos/builtin/packages/py-pychecker/package.py
+++ b/var/spack/repos/builtin/packages/py-pychecker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pycodestyle/package.py b/var/spack/repos/builtin/packages/py-pycodestyle/package.py
index 3bae7c4296..10f97547c5 100644
--- a/var/spack/repos/builtin/packages/py-pycodestyle/package.py
+++ b/var/spack/repos/builtin/packages/py-pycodestyle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,10 @@ class PyPycodestyle(PythonPackage):
     homepage = "https://github.com/PyCQA/pycodestyle"
     url      = "https://github.com/PyCQA/pycodestyle/archive/2.0.0.tar.gz"
 
+    version('2.3.1', '4185319f6137833eec9057dbf3293629')
+    version('2.3.0', '1b2019b3c39c20becadbb7fdec6dcb5a')
+    version('2.2.0', '6e21aab2e038c3dd38dca585011a6f38')
+    version('2.1.0', '1e606c687a6cf01d51305417d0e97824')
     version('2.0.0', '5c3e90001f538bf3b7896d60e92eb6f6')
     version('1.7.0', '31070a3a6391928893cbf5fa523eb8d9')
     version('1.6.2', '8df18246d82ddd3d19ffe7518f983955')
diff --git a/var/spack/repos/builtin/packages/py-pycparser/package.py b/var/spack/repos/builtin/packages/py-pycparser/package.py
index 256130b1b7..3fa5a0acb3 100644
--- a/var/spack/repos/builtin/packages/py-pycparser/package.py
+++ b/var/spack/repos/builtin/packages/py-pycparser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class PyPycparser(PythonPackage):
 
     import_modules = ['pycparser', 'pycparser.ply']
 
+    version('2.18', '72370da54358202a60130e223d488136')
     version('2.17', 'ca98dcb50bc1276f230118f6af5a40c7')
     version('2.13', 'e4fe1a2d341b22e25da0d22f034ef32f')
 
diff --git a/var/spack/repos/builtin/packages/py-pycrypto/package.py b/var/spack/repos/builtin/packages/py-pycrypto/package.py
index 948a4f7cbd..9bacd5b4ba 100644
--- a/var/spack/repos/builtin/packages/py-pycrypto/package.py
+++ b/var/spack/repos/builtin/packages/py-pycrypto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-pycurl/package.py b/var/spack/repos/builtin/packages/py-pycurl/package.py
index c111430b9e..85074d6341 100644
--- a/var/spack/repos/builtin/packages/py-pycurl/package.py
+++ b/var/spack/repos/builtin/packages/py-pycurl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pydatalog/package.py b/var/spack/repos/builtin/packages/py-pydatalog/package.py
index 9bd5c898a2..cbcedc385f 100644
--- a/var/spack/repos/builtin/packages/py-pydatalog/package.py
+++ b/var/spack/repos/builtin/packages/py-pydatalog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pydispatcher/package.py b/var/spack/repos/builtin/packages/py-pydispatcher/package.py
index 9e329ab70c..89efd4f463 100644
--- a/var/spack/repos/builtin/packages/py-pydispatcher/package.py
+++ b/var/spack/repos/builtin/packages/py-pydispatcher/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pydot/package.py b/var/spack/repos/builtin/packages/py-pydot/package.py
index c6067c00a1..ed941e9513 100644
--- a/var/spack/repos/builtin/packages/py-pydot/package.py
+++ b/var/spack/repos/builtin/packages/py-pydot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyelftools/package.py b/var/spack/repos/builtin/packages/py-pyelftools/package.py
index a7d52ee946..632ee37917 100644
--- a/var/spack/repos/builtin/packages/py-pyelftools/package.py
+++ b/var/spack/repos/builtin/packages/py-pyelftools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyepsg/package.py b/var/spack/repos/builtin/packages/py-pyepsg/package.py
new file mode 100644
index 0000000000..4771e56d4b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyepsg/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyepsg(PythonPackage):
+    """Provides simple access to http://epsg.io/."""
+
+    homepage = "https://pyepsg.readthedocs.io/en/latest/"
+    url      = "https://pypi.io/packages/source/p/pyepsg/pyepsg-0.3.2.tar.gz"
+
+    version('0.3.2', 'b0644187068a9b58378a5c58ad55b991')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-requests',   type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pyfasta/package.py b/var/spack/repos/builtin/packages/py-pyfasta/package.py
index 40a5fcf46e..ba0a69838a 100644
--- a/var/spack/repos/builtin/packages/py-pyfasta/package.py
+++ b/var/spack/repos/builtin/packages/py-pyfasta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,7 @@ class PyPyfasta(PythonPackage):
        access to fasta sequence files"""
 
     homepage = "https://pypi.python.org/pypi/pyfasta/"
-    url      = "https://pypi.python.org/packages/be/3f/794fbcdaaa2113f0a1d16a962463896c1a6bdab77bd63f33a8f16aae6cdc/pyfasta-0.5.2.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pyfasta/pyfasta-0.5.2.tar.gz"
 
     version('0.5.2', 'bf61ab997dca329675c3eb2ee7cdfcf2')
 
diff --git a/var/spack/repos/builtin/packages/py-pyfftw/package.py b/var/spack/repos/builtin/packages/py-pyfftw/package.py
index 4dd9fe1600..78a76f9a5d 100644
--- a/var/spack/repos/builtin/packages/py-pyfftw/package.py
+++ b/var/spack/repos/builtin/packages/py-pyfftw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyflakes/package.py b/var/spack/repos/builtin/packages/py-pyflakes/package.py
index 6f962ae4df..08c1229b7e 100644
--- a/var/spack/repos/builtin/packages/py-pyflakes/package.py
+++ b/var/spack/repos/builtin/packages/py-pyflakes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,9 @@ class PyPyflakes(PythonPackage):
     homepage = "https://github.com/PyCQA/pyflakes"
     url      = "https://github.com/PyCQA/pyflakes/archive/1.3.0.tar.gz"
 
+    version('1.6.0', '68eff61e54964e6389f8fb1d2122fc5b')
+    version('1.5.0', '1dee2ca8a0520061aac5a82f3b539fa0')
+    version('1.4.0', 'ed832ef1cbd59463e5f0f6340254f603')
     version('1.3.0', 'a76173deb7a84fe860c0b60e2fbcdfe2')
     version('1.2.3', '2ac2e148a5c46b6bb06c4785be76f7cc')
     version('1.2.2', 'fe759b9381a6500e67a2ddbbeb5161a4')
diff --git a/var/spack/repos/builtin/packages/py-pygdbmi/package.py b/var/spack/repos/builtin/packages/py-pygdbmi/package.py
new file mode 100644
index 0000000000..f8198015f8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pygdbmi/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPygdbmi(PythonPackage):
+    """Parse gdb machine interface output with Python"""
+
+    homepage = "https://github.com/cs01/pygdbmi"
+    url      = "https://pypi.io/packages/source/p/pygdbmi/pygdbmi-0.8.2.0.tar.gz"
+
+    version('0.8.2.0', 'e74d3d02fa5eef1223b5dedb13f9bbad')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pygments/package.py b/var/spack/repos/builtin/packages/py-pygments/package.py
index 8c6ee04db8..1909a2da11 100644
--- a/var/spack/repos/builtin/packages/py-pygments/package.py
+++ b/var/spack/repos/builtin/packages/py-pygments/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pygobject/package.py b/var/spack/repos/builtin/packages/py-pygobject/package.py
index 6c81418fce..1dd08a30d0 100644
--- a/var/spack/repos/builtin/packages/py-pygobject/package.py
+++ b/var/spack/repos/builtin/packages/py-pygobject/package.py
@@ -1,47 +1,32 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class PyPygobject(AutotoolsPackage):
+class PyPygobject(PythonPackage):
     """bindings for the GLib, and GObject,
        to be used in Python."""
 
     homepage = "https://pypi.python.org/pypi/pygobject"
 
-    url      = "http://ftp.gnome.org/pub/GNOME/sources/pygobject/2.28/pygobject-2.28.6.tar.bz2"
-
-    version('2.28.6', 'a43d783228dd32899e6908352b8308f3')
-    version('2.28.3', 'aa64900b274c4661a5c32e52922977f9')
+    version('3.28.3', '3bac63c86bb963aa401f97859464aa90')
+    version('2.28.6', '9415cb7f2b3a847f2310ccea258b101e')
+    version('2.28.3', 'aa64900b274c4661a5c32e52922977f9',
+            url='http://ftp.gnome.org/pub/GNOME/sources/pygobject/2.28/pygobject-2.28.3.tar.bz2')
 
     extends('python')
 
+    depends_on('py-setuptools', type=('build'))
     depends_on("libffi")
     depends_on('glib')
-    depends_on('py-py2cairo', type=('build', 'run'))
+    depends_on('python@2:2.99', when='@2:2.99', type=('build', 'run'))
+    depends_on('py-pycairo', type=('build', 'run'), when='@3:')
+    depends_on('py-py2cairo', type=('build', 'run'), when='@2:2.99')
     depends_on('gobject-introspection')
+    depends_on('gtkplus', when='@3:')
 
     patch('pygobject-2.28.6-introspection-1.patch', when='@2.28.3:2.28.6')
 
@@ -49,5 +34,22 @@ class PyPygobject(AutotoolsPackage):
     # for https://bugzilla.gnome.org/show_bug.cgi?id=668522
     patch('pygobject-2.28.6-gio-types-2.32.patch', when='@2.28.6')
 
+    def url_for_version(self, version):
+        url = 'http://ftp.gnome.org/pub/GNOME/sources/pygobject'
+        return url + '/%s/pygobject-%s.tar.xz' % (version.up_to(2), version)
+
+    # pygobject version 2 requires an autotools build
+    @when('@2:2.99')
+    def build(self, spec, prefix):
+        configure('--prefix=%s' % spec.prefix)
+
+    @when('@2:2.99')
     def install(self, spec, prefix):
         make('install', parallel=False)
+
+    @when('^python@3:')
+    def patch(self):
+        filter_file(
+            r'Pycairo_IMPORT',
+            r'//Pycairo_IMPORT',
+            'gi/pygi-foreign-cairo.c')
diff --git a/var/spack/repos/builtin/packages/py-pygpu/package.py b/var/spack/repos/builtin/packages/py-pygpu/package.py
new file mode 100644
index 0000000000..f5838c740b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pygpu/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPygpu(PythonPackage):
+    """Python packge for the libgpuarray C library."""
+
+    homepage = "http://deeplearning.net/software/libgpuarray/"
+    url      = "https://github.com/Theano/libgpuarray/archive/v0.6.1.tar.gz"
+
+    version('0.7.5', '2534011464555c3e99d14231db965c20')
+    version('0.7.4', '19f57cd381175162048c8154f5251546')
+    version('0.7.3', 'cb44aeb8482330974abdb36b0a477e5d')
+    version('0.7.2', '0f9d7748501bc5c71bf04aae2285ac4e')
+    version('0.7.1', '7eb5bb6689ddbc386a9d498f5c0027fb')
+    version('0.7.0', 'f71b066f21ef7666f3a851e96c26f52e')
+    version('0.6.9', '7f75c39f1436c920ed9c5ffde5631fc0')
+    version('0.6.2', '7f163bd5f48f399cd6e608ee3d528ee4')
+    version('0.6.1', 'cfcd1b54447f9d55b05514df62c70ae2')
+    version('0.6.0', '98a4ec1b4c8f225f0b89c18b899a000b')
+
+    depends_on('libgpuarray')
+    # not just build-time, requires pkg_resources
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-cython@0.25:', type=('build', 'run'))
+    depends_on('py-nose', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-mako', type=('build', 'run'))
+    depends_on('libcheck')
diff --git a/var/spack/repos/builtin/packages/py-pygtk/package.py b/var/spack/repos/builtin/packages/py-pygtk/package.py
index 5a05a3a402..28b2cacd27 100644
--- a/var/spack/repos/builtin/packages/py-pygtk/package.py
+++ b/var/spack/repos/builtin/packages/py-pygtk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,11 +15,18 @@ class PyPygtk(AutotoolsPackage):
     version('2.24.0', 'd27c7f245a9e027f6b6cd9acb7468e36')
 
     extends('python')
+
+    depends_on('pkgconfig', type=('build'))
     depends_on("libffi")
+    # atk@2.28.1 depends on meson which requires python 3
+    depends_on('atk@:2.20.0')
+    # PyGTK requires python 2
+    # Use py-pygobject@3: for GTK bindings for python 3
+    depends_on('python@2:2.99', type=('build', 'run'))
     depends_on('cairo')
     depends_on('glib')
     # for GTK 3.X use pygobject 3.X instead of pygtk
-    depends_on('gtkplus+X@2.24:2.99')
+    depends_on('gtkplus@2.24:2.99')
     depends_on('py-pygobject@2.28:2.99', type=('build', 'run'))
     depends_on('py-py2cairo', type=('build', 'run'))
 
diff --git a/var/spack/repos/builtin/packages/py-pylint/package.py b/var/spack/repos/builtin/packages/py-pylint/package.py
index fb6cb2946e..404767e909 100644
--- a/var/spack/repos/builtin/packages/py-pylint/package.py
+++ b/var/spack/repos/builtin/packages/py-pylint/package.py
@@ -1,44 +1,32 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class PyPylint(PythonPackage):
     """array processing for numbers, strings, records, and objects."""
+
     homepage = "https://pypi.python.org/pypi/pylint"
-    url      = "https://pypi.io/packages/source/p/pylint/pylint-1.7.2.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pylint/pylint-1.6.5.tar.gz"
 
-    version('1.7.2', '27ee752cdcfacb05bf4940947e6b35c6')
+    # version('1.7.2', '27ee752cdcfacb05bf4940947e6b35c6') # see dependencies
+    version('1.6.5', '31da2185bf59142479e4fa16d8a9e347')
     version('1.4.3', '5924c1c7ca5ca23647812f5971d0ea44')
     version('1.4.1', 'df7c679bdcce5019389038847e4de622')
 
     extends('python', ignore=r'bin/pytest')
-    depends_on('py-six', type=('build', 'run'))
     depends_on('py-astroid', type=('build', 'run'))
-    depends_on('py-logilab-common', type=('build', 'run'))
-    depends_on('py-setuptools', type='build')
-
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
+    # note there is no working version of astroid for this
+    depends_on('py-astroid@1.5.1:', type=('build', 'run'), when='@1.7:')
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-isort@4.2.5:')
+    depends_on('py-mccabe')
+    depends_on('py-editdistance')
+    depends_on('py-setuptools@17.1:', type='build')
+    # depends_on('py-setuptools-scm@1.15.0:', type='build')
+    depends_on('py-configparser', when='^python@:2.8')
+    depends_on('py-backports-functools-lru-cache', when='^python@:2.8')
+    depends_on('py-singledispatch', when='^python@:3.3.99')
diff --git a/var/spack/repos/builtin/packages/py-pymatgen/package.py b/var/spack/repos/builtin/packages/py-pymatgen/package.py
index 78343e74ff..65c4337083 100644
--- a/var/spack/repos/builtin/packages/py-pymatgen/package.py
+++ b/var/spack/repos/builtin/packages/py-pymatgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyminifier/package.py b/var/spack/repos/builtin/packages/py-pyminifier/package.py
index b4bc9e859b..4da150f949 100644
--- a/var/spack/repos/builtin/packages/py-pyminifier/package.py
+++ b/var/spack/repos/builtin/packages/py-pyminifier/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pymol/package.py b/var/spack/repos/builtin/packages/py-pymol/package.py
new file mode 100644
index 0000000000..1a23247499
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pymol/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPymol(PythonPackage):
+    """PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D
+       visualization of proteins, small molecules, density, surfaces, and
+       trajectories. It also includes molecular editing, ray tracing, and
+       movies. Open Source PyMOL is free to everyone!"""
+
+    homepage = "https://pymol.org"
+    url      = "https://sourceforge.net/projects/pymol/files/pymol/2/pymol-v2.1.0.tar.bz2"
+
+    version('2.1.0', 'ef2ab2ce11d65785ca3258b4e6982dfb')
+
+    depends_on('python+tk', type=('build', 'run'))
+    depends_on('tcl')
+    depends_on('tk')
+    depends_on('py-pmw')
+    depends_on('gl')
+    depends_on('glu')
+    depends_on('glew')
+    depends_on('libpng')
+    depends_on('freetype')
+    depends_on('libxml2')
+    depends_on('msgpack-c')
+    depends_on('py-pyqt', type=('build', 'run'))
+    depends_on('freeglut')
diff --git a/var/spack/repos/builtin/packages/py-pympler/package.py b/var/spack/repos/builtin/packages/py-pympler/package.py
index 25766d10c4..7498f9e32e 100644
--- a/var/spack/repos/builtin/packages/py-pympler/package.py
+++ b/var/spack/repos/builtin/packages/py-pympler/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pymysql/package.py b/var/spack/repos/builtin/packages/py-pymysql/package.py
new file mode 100644
index 0000000000..22346c4dd0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pymysql/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPymysql(PythonPackage):
+    """Pure-Python MySQL client library"""
+
+    homepage = "https://github.com/PyMySQL/PyMySQL/"
+    url      = "https://pypi.io/packages/source/p/pymysql/PyMySQL-0.9.2.tar.gz"
+
+    version('0.9.2', sha256='9ec760cbb251c158c19d6c88c17ca00a8632bac713890e465b2be01fdc30713f')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cryptography', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pynn/package.py b/var/spack/repos/builtin/packages/py-pynn/package.py
index 23e9ab13a4..a91adb259c 100644
--- a/var/spack/repos/builtin/packages/py-pynn/package.py
+++ b/var/spack/repos/builtin/packages/py-pynn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,11 @@ class PyPynn(PythonPackage):
 
     homepage = "http://neuralensemble.org/PyNN/"
     url      = "https://pypi.io/packages/source/P/PyNN/PyNN-0.8.3.tar.gz"
+    git      = "https://github.com/NeuralEnsemble/PyNN.git"
 
+    version('0.9.1', '3b8a6c63dc59d7ac751029f84dcaf7e6')
     version('0.8.3', '28c63f898093806a57198e9271ed7b82')
-    version('0.8beta', git='https://github.com/NeuralEnsemble/PyNN.git',
-        commit='ffb0cb1661f2b0f2778db8f71865978fe7a7a6a4')
+    version('0.8beta', commit='ffb0cb1661f2b0f2778db8f71865978fe7a7a6a4')
     version('0.8.1', '7fb165ed5af35a115cb9c60991645ae6')
     version('0.7.5', 'd8280544e4c9b34b40fd372b16342841')
 
@@ -45,7 +27,8 @@ class PyPynn(PythonPackage):
     depends_on('py-numpy@1.5:',         type=('build', 'run'))
     depends_on('py-quantities@0.10:',   type=('build', 'run'))
     depends_on('py-lazyarray@0.2.9:',   type=('build', 'run'))
-    depends_on('py-neo@0.3:',           type=('build', 'run'))
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-mock@1.0:', type='test')
+    depends_on('py-neo@0.3:0.4.1',      type=('build', 'run'), when="@:0.8.3")
+    depends_on('py-neo@0.5.0:',         type=('build', 'run'), when="@0.9.0:")
+
+    depends_on('py-mock@1.0:', type='test')
diff --git a/var/spack/repos/builtin/packages/py-pypar/package.py b/var/spack/repos/builtin/packages/py-pypar/package.py
index ee1aa2735d..28fcada1fc 100644
--- a/var/spack/repos/builtin/packages/py-pypar/package.py
+++ b/var/spack/repos/builtin/packages/py-pypar/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyparsing/package.py b/var/spack/repos/builtin/packages/py-pyparsing/package.py
index 0be88e638d..48626a37e4 100644
--- a/var/spack/repos/builtin/packages/py-pyparsing/package.py
+++ b/var/spack/repos/builtin/packages/py-pyparsing/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pypeflow/package.py b/var/spack/repos/builtin/packages/py-pypeflow/package.py
index 8eb353432c..d4abb9f330 100644
--- a/var/spack/repos/builtin/packages/py-pypeflow/package.py
+++ b/var/spack/repos/builtin/packages/py-pypeflow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,11 +11,9 @@ class PyPypeflow(PythonPackage):
     library written in Python."""
 
     homepage = "https://github.com/PacificBiosciences/pypeFLOW"
-    url      = "https://github.com/PacificBiosciences/pypeFLOW"
+    git      = "https://github.com/PacificBiosciences/pypeFLOW.git"
 
-    version('2017-05-04',
-            git='https://github.com/PacificBiosciences/pypeFLOW.git',
-            commit='f23a1b290876bbdf130611000934ae4247158073')
+    version('2017-05-04', commit='f23a1b290876bbdf130611000934ae4247158073')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-networkx@1.7:1.11', type=['build', 'run'])
diff --git a/var/spack/repos/builtin/packages/py-pyprof2html/package.py b/var/spack/repos/builtin/packages/py-pyprof2html/package.py
index efaa525267..275b52aa07 100644
--- a/var/spack/repos/builtin/packages/py-pyprof2html/package.py
+++ b/var/spack/repos/builtin/packages/py-pyprof2html/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyqi/package.py b/var/spack/repos/builtin/packages/py-pyqi/package.py
new file mode 100644
index 0000000000..21fecdec19
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyqi/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyqi(PythonPackage):
+    """pyqi (canonically pronounced pie chee) is a Python framework designed
+       to support wrapping general commands in multiple types of interfaces,
+       including at the command line, HTML, and API levels."""
+
+    homepage = "https://pyqi.readthedocs.io"
+    url      = "https://pypi.io/packages/source/p/pyqi/pyqi-0.3.2.tar.gz"
+
+    version('0.3.2', '9507c06eeb22a816d963c860ad8e92ae')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pyqt/package.py b/var/spack/repos/builtin/packages/py-pyqt/package.py
index 401cf8ded6..ce700d18bd 100644
--- a/var/spack/repos/builtin/packages/py-pyqt/package.py
+++ b/var/spack/repos/builtin/packages/py-pyqt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyrad/package.py b/var/spack/repos/builtin/packages/py-pyrad/package.py
index 0b56dd3631..de0a082930 100644
--- a/var/spack/repos/builtin/packages/py-pyrad/package.py
+++ b/var/spack/repos/builtin/packages/py-pyrad/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pysam/package.py b/var/spack/repos/builtin/packages/py-pysam/package.py
index 7c3cccd21a..513a41f778 100644
--- a/var/spack/repos/builtin/packages/py-pysam/package.py
+++ b/var/spack/repos/builtin/packages/py-pysam/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,18 @@ class PyPysam(PythonPackage):
        sets."""
 
     homepage = "https://pypi.python.org/pypi/pysam"
-    url      = "https://pypi.io/packages/source/p/pysam/pysam-0.11.2.2.tar.gz"
+    url      = "https://github.com/pysam-developers/pysam/archive/v0.14.1.tar.gz"
 
+    version('0.14.1', 'ad88fa5bbcc0fdf4a936734691d9c9d1')
+    version('0.13', 'a9b502dd1a7e6403e35e6972211688a2')
     version('0.11.2.2', '56230cd5f55b503845915b76c22d620a')
+    version('0.7.7', 'eaf9f37cbccc5e2708754d045909c1a0')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-cython@0.21:', type='build')
+    depends_on('curl')
     depends_on('bcftools')
+    depends_on('htslib')
+    depends_on('samtools')
+
+    depends_on('htslib@:1.6', when='@:0.13')
diff --git a/var/spack/repos/builtin/packages/py-pyscaf/package.py b/var/spack/repos/builtin/packages/py-pyscaf/package.py
index a32a1aee55..508de86ad9 100644
--- a/var/spack/repos/builtin/packages/py-pyscaf/package.py
+++ b/var/spack/repos/builtin/packages/py-pyscaf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyserial/package.py b/var/spack/repos/builtin/packages/py-pyserial/package.py
index 0ddc2c51de..cb747c2e27 100644
--- a/var/spack/repos/builtin/packages/py-pyserial/package.py
+++ b/var/spack/repos/builtin/packages/py-pyserial/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class PyPyserial(Package):
+class PyPyserial(PythonPackage):
     """Python Serial Port Extension"""
 
     homepage = "https://github.com/pyserial/pyserial"
diff --git a/var/spack/repos/builtin/packages/py-pyshp/package.py b/var/spack/repos/builtin/packages/py-pyshp/package.py
new file mode 100644
index 0000000000..f416310fba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyshp/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyshp(PythonPackage):
+    """The Python Shapefile Library (pyshp) reads and writes ESRI Shapefiles in
+    pure Python."""
+
+    homepage = "https://github.com/GeospatialPython/pyshp"
+    url      = "https://pypi.io/packages/source/p/pyshp/pyshp-1.2.12.tar.gz"
+
+    version('1.2.12', '63d33d151ac308f1db71ea0f22c30d8b')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pyside/package.py b/var/spack/repos/builtin/packages/py-pyside/package.py
index e799b4cb72..dc728bff77 100644
--- a/var/spack/repos/builtin/packages/py-pyside/package.py
+++ b/var/spack/repos/builtin/packages/py-pyside/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -31,7 +12,21 @@ class PyPyside(PythonPackage):
     homepage = "https://pypi.python.org/pypi/pyside"
     url      = "https://pypi.io/packages/source/P/PySide/PySide-1.2.2.tar.gz"
 
+    # More recent versions of PySide2 (for Qt5) have been taken under
+    # the offical Qt umbrella.  For more information, see:
+    # http://wiki.qt.io/Qt_for_Python_Development_Getting_Started
+
+    # Version 1.2.4 claims to not work with Python 3.5, mostly
+    # because it hasn't been tested.  Otherwise, it's the same as v1.2.3
+    # https://github.com/PySide/pyside-setup/issues/58
+    # Meanwhile, developers have moved onto pyside2 (for Qt5),
+    # and show little interest in certifying PySide 1.2.4 for Python.
     version('1.2.4', '3cb7174c13bd45e3e8f77638926cb8c0')  # rpath problems
+
+    # This is not available from pypi
+    # version('1.2.3', 'fa5d5438b045ede36104bba25a6ccc10')
+
+    # v1.2.2 does not work with Python3
     version('1.2.2', 'c45bc400c8a86d6b35f34c29e379e44d', preferred=True)
 
     depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pysocks/package.py b/var/spack/repos/builtin/packages/py-pysocks/package.py
index db734dd927..83661d93b0 100644
--- a/var/spack/repos/builtin/packages/py-pysocks/package.py
+++ b/var/spack/repos/builtin/packages/py-pysocks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pyspark/package.py b/var/spack/repos/builtin/packages/py-pyspark/package.py
new file mode 100644
index 0000000000..126de2af41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyspark/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPyspark(PythonPackage):
+    """Python bindings for Apache Spark"""
+
+    homepage = "http://spark.apache.org"
+    url      = "https://pypi.org/packages/source/p/pyspark/pyspark-2.3.0.tar.gz"
+
+    version('2.3.0', sha256='0b3536910e154c36a94239f0ba0a201f476aadc72006409e5787198ffd01986e')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-py4j', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pysqlite/package.py b/var/spack/repos/builtin/packages/py-pysqlite/package.py
new file mode 100644
index 0000000000..0f69acc3bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pysqlite/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPysqlite(PythonPackage):
+    """Python DB-API module for SQLite 3."""
+
+    homepage = "https://github.com/ghaering/pysqlite"
+    url      = "https://pypi.io/packages/source/p/pysqlite/pysqlite-2.8.3.tar.gz"
+
+    version('2.8.3', '033f17b8644577715aee55e8832ac9fc')
+
+    depends_on('python@2.7.0:2.7.999', type=('build', 'run'))
+    depends_on('sqlite', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pytables/package.py b/var/spack/repos/builtin/packages/py-pytables/package.py
index 5e782341d9..96033237b0 100644
--- a/var/spack/repos/builtin/packages/py-pytables/package.py
+++ b/var/spack/repos/builtin/packages/py-pytables/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-cov/package.py b/var/spack/repos/builtin/packages/py-pytest-cov/package.py
index 3621b54d0d..949696d3f4 100644
--- a/var/spack/repos/builtin/packages/py-pytest-cov/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-cov/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-flake8/package.py b/var/spack/repos/builtin/packages/py-pytest-flake8/package.py
index 4b2ec5e014..06066572ec 100644
--- a/var/spack/repos/builtin/packages/py-pytest-flake8/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-flake8/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py
index f27f121d8e..0782f761d4 100644
--- a/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-httpbin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-mock/package.py b/var/spack/repos/builtin/packages/py-pytest-mock/package.py
index 968816f6f4..d574f6ae84 100644
--- a/var/spack/repos/builtin/packages/py-pytest-mock/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-mock/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest-runner/package.py b/var/spack/repos/builtin/packages/py-pytest-runner/package.py
index 771902afd9..037ec724ae 100644
--- a/var/spack/repos/builtin/packages/py-pytest-runner/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-runner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,3 +17,4 @@ class PyPytestRunner(PythonPackage):
     version('2.11.1', 'bdb73eb18eca2727944a2dcf963c5a81')
 
     depends_on('py-setuptools', type='build')
+    depends_on('py-setuptools-scm@1.15:', type='build')
diff --git a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py
index 968601ab29..ad3c77c7ef 100644
--- a/var/spack/repos/builtin/packages/py-pytest-xdist/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest-xdist/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-pytest/package.py b/var/spack/repos/builtin/packages/py-pytest/package.py
index 098a9de79c..7e6c6f555c 100644
--- a/var/spack/repos/builtin/packages/py-pytest/package.py
+++ b/var/spack/repos/builtin/packages/py-pytest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,23 +10,31 @@ class PyPytest(PythonPackage):
     """pytest: simple powerful testing with Python."""
 
     homepage = "http://pytest.org/"
-    url      = "https://pypi.io/packages/source/p/pytest/pytest-3.0.7.tar.gz"
+    url      = "https://pypi.io/packages/source/p/pytest/pytest-3.7.2.tar.gz"
 
     import_modules = [
         '_pytest', '_pytest.assertion', '_pytest._code',
-        '_pytest.vendored_packages', 'pytest'
+        '_pytest.mark', 'pytest'
     ]
 
+    version('3.7.2', 'd12d0d556a21fd8633e105f1a8d5a0f9')
+    version('3.7.1', '2704e16bb2c11af494167f80a7cd37c4')
+    version('3.5.1', 'ffd870ee3ca561695d2f916f0f0f3c0b')
     version('3.0.7', '89c60546507dc7eb6e9e40a6e9f720bd')
     version('3.0.2', '61dc36e65a6f6c11c53b1388e043a9f5')
 
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
     # Most Python packages only require setuptools as a build dependency.
     # However, pytest requires setuptools during runtime as well.
     depends_on('py-setuptools', type=('build', 'run'))
-    depends_on('py-py@1.4.29:', type=('build', 'run'))
-    depends_on('py-hypothesis@3.5.2:', type=('build', 'run'))
-
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
-    # depends_on('py-mock', type='test')
-    # depends_on('py-requests', type='test')
+    depends_on('py-setuptools-scm', type='build')
+    depends_on('py-py@1.5.0:', type=('build', 'run'))
+    depends_on('py-six@1.10.0:', type=('build', 'run'))
+    depends_on('py-attrs@17.4.0:', type=('build', 'run'))
+    depends_on('py-more-itertools@4.0.0:', type=('build', 'run'))
+    depends_on('py-atomicwrites@1.0:', type=('build', 'run'))
+    depends_on('py-pluggy@0.7:', when='@3.7:', type=('build', 'run'))
+    depends_on('py-pluggy@0.5:0.6', when='@:3.6', type=('build', 'run'))
+    depends_on('py-funcsigs', when='^python@:2', type=('build', 'run'))
+    depends_on('py-pathlib2@2.2.0:', when='^python@:3.5', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-python-daemon/package.py b/var/spack/repos/builtin/packages/py-python-daemon/package.py
index ff47d32504..8fd6e38464 100644
--- a/var/spack/repos/builtin/packages/py-python-daemon/package.py
+++ b/var/spack/repos/builtin/packages/py-python-daemon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-python-engineio/package.py b/var/spack/repos/builtin/packages/py-python-engineio/package.py
new file mode 100644
index 0000000000..27735cb1ad
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-python-engineio/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPythonEngineio(PythonPackage):
+    """Engine.IO is the implementation of transport-based
+    cross-browser/cross-device bi-directional communication
+    layer for Socket.IO."""
+
+    homepage = "http://python-engineio.readthedocs.io/en/latest/"
+    url      = "https://github.com/miguelgrinberg/python-engineio/archive/v2.0.2.tar.gz"
+
+    version('2.0.2', 'b91c6fa900905f9a96b86c3e141e2754')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six@1.9.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-python-gitlab/package.py b/var/spack/repos/builtin/packages/py-python-gitlab/package.py
index ff769b421e..d27d250d99 100644
--- a/var/spack/repos/builtin/packages/py-python-gitlab/package.py
+++ b/var/spack/repos/builtin/packages/py-python-gitlab/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-python-levenshtein/package.py b/var/spack/repos/builtin/packages/py-python-levenshtein/package.py
new file mode 100644
index 0000000000..a19247c6fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-python-levenshtein/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPythonLevenshtein(PythonPackage):
+    """Python extension for computing string edit distances and
+    similarities."""
+
+    homepage = "https://github.com/ztane/python-Levenshtein"
+    url      = "https://pypi.io/packages/source/p/python-Levenshtein/python-Levenshtein-0.12.0.tar.gz"
+
+    version('0.12.0', 'e8cde197d6d304bbdc3adae66fec99fb')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-python-socketio/package.py b/var/spack/repos/builtin/packages/py-python-socketio/package.py
new file mode 100644
index 0000000000..169c960f9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-python-socketio/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPythonSocketio(PythonPackage):
+    """Python implementation of the Socket.IO realtime server."""
+
+    homepage = "https://github.com/miguelgrinberg/python-socketio"
+    url      = "https://pypi.io/packages/source/p/python-socketio/python-socketio-1.8.4.tar.gz"
+
+    version('1.8.4', '9de73990f6c32c701278c01b0fa1a0c3')
+
+    variant('eventlet', default=True,
+            description="Pulls in optional eventlet dependency, required"
+                        " for using the zmq implementation.")
+
+    depends_on('py-setuptools',                 type='build')
+    depends_on('py-six@1.9.0:',                 type=("build", "run"))
+    depends_on('py-python-engineio@1.2.1:',     type=("build", "run"))
+    depends_on('py-eventlet', when='+eventlet', type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-pythonqwt/package.py b/var/spack/repos/builtin/packages/py-pythonqwt/package.py
index 9f4c09b537..62551cfc9c 100644
--- a/var/spack/repos/builtin/packages/py-pythonqwt/package.py
+++ b/var/spack/repos/builtin/packages/py-pythonqwt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class PyPythonqwt(PythonPackage):
 
     version('0.5.5', 'a60c7da9fbca667337d14aca094b6fda')
 
-    variant('docs', default=False, description="Build documentation.")
+    variant('doc', default=False, description="Build documentation.")
 
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy@1.3:',   type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pytorch/package.py b/var/spack/repos/builtin/packages/py-pytorch/package.py
new file mode 100644
index 0000000000..d5df52c16f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pytorch/package.py
@@ -0,0 +1,72 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyPytorch(PythonPackage):
+    """Tensors and Dynamic neural networks in Python
+    with strong GPU acceleration."""
+
+    homepage = "http://pytorch.org/"
+    git      = "https://github.com/pytorch/pytorch.git"
+
+    version('0.4.0', tag='v0.4.0', submodules=True)
+    version('0.3.1', tag='v0.3.1', submodules=True)
+
+    variant('cuda', default='False', description='Add GPU support')
+    variant('cudnn', default='False', description='Add cuDNN support')
+    variant('nccl', default='False', description='Add NCCL support')
+    variant('mkldnn', default='False', description='Add Intel MKL DNN support')
+    variant('magma', default='False', description='Add MAGMA support')
+
+    conflicts('+cudnn', when='~cuda')
+    conflicts('+nccl', when='~cuda')
+    conflicts('+magma', when='~cuda')
+    conflicts('+mkldnn', when='@:0.3.2')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cffi', type='build')
+    depends_on('py-numpy', type=('run', 'build'))
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('py-pyyaml', type=('run', 'build'))
+    depends_on('py-typing', when='@0.3.2:', type=('run', 'build'))
+    depends_on('intel-mkl', when='+mkl')
+    depends_on('cuda', when='+cuda', type=('build', 'link', 'run'))
+    depends_on('cudnn', when='+cuda+cudnn')
+    depends_on('nccl', when='+cuda+nccl')
+    depends_on('magma+shared', when='+cuda+magma')
+
+    def setup_environment(self, build_env, run_env):
+        build_env.set('MAX_JOBS', make_jobs)
+
+        if '+cuda' in self.spec:
+            build_env.set('CUDA_HOME', self.spec['cuda'].prefix)
+        else:
+            build_env.set('NO_CUDA', 'TRUE')
+
+        if '+cudnn' in self.spec:
+            build_env.set('CUDNN_LIB_DIR',
+                          self.spec['cudnn'].prefix.lib)
+            build_env.set('CUDNN_INCLUDE_DIR',
+                          self.spec['cudnn'].prefix.include)
+        else:
+            build_env.set('NO_CUDNN', 'TRUE')
+
+        if '+nccl' in self.spec:
+            build_env.set('NCCL_ROOT_DIR', self.spec['nccl'].prefix)
+        else:
+            build_env.set('NO_SYSTEM_NCCL', 'TRUE')
+
+        if '+mkldnn' in self.spec:
+            build_env.set('MKLDNN_HOME', self.spec['intel-mkl'].prefix)
+        else:
+            build_env.set('NO_MKLDNN', 'TRUE')
+
+        build_env.set('NO_NNPACK', 'TRUE')
+
+        build_env.set('PYTORCH_BUILD_VERSION', str(self.version))
+        build_env.set('PYTORCH_BUILD_NUMBER', 0)
diff --git a/var/spack/repos/builtin/packages/py-pytz/package.py b/var/spack/repos/builtin/packages/py-pytz/package.py
index d946e767e9..de453868ae 100644
--- a/var/spack/repos/builtin/packages/py-pytz/package.py
+++ b/var/spack/repos/builtin/packages/py-pytz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,6 +19,7 @@ class PyPytz(PythonPackage):
     version('2016.10',  'cc9f16ba436efabdcef3c4d32ae4919c')
     version('2016.6.1', 'b6c28a3b968bc1d8badfb61b93874e03')
     version('2014.10',  'eb1cb941a20c5b751352c52486aa1dd7')
+    version('2014.9',   'd42bda2f4c1e873e02fbd1e4acfd1b8c')
     version('2015.4',   '417a47b1c432d90333e42084a605d3d8')
     version('2016.3',   'abae92c3301b27bd8a9f56b14f52cb29')
 
diff --git a/var/spack/repos/builtin/packages/py-pyutilib/package.py b/var/spack/repos/builtin/packages/py-pyutilib/package.py
new file mode 100644
index 0000000000..62024068f1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-pyutilib/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class PyPyutilib(PythonPackage):
+    """The PyUtilib project supports a collection of Python utilities,
+    including a well-developed component architecture and extensions to the
+    PyUnit testing framework. PyUtilib has been developed to support several
+    Python-centric projects, especially Pyomo. PyUtilib is available under the
+    BSD License."""
+
+    homepage = "https://github.com/PyUtilib/pyutilib"
+    url      = "https://github.com/PyUtilib/pyutilib/archive/5.5.1.tar.gz"
+
+    version('5.6.2', '60c6ea5083e512211984347ffeca19d2')
+    version('5.6.1', 'ddc7e896304b6fabe4d21eb5fdec386e')
+    version('5.6',   '5bfcdbf118264f1a1b8c6cac9dea8bca')
+    version('5.5.1', 'c4990cbced152d879812d109aaa857ff')
+    version('5.5',   '7940563bf951332cf836f418d67b2134')
+    version('5.4.1', 'b34b5798757e4ab73868b7655c5c8f8a')
+    version('5.4',   '9410e5a76885412310b03074d2f97e55')
+    version('5.3.5', '85e41e65f24f6711261229bcde6eb825')
+    version('5.3.4', '4fe1a8387c027f64b62ca99424275368')
+    version('5.3.3', '27a713ca8d49714244646e1ce38778b9')
+
+    depends_on('py-nose', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-pywavelets/package.py b/var/spack/repos/builtin/packages/py-pywavelets/package.py
index c542a23c1c..dd561b17f4 100644
--- a/var/spack/repos/builtin/packages/py-pywavelets/package.py
+++ b/var/spack/repos/builtin/packages/py-pywavelets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py
index 05ac4d2ac5..3651c6820d 100644
--- a/var/spack/repos/builtin/packages/py-pyyaml/package.py
+++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,4 +11,5 @@ class PyPyyaml(PythonPackage):
     homepage = "http://pyyaml.org/wiki/PyYAML"
     url      = "http://pyyaml.org/download/pyyaml/PyYAML-3.11.tar.gz"
 
+    version('3.12', '4c129761b661d181ebf7ff4eb2d79950')
     version('3.11', 'f50e08ef0fe55178479d3a618efe21db')
diff --git a/var/spack/repos/builtin/packages/py-qtawesome/package.py b/var/spack/repos/builtin/packages/py-qtawesome/package.py
index b5c08a3c60..3d9cd5f77c 100644
--- a/var/spack/repos/builtin/packages/py-qtawesome/package.py
+++ b/var/spack/repos/builtin/packages/py-qtawesome/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-qtconsole/package.py b/var/spack/repos/builtin/packages/py-qtconsole/package.py
index 07acca339b..37b05f9a1b 100644
--- a/var/spack/repos/builtin/packages/py-qtconsole/package.py
+++ b/var/spack/repos/builtin/packages/py-qtconsole/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,8 @@ class PyQtconsole(PythonPackage):
 
     version('4.2.1', 'c08ebebc7a60629ebadf685361ca0798')
 
-    variant('docs', default=False, description='Build documentation')
+    variant('doc', default=False, description='Build documentation')
 
-    depends_on('py-setuptools',          type='build')
     depends_on('py-ipykernel@4.1:',      type=('build', 'run'))
     depends_on('py-jupyter-client@4.1:', type=('build', 'run'))
     depends_on('py-jupyter-core',        type=('build', 'run'))
@@ -43,5 +23,4 @@ class PyQtconsole(PythonPackage):
     depends_on('py-traitlets',           type=('build', 'run'))
     depends_on('py-sphinx@1.3:',         type=('build', 'run'), when='+docs')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-mock', type='test', when='^python@2.7:2.8')
+    depends_on('py-mock', type='test', when='^python@2.7:2.8')
diff --git a/var/spack/repos/builtin/packages/py-qtpy/package.py b/var/spack/repos/builtin/packages/py-qtpy/package.py
index 020894d0e7..aef6a1deb1 100644
--- a/var/spack/repos/builtin/packages/py-qtpy/package.py
+++ b/var/spack/repos/builtin/packages/py-qtpy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-quantities/package.py b/var/spack/repos/builtin/packages/py-quantities/package.py
index d75aced6f9..c0afca77a7 100644
--- a/var/spack/repos/builtin/packages/py-quantities/package.py
+++ b/var/spack/repos/builtin/packages/py-quantities/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-quast/package.py b/var/spack/repos/builtin/packages/py-quast/package.py
new file mode 100644
index 0000000000..41e966b24b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-quast/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyQuast(PythonPackage):
+    """Quality Assessment Tool for Genome Assemblies"""
+
+    homepage = "http://cab.spbu.ru/software/quast"
+    url      = "https://github.com/ablab/quast/archive/quast_4.6.1.tar.gz"
+
+    version('4.6.3', '16d77acb2e0f6436b58d9df7b732fb76')
+    version('4.6.1', '37ccd34e0040c17aa6f990353a92475c')
+    version('4.6.0', 'c04d62c50ec4d9caa9d7388950b8d144')
+
+    depends_on('boost@1.56.0')
+    depends_on('perl@5.6.0:')
+    depends_on('python@2.5:,3.3:')
+    depends_on('py-setuptools',    type='build')
+    depends_on('py-matplotlib',    type=('build', 'run'))
+    depends_on('java',             type=('build', 'run'))
+    depends_on('perl-time-hires',  type=('build', 'run'))
+    depends_on('gnuplot',          type=('build', 'run'))
+    depends_on('mummer',           type=('build', 'run'))
+    depends_on('bedtools2',        type=('build', 'run'))
+    depends_on('bwa',              type=('build', 'run'))
+    depends_on('glimmer',          type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-radical-utils/package.py b/var/spack/repos/builtin/packages/py-radical-utils/package.py
index 85a4832e3e..1a04087ea0 100644
--- a/var/spack/repos/builtin/packages/py-radical-utils/package.py
+++ b/var/spack/repos/builtin/packages/py-radical-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-ranger/package.py b/var/spack/repos/builtin/packages/py-ranger/package.py
index 19f20c6d33..7a923fc638 100644
--- a/var/spack/repos/builtin/packages/py-ranger/package.py
+++ b/var/spack/repos/builtin/packages/py-ranger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-rasterio/package.py b/var/spack/repos/builtin/packages/py-rasterio/package.py
new file mode 100644
index 0000000000..567befd2a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-rasterio/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyRasterio(PythonPackage):
+    """Rasterio reads and writes geospatial raster data.
+    Geographic information systems use GeoTIFF and other formats to
+    organize and store gridded, or raster, datasets. Rasterio reads
+    and writes these formats and provides a Python API based on N-D
+    arrays."""
+
+    homepage = "https://github.com/mapbox/rasterio"
+    url      = "https://github.com/mapbox/rasterio/archive/1.0a12.zip"
+
+    version('1.0a12', 'e078ca02b3513b65a9be5bb3f528b4da')
+
+    variant('aws', default=False,
+        description='Enable testing with Amazon Web Services')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-cython', type='build')
+
+    # Only use py-enum34 with Python2
+    # depends_on('py-enum34', type='run', when='^python@:2.7')
+
+    depends_on('py-attrs', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-cligj', type=('build', 'run'))
+    depends_on('py-click', type=('build', 'run'))
+    depends_on('py-affine', type=('build', 'run'))
+    depends_on('py-snuggs', type=('build', 'run'))
+    depends_on('gdal')
+    depends_on('jpeg')
+
+    # (Commented out for now: py-boto3 is not yet a Spack package)
+    # Some (optional) tests use py-boto3 for Amazon Web Services
+    # depends_on('py-boto3', type=('build', 'run'), when='+aws')
diff --git a/var/spack/repos/builtin/packages/py-readme-renderer/package.py b/var/spack/repos/builtin/packages/py-readme-renderer/package.py
index 20691a12ec..becbc0e1d4 100644
--- a/var/spack/repos/builtin/packages/py-readme-renderer/package.py
+++ b/var/spack/repos/builtin/packages/py-readme-renderer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-regex/package.py b/var/spack/repos/builtin/packages/py-regex/package.py
index 14c40c50cc..e2aeb296bf 100644
--- a/var/spack/repos/builtin/packages/py-regex/package.py
+++ b/var/spack/repos/builtin/packages/py-regex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-reportlab/package.py b/var/spack/repos/builtin/packages/py-reportlab/package.py
new file mode 100644
index 0000000000..e8a1867947
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-reportlab/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyReportlab(PythonPackage):
+    """The ReportLab Toolkit. An Open Source Python library for generating
+    PDFs and graphics."""
+
+    homepage = "https://pypi.python.org/pypi/reportlab"
+    url      = "https://pypi.io/packages/source/r/reportlab/reportlab-3.4.0.tar.gz"
+
+    version('3.4.0', '3f2522cf3b69cd84426c216619bbff53')
diff --git a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py
new file mode 100644
index 0000000000..f19e9fe1d1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyRequestsToolbelt(PythonPackage):
+    """A toolbelt of useful classes and functions to be used with
+    python-requests"""
+
+    homepage = "https://toolbelt.readthedocs.org/"
+    url      = "https://github.com/requests/toolbelt/archive/0.8.0.tar.gz"
+
+    version('0.8.0', 'de9bf7fbcc6ae341a5c4fd9f8912bcac')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-requests@2.0.1:3.0.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-requests/package.py b/var/spack/repos/builtin/packages/py-requests/package.py
index 329c07758c..b5ba4b0d37 100644
--- a/var/spack/repos/builtin/packages/py-requests/package.py
+++ b/var/spack/repos/builtin/packages/py-requests/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -45,11 +26,11 @@ class PyRequests(PythonPackage):
     version('2.14.2', '4c3c169ed67466088a2a6947784fe444')
     version('2.13.0', '921ec6b48f2ddafc8bb6160957baf444')
     version('2.11.1', 'ad5f9c47b5c5dfdb28363ad7546b0763')
+    version('2.3.0',  '7449ffdc8ec9ac37bbcd286003c80f00')
 
     depends_on('py-setuptools', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest@2.8.0:',        type='test')
-    # depends_on('py-pytest-cov',           type='test')
-    # depends_on('py-pytest-httpbin@0.0.7', type='test')
-    # depends_on('py-pytest-mock',          type='test')
+    depends_on('py-pytest@2.8.0:',        type='test')
+    depends_on('py-pytest-cov',           type='test')
+    depends_on('py-pytest-httpbin@0.0.7', type='test')
+    depends_on('py-pytest-mock',          type='test')
diff --git a/var/spack/repos/builtin/packages/py-restview/package.py b/var/spack/repos/builtin/packages/py-restview/package.py
index bd63d64bf5..2f9c735bab 100644
--- a/var/spack/repos/builtin/packages/py-restview/package.py
+++ b/var/spack/repos/builtin/packages/py-restview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-rope/package.py b/var/spack/repos/builtin/packages/py-rope/package.py
index 5f0d27db23..879264707f 100644
--- a/var/spack/repos/builtin/packages/py-rope/package.py
+++ b/var/spack/repos/builtin/packages/py-rope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-rpy2/package.py b/var/spack/repos/builtin/packages/py-rpy2/package.py
index c607360f0a..9ae4464ea1 100644
--- a/var/spack/repos/builtin/packages/py-rpy2/package.py
+++ b/var/spack/repos/builtin/packages/py-rpy2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,14 +16,25 @@ class PyRpy2(PythonPackage):
     homepage = "https://pypi.python.org/pypi/rpy2"
     url = "https://pypi.io/packages/source/r/rpy2/rpy2-2.5.4.tar.gz"
 
-    version('2.5.4', '115a20ac30883f096da2bdfcab55196d')
+    version('2.9.4', '7df2562cdf43a0ccdd1e44ee1c16614f')
+    version('2.8.6', '85046aa58ba586622f67271fbca05933')
     version('2.5.6', 'a36e758b633ce6aec6a5f450bfee980f')
+    version('2.5.4', '115a20ac30883f096da2bdfcab55196d')
 
     # FIXME: Missing dependencies:
     # ld: cannot find -licuuc
     # ld: cannot find -licui18
 
-    depends_on('py-six', type=('build', 'run'))
+    # All versions
     depends_on('py-setuptools', type='build')
+    depends_on('r',             type=('build', 'run'))
+
+    # @2.9.0:
+    depends_on('r@3.3:',    when='@2.9.0:', type=('build', 'run'))
+    depends_on('python@3:', when='@2.9.0:', type=('build', 'run'))
+    depends_on('py-jinja2', when='@2.9.0:', type=('build', 'run'))
+    depends_on('py-six',    when='@2.9.0:', type=('build', 'run'))
 
-    depends_on('r')
+    # @:2.8.6
+    depends_on('r@2.8:', when='@:2.8.6', type=('build', 'run'))
+    depends_on('py-singledispatch', when='^python@:2',   type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-rsa/package.py b/var/spack/repos/builtin/packages/py-rsa/package.py
index 6cde68a33f..287d39279a 100644
--- a/var/spack/repos/builtin/packages/py-rsa/package.py
+++ b/var/spack/repos/builtin/packages/py-rsa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-rseqc/package.py b/var/spack/repos/builtin/packages/py-rseqc/package.py
new file mode 100644
index 0000000000..15563be2a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-rseqc/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyRseqc(PythonPackage):
+    """RSeQC package provides a number of useful modules that can
+    comprehensively evaluate high throughput sequence data especially RNA-seq
+    data."""
+
+    homepage = "http://rseqc.sourceforge.net"
+    url      = "https://pypi.io/packages/source/R/RSeQC/RSeQC-2.6.4.tar.gz"
+
+    version('2.6.4', '935779c452ffc84f3b8b9fb3d485c782')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-bx-python',  type=('build', 'run'))
+    depends_on('py-numpy',      type=('build', 'run'))
+    depends_on('py-pysam',      type=('build', 'run'))
+    depends_on('r',             type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-rtree/package.py b/var/spack/repos/builtin/packages/py-rtree/package.py
index 70eb46575c..e1be4c6aee 100644
--- a/var/spack/repos/builtin/packages/py-rtree/package.py
+++ b/var/spack/repos/builtin/packages/py-rtree/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-saga-python/package.py b/var/spack/repos/builtin/packages/py-saga-python/package.py
index 4eb83b1dc1..2890c16889 100644
--- a/var/spack/repos/builtin/packages/py-saga-python/package.py
+++ b/var/spack/repos/builtin/packages/py-saga-python/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-scandir/package.py b/var/spack/repos/builtin/packages/py-scandir/package.py
new file mode 100644
index 0000000000..09aa29a662
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-scandir/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyScandir(PythonPackage):
+    """scandir, a better directory iterator and faster os.walk()."""
+
+    homepage = "https://github.com/benhoyt/scandir"
+    url      = "https://pypi.io/packages/source/s/scandir/scandir-1.9.0.tar.gz"
+
+    import_modules = ['scandir']
+
+    version('1.9.0', '506c4cc5f38c00b301642a9cb0433910')
+    version('1.6',   '0180ddb97c96cbb2d4f25d2ae11c64ac')
+
+    depends_on('py-setuptools', type=('build'))
diff --git a/var/spack/repos/builtin/packages/py-scientificpython/package.py b/var/spack/repos/builtin/packages/py-scientificpython/package.py
index 45fedc825b..4926de0054 100644
--- a/var/spack/repos/builtin/packages/py-scientificpython/package.py
+++ b/var/spack/repos/builtin/packages/py-scientificpython/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py
index 40cbf740fe..f9a270f96d 100644
--- a/var/spack/repos/builtin/packages/py-scikit-image/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,3 +24,4 @@ class PyScikitImage(PythonPackage):
     depends_on('py-scipy', type=('build', 'run'))
     depends_on('py-matplotlib', type=('build', 'run'))
     depends_on('py-setuptools', type='build')
+    depends_on('py-cython@0.23.4:', type='build')
diff --git a/var/spack/repos/builtin/packages/py-scikit-learn/package.py b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
index 81f5de2737..9a5df494f2 100644
--- a/var/spack/repos/builtin/packages/py-scikit-learn/package.py
+++ b/var/spack/repos/builtin/packages/py-scikit-learn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,8 @@ class PyScikitLearn(PythonPackage):
     homepage = "https://pypi.python.org/pypi/scikit-learn"
     url      = "https://pypi.io/packages/source/s/scikit-learn/scikit-learn-0.18.1.tar.gz"
 
+    version('0.20.0', sha256='97d1d971f8ec257011e64b7d655df68081dd3097322690afa1a71a1d755f8c18')
+    version('0.19.1', 'b67143988c108862735a96cf2b1e827a')
     version('0.18.1', '6b0ff1eaa5010043895dd63d1e3c60c9')
     version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d')
     version('0.16.1', '363ddda501e3b6b61726aa40b8dbdb7e')
diff --git a/var/spack/repos/builtin/packages/py-scipy/package.py b/var/spack/repos/builtin/packages/py-scipy/package.py
index 3aced0bf4a..8b04bda75d 100644
--- a/var/spack/repos/builtin/packages/py-scipy/package.py
+++ b/var/spack/repos/builtin/packages/py-scipy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -49,9 +30,9 @@ class PyScipy(PythonPackage):
         'scipy.special._precompute'
     ]
 
-    # See https://github.com/spack/spack/issues/2737
-    version('0.19.1', '6b4d91b62f1926282b127194a06b72b3',
-            url="https://pypi.io/packages/source/s/scipy/scipy-0.19.1.tar.gz")
+    version('1.1.0', 'aa6bcc85276b6f25e17bcfc4dede8718')
+    version('1.0.0', '53fa34bd3733a9a4216842b6000f7316')
+    version('0.19.1', '6b4d91b62f1926282b127194a06b72b3')
     version('0.19.0', '91b8396231eec780222a57703d3ec550',
             url="https://pypi.io/packages/source/s/scipy/scipy-0.19.0.zip")
     version('0.18.1', '5fb5fb7ccb113ab3a039702b6c2f3327')
@@ -61,6 +42,7 @@ class PyScipy(PythonPackage):
 
     depends_on('python@2.6:2.8,3.2:')
     depends_on('py-setuptools', type='build')
+    depends_on('py-nose', type='test')
     depends_on('py-numpy@1.7.1:+blas+lapack', type=('build', 'run'))
 
     # NOTE: scipy picks up Blas/Lapack from numpy, see
@@ -68,17 +50,14 @@ class PyScipy(PythonPackage):
     depends_on('blas')
     depends_on('lapack')
 
-    # Tests require:
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose', type='test')
-
     def build_args(self, spec, prefix):
         args = []
 
         # Build in parallel
-        # Known problems with Python 3
+        # Known problems with Python 3.5+
+        # https://github.com/spack/spack/issues/7927
         # https://github.com/scipy/scipy/issues/7112
-        if not spec.satisfies('^python@3:'):
+        if not spec.satisfies('^python@3.5:'):
             args.extend(['-j', str(make_jobs)])
 
         return args
@@ -99,5 +78,5 @@ class PyScipy(PythonPackage):
         # ImportError: Error importing scipy: you should not try to import
         #       scipy from its source directory; please exit the scipy
         #       source tree, and relaunch your python interpreter from there.
-        with working_dir('..'):
+        with working_dir('spack-test', create=True):
             python('-c', 'import scipy; scipy.test("full", verbose=2)')
diff --git a/var/spack/repos/builtin/packages/py-seaborn/package.py b/var/spack/repos/builtin/packages/py-seaborn/package.py
index d0bd755343..129de71574 100644
--- a/var/spack/repos/builtin/packages/py-seaborn/package.py
+++ b/var/spack/repos/builtin/packages/py-seaborn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,6 +17,7 @@ class PySeaborn(PythonPackage):
     homepage = "http://seaborn.pydata.org/"
     url      = "https://pypi.io/packages/source/s/seaborn/seaborn-0.7.1.tar.gz"
 
+    version('0.9.0', '76c83f794ca320fb6b23a7c6192d5e185a5fcf4758966a0c0a54baee46d41e2f')
     version('0.7.1', 'ef07e29e0f8a1f2726abe506c1a36e93')
 
     depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-setuptools-git/package.py b/var/spack/repos/builtin/packages/py-setuptools-git/package.py
new file mode 100644
index 0000000000..23569c4534
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-setuptools-git/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySetuptoolsGit(PythonPackage):
+    """Setuptools revision control system plugin for Git"""
+
+    homepage = "https://pypi.python.org/pypi/setuptools-git"
+    url      = "https://pypi.io/packages/source/s/setuptools-git/setuptools-git-1.2.tar.gz"
+
+    version('1.2', '40b2ef7687a384ea144503c2e5bc67e2')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('git')
diff --git a/var/spack/repos/builtin/packages/py-setuptools-scm/package.py b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py
new file mode 100644
index 0000000000..dd2321fbd0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-setuptools-scm/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySetuptoolsScm(PythonPackage):
+    """The blessed package to manage your versions by scm tags."""
+
+    homepage = "https://github.com/pypa/setuptools_scm"
+    url      = "https://pypi.io/packages/source/s/setuptools_scm/setuptools_scm-3.1.0.tar.gz"
+
+    import_modules = ['setuptools_scm']
+
+    version('3.1.0',  '52a8dee23c9e5f7d7d18094563db516c')
+    version('1.15.6', 'f17493d53f0d842bb0152f214775640b')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py
index de7b47367b..c37d62414b 100644
--- a/var/spack/repos/builtin/packages/py-setuptools/package.py
+++ b/var/spack/repos/builtin/packages/py-setuptools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,17 +10,24 @@ class PySetuptools(PythonPackage):
     """A Python utility that aids in the process of downloading, building,
        upgrading, installing, and uninstalling Python packages."""
 
-    homepage = "https://pypi.python.org/pypi/setuptools"
-    url      = "https://pypi.io/packages/source/s/setuptools/setuptools-25.2.0.tar.gz"
+    homepage = "https://github.com/pypa/setuptools"
+    url      = "https://pypi.io/packages/source/s/setuptools/setuptools-40.2.0.zip"
 
-    import_modules = ['pkg_resources', 'setuptools', 'setuptools.command']
+    import_modules = [
+        'setuptools', 'pkg_resources', 'setuptools._vendor',
+        'setuptools.command', 'setuptools.extern',
+        'setuptools._vendor.packaging', 'pkg_resources._vendor',
+        'pkg_resources.extern', 'pkg_resources._vendor.packaging',
+        'easy_install'
+    ]
 
-    version('35.0.2', 'c368b4970d3ad3eab5afe4ef4dbe2437',
-            url="https://pypi.io/packages/source/s/setuptools/setuptools-35.0.2.zip")
-    version('34.4.1', '5f9b07aeaafd29eac2548fc0b89a4934',
-            url="https://pypi.io/packages/source/s/setuptools/setuptools-34.4.1.zip")
-    version('34.2.0', '41b630da4ea6cfa5894d9eb3142922be',
-            url="https://pypi.io/packages/source/s/setuptools/setuptools-34.2.0.zip")
+    version('40.4.3', sha256='acbc5740dd63f243f46c2b4b8e2c7fd92259c2ddb55a4115b16418a2ed371b15')
+    version('40.2.0', '592efabea3a65d8e97a025ed52f69b12')
+    version('39.2.0', 'dd4e3fa83a21bf7bf9c51026dc8a4e59')
+    version('39.0.1', '75310b72ca0ab4e673bf7679f69d7a62')
+    version('35.0.2', 'c368b4970d3ad3eab5afe4ef4dbe2437')
+    version('34.4.1', '5f9b07aeaafd29eac2548fc0b89a4934')
+    version('34.2.0', '41b630da4ea6cfa5894d9eb3142922be')
     version('25.2.0', 'a0dbb65889c46214c691f6c516cf959c')
     version('20.7.0', '5d12b39bf3e75e80fdce54e44b255615')
     version('20.6.7', '45d6110f3ec14924e44c33411db64fe6')
@@ -49,11 +37,29 @@ class PySetuptools(PythonPackage):
     version('16.0',   '0ace0b96233516fc5f7c857d086aa3ad')
     version('11.3.1', '01f69212e019a2420c1693fb43593930')
 
-    depends_on('python@2.6:2.8,3.3:')
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
 
     # Previously, setuptools vendored all of its dependencies to allow
     # easy bootstrapping. As of version 34.0.0, this is no longer done
-    # and the dependencies need to be installed externally.
-    depends_on('py-packaging@16.8:', when='@34.0.0:', type=('build', 'run'))
-    depends_on('py-six@1.6.0:',      when='@34.0.0:', type=('build', 'run'))
-    depends_on('py-appdirs@1.4.0:',  when='@34.0.0:', type=('build', 'run'))
+    # and the dependencies need to be installed externally. As of version
+    # 36.0.0, setuptools now vendors its dependencies again. See
+    # https://github.com/pypa/setuptools/issues/980 for the reason they
+    # reverted back to vendoring again.
+    depends_on('py-packaging@16.8:', when='@34:35', type=('build', 'run'))
+    depends_on('py-six@1.6.0:',      when='@34:35', type=('build', 'run'))
+    depends_on('py-appdirs@1.4.0:',  when='@34:35', type=('build', 'run'))
+
+    def url_for_version(self, version):
+        url = 'https://pypi.io/packages/source/s/setuptools/setuptools-{0}'
+        url = url.format(version)
+
+        if version > Version('32.1.2'):
+            url += '.zip'
+        else:
+            url += '.tar.gz'
+
+        return url
+
+    def test(self):
+        # Unit tests require pytest, creating a circular dependency
+        pass
diff --git a/var/spack/repos/builtin/packages/py-sfepy/package.py b/var/spack/repos/builtin/packages/py-sfepy/package.py
new file mode 100644
index 0000000000..efd3305bf4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-sfepy/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySfepy(PythonPackage):
+    """SfePy (http://sfepy.org) is a software for solving systems of coupled
+    partial differential equations (PDEs) by the finite element method in 1D,
+    2D and 3D. It can be viewed both as black-box PDE solver, and as a Python
+    package which can be used for building custom applications.
+    """
+
+    homepage = "http://sfepy.org"
+    url      = "https://github.com/sfepy/sfepy/archive/release_2017.3.tar.gz"
+
+    version('2017.3', '65ab606a9fe80fccf17a7eb5ab8fd025')
+
+    variant('petsc', default=False, description='Enable PETSc support')
+
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six', type='run')
+    depends_on('py-scipy', type='run')
+    depends_on('py-matplotlib', type='run')
+    depends_on('py-sympy', type='run')
+    depends_on('hdf5+hl', type='run')
+    depends_on('py-pytables', type='run')
+    depends_on('py-petsc4py', type='run', when='+petsc')
diff --git a/var/spack/repos/builtin/packages/py-sh/package.py b/var/spack/repos/builtin/packages/py-sh/package.py
index 8dc74c0740..4fd4ecb8bf 100644
--- a/var/spack/repos/builtin/packages/py-sh/package.py
+++ b/var/spack/repos/builtin/packages/py-sh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-shapely/package.py b/var/spack/repos/builtin/packages/py-shapely/package.py
new file mode 100644
index 0000000000..ba82ef2229
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-shapely/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyShapely(PythonPackage):
+    """Manipulation and analysis of geometric objects in the Cartesian plane.
+    """
+
+    homepage = "https://github.com/Toblerity/Shapely"
+    url      = "https://pypi.io/packages/source/S/Shapely/Shapely-1.6.4.tar.gz"
+
+    version('1.6.4', '7581ef2d0fb346f9ed157f3efc75f6a4')
+
+    depends_on('python@2.6.0:2.8,3.4.0:', type=('build', 'run'))
+    depends_on('py-setuptools',     type='build')
+    depends_on('py-cython@0.19:',   type='build')
+    depends_on('py-numpy@1.4.1:',   type=('build', 'run'))
+    depends_on('geos@3.3:')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('GEOS_CONFIG', self.spec['geos'].prefix)
+        spack_env.prepend_path('LD_LIBRARY_PATH', self.spec['geos'].prefix.lib)
diff --git a/var/spack/repos/builtin/packages/py-shiboken/package.py b/var/spack/repos/builtin/packages/py-shiboken/package.py
index cf04385c62..02197e7571 100644
--- a/var/spack/repos/builtin/packages/py-shiboken/package.py
+++ b/var/spack/repos/builtin/packages/py-shiboken/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/py-simplegeneric/package.py b/var/spack/repos/builtin/packages/py-simplegeneric/package.py
index a704436281..5fc961ccc0 100644
--- a/var/spack/repos/builtin/packages/py-simplegeneric/package.py
+++ b/var/spack/repos/builtin/packages/py-simplegeneric/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-simplejson/package.py b/var/spack/repos/builtin/packages/py-simplejson/package.py
index 6894d62044..1b7ad7e071 100644
--- a/var/spack/repos/builtin/packages/py-simplejson/package.py
+++ b/var/spack/repos/builtin/packages/py-simplejson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-singledispatch/package.py b/var/spack/repos/builtin/packages/py-singledispatch/package.py
index 6007fda635..ca9ed4513c 100644
--- a/var/spack/repos/builtin/packages/py-singledispatch/package.py
+++ b/var/spack/repos/builtin/packages/py-singledispatch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sip/package.py b/var/spack/repos/builtin/packages/py-sip/package.py
index 4c4a5af463..afa4aeee9b 100644
--- a/var/spack/repos/builtin/packages/py-sip/package.py
+++ b/var/spack/repos/builtin/packages/py-sip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/py-six/package.py b/var/spack/repos/builtin/packages/py-six/package.py
index 2f0bda16c6..acbc674d7b 100644
--- a/var/spack/repos/builtin/packages/py-six/package.py
+++ b/var/spack/repos/builtin/packages/py-six/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,14 @@ class PySix(PythonPackage):
     """Python 2 and 3 compatibility utilities."""
 
     homepage = "https://pypi.python.org/pypi/six"
-    url      = "https://pypi.io/packages/source/s/six/six-1.10.0.tar.gz"
+    url      = "https://pypi.io/packages/source/s/six/six-1.11.0.tar.gz"
 
     import_modules = ['six']
 
+    version('1.11.0', 'd12789f9baf7e9fb2524c0c64f1773f8')
     version('1.10.0', '34eed507548117b2ab523ab14b2f8b55')
     version('1.9.0',  '476881ef4012262dfc8adc645ee786c4')
+    version('1.8.0',  '1626eb24cc889110c38f7e786ec69885')
 
     extends('python', ignore=r'bin/pytest')
 
diff --git a/var/spack/repos/builtin/packages/py-slepc4py/package.py b/var/spack/repos/builtin/packages/py-slepc4py/package.py
index f9603abd9b..279f805052 100644
--- a/var/spack/repos/builtin/packages/py-slepc4py/package.py
+++ b/var/spack/repos/builtin/packages/py-slepc4py/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py b/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py
new file mode 100644
index 0000000000..ffece8a2ac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-slurm-pipeline/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySlurmPipeline(PythonPackage):
+    """A Python class for scheduling SLURM jobs"""
+
+    homepage = "https://github.com/acorg/slurm-pipeline"
+    url      = "https://pypi.io/packages/source/s/slurm-pipeline/slurm-pipeline-1.1.13.tar.gz"
+
+    version('2.0.9',  '7f97d2410db441081b79ac5c3395b8d0')
+    version('1.1.13', 'd1f8c78a64718ec5e2e40ba1b6816017')
+
+    depends_on('py-setuptools', type='build')
+    # using open range although requirements*.txt give explicit versions
+    # test dependencies are omitted, see #7681
+    depends_on('py-six@1.10.0:', type=('build', 'run'))
+    # six only required for python 2, change when ^-dependencies work, cf #2793
+    # depends_on('py-six@1.10.0:', type=('build', 'run'), when='^python@:2.8')
diff --git a/var/spack/repos/builtin/packages/py-sncosmo/package.py b/var/spack/repos/builtin/packages/py-sncosmo/package.py
index 87c1f44fad..d44724d41c 100644
--- a/var/spack/repos/builtin/packages/py-sncosmo/package.py
+++ b/var/spack/repos/builtin/packages/py-sncosmo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py
index 5122d4600a..19e3d99afe 100644
--- a/var/spack/repos/builtin/packages/py-snowballstemmer/package.py
+++ b/var/spack/repos/builtin/packages/py-snowballstemmer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-snuggs/package.py b/var/spack/repos/builtin/packages/py-snuggs/package.py
new file mode 100644
index 0000000000..7224d9e7bf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-snuggs/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PySnuggs(PythonPackage):
+    """Snuggs are s-expressions for Numpy"""
+
+    homepage = "https://github.com/mapbox/snuggs"""
+    url      = "https://github.com/mapbox/snuggs/archive/1.4.1.zip"
+
+    version('1.4.1', 'bfc4058c32faa4ef76ab7946755557cc')
+
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-click', type=('build', 'run'))
+    depends_on('py-pyparsing', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-spectra/package.py b/var/spack/repos/builtin/packages/py-spectra/package.py
index 9584b659f8..37891536d9 100644
--- a/var/spack/repos/builtin/packages/py-spectra/package.py
+++ b/var/spack/repos/builtin/packages/py-spectra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,7 +12,9 @@ class PySpectra(PythonPackage):
     homepage = "https://pypi.python.org/pypi/spectra/0.0.8"
     url      = "https://pypi.io/packages/source/s/spectra/spectra-0.0.8.tar.gz"
 
+    version('0.0.11', sha256='8eb362a5187cb63cee13cd01186799c0c791a3ad3bec57b279132e12521762b8')
     version('0.0.8', '83020b29e584389f24c7720f38f0136c')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-colormath', type=('build', 'run'))
+    depends_on('py-colormath@3.0.0:', type=('build', 'run'), when='@0.0.11:')
diff --git a/var/spack/repos/builtin/packages/py-spefile/package.py b/var/spack/repos/builtin/packages/py-spefile/package.py
index dbb8937dc8..c6b4adba1f 100644
--- a/var/spack/repos/builtin/packages/py-spefile/package.py
+++ b/var/spack/repos/builtin/packages/py-spefile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,11 @@ class PySpefile(PythonPackage):
        analysis of x-ray scattering experiments"""
 
     homepage = "https://github.com/conda-forge/spefile-feedstock"
-    url      = "https://github.com/conda-forge/spefile-feedstock.git"
+    git      = "https://github.com/conda-forge/spefile-feedstock.git"
 
     import_modules = ['spefile']
 
-    version('1.6', git='https://github.com/conda-forge/spefile-feedstock.git',
-            commit='24394e066da8dee5e7608f556ca0203c9db217f9')
+    version('1.6', commit='24394e066da8dee5e7608f556ca0203c9db217f9')
 
     depends_on('py-setuptools', type='build')
     depends_on('py-numpy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-spglib/package.py b/var/spack/repos/builtin/packages/py-spglib/package.py
index 604aa0faf2..271ca68e82 100644
--- a/var/spack/repos/builtin/packages/py-spglib/package.py
+++ b/var/spack/repos/builtin/packages/py-spglib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py
index faaa9811df..878b18195c 100644
--- a/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinx-bootstrap-theme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py b/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py
index bd922fadf7..bb799915aa 100644
--- a/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinx-rtd-theme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinx/package.py b/var/spack/repos/builtin/packages/py-sphinx/package.py
index d99ee12f0e..3f0268732f 100644
--- a/var/spack/repos/builtin/packages/py-sphinx/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,6 +21,7 @@ class PySphinx(PythonPackage):
         'sphinx.environment.collectors', 'sphinx.environment.adapters'
     ]
 
+    version('1.7.4', '95f3b83f521314600e5b09e99cf32c46')
     version('1.6.3', 'c5ad61f4e0974375ca2c2b58ef8d5411')
     version('1.6.1', '26cb1cdca7aa4afc8c925d926b6268e7')
     version('1.5.5', 'f9581b3556df9722143c47290273bcf8')
@@ -51,6 +33,9 @@ class PySphinx(PythonPackage):
     # Sphinx requires at least Python 2.7 or 3.4 to run
     depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
 
+    # See here for upstream list of dependencies:
+    # https://github.com/sphinx-doc/sphinx/blob/master/setup.py
+
     # Most Python packages only require py-setuptools as a build dependency.
     # However, py-sphinx requires py-setuptools during runtime as well.
     depends_on('py-setuptools',               type=('build', 'run'))
@@ -65,6 +50,8 @@ class PySphinx(PythonPackage):
     depends_on('py-imagesize', when='@1.4:',  type=('build', 'run'))
     depends_on('py-requests@2.0.0:',          type=('build', 'run'))
     depends_on('py-sphinx-rtd-theme@0.1:',    type=('build', 'run'))  # optional as of 1.4
+    # See: https://github.com/sphinx-doc/sphinx/commit/854a227501a7582510eba41a208d25816f754e0c
+    depends_on('py-packaging', type=('build', 'run'), when='@1.7.4:')
 
     # Sphinx v1.6+ no longer includes websupport by default:
     # http://www.sphinx-doc.org/en/stable/changes.html
@@ -78,8 +65,7 @@ class PySphinx(PythonPackage):
     #            type=('build', 'run'))
     depends_on('py-typing', when='@1.6:', type=('build', 'run'))
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest',     type='test')
-    # depends_on('py-mock',       type='test')
-    # depends_on('py-simplejson', type='test')
-    # depends_on('py-html5lib',   type='test')
+    depends_on('py-pytest',     type='test')
+    depends_on('py-mock',       type='test')
+    depends_on('py-simplejson', type='test')
+    depends_on('py-html5lib',   type='test')
diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py
index e643a8d933..b0dc62142b 100644
--- a/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-bibtex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py
index d9dbafb3e3..bc8cd15609 100644
--- a/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-programoutput/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py
index b75f894c1d..f823a0fadb 100644
--- a/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py
+++ b/var/spack/repos/builtin/packages/py-sphinxcontrib-websupport/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,6 +23,5 @@ class PySphinxcontribWebsupport(PythonPackage):
 
     depends_on('py-setuptools', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-pytest', type='test')
-    # depends_on('py-mock',   type='test')
+    depends_on('py-pytest', type='test')
+    depends_on('py-mock',   type='test')
diff --git a/var/spack/repos/builtin/packages/py-spyder/package.py b/var/spack/repos/builtin/packages/py-spyder/package.py
index 58bc3f9fce..57ce28a28a 100644
--- a/var/spack/repos/builtin/packages/py-spyder/package.py
+++ b/var/spack/repos/builtin/packages/py-spyder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class PySpyder(PythonPackage):
     version('3.1.3', '4b9b7c8c3e6dc00001e6e98473473c36')
     version('2.3.9', 'dd01e07a77123c128ff79ba57b97c1d7')
 
-    depends_on('py-setuptools',       type='build')
+    depends_on('python@2.7.0:2.8.0,3.3.0:', type=('build', 'run'))
     depends_on('py-rope@0.9.4:',      type=('build', 'run'), when='^python@:3')
     # depends_on('py-rope_py3k',    type=('build', 'run'), when='^python@3:')
     depends_on('py-jedi@0.9.0',       type=('build', 'run'))
@@ -44,12 +25,21 @@ class PySpyder(PythonPackage):
     depends_on('py-qtconsole@4.2.0:', type=('build', 'run'))
     depends_on('py-nbconvert',        type=('build', 'run'))
     depends_on('py-sphinx',           type=('build', 'run'))
-    depends_on('py-pycodestyle',      type=('build', 'run'))
+    # The pycodestyle dependency is split in two, because internally it
+    # changes its name from pep8 to pycodestyle, and spyder does not cope
+    # with this change until @3.2.0
+    # https://github.com/PyCQA/pycodestyle/issues/466
+    # https://github.com/spyder-ide/spyder/blob/master/CHANGELOG.md#version-32-2017-07-24
+    depends_on('py-pycodestyle@:1.7.1', when='@:3.1.99', type=('build', 'run'))
+    depends_on('py-pycodestyle@2.1.0:', when='@3.2.0:',  type=('build', 'run'))
     depends_on('py-pylint',           type=('build', 'run'))
     depends_on('py-psutil',           type=('build', 'run'))
     depends_on('py-qtawesome@0.4.1:', type=('build', 'run'))
     depends_on('py-qtpy@1.1.0:',      type=('build', 'run'))
-    depends_on('py-zmq',              type=('build', 'run'))
-    depends_on('py-chardet@2:',       type=('build', 'run'))
+    # technically this is a transitive dependency in order for py-pyqt
+    # to pick up webkit, but this is the easier solution (see #9207)
+    depends_on('qt+webkit',           type=('build', 'run'))
     depends_on('py-pickleshare',      type=('build', 'run'))
+    depends_on('py-zmq',              type=('build', 'run'))
+    depends_on('py-chardet@2.0.0:',   type=('build', 'run'))
     depends_on('py-numpydoc',         type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-spykeutils/package.py b/var/spack/repos/builtin/packages/py-spykeutils/package.py
index cdccc3be67..466ec83895 100644
--- a/var/spack/repos/builtin/packages/py-spykeutils/package.py
+++ b/var/spack/repos/builtin/packages/py-spykeutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py
index 8f60538c77..16ce8b76c9 100644
--- a/var/spack/repos/builtin/packages/py-sqlalchemy/package.py
+++ b/var/spack/repos/builtin/packages/py-sqlalchemy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-statsmodels/package.py b/var/spack/repos/builtin/packages/py-statsmodels/package.py
index 641dc197af..b206410d39 100644
--- a/var/spack/repos/builtin/packages/py-statsmodels/package.py
+++ b/var/spack/repos/builtin/packages/py-statsmodels/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-stevedore/package.py b/var/spack/repos/builtin/packages/py-stevedore/package.py
new file mode 100644
index 0000000000..5cd8c5ec43
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-stevedore/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyStevedore(PythonPackage):
+    """Manage Dynamic Plugins for Python Applications."""
+
+    homepage = "https://docs.openstack.org/stevedore/latest/"
+    url      = "https://pypi.io/packages/source/s/stevedore/stevedore-1.28.0.tar.gz"
+
+    version('1.28.0', 'b736a71431a2ff5831bbff4a6ccec0c1')
+
+    depends_on('python@2.6:')
+
+    depends_on('py-six@1.10.0:', type=('build', 'run'))
+    depends_on('py-pbr@2.0.0:2.1.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-storm/package.py b/var/spack/repos/builtin/packages/py-storm/package.py
index 8552413694..2274a5d3ea 100644
--- a/var/spack/repos/builtin/packages/py-storm/package.py
+++ b/var/spack/repos/builtin/packages/py-storm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-subprocess32/package.py b/var/spack/repos/builtin/packages/py-subprocess32/package.py
index 66c6e3b86d..831f0ae428 100644
--- a/var/spack/repos/builtin/packages/py-subprocess32/package.py
+++ b/var/spack/repos/builtin/packages/py-subprocess32/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-symengine/package.py b/var/spack/repos/builtin/packages/py-symengine/package.py
index 6de1c159c3..021604a88b 100644
--- a/var/spack/repos/builtin/packages/py-symengine/package.py
+++ b/var/spack/repos/builtin/packages/py-symengine/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,11 @@ class PySymengine(PythonPackage):
     """Python wrappers for SymEngine, a symbolic manipulation library."""
 
     homepage = "https://github.com/symengine/symengine.py"
-    url = "https://github.com/symengine/symengine.py/archive/v0.2.0.tar.gz"
+    url      = "https://github.com/symengine/symengine.py/archive/v0.2.0.tar.gz"
+    git      = "https://github.com/symengine/symengine.py.git"
 
+    version('develop', branch='master')
     version('0.2.0', 'e1d114fa12be4c8c7e9f24007e07718c')
-    version('develop', git='https://github.com/symengine/symengine.py.git')
 
     # Build dependencies
     depends_on('python@2.7:2.8,3.3:')
diff --git a/var/spack/repos/builtin/packages/py-symfit/package.py b/var/spack/repos/builtin/packages/py-symfit/package.py
index 6ecf2ebee6..a876ef689d 100644
--- a/var/spack/repos/builtin/packages/py-symfit/package.py
+++ b/var/spack/repos/builtin/packages/py-symfit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-sympy/package.py b/var/spack/repos/builtin/packages/py-sympy/package.py
index 2a6758bbf6..f9289f9b0f 100644
--- a/var/spack/repos/builtin/packages/py-sympy/package.py
+++ b/var/spack/repos/builtin/packages/py-sympy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,8 @@ class PySympy(PythonPackage):
     homepage = "https://pypi.python.org/pypi/sympy"
     url      = "https://pypi.io/packages/source/s/sympy/sympy-0.7.6.tar.gz"
 
-    version('0.7.6', '3d04753974306d8a13830008e17babca')
+    version('1.1.1', 'c410a9c2346878716d16ec873d72e72a')
     version('1.0', '43e797de799f00f9e8fd2307dba9fab1')
+    version('0.7.6', '3d04753974306d8a13830008e17babca')
 
     depends_on('py-mpmath', when='@1.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-tabulate/package.py b/var/spack/repos/builtin/packages/py-tabulate/package.py
index 7083d69506..6a3058a769 100644
--- a/var/spack/repos/builtin/packages/py-tabulate/package.py
+++ b/var/spack/repos/builtin/packages/py-tabulate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tappy/package.py
index 3600e56fc8..ae2c5b360b 100644
--- a/var/spack/repos/builtin/packages/py-tappy/package.py
+++ b/var/spack/repos/builtin/packages/py-tappy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-terminado/package.py b/var/spack/repos/builtin/packages/py-terminado/package.py
index 0cf4e582f2..f77097c4d8 100644
--- a/var/spack/repos/builtin/packages/py-terminado/package.py
+++ b/var/spack/repos/builtin/packages/py-terminado/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-testinfra/package.py b/var/spack/repos/builtin/packages/py-testinfra/package.py
new file mode 100644
index 0000000000..e866245794
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-testinfra/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyTestinfra(PythonPackage):
+    """With Testinfra you can write unit tests in Python to test actual state
+    of your servers configured by management tools like Salt, Ansible, Puppet,
+    Chef and so on."""
+
+    homepage = "https://testinfra.readthedocs.io"
+    url      = "https://pypi.python.org/packages/source/t/testinfra/testinfra-1.11.1.tar.gz"
+
+    version('1.13.0', '1e0a135c784207f8609e7730901f1291')
+    version('1.12.0', '9784c01d7af3d624c6ec3cd25cce2011')
+    version('1.11.1', 'c64ce6b16661d647c62c9508de419f5f')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-importlib', when='^python@2.6.0:2.6.999', type=('build', 'run'))
+    depends_on('py-pytest@:3.0.1,3.0.3:', type=('build', 'run'))
+    depends_on('py-six@1.4:', type=('build', 'run'))
+
+    # Required for testing remote systems
+    depends_on('py-paramiko', type=('build', 'run'))
+
+    # Required for parallel execution
+    depends_on('py-pytest-xdist', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-tetoolkit/package.py b/var/spack/repos/builtin/packages/py-tetoolkit/package.py
new file mode 100644
index 0000000000..c43950c518
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-tetoolkit/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyTetoolkit(PythonPackage):
+    """TEToolkit is a software package that utilizes both unambiguously
+       (uniquely) and ambiguously (multi-) mapped reads to perform
+       differential enrichment analyses from high throughput sequencing
+       experiments."""
+
+    homepage = "http://hammelllab.labsites.cshl.edu/software"
+    url      = "https://pypi.io/packages/source/T/TEToolkit/TEToolkit-1.5.1.tar.gz"
+
+    version('1.5.1', '05745b2d5109911e95593e423446a831')
+
+    depends_on('py-setuptools')
+    depends_on('python@2.7:', type=('build', 'run'))
+    depends_on('py-pysam', type=('build', 'run'))
+    depends_on('r-deseq', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-theano/package.py b/var/spack/repos/builtin/packages/py-theano/package.py
index 4fe8920dd5..a808fa896b 100644
--- a/var/spack/repos/builtin/packages/py-theano/package.py
+++ b/var/spack/repos/builtin/packages/py-theano/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,13 @@ class PyTheano(PythonPackage):
     and GPUs."""
 
     homepage = "http://deeplearning.net/software/theano/"
-    url = "https://pypi.io/packages/source/T/Theano/Theano-0.8.2.tar.gz"
+    url      = "https://pypi.io/packages/source/T/Theano/Theano-0.8.2.tar.gz"
+    git      = "https://github.com/Theano/Theano.git"
 
+    version('master', branch='master')
+    version('1.0.2', 'fcae24dfa76babe15f5f3c556d67c9f2')
+    version('1.0.1', 'a38b36c0fdc3126c574163db0a253e69')
     version('0.8.2', 'f2d0dfe7df141115201077cd933b2c52')
-    version('master', git='https://github.com/Theano/Theano.git', branch='master')
 
     variant('gpu', default=False,
             description='Builds with support for GPUs via CUDA and cuDNN')
@@ -48,8 +32,9 @@ class PyTheano(PythonPackage):
     depends_on('blas')
 
     depends_on('cuda', when='+gpu')
+    depends_on('cudnn', when='+gpu')
+    depends_on('py-pygpu', when='+gpu', type=('build', 'run'))
     depends_on('libgpuarray', when='+gpu')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('py-nose@1.3.0:', type='test')
-    # depends_on('py-nose-parameterized@0.5.0:', type='test')
+    depends_on('py-nose@1.3.0:', type='test')
+    depends_on('py-nose-parameterized@0.5.0:', type='test')
diff --git a/var/spack/repos/builtin/packages/py-tifffile/package.py b/var/spack/repos/builtin/packages/py-tifffile/package.py
index b0dfb7ed1d..d8f863ef15 100644
--- a/var/spack/repos/builtin/packages/py-tifffile/package.py
+++ b/var/spack/repos/builtin/packages/py-tifffile/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-toml/package.py b/var/spack/repos/builtin/packages/py-toml/package.py
new file mode 100644
index 0000000000..22c8c3065a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-toml/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyToml(PythonPackage):
+    """A Python library for parsing and creating TOML configuration files.
+    For more information on the TOML standard, see
+    https://github.com/toml-lang/toml.git"""
+
+    homepage = "https://github.com/uiri/toml.git"
+    url      = "https://github.com/uiri/toml/archive/0.9.3.tar.gz"
+
+    version('0.9.3', '58e3023a17509dcf4f50581bfc70ff23')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('python@2.6:2.8,3.3:', type=('build', 'run'))
+
+    phases = ['build', 'check', 'install']
diff --git a/var/spack/repos/builtin/packages/py-tomopy/package.py b/var/spack/repos/builtin/packages/py-tomopy/package.py
index acba1ddcac..1b5d8f2e79 100644
--- a/var/spack/repos/builtin/packages/py-tomopy/package.py
+++ b/var/spack/repos/builtin/packages/py-tomopy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/py-toolz/package.py b/var/spack/repos/builtin/packages/py-toolz/package.py
new file mode 100644
index 0000000000..671a5dbfee
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-toolz/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyToolz(PythonPackage):
+    """A set of utility functions for iterators, functions, and dictionaries"""
+
+    homepage = "http://github.com/pytoolz/toolz/"
+    url      = "https://pypi.io/packages/source/t/toolz/toolz-0.9.0.tar.gz"
+
+    import_modules = ['toolz', 'tlz', 'toolz.curried', 'toolz.sandbox']
+
+    version('0.9.0', '6fd07249389dd0b3bfe71d4282314328')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-tornado/package.py b/var/spack/repos/builtin/packages/py-tornado/package.py
index ce1c88a2bb..c480b27470 100644
--- a/var/spack/repos/builtin/packages/py-tornado/package.py
+++ b/var/spack/repos/builtin/packages/py-tornado/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-tqdm/package.py b/var/spack/repos/builtin/packages/py-tqdm/package.py
index 1d1b2486c3..b9c3d69562 100644
--- a/var/spack/repos/builtin/packages/py-tqdm/package.py
+++ b/var/spack/repos/builtin/packages/py-tqdm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-traceback2/package.py b/var/spack/repos/builtin/packages/py-traceback2/package.py
new file mode 100644
index 0000000000..86f61b17c5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-traceback2/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyTraceback2(PythonPackage):
+    """Backports of the traceback module"""
+
+    homepage = "https://github.com/testing-cabal/traceback2"
+    url      = "https://pypi.io/packages/source/t/traceback2/traceback2-1.4.0.tar.gz"
+
+    version('1.4.0', '9e9723f4d70bfc6308fa992dd193c400')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-linecache2', type=('build', 'run'))
+    depends_on('py-pbr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-traitlets/package.py b/var/spack/repos/builtin/packages/py-traitlets/package.py
index db90d28a66..b8d7b418e1 100644
--- a/var/spack/repos/builtin/packages/py-traitlets/package.py
+++ b/var/spack/repos/builtin/packages/py-traitlets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-tuiview/package.py b/var/spack/repos/builtin/packages/py-tuiview/package.py
index 1223666d90..f9baeef8b8 100644
--- a/var/spack/repos/builtin/packages/py-tuiview/package.py
+++ b/var/spack/repos/builtin/packages/py-tuiview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-twisted/package.py b/var/spack/repos/builtin/packages/py-twisted/package.py
index e596adec97..7b03f54f8f 100644
--- a/var/spack/repos/builtin/packages/py-twisted/package.py
+++ b/var/spack/repos/builtin/packages/py-twisted/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-typing/package.py b/var/spack/repos/builtin/packages/py-typing/package.py
index 656eabe6f6..c1f593f07a 100644
--- a/var/spack/repos/builtin/packages/py-typing/package.py
+++ b/var/spack/repos/builtin/packages/py-typing/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-tzlocal/package.py b/var/spack/repos/builtin/packages/py-tzlocal/package.py
index fad9c19f3b..90f31cb205 100644
--- a/var/spack/repos/builtin/packages/py-tzlocal/package.py
+++ b/var/spack/repos/builtin/packages/py-tzlocal/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-udunits/package.py b/var/spack/repos/builtin/packages/py-udunits/package.py
new file mode 100644
index 0000000000..eddfd4cc08
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-udunits/package.py
@@ -0,0 +1,50 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class PyUdunits(PythonPackage):
+    """The MetOffice cf_units Python interface to the UDUNITS-2 Library."""
+    homepage = "https://github.com/SciTools/cf_units"
+    url      = "https://github.com/SciTools/cf_units/archive/v1.1.3.tar.gz"
+
+    version('1.1.3', '61ea2239c87b4c1d5d30147800a9e750')
+
+    maintainers = ['citibeth']
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-netcdf4', type=('build', 'run'))
+    depends_on('udunits2')
+
+    # See: https://github.com/SciTools/cf_units/blob/master/cf_units/etc/site.cfg.template
+    # udunits2_path = /path/to/libudunits2.so
+    # udunits2_xml_path = /path/to/udunits2.xml
+    site_cfg_template = """[System]
+udunits2_path = %s
+udunits2_xml_path = %s
+"""
+
+    @run_after('install')
+    def configure_template(self):
+        spec = self.spec
+
+        cfg_templates = find(spec.prefix, ['site.cfg.template'])
+        if len(cfg_templates) != 1:
+            tty.die(
+                'Found %d instances of site.cfg.template, wanted 1' %
+                len(cfg_templates))
+        cfg_template = cfg_templates[0]
+
+        cfg = os.path.join(os.path.split(cfg_template)[0], 'site.cfg')
+
+        udunits2_xml_path = os.path.join(
+            spec['udunits2'].prefix, 'share', 'udunits', 'udunits2.xml')
+
+        with open(cfg, 'w') as fout:
+            fout.write(self.site_cfg_template %
+                       (spec['udunits2'].libs, udunits2_xml_path))
diff --git a/var/spack/repos/builtin/packages/py-umi-tools/package.py b/var/spack/repos/builtin/packages/py-umi-tools/package.py
new file mode 100644
index 0000000000..d837ba6be6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-umi-tools/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyUmiTools(PythonPackage):
+    """Tools for handling Unique Molecular Identifiers in NGS data sets"""
+
+    homepage = "https://github.com/CGATOxford/UMI-tools"
+    url      = "https://github.com/CGATOxford/UMI-tools/archive/0.5.3.tar.gz"
+
+    version('0.5.3', '08bdebe30f84867d352ff5e1a2fe4d94')
+
+    depends_on('python@2.7:')
+    depends_on('py-setuptools@1.1:',   type='build')
+    depends_on('py-numpy@1.7:',        type=('build', 'run'))
+    depends_on('py-pandas@0.12:',      type=('build', 'run'))
+    depends_on('py-pysam@0.8.4:',      type=('build', 'run'))
+    depends_on('py-future',            type=('build', 'run'))
+    depends_on('py-six',               type=('build', 'run'))
+    depends_on('py-regex',             type=('build', 'run'))
+    depends_on('py-scipy',             type=('build', 'run'))
+    depends_on('py-matplotlib',        type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-unittest2/package.py b/var/spack/repos/builtin/packages/py-unittest2/package.py
index bdac19d855..635ba1ceda 100644
--- a/var/spack/repos/builtin/packages/py-unittest2/package.py
+++ b/var/spack/repos/builtin/packages/py-unittest2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,3 +17,6 @@ class PyUnittest2(PythonPackage):
 
     depends_on('py-setuptools', type='build')
     depends_on('py-enum34', when='^python@:3.3', type=('build', 'run'))
+    depends_on('py-traceback2', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
+    depends_on('py-argparse', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py
index 1c30595d97..932d665b2f 100644
--- a/var/spack/repos/builtin/packages/py-unittest2py3k/package.py
+++ b/var/spack/repos/builtin/packages/py-unittest2py3k/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-urllib3/package.py b/var/spack/repos/builtin/packages/py-urllib3/package.py
index 000c6ef1e6..224ee6197d 100644
--- a/var/spack/repos/builtin/packages/py-urllib3/package.py
+++ b/var/spack/repos/builtin/packages/py-urllib3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-urwid/package.py b/var/spack/repos/builtin/packages/py-urwid/package.py
index 46895ac2ee..c5f106809a 100644
--- a/var/spack/repos/builtin/packages/py-urwid/package.py
+++ b/var/spack/repos/builtin/packages/py-urwid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-vcversioner/package.py b/var/spack/repos/builtin/packages/py-vcversioner/package.py
index fa4e2565b8..8c863ae58f 100644
--- a/var/spack/repos/builtin/packages/py-vcversioner/package.py
+++ b/var/spack/repos/builtin/packages/py-vcversioner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py b/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py
new file mode 100644
index 0000000000..ecc7abfe4f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-virtualenv-clone/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyVirtualenvClone(PythonPackage):
+    """A script for cloning a non-relocatable virtualenv."""
+
+    homepage = "https://github.com/edwardgeorge/virtualenv-clone"
+    url      = "https://pypi.io/packages/source/v/virtualenv-clone/virtualenv-clone-0.2.6.tar.gz"
+
+    version('0.2.6', 'fb03cd8c7a2be75937a13756d14068fc')
+
+    depends_on('python@2.6:')
+    # not just build-time, requires pkg_resources
+    depends_on('py-setuptools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-virtualenv/package.py b/var/spack/repos/builtin/packages/py-virtualenv/package.py
index a91117e616..a4108b51ee 100644
--- a/var/spack/repos/builtin/packages/py-virtualenv/package.py
+++ b/var/spack/repos/builtin/packages/py-virtualenv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class PyVirtualenv(PythonPackage):
     homepage = "https://virtualenv.pypa.io/"
     url      = "https://pypi.io/packages/source/v/virtualenv/virtualenv-15.1.0.tar.gz"
 
+    version('16.0.0', '4feb74ee26255dd7e62e36ce96bcc4c6')
     version('15.1.0', '44e19f4134906fe2d75124427dc9b716')
     version('15.0.1', '28d76a0d9cbd5dc42046dd14e76a6ecc')
     version('13.0.1', '1ffc011bde6667f0e37ecd976f4934db')
diff --git a/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py b/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py
new file mode 100644
index 0000000000..009358344a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-virtualenvwrapper/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyVirtualenvwrapper(PythonPackage):
+    """virtualenvwrapper is a set of extensions to Ian Bicking's
+    virtualenv tool. The extensions include wrappers for creating and
+    deleting virtual environments and otherwise managing your development
+    workflow, making it easier to work on more than one project at a time
+    without introducing conflicts in their dependencies."""
+
+    homepage = "https://bitbucket.org/virtualenvwrapper/virtualenvwrapper.git"
+    url      = "https://pypi.io/packages/source/v/virtualenvwrapper/virtualenvwrapper-4.8.2.tar.gz"
+
+    version('4.8.2', '8e3af0e0d42733f15c5e36df484a952e')
+
+    depends_on('python@2.6:')
+    depends_on('py-virtualenv', type=('build', 'run'))
+    depends_on('py-virtualenv-clone', type=('build', 'run'))
+    depends_on('py-stevedore', type=('build', 'run'))
+    # not just build-time, requires pkg_resources
+    depends_on('py-setuptools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-vsc-base/package.py b/var/spack/repos/builtin/packages/py-vsc-base/package.py
index 2cd0ff4b46..f2ca078d60 100644
--- a/var/spack/repos/builtin/packages/py-vsc-base/package.py
+++ b/var/spack/repos/builtin/packages/py-vsc-base/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-vsc-install/package.py b/var/spack/repos/builtin/packages/py-vsc-install/package.py
index 09e9c885cf..9b74392146 100644
--- a/var/spack/repos/builtin/packages/py-vsc-install/package.py
+++ b/var/spack/repos/builtin/packages/py-vsc-install/package.py
@@ -1,25 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Kenneth Hoste
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Kenneth Hoste, kenneth.hoste@gmail.com
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-wcsaxes/package.py b/var/spack/repos/builtin/packages/py-wcsaxes/package.py
index 16fa376dc7..c3109c498a 100644
--- a/var/spack/repos/builtin/packages/py-wcsaxes/package.py
+++ b/var/spack/repos/builtin/packages/py-wcsaxes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-wcwidth/package.py b/var/spack/repos/builtin/packages/py-wcwidth/package.py
index ca4b7740b5..4bb68362a7 100644
--- a/var/spack/repos/builtin/packages/py-wcwidth/package.py
+++ b/var/spack/repos/builtin/packages/py-wcwidth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-webkit-server/package.py b/var/spack/repos/builtin/packages/py-webkit-server/package.py
index 66850b9682..db1e45e088 100644
--- a/var/spack/repos/builtin/packages/py-webkit-server/package.py
+++ b/var/spack/repos/builtin/packages/py-webkit-server/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class PyWebkitServer(PythonPackage):
 
     homepage = "https://github.com/niklasb/webkit-server"
     url      = "https://pypi.io/packages/source/w/webkit-server/webkit-server-1.0.tar.gz"
+    git      = "https://github.com/niklasb/webkit-server.git"
 
-    version('develop', git="https://github.com/niklasb/webkit-server", branch="master")
+    version('develop', branch='master')
     version('1.0', '8463245c2b4f0264d934c0ae20bd4654')
diff --git a/var/spack/repos/builtin/packages/py-weblogo/package.py b/var/spack/repos/builtin/packages/py-weblogo/package.py
new file mode 100644
index 0000000000..1b27ac5686
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-weblogo/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyWeblogo(PythonPackage):
+    """WebLogo is a web based application designed to make the generation of
+    sequence logos as easy and painless as possible."""
+
+    homepage = "http://weblogo.threeplusone.com"
+    url      = "https://pypi.io/packages/source/w/weblogo/weblogo-3.6.0.tar.gz"
+
+    version('3.6.0', 'd0764f218057543fa664d2ae17d37b6d')
+
+    depends_on('py-setuptools', type='build')
+    depends_on('ghostscript', type=('build', 'run'))
+    depends_on('pdf2svg', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-werkzeug/package.py b/var/spack/repos/builtin/packages/py-werkzeug/package.py
index 30573a7ff2..f2941f80fc 100644
--- a/var/spack/repos/builtin/packages/py-werkzeug/package.py
+++ b/var/spack/repos/builtin/packages/py-werkzeug/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-wheel/package.py b/var/spack/repos/builtin/packages/py-wheel/package.py
index f0a15f0886..03e91849ad 100644
--- a/var/spack/repos/builtin/packages/py-wheel/package.py
+++ b/var/spack/repos/builtin/packages/py-wheel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py
index 206f940b57..32cfc4581a 100644
--- a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py
+++ b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-wrapt/package.py b/var/spack/repos/builtin/packages/py-wrapt/package.py
index 5b81eef2e1..a73a0ee70a 100644
--- a/var/spack/repos/builtin/packages/py-wrapt/package.py
+++ b/var/spack/repos/builtin/packages/py-wrapt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xarray/package.py b/var/spack/repos/builtin/packages/py-xarray/package.py
index 27017a9227..ade407dbb9 100644
--- a/var/spack/repos/builtin/packages/py-xarray/package.py
+++ b/var/spack/repos/builtin/packages/py-xarray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xattr/package.py b/var/spack/repos/builtin/packages/py-xattr/package.py
new file mode 100644
index 0000000000..c6ee55760f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-xattr/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyXattr(PythonPackage):
+    """A python interface to access extended file attributes,
+        sans libattr dependency"""
+
+    homepage = "http://pyxattr.k1024.org/"
+    git      = "https://github.com/fwang2/pyxattr.git"
+
+    version('develop', branch='dev')
+
+    depends_on('python@2.7:')
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-xdot/package.py b/var/spack/repos/builtin/packages/py-xdot/package.py
new file mode 100644
index 0000000000..f840919294
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-xdot/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyXdot(PythonPackage):
+    """xdot.py is an interactive viewer for graphs written in Graphviz's
+    dot language."""
+
+    homepage = "https://github.com/jrfonseca/xdot.py"
+    url      = "https://github.com/jrfonseca/xdot.py/archive/0.9.tar.gz"
+    git      = "https://github.com/jrfonseca/xdot.py.git"
+
+    version('master', branch="master")
+    version('1.0', '4e60c42d009a8802db6c1b4dab519863')
+    version('0.9', '19c78311d73b0f9ea059a6febf42eeea')
+
+    # setuptools is required at runtime to avoid:
+    # No module named 'pkg_resources'
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('python@3:', type=('build', 'run'))
+    depends_on('py-pygobject', type=('build', 'run'))
+    depends_on('py-pycairo', type=('build', 'run'))
+    depends_on('pango', type=('build', 'run'))
+    depends_on('atk', type=('build', 'run'))
+    depends_on('gdk-pixbuf', type=('build', 'run'))
+    depends_on('gtkplus', type=('build', 'run'))
+
+    @run_after('install')
+    def post_install(self):
+        spec = self.spec
+        repo_paths = '%s:%s:%s:%s' % (
+            join_path(spec['pango'].prefix.lib, 'girepository-1.0'),
+            join_path(spec['atk'].prefix.lib, 'girepository-1.0'),
+            join_path(spec['gdk-pixbuf'].prefix.lib, 'girepository-1.0'),
+            join_path(spec['gtkplus'].prefix.lib, 'girepository-1.0'))
+        dst = join_path(spec.prefix, spec['python'].package.site_packages_dir,
+                        'xdot/__init__.py')
+        filter_file("import sys",
+                    "import sys\nimport os\nos.environ['GI_TYPELIB_PATH']" +
+                    " = '%s'" % repo_paths, dst)
+        # regenerate the byte-compiled __init__.py
+        python3 = spec['python'].command
+        python3('-m', 'compileall', dst)
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+        run_env.prepend_path('GI_TYPELIB_PATH',
+                             join_path(spec['pango'].prefix.lib,
+                                       'girepository-1.0'))
+        run_env.prepend_path('GI_TYPELIB_PATH',
+                             join_path(spec['atk'].prefix.lib,
+                                       'girepository-1.0'))
+        run_env.prepend_path('GI_TYPELIB_PATH',
+                             join_path(spec['gdk-pixbuf'].prefix.lib,
+                                       'girepository-1.0'))
+        run_env.prepend_path('GI_TYPELIB_PATH',
+                             join_path(spec['gtkplus'].prefix.lib,
+                                       'girepository-1.0'))
diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py
index 3fc22a7865..9117728b98 100644
--- a/var/spack/repos/builtin/packages/py-xlrd/package.py
+++ b/var/spack/repos/builtin/packages/py-xlrd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xlsxwriter/package.py b/var/spack/repos/builtin/packages/py-xlsxwriter/package.py
index 97170d76d5..af6dd10d7c 100644
--- a/var/spack/repos/builtin/packages/py-xlsxwriter/package.py
+++ b/var/spack/repos/builtin/packages/py-xlsxwriter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xmlrunner/package.py b/var/spack/repos/builtin/packages/py-xmlrunner/package.py
index 104d6113c0..aa469b6b40 100644
--- a/var/spack/repos/builtin/packages/py-xmlrunner/package.py
+++ b/var/spack/repos/builtin/packages/py-xmlrunner/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xopen/package.py b/var/spack/repos/builtin/packages/py-xopen/package.py
index 4b6df42419..0d2121e855 100644
--- a/var/spack/repos/builtin/packages/py-xopen/package.py
+++ b/var/spack/repos/builtin/packages/py-xopen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xpyb/package.py b/var/spack/repos/builtin/packages/py-xpyb/package.py
index 60f69610c3..11e73d24b0 100644
--- a/var/spack/repos/builtin/packages/py-xpyb/package.py
+++ b/var/spack/repos/builtin/packages/py-xpyb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py b/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py
index 09c9f6da47..18b08b266f 100644
--- a/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py
+++ b/var/spack/repos/builtin/packages/py-xvfbwrapper/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-yamlreader/package.py b/var/spack/repos/builtin/packages/py-yamlreader/package.py
new file mode 100644
index 0000000000..66c7be55ed
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-yamlreader/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyYamlreader(PythonPackage):
+    """Yamlreader merges YAML data from a directory, a list of files or a
+    file glob."""
+
+    homepage = "http://pyyaml.org/wiki/PyYAML"
+    url      = "https://pypi.io/packages/source/y/yamlreader/yamlreader-3.0.4.tar.gz"
+
+    version('3.0.4', '542179b5b5bedae941245b8b673119db')
+
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-pyyaml', type=('build', 'run'))
+    depends_on('py-six', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/py-yapf/package.py b/var/spack/repos/builtin/packages/py-yapf/package.py
index 76121cf2d2..1b71fbe2ba 100644
--- a/var/spack/repos/builtin/packages/py-yapf/package.py
+++ b/var/spack/repos/builtin/packages/py-yapf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-yt/package.py b/var/spack/repos/builtin/packages/py-yt/package.py
index 6c8aa1797f..9344fe7463 100644
--- a/var/spack/repos/builtin/packages/py-yt/package.py
+++ b/var/spack/repos/builtin/packages/py-yt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -35,24 +16,21 @@ class PyYt(PythonPackage):
        interdisciplinary community.
     """
     homepage = "http://yt-project.org"
-    url = "https://bitbucket.org/yt_analysis/yt"
+    url      = "https://github.com/yt-project/yt/archive/yt-3.4.0.tar.gz"
+    git      = "https://github.com/yt-project/yt.git"
+
+    version("develop", branch="master")
 
-    version("3.3.5", "2ad314ff3d3261e41825d15db027b0e7",
-            url="https://bitbucket.org/yt_analysis/yt/get/yt-3.3.5.tar.gz")
-    version("3.3.4", "3a84e56dfd82f9dd923f3fb8490e679c",
-            url="https://bitbucket.org/yt_analysis/yt/get/yt-3.3.4.tar.gz")
-    version("3.3.1", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-3.3.1", commit="9bc3d0e9b750c923d44d73c447df64fc431f5838")
-    version("3.2.3", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-3.2.3", commit="83d2c1e9313e7d83eb5b96888451ff2646fd8ff3")
-    version("3.1.0", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-3.1.0", commit="fd7cdc4836188a3badf81adb477bcc1b9632e485")
-    version("3.0.2", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-3.0.2", commit="511887af4c995a78fe606e58ce8162c88380ecdc")
-    version("2.6.3", hg="https://bitbucket.org/yt_analysis/yt",
-            tag="yt-2.6.3", commit="816186f16396a16853810ac9ebcde5057d8d5b1a")
-    version("development", hg="https://bitbucket.org/yt_analysis/yt",
-            branch="yt")
+    version('3.4.1', sha256='b9a73ade3726a8163fc992999c8c1010ca89473131901fe4d48b820ab2ced486')
+    version('3.4.0', sha256='2120793a76864cf3165b2b7290ef719e358fa57501ee8721941e7cfc434cfb2b')
+    version('3.3.5', sha256='2ebe4bbefd9f5367563ce4d7eb87d3f6ef0de1f97ed1c03106d9541e71b7e1ca')
+    version('3.3.4', sha256='2842bab891cfbf3269a3c4bd8f22fef23c9a15a790ba48c6490730cb51ce9b0e')
+    version('3.3.3', sha256='7b9244089e92b1d32cef791cd72760bb8c80b391eaec29672a5377c33f932d88')
+    version('3.3.2', sha256='d323419ad3919e86d2af1738c846021fd7f5b5dc5c06059cdf3a2bc63226466a')
+    version('3.3.1', sha256='7ac68d5e05e2b57fb3635f1027f3201094f3547d584e72ab55fedbfd3bc09a36')
+    version('3.3.0', sha256='e6be799c0d9a83a06649f0d77a61ad9c23b94b34f94e16724e2b18f5c7513c33')
+    version('3.2.3', sha256='96476d17e9ce35f0d4380b2ddb398fe729e39f1f3894602ff07e49844541e5ca')
+    version('3.2.2', sha256='498ed77b3dae8c54929602d4931f3c3e0a3420a9b500cbd870f50b1e0efea8c3')
 
     variant("astropy", default=True, description="enable astropy support")
     variant("h5py", default=True, description="enable h5py support")
diff --git a/var/spack/repos/builtin/packages/py-ytopt/package.py b/var/spack/repos/builtin/packages/py-ytopt/package.py
new file mode 100644
index 0000000000..ec70d6c06d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-ytopt/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyYtopt(PythonPackage):
+    """Ytopt package implements search using Random Forest (SuRF), an autotuning
+       search method developed within Y-Tune ECP project."""
+
+    homepage = "https://xgitlab.cels.anl.gov/pbalapra/ytopt"
+    url      = "https://xgitlab.cels.anl.gov/pbalapra/ytopt/raw/release/dist/ytopt-0.1.0.tar.gz"
+
+    version('0.1.0', sha256='c7081fe3585a5b7a25bcb84733cd2326b72de3bfc4f84d6ad110341f24c3e612')
+
+    depends_on('py-scikit-learn', type=('build', 'run'))
+    depends_on('py-scikit-optimize', type=('build', 'run'))	
+
+    def build_args(self, spec, prefix):
+        args = []
+        return args
diff --git a/var/spack/repos/builtin/packages/py-zmq/package.py b/var/spack/repos/builtin/packages/py-zmq/package.py
index d5734d8a33..51a13ddaf2 100644
--- a/var/spack/repos/builtin/packages/py-zmq/package.py
+++ b/var/spack/repos/builtin/packages/py-zmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/py-zope-event/package.py b/var/spack/repos/builtin/packages/py-zope-event/package.py
new file mode 100644
index 0000000000..a2f0e6ecc1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-zope-event/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyZopeEvent(PythonPackage):
+    """Very basic event publishing system."""
+
+    homepage = "http://github.com/zopefoundation/zope.event"
+    url      = "https://pypi.io/packages/source/z/zope.event/zope.event-4.3.0.tar.gz"
+
+    # FIXME: No idea why this import test fails.
+    # Maybe some kind of namespace issue?
+    # import_modules = ['zope.event']
+
+    version('4.3.0', '8ca737960741c6fd112972f3313303bd')
+
+    depends_on('py-setuptools', type='build')
diff --git a/var/spack/repos/builtin/packages/py-zope-interface/package.py b/var/spack/repos/builtin/packages/py-zope-interface/package.py
new file mode 100644
index 0000000000..0fd1b3bee5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-zope-interface/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class PyZopeInterface(PythonPackage):
+    """This package provides an implementation of "object interfaces" for
+    Python. Interfaces are a mechanism for labeling objects as conforming to a
+    given API or contract. So, this package can be considered as implementation
+    of the Design By Contract methodology support in Python."""
+
+    homepage = "https://github.com/zopefoundation/zope.interface"
+    url      = "https://pypi.io/packages/source/z/zope.interface/zope.interface-4.5.0.tar.gz"
+
+    # FIXME: No idea why these import tests fail.
+    # Maybe some kind of namespace issue?
+    # import_modules = ['zope.interface', 'zope.interface.common']
+
+    version('4.5.0', '7b669cd692d817772c61d2e3ad0f1e71')
+
+    depends_on('python@2.7:2.8,3.4:', type=('build', 'run'))
+
+    depends_on('py-setuptools', type='build')
+    depends_on('py-zope-event', type='test')
+    depends_on('py-nose', type='test')
+    depends_on('py-coverage', type='test')
diff --git a/var/spack/repos/builtin/packages/pythia6/CMakeLists.txt b/var/spack/repos/builtin/packages/pythia6/CMakeLists.txt
new file mode 100644
index 0000000000..9362f03668
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pythia6/CMakeLists.txt
@@ -0,0 +1,115 @@
+# ======================================================================
+#  pythia6 main build file
+#
+#  setup cmake
+#  cd .../path/to/build/directory
+#  cmake [-DCMAKE_INSTALL_PREFIX=/install/path]
+#        [-DCMAKE_BUILD_TYPE=<RelWithDebInfo|Debug|Release|MinSizeRel> ]
+#        [-Drun_long_tests:BOOL=ON]
+#        .../path/to/pythia/source
+#  make
+#  make test
+#  make install
+# ======================================================================
+
+# use cmake 2.6 or later
+cmake_minimum_required (VERSION 2.6)
+
+project(pythia6 C Fortran)
+message(STATUS "pythia version is ${PYTHIA6_VERSION}")
+
+enable_testing()
+
+#build all libraries in a single directory to enable testing
+set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
+
+# set compiler flags
+# default GNU compiler flags:
+# DEBUG           -g
+# RELEASE         -O3 -DNDEBUG
+# MINSIZEREL      -Os -DNDEBUG
+# RELWITHDEBINFO  -O2 -g
+set( CMAKE_C_FLAGS_DEBUG "-g -O0" )
+set( CMAKE_C_FLAGS_RELWITHDEBINFO "-O3 -g -DNDEBUG -fno-omit-frame-pointer" )
+set( CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" )
+set( CMAKE_Fortran_FLAGS_DEBUG "-g -O0 -fno-second-underscore" )
+set( CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-O3 -g -DNDEBUG -fno-omit-frame-pointer -fno-second-underscore" )
+set( CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -fno-second-underscore" )
+
+message(STATUS "CMAKE_Fortran_COMPILER_INIT = ${CMAKE_Fortran_COMPILER_INIT}")
+message(STATUS "CMAKE_Fortran_COMPILER_FULLPATH = ${CMAKE_Fortran_COMPILER_FULLPATH}")
+message(STATUS "CMAKE_Fortran_COMPILER = ${CMAKE_Fortran_COMPILER}")
+
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "" FORCE)
+endif()
+message(STATUS "cmake build type set to ${CMAKE_BUILD_TYPE}")
+
+message("ENV_FLAGS = $ENV{FFLAGS}")
+string(TOUPPER ${CMAKE_BUILD_TYPE} BTYPE_UC )
+if( ${BTYPE_UC} MATCHES "DEBUG")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS_DEBUG}")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS_DEBUG}")
+elseif( ${BTYPE_UC} MATCHES "RELEASE")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS_RELEASE}")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS_RELEASE}")
+elseif( ${BTYPE_UC} MATCHES "RELWITHDEBINFO")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS_RELWITHDEBINFO}")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS_RELWITHDEBINFO}")
+endif()
+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} $ENV{CFLAGS}")
+set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} $ENV{FFLAGS}")
+message("CMAKE_C_FLAGS = ${CMAKE_C_FLAGS}")
+message("CMAKE_Fortran_FLAGS = ${CMAKE_Fortran_FLAGS}")
+
+# source
+# shared library
+file(GLOB src_files *.c *.F *.f)
+add_library(Pythia6 SHARED ${src_files})
+
+# Installation:
+# Library.
+install(TARGETS Pythia6 DESTINATION lib)
+
+# Include-able file.
+install( FILES example/main60.f
+         DESTINATION include )
+
+# Documentation.
+install(DIRECTORY doc DESTINATION .)
+
+# Examples
+install(DIRECTORY example DESTINATION .)
+
+# tests
+macro( pythia_test testname )
+  set ( package_library_list ${PROJECT_BINARY_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}CLHEP-${PACKAGE}-${VERSION}${CMAKE_STATIC_LIBRARY_SUFFIX} )
+  link_libraries( Pythia6 )
+  message( STATUS "building ${testname} from ${CMAKE_CURRENT_SOURCE_DIR}/example in ${CMAKE_CURRENT_BINARY_DIR}" )
+  add_executable(${testname} example/${testname}.f)
+  add_test( ${testname} ${CMAKE_CURRENT_BINARY_DIR}/${testname} )
+endmacro( pythia_test )
+
+pythia_test( main61 )
+pythia_test( main63 )
+pythia_test( main66 )
+pythia_test( main67 )
+pythia_test( main68 )
+pythia_test( main69 )
+pythia_test( main71 )
+pythia_test( main72 )
+pythia_test( main73 )
+pythia_test( main75 )
+pythia_test( main77 )
+pythia_test( main78 )
+pythia_test( main81 )
+
+# these examples take a while to run
+if( run_long_tests )
+  pythia_test( main62 )
+  pythia_test( main64 )
+  pythia_test( main65 )
+  pythia_test( main70 )
+  pythia_test( main74 )
+  pythia_test( main79 )
+endif( run_long_tests )
diff --git a/var/spack/repos/builtin/packages/pythia6/package.py b/var/spack/repos/builtin/packages/pythia6/package.py
new file mode 100644
index 0000000000..800073bf41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pythia6/package.py
@@ -0,0 +1,154 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import numbers
+import os
+from six import iteritems
+from six.moves.urllib.parse import urlparse
+
+
+def _is_integral(x):
+    """Accepts only integral values."""
+    try:
+        return isinstance(int(x), numbers.Integral) and \
+            (not isinstance(x, bool)) and \
+            int(x) == x
+    except ValueError:
+        return False
+
+
+class Pythia6(CMakePackage):
+    """PYTHIA is a program for the generation of high-energy physics events,
+    i.e. for the description of collisions at high energies between elementary
+    particles such as e+, e-, p and pbar in various combinations.
+
+    PYTHIA6 is a Fortran package which is no longer maintained: new
+    prospective users should use Pythia8 instead.
+
+    This recipe includes patches required to interoperate with Root.
+    """
+
+    homepage = 'https://pythiasix.hepforge.org/'
+    url = 'http://www.hepforge.org/archive/pythiasix/pythia-6.4.28.tgz'
+
+    version('6.4.28',
+            sha256='01cbff47e99365b5e46f6d62c1735d3cae1932c4710604850d59f538cb758020')
+
+    # Root's TPythia6 interface requires extra sources to be built into
+    # the Pythia6 library.
+    variant('root', default=False,
+            description='Build extra (non OEM) code to allow use by Root.')
+
+    # The maximum number of particles (NMXHEP) supported by the arrays
+    # in the /HEPEVT/ COMMON block may need tweaking if pythia6 is
+    # intended to be used with other code with different requirements.
+    variant('nmxhep', default=4000, values=_is_integral, description='Extent of particle arrays in the /HEPEVT/ COMMON block.')
+
+    # In the unlikely event of new versions >6.4.28,
+    # pythia6_common_address.c should be checked for accuracy against
+    # the definitions of the relevant COMMON blocks in the Pythia6
+    # Fortran source, and patched if necessaary.
+    resource(
+        name='root-pythia6-shim',
+        url='https://root.cern.ch/download/pythia6.tar.gz',
+        sha256='d613dcb27c905710e2f13a934913cc5545e3e5d0e477e580107385d9ef260056',
+        when='+root',
+        destination='.',
+        placement={'pythia6_common_address.c': 'pythia6_common_address.c',
+                   'tpythia6_called_from_cc.F': 'tpythia6_called_from_cc.F'}
+    )
+
+    # Download examples separately.
+    examples \
+        = {'main60.f':
+           'd713b8b267c4405cc9d31c58bba267ae3378902a26fa52393003bf35fd56902c',
+           'main61.f':
+           'e2a3d5524e43d16f60d9edc6e7198d41006d1ba127fb7b0e265aa509e13128b4',
+           'main62.f':
+           'dce822a72fe2d6cfb6d43c479ba98928fb0a39290a6ee26fdcacc66229313045',
+           'main63.f':
+           'b2dd343b3cd7969979b80c564d82b92e0d776d66bb19d346b52f2af27adeb62d',
+           'main64.f':
+           'a35f2f232e6e0d68d67fd350d4d46b0a353f5c7811de0c2db47ae16d17ed1843',
+           'main65.f':
+           '03c81e0bbd77710b0461e18265e80e3bd51360b9f416c86013401f882ac39a5e',
+           'main66.f':
+           '50dd9221a7e84ee7c5005db6758e5880d190eab8cce8a52e7c7b29e9fee8d3da',
+           'main67.f':
+           '1984aa90fe4e3d628c3bcceaa6fca1b08231d835158d975fa171337d55ca4a2f',
+           'main68.f':
+           'c8d6def1298477ffec6a1d98c7e02dcee0debe6badc7c63f752f9194b82f212d',
+           'main69.f':
+           'd14399d43f8c4b670907558849d3e5a4d7625d027de3c10002185c58b20b061a',
+           'main71.f':
+           '2e47af778003b0596e8999f0914033c6eda7335211b9e96ac3075d45a3cde12e',
+           'main72.f':
+           'e27ce2af68b40436c51c65767ebb5ff0955ab8dfdfc5fc5c217ae73cd53070da',
+           'main73.f':
+           '567db2d1a66896ce5103ffa7e10742442b0e934088883e91339536e0249772c4',
+           'main75.f':
+           'b850986c43a5af1e7d13b66d22b01584e3c68bb338be32eac39e31f971b80be4',
+           'main77.f':
+           '0679852c4f35719531ad38dc1dbb374b884181eb5e483c36d8867ccb449177a4',
+           'main78.f':
+           '5babc59fe6a0bd57d97ec398cf01745bc9b72ce6ce0711e934d53c7821e21912',
+           'main79.f':
+           '27ca84d6d0877f3605cbc1b865c3e1f571e7d2c9301094a4122e726a903dbead',
+           'main81.f':
+           'b02fecd1cd0f9ba16eaae53e9da0ba602569fdf0e46856cccdfb4c5b7ba33e8b',
+           'ttbar.lhe':
+           'fb0d43175cc392b19c2b6633dcf673d0b56229b60bec92df4aa782c7196b149c'}
+
+    for example, checksum in iteritems(examples):
+        resource(name=example,
+                 url='http://pythiasix.hepforge.org/examples/{0}'.
+                 format(example),
+                 sha256=checksum,
+                 expand=False,
+                 destination='example',
+                 placement={example: example}
+             )
+
+    # Docs.
+    docs \
+        = {'http://www.hepforge.org/archive/pythiasix/update_notes-6.4.28.txt':
+            'a229be4ba9a4eb65a9d53600a5f388b620038d56694c6cb4671c2be224b67751',
+           'http://home.thep.lu.se/~torbjorn/pythia6/lutp0613man2.pdf':
+           '03d637310ea80f0d7aea761492bd38452c602890d8cf913a1ec9edacd79fa43d',
+           'https://pythiasix.hepforge.org/pythia6-announcement.txt':
+           '2a52def41f0c93e32e0db58dbcf072b987ebfbd32e42ccfc1f9382fcf65f1271'}
+
+    for docurl, checksum in iteritems(docs):
+        doc = os.path.basename(urlparse(docurl).path)
+        resource(name=doc,
+                 url=docurl,
+                 sha256=checksum,
+                 expand=False,
+                 destination='doc',
+                 placement={doc: doc}
+             )
+
+    # The included patch customizes some routines provided in dummy form
+    # by the original source to be useful out of the box in the vast
+    # majority of cases. If your case is different, platform- or
+    # variant-based adjustments should be made.
+    patch('pythia6.patch', level=0)
+
+    def patch(self):
+        # Use our provided CMakeLists.txt. The Makefile provided with
+        # the source is GCC (gfortran) specific, and would have required
+        # additional patching for the +root variant.
+        llnl.util.filesystem.copy(os.path.join(os.path.dirname(__file__),
+                                               'CMakeLists.txt'),
+                                  self.stage.source_path)
+        # Apply the variant value at the relevant place in the source.
+        filter_file(r'^(\s+PARAMETER\s*\(\s*NMXHEP\s*=\s*)\d+',
+                    r'\1{0}'.format(self.spec.variants['nmxhep'].value),
+                    'pyhepc.f')
+
+    def cmake_args(self):
+        args = ['-DPYTHIA6_VERSION={0}'.format(self.version.dotted)]
+        return args
diff --git a/var/spack/repos/builtin/packages/pythia6/pythia6.patch b/var/spack/repos/builtin/packages/pythia6/pythia6.patch
new file mode 100644
index 0000000000..5d45541e07
--- /dev/null
+++ b/var/spack/repos/builtin/packages/pythia6/pythia6.patch
@@ -0,0 +1,278 @@
+diff -Naur pytime.f pytime.f
+--- pytime.f	2018-08-23 11:24:27.000000000 -0500
++++ pytime.f	2018-08-23 11:46:08.189999826 -0500
+@@ -1,4 +1,3 @@
+- 
+ C*********************************************************************
+  
+ C...PYTIME
+@@ -59,17 +58,18 @@
+ C      IDATI(6)=ISEC
+  
+ C...Example 4: GNU LINUX libU77, SunOS.
+-C      CALL IDATE(IDTEMP)
+-C      IDATI(1)=IDTEMP(3)
+-C      IDATI(2)=IDTEMP(2)
+-C      IDATI(3)=IDTEMP(1)
+-C      CALL ITIME(IDTEMP)
+-C      IDATI(4)=IDTEMP(1)
+-C      IDATI(5)=IDTEMP(2)
+-C      IDATI(6)=IDTEMP(3)
++      CALL IDATE(IDTEMP)
++      IDATI(1)=IDTEMP(3)
++      IDATI(2)=IDTEMP(2)
++      IDATI(3)=IDTEMP(1)
++      CALL ITIME(IDTEMP)
++      IDATI(4)=IDTEMP(1)
++      IDATI(5)=IDTEMP(2)
++      IDATI(6)=IDTEMP(3)
+  
+ C...Common code to ensure right century.
+       IDATI(1)=2000+MOD(IDATI(1),100)
+  
+       RETURN
+       END
++ 
+diff -Naur upevnt.f upevnt.f
+--- upevnt.f	2018-08-23 11:24:27.000000000 -0500
++++ upevnt.f	2018-08-23 11:46:08.189999826 -0500
+@@ -1,56 +1,3 @@
+-
+-C...Old example: handles a simple Pythia 6.4 initialization file.
+- 
+-c      SUBROUTINE UPINIT
+- 
+-C...Double precision and integer declarations.
+-c      IMPLICIT DOUBLE PRECISION(A-H, O-Z)
+-c      IMPLICIT INTEGER(I-N)
+- 
+-C...Commonblocks.
+-c      COMMON/PYDAT1/MSTU(200),PARU(200),MSTJ(200),PARJ(200)
+-c      COMMON/PYPARS/MSTP(200),PARP(200),MSTI(200),PARI(200)
+-c      SAVE /PYDAT1/,/PYPARS/
+- 
+-C...User process initialization commonblock.
+-c      INTEGER MAXPUP
+-c      PARAMETER (MAXPUP=100)
+-c      INTEGER IDBMUP,PDFGUP,PDFSUP,IDWTUP,NPRUP,LPRUP
+-c      DOUBLE PRECISION EBMUP,XSECUP,XERRUP,XMAXUP
+-c      COMMON/HEPRUP/IDBMUP(2),EBMUP(2),PDFGUP(2),PDFSUP(2),
+-c     &IDWTUP,NPRUP,XSECUP(MAXPUP),XERRUP(MAXPUP),XMAXUP(MAXPUP),
+-c     &LPRUP(MAXPUP)
+-c      SAVE /HEPRUP/
+- 
+-C...Read info from file.
+-c      IF(MSTP(161).GT.0) THEN
+-c        READ(MSTP(161),*,END=110,ERR=110) IDBMUP(1),IDBMUP(2),EBMUP(1),
+-c     &  EBMUP(2),PDFGUP(1),PDFGUP(2),PDFSUP(1),PDFSUP(2),IDWTUP,NPRUP
+-c        DO 100 IPR=1,NPRUP
+-c          READ(MSTP(161),*,END=110,ERR=110) XSECUP(IPR),XERRUP(IPR),
+-c     &    XMAXUP(IPR),LPRUP(IPR)
+-c  100   CONTINUE
+-c        RETURN
+-C...Error or prematurely reached end of file.
+-c  110   WRITE(MSTU(11),5000)
+-c        STOP
+- 
+-C...Else not implemented.
+-c      ELSE
+-c        WRITE(MSTU(11),5100)
+-c        STOP
+-c      ENDIF
+- 
+-C...Format for error printout.
+-c 5000 FORMAT(1X,'Error: UPINIT routine failed to read information'/
+-c     &1X,'Execution stopped!')
+-c 5100 FORMAT(1X,'Error: You have not implemented UPINIT routine'/
+-c     &1X,'Dummy routine in PYTHIA file called instead.'/
+-c     &1X,'Execution stopped!')
+- 
+-c      RETURN
+-c      END
+- 
+ C*********************************************************************
+  
+ C...UPEVNT
+@@ -120,3 +67,54 @@
+  
+       RETURN
+       END
++
++C...Old example: handles a simple Pythia 6.4 event file.
++ 
++c      SUBROUTINE UPEVNT
++ 
++C...Double precision and integer declarations.
++c      IMPLICIT DOUBLE PRECISION(A-H, O-Z)
++c      IMPLICIT INTEGER(I-N)
++ 
++C...Commonblocks.
++c      COMMON/PYDAT1/MSTU(200),PARU(200),MSTJ(200),PARJ(200)
++c      COMMON/PYPARS/MSTP(200),PARP(200),MSTI(200),PARI(200)
++c      SAVE /PYDAT1/,/PYPARS/
++ 
++C...User process event common block.
++c      INTEGER MAXNUP
++c      PARAMETER (MAXNUP=500)
++c      INTEGER NUP,IDPRUP,IDUP,ISTUP,MOTHUP,ICOLUP
++c      DOUBLE PRECISION XWGTUP,SCALUP,AQEDUP,AQCDUP,PUP,VTIMUP,SPINUP
++c      COMMON/HEPEUP/NUP,IDPRUP,XWGTUP,SCALUP,AQEDUP,AQCDUP,IDUP(MAXNUP),
++c     &ISTUP(MAXNUP),MOTHUP(2,MAXNUP),ICOLUP(2,MAXNUP),PUP(5,MAXNUP),
++c     &VTIMUP(MAXNUP),SPINUP(MAXNUP)
++c      SAVE /HEPEUP/
++ 
++C...Read info from file.
++c      IF(MSTP(162).GT.0) THEN
++c        READ(MSTP(162),*,END=110,ERR=110) NUP,IDPRUP,XWGTUP,SCALUP,
++c     &  AQEDUP,AQCDUP
++c        DO 100 I=1,NUP
++c          READ(MSTP(162),*,END=110,ERR=110) IDUP(I),ISTUP(I),
++c     &    MOTHUP(1,I),MOTHUP(2,I),ICOLUP(1,I),ICOLUP(2,I),
++c     &    (PUP(J,I),J=1,5),VTIMUP(I),SPINUP(I)
++c  100   CONTINUE
++c        RETURN
++C...Special when reached end of file or other error.
++c  110   NUP=0
++ 
++C...Else not implemented.
++c      ELSE
++c        WRITE(MSTU(11),5000)
++c        STOP
++c      ENDIF
++ 
++C...Format for error printout.
++c 5000 FORMAT(1X,'Error: You have not implemented UPEVNT routine'/
++c     &1X,'Dummy routine in PYTHIA file called instead.'/
++c     &1X,'Execution stopped!')
++ 
++c      RETURN
++c      END
++ 
+diff -Naur upinit.f upinit.f
+--- upinit.f	2018-08-23 11:24:27.000000000 -0500
++++ upinit.f	2018-08-23 11:46:08.190999819 -0500
+@@ -1,4 +1,3 @@
+- 
+ C*********************************************************************
+  
+ C...UPINIT
+@@ -64,3 +63,56 @@
+  
+       RETURN
+       END
++
++C...Old example: handles a simple Pythia 6.4 initialization file.
++ 
++c      SUBROUTINE UPINIT
++ 
++C...Double precision and integer declarations.
++c      IMPLICIT DOUBLE PRECISION(A-H, O-Z)
++c      IMPLICIT INTEGER(I-N)
++ 
++C...Commonblocks.
++c      COMMON/PYDAT1/MSTU(200),PARU(200),MSTJ(200),PARJ(200)
++c      COMMON/PYPARS/MSTP(200),PARP(200),MSTI(200),PARI(200)
++c      SAVE /PYDAT1/,/PYPARS/
++ 
++C...User process initialization commonblock.
++c      INTEGER MAXPUP
++c      PARAMETER (MAXPUP=100)
++c      INTEGER IDBMUP,PDFGUP,PDFSUP,IDWTUP,NPRUP,LPRUP
++c      DOUBLE PRECISION EBMUP,XSECUP,XERRUP,XMAXUP
++c      COMMON/HEPRUP/IDBMUP(2),EBMUP(2),PDFGUP(2),PDFSUP(2),
++c     &IDWTUP,NPRUP,XSECUP(MAXPUP),XERRUP(MAXPUP),XMAXUP(MAXPUP),
++c     &LPRUP(MAXPUP)
++c      SAVE /HEPRUP/
++ 
++C...Read info from file.
++c      IF(MSTP(161).GT.0) THEN
++c        READ(MSTP(161),*,END=110,ERR=110) IDBMUP(1),IDBMUP(2),EBMUP(1),
++c     &  EBMUP(2),PDFGUP(1),PDFGUP(2),PDFSUP(1),PDFSUP(2),IDWTUP,NPRUP
++c        DO 100 IPR=1,NPRUP
++c          READ(MSTP(161),*,END=110,ERR=110) XSECUP(IPR),XERRUP(IPR),
++c     &    XMAXUP(IPR),LPRUP(IPR)
++c  100   CONTINUE
++c        RETURN
++C...Error or prematurely reached end of file.
++c  110   WRITE(MSTU(11),5000)
++c        STOP
++ 
++C...Else not implemented.
++c      ELSE
++c        WRITE(MSTU(11),5100)
++c        STOP
++c      ENDIF
++ 
++C...Format for error printout.
++c 5000 FORMAT(1X,'Error: UPINIT routine failed to read information'/
++c     &1X,'Execution stopped!')
++c 5100 FORMAT(1X,'Error: You have not implemented UPINIT routine'/
++c     &1X,'Dummy routine in PYTHIA file called instead.'/
++c     &1X,'Execution stopped!')
++ 
++c      RETURN
++c      END
++ 
+diff -Naur upveto.f upveto.f
+--- upveto.f	2018-08-23 11:24:27.000000000 -0500
++++ upveto.f	2018-08-23 11:46:08.190999819 -0500
+@@ -1,54 +1,3 @@
+-
+-C...Old example: handles a simple Pythia 6.4 event file.
+- 
+-c      SUBROUTINE UPEVNT
+- 
+-C...Double precision and integer declarations.
+-c      IMPLICIT DOUBLE PRECISION(A-H, O-Z)
+-c      IMPLICIT INTEGER(I-N)
+- 
+-C...Commonblocks.
+-c      COMMON/PYDAT1/MSTU(200),PARU(200),MSTJ(200),PARJ(200)
+-c      COMMON/PYPARS/MSTP(200),PARP(200),MSTI(200),PARI(200)
+-c      SAVE /PYDAT1/,/PYPARS/
+- 
+-C...User process event common block.
+-c      INTEGER MAXNUP
+-c      PARAMETER (MAXNUP=500)
+-c      INTEGER NUP,IDPRUP,IDUP,ISTUP,MOTHUP,ICOLUP
+-c      DOUBLE PRECISION XWGTUP,SCALUP,AQEDUP,AQCDUP,PUP,VTIMUP,SPINUP
+-c      COMMON/HEPEUP/NUP,IDPRUP,XWGTUP,SCALUP,AQEDUP,AQCDUP,IDUP(MAXNUP),
+-c     &ISTUP(MAXNUP),MOTHUP(2,MAXNUP),ICOLUP(2,MAXNUP),PUP(5,MAXNUP),
+-c     &VTIMUP(MAXNUP),SPINUP(MAXNUP)
+-c      SAVE /HEPEUP/
+- 
+-C...Read info from file.
+-c      IF(MSTP(162).GT.0) THEN
+-c        READ(MSTP(162),*,END=110,ERR=110) NUP,IDPRUP,XWGTUP,SCALUP,
+-c     &  AQEDUP,AQCDUP
+-c        DO 100 I=1,NUP
+-c          READ(MSTP(162),*,END=110,ERR=110) IDUP(I),ISTUP(I),
+-c     &    MOTHUP(1,I),MOTHUP(2,I),ICOLUP(1,I),ICOLUP(2,I),
+-c     &    (PUP(J,I),J=1,5),VTIMUP(I),SPINUP(I)
+-c  100   CONTINUE
+-c        RETURN
+-C...Special when reached end of file or other error.
+-c  110   NUP=0
+- 
+-C...Else not implemented.
+-c      ELSE
+-c        WRITE(MSTU(11),5000)
+-c        STOP
+-c      ENDIF
+- 
+-C...Format for error printout.
+-c 5000 FORMAT(1X,'Error: You have not implemented UPEVNT routine'/
+-c     &1X,'Dummy routine in PYTHIA file called instead.'/
+-c     &1X,'Execution stopped!')
+- 
+-c      RETURN
+-c      END
+- 
+ C*********************************************************************
+  
+ C...UPVETO
+@@ -98,3 +47,4 @@
+  
+       RETURN
+       END
++ 
diff --git a/var/spack/repos/builtin/packages/python/gcc-8-2.7.14.patch b/var/spack/repos/builtin/packages/python/gcc-8-2.7.14.patch
new file mode 100644
index 0000000000..72c879cdea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/python/gcc-8-2.7.14.patch
@@ -0,0 +1,35 @@
+diff --git a/Include/objimpl.h b/Include/objimpl.h
+index 5f2868332955..cbf6bc3f8763 100644
+--- a/Include/objimpl.h
++++ b/Include/objimpl.h
+@@ -248,6 +248,20 @@ PyAPI_FUNC(PyVarObject *) _PyObject_GC_Resize(PyVarObject *, Py_ssize_t);
+ /* for source compatibility with 2.2 */
+ #define _PyObject_GC_Del PyObject_GC_Del
+ 
++/*
++ * Former over-aligned definition of PyGC_Head, used to compute the size of the
++ * padding for the new version below.
++ */
++union _gc_head;
++union _gc_head_old {
++    struct {
++        union _gc_head_old *gc_next;
++        union _gc_head_old *gc_prev;
++        Py_ssize_t gc_refs;
++    } gc;
++    long double dummy;
++};
++
+ /* GC information is stored BEFORE the object structure. */
+ typedef union _gc_head {
+     struct {
+@@ -255,7 +269,8 @@ typedef union _gc_head {
+         union _gc_head *gc_prev;
+         Py_ssize_t gc_refs;
+     } gc;
+-    long double dummy;  /* force worst-case alignment */
++    double dummy; /* Force at least 8-byte alignment. */
++    char dummy_padding[sizeof(union _gc_head_old)];
+ } PyGC_Head;
+ 
+ extern PyGC_Head *_PyGC_generation0;
diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py
index c77756a78f..6d8823cc64 100644
--- a/var/spack/repos/builtin/packages/python/package.py
+++ b/var/spack/repos/builtin/packages/python/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import ast
 import os
 import platform
@@ -30,12 +11,14 @@ import sys
 
 import llnl.util.tty as tty
 from llnl.util.lang import match_predicate
-from llnl.util.filesystem import force_remove
+from llnl.util.filesystem import (force_remove, get_filetype,
+                                  path_contains_subdirectory)
 
-import spack
-from spack import *
-from spack.util.prefix import Prefix
+import spack.store
 import spack.util.spack_json as sjson
+from spack.util.environment import is_system_path
+from spack.util.prefix import Prefix
+from spack import *
 
 
 class Python(AutotoolsPackage):
@@ -46,6 +29,10 @@ class Python(AutotoolsPackage):
     list_url = "https://www.python.org/downloads/"
     list_depth = 1
 
+    version('3.7.0', '41b6595deb4147a1ed517a7d9a580271')
+    version('3.6.5', 'ab25d24b1f8cc4990ade979f6dc37883')
+    version('3.6.4', '9de6494314ea199e3633211696735f65')
+    version('3.6.3', 'e9180c69ed9a878a4a8a3ab221e32fa9')
     version('3.6.2', 'e1a36bfffdd1d3a780b1825daf16e56c')
     version('3.6.1', '2d0fc9f3a5940707590e07f03ecb08b9')
     version('3.6.0', '3f7062ccf8be76491884d0e47ac8b251')
@@ -56,7 +43,8 @@ class Python(AutotoolsPackage):
     version('3.3.6', 'cdb3cd08f96f074b3f3994ccb51063e9')
     version('3.2.6', '23815d82ae706e9b781ca65865353d39')
     version('3.1.5', '02196d3fc7bc76bdda68aa36b0dd16ab')
-    version('2.7.14', 'cee2e4b33ad3750da77b2e85f2f8b724', preferred=True)
+    version('2.7.15', '045fb3440219a1f6923fefdabde63342', preferred=True)
+    version('2.7.14', 'cee2e4b33ad3750da77b2e85f2f8b724')
     version('2.7.13', '17add4bf0ad0ec2f08e0cae6d205c700')
     version('2.7.12', '88d61f82e3616a4be952828b3694109d')
     version('2.7.11', '6b6076ec9e93f05dd63e47eb9c15728b')
@@ -83,6 +71,18 @@ class Python(AutotoolsPackage):
     variant('pic', default=True,
             description='Produce position-independent code (for shared libs)')
 
+    variant('dbm', default=True, description='Provide support for dbm')
+    variant(
+        'optimizations',
+        default=False,
+        description='Enable expensive build-time optimizations, if available'
+    )
+    # See https://legacy.python.org/dev/peps/pep-0394/
+    variant('pythoncmd', default=True,
+            description="Symlink 'python3' executable to 'python' "
+            "(not PEP 394 compliant)")
+
+    depends_on("pkgconfig", type="build")
     depends_on("openssl")
     depends_on("bzip2")
     depends_on("readline")
@@ -91,6 +91,11 @@ class Python(AutotoolsPackage):
     depends_on("zlib")
     depends_on("tk", when="+tk")
     depends_on("tcl", when="+tk")
+    depends_on("gdbm", when='+dbm')
+
+    # https://docs.python.org/3/whatsnew/3.7.html#build-changes
+    depends_on("libffi", when="@3.7:")
+    depends_on("openssl@1.0.2:", when="@3.7:")
 
     # Patch does not work for Python 3.1
     patch('ncurses.patch', when='@:2.8,3.2:')
@@ -99,10 +104,25 @@ class Python(AutotoolsPackage):
     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")
 
+    # Fixes an alignment problem with more aggressive optimization in gcc8
+    # https://github.com/python/cpython/commit/0b91f8a668201fc58fa732b8acc496caedfdbae0
+    patch('gcc-8-2.7.14.patch', when="@2.7.14 %gcc@8:")
+
+    # For more information refer to this bug report:
+    # https://bugs.python.org/issue29712
+    conflicts(
+        '@:2.8 +shared',
+        when='+optimizations',
+        msg='+optimizations is incompatible with +shared in python@2.X'
+    )
+
     _DISTUTIL_VARS_TO_SAVE = ['LDSHARED']
     _DISTUTIL_CACHE_FILENAME = 'sysconfig.json'
     _distutil_vars = None
 
+    # An in-source build with --enable-optimizations fails for python@3.X
+    build_directory = 'spack-build'
+
     @when('@2.7:2.8,3.4:')
     def patch(self):
         # NOTE: Python's default installation procedure makes it possible for a
@@ -117,7 +137,6 @@ class Python(AutotoolsPackage):
 
     def setup_environment(self, spack_env, run_env):
         spec = self.spec
-        prefix = self.prefix
 
         # TODO: The '--no-user-cfg' option for Python installation is only in
         # Python v2.7 and v3.4+ (see https://bugs.python.org/issue1180) and
@@ -128,8 +147,6 @@ class Python(AutotoolsPackage):
                       'user configurations are present.').format(self.version))
 
         # Need this to allow python build to find the Python installation.
-        spack_env.set('PYTHONHOME', prefix)
-        spack_env.set('PYTHONPATH', prefix)
         spack_env.set('MACOSX_DEPLOYMENT_TARGET', platform.mac_ver()[0])
 
     def configure_args(self):
@@ -137,15 +154,45 @@ class Python(AutotoolsPackage):
 
         # setup.py needs to be able to read the CPPFLAGS and LDFLAGS
         # as it scans for the library and headers to build
-        dep_pfxs = [dspec.prefix for dspec in spec.dependencies('link')]
-        config_args = [
-            '--with-threads',
-            'CPPFLAGS=-I{0}'.format(' -I'.join(dp.include for dp in dep_pfxs)),
-            'LDFLAGS=-L{0}'.format(' -L'.join(dp.lib for dp in dep_pfxs)),
-        ]
+        link_deps = spec.dependencies('link')
+
+        # Header files are often included assuming they reside in a
+        # subdirectory of prefix.include, e.g. #include <openssl/ssl.h>,
+        # which is why we don't use HeaderList here. The header files of
+        # libffi reside in prefix.lib but the configure script of Python
+        # finds them using pkg-config.
+        cppflags = '-I' + ' -I'.join(dep.prefix.include
+                                     for dep in link_deps
+                                     if dep.name != 'libffi')
+
+        # Currently, the only way to get SpecBuildInterface wrappers of the
+        # dependencies (which we need to get their 'libs') is to get them
+        # using spec.__getitem__.
+        ldflags = ' '.join(spec[dep.name].libs.search_flags
+                           for dep in link_deps)
+
+        config_args = ['CPPFLAGS=' + cppflags, 'LDFLAGS=' + ldflags]
+
+        # https://docs.python.org/3/whatsnew/3.7.html#build-changes
+        if spec.satisfies('@:3.6'):
+            config_args.append('--with-threads')
+
+        if '^libffi' in spec:
+            config_args.append('--with-system-ffi')
+        else:
+            config_args.append('--without-system-ffi')
+
+        if spec.satisfies('@2.7.13:2.8,3.5.3:', strict=True) \
+                and '+optimizations' in spec:
+            config_args.append('--enable-optimizations')
+
         if spec.satisfies('%gcc platform=darwin'):
             config_args.append('--disable-toolbox-glue')
 
+        if spec.satisfies('%intel', strict=True) and \
+                spec.satisfies('@2.7.12:2.8,3.5.2:', strict=True):
+            config_args.append('--with-icc')
+
         if '+shared' in spec:
             config_args.append('--enable-shared')
         else:
@@ -202,6 +249,12 @@ class Python(AutotoolsPackage):
                 os.symlink(os.path.join(src, f),
                            os.path.join(dst, f))
 
+        if spec.satisfies('@3:') and spec.satisfies('+pythoncmd'):
+            os.symlink(os.path.join(prefix.bin, 'python3'),
+                       os.path.join(prefix.bin, 'python'))
+            os.symlink(os.path.join(prefix.bin, 'python3-config'),
+                       os.path.join(prefix.bin, 'python-config'))
+
     # TODO: Once better testing support is integrated, add the following tests
     # https://wiki.python.org/moin/TkInter
     #
@@ -352,37 +405,32 @@ class Python(AutotoolsPackage):
         on the version of Python and how it was installed.
 
         In general, Python 2 comes with ``python`` and ``python2`` commands,
-        while Python 3 only comes with a ``python3`` command.
+        while Python 3 only comes with a ``python3`` command. However, some
+        package managers will symlink ``python`` to ``python3``, while others
+        may contain ``python3.6``, ``python3.5``, and ``python3.4`` in the
+        same directory.
 
-        :returns: The Python command
-        :rtype: Executable
+        Returns:
+            Executable: the Python command
         """
         # We need to be careful here. If the user is using an externally
-        # installed python, all 3 commands could be in the same directory.
-
-        # Search for `python2` iff using Python 2
-        if (self.spec.satisfies('@:2') and
-                os.path.exists(os.path.join(self.prefix.bin, 'python2'))):
-            command = 'python2'
-        # Search for `python3` iff using Python 3
-        elif (self.spec.satisfies('@3:') and
-                os.path.exists(os.path.join(self.prefix.bin, 'python3'))):
-            command = 'python3'
-        # If neither were found, try `python`
-        elif os.path.exists(os.path.join(self.prefix.bin, 'python')):
-            command = 'python'
+        # installed python, several different commands could be located
+        # in the same directory. Be as specific as possible. Search for:
+        #
+        # * python3.6
+        # * python3
+        # * python
+        #
+        # in that order if using python@3.6.5, for example.
+        version = self.spec.version
+        for ver in [version.up_to(2), version.up_to(1), '']:
+            path = os.path.join(self.prefix.bin, 'python{0}'.format(ver))
+            if os.path.exists(path):
+                return Executable(path)
         else:
             msg = 'Unable to locate {0} command in {1}'
             raise RuntimeError(msg.format(self.name, self.prefix.bin))
 
-        # The python command may be a symlink if it was installed
-        # with Homebrew. Since some packages try to determine the
-        # location of libraries and headers based on the path,
-        # return the realpath
-        path = os.path.realpath(os.path.join(self.prefix.bin, command))
-
-        return Executable(path)
-
     def print_string(self, string):
         """Returns the appropriate print string depending on the
         version of Python.
@@ -461,7 +509,7 @@ class Python(AutotoolsPackage):
                 return LibraryList(os.path.join(frameworkprefix, ldlibrary))
             else:
                 msg = 'Unable to locate {0} libraries in {1}'
-                raise RuntimeError(msg.format(self.name, libdir))
+                raise RuntimeError(msg.format(ldlibrary, libdir))
         else:
             library = self.get_config_var('LIBRARY')
 
@@ -471,7 +519,7 @@ class Python(AutotoolsPackage):
                 return LibraryList(os.path.join(frameworkprefix, library))
             else:
                 msg = 'Unable to locate {0} libraries in {1}'
-                raise RuntimeError(msg.format(self.name, libdir))
+                raise RuntimeError(msg.format(library, libdir))
 
     @property
     def headers(self):
@@ -504,11 +552,19 @@ class Python(AutotoolsPackage):
         """Set PYTHONPATH to include the site-packages directory for the
         extension and any other python extensions it depends on."""
 
+        # If we set PYTHONHOME, we must also ensure that the corresponding
+        # python is found in the build environment. This to prevent cases
+        # where a system provided python is run against the standard libraries
+        # of a Spack built python. See issue #7128
         spack_env.set('PYTHONHOME', self.home)
 
+        path = os.path.dirname(self.command.path)
+        if not is_system_path(path):
+            spack_env.prepend_path('PATH', path)
+
         python_paths = []
         for d in dependent_spec.traverse(
-                deptype=('build', 'run'), deptype_query='run'):
+                deptype=('build', 'run', 'test')):
             if d.package.extends(self.spec):
                 python_paths.append(join_path(d.prefix,
                                               self.site_packages_dir))
@@ -628,33 +684,49 @@ class Python(AutotoolsPackage):
                         "sys.path[p:p]=new; "
                         "sys.__egginsert = p+len(new)\n")
 
-    def activate(self, ext_pkg, **args):
+    def activate(self, ext_pkg, view, **args):
         ignore = self.python_ignore(ext_pkg, args)
         args.update(ignore=ignore)
 
-        extensions_layout = args.get("extensions_layout",
-                                     spack.store.extensions)
-
-        super(Python, self).activate(ext_pkg, **args)
+        super(Python, self).activate(ext_pkg, view, **args)
 
+        extensions_layout = view.extensions_layout
         exts = extensions_layout.extension_map(self.spec)
         exts[ext_pkg.name] = ext_pkg.spec
 
-        self.write_easy_install_pth(
-            exts,
-            prefix=extensions_layout.extendee_target_directory(self))
+        self.write_easy_install_pth(exts, prefix=view.root)
 
-    def deactivate(self, ext_pkg, **args):
+    def deactivate(self, ext_pkg, view, **args):
         args.update(ignore=self.python_ignore(ext_pkg, args))
-        super(Python, self).deactivate(ext_pkg, **args)
 
-        extensions_layout = args.get("extensions_layout",
-                                     spack.store.extensions)
+        super(Python, self).deactivate(ext_pkg, view, **args)
 
+        extensions_layout = view.extensions_layout
         exts = extensions_layout.extension_map(self.spec)
         # Make deactivate idempotent
         if ext_pkg.name in exts:
             del exts[ext_pkg.name]
-            self.write_easy_install_pth(
-                exts,
-                prefix=extensions_layout.extendee_target_directory(self))
+            self.write_easy_install_pth(exts, prefix=view.root)
+
+    def add_files_to_view(self, view, merge_map):
+        bin_dir = self.spec.prefix.bin
+        for src, dst in merge_map.items():
+            if not path_contains_subdirectory(src, bin_dir):
+                view.link(src, dst)
+            elif not os.path.islink(src):
+                copy(src, dst)
+                if 'script' in get_filetype(src):
+                    filter_file(
+                        self.spec.prefix, os.path.abspath(view.root), dst)
+            else:
+                orig_link_target = os.path.realpath(src)
+                new_link_target = os.path.abspath(merge_map[orig_link_target])
+                view.link(new_link_target, dst)
+
+    def remove_files_from_view(self, view, merge_map):
+        bin_dir = self.spec.prefix.bin
+        for src, dst in merge_map.items():
+            if not path_contains_subdirectory(src, bin_dir):
+                view.remove_file(src, dst)
+            else:
+                os.remove(dst)
diff --git a/var/spack/repos/builtin/packages/qbank/package.py b/var/spack/repos/builtin/packages/qbank/package.py
index b56be62bad..30133052b4 100644
--- a/var/spack/repos/builtin/packages/qbank/package.py
+++ b/var/spack/repos/builtin/packages/qbank/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/qbox/package.py b/var/spack/repos/builtin/packages/qbox/package.py
index 7945370997..0bd70f4445 100644
--- a/var/spack/repos/builtin/packages/qbox/package.py
+++ b/var/spack/repos/builtin/packages/qbox/package.py
@@ -1,29 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import shutil
 from spack import *
 
 
@@ -88,6 +67,6 @@ class Qbox(MakefilePackage):
     def install(self, spec, prefix):
         mkdir(prefix.src)
         install('src/qb', prefix.src)
-        shutil.move('test', prefix)
-        shutil.move('xml', prefix)
-        shutil.move('util', prefix)
+        install_tree('test', prefix)
+        install_tree('xml', prefix)
+        install_tree('util', prefix)
diff --git a/var/spack/repos/builtin/packages/qhull/package.py b/var/spack/repos/builtin/packages/qhull/package.py
index 3e3e033025..9bdfcab341 100644
--- a/var/spack/repos/builtin/packages/qhull/package.py
+++ b/var/spack/repos/builtin/packages/qhull/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/qmcpack/package.py b/var/spack/repos/builtin/packages/qmcpack/package.py
index 360ae0a51d..0e9169a481 100644
--- a/var/spack/repos/builtin/packages/qmcpack/package.py
+++ b/var/spack/repos/builtin/packages/qmcpack/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import llnl.util.tty as tty
 
 
 class Qmcpack(CMakePackage):
@@ -31,16 +13,21 @@ class Qmcpack(CMakePackage):
 
     # Package information
     homepage = "http://www.qmcpack.org/"
-    url      = "https://github.com/QMCPACK/qmcpack.git"
-
-    # This download method is untrusted, and is not recommended
-    # by the Spack manual. However, it is easier to maintain
-    # because github hashes can occasionally change
-    version('3.2.0', git=url, tag='v3.2.0')
-    version('3.1.1', git=url, tag='v3.1.1')
-    version('3.1.0', git=url, tag='v3.1.0')
-    version('3.0.0', git=url, tag='v3.0.0')
-    version('develop', git=url)
+    git      = "https://github.com/QMCPACK/qmcpack.git"
+
+    tags = ['ecp', 'ecp-apps']
+
+    # This download method is untrusted, and is not recommended by the
+    # Spack manual. However, it is easier to maintain because github hashes
+    # can occasionally change.
+    # NOTE: 12/19/2017 QMCPACK 3.0.0 does not build properly with Spack.
+    version('develop')
+    version('3.5.0', tag='v3.5.0')
+    version('3.4.0', tag='v3.4.0')
+    version('3.3.0', tag='v3.3.0')
+    version('3.2.0', tag='v3.2.0')
+    version('3.1.1', tag='v3.1.1')
+    version('3.1.0', tag='v3.1.0')
 
     # These defaults match those in the QMCPACK manual
     variant('debug', default=False, description='Build debug version')
@@ -57,11 +44,13 @@ class Qmcpack(CMakePackage):
                         'Array-of-Structure code. Only for CPU code'
                         'and only in mixed precision')
     variant('timers', default=False,
-             description='Build with support for timers')
+            description='Build with support for timers')
     variant('da', default=False,
             description='Install with support for basic data analysis tools')
     variant('gui', default=False,
             description='Install with Matplotlib (long installation time)')
+    variant('qe', default=True,
+            description='Install with patched Quantum Espresso 6.3.0')
 
     # cuda variant implies mixed precision variant by default, but there is
     # no way to express this in variant syntax, need something like
@@ -72,7 +61,9 @@ class Qmcpack(CMakePackage):
     conflicts('^openblas+ilp64')
     conflicts('^intel-mkl+ilp64')
 
-    # Dependencies match those in the QMCPACK manual
+    # Dependencies match those in the QMCPACK manual.
+    # FIXME: once concretizer can unite unconditional and conditional
+    # dependencies the some of the '~mpi' will not be necessary.
     depends_on('cmake@3.4.3:', type='build')
     depends_on('mpi', when='+mpi')
     depends_on('libxml2')
@@ -90,23 +81,41 @@ class Qmcpack(CMakePackage):
     # qmcpack data analysis tools
     # basic command line tool based on Python and NumPy
     # blas and lapack patching fails often and so are disabled at this time
-    depends_on('py-numpy~blas~lapack', type='run', when='+da')
+    depends_on('py-numpy~blas~lapack', when='+da', type='run')
 
-    # GUI is optional fpr data anlysis
+    # GUI is optional for data anlysis
     # py-matplotlib leads to a long complex DAG for dependencies
-    depends_on('py-matplotlib', type='run', when='+gui')
+    depends_on('py-matplotlib', when='+gui', type='run')
 
     # B-spline basis calculation require a patched version of
-    # Quantum Espresso 5.3.0 (see QMCPACK manual)
-    patch_url = 'https://raw.githubusercontent.com/QMCPACK/qmcpack/develop/external_codes/quantum_espresso/add_pw2qmcpack_to_espresso-5.3.0.diff'
-    patch_checksum = '0d8d7ba805313ddd4c02ee32c96d2f12e7091e9e82e22671d3ad5a24247860c4'
-    depends_on('espresso@5.3.0~elpa',
-               patches=patch(patch_url, sha256=patch_checksum),
-               when='+mpi')
-
-    depends_on('espresso@5.3.0~elpa~scalapack~mpi',
-               patches=patch(patch_url, sha256=patch_checksum),
-               when='~mpi')
+    # Quantum Espresso 6.3 (see QMCPACK manual)
+    # Building explicitly without ELPA due to issues in Quantum Espresso
+    # Spack package
+    patch_url = 'https://raw.githubusercontent.com/QMCPACK/qmcpack/develop/external_codes/quantum_espresso/add_pw2qmcpack_to_qe-6.3.diff'
+    patch_checksum = '2ee346e24926479f5e96f8dc47812173a8847a58354bbc32cf2114af7a521c13'
+    depends_on('quantum-espresso@6.3~elpa+hdf5',
+               patches=patch(patch_url, sha256=patch_checksum, when='+qe'),
+                   when='+qe+mpi', type='run')
+
+    depends_on('quantum-espresso@6.3~elpa~scalapack~mpi+hdf5',
+               patches=patch(patch_url, sha256=patch_checksum, when='+qe'),
+                   when='+qe~mpi', type='run')
+
+    # Backport several patches from recent versions of QMCPACK
+    # The test_numerics unit test is broken prior to QMCPACK 3.3.0
+    patch_url = 'https://patch-diff.githubusercontent.com/raw/QMCPACK/qmcpack/pull/621.patch'
+    patch_checksum = 'e2ff7a6f0f006856085d4aab6d31f32f16353e41f760a33a7ef75f3ecce6a5d6'
+    patch(patch_url, sha256=patch_checksum, when='@3.1.0:3.3.0')
+
+    # FindMKL.cmake has an issues prior to QMCPACK 3.3.0
+    patch_url = 'https://patch-diff.githubusercontent.com/raw/QMCPACK/qmcpack/pull/623.patch'
+    patch_checksum = '3eb9dec05fd1a544318ff84cd8b5926cfc6b46b375c7f3b012ccf0b50cf617b7'
+    patch(patch_url, sha256=patch_checksum, when='@3.1.0:3.3.0')
+
+    # git-rev files for not git builds issues prior to QMCPACK 3.3.0
+    patch_url = 'https://patch-diff.githubusercontent.com/raw/QMCPACK/qmcpack/pull/643.patch'
+    patch_checksum = 'c066c79901a612cf8848135e0d544efb114534cca70b90bfccc8ed989d3d9dde'
+    patch(patch_url, sha256=patch_checksum, when='@3.1.0:3.3.0')
 
     def patch(self):
         # FindLibxml2QMC.cmake doesn't check the environment by default
@@ -116,22 +125,23 @@ class Qmcpack(CMakePackage):
                     'CMake/FindLibxml2QMC.cmake')
 
     def cmake_args(self):
+        spec = self.spec
         args = []
 
-        if '+mpi' in self.spec:
-            mpi = self.spec['mpi']
+        if '+mpi' in spec:
+            mpi = spec['mpi']
             args.append('-DCMAKE_C_COMPILER={0}'.format(mpi.mpicc))
             args.append('-DCMAKE_CXX_COMPILER={0}'.format(mpi.mpicxx))
             args.append('-DMPI_BASE_DIR:PATH={0}'.format(mpi.prefix))
 
         # Currently FFTW_HOME and LIBXML2_HOME are used by CMake.
         # Any CMake warnings about other variables are benign.
-        xml2_prefix = self.spec['libxml2'].prefix
+        xml2_prefix = spec['libxml2'].prefix
         args.append('-DLIBXML2_HOME={0}'.format(xml2_prefix))
         args.append('-DLibxml2_INCLUDE_DIRS={0}'.format(xml2_prefix.include))
         args.append('-DLibxml2_LIBRARY_DIRS={0}'.format(xml2_prefix.lib))
 
-        fftw_prefix = self.spec['fftw'].prefix
+        fftw_prefix = spec['fftw'].prefix
         args.append('-DFFTW_HOME={0}'.format(fftw_prefix))
         args.append('-DFFTW_INCLUDE_DIRS={0}'.format(fftw_prefix.include))
         args.append('-DFFTW_LIBRARY_DIRS={0}'.format(fftw_prefix.lib))
@@ -140,15 +150,15 @@ class Qmcpack(CMakePackage):
         args.append('-DHDF5_ROOT={0}'.format(self.spec['hdf5'].prefix))
 
         # Default is MPI, serial version is convenient for cases, e.g. laptops
-        if '+mpi' in self.spec:
+        if '+mpi' in spec:
             args.append('-DQMC_MPI=1')
-        elif '~mpi' in self.spec:
+        elif '~mpi' in spec:
             args.append('-DQMC_MPI=0')
 
         # Default is real-valued single particle orbitals
-        if '+complex' in self.spec:
+        if '+complex' in spec:
             args.append('-DQMC_COMPLEX=1')
-        elif '~complex' in self.spec:
+        elif '~complex' in spec:
             args.append('-DQMC_COMPLEX=0')
 
         # When '-DQMC_CUDA=1', CMake automatically sets:
@@ -157,44 +167,66 @@ class Qmcpack(CMakePackage):
         # There is a double-precision CUDA path, but it is not as well
         # tested.
 
-        if '+cuda' in self.spec:
+        if '+cuda' in spec:
             args.append('-DQMC_CUDA=1')
-        elif '~cuda' in self.spec:
+        elif '~cuda' in spec:
             args.append('-DQMC_CUDA=0')
 
         # Mixed-precision versues double-precision CPU and GPU code
-        if '+mixed' in self.spec:
+        if '+mixed' in spec:
             args.append('-DQMC_MIXED_PRECISION=1')
-        elif '~mixed' in self.spec:
+        elif '~mixed' in spec:
             args.append('-DQMC_MIXED_PRECISION=0')
 
         # New Structure-of-Array (SOA) code, much faster than default
         # Array-of-Structure (AOS) code.
         # No support for local atomic orbital basis.
-        if '+soa' in self.spec:
+        if '+soa' in spec:
             args.append('-DENABLE_SOA=1')
-        elif '~soa' in self.spec:
+        elif '~soa' in spec:
             args.append('-DENABLE_SOA=0')
 
         # Manual Timers
-        if '+timers' in self.spec:
+        if '+timers' in spec:
             args.append('-DENABLE_TIMERS=1')
-        elif '~timers' in self.spec:
+        elif '~timers' in spec:
             args.append('-DENABLE_TIMERS=0')
 
-    #     # Proper MKL detection not working.
-    #     # Include MKL flags
-    #     if 'intel-mkl' in self.spec:
-    #         args.append('-DBLA_VENDOR=Intel10_64lp_seq')
-    #         args.append('-DQMC_INCLUDE={0}'.format(join_path(env['MKLROOT'],'include')))
-        return args
+        # Proper detection of optimized BLAS and LAPACK.
+        # Based on the code from the deal II Spack package:
+        # https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/dealii/package.py
+        #
+        # Basically, we override CMake's auto-detection mechanism
+        # and use the Spack's interface instead
+        lapack_blas = spec['lapack'].libs + spec['blas'].libs
+        args.extend([
+            '-DLAPACK_FOUND=true',
+            '-DLAPACK_LIBRARIES=%s' % lapack_blas.joined(';')
+        ])
+
+        # Additionally, we need to pass the BLAS+LAPACK include directory for
+        # header files. This is to insure vectorized math and FFT libraries
+        # get properly detected. Intel MKL requires special case due to
+        # differences in Darwin vs. Linux $MKLROOT naming schemes. This section
+        # of code is intentionally redundant for backwards compatibility.
+        if 'intel-mkl' in self.spec:
+            lapack_dir = format(join_path(env['MKLROOT'], 'include'))
+            # Next two lines were introduced in QMCPACK 3.5.0 and later.
+            # Prior to v3.5.0, these lines should be benign.
+            args.append('-DENABLE_MKL=1')
+            args.append('-DMKL_ROOT=%s' % env['MKLROOT'])
+        else:
+            lapack_dir = ':'.join((
+                spec['lapack'].prefix.include,
+                spec['blas'].prefix.include
+            ))
+
+        args.extend([
+            '-DCMAKE_CXX_FLAGS=-I%s' % lapack_dir,
+            '-DCMAKE_C_FLAGS=-I%s' % lapack_dir
+        ])
 
-    # def setup_environment(self, spack_env, run_env):
-    #     # Add MKLROOT/lib to the CMAKE_PREFIX_PATH to enable CMake to find
-    #     # MKL libraries. MKLROOT environment variable must be defined for
-    #     # this to work properly.
-    #     if 'intel-mkl' in self.spec:
-    #         spack_env.append_path('CMAKE_PREFIX_PATH',format(join_path(env['MKLROOT'],'lib')))
+        return args
 
     def install(self, spec, prefix):
         """Make the install targets"""
@@ -228,7 +260,19 @@ class Qmcpack(CMakePackage):
     def check(self):
         """Run ctest after building binary.
         It can take over 24 hours to run all the regression tests, here we
-        only run the unit tests and short tests."""
+        only run the unit tests and short tests. If the unit tests fail,
+        the QMCPACK installation aborts. On the other hand, the short tests
+        are too strict and often fail, but are still useful to run. In the
+        future, the short tests will be more reasonable in terms of quality
+        assurance (i.e. they will not be so strict), but will be sufficient to
+        validate QMCPACK in production."""
+
         with working_dir(self.build_directory):
             ctest('-L', 'unit')
-            ctest('-R', 'short')
+            try:
+                ctest('-R', 'short')
+            except ProcessError:
+                warn  = 'Unit tests passed, but short tests have failed.\n'
+                warn += 'Please review failed tests before proceeding\n'
+                warn += 'with production calculations.\n'
+                tty.msg(warn)
diff --git a/var/spack/repos/builtin/packages/qmd-progress/package.py b/var/spack/repos/builtin/packages/qmd-progress/package.py
index a880609e76..ea87217689 100644
--- a/var/spack/repos/builtin/packages/qmd-progress/package.py
+++ b/var/spack/repos/builtin/packages/qmd-progress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,12 @@ class QmdProgress(CMakePackage):
     commonly used in quantum chemistry packages."""
 
     homepage = "https://github.com/lanl/qmd-progress"
-    url      = "https://github.com/lanl/qmd-progress"
+    url      = "https://github.com/lanl/qmd-progress/tarball/v1.1.0"
+    git      = "https://github.com/lanl/qmd-progress.git"
 
-    version('develop', git='https://github.com/lanl/qmd-progress', branch='master')
-    version('1.0.0', git='https://github.com/lanl/qmd-progress', tag='v1.0.0')
+    version('develop', branch='master')
+    version('1.1.0', 'dda155134f0925629bf116e562c0a4bd')
+    version('1.0.0', 'c950bead2719a47a78864e3376ba143e')
 
     variant('graphlib', default=False, description='Build with Metis Suppport')
     variant('mpi', default=True, description='Build with MPI Support')
diff --git a/var/spack/repos/builtin/packages/qorts/QoRTs.sh b/var/spack/repos/builtin/packages/qorts/QoRTs.sh
new file mode 100644
index 0000000000..d847e76e05
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qorts/QoRTs.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the QoRTs jar file
+java -jar QoRTs.jar "$@"
diff --git a/var/spack/repos/builtin/packages/qorts/package.py b/var/spack/repos/builtin/packages/qorts/package.py
new file mode 100644
index 0000000000..5b1c811e5f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qorts/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class Qorts(RPackage):
+    """The QoRTs software package is a fast, efficient, and portable
+    multifunction toolkit designed to assist in the analysis, quality
+    control, and data management of RNA-Seq and DNA-Seq datasets. Its
+    primary function is to aid in the detection and identification of
+    errors, biases, and artifacts produced by high-throughput sequencing
+    technology."""
+
+    homepage = "https://github.com/hartleys/QoRTs"
+    url      = "https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs_1.2.42.tar.gz"
+
+    version('1.2.42', '7d46162327b0da70bfe483fe2f2b7829')
+
+    depends_on('java', type='run')
+
+    resource(
+        name='QoRTs.jar',
+        url='https://github.com/hartleys/QoRTs/releases/download/v1.2.42/QoRTs.jar',
+        md5='918df4291538218c12caa3ab98c535e9',
+        placement='jarfile',
+        expand=False
+    )
+
+    @run_after('install')
+    def install_jar(self):
+        install_tree(join_path(self.stage.source_path, 'jarfile'),
+                     self.prefix.bin)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "QoRTs.sh")
+        script = self.prefix.bin.QoRTs
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = self.spec['java'].prefix.bin.java
+        kwargs = {'backup': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('QoRTs.jar', join_path(self.prefix.bin, 'QoRTs.jar'),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py
index 0856a4efb0..915f6615e8 100644
--- a/var/spack/repos/builtin/packages/qrupdate/package.py
+++ b/var/spack/repos/builtin/packages/qrupdate/package.py
@@ -1,31 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import sys
 from spack import *
 
 
-class Qrupdate(Package):
+class Qrupdate(MakefilePackage):
     """qrupdate is a Fortran library for fast updates of QR and
     Cholesky decompositions."""
 
@@ -37,7 +20,30 @@ class Qrupdate(Package):
     depends_on("blas")
     depends_on("lapack")
 
+    def edit(self, spec, prefix):
+        # BSD "install" does not understand GNU -D flag.
+        # We will create the parent directory ourselves.
+        makefile = FileFilter('src/Makefile')
+        if (sys.platform == 'darwin'):
+            makefile.filter('-D', '')
+        return
+
     def install(self, spec, prefix):
+        lapack_blas = spec['lapack'].libs + spec['blas'].libs
         # Build static and dynamic libraries
-        make("lib", "solib")
+        make('lib', 'solib',
+             'BLAS={0}'.format(lapack_blas.ld_flags),
+             'LAPACK={0}'.format(lapack_blas.ld_flags))
+        # "INSTALL" confuses "make install" on case-insensitive filesystems
+        if os.path.isfile("INSTALL"):
+            os.remove("INSTALL")
+        # create lib folder:
+        if (sys.platform == 'darwin'):
+            mkdirp(prefix.lib)
         make("install", "PREFIX=%s" % prefix)
+
+    @run_after('install')
+    def fix_darwin_install(self):
+        # The shared libraries are not installed correctly on Darwin:
+        if (sys.platform == 'darwin'):
+            fix_darwin_install_name(self.spec.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/qt-creator/package.py b/var/spack/repos/builtin/packages/qt-creator/package.py
index c7484f9643..05581edae4 100644
--- a/var/spack/repos/builtin/packages/qt-creator/package.py
+++ b/var/spack/repos/builtin/packages/qt-creator/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py
index fe29ced8a9..f956d77219 100644
--- a/var/spack/repos/builtin/packages/qt/package.py
+++ b/var/spack/repos/builtin/packages/qt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import platform
 import os
@@ -36,6 +17,8 @@ class Qt(Package):
     list_url = 'http://download.qt.io/archive/qt/'
     list_depth = 3
 
+    version('5.11.2', 'c6104b840b6caee596fa9a35bc5f57f67ed5a99d6a36497b6fe66f990a53ca81')
+    version('5.10.0', 'c5e275ab0ed7ee61d0f4b82cd471770d')
     version('5.9.1',  '77b4af61c49a09833d4df824c806acaf')
     version('5.9.0',  '9c8bc8b828c2b56721980368266df9d9')
     version('5.8.0',  'a9f2494f75f966e2f22358ec367d8f41')
@@ -66,7 +49,13 @@ class Qt(Package):
     variant('opengl',     default=False,
             description="Build with OpenGL support.")
 
+    # fix installation of pkgconfig files
+    # see https://github.com/Homebrew/homebrew-core/pull/5951
+    patch('restore-pc-files.patch', when='@5.9: platform=darwin')
+
+    patch('qt3accept.patch', when='@3.3.8b')
     patch('qt3krell.patch', when='@3.3.8b+krellpatch')
+    patch('qt3ptrdiff.patch', when='@3.3.8b')
 
     # see https://bugreports.qt.io/browse/QTBUG-57656
     patch('QTBUG-57656.patch', when='@5.8.0')
@@ -83,6 +72,12 @@ class Qt(Package):
     patch('qt4-pcre-include-conflict.patch', when='@4')
     patch('qt4-el-capitan.patch', when='@4')
 
+    # Allow Qt's configure script to build the webkit option with more
+    # recent versions of gcc.
+    # https://github.com/spack/spack/issues/9205
+    # https://github.com/spack/spack/issues/9209
+    patch('qt4-gcc-and-webkit.patch', when='@4')
+
     # Use system openssl for security.
     depends_on("openssl")
     depends_on("glib", when='@4:')
@@ -96,21 +91,36 @@ class Qt(Package):
     depends_on("libmng")
     depends_on("jpeg")
     depends_on("icu4c")
-    depends_on("fontconfig")
+    depends_on("fontconfig", when=(sys.platform != 'darwin'))  # (Unix only)
     depends_on("freetype")
-    # FIXME:
-    # depends_on("freetype", when='@5.8:') and '-system-freetype'
-    # -system-harfbuzz
-    # -system-pcre
+
+    # Core options:
+    # -doubleconversion  [system/qt/no]
+    # -iconv             [posix/sun/gnu/no] (Unix only)
+    # -pcre              [system/qt]
+
+    # Gui, printing, widget options:
+    # -harfbuzz          [system/qt/no]
+    # -xkbcommon-x11     [system/qt/no]
+    # -system-xkbcommon
+
+    # Database options:
+    # -sqlite            [system/qt]
+
+    # Qt3D options:
+    # -assimp            [system/qt/no]
 
     # QtQml
     depends_on("python", when='@5.7.0:', type='build')
 
     # OpenGL hardware acceleration
-    depends_on("mesa", when='@4:+opengl')
+    depends_on("gl@3.2:", when='@4:+opengl')
     depends_on("libxcb", when=sys.platform != 'darwin')
     depends_on("libx11", when=sys.platform != 'darwin')
 
+    if sys.platform != 'darwin':
+        depends_on("libxext", when='@3:4.99')
+
     # Webkit
     depends_on("flex", when='+webkit', type='build')
     depends_on("bison", when='+webkit', type='build')
@@ -121,6 +131,17 @@ class Qt(Package):
     # depends_on("pulse", when='+multimedia')
     # depends_on("flac", when='+multimedia')
     # depends_on("ogg", when='+multimedia')
+    # -pulseaudio                [auto] (Unix only)
+    # -alsa                      [auto] (Unix only)
+
+    # Webengine options:
+    # -webengine-alsa            [auto] (Linux only)
+    # -webengine-pulseaudio      [auto] (Linux only)
+    # -webengine-embedded-build  [auto] (Linux only)
+    # -webengine-icu             [system/qt] (Linux only)
+    # -webengine-ffmpeg          [system/qt] (Linux only)
+    # -webengine-opus            [system/qt] (Linux only)
+    # -webengine-webp            [system/qt] (Linux only)
 
     use_xcode = True
 
@@ -146,7 +167,9 @@ class Qt(Package):
         elif version >= Version('2.1'):
             url += 'x11-'
 
-        if version >= Version('4.0'):
+        if version >= Version('5.10.0'):
+            url += 'src-'
+        elif version >= Version('4.0'):
             url += 'opensource-src-'
         elif version >= Version('3'):
             url += 'free-'
@@ -198,6 +221,7 @@ class Qt(Package):
 
     @property
     def common_config_args(self):
+        # incomplete list is here http://doc.qt.io/qt-5/configure-options.html
         config_args = [
             '-prefix', self.prefix,
             '-v',
@@ -208,12 +232,14 @@ class Qt(Package):
             '-confirm-license',
             '-openssl-linked',
             '-optimized-qmake',
-            '-fontconfig',
             '-system-freetype',
             '-I{0}/freetype2'.format(self.spec['freetype'].prefix.include),
             '-no-pch'
         ]
 
+        if sys.platform != 'darwin':
+            config_args.append('-fontconfig')
+
         if '@:5.7.1' in self.spec:
             config_args.append('-no-openvg')
         else:
@@ -243,7 +269,6 @@ class Qt(Package):
             config_args.append('-I%s/dbus-1.0/include' % dbus.lib)
             config_args.append('-I%s/dbus-1.0' % dbus.include)
             config_args.append('-L%s' % dbus.lib)
-            config_args.append('-ldbus-1')
         else:
             config_args.append('-no-dbus')
 
@@ -255,6 +280,8 @@ class Qt(Package):
                 '-no-alsa',
             ])
 
+        # FIXME: else: -system-xcb ?
+
         if '@4' in self.spec and sys.platform == 'darwin':
             config_args.append('-cocoa')
 
@@ -333,6 +360,17 @@ class Qt(Package):
                 '-skip', 'webengine',
             ])
 
+        if '~opengl' in self.spec and self.spec.satisfies('@5.10:'):
+            config_args.extend([
+                '-skip', 'webglplugin',
+            ])
+
+        if self.version > Version('5.8'):
+            # relies on a system installed wayland, i.e. no spack package yet
+            # https://wayland.freedesktop.org/ubuntu16.04.html
+            # https://wiki.qt.io/QtWayland
+            config_args.extend(['-skip', 'wayland'])
+
         configure('-no-eglfs',
                   '-no-directfb',
                   '-{0}gtk'.format('' if '+gtk' in self.spec else 'no-'),
diff --git a/var/spack/repos/builtin/packages/qt/qt3accept.patch b/var/spack/repos/builtin/packages/qt/qt3accept.patch
new file mode 100644
index 0000000000..32dfb9df08
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt3accept.patch
@@ -0,0 +1,38 @@
+--- qt-x11-free-3.3.8b/configure	2008-01-15 13:09:15.000000000 -0600
++++ qt-x11-free-3.3.8b-fixes/configure	2015-07-08 15:49:03.379560633 -0500
+@@ -2339,7 +2339,7 @@
+         else
+             echo "Do you accept the terms of the $TheLicense? \c"
+         fi
+-        read acceptance
++        acceptance=yes
+         echo
+ 	if [ "$acceptance" = yes ]; then
+ 	    break
+@@ -2397,7 +2397,7 @@
+ 	else
+ 	    echo "Do you accept the terms of $affix license? \c"
+ 	fi
+-	read acceptance
++        acceptance=yes
+ 	echo
+ 	if [ "$acceptance" = "yes" ]; then
+ 	    break
+@@ -2443,7 +2443,7 @@
+ 	else
+ 	    echo "Do you accept the terms of the license? \c"
+ 	fi
+-	read acceptance
++        acceptance=yes
+ 	echo
+ 	if [ "$acceptance" = "yes" ]; then
+ 	    break
+@@ -2524,7 +2524,7 @@
+ 	else
+ 	    echo "Do you accept the terms of the $Platform License? \c"
+ 	fi
+-	read acceptance
++        acceptance=yes
+ 	echo
+ 	if [ "$acceptance" = "yes" ]; then
+ 	    break
diff --git a/var/spack/repos/builtin/packages/qt/qt3krell.patch b/var/spack/repos/builtin/packages/qt/qt3krell.patch
index 3333eeacd4..cee94b3cbc 100644
--- a/var/spack/repos/builtin/packages/qt/qt3krell.patch
+++ b/var/spack/repos/builtin/packages/qt/qt3krell.patch
@@ -1,23 +1,3 @@
---- qt-x11-free-3.3.8b/src/tools/qmap.h	2008-01-15 13:09:13.000000000 -0600
-+++ qt-x11-free-3.3.8b-fixes/src/tools/qmap.h	2015-07-08 15:47:34.757565247 -0500
-@@ -52,6 +52,7 @@
- #ifndef QT_NO_STL
- #include <iterator>
- #include <map>
-+#include <cstddef>
- #endif
- 
- //#define QT_CHECK_MAP_RANGE
---- qt-x11-free-3.3.8b/src/tools/qvaluelist.h	2008-01-15 13:09:13.000000000 -0600
-+++ qt-x11-free-3.3.8b-fixes/src/tools/qvaluelist.h	2015-07-08 15:47:34.758565247 -0500
-@@ -50,6 +50,7 @@
- #ifndef QT_NO_STL
- #include <iterator>
- #include <list>
-+#include <cstddef>
- #endif
- 
- //#define QT_CHECK_VALUELIST_RANGE
 --- qt-x11-free-3.3.8b/src/tools/qvaluevector.h	2008-01-15 13:09:13.000000000 -0600
 +++ qt-x11-free-3.3.8b-fixes/src/tools/qvaluevector.h	2015-07-08 15:47:34.758565247 -0500
 @@ -47,6 +47,7 @@
@@ -28,41 +8,3 @@
  #endif
  
  template <class T>
---- qt-x11-free-3.3.8b/configure	2008-01-15 13:09:15.000000000 -0600
-+++ qt-x11-free-3.3.8b-fixes/configure	2015-07-08 15:49:03.379560633 -0500
-@@ -2339,7 +2339,7 @@
-         else
-             echo "Do you accept the terms of the $TheLicense? \c"
-         fi
--        read acceptance
-+        acceptance=yes
-         echo
- 	if [ "$acceptance" = yes ]; then
- 	    break
-@@ -2397,7 +2397,7 @@
- 	else
- 	    echo "Do you accept the terms of $affix license? \c"
- 	fi
--	read acceptance
-+        acceptance=yes
- 	echo
- 	if [ "$acceptance" = "yes" ]; then
- 	    break
-@@ -2443,7 +2443,7 @@
- 	else
- 	    echo "Do you accept the terms of the license? \c"
- 	fi
--	read acceptance
-+        acceptance=yes
- 	echo
- 	if [ "$acceptance" = "yes" ]; then
- 	    break
-@@ -2524,7 +2524,7 @@
- 	else
- 	    echo "Do you accept the terms of the $Platform License? \c"
- 	fi
--	read acceptance
-+        acceptance=yes
- 	echo
- 	if [ "$acceptance" = "yes" ]; then
- 	    break
diff --git a/var/spack/repos/builtin/packages/qt/qt3ptrdiff.patch b/var/spack/repos/builtin/packages/qt/qt3ptrdiff.patch
new file mode 100644
index 0000000000..5043e4b5a8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt3ptrdiff.patch
@@ -0,0 +1,20 @@
+--- a/src/tools/qmap.h	2008-01-16 06:09:13.000000000 +1100
++++ b/src/tools/qmap.h	2018-01-07 11:32:38.720893324 +1100
+@@ -52,6 +52,7 @@
+ #ifndef QT_NO_STL
+ #include <iterator>
+ #include <map>
++#include <stddef.h>
+ #endif
+ 
+ //#define QT_CHECK_MAP_RANGE
+--- a/src/tools/qvaluelist.h	2008-01-16 06:09:13.000000000 +1100
++++ b/src/tools/qvaluelist.h	2018-01-07 11:33:03.393206961 +1100
+@@ -50,6 +50,7 @@
+ #ifndef QT_NO_STL
+ #include <iterator>
+ #include <list>
++#include <stddef.h>
+ #endif
+ 
+ //#define QT_CHECK_VALUELIST_RANGE
diff --git a/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch b/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
index 370edf7fa5..a4b652e401 100644
--- a/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
+++ b/var/spack/repos/builtin/packages/qt/qt4-corewlan-new-osx.patch
@@ -1,16 +1,16 @@
 diff -Nr -U5 qt-everywhere-opensource-src-4.8.6/src/plugins/bearer/corewlan/corewlan.pro qt-everywhere-opensource-src-4.8.6.corewlan-new-osx/src/plugins/bearer/corewlan/corewlan.pro
 --- qt-everywhere-opensource-src-4.8.6/src/plugins/bearer/corewlan/corewlan.pro	2014-04-10 14:37:12.000000000 -0400
 +++ qt-everywhere-opensource-src-4.8.6.corewlan-new-osx/src/plugins/bearer/corewlan/corewlan.pro	2015-12-02 12:21:34.608585392 -0500
-@@ -3,11 +3,11 @@
- 
+@@ -3,9 +3,9 @@
+
  QT = core network
  LIBS += -framework Foundation -framework SystemConfiguration
- 
+
  contains(QT_CONFIG, corewlan) {
 -    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, "/Developer/SDKs/MacOSX10\.[67]\.sdk") {
-+    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, ".*MacOSX10\.([6789]|1[01])\.sdk") {
++    isEmpty(QMAKE_MAC_SDK)|contains(QMAKE_MAC_SDK, ".*MacOSX10\.([6789]|1[0123])\.sdk") {
           LIBS += -framework CoreWLAN -framework Security
      }
  }
- 
+
  HEADERS += qcorewlanengine.h \
diff --git a/var/spack/repos/builtin/packages/qt/qt4-gcc-and-webkit.patch b/var/spack/repos/builtin/packages/qt/qt4-gcc-and-webkit.patch
new file mode 100644
index 0000000000..38a1c350f3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/qt4-gcc-and-webkit.patch
@@ -0,0 +1,20 @@
+--- a/configure.orig	2018-09-18 07:02:33.866633000 +1000
++++ b/configure	2018-09-18 07:05:21.935194000 +1000
+@@ -7708,7 +7708,7 @@
+ 
+ 	# Check gcc's version
+ 	case "$(${QMAKE_CONF_COMPILER} -dumpversion)" in
+-	    4*)
++	    [4-8]*)
+ 		;;
+ 	    3.4*)
+ 		canBuildQtXmlPatterns="no"
+@@ -7729,7 +7729,7 @@
+     *-g++*)
+ 	# Check gcc's version
+ 	case "$(${QMAKE_CONF_COMPILER} -dumpversion)" in
+-	    4*|3.4*)
++	    [4-8]*|3.4*)
+ 		;;
+             3.3*)
+                 canBuildWebKit="no"
diff --git a/var/spack/repos/builtin/packages/qt/restore-pc-files.patch b/var/spack/repos/builtin/packages/qt/restore-pc-files.patch
new file mode 100644
index 0000000000..35fbaddd43
--- /dev/null
+++ b/var/spack/repos/builtin/packages/qt/restore-pc-files.patch
@@ -0,0 +1,15 @@
+Partially reverts <https://codereview.qt-project.org/#/c/140954/>.
+
+diff --git i/qtbase/mkspecs/features/qt_module.prf w/qtbase/mkspecs/features/qt_module.prf
+index bb28af97..36bb6483 100644
+--- i/qtbase/mkspecs/features/qt_module.prf
++++ w/qtbase/mkspecs/features/qt_module.prf
+@@ -245,7 +245,7 @@ load(qt_installs)
+ load(qt_targets)
+
+ # this builds on top of qt_common
+-!internal_module:!lib_bundle:if(unix|mingw) {
++!internal_module:if(unix|mingw) {
+     CONFIG += create_pc
+     QMAKE_PKGCONFIG_DESTDIR = pkgconfig
+     host_build: \
diff --git a/var/spack/repos/builtin/packages/qtgraph/package.py b/var/spack/repos/builtin/packages/qtgraph/package.py
index 742b51dd1f..012bce84f2 100644
--- a/var/spack/repos/builtin/packages/qtgraph/package.py
+++ b/var/spack/repos/builtin/packages/qtgraph/package.py
@@ -1,45 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-##############################################################################
-# Copyright (c) 2015-2017 Krell Institute. All Rights Reserved.
-#
-# This program is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by the Free
-# Software Foundation; either version 2 of the License, or (at your option)
-# any later version.
-#
-# 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 GNU General Public License for
-# more details.
-#
-# You should have received a copy of the GNU 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import os
 
 
 class Qtgraph(QMakePackage):
@@ -49,25 +14,34 @@ class Qtgraph(QMakePackage):
        libgvc within the Qt Graphics View Framework."""
 
     homepage = "https://github.com/OpenSpeedShop/QtGraph"
+    git      = "https://github.com/OpenSpeedShop/QtGraph.git"
 
-    url      = "https://github.com/OpenSpeedShop/QtGraph.git"
-    version('1.0.0', branch='master',
-            git='https://github.com/OpenSpeedShop/QtGraph.git')
+    version('develop', branch='master')
+    version('1.0.0.0', branch='1.0.0.0')
 
     # qtgraph depends on these packages
-    depends_on('qt@4.8.6:')
-    depends_on('graphviz')
+    depends_on('qt@4.8.6:', when='@develop')
+    depends_on('qt@5.10.0', when='@1.0.0.0:')
+
+    depends_on("graphviz@2.40.1:", when='@develop')
+    depends_on("graphviz@2.40.1", when='@1.0.0.0:')
 
     def setup_environment(self, spack_env, run_env):
         """Set up the compile and runtime environments for a package."""
         spack_env.set('GRAPHVIZ_ROOT', self.spec['graphviz'].prefix)
         spack_env.set('INSTALL_ROOT', self.prefix)
 
+        # What library suffix should be used based on library existence
+        if os.path.isdir(self.prefix.lib64):
+            lib_dir = self.prefix.lib64
+        else:
+            lib_dir = self.prefix.lib
+
         # The implementor has set up the library and include paths in
         # a non-conventional way.  We reflect that here.
         run_env.prepend_path(
             'LD_LIBRARY_PATH', join_path(
-                self.prefix.lib64,
+                lib_dir,
                 '{0}'.format(self.spec['qt'].version.up_to(3))))
 
         run_env.prepend_path('CPATH', self.prefix.include.QtGraph)
diff --git a/var/spack/repos/builtin/packages/qthreads/package.py b/var/spack/repos/builtin/packages/qthreads/package.py
index b06e824681..f1796099aa 100644
--- a/var/spack/repos/builtin/packages/qthreads/package.py
+++ b/var/spack/repos/builtin/packages/qthreads/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/espresso/dspev_drv_elpa.patch b/var/spack/repos/builtin/packages/quantum-espresso/dspev_drv_elpa.patch
index 153bcf2ef5..153bcf2ef5 100644
--- a/var/spack/repos/builtin/packages/espresso/dspev_drv_elpa.patch
+++ b/var/spack/repos/builtin/packages/quantum-espresso/dspev_drv_elpa.patch
diff --git a/var/spack/repos/builtin/packages/espresso/package.py b/var/spack/repos/builtin/packages/quantum-espresso/package.py
index 23014710a1..7c1310ec31 100644
--- a/var/spack/repos/builtin/packages/espresso/package.py
+++ b/var/spack/repos/builtin/packages/quantum-espresso/package.py
@@ -1,34 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import glob
 import os.path
 
 from spack import *
 
 
-class Espresso(Package):
+class QuantumEspresso(Package):
     """Quantum-ESPRESSO is an integrated suite of Open-Source computer codes
     for electronic-structure calculations and materials modeling at the
     nanoscale. It is based on density-functional theory, plane waves, and
@@ -36,20 +17,12 @@ class Espresso(Package):
     """
 
     homepage = 'http://quantum-espresso.org'
-    url = 'http://www.qe-forge.org/gf/download/frsrelease/204/912/espresso-5.3.0.tar.gz'
+    url      = 'https://github.com/QEF/q-e/archive/qe-6.2.0.tar.gz'
 
-    version(
-        '6.1.0',
-        'db398edcad76e085f8c8a3f6ecb7aaab',
-        url='http://www.qe-forge.org/gf/download/frsrelease/240/1075/qe-6.1.tar.gz'
-    )
-
-    version(
-        '5.4.0',
-        '8bb78181b39bd084ae5cb7a512c1cfe7',
-        url='http://www.qe-forge.org/gf/download/frsrelease/211/968/espresso-5.4.0.tar.gz'
-    )
-    version('5.3.0', '6848fcfaeb118587d6be36bd10b7f2c3')
+    version('6.2.0', '972176a58d16ae8cf0c9a308479e2b97')
+    version('6.1.0', '3fe861dcb5f6ec3d15f802319d5d801b')
+    version('5.4',   '085f7e4de0952e266957bbc79563c54e')
+    version('5.3',   'be3f8778e302cffb89258a5f936a7592')
 
     variant('mpi', default=True, description='Builds with mpi support')
     variant('openmp', default=False, description='Enables openMP support')
@@ -71,8 +44,8 @@ class Espresso(Package):
     depends_on('elpa~openmp', when='+elpa~openmp')
     depends_on('hdf5', when='+hdf5')
 
-    patch('dspev_drv_elpa.patch', when='@6.1 ^elpa@2016.05.004')
-    patch('dspev_drv_elpa.patch', when='@6.1 ^elpa@2016.05.003')
+    patch('dspev_drv_elpa.patch', when='@6.1.0:+elpa ^elpa@2016.05.004')
+    patch('dspev_drv_elpa.patch', when='@6.1.0:+elpa ^elpa@2016.05.003')
 
     # We can't ask for scalapack or elpa if we don't want MPI
     conflicts(
@@ -154,6 +127,24 @@ class Espresso(Package):
 
         configure(*options)
 
+        # Apparently the build system of QE is so broken that:
+        #
+        # 1. The variable reported on stdout as HDF5_LIBS is actually
+        #    called HDF5_LIB (singular)
+        # 2. The link flags omit a few `-L` from the line, and this
+        #    causes the linker to break
+        #
+        # Below we try to match the entire HDF5_LIB line and substitute
+        # with the list of libraries that needs to be linked.
+        if '+hdf5' in spec:
+            make_inc = join_path(self.stage.source_path, 'make.inc')
+            hdf5_libs = ' '.join(spec['hdf5:hl,fortran'].libs)
+            filter_file(
+                'HDF5_LIB([\s]*)=([\s\w\-\/.,]*)',
+                'HDF5_LIB = {0}'.format(hdf5_libs),
+                make_inc
+            )
+
         make('all')
 
         if 'platform=darwin' in spec:
diff --git a/var/spack/repos/builtin/packages/quinoa/package.py b/var/spack/repos/builtin/packages/quinoa/package.py
index 5a47d355d9..61a933b378 100644
--- a/var/spack/repos/builtin/packages/quinoa/package.py
+++ b/var/spack/repos/builtin/packages/quinoa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,12 +15,12 @@ class Quinoa(CMakePackage):
     """
 
     homepage = "http://quinoacomputing.org"
-    url      = "https://github.com/quinoacomputing/quinoa/tarball/quinoa_v0.1"
+    git      = "https://github.com/quinoacomputing/quinoa.git"
 
-    version('develop', git='https://github.com/quinoacomputing/quinoa', branch='master')
+    version('develop', branch='master')
 
     depends_on('hdf5+mpi')
-    depends_on("charm backend=mpi")
+    depends_on("charmpp backend=mpi")
     depends_on("trilinos+exodus")
     depends_on("boost")
     depends_on("hypre~internal-superlu")
diff --git a/var/spack/repos/builtin/packages/qwt/package.py b/var/spack/repos/builtin/packages/qwt/package.py
index cef42d73e1..1d996a6246 100644
--- a/var/spack/repos/builtin/packages/qwt/package.py
+++ b/var/spack/repos/builtin/packages/qwt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-a4/package.py b/var/spack/repos/builtin/packages/r-a4/package.py
index 248e0c41f8..18b13c506e 100644
--- a/var/spack/repos/builtin/packages/r-a4/package.py
+++ b/var/spack/repos/builtin/packages/r-a4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4(RPackage):
     """Automated Affymetrix Array Analysis Umbrella Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4/"
-    url      = "https://git.bioconductor.org/packages/a4"
-    list_url = homepage
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4')
+    git      = "https://git.bioconductor.org/packages/a4.git"
+
+    version('1.24.0', commit='79b5143652176787c85a0d587b3bbfad6b4a19f4')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-a4base', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4base/package.py b/var/spack/repos/builtin/packages/r-a4base/package.py
index bc18cae16d..0e76c245f3 100644
--- a/var/spack/repos/builtin/packages/r-a4base/package.py
+++ b/var/spack/repos/builtin/packages/r-a4base/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4base(RPackage):
     """Automated Affymetrix Array Analysis."""
 
     homepage = "https://www.bioconductor.org/packages/a4Base/"
-    url      = "'https://git.bioconductor.org/packages/a4Base'"
-    list_url = homepage
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Base', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6')
+    git      = "https://git.bioconductor.org/packages/a4Base.git"
+
+    version('1.24.0', commit='f674afe424a508df2c8ee6c87a06fbd4aa410ef6')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4classif/package.py b/var/spack/repos/builtin/packages/r-a4classif/package.py
index 18a2e1b390..8a2a5c40f5 100644
--- a/var/spack/repos/builtin/packages/r-a4classif/package.py
+++ b/var/spack/repos/builtin/packages/r-a4classif/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class RA4classif(RPackage):
     """Automated Affymetrix Array Analysis Classification Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Classif/"
-    url      = "https://git.bioconductor.org/packages/a4Classif"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/a4Classif.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Classif', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1')
+    version('1.24.0', commit='ca06bf274c87a73fc12c29a6eea4b90289fe30b1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-a4core', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4core/package.py b/var/spack/repos/builtin/packages/r-a4core/package.py
index d01514d499..df2142be36 100644
--- a/var/spack/repos/builtin/packages/r-a4core/package.py
+++ b/var/spack/repos/builtin/packages/r-a4core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4core(RPackage):
     """Automated Affymetrix Array Analysis Core Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Core/"
-    url      = "https://git.bioconductor.org/packages/a4Core"
+    git      = "https://git.bioconductor.org/packages/a4Core.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Core', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3')
+    version('1.24.0', commit='c871faa3e1ab6be38a9ea3018816cf31b58b0ed3')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4preproc/package.py b/var/spack/repos/builtin/packages/r-a4preproc/package.py
index 3410b0640b..08530cf7b4 100644
--- a/var/spack/repos/builtin/packages/r-a4preproc/package.py
+++ b/var/spack/repos/builtin/packages/r-a4preproc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4preproc(RPackage):
     """Automated Affymetrix Array Analysis Preprocessing Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Preproc/"
-    url      = "https://git.bioconductor.org/packages/a4Preproc"
+    git      = "https://git.bioconductor.org/packages/a4Preproc.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Preproc', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
+    version('1.24.0', commit='651014b8102807aea4f1274e34e083e70b5e7ee7')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-a4reporting/package.py b/var/spack/repos/builtin/packages/r-a4reporting/package.py
index 352d35b38a..f0f9f32065 100644
--- a/var/spack/repos/builtin/packages/r-a4reporting/package.py
+++ b/var/spack/repos/builtin/packages/r-a4reporting/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RA4reporting(RPackage):
     """Automated Affymetrix Array Analysis Reporting Package."""
 
     homepage = "https://www.bioconductor.org/packages/a4Reporting"
-    url      = "https://git.bioconductor.org/packages/a4Reporting"
-    list_url = homepage
-    version('1.24.0', git='https://git.bioconductor.org/packages/a4Reporting', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
+    git      = "https://git.bioconductor.org/packages/a4Reporting.git"
+
+    version('1.24.0', commit='bf22c4d50daf40fc9eaf8c476385bf4a24a5b5ce')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-annaffy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-abadata/package.py b/var/spack/repos/builtin/packages/r-abadata/package.py
index 0d92e3e540..aa9796e383 100644
--- a/var/spack/repos/builtin/packages/r-abadata/package.py
+++ b/var/spack/repos/builtin/packages/r-abadata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-abaenrichment/package.py b/var/spack/repos/builtin/packages/r-abaenrichment/package.py
index c3e903e248..c43a85c214 100644
--- a/var/spack/repos/builtin/packages/r-abaenrichment/package.py
+++ b/var/spack/repos/builtin/packages/r-abaenrichment/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,9 +23,9 @@ class RAbaenrichment(RPackage):
     user-defined brain regions."""
 
     homepage = "https://bioconductor.org/packages/ABAEnrichment/"
-    url      = "https://git.bioconductor.org/packages/ABAEnrichment"
+    git      = "https://git.bioconductor.org/packages/ABAEnrichment.git"
 
-    version('1.6.0', git='https://git.bioconductor.org/packages/ABAEnrichment', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')
+    version('1.6.0', commit='d2a0467dcb7aa6e103e3b83dccd6510b0e142ac1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.6.0')
     depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py
index 768e930f4b..d9e7b2d821 100644
--- a/var/spack/repos/builtin/packages/r-abind/package.py
+++ b/var/spack/repos/builtin/packages/r-abind/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-absseq/package.py b/var/spack/repos/builtin/packages/r-absseq/package.py
index e3a094c97c..46bcf022f0 100644
--- a/var/spack/repos/builtin/packages/r-absseq/package.py
+++ b/var/spack/repos/builtin/packages/r-absseq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RAbsseq(RPackage):
     of dispersion across expression level."""
 
     homepage = "https://www.bioconductor.org/packages/ABSSeq/"
-    url      = "https://git.bioconductor.org/packages/ABSSeq"
+    git      = "https://git.bioconductor.org/packages/ABSSeq.git"
 
-    version('1.22.8', git='https://git.bioconductor.org/packages/ABSSeq', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a')
+    version('1.22.8', commit='a67ba49bc156a4522092519644f3ec83d58ebd6a')
 
     depends_on('r@3.4.0:3.4.9', when='@1.22.8')
     depends_on('r-locfit', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-acde/package.py b/var/spack/repos/builtin/packages/r-acde/package.py
index fd8677d42e..6abcd589ae 100644
--- a/var/spack/repos/builtin/packages/r-acde/package.py
+++ b/var/spack/repos/builtin/packages/r-acde/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-acepack/package.py b/var/spack/repos/builtin/packages/r-acepack/package.py
index be5d20f6ad..29a91b8a11 100644
--- a/var/spack/repos/builtin/packages/r-acepack/package.py
+++ b/var/spack/repos/builtin/packages/r-acepack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-acgh/package.py b/var/spack/repos/builtin/packages/r-acgh/package.py
index f2e923ca3e..54db729af3 100644
--- a/var/spack/repos/builtin/packages/r-acgh/package.py
+++ b/var/spack/repos/builtin/packages/r-acgh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RAcgh(RPackage):
     printing and plotting aCGH objects."""
 
     homepage = "https://www.bioconductor.org/packages/aCGH/"
-    url      = "https://git.bioconductor.org/packages/aCGH"
+    git      = "https://git.bioconductor.org/packages/aCGH.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/aCGH', commit='be2ed339449f55c8d218e10c435e4ad356683693')
+    version('1.54.0', commit='be2ed339449f55c8d218e10c435e4ad356683693')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-cluster', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-acme/package.py b/var/spack/repos/builtin/packages/r-acme/package.py
index 168f2044d5..d4263bfcc8 100644
--- a/var/spack/repos/builtin/packages/r-acme/package.py
+++ b/var/spack/repos/builtin/packages/r-acme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,9 +18,9 @@ class RAcme(RPackage):
     experiments quite easily with enough memory."""
 
     homepage = "https://www.bioconductor.org/packages/ACME/"
-    url      = "https://git.bioconductor.org/packages/ACME"
+    git      = "https://git.bioconductor.org/packages/ACME.git"
 
-    version('2.32.0', git='https://git.bioconductor.org/packages/ACME', commit='76372255d7714a0c8128a11c028bf70214dac407')
+    version('2.32.0', commit='76372255d7714a0c8128a11c028bf70214dac407')
 
     depends_on('r@3.4.0:3.4.9', when='@2.32.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ada/package.py b/var/spack/repos/builtin/packages/r-ada/package.py
index fbd4c0f167..eecb780fb0 100644
--- a/var/spack/repos/builtin/packages/r-ada/package.py
+++ b/var/spack/repos/builtin/packages/r-ada/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-adabag/package.py b/var/spack/repos/builtin/packages/r-adabag/package.py
index 407d0ad1ab..1e07829d5c 100644
--- a/var/spack/repos/builtin/packages/r-adabag/package.py
+++ b/var/spack/repos/builtin/packages/r-adabag/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ade4/package.py b/var/spack/repos/builtin/packages/r-ade4/package.py
index 39b21c3373..b3acb086e9 100644
--- a/var/spack/repos/builtin/packages/r-ade4/package.py
+++ b/var/spack/repos/builtin/packages/r-ade4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-adegenet/package.py b/var/spack/repos/builtin/packages/r-adegenet/package.py
index 64c475bc1f..754fb4ac22 100644
--- a/var/spack/repos/builtin/packages/r-adegenet/package.py
+++ b/var/spack/repos/builtin/packages/r-adegenet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-adsplit/package.py b/var/spack/repos/builtin/packages/r-adsplit/package.py
index f862b1e581..d2a9f44352 100644
--- a/var/spack/repos/builtin/packages/r-adsplit/package.py
+++ b/var/spack/repos/builtin/packages/r-adsplit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RAdsplit(RPackage):
     significance of the supporting gene set is determined."""
 
     homepage = "https://www.bioconductor.org/packages/adSplit/"
-    url      = "https://git.bioconductor.org/packages/adSplit"
+    git      = "https://git.bioconductor.org/packages/adSplit.git"
 
-    version('1.46.0', git='https://git.bioconductor.org/packages/adSplit', commit='7e81a83f34d371447f491b3a146bf6851e260c7c')
+    version('1.46.0', commit='7e81a83f34d371447f491b3a146bf6851e260c7c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.46.0')
     depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aer/package.py b/var/spack/repos/builtin/packages/r-aer/package.py
new file mode 100644
index 0000000000..830d4d74c6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-aer/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAer(RPackage):
+    """Functions, data sets, examples, demos, and vignettes
+    for the book Christian Kleiber and Achim Zeileis (2008),
+    Applied Econometrics with R, Springer-Verlag, New York.
+    ISBN 978-0-387-77316-2."""
+
+    homepage = "https://cran.r-project.org/web/packages/AER/index.html"
+    url      = "https://cran.r-project.org/src/contrib/AER_1.2-5.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/AER"
+
+    version('1.2-5', '419df9dc8ee6e5edd79678fee06719ae')
+
+    depends_on('r@2.13.0:', type=('build', 'run'))
+    depends_on('r-car@2.10-19:', type=('build', 'run'))
+    depends_on('r-lmtest', type=('build', 'run'))
+    depends_on('r-sandwich', type=('build', 'run'))
+    depends_on('r-survival@2.37-5:', type=('build', 'run'))
+    depends_on('r-zoo', type=('build', 'run'))
+    depends_on('r-formula', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affxparser/package.py b/var/spack/repos/builtin/packages/r-affxparser/package.py
index 1fd1dc5e85..79522cac96 100644
--- a/var/spack/repos/builtin/packages/r-affxparser/package.py
+++ b/var/spack/repos/builtin/packages/r-affxparser/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,9 +17,8 @@ class RAffxparser(RPackage):
     from a set of CEL files into a convenient list structure."""
 
     homepage = "https://www.bioconductor.org/packages/affxparser/"
-    url      = "https://git.bioconductor.org/packages/affxparser"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/affxparser.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/affxparser', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa')
+    version('1.48.0', commit='2461ea88f310b59c4a9a997a4b3dadedbd65a4aa')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
diff --git a/var/spack/repos/builtin/packages/r-affy/package.py b/var/spack/repos/builtin/packages/r-affy/package.py
index 6be405c38b..eb361b1b95 100644
--- a/var/spack/repos/builtin/packages/r-affy/package.py
+++ b/var/spack/repos/builtin/packages/r-affy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class RAffy(RPackage):
        functions. 'affy' is fully functional without it."""
 
     homepage = "https://bioconductor.org/packages/affy/"
-    url      = "https://git.bioconductor.org/packages/affy"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/affy.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/affy', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
+    version('1.54.0', commit='a815f02906fcf491b28ed0a356d6fce95a6bd20e')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affycomp/package.py b/var/spack/repos/builtin/packages/r-affycomp/package.py
index 16593472ad..329ffe1ed2 100644
--- a/var/spack/repos/builtin/packages/r-affycomp/package.py
+++ b/var/spack/repos/builtin/packages/r-affycomp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAffycomp(RPackage):
     expression measures for Affymetrix Oligonucleotide Arrays."""
 
     homepage = "https://www.bioconductor.org/packages/affycomp/"
-    url      = "https://git.bioconductor.org/packages/affycomp"
+    git      = "https://git.bioconductor.org/packages/affycomp.git"
 
-    version('1.52.0', git='https://git.bioconductor.org/packages/affycomp', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790')
+    version('1.52.0', commit='1b97a1cb21ec93bf1e5c88d5d55b988059612790')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affycompatible/package.py b/var/spack/repos/builtin/packages/r-affycompatible/package.py
index 68f6f5c450..de43dc9f9b 100644
--- a/var/spack/repos/builtin/packages/r-affycompatible/package.py
+++ b/var/spack/repos/builtin/packages/r-affycompatible/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,9 @@ class RAffycompatible(RPackage):
     (AGCC)-compatible sample annotation files."""
 
     homepage = "https://www.bioconductor.org/packages/AffyCompatible/"
-    url      = "https://git.bioconductor.org/packages/AffyCompatible"
+    git      = "https://git.bioconductor.org/packages/AffyCompatible.git"
 
-    version('1.36.0', 'https://git.bioconductor.org/packages/AffyCompatible', commit='dbbfd43a54ae1de6173336683a9461084ebf38c3')
+    version('1.36.0', commit='dbbfd43a54ae1de6173336683a9461084ebf38c3')
 
     depends_on('r@3.4.0:3.4.9', when=('@1.36.0'))
     depends_on('r-xml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affycontam/package.py b/var/spack/repos/builtin/packages/r-affycontam/package.py
index c2c08be3d6..f44105ce13 100644
--- a/var/spack/repos/builtin/packages/r-affycontam/package.py
+++ b/var/spack/repos/builtin/packages/r-affycontam/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAffycontam(RPackage):
     effectiveness."""
 
     homepage = "https://www.bioconductor.org/packages/affyContam/"
-    url      = "https://git.bioconductor.org/packages/affyContam"
+    git      = "https://git.bioconductor.org/packages/affyContam.git"
 
-    version('1.34.0', git='https://git.bioconductor.org/packages/affyContam', commit='03529f26d059c19e069cdda358dbf7789b6d4c40')
+    version('1.34.0', commit='03529f26d059c19e069cdda358dbf7789b6d4c40')
 
     depends_on('r@3.4.0:3.4.9', when=('@1.34.0'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affycoretools/package.py b/var/spack/repos/builtin/packages/r-affycoretools/package.py
index 303b7255f8..b2023e7084 100644
--- a/var/spack/repos/builtin/packages/r-affycoretools/package.py
+++ b/var/spack/repos/builtin/packages/r-affycoretools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAffycoretools(RPackage):
     the more common analyses that a core Biostatistician might see."""
 
     homepage = "https://www.bioconductor.org/packages/affycoretools/"
-    url      = "https://git.bioconductor.org/packages/affycoretools"
+    git      = "https://git.bioconductor.org/packages/affycoretools.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/affycoretools', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99')
+    version('1.48.0', commit='e0d52e34eead1ac45d3e60c59efd940e4889eb99')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affydata/package.py b/var/spack/repos/builtin/packages/r-affydata/package.py
index 9fa647f282..ac720a1793 100644
--- a/var/spack/repos/builtin/packages/r-affydata/package.py
+++ b/var/spack/repos/builtin/packages/r-affydata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-affyexpress/package.py b/var/spack/repos/builtin/packages/r-affyexpress/package.py
index 0e3a8f19d7..ec99f7bdce 100644
--- a/var/spack/repos/builtin/packages/r-affyexpress/package.py
+++ b/var/spack/repos/builtin/packages/r-affyexpress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RAffyexpress(RPackage):
     expressed genes in the Affymetrix gene expression data."""
 
     homepage = "https://www.bioconductor.org/packages/AffyExpress/"
-    url      = "https://git.bioconductor.org/packages/AffyExpress"
+    git      = "https://git.bioconductor.org/packages/AffyExpress.git"
 
-    version('1.42.0', git='https://git.bioconductor.org/packages/AffyExpress', commit='f5c5cf6173f4419e25f4aeff5e6b705a40abc371')
+    version('1.42.0', commit='f5c5cf6173f4419e25f4aeff5e6b705a40abc371')
 
     depends_on('r@3.4.0:3.4.9', when='@1.42.0')
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyilm/package.py b/var/spack/repos/builtin/packages/r-affyilm/package.py
index 7b854bc262..baa61ac6e0 100644
--- a/var/spack/repos/builtin/packages/r-affyilm/package.py
+++ b/var/spack/repos/builtin/packages/r-affyilm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RAffyilm(RPackage):
     of the Langmuir model."""
 
     homepage = "https://www.bioconductor.org/packages/affyILM/"
-    url      = "https://git.bioconductor.org/packages/affyILM"
+    git      = "https://git.bioconductor.org/packages/affyILM.git"
 
-    version('1.28.0', git='https://git.bioconductor.org/packages/affyILM', commit='307bee3ebc599e0ea4a1d6fa8d5511ccf8bef7de')
+    version('1.28.0', commit='307bee3ebc599e0ea4a1d6fa8d5511ccf8bef7de')
 
     depends_on('r@3.4.0:3.4.9', when='@1.28.0')
     depends_on('r-gcrma', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyio/package.py b/var/spack/repos/builtin/packages/r-affyio/package.py
index ed1f9ff265..973fdd757c 100644
--- a/var/spack/repos/builtin/packages/r-affyio/package.py
+++ b/var/spack/repos/builtin/packages/r-affyio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RAffyio(RPackage):
        formats."""
 
     homepage = "https://bioconductor.org/packages/affyio/"
-    url      = "https://git.bioconductor.org/packages/affyio"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/affyio.git"
+
+    version('1.46.0', commit='977597f2772e08273d86579486f452170566c880')
 
-    version('1.46.0', git='https://git.bioconductor.org/packages/affyio', commit='977597f2772e08273d86579486f452170566c880')
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@1.46.0')
diff --git a/var/spack/repos/builtin/packages/r-affypdnn/package.py b/var/spack/repos/builtin/packages/r-affypdnn/package.py
index 6fa1136468..f7cfaa20a6 100644
--- a/var/spack/repos/builtin/packages/r-affypdnn/package.py
+++ b/var/spack/repos/builtin/packages/r-affypdnn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAffypdnn(RPackage):
     described by Li Zhang et al."""
 
     homepage = "https://www.bioconductor.org/packages/affypdnn/"
-    url      = "https://git.bioconductor.org/packages/affypdnn"
+    git      = "https://git.bioconductor.org/packages/affypdnn.git"
 
-    version('1.50.0', git='https://git.bioconductor.org/packages/affypdnn', commit='97ff68e9f51f31333c0330435ea23b212b3ed18a')
+    version('1.50.0', commit='97ff68e9f51f31333c0330435ea23b212b3ed18a')
 
     depends_on('r@3.4.0:3.4.9', when='@1.50.0')
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyplm/package.py b/var/spack/repos/builtin/packages/r-affyplm/package.py
index f73b7ca19f..1690ce430b 100644
--- a/var/spack/repos/builtin/packages/r-affyplm/package.py
+++ b/var/spack/repos/builtin/packages/r-affyplm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RAffyplm(RPackage):
     PLM based quality assessment tools."""
 
     homepage = "https://www.bioconductor.org/packages/affyPLM/"
-    url      = "https://git.bioconductor.org/packages/affyPLM"
+    git      = "https://git.bioconductor.org/packages/affyPLM.git"
 
-    version('1.52.1', git='https://git.bioconductor.org/packages/affyPLM', commit='e8613a6018c4ee58045df6bf19128844f50a1f43')
+    version('1.52.1', commit='e8613a6018c4ee58045df6bf19128844f50a1f43')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.1')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyqcreport/package.py b/var/spack/repos/builtin/packages/r-affyqcreport/package.py
index a7b9f2aa3c..cb78a3d887 100644
--- a/var/spack/repos/builtin/packages/r-affyqcreport/package.py
+++ b/var/spack/repos/builtin/packages/r-affyqcreport/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RAffyqcreport(RPackage):
     quality of a set of arrays in an AffyBatch object."""
 
     homepage = "https://www.bioconductor.org/packages/affyQCReport/"
-    url      = "https://git.bioconductor.org/packages/affyQCReport"
+    git      = "https://git.bioconductor.org/packages/affyQCReport.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/affyQCReport', commit='5572e9981dc874b78b4adebf58080cac3fbb69e1')
+    version('1.54.0', commit='5572e9981dc874b78b4adebf58080cac3fbb69e1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
index 0a5d5f315c..b3cbabcc12 100644
--- a/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
+++ b/var/spack/repos/builtin/packages/r-affyrnadegradation/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,9 @@ class RAffyrnadegradation(RPackage):
     by RNA degradation."""
 
     homepage = "https://www.bioconductor.org/packages/AffyRNADegradation/"
-    url      = "https://git.bioconductor.org/packages/AffyRNADegradation"
+    git      = "https://git.bioconductor.org/packages/AffyRNADegradation.git"
 
-    version('1.22.0', git='https://git.bioconductor.org/packages/AffyRNADegradation', commit='0fa78f8286494711a239ded0ba587b0de47c15d3')
+    version('1.22.0', commit='0fa78f8286494711a239ded0ba587b0de47c15d3')
 
     depends_on('r@3.4.0:3.4.9', when='@1.22.0')
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-agdex/package.py b/var/spack/repos/builtin/packages/r-agdex/package.py
index 8abec46a01..85275712fb 100644
--- a/var/spack/repos/builtin/packages/r-agdex/package.py
+++ b/var/spack/repos/builtin/packages/r-agdex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAgdex(RPackage):
     for cross-species genomics."""
 
     homepage = "http://bioconductor.org/packages/AGDEX/"
-    url      = "https://git.bioconductor.org/packages/AGDEX"
+    git      = "https://git.bioconductor.org/packages/AGDEX.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/AGDEX', commit='29c6bcfa6919a5c6d8bcb36b44e75145a60ce7b5')
+    version('1.24.0', commit='29c6bcfa6919a5c6d8bcb36b44e75145a60ce7b5')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-agilp/package.py b/var/spack/repos/builtin/packages/r-agilp/package.py
index 15aba2cdce..9b90fca17a 100644
--- a/var/spack/repos/builtin/packages/r-agilp/package.py
+++ b/var/spack/repos/builtin/packages/r-agilp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,8 @@ class RAgilp(RPackage):
     """Agilent expression array processing package."""
 
     homepage = "http://bioconductor.org/packages/agilp/"
-    url      = "https://git.bioconductor.org/packages/agilp"
+    git      = "https://git.bioconductor.org/packages/agilp.git"
 
-    version('3.8.0', git='https://git.bioconductor.org/packages/agilp', commit='c772a802af1b4c0741f2edd78053a0425160ea53')
+    version('3.8.0', commit='c772a802af1b4c0741f2edd78053a0425160ea53')
 
     depends_on('r@3.4.0:3.4.9', when='@3.8.0')
diff --git a/var/spack/repos/builtin/packages/r-agimicrorna/package.py b/var/spack/repos/builtin/packages/r-agimicrorna/package.py
index b672f784bc..c509634f77 100644
--- a/var/spack/repos/builtin/packages/r-agimicrorna/package.py
+++ b/var/spack/repos/builtin/packages/r-agimicrorna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RAgimicrorna(RPackage):
     """Processing and Analysis of Agilent microRNA data."""
 
     homepage = "https://www.bioconductor.org/packages/AgiMicroRna/"
-    url      = "https://git.bioconductor.org/packages/AgiMicroRna"
+    git      = "https://git.bioconductor.org/packages/AgiMicroRna.git"
 
-    version('2.26.0', git='https://git.bioconductor.org/packages/AgiMicroRna', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053')
+    version('2.26.0', commit='6dd74bae47986f2a23d03e3f1f9f78f701dd8053')
 
     depends_on('r@3.4.0:3.4.9', when='@2.26.0')
     depends_on('r-affycoretools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aims/package.py b/var/spack/repos/builtin/packages/r-aims/package.py
index 4a724804ae..9d87e99052 100644
--- a/var/spack/repos/builtin/packages/r-aims/package.py
+++ b/var/spack/repos/builtin/packages/r-aims/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RAims(RPackage):
     as well as on dataset of gene expression data."""
 
     homepage = "http://bioconductor.org/packages/AIMS/"
-    url      = "https://git.bioconductor.org/packages/AIMS"
+    git      = "https://git.bioconductor.org/packages/AIMS.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/AIMS', commit='86b866c20e191047492c51b43e3f73082c3f8357')
+    version('1.8.0', commit='86b866c20e191047492c51b43e3f73082c3f8357')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-e1071', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aldex2/package.py b/var/spack/repos/builtin/packages/r-aldex2/package.py
index ab046f82ec..1a1912a32e 100644
--- a/var/spack/repos/builtin/packages/r-aldex2/package.py
+++ b/var/spack/repos/builtin/packages/r-aldex2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,9 +20,9 @@ class RAldex2(RPackage):
     and fdr values calculated by the Benjamini Hochberg correction."""
 
     homepage = "http://bioconductor.org/packages/ALDEx2/"
-    url      = "https://git.bioconductor.org/packages/ALDEx2"
+    git      = "https://git.bioconductor.org/packages/ALDEx2.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/ALDEx2', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
+    version('1.8.0', commit='24104824ca2402ad4f54fbf1ed9cee7fac2aaaf1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
index f7e95e519c..6e5b2a4088 100644
--- a/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
+++ b/var/spack/repos/builtin/packages/r-allelicimbalance/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAllelicimbalance(RPackage):
     investigation using RNA-seq data."""
 
     homepage = "http://bioconductor.org/packages/AllelicImbalance/"
-    url      = "https://git.bioconductor.org/packages/AllelicImbalance"
+    git      = "https://git.bioconductor.org/packages/AllelicImbalance.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/AllelicImbalance', commit='35958534945819baafde0e13d1eb4d05a514142c')
+    version('1.14.0', commit='35958534945819baafde0e13d1eb4d05a514142c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.14.0')
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-alpine/package.py b/var/spack/repos/builtin/packages/r-alpine/package.py
index 9d28ec66e7..2d3666642e 100644
--- a/var/spack/repos/builtin/packages/r-alpine/package.py
+++ b/var/spack/repos/builtin/packages/r-alpine/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAlpine(RPackage):
     transcript abundance estimation."""
 
     homepage = "http://bioconductor.org/packages/alpine/"
-    url      = "https://git.bioconductor.org/packages/alpine"
+    git      = "https://git.bioconductor.org/packages/alpine.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/alpine', commit='896872e6071769e1ac2cf786974edb8b875c45eb')
+    version('1.2.0', commit='896872e6071769e1ac2cf786974edb8b875c45eb')
 
     depends_on('r@3.4.0:3.4.9', when='@1.2.0')
     depends_on('r-biostrings', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-als/package.py b/var/spack/repos/builtin/packages/r-als/package.py
index 12f1905614..9102e21b32 100644
--- a/var/spack/repos/builtin/packages/r-als/package.py
+++ b/var/spack/repos/builtin/packages/r-als/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-alsace/package.py b/var/spack/repos/builtin/packages/r-alsace/package.py
index 0573dde123..cc6eb65902 100644
--- a/var/spack/repos/builtin/packages/r-alsace/package.py
+++ b/var/spack/repos/builtin/packages/r-alsace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,9 +16,9 @@ class RAlsace(RPackage):
     retention time correction, etcetera."""
 
     homepage = "https://www.bioconductor.org/packages/alsace/"
-    url      = "https://git.bioconductor.org/packages/alsace"
+    git      = "https://git.bioconductor.org/packages/alsace.git"
 
-    version('1.12.0', git='https://git.bioconductor.org/packages/alsace', commit='1364c65bbff05786d05c02799fd44fd57748fae3')
+    version('1.12.0', commit='1364c65bbff05786d05c02799fd44fd57748fae3')
 
     depends_on('r-als', type=('build', 'run'))
     depends_on('r-ptw', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
index 8f9770d68a..9853b0cda8 100644
--- a/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
+++ b/var/spack/repos/builtin/packages/r-altcdfenvs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RAltcdfenvs(RPackage):
     """Convenience data structures and functions to handle cdfenvs."""
 
     homepage = "https://www.bioconductor.org/packages/altcdfenvs/"
-    url      = "https://git.bioconductor.org/packages/altcdfenvs"
+    git      = "https://git.bioconductor.org/packages/altcdfenvs.git"
 
-    version('2.38.0', git='https://git.bioconductor.org/packages/altcdfenvs', commit='2e92b9da76dbe50af4bf33c525134e29e9809291')
+    version('2.38.0', commit='2e92b9da76dbe50af4bf33c525134e29e9809291')
 
     depends_on('r@3.4.0:3.4.9', when='@2.38.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-amap/package.py b/var/spack/repos/builtin/packages/r-amap/package.py
new file mode 100644
index 0000000000..d783a8220a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-amap/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAmap(RPackage):
+    """Tools for Clustering and Principal Component Analysis
+       (With robust methods, and parallelized functions)."""
+
+    homepage = "http://mulcyber.toulouse.inra.fr/projects/amap/"
+    url      = "https://cran.rstudio.com/src/contrib/amap_0.8-16.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/amap/"
+
+    version('0.8-16', sha256='d3775ad7f660581f7d2f070e426be95ae0d6743622943e6f5491988e5217d4e2')
+
+    depends_on('r@2.10.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ampliqueso/package.py b/var/spack/repos/builtin/packages/r-ampliqueso/package.py
index a703caf19e..ec0ec337e1 100644
--- a/var/spack/repos/builtin/packages/r-ampliqueso/package.py
+++ b/var/spack/repos/builtin/packages/r-ampliqueso/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAmpliqueso(RPackage):
     amplicon sequencing panels, such as AmpliSeq."""
 
     homepage = "https://www.bioconductor.org/packages/ampliQueso/"
-    url      = "https://git.bioconductor.org/packages/ampliQueso"
+    git      = "https://git.bioconductor.org/packages/ampliQueso.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/ampliQueso', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b')
+    version('1.14.0', commit='9a4c26ec594171279aba8ab7fe59c4a2ea09b06b')
 
     depends_on('r@3.4.0:3.4.9', when='@1.14.0')
     depends_on('r-samr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-analysispageserver/package.py b/var/spack/repos/builtin/packages/r-analysispageserver/package.py
index 4245dbed56..f37f3b0daa 100644
--- a/var/spack/repos/builtin/packages/r-analysispageserver/package.py
+++ b/var/spack/repos/builtin/packages/r-analysispageserver/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAnalysispageserver(RPackage):
     of customizable R analyses via the web."""
 
     homepage = "https://www.bioconductor.org/packages/AnalysisPageServer/"
-    url      = "https://git.bioconductor.org/packages/AnalysisPageServer"
+    git      = "https://git.bioconductor.org/packages/AnalysisPageServer.git"
 
-    version('1.10.0', git='https://git.bioconductor.org/packages/AnalysisPageServer', commit='876c87073be116fa15a1afdd407e21152eb80d50')
+    version('1.10.0', commit='876c87073be116fa15a1afdd407e21152eb80d50')
 
     depends_on('r@3.4.0:3.4.9', when='@1.10.0')
     depends_on('r-log4r', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-anaquin/package.py b/var/spack/repos/builtin/packages/r-anaquin/package.py
index 678084df09..2cf761c2b0 100644
--- a/var/spack/repos/builtin/packages/r-anaquin/package.py
+++ b/var/spack/repos/builtin/packages/r-anaquin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RAnaquin(RPackage):
     modelling and visualization of spike-in controls."""
 
     homepage = "https://www.bioconductor.org/packages/Anaquin/"
-    url      = "https://git.bioconductor.org/packages/Anaquin"
+    git      = "https://git.bioconductor.org/packages/Anaquin.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/Anaquin', commit='584d1970cc9dc1d354f9a6d7c1306bd7e8567119')
+    version('1.2.0', commit='584d1970cc9dc1d354f9a6d7c1306bd7e8567119')
 
     depends_on('r@3.4.0:3.4.9', when='@1.2.0')
     depends_on('r-deseq2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aneufinder/package.py b/var/spack/repos/builtin/packages/r-aneufinder/package.py
index 6be07235a1..4123db13c5 100644
--- a/var/spack/repos/builtin/packages/r-aneufinder/package.py
+++ b/var/spack/repos/builtin/packages/r-aneufinder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RAneufinder(RPackage):
     export and analysis from whole-genome single cell sequencing data."""
 
     homepage = "https://www.bioconductor.org/packages/AneuFinder/"
-    url      = "https://git.bioconductor.org/packages/AneuFinder"
+    git      = "https://git.bioconductor.org/packages/AneuFinder.git"
 
-    version('1.4.0', git='https://git.bioconductor.org/packages/AneuFinder', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e')
+    version('1.4.0', commit='e5bdf4d5e4f84ee5680986826ffed636ed853b8e')
 
     depends_on('r@3.4.0:3.4.9', when='@1.4.0')
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
index a61e7cd4cd..dde20609af 100644
--- a/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
+++ b/var/spack/repos/builtin/packages/r-aneufinderdata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,8 @@ class RAneufinderdata(RPackage):
     purposes in the AneuFinder package."""
 
     homepage = "https://www.bioconductor.org/packages/AneuFinderData/"
-    url      = "https://git.bioconductor.org/packages/AneuFinderData"
+    git      = "https://git.bioconductor.org/packages/AneuFinderData.git"
 
-    version('1.4.0', git='https://git.bioconductor.org/packages/AneuFinderData', commit='55c8807ee4a37a2eb6d0defafaf843f980b22c40')
+    version('1.4.0', commit='55c8807ee4a37a2eb6d0defafaf843f980b22c40')
 
     depends_on('r@3.4.0:3.4.9', when='@1.4.0')
diff --git a/var/spack/repos/builtin/packages/r-animation/package.py b/var/spack/repos/builtin/packages/r-animation/package.py
new file mode 100644
index 0000000000..c0d592c518
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-animation/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RAnimation(RPackage):
+    """Provides functions for animations in statistics, covering topics
+    in probability theory, mathematical statistics, multivariate statistics,
+    non-parametric statistics, sampling survey, linear models, time series,
+    computational statistics, data mining and machine learning.
+    These functions maybe helpful in teaching statistics and data analysis."""
+
+    homepage = "https://cran.r-project.org/package=animation"
+    url = "https://cran.r-project.org/src/contrib/animation_2.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/animation"
+
+    version('2.5', sha256='b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f')
+
+    extends('r')
+    depends_on('r', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annaffy/package.py b/var/spack/repos/builtin/packages/r-annaffy/package.py
index f4bfd87d3e..af47b5f193 100644
--- a/var/spack/repos/builtin/packages/r-annaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-annaffy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 #
 from spack import *
@@ -35,9 +16,9 @@ class RAnnaffy(RPackage):
     using various criteria."""
 
     homepage = "https://www.bioconductor.org/packages/annaffy/"
-    url      = "https://git.bioconductor.org/packages/annaffy"
+    git      = "https://git.bioconductor.org/packages/annaffy.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/annaffy', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0')
+    version('1.48.0', commit='89a03c64ac9df5d963ed60b87893a3fffa6798a0')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotate/package.py b/var/spack/repos/builtin/packages/r-annotate/package.py
index 7c49849f01..09e367cb35 100644
--- a/var/spack/repos/builtin/packages/r-annotate/package.py
+++ b/var/spack/repos/builtin/packages/r-annotate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,14 @@ class RAnnotate(RPackage):
     """Using R enviroments for annotation."""
 
     homepage = "https://www.bioconductor.org/packages/annotate/"
-    url      = "https://git.bioconductor.org/packages/annotate"
-    list_url = homepage
-    version('1.54.0', git='https://git.bioconductor.org/packages/annotate', commit='860cc5b696795a31b18beaf4869f9c418d74549e')
+    git      = "https://git.bioconductor.org/packages/annotate.git"
+
+    version('1.58.0', commit='d1b5dd5feb8793f4f816d9a4aecbebb5ec7df7bc')
+    version('1.54.0', commit='860cc5b696795a31b18beaf4869f9c418d74549e')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-xtable', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotationdbi/package.py b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
index 2b55b95a63..d6a66236ce 100644
--- a/var/spack/repos/builtin/packages/r-annotationdbi/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationdbi/package.py
@@ -1,29 +1,8 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-#
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,11 +11,13 @@ class RAnnotationdbi(RPackage):
     annotation data packages using SQLite data storage."""
 
     homepage = "https://www.bioconductor.org/packages/AnnotationDbi/"
-    url      = "https://git.bioconductor.org/packages/AnnotationDbi"
-    list_url = homepage
-    version('1.38.2', git='https://git.bioconductor.org/packages/AnnotationDbi', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36')
+    git      = "https://git.bioconductor.org/packages/AnnotationDbi.git"
+
+    version('1.42.1', commit='71085b47ea2e1ef929bebe8b17eb8e8a573f98e3')
+    version('1.38.2', commit='67d46facba8c15fa5f0eb47c4e39b53dbdc67c36')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.38.2')
+    depends_on('r@3.4.0:3.4.9', when='@1.38.2', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.42.1', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotationfilter/package.py b/var/spack/repos/builtin/packages/r-annotationfilter/package.py
index ff82f8a3c0..b6c39cac1e 100644
--- a/var/spack/repos/builtin/packages/r-annotationfilter/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationfilter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RAnnotationfilter(RPackage):
        packages."""
 
     homepage = "https://bioconductor.org/packages/AnnotationFilter/"
-    url      = "https://git.bioconductor.org/packages/AnnotationFilter"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/AnnotationFilter.git"
 
-    version('1.0.0', git='https://git.bioconductor.org/packages/AnnotationFilter', commit='a9f79b26defe3021eea60abe16ce1fa379813ec9')
+    version('1.0.0', commit='a9f79b26defe3021eea60abe16ce1fa379813ec9')
 
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-lazyeval', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotationforge/package.py b/var/spack/repos/builtin/packages/r-annotationforge/package.py
index 57a69306c3..41dfa85c25 100644
--- a/var/spack/repos/builtin/packages/r-annotationforge/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationforge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RAnnotationforge(RPackage):
     with AnnotationDbi."""
 
     homepage = "https://www.bioconductor.org/packages/AnnotationForge/"
-    url      = "https://git.bioconductor.org/packages/AnnotationForge"
+    git      = "https://git.bioconductor.org/packages/AnnotationForge.git"
 
-    version('1.18.2', git='https://git.bioconductor.org/packages/AnnotationForge', commit='44ca3d4ef9e9825c14725ffdbbaa57ea059532e1')
+    version('1.18.2', commit='44ca3d4ef9e9825c14725ffdbbaa57ea059532e1')
 
     depends_on('r@3.4.0:3.4.9', when='@1.18.2')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-annotationhub/package.py b/var/spack/repos/builtin/packages/r-annotationhub/package.py
index ccda18a203..92fe597a94 100644
--- a/var/spack/repos/builtin/packages/r-annotationhub/package.py
+++ b/var/spack/repos/builtin/packages/r-annotationhub/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,10 +17,9 @@ class RAnnotationhub(RPackage):
        quick and reproducible access."""
 
     homepage = "https://bioconductor.org/packages/AnnotationHub/"
-    url      = "https://git.bioconductor.org/packages/AnnotationHub"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/AnnotationHub.git"
 
-    version('2.8.3', git='https://git.bioconductor.org/packages/AnnotationHub', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
+    version('2.8.3', commit='8aa9c64262a8d708d2bf1c82f82dfc3d7d4ccc0c')
 
     depends_on('r-rsqlite', type=('build', 'run'))
     depends_on('r-biocinstaller', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ape/package.py b/var/spack/repos/builtin/packages/r-ape/package.py
index 17a0f0ff23..63f1dfed6b 100644
--- a/var/spack/repos/builtin/packages/r-ape/package.py
+++ b/var/spack/repos/builtin/packages/r-ape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -46,6 +27,10 @@ class RApe(RPackage):
     url      = "https://cran.r-project.org/src/contrib/ape_4.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/ape"
 
+    version('5.0', '82fd2786a502f070ca020797f7b19fa4')
     version('4.1', 'a9ed416d6d172d4b9682556cf692d7c2')
 
     depends_on('r@3.2:')
+    depends_on('r-nlme', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-argparse/package.py b/var/spack/repos/builtin/packages/r-argparse/package.py
new file mode 100644
index 0000000000..c722eae792
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-argparse/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RArgparse(RPackage):
+    """A command line parser to be used with Rscript to write "#!"
+       shebang scripts that gracefully accept positional and optional
+       arguments and automatically generate usage."""
+
+    homepage = "https://github.com/trevorld/argparse"
+    url      = "https://cran.r-project.org/src/contrib/argparse_1.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/argparse"
+
+    version('1.1.1', sha256='441449f0816411a868fd1b15cf4b2bc45931bbd4b67d6592dbe48875905cf93b')
+
+    depends_on('r-proto@1:', type=('build', 'run'))
+    depends_on('r-findpython', type=('build', 'run'))
+    depends_on('r-getopt', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-assertthat/package.py b/var/spack/repos/builtin/packages/r-assertthat/package.py
index 37e0424d1a..331e13d887 100644
--- a/var/spack/repos/builtin/packages/r-assertthat/package.py
+++ b/var/spack/repos/builtin/packages/r-assertthat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-backports/package.py b/var/spack/repos/builtin/packages/r-backports/package.py
index 02c0c6fc1b..97303b92da 100644
--- a/var/spack/repos/builtin/packages/r-backports/package.py
+++ b/var/spack/repos/builtin/packages/r-backports/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bamsignals/package.py b/var/spack/repos/builtin/packages/r-bamsignals/package.py
index 29a7fda80d..78310f5f4c 100644
--- a/var/spack/repos/builtin/packages/r-bamsignals/package.py
+++ b/var/spack/repos/builtin/packages/r-bamsignals/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RBamsignals(RPackage):
     profiles. It also handles paired-end data."""
 
     homepage = "https://www.bioconductor.org/packages/bamsignals/"
-    url      = "https://git.bioconductor.org/packages/bamsignals"
+    git      = "https://git.bioconductor.org/packages/bamsignals.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/bamsignals', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23')
+    version('1.8.0', commit='b123b83e8e026c9ec91209d4498aff3e95a5de23')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-base64/package.py b/var/spack/repos/builtin/packages/r-base64/package.py
index 6a693e12a7..6a599a62f0 100644
--- a/var/spack/repos/builtin/packages/r-base64/package.py
+++ b/var/spack/repos/builtin/packages/r-base64/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-base64enc/package.py b/var/spack/repos/builtin/packages/r-base64enc/package.py
index 3566baab7a..7424fefe8f 100644
--- a/var/spack/repos/builtin/packages/r-base64enc/package.py
+++ b/var/spack/repos/builtin/packages/r-base64enc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bbmisc/package.py b/var/spack/repos/builtin/packages/r-bbmisc/package.py
new file mode 100644
index 0000000000..f8cee5cec6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bbmisc/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBbmisc(RPackage):
+    """Miscellaneous helper functions for and from B. Bischl and some other
+       guys, mainly for package development."""
+
+    homepage = "https://github.com/berndbischl/BBmisc"
+    url      = "https://cran.r-project.org/src/contrib/BBmisc_1.11.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/BBmisc"
+
+    version('1.11', '681642628037406beb6088d5f773473d')
+
+    depends_on('r-checkmate@1.8.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-beanplot/package.py b/var/spack/repos/builtin/packages/r-beanplot/package.py
index 3ddb95f59e..34760038fb 100644
--- a/var/spack/repos/builtin/packages/r-beanplot/package.py
+++ b/var/spack/repos/builtin/packages/r-beanplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bh/package.py b/var/spack/repos/builtin/packages/r-bh/package.py
index bcf4f600a6..54ed774931 100644
--- a/var/spack/repos/builtin/packages/r-bh/package.py
+++ b/var/spack/repos/builtin/packages/r-bh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-biasedurn/package.py b/var/spack/repos/builtin/packages/r-biasedurn/package.py
new file mode 100644
index 0000000000..258788ebdd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biasedurn/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBiasedurn(RPackage):
+    """Statistical models of biased sampling in the form of univariate and
+       multivariate noncentral hypergeometric distributions, including
+       Wallenius' noncentral hypergeometric distribution and Fisher's
+       noncentral hypergeometric distribution (also called extended
+       hypergeometric distribution). See vignette("UrnTheory") for
+       explanation of these distributions."""
+
+    homepage = "http://www.agner.org/random/"
+    url      = "https://cran.rstudio.com/src/contrib/BiasedUrn_1.07.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/BiasedUrn/"
+
+    version('1.07', sha256='2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e')
diff --git a/var/spack/repos/builtin/packages/r-bindr/package.py b/var/spack/repos/builtin/packages/r-bindr/package.py
new file mode 100644
index 0000000000..e874ac264f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bindr/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBindr(RPackage):
+    """Provides a simple interface for creating active bindings where the
+       bound function accepts additional arguments."""
+
+    homepage = "https://github.com/krlmlr/bindr"
+    url      = "https://cran.r-project.org/src/contrib/bindr_0.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/bindr"
+
+    version('0.1', 'f3897a70cbad2d2981272772fa30bb59')
diff --git a/var/spack/repos/builtin/packages/r-bindrcpp/package.py b/var/spack/repos/builtin/packages/r-bindrcpp/package.py
new file mode 100644
index 0000000000..78d50af84e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bindrcpp/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBindrcpp(RPackage):
+    """Provides an easy way to fill an environment with active bindings that
+       call a C++ function."""
+
+    homepage = "https://github.com/krlmlr/bindrcpp"
+    url      = "https://cran.r-project.org/src/contrib/bindrcpp_0.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/bindrcpp"
+
+    version('0.2.2', '48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467')
+    version('0.2', '2ed7f19fd9a12587f882d90060e7a343')
+
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-bindr', type=('build', 'run'))
+    depends_on('r-plogr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biobase/package.py b/var/spack/repos/builtin/packages/r-biobase/package.py
index 035d0ddcad..015522735c 100644
--- a/var/spack/repos/builtin/packages/r-biobase/package.py
+++ b/var/spack/repos/builtin/packages/r-biobase/package.py
@@ -1,40 +1,23 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
 
 class RBiobase(RPackage):
     """Functions that are needed by many other packages
- or which replace R functions."""
+    or which replace R functions."""
 
     homepage = "https://www.bioconductor.org/packages/Biobase/"
-    url      = "https://git.bioconductor.org/packages/Biobase"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/Biobase.git"
 
-    version('2.36.2', git='https://git.bioconductor.org/packages/Biobase', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075')
+    version('2.40.0', commit='6555edbbcb8a04185ef402bfdea7ed8ac72513a5')
+    version('2.38.0', commit='83f89829e0278ac014b0bc6664e621ac147ba424')
+    version('2.36.2', commit='15f50912f3fa08ccb15c33b7baebe6b8a59ce075')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@2.36.2')
+    depends_on('r-biocgenerics@0.16.1:', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.36.2', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.40.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocgenerics/package.py b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
index 2d101b09e1..b6758db358 100644
--- a/var/spack/repos/builtin/packages/r-biocgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-biocgenerics/package.py
@@ -1,37 +1,20 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class RBiocgenerics(RPackage):
     """S4 generic functions needed by many Bioconductor packages."""
+
     homepage = "https://www.bioconductor.org/packages/BiocGenerics/"
-    url      = "https://git.bioconductor.org/packages/BiocGenerics"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BiocGenerics.git"
 
-    version('0.22.1', git='https://git.bioconductor.org/packages/BiocGenerics', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
+    version('0.26.0', commit='5b2a6df639e48c3cd53789e0b174aec9dda6b67d')
+    version('0.24.0', commit='3db111e8c1f876267da89f4f0c5406a9d5c31cd1')
+    version('0.22.1', commit='9c90bb8926885289d596a81ff318ee3745cbb6ad')
 
-    depends_on('r@3.4.0:3.4.9', when='@0.22.1')
+    depends_on('r@3.4.0:3.4.9', when='@0.22.1', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@0.26.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocinstaller/package.py b/var/spack/repos/builtin/packages/r-biocinstaller/package.py
index b2248f87ac..a3cc8e471e 100644
--- a/var/spack/repos/builtin/packages/r-biocinstaller/package.py
+++ b/var/spack/repos/builtin/packages/r-biocinstaller/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,8 @@ class RBiocinstaller(RPackage):
     and (some) github packages."""
 
     homepage = "https://bioconductor.org/packages/BiocInstaller/"
-    url      = "https://git.bioconductor.org/packages/BiocInstaller"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BiocInstaller.git"
 
-    version('1.26.1', git='https://git.bioconductor.org/packages/BiocInstaller', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
+    version('1.26.1', commit='9049b82a77aefa98e3f8e4dd7068317505d70e98')
 
     depends_on('r@3.4.0:3.4.9', when='@1.26.1')
diff --git a/var/spack/repos/builtin/packages/r-biocparallel/package.py b/var/spack/repos/builtin/packages/r-biocparallel/package.py
index 769c8b9b16..37d0b93375 100644
--- a/var/spack/repos/builtin/packages/r-biocparallel/package.py
+++ b/var/spack/repos/builtin/packages/r-biocparallel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,13 @@ class RBiocparallel(RPackage):
        objects."""
 
     homepage = "https://bioconductor.org/packages/BiocParallel/"
-    url      = "https://git.bioconductor.org/packages/BiocParallel"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BiocParallel.git"
 
-    version('1.10.1', git='https://git.bioconductor.org/packages/BiocParallel', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
+    version('1.14.2', commit='1d5a44960b19e9dbbca04c7290c8c58b0a7fc299')
+    version('1.10.1', commit='a76c58cf99fd585ba5ea33065649e68f1afe0a7d')
 
     depends_on('r-futile-logger', type=('build', 'run'))
     depends_on('r-snow', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.10.1')
+    depends_on('r-bh', type=('build', 'link', 'run'), when='@1.14.2:')
+    depends_on('r@3.4.0:3.4.9', when='@1.10.1', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.14.2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biocstyle/package.py b/var/spack/repos/builtin/packages/r-biocstyle/package.py
new file mode 100644
index 0000000000..411b2549fa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biocstyle/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBiocstyle(RPackage):
+    """Provides standard formatting styles for Bioconductor PDF and HTML
+    documents. Package vignettes illustrate use and functionality."""
+
+    homepage = "https://www.bioconductor.org/packages/BiocStyle/"
+    git      = "https://git.bioconductor.org/packages/BiocStyle.git"
+
+    version('2.4.1', commit='ef10764b68ac23a3a7a8ec3b6a6436187309c138')
+
+    depends_on('r-bookdown', type=('build', 'run'))
+    depends_on('r-knitr@1.12:', type=('build', 'run'))
+    depends_on('r-rmarkdown@1.2:', type=('build', 'run'))
+    depends_on('r-yaml', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.4.1')
diff --git a/var/spack/repos/builtin/packages/r-biom-utils/package.py b/var/spack/repos/builtin/packages/r-biom-utils/package.py
new file mode 100644
index 0000000000..7bd3d2471d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biom-utils/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBiomUtils(RPackage):
+    """Provides utilities to facilitate import, export and computation with
+    the BIOM (Biological Observation Matrix) format (http://biom-format.org).
+    """
+
+    homepage = "https://github.com/braithwaite/BIOM.utils/"
+    url      = "https://cran.r-project.org/src/contrib/BIOM.utils_0.9.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/biom/"
+
+    version('0.9', sha256='e7024469fb38e275aa78fbfcce15b9a7661317f632a7e9b8124695e076839375')
+
+    depends_on('r@3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biomart/package.py b/var/spack/repos/builtin/packages/r-biomart/package.py
index d9c15151bd..b74a6794ba 100644
--- a/var/spack/repos/builtin/packages/r-biomart/package.py
+++ b/var/spack/repos/builtin/packages/r-biomart/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,11 +21,17 @@ class RBiomart(RPackage):
        online queries from gene annotation to database mining."""
 
     homepage = "https://bioconductor.org/packages/biomaRt/"
-    url      = "https://git.bioconductor.org/packages/biomaRt"
+    git      = "https://git.bioconductor.org/packages/biomaRt.git"
 
-    version('2.32.1', git='https://git.bioconductor.org/packages/biomaRt', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
+    version('2.36.1', commit='5634e57e20199f9dc1f8b927eb3893143fc02f4f')
+    version('2.34.2', commit='a7030915fbc6120cc6812aefdedba423a207459b')
+    version('2.32.1', commit='f84d74424fa599f6d08f8db4612ca09914a9087f')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@2.32.1')
+    depends_on('r-progress', type=('build', 'run'), when='@2.34.2:')
+    depends_on('r-stringr', type=('build', 'run'), when='@2.34.2:')
+    depends_on('r-httr', type=('build', 'run'), when='@2.34.2:')
+    depends_on('r@3.4.0:3.4.9', when='@2.32.1:2.35.9', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.36.1', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biomformat/package.py b/var/spack/repos/builtin/packages/r-biomformat/package.py
new file mode 100644
index 0000000000..29c1d4e75c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-biomformat/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBiomformat(RPackage):
+    """This is an R package for interfacing with the BIOM format. This
+    package includes basic tools for reading biom-format files, accessing
+    and subsetting data tables from a biom object (which is more complex
+    than a single table), as well as limited support for writing a
+    biom-object back to a biom-format file. The design of this API is
+    intended to match the python API and other tools included with the
+    biom-format project, but with a decidedly "R flavor" that should be
+    familiar to R users. This includes S4 classes and methods, as well
+    as extensions of common core functions/methods."""
+
+    homepage = "https://www.bioconductor.org/packages/biomformat/"
+    git      = "https://git.bioconductor.org/packages/biomformat.git"
+
+    version('1.4.0', commit='83b4b1883bc56ea93a0a6ca90fc1b18712ef0f1a')
+
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-rhdf5', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.4.0')
diff --git a/var/spack/repos/builtin/packages/r-biostrings/package.py b/var/spack/repos/builtin/packages/r-biostrings/package.py
index fee137c11b..b6337f29b8 100644
--- a/var/spack/repos/builtin/packages/r-biostrings/package.py
+++ b/var/spack/repos/builtin/packages/r-biostrings/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,13 +12,18 @@ class RBiostrings(RPackage):
        or sets of sequences."""
 
     homepage = "https://bioconductor.org/packages/Biostrings/"
-    url      = "https://git.bioconductor.org/packages/Biostrings"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/Biostrings.git"
 
-    version('2.44.2', git='https://git.bioconductor.org/packages/Biostrings', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
+    version('2.48.0', commit='aa3599a7d259d658014d087b86d71ab1deb5f12b')
+    version('2.44.2', commit='e4a2b320fb21c5cab3ece7b3c6fecaedfb1e5200')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.15.6:', when='@2.48.0', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@2.48.0', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.24:', when='@2.48.0', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@2.44.2')
+    depends_on('r-xvector@0.19.8:', when='@2.48.0', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.44.2', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.48.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-biovizbase/package.py b/var/spack/repos/builtin/packages/r-biovizbase/package.py
index ee87f87625..0535c052d9 100644
--- a/var/spack/repos/builtin/packages/r-biovizbase/package.py
+++ b/var/spack/repos/builtin/packages/r-biovizbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RBiovizbase(RPackage):
     and encourages consistency."""
 
     homepage = "http://bioconductor.org/packages/biovizBase/"
-    url      = "https://git.bioconductor.org/packages/biovizBase"
+    git      = "https://git.bioconductor.org/packages/biovizBase.git"
 
-    version('1.24.0', git='https://git.bioconductor.org/packages/biovizBase', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
+    version('1.24.0', commit='ae9cd2ff665b74a8f45ed9c1d17fc0a778b4af6c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.24.0')
     depends_on('r-scales', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-bit/package.py b/var/spack/repos/builtin/packages/r-bit/package.py
index aed6d724a6..0d178c10f8 100644
--- a/var/spack/repos/builtin/packages/r-bit/package.py
+++ b/var/spack/repos/builtin/packages/r-bit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bit64/package.py b/var/spack/repos/builtin/packages/r-bit64/package.py
index 85c631e1ba..a8e8501f2f 100644
--- a/var/spack/repos/builtin/packages/r-bit64/package.py
+++ b/var/spack/repos/builtin/packages/r-bit64/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bitops/package.py b/var/spack/repos/builtin/packages/r-bitops/package.py
index ec0b45f454..2d61f87d17 100644
--- a/var/spack/repos/builtin/packages/r-bitops/package.py
+++ b/var/spack/repos/builtin/packages/r-bitops/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-blob/package.py b/var/spack/repos/builtin/packages/r-blob/package.py
index b77399f775..85e33a1ac4 100644
--- a/var/spack/repos/builtin/packages/r-blob/package.py
+++ b/var/spack/repos/builtin/packages/r-blob/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-bookdown/package.py b/var/spack/repos/builtin/packages/r-bookdown/package.py
new file mode 100644
index 0000000000..94d2ed08fa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-bookdown/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBookdown(RPackage):
+    """Output formats and utilities for authoring books and technical
+    documents with R Markdown."""
+
+    homepage = "https://cran.r-project.org/package=bookdown"
+    url      = "https://cran.rstudio.com/src/contrib/bookdown_0.5.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/bookdown"
+
+    version('0.5', '7bad360948e2b22d28397870b9319f17')
+
+    depends_on('r-yaml@2.1.14:', type=('build', 'run'))
+    depends_on('r-rmarkdown@1.5:', type=('build', 'run'))
+    depends_on('r-knitr@1.16:', type=('build', 'run'))
+    depends_on('r-htmltools@0.3.6:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-boot/package.py b/var/spack/repos/builtin/packages/r-boot/package.py
index 2e2802893d..52df4caee5 100644
--- a/var/spack/repos/builtin/packages/r-boot/package.py
+++ b/var/spack/repos/builtin/packages/r-boot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-brew/package.py b/var/spack/repos/builtin/packages/r-brew/package.py
index e3cf99a095..bf765a6627 100644
--- a/var/spack/repos/builtin/packages/r-brew/package.py
+++ b/var/spack/repos/builtin/packages/r-brew/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-broom/package.py b/var/spack/repos/builtin/packages/r-broom/package.py
new file mode 100644
index 0000000000..2daad5e49e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-broom/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RBroom(RPackage):
+    """Convert statistical analysis objects from R into tidy data frames, so
+       that they can more easily be combined, reshaped and otherwise processed
+       with tools like 'dplyr', 'tidyr' and 'ggplot2'. The package provides
+       three S3 generics: tidy, which summarizes a model's statistical
+       findings such as coefficients of a regression; augment, which adds
+       columns to the original data such as predictions, residuals and cluster
+       assignments; and glance, which provides a one-row summary of
+       model-level statistics."""
+
+    homepage = "http://github.com/tidyverse/broom"
+    url      = "https://cran.r-project.org/src/contrib/broom_0.4.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/broom"
+    version('0.4.2', '6eabab1f2eaec10f93cf9aa56d6a61de')
+
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-psych', type=('build', 'run'))
+    depends_on('r-stringr', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-bsgenome/package.py b/var/spack/repos/builtin/packages/r-bsgenome/package.py
index 3758992266..3b2de6aeb7 100644
--- a/var/spack/repos/builtin/packages/r-bsgenome/package.py
+++ b/var/spack/repos/builtin/packages/r-bsgenome/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,18 +11,21 @@ class RBsgenome(RPackage):
        packages."""
 
     homepage = "https://www.bioconductor.org/packages/BSgenome/"
-    url      = "https://git.bioconductor.org/packages/BSgenome"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/BSgenome.git"
 
-    version('1.44.2', git='https://git.bioconductor.org/packages/BSgenome', commit='105b00588a758d5ec7c347a7dff2756aea4516a0')
+    version('1.46.0', commit='bdfbd6d09820993585b8231ddea5e11c99008dc5')
+    version('1.44.2', commit='105b00588a758d5ec7c347a7dff2756aea4516a0')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-genomeinfodb', type=('build', 'run'))
-    depends_on('r-genomicranges', type=('build', 'run'))
-    depends_on('r-biostrings', type=('build', 'run'))
-    depends_on('r-rtracklayer', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.13.8:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.9.36:', type=('build', 'run'))
+    depends_on('r-iranges@2.1.33:', type=('build', 'run'), when='@1.44.2')
+    depends_on('r-iranges@2.11.16:', type=('build', 'run'), when='@1.46.0')
+    depends_on('r-genomeinfodb@1.11.4:', type=('build', 'run'), when='@1.44.2')
+    depends_on('r-genomeinfodb@1.13.1:', type=('build', 'run'), when='@1.46.0')
+    depends_on('r-genomicranges@1.27.6:', type=('build', 'run'), when='@1.44.2')
+    depends_on('r-genomicranges@1.29.14:', type=('build', 'run'), when='@1.46.0')
+    depends_on('r-biostrings@2.35.3:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.25.8:', type=('build', 'run'))
     depends_on('r-rsamtools', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.44.2')
+    depends_on('r@3.4.0:3.4.9', when='@1.44.2:')
diff --git a/var/spack/repos/builtin/packages/r-bumphunter/package.py b/var/spack/repos/builtin/packages/r-bumphunter/package.py
index bc36a53485..8b952a7d97 100644
--- a/var/spack/repos/builtin/packages/r-bumphunter/package.py
+++ b/var/spack/repos/builtin/packages/r-bumphunter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class RBumphunter(RPackage):
     """Tools for finding bumps in genomic data"""
 
     homepage = "http://bioconductor.org/packages/bumphunter/"
-    url      = "https://git.bioconductor.org/packages/bumphunter"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/bumphunter.git"
 
-    version('1.16.0', git='https://git.bioconductor.org/packages/bumphunter', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a')
+    version('1.16.0', commit='1c3ab4d1fd2d75b1586ccef12665960b3602080a')
 
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-c50/package.py b/var/spack/repos/builtin/packages/r-c50/package.py
index e5ee2d285a..6e4a6f6b77 100644
--- a/var/spack/repos/builtin/packages/r-c50/package.py
+++ b/var/spack/repos/builtin/packages/r-c50/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-callr/package.py b/var/spack/repos/builtin/packages/r-callr/package.py
index f69ed861ce..2cee5cd308 100644
--- a/var/spack/repos/builtin/packages/r-callr/package.py
+++ b/var/spack/repos/builtin/packages/r-callr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,5 +13,7 @@ class RCallr(RPackage):
 
     homepage = "https://github.com/MangoTheCat/callr"
     url      = "https://cran.r-project.org/src/contrib/callr_1.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/callr/"
 
+    version('3.0.0', sha256='e36361086c65660a6ecbbc09b5ecfcddee6b59caf75e983e48b21d3b8defabe7')
     version('1.0.0', 'd9af99bb95696310fa1e5d1cb7166c91')
diff --git a/var/spack/repos/builtin/packages/r-car/package.py b/var/spack/repos/builtin/packages/r-car/package.py
index aa5a776e37..e02a46e45e 100644
--- a/var/spack/repos/builtin/packages/r-car/package.py
+++ b/var/spack/repos/builtin/packages/r-car/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-caret/package.py b/var/spack/repos/builtin/packages/r-caret/package.py
index 89dcc691ea..95bcf03130 100644
--- a/var/spack/repos/builtin/packages/r-caret/package.py
+++ b/var/spack/repos/builtin/packages/r-caret/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-category/package.py b/var/spack/repos/builtin/packages/r-category/package.py
index 026f0c5987..0b2949ef25 100644
--- a/var/spack/repos/builtin/packages/r-category/package.py
+++ b/var/spack/repos/builtin/packages/r-category/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RCategory(RPackage):
     """A collection of tools for performing category analysis."""
 
     homepage = "https://www.bioconductor.org/packages/Category/"
-    url      = "https://git.bioconductor.org/packages/Category"
+    git      = "https://git.bioconductor.org/packages/Category.git"
 
-    version('2.42.1', git='https://git.bioconductor.org/packages/Category', commit='382c817a2371671a72f8f949dfb4050361ebabcd')
+    version('2.42.1', commit='382c817a2371671a72f8f949dfb4050361ebabcd')
 
     depends_on('r@3.4.0:3.4.9', when='@2.42.1')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-catools/package.py b/var/spack/repos/builtin/packages/r-catools/package.py
index 2253b1e0ec..2c19850222 100644
--- a/var/spack/repos/builtin/packages/r-catools/package.py
+++ b/var/spack/repos/builtin/packages/r-catools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-cdcfluview/package.py b/var/spack/repos/builtin/packages/r-cdcfluview/package.py
new file mode 100644
index 0000000000..541441c38a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cdcfluview/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCdcfluview(RPackage):
+    """The 'U.S.' Centers for Disease Control ('CDC') maintains a portal
+    <http://gis.cdc.gov/grasp/fluview/fluportaldashboard.html> for accessing
+    state, regional and national influenza statistics as well as Mortality
+    Surveillance Data. The web interface makes it difficult and time-consuming
+    to select and retrieve influenza data. Tools are provided to access the
+    data provided by the portal's underlying 'API'."""
+
+    homepage = "https://cran.r-project.org/package=cdcfluview"
+    url      = "https://cran.r-project.org/src/contrib/cdcfluview_0.7.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/cdcfluview"
+
+    version('0.7.0', 'd592606fab3da3536f39a15c0fdbcd17')
+
+    depends_on('r-httr', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-sf', type=('build', 'run'))
+    depends_on('r-xml2', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-readr', type=('build', 'run'))
+    depends_on('r-mmwrweek', type=('build', 'run'))
+    depends_on('r-units@0.4-6:', type=('build', 'run'))
+    depends_on('r@3.2.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-cellranger/package.py b/var/spack/repos/builtin/packages/r-cellranger/package.py
index 5b57c221f9..ca5e60048d 100644
--- a/var/spack/repos/builtin/packages/r-cellranger/package.py
+++ b/var/spack/repos/builtin/packages/r-cellranger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-checkmate/package.py b/var/spack/repos/builtin/packages/r-checkmate/package.py
index 278937335a..0aff1514d4 100644
--- a/var/spack/repos/builtin/packages/r-checkmate/package.py
+++ b/var/spack/repos/builtin/packages/r-checkmate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py
index 6d3d9cc830..517eed195a 100644
--- a/var/spack/repos/builtin/packages/r-checkpoint/package.py
+++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-chemometrics/package.py b/var/spack/repos/builtin/packages/r-chemometrics/package.py
new file mode 100644
index 0000000000..4bf7932e2b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-chemometrics/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RChemometrics(RPackage):
+    """R companion to the book "Introduction to Multivariate Statistical Analysis
+    in Chemometrics" written by K. Varmuza and P. Filzmoser (2009)."""
+
+    homepage = "https://cran.r-project.org/web/packages/chemometrics/index.html"
+    url      = "https://cran.r-project.org/src/contrib/chemometrics_1.4.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/chemometrics"
+
+    version('1.4.2', '8137b0ca4004add9cc2ea81d2c54427f')
+    version('1.4.1', '1e5a89442bb4a61db0da884eedd74fc2')
+    version('1.3.9', '2b619791896db1513ca3d714acb68af3')
+    version('1.3.8', '7fad828bd094b5485fbf20bdf7d3d0d1')
+    version('1.3.7', 'a9e2f32efb1545421dd96185fd849184')
+
+    depends_on('r@2.10:', type=('build', 'run'))
+    depends_on('r-rpart', type=('build', 'run'))
+    depends_on('r-mclust', type=('build', 'run'))
+    depends_on('r-lars', type=('build', 'run'))
+    depends_on('r-robustbase', type=('build', 'run'))
+    depends_on('r-e1071', type=('build', 'run'))
+    depends_on('r-pls', type=('build', 'run'))
+    depends_on('r-som', type=('build', 'run'))
+    depends_on('r-pcapp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-chron/package.py b/var/spack/repos/builtin/packages/r-chron/package.py
index 0a2566c0b1..b7fcc3777f 100644
--- a/var/spack/repos/builtin/packages/r-chron/package.py
+++ b/var/spack/repos/builtin/packages/r-chron/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-circlize/package.py b/var/spack/repos/builtin/packages/r-circlize/package.py
index 628c042d7d..5740e14d2b 100644
--- a/var/spack/repos/builtin/packages/r-circlize/package.py
+++ b/var/spack/repos/builtin/packages/r-circlize/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-class/package.py b/var/spack/repos/builtin/packages/r-class/package.py
index 3b35634302..a0cc01075c 100644
--- a/var/spack/repos/builtin/packages/r-class/package.py
+++ b/var/spack/repos/builtin/packages/r-class/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-classint/package.py b/var/spack/repos/builtin/packages/r-classint/package.py
new file mode 100644
index 0000000000..7009519294
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-classint/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RClassint(RPackage):
+    """Selected commonly used methods for choosing univariate class intervals
+       for mapping or other graphics purposes."""
+
+    homepage = "https://cran.r-project.org/package=classInt"
+    url      = "https://cran.r-project.org/src/contrib/classInt_0.1-24.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/classInt"
+
+    version('0.1-24', '45f1bde3ec7601ce17c99189be5c0fd5')
+
+    depends_on('r-e1071', type=('build', 'run'))
+    depends_on('r-class', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-cli/package.py b/var/spack/repos/builtin/packages/r-cli/package.py
new file mode 100644
index 0000000000..2b48e5fdb4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cli/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCli(RPackage):
+    """A suite of tools designed to build attractive command line interfaces
+       ('CLIs'). Includes tools for drawing rules, boxes, trees, and
+       'Unicode' symbols with 'ASCII' alternatives."""
+
+    homepage = "https://github.com/r-lib/cli#readme"
+    url      = "https://cran.r-project.org/src/contrib/cli_1.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/cli"
+
+    version('1.0.0', 'e6c4169541d394d6d435c4b430b1dd77')
+
+    depends_on('r-assertthat', type=('build', 'run'))
+    depends_on('r-crayon', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-clipr/package.py b/var/spack/repos/builtin/packages/r-clipr/package.py
index a5b6ce9993..c87ffa1f3c 100644
--- a/var/spack/repos/builtin/packages/r-clipr/package.py
+++ b/var/spack/repos/builtin/packages/r-clipr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-cluster/package.py b/var/spack/repos/builtin/packages/r-cluster/package.py
index e59a486434..cdde5da74f 100644
--- a/var/spack/repos/builtin/packages/r-cluster/package.py
+++ b/var/spack/repos/builtin/packages/r-cluster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RCluster(RPackage):
     (1990) "Finding Groups in Data"."""
 
     homepage = "https://cran.r-project.org/web/packages/cluster/index.html"
-    url      = "https://cran.rstudio.com/src/contrib/cluster_2.0.6.tar.gz"
+    url      = "https://cran.rstudio.com/src/contrib/cluster_2.0.7-1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/cluster"
 
-    version('2.0.6', 'e7d0660b05c65f4d886ebf7f046939ab')
+    version('2.0.7-1', 'a37add21b91d3e4f3883d005331e0d45')
     version('2.0.5', '7330f209ebce960bdee1a6d6679cb85a')
     version('2.0.4', 'bb4deceaafb1c42bb1278d5d0dc11e59')
diff --git a/var/spack/repos/builtin/packages/r-clusterprofiler/package.py b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
new file mode 100644
index 0000000000..5a1f51dc95
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-clusterprofiler/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RClusterprofiler(RPackage):
+    """This package implements methods to analyze and visualize functional
+    profiles (GO and KEGG) of gene and gene clusters."""
+
+    homepage = "https://www.bioconductor.org/packages/clusterProfiler/"
+    git      = "https://git.bioconductor.org/packages/clusterProfiler.git"
+
+    version('3.4.4', commit='b86b00e8405fe130e439362651a5567736e2d9d7')
+
+    depends_on('r@3.4.0:3.4.9', when='@3.4.4')
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-rvcheck', type=('build', 'run'))
+    depends_on('r-qvalue', type=('build', 'run'))
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-gosemsim', type=('build', 'run'))
+    depends_on('r-go-db', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-dose', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-cner/package.py b/var/spack/repos/builtin/packages/r-cner/package.py
new file mode 100644
index 0000000000..8a96c0b086
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-cner/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCner(RPackage):
+    """"Large-scale identification and advanced visualization of sets of
+        conserved noncoding elements."""
+
+    homepage = "https://bioconductor.org/packages/CNEr/"
+    git      = "https://git.bioconductor.org/packages/CNEr.git"
+
+    version('1.14.0', commit='b8634d65c51728c815127e22b45eba7c9b9db897')
+
+    depends_on('r-biostrings@2.33.4:', type=('build', 'run'))
+    depends_on('r-dbi@0.7:', type=('build', 'run'))
+    depends_on('r-rsqlite@0.11.4:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.23.16:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.25.5:', type=('build', 'run'))
+    depends_on('r-xvector@0.5.4:', type=('build', 'run'))
+    depends_on('r-genomicalignments@1.1.9:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
+    depends_on('r-iranges@2.5.27:', type=('build', 'run'))
+    depends_on('r-readr@0.2.2:', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-reshape2@1.4.1:', type=('build', 'run'))
+    depends_on('r-ggplot2@2.1.0:', type=('build', 'run'))
+    depends_on('r-powerlaw@0.60.3:', type=('build', 'run'))
+    depends_on('r-annotate@1.50.0:', type=('build', 'run'))
+    depends_on('r-go-db@3.3.0:', type=('build', 'run'))
+    depends_on('r-keggrest@1.14.0:', type=('build', 'run'))
+    depends_on('r-utils@2.3.0:', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.14.0')
diff --git a/var/spack/repos/builtin/packages/r-coda/package.py b/var/spack/repos/builtin/packages/r-coda/package.py
index 82c1887a32..de5e8e112f 100644
--- a/var/spack/repos/builtin/packages/r-coda/package.py
+++ b/var/spack/repos/builtin/packages/r-coda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-codetools/package.py b/var/spack/repos/builtin/packages/r-codetools/package.py
index ce78dd590b..a32e9ddc77 100644
--- a/var/spack/repos/builtin/packages/r-codetools/package.py
+++ b/var/spack/repos/builtin/packages/r-codetools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-coin/package.py b/var/spack/repos/builtin/packages/r-coin/package.py
index 8c7a3a348e..f9688bbb86 100644
--- a/var/spack/repos/builtin/packages/r-coin/package.py
+++ b/var/spack/repos/builtin/packages/r-coin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-colorspace/package.py b/var/spack/repos/builtin/packages/r-colorspace/package.py
index 70e3ea63a7..137f0441d2 100644
--- a/var/spack/repos/builtin/packages/r-colorspace/package.py
+++ b/var/spack/repos/builtin/packages/r-colorspace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-complexheatmap/package.py b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
index 04c88f8ef8..e4c0025f58 100644
--- a/var/spack/repos/builtin/packages/r-complexheatmap/package.py
+++ b/var/spack/repos/builtin/packages/r-complexheatmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RComplexheatmap(RPackage):
        multiple heatmaps and supports self-defined annotation graphics."""
 
     homepage = "https://bioconductor.org/packages/ComplexHeatmap/"
-    url      = "https://git.bioconductor.org/packages/ComplexHeatmap"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ComplexHeatmap.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/ComplexHeatmap', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34')
+    version('1.14.0', commit='0acd8974fb5cedde8cd96efea6dfa39324d25b34')
 
     depends_on('r-circlize', type=('build', 'run'))
     depends_on('r-getoptlong', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-corpcor/package.py b/var/spack/repos/builtin/packages/r-corpcor/package.py
index b07e333ad7..2be6972de0 100644
--- a/var/spack/repos/builtin/packages/r-corpcor/package.py
+++ b/var/spack/repos/builtin/packages/r-corpcor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-corrplot/package.py b/var/spack/repos/builtin/packages/r-corrplot/package.py
index 52408e5ae7..cf053e7733 100644
--- a/var/spack/repos/builtin/packages/r-corrplot/package.py
+++ b/var/spack/repos/builtin/packages/r-corrplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-covr/package.py b/var/spack/repos/builtin/packages/r-covr/package.py
index 5e3d8fff21..dc6430bafd 100644
--- a/var/spack/repos/builtin/packages/r-covr/package.py
+++ b/var/spack/repos/builtin/packages/r-covr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-cowplot/package.py b/var/spack/repos/builtin/packages/r-cowplot/package.py
index cb49c52acb..17a7d8f80e 100644
--- a/var/spack/repos/builtin/packages/r-cowplot/package.py
+++ b/var/spack/repos/builtin/packages/r-cowplot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-crayon/package.py b/var/spack/repos/builtin/packages/r-crayon/package.py
index de1140df3b..d74f993f3e 100644
--- a/var/spack/repos/builtin/packages/r-crayon/package.py
+++ b/var/spack/repos/builtin/packages/r-crayon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-crosstalk/package.py b/var/spack/repos/builtin/packages/r-crosstalk/package.py
new file mode 100644
index 0000000000..aa92cb027c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-crosstalk/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCrosstalk(RPackage):
+    """Provides building blocks for allowing HTML widgets to communicate with
+    each other, with Shiny or without (i.e. static .html files)."""
+
+    homepage = "https://cran.r-project.org/web/packages/crosstalk/index.html"
+    url      = "https://cran.r-project.org/src/contrib/crosstalk_1.0.0.tar.gz"
+
+    version('1.0.0', 'c13c21b81af2154be3f08870fd3a7077')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-htmltools', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-lazyeval', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-shiny', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ctc/package.py b/var/spack/repos/builtin/packages/r-ctc/package.py
new file mode 100644
index 0000000000..c4ceb4d471
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ctc/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RCtc(RPackage):
+    """Tools for export and import classification trees and clusters
+       to other programs"""
+
+    homepage = "https://www.bioconductor.org/packages/release/bioc/html/ctc.html"
+    git      = "https://git.bioconductor.org/packages/ctc.git"
+
+    version('1.54.0', commit='0c3df81dfc8fabe12e11884bed44b64e11fd6d4e')
+
+    depends_on('r-amap', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.54.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-cubature/package.py b/var/spack/repos/builtin/packages/r-cubature/package.py
index 9f09069094..2701f470e4 100644
--- a/var/spack/repos/builtin/packages/r-cubature/package.py
+++ b/var/spack/repos/builtin/packages/r-cubature/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-cubist/package.py b/var/spack/repos/builtin/packages/r-cubist/package.py
index 8fd4639fc5..a5472f2965 100644
--- a/var/spack/repos/builtin/packages/r-cubist/package.py
+++ b/var/spack/repos/builtin/packages/r-cubist/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-curl/package.py b/var/spack/repos/builtin/packages/r-curl/package.py
index 0b53d436fd..3951059736 100644
--- a/var/spack/repos/builtin/packages/r-curl/package.py
+++ b/var/spack/repos/builtin/packages/r-curl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-data-table/package.py b/var/spack/repos/builtin/packages/r-data-table/package.py
index fad200eeb1..9726785a54 100644
--- a/var/spack/repos/builtin/packages/r-data-table/package.py
+++ b/var/spack/repos/builtin/packages/r-data-table/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,7 @@ class RDataTable(RPackage):
     url      = "https://cran.r-project.org/src/contrib/data.table_1.10.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/data.table"
 
+    version('1.10.4-3', '081da241d06f30ae4a2bc60efb409893')
     version('1.10.4-2', '4a2d3541f241088d0979522b4083a765')
     version('1.10.0', 'f0e08dd5ba1b3f46c59dd1574fe497c1')
     version('1.9.6',  'b1c0c7cce490bdf42ab288541cc55372')
diff --git a/var/spack/repos/builtin/packages/r-dbi/package.py b/var/spack/repos/builtin/packages/r-dbi/package.py
index 00b38984e1..5c4c8493ab 100644
--- a/var/spack/repos/builtin/packages/r-dbi/package.py
+++ b/var/spack/repos/builtin/packages/r-dbi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dbplyr/package.py b/var/spack/repos/builtin/packages/r-dbplyr/package.py
new file mode 100644
index 0000000000..7f0dcf7577
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dbplyr/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDbplyr(RPackage):
+    """A 'dplyr' back end for databases that allows you to work with remote
+       database tables as if they are in-memory data frames. Basic features
+       works with any database that has a 'DBI' back end; more advanced
+       features require 'SQL' translation to be provided by the package
+       author."""
+
+    homepage = "https://github.com/tidyverse/dbplyr"
+    url      = "https://cran.r-project.org/src/contrib/dbplyr_1.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/dbplyr"
+
+    version('1.1.0', 'a66a08d1046e3e44bfe17e65ce72a1d0')
+
+    depends_on('r-assertthat', type=('build', 'run'))
+    depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-glue', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'))
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-r6', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-delayedarray/package.py b/var/spack/repos/builtin/packages/r-delayedarray/package.py
index 8cbeb0296b..c6c32aa888 100644
--- a/var/spack/repos/builtin/packages/r-delayedarray/package.py
+++ b/var/spack/repos/builtin/packages/r-delayedarray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,13 +24,20 @@ class RDelayedarray(RPackage):
        frames."""
 
     homepage = "https://bioconductor.org/packages/DelayedArray/"
-    url      = "https://git.bioconductor.org/packages/DelayedArray"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/DelayedArray.git"
 
-    version('0.2.7', git='https://git.bioconductor.org/packages/DelayedArray', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
+    version('0.6.5', commit='7d1cb6477cb024c38bf1ee0c9155e010249ed94e')
+    version('0.4.1', commit='ffe932ef8c255614340e4856fc6e0b44128a27a1')
+    version('0.2.7', commit='909c2ce1665ebae2543172ead50abbe10bd42bc4')
 
+    depends_on('r-biocparallel', when='@0.6.5:', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', when='@0.6.5', type=('build', 'run'))
+    depends_on('r-s4vectors@0.14.3:', when='@0.2.7', type=('build', 'run'))
+    depends_on('r-s4vectors@0.15.3:', when='@0.4.1', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.43:', when='@0.6.5', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.11.17:', when='@0.4.1:', type=('build', 'run'))
     depends_on('r-matrixstats', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@0.2.7')
+    depends_on('r@3.4.0:3.4.9', when='@0.2.7', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@0.6.5', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-deldir/package.py b/var/spack/repos/builtin/packages/r-deldir/package.py
index d02ecb19ce..7a2a5c6de0 100644
--- a/var/spack/repos/builtin/packages/r-deldir/package.py
+++ b/var/spack/repos/builtin/packages/r-deldir/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dendextend/package.py b/var/spack/repos/builtin/packages/r-dendextend/package.py
index 5d98e012fc..73f085b7b7 100644
--- a/var/spack/repos/builtin/packages/r-dendextend/package.py
+++ b/var/spack/repos/builtin/packages/r-dendextend/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-deoptim/package.py b/var/spack/repos/builtin/packages/r-deoptim/package.py
index 298b790693..7a4daac46b 100644
--- a/var/spack/repos/builtin/packages/r-deoptim/package.py
+++ b/var/spack/repos/builtin/packages/r-deoptim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-deoptimr/package.py b/var/spack/repos/builtin/packages/r-deoptimr/package.py
index af95c081e0..e2ec25a988 100644
--- a/var/spack/repos/builtin/packages/r-deoptimr/package.py
+++ b/var/spack/repos/builtin/packages/r-deoptimr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-deseq/package.py b/var/spack/repos/builtin/packages/r-deseq/package.py
index 900c82499a..78886d4f03 100644
--- a/var/spack/repos/builtin/packages/r-deseq/package.py
+++ b/var/spack/repos/builtin/packages/r-deseq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,9 @@ class RDeseq(RPackage):
     distribution."""
 
     homepage = "https://www.bioconductor.org/packages/DESeq/"
-    url      = "https://git.bioconductor.org/packages/DESeq"
+    git      = "https://git.bioconductor.org/packages/DESeq.git"
 
-    version('1.28.0', git='https://git.bioconductor.org/packages/DESeq', commit='738371466e6ccf00179fd35b617c8ba0e1e91630')
+    version('1.28.0', commit='738371466e6ccf00179fd35b617c8ba0e1e91630')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-deseq2/package.py b/var/spack/repos/builtin/packages/r-deseq2/package.py
index 96a2426c4f..2a470b808d 100644
--- a/var/spack/repos/builtin/packages/r-deseq2/package.py
+++ b/var/spack/repos/builtin/packages/r-deseq2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,11 +13,12 @@ class RDeseq2(RPackage):
     distribution."""
 
     homepage = "https://www.bioconductor.org/packages/DESeq2/"
-    url      = "https://git.bioconductor.org/packages/DESeq2"
+    git      = "https://git.bioconductor.org/packages/DESeq2.git"
 
-    version('1.16.1', git='https://git.bioconductor.org/packages/DESeq2', commit='0a815574382704a08ef8b906eceb0296f81cded5')
+    version('1.20.0', commit='7e88ea5c5e68473824ce0af6e10f19e22374cb7c')
+    version('1.18.1', commit='ef65091d46436af68915124b752f5e1cc55e93a7')
+    version('1.16.1', commit='0a815574382704a08ef8b906eceb0296f81cded5')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.16.1')
     depends_on("r-rcpparmadillo", type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
@@ -51,3 +33,5 @@ class RDeseq2(RPackage):
     depends_on('r-ggplot2', type=('build', 'run'))
     depends_on('r-hmisc', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.16.1:1.19', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.20.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-desolve/package.py b/var/spack/repos/builtin/packages/r-desolve/package.py
index bbcbebcd53..11642809e1 100644
--- a/var/spack/repos/builtin/packages/r-desolve/package.py
+++ b/var/spack/repos/builtin/packages/r-desolve/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-devtools/package.py b/var/spack/repos/builtin/packages/r-devtools/package.py
index 7b9b789eb3..68bb13ed76 100644
--- a/var/spack/repos/builtin/packages/r-devtools/package.py
+++ b/var/spack/repos/builtin/packages/r-devtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-diagrammer/package.py b/var/spack/repos/builtin/packages/r-diagrammer/package.py
index 650ab64a3f..a5c7c58787 100644
--- a/var/spack/repos/builtin/packages/r-diagrammer/package.py
+++ b/var/spack/repos/builtin/packages/r-diagrammer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dicekriging/package.py b/var/spack/repos/builtin/packages/r-dicekriging/package.py
new file mode 100644
index 0000000000..6dcfddda69
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dicekriging/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDicekriging(RPackage):
+    """Estimation, validation and prediction of kriging models. Important
+       functions : km, print.km, plot.km, predict.km."""
+
+    homepage = "http://dice.emse.fr/"
+    url      = "https://cran.r-project.org/src/contrib/DiceKriging_1.5.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/DiceKriging"
+
+    version('1.5.5', 'ee3e2d7a91d4a712467ef4f0b69c2844')
diff --git a/var/spack/repos/builtin/packages/r-dichromat/package.py b/var/spack/repos/builtin/packages/r-dichromat/package.py
index b40cff31dd..1364e90113 100644
--- a/var/spack/repos/builtin/packages/r-dichromat/package.py
+++ b/var/spack/repos/builtin/packages/r-dichromat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-diffusionmap/package.py b/var/spack/repos/builtin/packages/r-diffusionmap/package.py
new file mode 100644
index 0000000000..c4011ff844
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-diffusionmap/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDiffusionmap(RPackage):
+    """Allows to display a progress bar in the R console for long running
+    computations taking place in c++ code, and support for interrupting those
+    computations even in multithreaded code, typically using OpenMP."""
+
+    homepage = "https://cran.r-project.org/web/packages/diffusionMap/index.html"
+    url      = "https://cran.r-project.org/src/contrib/diffusionMap_1.1-0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/diffusionMap"
+
+    version('1.1-0', 'cc7d728087ba08d9299ae3a64a8d8919')
+    version('1.0-0', 'bca462e6efe45c5eaa48d38621f0bd6f')
+    version('0.0-2', 'b599f47ebf30127e34ce2219dc3e43ae')
+    version('0.0-1', '20c2cc2fffb5237d5c0216207016c2a1')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-scatterplot3d', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-digest/package.py b/var/spack/repos/builtin/packages/r-digest/package.py
index 78b96e03f4..db1678ed1e 100644
--- a/var/spack/repos/builtin/packages/r-digest/package.py
+++ b/var/spack/repos/builtin/packages/r-digest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-diptest/package.py b/var/spack/repos/builtin/packages/r-diptest/package.py
index 96d9eea734..1afe05803b 100644
--- a/var/spack/repos/builtin/packages/r-diptest/package.py
+++ b/var/spack/repos/builtin/packages/r-diptest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
new file mode 100644
index 0000000000..ce634abf12
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dirichletmultinomial/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDirichletmultinomial(RPackage):
+    """Dirichlet-multinomial mixture models can be used to describe
+    variability in microbial metagenomic data.
+
+    This package is an interface to code originally made available by
+    Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed
+    further in the man page for this package, ?DirichletMultinomial."""
+
+    homepage = "https://bioconductor.org/packages/DirichletMultinomial/"
+    git      = "https://git.bioconductor.org/packages/DirichletMultinomial.git"
+
+    version('1.20.0', commit='251529f301da1482551142240aeb6baf8dab2272')
+
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('gsl')
+    depends_on('r@3.4.0:')
diff --git a/var/spack/repos/builtin/packages/r-dismo/package.py b/var/spack/repos/builtin/packages/r-dismo/package.py
new file mode 100644
index 0000000000..db2db94130
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dismo/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDismo(RPackage):
+    """Functions for species distribution modeling, that is, predicting
+       entire geographic distributions form occurrences at a number of sites
+       and the environment at these sites."""
+
+    homepage = "https://cran.r-project.org/package=dismo"
+    url      = "https://cran.r-project.org/src/contrib/dismo_1.1-4.tar.gz"
+
+    version('1.1-4', sha256='f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8')
+
+    depends_on('r@3.2.0:', type=('build', 'run'))
+    depends_on('r-raster@2.5-2:', type=('build', 'run'))
+    depends_on('r-sp@1.2-0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-dnacopy/package.py b/var/spack/repos/builtin/packages/r-dnacopy/package.py
index ade0424829..2f1900f361 100644
--- a/var/spack/repos/builtin/packages/r-dnacopy/package.py
+++ b/var/spack/repos/builtin/packages/r-dnacopy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,6 @@ class RDnacopy(RPackage):
     with abnormal copy number."""
 
     homepage = "https://www.bioconductor.org/packages/DNAcopy/"
-    url      = "https://git.bioconductor.org/packages/DNAcopy"
+    git      = "https://git.bioconductor.org/packages/DNAcopy.git"
 
-    version('1.50.1', git='https://git.bioconductor.org/packages/DNAcopy', commit='a20153029e28c009df813dbaf13d9f519fafa4e8')
+    version('1.50.1', commit='a20153029e28c009df813dbaf13d9f519fafa4e8')
diff --git a/var/spack/repos/builtin/packages/r-do-db/package.py b/var/spack/repos/builtin/packages/r-do-db/package.py
new file mode 100644
index 0000000000..3dd7c8b258
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-do-db/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDoDb(RPackage):
+    """A set of annotation maps describing the entire Disease
+    Ontology assembled using data from DO."""
+
+    homepage = "https://bioconductor.org/packages/DO.db/"
+    url      = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/DO.db_2.9.tar.gz"
+
+    version('2.9', '63dda6d46d2fe40c52a2e79260a7fb9d')
+
+    depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-domc/package.py b/var/spack/repos/builtin/packages/r-domc/package.py
index 9ed4841520..2fd58884d5 100644
--- a/var/spack/repos/builtin/packages/r-domc/package.py
+++ b/var/spack/repos/builtin/packages/r-domc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-doparallel/package.py b/var/spack/repos/builtin/packages/r-doparallel/package.py
index 1690db07a7..06bc2bf0a7 100644
--- a/var/spack/repos/builtin/packages/r-doparallel/package.py
+++ b/var/spack/repos/builtin/packages/r-doparallel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dorng/package.py b/var/spack/repos/builtin/packages/r-dorng/package.py
index 7ac9556d9b..ba094688ad 100644
--- a/var/spack/repos/builtin/packages/r-dorng/package.py
+++ b/var/spack/repos/builtin/packages/r-dorng/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dose/package.py b/var/spack/repos/builtin/packages/r-dose/package.py
new file mode 100644
index 0000000000..96bbf34451
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dose/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDose(RPackage):
+    """This package implements five methods proposed by Resnik, Schlicker,
+    Jiang, Lin and Wang respectively for measuring semantic similarities
+    among DO terms and gene products. Enrichment analyses including
+    hypergeometric model and gene set enrichment analysis are also
+    implemented for discovering disease associations of high-throughput
+    biological data."""
+
+    homepage = "https://www.bioconductor.org/packages/DOSE/"
+    git      = "https://git.bioconductor.org/packages/DOSE.git"
+
+    version('3.2.0', commit='71f563fc39d02dfdf65184c94e0890a63b96b86b')
+
+    depends_on('r@3.4.0:3.4.9', when='@3.2.0')
+    depends_on('r-scales', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-qvalue', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
+    depends_on('r-gosemsim', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-fgsea', type=('build', 'run'))
+    depends_on('r-do-db', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-downloader/package.py b/var/spack/repos/builtin/packages/r-downloader/package.py
index d71c17e304..6a0293b8c6 100644
--- a/var/spack/repos/builtin/packages/r-downloader/package.py
+++ b/var/spack/repos/builtin/packages/r-downloader/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dplyr/package.py b/var/spack/repos/builtin/packages/r-dplyr/package.py
index fa68988692..72a34222cb 100644
--- a/var/spack/repos/builtin/packages/r-dplyr/package.py
+++ b/var/spack/repos/builtin/packages/r-dplyr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,18 +10,26 @@ class RDplyr(RPackage):
     """A fast, consistent tool for working with data frame like objects, both
     in memory and out of memory."""
 
-    homepage = "https://github.com/hadley/dplyr"
-    url      = "https://cran.rstudio.com/src/contrib/dplyr_0.7.3.tar.gz"
+    homepage = "https://cran.r-project.org/package=dplyr"
+    url      = "https://cran.r-project.org/src/contrib/dplyr_0.7.6.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/dplyr"
 
+    version('0.7.5', sha256='2fbd8f316a59670076d43a0fe854654621941ee5f621ea5f0185a3f5daafda50')
+    version('0.7.4', '9edee9b2db9831c2438054d0d2c1647d')
     version('0.7.3', 'f9760b796917747e9dcd927ebb531c7d')
     version('0.5.0', '1fcafcacca70806eea2e6d465cdb94ef')
 
+    depends_on('r-tidyselect@0.2.3', type=('build', 'run'))
     depends_on('r-assertthat', type=('build', 'run'))
+    depends_on('r-bindr@0.1.1', type=('build', 'run'))
     depends_on('r-r6', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
     depends_on('r-tibble', type=('build', 'run'))
     depends_on('r-magrittr', type=('build', 'run'))
     depends_on('r-lazyeval', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-bindrcpp', type=('build', 'run'))
+    depends_on('r-glue', type=('build', 'run'))
+    depends_on('r-pkgconfig', type=('build', 'run'))
+    depends_on('r-plogr', type=('build', 'run'))
     depends_on('r-bh', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-dt/package.py b/var/spack/repos/builtin/packages/r-dt/package.py
index a2d01900e1..3a68487f43 100644
--- a/var/spack/repos/builtin/packages/r-dt/package.py
+++ b/var/spack/repos/builtin/packages/r-dt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-dtw/package.py b/var/spack/repos/builtin/packages/r-dtw/package.py
new file mode 100644
index 0000000000..a752f202d6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-dtw/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RDtw(RPackage):
+    """A comprehensive implementation of dynamic time warping (DTW) algorithms
+    in R. DTW computes the optimal (least cumulative distance) alignment
+    between points of two time series."""
+
+    homepage = "https://cran.r-project.org/web/packages/dtw/index.html"
+    url      = "https://cran.r-project.org/src/contrib/dtw_1.18-1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/dtw"
+
+    version('1.18-1', '5e9995a198a62f28045c29461265d536')
+    version('1.17-1', 'e8be988fe528acd6b44afdf5aa06b745')
+    version('1.16',   '260bd22d9db429394eb39739db4a4686')
+    version('1.15',   'd3b6fdb0b866ff2e5b178c37bcfc7c55')
+    version('1.14-3', 'a7b878e8dda7a61df22356d0a81540c5')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-proxy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-dygraphs/package.py b/var/spack/repos/builtin/packages/r-dygraphs/package.py
index 91e2dc5504..eeb0f08481 100644
--- a/var/spack/repos/builtin/packages/r-dygraphs/package.py
+++ b/var/spack/repos/builtin/packages/r-dygraphs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-e1071/package.py b/var/spack/repos/builtin/packages/r-e1071/package.py
index 7be5264895..94b6a60ef9 100644
--- a/var/spack/repos/builtin/packages/r-e1071/package.py
+++ b/var/spack/repos/builtin/packages/r-e1071/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-edger/package.py b/var/spack/repos/builtin/packages/r-edger/package.py
index 2d9da861db..cc94490e97 100644
--- a/var/spack/repos/builtin/packages/r-edger/package.py
+++ b/var/spack/repos/builtin/packages/r-edger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,11 +16,13 @@ class REdger(RPackage):
        SAGE and CAGE."""
 
     homepage = "https://bioconductor.org/packages/edgeR/"
-    url      = "https://git.bioconductor.org/packages/edgeR"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/edgeR.git"
 
-    version('3.18.1', git='https://git.bioconductor.org/packages/edgeR', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
+    version('3.22.3', commit='e82e54afc9398ac54dc4caba0f7ae5c43e572203')
+    version('3.18.1', commit='101106f3fdd9e2c45d4a670c88f64c12e97a0495')
 
     depends_on('r-limma', type=('build', 'run'))
     depends_on('r-locfit', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'link', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@3.22.3')
     depends_on('r@3.4.0:3.4.9', when='@3.18.1')
diff --git a/var/spack/repos/builtin/packages/r-ellipse/package.py b/var/spack/repos/builtin/packages/r-ellipse/package.py
index 52393ed66a..555e5cd985 100644
--- a/var/spack/repos/builtin/packages/r-ellipse/package.py
+++ b/var/spack/repos/builtin/packages/r-ellipse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ensembldb/package.py b/var/spack/repos/builtin/packages/r-ensembldb/package.py
index c6f424a855..c1e5b219ef 100644
--- a/var/spack/repos/builtin/packages/r-ensembldb/package.py
+++ b/var/spack/repos/builtin/packages/r-ensembldb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,10 +18,9 @@ class REnsembldb(RPackage):
        region or transcript models of lincRNA genes."""
 
     homepage = "https://bioconductor.org/packages/ensembldb/"
-    url      = "https://git.bioconductor.org/packages/ensembldb"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ensembldb.git"
 
-    version('2.0.4', git='https://git.bioconductor.org/packages/ensembldb', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
+    version('2.0.4', commit='514623d71e3cca7a4e547adb579b5a958702ef86')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ergm/package.py b/var/spack/repos/builtin/packages/r-ergm/package.py
index 419119e2b0..cea98327f7 100644
--- a/var/spack/repos/builtin/packages/r-ergm/package.py
+++ b/var/spack/repos/builtin/packages/r-ergm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-evaluate/package.py b/var/spack/repos/builtin/packages/r-evaluate/package.py
index d32bff7319..8edc12743e 100644
--- a/var/spack/repos/builtin/packages/r-evaluate/package.py
+++ b/var/spack/repos/builtin/packages/r-evaluate/package.py
@@ -1,28 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-expm/package.py b/var/spack/repos/builtin/packages/r-expm/package.py
index 48080163de..2f68a851ab 100644
--- a/var/spack/repos/builtin/packages/r-expm/package.py
+++ b/var/spack/repos/builtin/packages/r-expm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-factoextra/package.py b/var/spack/repos/builtin/packages/r-factoextra/package.py
index 518f4d6a63..8bffeafbc9 100644
--- a/var/spack/repos/builtin/packages/r-factoextra/package.py
+++ b/var/spack/repos/builtin/packages/r-factoextra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-factominer/package.py b/var/spack/repos/builtin/packages/r-factominer/package.py
index d2abf10ff7..f9aa8a7d77 100644
--- a/var/spack/repos/builtin/packages/r-factominer/package.py
+++ b/var/spack/repos/builtin/packages/r-factominer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-fastcluster/package.py b/var/spack/repos/builtin/packages/r-fastcluster/package.py
new file mode 100644
index 0000000000..303219e630
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fastcluster/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFastcluster(RPackage):
+    """This is a two-in-one package which provides interfaces to both R
+       and 'Python'. It implements fast hierarchical, agglomerative
+       clustering routines. Part of the functionality is designed as drop-in
+       replacement for existing routines: linkage() in the 'SciPy' package
+       'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the
+       'flashClust' package. It provides the same functionality with the
+       benefit of a much faster implementation. Moreover, there are
+       memory-saving routines for clustering of vector data, which go beyond
+       what the existing packages provide. For information on how to install
+       the 'Python' files, see the file INSTALL in the source distribution."""
+
+    homepage = "http://danifold.net/fastcluster.html"
+    url      = "https://cran.r-project.org/src/contrib/fastcluster_1.1.25.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/fastcluster/"
+
+    version('1.1.25', sha256='f3661def975802f3dd3cec5b2a1379f3707eacff945cf448e33aec0da1ed4205')
+
+    depends_on('r@3.0.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-fastmatch/package.py b/var/spack/repos/builtin/packages/r-fastmatch/package.py
new file mode 100644
index 0000000000..73f849db91
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fastmatch/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFastmatch(RPackage):
+    """Package providing a fast match() replacement for cases that require
+       repeated look-ups. It is slightly faster that R's built-in match()
+       function on first match against a table, but extremely fast on any
+       subsequent lookup as it keeps the hash table in memory."""
+
+    homepage = "http://www.rforge.net/fastmatch"
+    url      = "https://cran.r-project.org/src/contrib/fastmatch_1.1-0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/fastmatch"
+
+    version('1.1-0', '900c2363c15059ac9d63c4c71ea2d6b2')
diff --git a/var/spack/repos/builtin/packages/r-ff/package.py b/var/spack/repos/builtin/packages/r-ff/package.py
index 1bb7250658..aa68be9562 100644
--- a/var/spack/repos/builtin/packages/r-ff/package.py
+++ b/var/spack/repos/builtin/packages/r-ff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-fftwtools/package.py b/var/spack/repos/builtin/packages/r-fftwtools/package.py
new file mode 100644
index 0000000000..237d40035e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fftwtools/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFftwtools(RPackage):
+    """Provides a wrapper for several 'FFTW' functions. This package provides
+       access to the two-dimensional 'FFT', the multivariate 'FFT', and the
+       one-dimensional real to complex 'FFT' using the 'FFTW3' library. The
+       package includes the functions fftw() and mvfftw() which are designed
+       to mimic the functionality of the R functions fft() and mvfft().
+       The 'FFT' functions have a parameter that allows them to not return
+       the redundant complex conjugate when the input is real data."""
+
+    homepage = "https://github.com/krahim/fftwtools"
+    url      = "https://cran.r-project.org/src/contrib/fftwtools_0.9-8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/fftwtools"
+
+    version('0.9-8', '2d1258fbaf0940b57ed61c8d6cd6694d')
+
+    depends_on('fftw')
diff --git a/var/spack/repos/builtin/packages/r-fgsea/package.py b/var/spack/repos/builtin/packages/r-fgsea/package.py
new file mode 100644
index 0000000000..938a15bf6f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fgsea/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFgsea(RPackage):
+    """The package implements an algorithm for fast gene set enrichment
+    analysis. Using the fast algorithm allows to make more permutations
+    and get more fine grained p-values, which allows to use accurate
+    stantard approaches to multiple hypothesis correction."""
+
+    homepage = "https://www.bioconductor.org/packages/fgsea/"
+    git      = "https://git.bioconductor.org/packages/fgsea.git"
+
+    version('1.2.1', commit='99b04eef664204d0dca4b9f8027cd7eefb006b72')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.2.1')
+    depends_on('r-fastmatch', type=('build', 'run'))
+    depends_on('r-gridextra', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py
index b7cfbb19ce..0220fbc6bb 100644
--- a/var/spack/repos/builtin/packages/r-filehash/package.py
+++ b/var/spack/repos/builtin/packages/r-filehash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-findpython/package.py b/var/spack/repos/builtin/packages/r-findpython/package.py
new file mode 100644
index 0000000000..e5a298b09a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-findpython/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFindpython(RPackage):
+    """Package designed to find an acceptable python binary."""
+
+    homepage = "https://github.com/trevorld/findpython"
+    url      = "https://cran.r-project.org/src/contrib/findpython_1.0.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/findpython"
+
+    version('1.0.3', sha256='5486535ae2f0a123b630d8eabf93a61b730765f55dfcc8ef4f6e56e7c49408f8')
+
+    depends_on('python', type='run')
diff --git a/var/spack/repos/builtin/packages/r-fit-models/package.py b/var/spack/repos/builtin/packages/r-fit-models/package.py
new file mode 100644
index 0000000000..32c2b96f9e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fit-models/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFitModels(RPackage):
+    """Compare Fitted Models"""
+
+    homepage = "https://cran.r-project.org/package=fit.models"
+    url      = "https://cran.r-project.org/src/contrib/fit.models_0.5-14.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/fit.models"
+
+    version('0.5-14', '159b5c57953db4c917bc186ddacdff51')
+    version('0.5-13', 'c9ff87e98189bcc3be597e3833408497')
+
+    depends_on('r-lattice', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-flashclust/package.py b/var/spack/repos/builtin/packages/r-flashclust/package.py
index cfaee392db..c36ad50cf8 100644
--- a/var/spack/repos/builtin/packages/r-flashclust/package.py
+++ b/var/spack/repos/builtin/packages/r-flashclust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-flexclust/package.py b/var/spack/repos/builtin/packages/r-flexclust/package.py
new file mode 100644
index 0000000000..338bfd4d07
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-flexclust/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFlexclust(RPackage):
+    """The main function kcca implements a general framework for k-centroids
+    cluster analysis supporting arbitrary distance measures and centroid
+    computation. Further cluster methods include hard competitive learning,
+    neural gas, and QT clustering. There are numerous visualization methods for
+    cluster results (neighborhood graphs, convex cluster hulls, barcharts of
+    centroids, ...), and bootstrap methods for the analysis of cluster
+    stability."""
+
+    homepage = "https://cran.r-project.org/package=flexclust"
+    url      = "https://cran.rstudio.com/src/contrib/flexclust_1.3-5.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/flexclust"
+
+    version('1.3-5', '90226a0e3a4f256f392a278e9543f8f4')
+
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-modeltools', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-flexmix/package.py b/var/spack/repos/builtin/packages/r-flexmix/package.py
index 82ea3f068a..f41e959b7c 100644
--- a/var/spack/repos/builtin/packages/r-flexmix/package.py
+++ b/var/spack/repos/builtin/packages/r-flexmix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-fnn/package.py b/var/spack/repos/builtin/packages/r-fnn/package.py
new file mode 100644
index 0000000000..984024a5d0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-fnn/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RFnn(RPackage):
+    """Cover-tree and kd-tree fast k-nearest neighbor search algorithms and
+    related applications including KNN classification, regression and
+    information measures are implemented."""
+
+    homepage = "https://cran.r-project.org/web/packages/FNN/index.html"
+    url      = "https://cran.r-project.org/src/contrib/FNN_1.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/FNN"
+
+    version('1.1',   '8ba8f5b8be271785593e13eae7b8c393')
+    version('1.0',   'e9a47dc69d1ba55165be0877b8443fe0')
+    version('0.6-4', '1c105df9763ceb7b13989cdbcb542fcc')
+    version('0.6-3', 'f0f0184e50f9f30a36ed5cff24d6cff2')
+    version('0.6-2', '20648ba934ea32b1b00dafb75e1a830c')
+
+    depends_on('r@3.0.0:', type=('build', 'run'))
+    depends_on('r-mvtnorm', type=('build', 'run'))
+    depends_on('r-chemometrics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-forcats/package.py b/var/spack/repos/builtin/packages/r-forcats/package.py
new file mode 100644
index 0000000000..3497da1f8b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-forcats/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RForcats(RPackage):
+    """Helpers for reordering factor levels (including moving specified levels
+       to front, ordering by first appearance, reversing, and randomly
+       shuffling), and tools for modifying factor levels (including collapsing
+       rare levels into other, 'anonymising', and manually 'recoding')."""
+
+    homepage = "http://forcats.tidyverse.org/"
+    url      = "https://cran.r-project.org/src/contrib/forcats_0.2.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/forcats"
+
+    version('0.2.0', 'e4ba2c0a59dcdfcc02274c519bf3dbfc')
+
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-foreach/package.py b/var/spack/repos/builtin/packages/r-foreach/package.py
index bf542efaea..b7ffbcc256 100644
--- a/var/spack/repos/builtin/packages/r-foreach/package.py
+++ b/var/spack/repos/builtin/packages/r-foreach/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-forecast/package.py b/var/spack/repos/builtin/packages/r-forecast/package.py
index e6549a30dd..d491a3bc20 100644
--- a/var/spack/repos/builtin/packages/r-forecast/package.py
+++ b/var/spack/repos/builtin/packages/r-forecast/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-foreign/package.py b/var/spack/repos/builtin/packages/r-foreign/package.py
index f43e0ad0e4..4974ec76d7 100644
--- a/var/spack/repos/builtin/packages/r-foreign/package.py
+++ b/var/spack/repos/builtin/packages/r-foreign/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-formatr/package.py b/var/spack/repos/builtin/packages/r-formatr/package.py
index e6fa3c6824..7e495ca821 100644
--- a/var/spack/repos/builtin/packages/r-formatr/package.py
+++ b/var/spack/repos/builtin/packages/r-formatr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-formula/package.py b/var/spack/repos/builtin/packages/r-formula/package.py
index 499ebfa8da..9f756f8917 100644
--- a/var/spack/repos/builtin/packages/r-formula/package.py
+++ b/var/spack/repos/builtin/packages/r-formula/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-fpc/package.py b/var/spack/repos/builtin/packages/r-fpc/package.py
index 4628970171..26901c8035 100644
--- a/var/spack/repos/builtin/packages/r-fpc/package.py
+++ b/var/spack/repos/builtin/packages/r-fpc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-fracdiff/package.py b/var/spack/repos/builtin/packages/r-fracdiff/package.py
index c5ed63b240..4666832c17 100644
--- a/var/spack/repos/builtin/packages/r-fracdiff/package.py
+++ b/var/spack/repos/builtin/packages/r-fracdiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-futile-logger/package.py b/var/spack/repos/builtin/packages/r-futile-logger/package.py
index 93d735f027..e2e3cf2667 100644
--- a/var/spack/repos/builtin/packages/r-futile-logger/package.py
+++ b/var/spack/repos/builtin/packages/r-futile-logger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-futile-options/package.py b/var/spack/repos/builtin/packages/r-futile-options/package.py
index 9d0ee93d13..881d6f8ad1 100644
--- a/var/spack/repos/builtin/packages/r-futile-options/package.py
+++ b/var/spack/repos/builtin/packages/r-futile-options/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,5 +11,6 @@ class RFutileOptions(RPackage):
 
     homepage = "https://cran.rstudio.com/web/packages/futile.options/index.html"
     url      = "https://cran.rstudio.com/src/contrib/futile.options_1.0.0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/futile.options"
 
     version('1.0.0', '8fd845774bbce56f41f7c43c3b4c13ba')
diff --git a/var/spack/repos/builtin/packages/r-gbm/package.py b/var/spack/repos/builtin/packages/r-gbm/package.py
index cddc0c77be..5309583922 100644
--- a/var/spack/repos/builtin/packages/r-gbm/package.py
+++ b/var/spack/repos/builtin/packages/r-gbm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gcrma/package.py b/var/spack/repos/builtin/packages/r-gcrma/package.py
index b54315796a..8f9fe9ff1f 100644
--- a/var/spack/repos/builtin/packages/r-gcrma/package.py
+++ b/var/spack/repos/builtin/packages/r-gcrma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class RGcrma(RPackage):
     """Background adjustment using sequence information"""
 
     homepage = "https://bioconductor.org/packages/gcrma/"
-    url      = "https://git.bioconductor.org/packages/gcrma"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/gcrma.git"
 
-    version('2.48.0', git='https://git.bioconductor.org/packages/gcrma', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4')
+    version('2.48.0', commit='3ea0eb0b5c15ffb24df76620667ae7996ed715b4')
 
     depends_on('r-affy', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gdata/package.py b/var/spack/repos/builtin/packages/r-gdata/package.py
index e07fc8d360..a093ae4485 100644
--- a/var/spack/repos/builtin/packages/r-gdata/package.py
+++ b/var/spack/repos/builtin/packages/r-gdata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gdsfmt/package.py b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
new file mode 100644
index 0000000000..b2a98aa726
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gdsfmt/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGdsfmt(RPackage):
+    """This package provides a high-level R interface to CoreArray Genomic
+       Data Structure (GDS) data files, which are portable across platforms
+       with hierarchical structure to store multiple scalable array-oriented
+       data sets with metadata information. It is suited for large-scale
+       datasets, especially for data which are much larger than the available
+       random-access memory. The gdsfmt package offers the efficient
+       operations specifically designed for integers of less than 8 bits,
+       since a diploid genotype, like single-nucleotide polymorphism (SNP),
+       usually occupies fewer bits than a byte. Data compression and
+       decompression are available with relatively efficient random access.
+       It is also allowed to read a GDS file in parallel with multiple R
+       processes supported by the package parallel."""
+
+    homepage = "http://bioconductor.org/packages/gdsfmt/"
+    git      = "https://git.bioconductor.org/packages/gdsfmt.git"
+
+    version('1.14.1', commit='15743647b7eea5b82d3284858b4591fb6e59959d')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.14.1')
diff --git a/var/spack/repos/builtin/packages/r-geiger/package.py b/var/spack/repos/builtin/packages/r-geiger/package.py
index c2ce69ef37..8bb6f8a3c7 100644
--- a/var/spack/repos/builtin/packages/r-geiger/package.py
+++ b/var/spack/repos/builtin/packages/r-geiger/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-genefilter/package.py b/var/spack/repos/builtin/packages/r-genefilter/package.py
index e5b631d778..afe1e1edf6 100644
--- a/var/spack/repos/builtin/packages/r-genefilter/package.py
+++ b/var/spack/repos/builtin/packages/r-genefilter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,14 @@ class RGenefilter(RPackage):
     """Some basic functions for filtering genes"""
 
     homepage = "https://bioconductor.org/packages/genefilter/"
-    url      = "https://git.bioconductor.org/packages/genefilter"
-    list_url = homepage
-    version('1.58.1', git='https://git.bioconductor.org/packages/genefilter', commit='ace2556049677f60882adfe91f8cc96791556fc2')
+    git      = "https://git.bioconductor.org/packages/genefilter.git"
+
+    version('1.62.0', commit='eb119894f015c759f93f458af7733bdb770a22ad')
+    version('1.58.1', commit='ace2556049677f60882adfe91f8cc96791556fc2')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.58.1')
     depends_on('r-s4vectors', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-annotate', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.58.1', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.62.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genelendatabase/package.py b/var/spack/repos/builtin/packages/r-genelendatabase/package.py
new file mode 100644
index 0000000000..003bc11e9d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-genelendatabase/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGenelendatabase(RPackage):
+    """Length of mRNA transcripts for a number of genomes and gene ID
+       formats, largely based on UCSC table browser"""
+
+    homepage = "https://bioconductor.org/packages/release/data/experiment/html/geneLenDataBase.html"
+    git      = "https://git.bioconductor.org/packages/geneLenDataBase.git"
+
+    version('1.16.0', commit='c2a8b2359c6c59388853d6f6d15d71dffb17a198')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.16.0:', type=('build', 'run'))
+    depends_on('r-rtracklayer', type=('build', 'run'))
+    depends_on('r-genomicfeatures@1.3.15:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-geneplotter/package.py b/var/spack/repos/builtin/packages/r-geneplotter/package.py
index 940c87e01f..46918c492a 100644
--- a/var/spack/repos/builtin/packages/r-geneplotter/package.py
+++ b/var/spack/repos/builtin/packages/r-geneplotter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,14 +10,16 @@ class RGeneplotter(RPackage):
     """Functions for plotting genomic data."""
 
     homepage = "https://www.bioconductor.org/packages/geneplotter/"
-    url      = "https://git.bioconductor.org/packages/geneplotter"
+    git      = "https://git.bioconductor.org/packages/geneplotter.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/geneplotter', commit='efdd946e092e44e35fde1eb4bcc5ec1d52090940')
+    version('1.58.0', commit='2b3f44804d61a40cfe7eaedf74ac9f5a054f7fde')
+    version('1.54.0', commit='efdd946e092e44e35fde1eb4bcc5ec1d52090940')
 
-    depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-lattice', type=('build', 'run'))
     depends_on('r-annotate', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
     depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.54.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.58.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genie3/package.py b/var/spack/repos/builtin/packages/r-genie3/package.py
new file mode 100644
index 0000000000..b2942ffc89
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-genie3/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGenie3(RPackage):
+    """This package implements the GENIE3 algorithm for inferring gene
+    regulatory networks from expression data."""
+
+    homepage = "https://bioconductor.org/packages/GENIE3/"
+    git      = "https://git.bioconductor.org/packages/GENIE3.git"
+
+    version('1.2.0', commit='cafe6a1a85095cda6cc3c812eb6f53501fcbaf93')
+
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r@3.5.0:', when='@1.2.0')
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
index 85a161a01b..a13b969c73 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,14 +13,19 @@ class RGenomeinfodb(RPackage):
        names in their natural, rather than lexicographic, order."""
 
     homepage = "https://bioconductor.org/packages/GenomeInfoDb/"
-    url      = "https://git.bioconductor.org/packages/GenomeInfoDb"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomeInfoDb.git"
 
-    version('1.12.3', git='https://git.bioconductor.org/packages/GenomeInfoDb', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
+    version('1.16.0', commit='6543dad89bbc2c275010b329eb114b237fd712fa')
+    version('1.14.0', commit='4978308a57d887b764cc4ce83724ca1758f580f6')
+    version('1.12.3', commit='2deef3f0571b7f622483257bc22d2509ab5a0369')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.13.8:', when='@1.16.0', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@1.16.0', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.12:', when='@1.16.0', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-genomeinfodbdata', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.12.3')
+    depends_on('r@3.4.0:3.4.9', when='@1.12.3', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
index 8e231ac43c..cf74104950 100644
--- a/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
+++ b/var/spack/repos/builtin/packages/r-genomeinfodbdata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,11 @@ class RGenomeinfodbdata(RPackage):
     """for mapping between NCBI taxonomy ID and species. Used by functions
        in the GenomeInfoDb package."""
 
-    homepage = "http://www.example.co://bioconductor.org/packages/3.5/data/annotation/html/GenomeInfoDbData.html"
+    homepage = "https://bioconductor.org/packages/GenomeInfoDbData/"
     url      = "https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GenomeInfoDbData_0.99.0.tar.gz"
 
+    version('1.1.0', '6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c',
+            url='https://bioconductor.org/packages/release/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz')
     version('0.99.0', '85977b51061dd02a90153db887040d05')
-    depends_on('r@3.4.0:3.4.9', when='@0.99.0')
+    depends_on('r@3.4.0:3.4.9', when='@0.99.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.1.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomicalignments/package.py b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
index 4a26b91538..9f66a1aba8 100644
--- a/var/spack/repos/builtin/packages/r-genomicalignments/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicalignments/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,18 +13,29 @@ class RGenomicalignments(RPackage):
     detection, and working with the nucleotide content of the alignments."""
 
     homepage = "https://bioconductor.org/packages/GenomicAlignments/"
-    url      = "https://git.bioconductor.org/packages/GenomicAlignments"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomicAlignments.git"
 
-    version('1.12.2', git='https://git.bioconductor.org/packages/GenomicAlignments', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
+    version('1.16.0', commit='db032a459e5cf05a2a5c2059662a541827112974')
+    version('1.14.2', commit='57b0b35d8b36069d4d94af86af051f0129b28eef')
+    version('1.12.2', commit='b5d6f19e4a89b6c1c3e9e58e5ea4eb13870874ef')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-genomeinfodb', type=('build', 'run'))
-    depends_on('r-genomicranges', type=('build', 'run'))
-    depends_on('r-summarizedexperiment', type=('build', 'run'))
-    depends_on('r-biostrings', type=('build', 'run'))
-    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.15.3:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.13.13:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.28:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-iranges@2.5.36:', when='@1.12.2', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', when='@1.14.2', type=('build', 'run'))
+    depends_on('r-iranges@2.13.25:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.11.5:', when='@1.12.2', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.13.1:', when='@1.14.2:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.27.19:', when='@1.12.2', type=('build', 'run'))
+    depends_on('r-genomicranges@1.29.14:', when='@1.14.2', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.19:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-summarizedexperiment@1.5.3:', type=('build', 'run'))
+    depends_on('r-summarizedexperiment@1.9.13:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', when='@1.16.0', type=('build', 'run'))
+    depends_on('r-rsamtools@1.21.4:', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', when='@1.16.0', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.12.2')
+    depends_on('r@3.4.0:3.4.9', when='@1.12.2:1.15.9', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.16.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
index a9e4bf5143..9531e36ccd 100644
--- a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,23 +17,34 @@ class RGenomicfeatures(RPackage):
        desired features in a convenient format."""
 
     homepage = "http://bioconductor.org/packages/GenomicFeatures/"
-    url      = "https://git.bioconductor.org/packages/GenomicFeatures"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomicFeatures.git"
 
-    version('1.28.5', git='https://git.bioconductor.org/packages/GenomicFeatures', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
+    version('1.32.2', commit='8487aedc8be85a99f0c3fc90cd62430b3fec3a03')
+    version('1.28.5', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.29:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.23:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.4:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.17:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-annotationdbi@1.41.4:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-dbi', type=('build', 'run'))
-    depends_on('r-rsqlite', type=('build', 'run'))
+    depends_on('r-rsqlite@2.0:', when='@1.28.5:', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-rtracklayer', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.39.7:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biomart', type=('build', 'run'))
+    depends_on('r-biomart@2.17.1:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.28.5')
+    depends_on('r-biobase@2.15.1:', when='@1.32.2', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.28.5', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.32.2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-genomicranges/package.py b/var/spack/repos/builtin/packages/r-genomicranges/package.py
index bd3f685acd..d362b57909 100644
--- a/var/spack/repos/builtin/packages/r-genomicranges/package.py
+++ b/var/spack/repos/builtin/packages/r-genomicranges/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,14 +19,23 @@ class RGenomicranges(RPackage):
        infrastructure."""
 
     homepage = "https://bioconductor.org/packages/GenomicRanges/"
-    url      = "https://git.bioconductor.org/packages/GenomicRanges"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GenomicRanges.git"
 
-    version('1.28.6', git='https://git.bioconductor.org/packages/GenomicRanges', commit='197472d618f3ed04c795dc6ed435500c29619563')
+    version('1.32.6', commit='31426be0fd6b76f7858971dc45aaf6e6d1dbac4e')
+    version('1.30.3', commit='e99979054bc50ed8c0109bc54563036c1b368997')
+    version('1.28.6', commit='197472d618f3ed04c795dc6ed435500c29619563')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r-iranges', type=('build', 'run'))
-    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.21.2:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.3:', when='@1.32.6', type=('build', 'run'))
+    depends_on('r-s4vectors@0.9.47:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.32:', when='@1.32.6', type=('build', 'run'))
+    depends_on('r-iranges@2.9.11:', when='@1.28.6', type=('build', 'run'))
+    depends_on('r-iranges@2.11.16:', when='@1.30.3', type=('build', 'run'))
+    depends_on('r-iranges@2.14.4:', when='@1.32.6', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.11.5:', when='@1.28.6', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.13.1:', when='@1.30.3', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.2:', when='@1.32.6', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.28.6')
+    depends_on('r-xvector@0.19.8:', when='@1.32.6', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.28.6', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.32.6', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-geomorph/package.py b/var/spack/repos/builtin/packages/r-geomorph/package.py
index 1cb82c9d7e..cb9e3605de 100644
--- a/var/spack/repos/builtin/packages/r-geomorph/package.py
+++ b/var/spack/repos/builtin/packages/r-geomorph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-geoquery/package.py b/var/spack/repos/builtin/packages/r-geoquery/package.py
index fd2c497430..af3629e5ed 100644
--- a/var/spack/repos/builtin/packages/r-geoquery/package.py
+++ b/var/spack/repos/builtin/packages/r-geoquery/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RGeoquery(RPackage):
        GEOquery is the bridge between GEO and BioConductor."""
 
     homepage = "https://bioconductor.org/packages/GEOquery/"
-    url      = "https://git.bioconductor.org/packages/GEOquery"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/GEOquery.git"
 
-    version('2.42.0', git='https://git.bioconductor.org/packages/GEOquery', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb')
+    version('2.42.0', commit='c26adef8d3ddbd6932a3170f2f84f6e4327641fb')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-xml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-geosphere/package.py b/var/spack/repos/builtin/packages/r-geosphere/package.py
index ee93217fb5..f6a3f233a1 100644
--- a/var/spack/repos/builtin/packages/r-geosphere/package.py
+++ b/var/spack/repos/builtin/packages/r-geosphere/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-getopt/package.py b/var/spack/repos/builtin/packages/r-getopt/package.py
new file mode 100644
index 0000000000..a1e1286b6c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-getopt/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGetopt(RPackage):
+    """Package designed to be used with Rscript to write "#!" shebang scripts
+       that accept short and long flags/options. Many users will prefer using
+       instead the packages optparse or argparse which add extra features like
+       automatically generated help option and usage, support for default
+       values, positional argument support, etc."""
+
+    homepage = "https://github.com/trevorld/getopt"
+    url      = "https://cran.r-project.org/src/contrib/getopt_1.20.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/getopt"
+
+    version('1.20.1', '323cf2846e306f49236b8174bc3d4e47')
diff --git a/var/spack/repos/builtin/packages/r-getoptlong/package.py b/var/spack/repos/builtin/packages/r-getoptlong/package.py
index b4c4a8f4e6..61d6cb7977 100644
--- a/var/spack/repos/builtin/packages/r-getoptlong/package.py
+++ b/var/spack/repos/builtin/packages/r-getoptlong/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggally/package.py b/var/spack/repos/builtin/packages/r-ggally/package.py
index f06d8257d3..26dacf1378 100644
--- a/var/spack/repos/builtin/packages/r-ggally/package.py
+++ b/var/spack/repos/builtin/packages/r-ggally/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggbio/package.py b/var/spack/repos/builtin/packages/r-ggbio/package.py
index 8c5f27885a..30ebcf23d8 100644
--- a/var/spack/repos/builtin/packages/r-ggbio/package.py
+++ b/var/spack/repos/builtin/packages/r-ggbio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,10 +18,9 @@ class RGgbio(RPackage):
        and several splicing summaries."""
 
     homepage = "http://bioconductor.org/packages/ggbio/"
-    url      = "https://git.bioconductor.org/packages/ggbio"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ggbio.git"
 
-    version('1.24.1', git='https://git.bioconductor.org/packages/ggbio', commit='ef04c1bca1330f37152bcc21080cbde94849a094')
+    version('1.24.1', commit='ef04c1bca1330f37152bcc21080cbde94849a094')
 
     depends_on('r-gridextra', type=('build', 'run'))
     depends_on('r-scales', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ggdendro/package.py b/var/spack/repos/builtin/packages/r-ggdendro/package.py
index e86180d4ac..d0b0562f39 100644
--- a/var/spack/repos/builtin/packages/r-ggdendro/package.py
+++ b/var/spack/repos/builtin/packages/r-ggdendro/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggjoy/package.py b/var/spack/repos/builtin/packages/r-ggjoy/package.py
new file mode 100644
index 0000000000..aa3ca2477b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggjoy/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGgjoy(RPackage):
+    """Joyplots provide a convenient way of visualizing changes in distributions
+    over time or space."""
+
+    homepage = "https://cran.r-project.org/web/packages/ggjoy/index.html"
+    url      = "https://cran.r-project.org/src/contrib/ggjoy_0.4.0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/ggjoy"
+
+    version('0.4.0', 'c63782e2395a9cfc435d08e078e6596b')
+    version('0.3.0', '59bd34a846270d43f2eeb1e90b03a127')
+    version('0.2.0', '8584cd154e228f8505b324e91d2e50d7')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-ggridges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ggmap/package.py b/var/spack/repos/builtin/packages/r-ggmap/package.py
index a3c16f7a45..4fe5a9e583 100644
--- a/var/spack/repos/builtin/packages/r-ggmap/package.py
+++ b/var/spack/repos/builtin/packages/r-ggmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggplot2/package.py b/var/spack/repos/builtin/packages/r-ggplot2/package.py
index c2c5e49832..0836103e41 100644
--- a/var/spack/repos/builtin/packages/r-ggplot2/package.py
+++ b/var/spack/repos/builtin/packages/r-ggplot2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggpubr/package.py b/var/spack/repos/builtin/packages/r-ggpubr/package.py
index ebc505bf5b..66f10d03f9 100644
--- a/var/spack/repos/builtin/packages/r-ggpubr/package.py
+++ b/var/spack/repos/builtin/packages/r-ggpubr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggrepel/package.py b/var/spack/repos/builtin/packages/r-ggrepel/package.py
index a44a22ee1e..075b081535 100644
--- a/var/spack/repos/builtin/packages/r-ggrepel/package.py
+++ b/var/spack/repos/builtin/packages/r-ggrepel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggridges/package.py b/var/spack/repos/builtin/packages/r-ggridges/package.py
new file mode 100644
index 0000000000..c5f686282d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ggridges/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGgridges(RPackage):
+    """Ridgeline plots provide a convenient way of visualizing changes in
+    distributions over time or space."""
+
+    homepage = "https://cran.r-project.org/web/packages/ggridges/index.html"
+    url      = "https://cran.r-project.org/src/contrib/ggridges_0.4.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/ggridges"
+
+    version('0.4.1', '21d53b3f7263beb17f629f0ebfb7b67a')
+    version('0.4.0', 'da94ed1ee856a7fa5fb87712c84ec4c9')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-ggplot2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ggsci/package.py b/var/spack/repos/builtin/packages/r-ggsci/package.py
index 1fedf202ee..2cec0a6496 100644
--- a/var/spack/repos/builtin/packages/r-ggsci/package.py
+++ b/var/spack/repos/builtin/packages/r-ggsci/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ggvis/package.py b/var/spack/repos/builtin/packages/r-ggvis/package.py
index c0dab6b8e4..6c2dffcc42 100644
--- a/var/spack/repos/builtin/packages/r-ggvis/package.py
+++ b/var/spack/repos/builtin/packages/r-ggvis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gistr/package.py b/var/spack/repos/builtin/packages/r-gistr/package.py
index 7cbe2ecafe..500d9cb0de 100644
--- a/var/spack/repos/builtin/packages/r-gistr/package.py
+++ b/var/spack/repos/builtin/packages/r-gistr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-git2r/package.py b/var/spack/repos/builtin/packages/r-git2r/package.py
index 3fa8baab7c..ad9545b6a2 100644
--- a/var/spack/repos/builtin/packages/r-git2r/package.py
+++ b/var/spack/repos/builtin/packages/r-git2r/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-glimma/package.py b/var/spack/repos/builtin/packages/r-glimma/package.py
new file mode 100644
index 0000000000..5fe40e6594
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-glimma/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGlimma(RPackage):
+    """This package generates interactive visualisations for analysis of
+       RNA-sequencing data using output from limma, edgeR or DESeq2 packages
+       in an HTML page. The interactions are built on top of the popular
+       static representations of analysis results in order to provide
+       additional information."""
+
+    homepage = "https://bioconductor.org/packages/release/bioc/html/Glimma.html"
+    git      = "https://git.bioconductor.org/packages/Glimma.git"
+
+    version('1.8.2', commit='f4aa1f05c2890d04b01ad4c0ab27f2f729f2c969')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.8.2:', type=('build', 'run'))
+    depends_on('r-edger', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-glmnet/package.py b/var/spack/repos/builtin/packages/r-glmnet/package.py
index 4e531165be..7f79e5f023 100644
--- a/var/spack/repos/builtin/packages/r-glmnet/package.py
+++ b/var/spack/repos/builtin/packages/r-glmnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-globaloptions/package.py b/var/spack/repos/builtin/packages/r-globaloptions/package.py
index 7785d4f3a1..3aef7c1f65 100644
--- a/var/spack/repos/builtin/packages/r-globaloptions/package.py
+++ b/var/spack/repos/builtin/packages/r-globaloptions/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-glue/package.py b/var/spack/repos/builtin/packages/r-glue/package.py
new file mode 100644
index 0000000000..bfd92fcdbd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-glue/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGlue(RPackage):
+    """An implementation of interpreted string literals, inspired by Python's
+       Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/>
+       and Docstrings <https://www.python.org/dev/peps/pep-0257/> and Julia's
+       Triple-Quoted String Literals <https://docs.julialang.org/en/stable/
+       manual/strings/#triple-quoted-string-literals>."""
+
+    homepage = "https://github.com/tidyverse/glue"
+    url      = "https://cran.r-project.org/src/contrib/glue_1.2.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/glue"
+
+    version('1.2.0', '77d06b6d86abc882fa1c0599e457c5e2')
diff --git a/var/spack/repos/builtin/packages/r-gmodels/package.py b/var/spack/repos/builtin/packages/r-gmodels/package.py
index ce4a8c9692..a9fd5541c0 100644
--- a/var/spack/repos/builtin/packages/r-gmodels/package.py
+++ b/var/spack/repos/builtin/packages/r-gmodels/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gmp/package.py b/var/spack/repos/builtin/packages/r-gmp/package.py
index 18e394f1ac..6aaa8d683c 100644
--- a/var/spack/repos/builtin/packages/r-gmp/package.py
+++ b/var/spack/repos/builtin/packages/r-gmp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-go-db/package.py b/var/spack/repos/builtin/packages/r-go-db/package.py
index af5df1ce3b..61cd6d35dc 100644
--- a/var/spack/repos/builtin/packages/r-go-db/package.py
+++ b/var/spack/repos/builtin/packages/r-go-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-googlevis/package.py b/var/spack/repos/builtin/packages/r-googlevis/package.py
index 4d7cfbd259..ac12962998 100644
--- a/var/spack/repos/builtin/packages/r-googlevis/package.py
+++ b/var/spack/repos/builtin/packages/r-googlevis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-goplot/package.py b/var/spack/repos/builtin/packages/r-goplot/package.py
new file mode 100644
index 0000000000..f9b86de5bd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-goplot/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack import *
+
+
+class RGoplot(RPackage):
+    """Implementation of multilayered visualizations for enhanced graphical
+       representation of functional analysis data. It combines and integrates
+       omics data derived from expression and functional annotation enrichment
+       analyses. Its plotting functions have been developed with an
+       hierarchical structure in mind: starting from a general overview to
+       identify the most enriched categories (modified bar plot, bubble plot)
+       to a more detailed one displaying different types of relevant
+       information for the molecules in a given set of categories
+       (circle plot, chord plot, cluster plot, Venn diagram, heatmap)."""
+
+    homepage = "https://github.com/wencke/wencke.github.io/issues"
+    url      = "https://cran.r-project.org/src/contrib/GOplot_1.0.2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/GOplot"
+
+    version('1.0.2', sha256='3ddaa2b6d1297ad6daad30d18af708adf43d86e8804b1b92fa29dfbf26d80df9')
+
+    depends_on('r@3.2.3:', type=('build', 'run'))
+    depends_on('r-ggplot2@2.0.0:', type=('build', 'run'))
+    depends_on('r-ggdendro@0.1-17:', type=('build', 'run'))
+    depends_on('r-gridextra@2.0.0:', type=('build', 'run'))
+    depends_on('r-rcolorbrewer@1.1-2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gosemsim/package.py b/var/spack/repos/builtin/packages/r-gosemsim/package.py
new file mode 100644
index 0000000000..b425445b0c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gosemsim/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGosemsim(RPackage):
+    """The semantic comparisons of Gene Ontology (GO) annotations provide
+    quantitative ways to compute similarities between genes and gene
+    groups, and have became important basis for many bioinformatics
+    analysis approaches. GOSemSim is an R package for semantic similarity
+    computation among GO terms, sets of GO terms, gene products and gene
+    clusters. GOSemSim implemented five methods proposed by Resnik,
+    Schlicker, Jiang, Lin and Wang respectively."""
+
+    homepage = "https://www.bioconductor.org/packages/GOSemSim/"
+    git      = "https://git.bioconductor.org/packages/GOSemSim.git"
+
+    version('2.2.0', commit='247434790e6c8cf99e5643f569390362b8c87c52')
+
+    depends_on('r@3.4.0:3.4.9', when='@2.2.0')
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-go-db', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-goseq/package.py b/var/spack/repos/builtin/packages/r-goseq/package.py
new file mode 100644
index 0000000000..5801169f1f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-goseq/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGoseq(RPackage):
+    """Detects Gene Ontology and/or other user defined categories which are
+       over/under represented in RNA-seq data"""
+
+    homepage = "https://bioconductor.org/packages/release/bioc/html/goseq.html"
+    git      = "https://git.bioconductor.org/packages/goseq.git"
+
+    version('1.32.0', commit='32fcbe647eea17d7d0d7a262610811502c421d36')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.32.0:', type=('build', 'run'))
+    depends_on('r-biasedurn', type=('build', 'run'))
+    depends_on('r-genelendatabase@1.9.2:', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-go-db', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gostats/package.py b/var/spack/repos/builtin/packages/r-gostats/package.py
index ef4231fc7d..36ca8a63d0 100644
--- a/var/spack/repos/builtin/packages/r-gostats/package.py
+++ b/var/spack/repos/builtin/packages/r-gostats/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class RGostats(RPackage):
     testing and other simple calculations."""
 
     homepage = "https://www.bioconductor.org/packages/GOstats/"
-    url      = "https://git.bioconductor.org/packages/GOstats"
+    git      = "https://git.bioconductor.org/packages/GOstats.git"
 
-    version('2.42.0', git='https://git.bioconductor.org/packages/GOstats', commit='8b29709064a3b66cf1d963b2be0c996fb48c873e')
+    version('2.42.0', commit='8b29709064a3b66cf1d963b2be0c996fb48c873e')
 
     depends_on('r@3.4.1:3.4.9', when='@2.42.0')
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gplots/package.py b/var/spack/repos/builtin/packages/r-gplots/package.py
index 21c3738caa..ff81686ba3 100644
--- a/var/spack/repos/builtin/packages/r-gplots/package.py
+++ b/var/spack/repos/builtin/packages/r-gplots/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 #
 from spack import *
diff --git a/var/spack/repos/builtin/packages/r-graph/package.py b/var/spack/repos/builtin/packages/r-graph/package.py
index a7b6140de8..88760e05bc 100644
--- a/var/spack/repos/builtin/packages/r-graph/package.py
+++ b/var/spack/repos/builtin/packages/r-graph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RGraph(RPackage):
     """A package that implements some simple graph handling capabilities."""
 
     homepage = "https://www.bioconductor.org/packages/graph/"
-    url      = "https://git.bioconductor.org/packages/graph"
+    git      = "https://git.bioconductor.org/packages/graph.git"
 
-    version('1.54.0', git='https://git.bioconductor.org/packages/graph', commit='2a8b08520096241620421078fc1098f4569c7301')
+    version('1.54.0', commit='2a8b08520096241620421078fc1098f4569c7301')
 
     depends_on('r@3.4.0:3.4.9', when='@1.54.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gridbase/package.py b/var/spack/repos/builtin/packages/r-gridbase/package.py
index 4353f16819..ed8e0b0267 100644
--- a/var/spack/repos/builtin/packages/r-gridbase/package.py
+++ b/var/spack/repos/builtin/packages/r-gridbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gridextra/package.py b/var/spack/repos/builtin/packages/r-gridextra/package.py
index 2b64580c4e..27c66a10ba 100644
--- a/var/spack/repos/builtin/packages/r-gridextra/package.py
+++ b/var/spack/repos/builtin/packages/r-gridextra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gseabase/package.py b/var/spack/repos/builtin/packages/r-gseabase/package.py
index b02b16289b..6dbe982b5d 100644
--- a/var/spack/repos/builtin/packages/r-gseabase/package.py
+++ b/var/spack/repos/builtin/packages/r-gseabase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RGseabase(RPackage):
     Set Enrichment Analysis (GSEA)."""
 
     homepage = "https://www.bioconductor.org/packages/GSEABase/"
-    url      = "https://git.bioconductor.org/packages/GSEABase"
+    git      = "https://git.bioconductor.org/packages/GSEABase.git"
 
-    version('1.38.2', git='https://git.bioconductor.org/packages/GSEABase', commit='84c9f10c316163118ca990900a7a67555b96e75b')
+    version('1.38.2', commit='84c9f10c316163118ca990900a7a67555b96e75b')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.2')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gss/package.py b/var/spack/repos/builtin/packages/r-gss/package.py
new file mode 100644
index 0000000000..9d65dd1d32
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-gss/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RGss(RPackage):
+    """A comprehensive package for structural multivariate function
+    estimation using smoothing splines."""
+
+    homepage = "https://cran.r-project.org/package=gss"
+    url      = "https://cran.rstudio.com/src/contrib/gss_2.1-7.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/gss"
+
+    version('2.1-7', '4a6bd96339d22b40c932895b64504fb2')
diff --git a/var/spack/repos/builtin/packages/r-gsubfn/package.py b/var/spack/repos/builtin/packages/r-gsubfn/package.py
index 858f7f2e39..ffe55f94a7 100644
--- a/var/spack/repos/builtin/packages/r-gsubfn/package.py
+++ b/var/spack/repos/builtin/packages/r-gsubfn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gtable/package.py b/var/spack/repos/builtin/packages/r-gtable/package.py
index 498e5ba2c3..e3400d641b 100644
--- a/var/spack/repos/builtin/packages/r-gtable/package.py
+++ b/var/spack/repos/builtin/packages/r-gtable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gtools/package.py b/var/spack/repos/builtin/packages/r-gtools/package.py
index 0c74d8449a..e42aae0220 100644
--- a/var/spack/repos/builtin/packages/r-gtools/package.py
+++ b/var/spack/repos/builtin/packages/r-gtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-gtrellis/package.py b/var/spack/repos/builtin/packages/r-gtrellis/package.py
index 64526035db..a1558c9cbd 100644
--- a/var/spack/repos/builtin/packages/r-gtrellis/package.py
+++ b/var/spack/repos/builtin/packages/r-gtrellis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,9 @@ class RGtrellis(RPackage):
        graphics in the plot."""
 
     homepage = "https://bioconductor.org/packages/gtrellis/"
-    url      = "https://git.bioconductor.org/packages/gtrellis"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/gtrellis.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/gtrellis', commit='f813b420a008c459f63a2a13e5e64c5507c4c472')
+    version('1.8.0', commit='f813b420a008c459f63a2a13e5e64c5507c4c472')
 
     depends_on('r-iranges', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-gviz/package.py b/var/spack/repos/builtin/packages/r-gviz/package.py
index ddb56cc681..23b886a34b 100644
--- a/var/spack/repos/builtin/packages/r-gviz/package.py
+++ b/var/spack/repos/builtin/packages/r-gviz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,9 +16,9 @@ class RGviz(RPackage):
     together with your data."""
 
     homepage = "http://bioconductor.org/packages/Gviz/"
-    url      = "https://git.bioconductor.org/packages/Gviz"
+    git      = "https://git.bioconductor.org/packages/Gviz.git"
 
-    version('1.20.0', git='https://git.bioconductor.org/packages/Gviz', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c')
+    version('1.20.0', commit='299b8255e1b03932cebe287c3690d58c88f5ba5c')
 
     depends_on('r@3.4.0:3.4.9', when='@1.20.0')
     depends_on('r-s4vectors', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-haven/package.py b/var/spack/repos/builtin/packages/r-haven/package.py
new file mode 100644
index 0000000000..dab9e486b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-haven/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RHaven(RPackage):
+    """Import foreign statistical formats into R via the embedded 'ReadStat' C
+       library, <https://github.com/WizardMac/ReadStat>."""
+
+    homepage = "http://haven.tidyverse.org/"
+    url      = "https://cran.r-project.org/src/contrib/haven_1.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/haven"
+
+    version('1.1.0', '8edd4b7683f8c36b5bb68582ac1b8733')
+
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-readr', type=('build', 'run'))
+    depends_on('r-hms', type=('build', 'run'))
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-forcats', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-hexbin/package.py b/var/spack/repos/builtin/packages/r-hexbin/package.py
index 179914fca3..8f71d729d4 100644
--- a/var/spack/repos/builtin/packages/r-hexbin/package.py
+++ b/var/spack/repos/builtin/packages/r-hexbin/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-highr/package.py b/var/spack/repos/builtin/packages/r-highr/package.py
index cc89cfd80b..fe8606ca59 100644
--- a/var/spack/repos/builtin/packages/r-highr/package.py
+++ b/var/spack/repos/builtin/packages/r-highr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-hmisc/package.py b/var/spack/repos/builtin/packages/r-hmisc/package.py
index 436c3279ec..11cc890764 100644
--- a/var/spack/repos/builtin/packages/r-hmisc/package.py
+++ b/var/spack/repos/builtin/packages/r-hmisc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,10 @@ class RHmisc(RPackage):
     code, and recoding variables."""
 
     homepage = "http://biostat.mc.vanderbilt.edu/Hmisc"
-    url      = "https://cran.rstudio.com/src/contrib/Hmisc_4.0-3.tar.gz"
+    url      = "https://cran.rstudio.com/src/contrib/Hmisc_4.1-1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/Hmisc"
 
+    version('4.1-1', 'd255611f2b108d3cc0212b8a98fef6e3')
     version('4.0-3', '7091924db1e473419d8116c3335f82da')
 
     depends_on('r-lattice', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-hms/package.py b/var/spack/repos/builtin/packages/r-hms/package.py
index cf3a4a88c3..caf95888d5 100644
--- a/var/spack/repos/builtin/packages/r-hms/package.py
+++ b/var/spack/repos/builtin/packages/r-hms/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-htmltable/package.py b/var/spack/repos/builtin/packages/r-htmltable/package.py
index f142a5221a..d2b832d151 100644
--- a/var/spack/repos/builtin/packages/r-htmltable/package.py
+++ b/var/spack/repos/builtin/packages/r-htmltable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,13 +16,15 @@ class RHtmltable(RPackage):
     compatible with HTML/'LaTeX'."""
 
     homepage = "https://CRAN.R-project.org/package=htmlTable"
-    url      = "https://cran.rstudio.com/src/contrib/htmlTable_1.9.tar.gz"
+    url      = "https://cran.rstudio.com/src/contrib/htmlTable_1.11.2.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/htmlTable"
 
+    version('1.11.2', '473e6d486e7714f8dd7f16a31480c896')
     version('1.9', '08c62c19e1ffe570e7d8fa57db5094b9')
 
     depends_on('r-stringr', type=('build', 'run'))
-    depends_on('r-knitr', type=('build', 'run'))
-    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-knitr@1.6:', type=('build', 'run'))
+    depends_on('r-magrittr@1.5:', type=('build', 'run'))
     depends_on('r-checkmate', type=('build', 'run'))
     depends_on('r-htmlwidgets', type=('build', 'run'))
+    depends_on('r-rstudioapi@0.6:', type=('build', 'run'), when="@1.11.0:")
diff --git a/var/spack/repos/builtin/packages/r-htmltools/package.py b/var/spack/repos/builtin/packages/r-htmltools/package.py
index 865c2f79ae..4bedff2115 100644
--- a/var/spack/repos/builtin/packages/r-htmltools/package.py
+++ b/var/spack/repos/builtin/packages/r-htmltools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py
index 1dcbbe5062..4416678974 100644
--- a/var/spack/repos/builtin/packages/r-htmlwidgets/package.py
+++ b/var/spack/repos/builtin/packages/r-htmlwidgets/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-httpuv/package.py b/var/spack/repos/builtin/packages/r-httpuv/package.py
index 59ba283621..ac2967c491 100644
--- a/var/spack/repos/builtin/packages/r-httpuv/package.py
+++ b/var/spack/repos/builtin/packages/r-httpuv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-httr/package.py b/var/spack/repos/builtin/packages/r-httr/package.py
index a533f6cbd9..f3f5426fdd 100644
--- a/var/spack/repos/builtin/packages/r-httr/package.py
+++ b/var/spack/repos/builtin/packages/r-httr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-hwriter/package.py b/var/spack/repos/builtin/packages/r-hwriter/package.py
index df8a2129db..348dec8b56 100644
--- a/var/spack/repos/builtin/packages/r-hwriter/package.py
+++ b/var/spack/repos/builtin/packages/r-hwriter/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-hypergraph/package.py b/var/spack/repos/builtin/packages/r-hypergraph/package.py
index b6fc0df172..8da1131197 100644
--- a/var/spack/repos/builtin/packages/r-hypergraph/package.py
+++ b/var/spack/repos/builtin/packages/r-hypergraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RHypergraph(RPackage):
     representing and manipulating hypergraphs."""
 
     homepage = "https://www.bioconductor.org/packages/hypergraph/"
-    url      = "https://git.bioconductor.org/packages/hypergraph"
+    git      = "https://git.bioconductor.org/packages/hypergraph.git"
 
-    version('1.48.0', git='https://git.bioconductor.org/packages/hypergraph', commit='a4c19ea0b5f15204f706a7bfdea5363706382820')
+    version('1.48.0', commit='a4c19ea0b5f15204f706a7bfdea5363706382820')
 
     depends_on('r@3.4.0:3.4.9', when='@1.48.0')
     depends_on('r-graph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ica/package.py b/var/spack/repos/builtin/packages/r-ica/package.py
new file mode 100644
index 0000000000..10e46c971e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ica/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RIca(RPackage):
+    """Independent Component Analysis (ICA) using various algorithms: FastICA,
+    Information-Maximization (Infomax), and Joint Approximate Diagonalization
+    of Eigenmatrices (JADE)."""
+
+    homepage = "https://cran.r-project.org/web/packages/ica/index.html"
+    url      = "https://cran.r-project.org/src/contrib/ica_1.0-1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/ica"
+
+    depends_on('r@3.4.0:3.4.9')
+    version('1.0-1', '15c8d5afeec2804beec55dd14abc585d')
+    version('1.0-0', '3ade2b3b00eb39c348d802f24d2afd1d')
diff --git a/var/spack/repos/builtin/packages/r-igraph/package.py b/var/spack/repos/builtin/packages/r-igraph/package.py
index b8a715b9ae..9d14815389 100644
--- a/var/spack/repos/builtin/packages/r-igraph/package.py
+++ b/var/spack/repos/builtin/packages/r-igraph/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,11 +15,12 @@ class RIgraph(RPackage):
     url      = "https://cran.r-project.org/src/contrib/igraph_1.0.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/igraph"
 
+    version('1.1.2', 'ca1617aea272852d2856c4661ad1c7d8')
     version('1.0.1', 'ea33495e49adf4a331e4ba60ba559065')
 
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-magrittr', type=('build', 'run'))
-    depends_on('r-nmf', type=('build', 'run'))
+    depends_on('r-pkgconfig', type=('build', 'run'))
     depends_on('r-irlba', type=('build', 'run'))
     depends_on('gmp')
     depends_on('libxml2')
diff --git a/var/spack/repos/builtin/packages/r-illuminaio/package.py b/var/spack/repos/builtin/packages/r-illuminaio/package.py
index 9d0993fb8f..8e578421c6 100644
--- a/var/spack/repos/builtin/packages/r-illuminaio/package.py
+++ b/var/spack/repos/builtin/packages/r-illuminaio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class RIlluminaio(RPackage):
        IDAT."""
 
     homepage = "http://bioconductor.org/packages/illuminaio/"
-    url      = "https://git.bioconductor.org/packages/illuminaio"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/illuminaio.git"
 
-    version('0.18.0', git='https://git.bioconductor.org/packages/illuminaio', commit='e6b8ab1f8eacb760aebdb4828e9cfbf07da06eda')
+    version('0.18.0', commit='e6b8ab1f8eacb760aebdb4828e9cfbf07da06eda')
 
     depends_on('r-base64', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@0.18.0')
diff --git a/var/spack/repos/builtin/packages/r-impute/package.py b/var/spack/repos/builtin/packages/r-impute/package.py
index b8bf956ac1..76cfb9be9b 100644
--- a/var/spack/repos/builtin/packages/r-impute/package.py
+++ b/var/spack/repos/builtin/packages/r-impute/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,8 @@ class RImpute(RPackage):
     """Imputation for microarray data (currently KNN only)."""
 
     homepage = "https://www.bioconductor.org/packages/impute/"
-    url      = "https://git.bioconductor.org/packages/impute"
+    git      = "https://git.bioconductor.org/packages/impute.git"
 
-    version('1.50.1', git='https://git.bioconductor.org/packages/impute', commit='31d1cc141797afdc83743e1d95aab8a90ee19b71')
+    version('1.50.1', commit='31d1cc141797afdc83743e1d95aab8a90ee19b71')
 
     depends_on('r@3.4.0:3.4.9', when='@1.50.1')
diff --git a/var/spack/repos/builtin/packages/r-influencer/package.py b/var/spack/repos/builtin/packages/r-influencer/package.py
index 53f1ba67a7..ded5558e98 100644
--- a/var/spack/repos/builtin/packages/r-influencer/package.py
+++ b/var/spack/repos/builtin/packages/r-influencer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-inline/package.py b/var/spack/repos/builtin/packages/r-inline/package.py
index 235aacfe19..54e32607b3 100644
--- a/var/spack/repos/builtin/packages/r-inline/package.py
+++ b/var/spack/repos/builtin/packages/r-inline/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
index 8b64962096..8a5a6a038d 100644
--- a/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
+++ b/var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class RInteractivedisplaybase(RPackage):
        Bioconductor objects."""
 
     homepage = "https://bioconductor.org/packages/interactiveDisplayBase/"
-    url      = "https://git.bioconductor.org/packages/interactiveDisplayBase"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/interactiveDisplayBase.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/interactiveDisplayBase', commit='e2ccc7eefdd904e3b1032dc6b3f4a28d08c1cd40')
+    version('1.14.0', commit='e2ccc7eefdd904e3b1032dc6b3f4a28d08c1cd40')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-shiny', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ipred/package.py b/var/spack/repos/builtin/packages/r-ipred/package.py
index 97d84f5361..825046560f 100644
--- a/var/spack/repos/builtin/packages/r-ipred/package.py
+++ b/var/spack/repos/builtin/packages/r-ipred/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-iranges/package.py b/var/spack/repos/builtin/packages/r-iranges/package.py
index c53b2773a7..5a79d0973b 100644
--- a/var/spack/repos/builtin/packages/r-iranges/package.py
+++ b/var/spack/repos/builtin/packages/r-iranges/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,10 +19,17 @@ class RIranges(RPackage):
     i.e., collections of atomic vectors and DataFrames."""
 
     homepage = "https://www.bioconductor.org/packages/IRanges/"
-    url      = "https://git.bioconductor.org/packages/IRanges"
-    list_url = homepage
-    version('2.10.5', git='https://git.bioconductor.org/packages/IRanges', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614')
+    git      = "https://git.bioconductor.org/packages/IRanges.git"
+
+    version('2.14.10', commit='c76118a38e84c7c764141adbd66ee350d0882bc9')
+    version('2.12.0', commit='1b1748655a8529ba87ad0f223f035ef0c08e7fcd')
+    version('2.10.5', commit='b00d1d5025e3c480d17c13100f0da5a0132b1614')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r-s4vectors', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@2.10.5')
+    depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@2.10.5')
+    depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@2.12.0')
+    depends_on('r-biocgenerics@0.25.3:', type=('build', 'run'), when='@2.14.10')
+    depends_on('r-s4vectors@0.13.17:', type=('build', 'run'), when='@2.10.5')
+    depends_on('r-s4vectors@0.15.5:', type=('build', 'run'), when='@2.12.0')
+    depends_on('r-s4vectors@0.18.2:', type=('build', 'run'), when='@2.14.10')
+    depends_on('r@3.4.0:3.4.9', when='@2.10.5', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.14.10', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-irdisplay/package.py b/var/spack/repos/builtin/packages/r-irdisplay/package.py
index 1edbf40c1a..293c0bc7c0 100644
--- a/var/spack/repos/builtin/packages/r-irdisplay/package.py
+++ b/var/spack/repos/builtin/packages/r-irdisplay/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-irkernel/package.py b/var/spack/repos/builtin/packages/r-irkernel/package.py
index 62daf2e0ca..2ab4c2d01e 100644
--- a/var/spack/repos/builtin/packages/r-irkernel/package.py
+++ b/var/spack/repos/builtin/packages/r-irkernel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,10 +11,9 @@ class RIrkernel(RPackage):
     """R kernel for Jupyter"""
 
     homepage = "https://irkernel.github.io/"
+    git      = "https://github.com/IRkernel/IRkernel.git"
 
-    # Git repository
-    version('master', git='https://github.com/IRkernel/IRkernel.git',
-        tag='0.7')
+    version('master', tag='0.7')
 
     depends_on('r-repr', type=('build', 'run'))
     depends_on('r-irdisplay', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-irlba/package.py b/var/spack/repos/builtin/packages/r-irlba/package.py
index 21e3df5e9f..3062b2411d 100644
--- a/var/spack/repos/builtin/packages/r-irlba/package.py
+++ b/var/spack/repos/builtin/packages/r-irlba/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-iso/package.py b/var/spack/repos/builtin/packages/r-iso/package.py
index f4be39ee6e..bf9e428eb3 100644
--- a/var/spack/repos/builtin/packages/r-iso/package.py
+++ b/var/spack/repos/builtin/packages/r-iso/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-iterators/package.py b/var/spack/repos/builtin/packages/r-iterators/package.py
index 1e864864e3..3b337cfa29 100644
--- a/var/spack/repos/builtin/packages/r-iterators/package.py
+++ b/var/spack/repos/builtin/packages/r-iterators/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-janitor/package.py b/var/spack/repos/builtin/packages/r-janitor/package.py
new file mode 100644
index 0000000000..eeb66b3c41
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-janitor/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RJanitor(RPackage):
+    """The main janitor functions can: perfectly format data.frame column
+       names; provide quick one- and two-variable tabulations (i.e., frequency
+       tables and crosstabs); and isolate duplicate records. Other janitor
+       functions nicely format the tabulation results. These
+       tabulate-and-report functions approximate popular features of SPSS and
+       Microsoft Excel. This package follows the principles of the "tidyverse"
+       and works well with the pipe function %>%. janitor was built with
+       beginning-to-intermediate R users in mind and is optimized for
+       user-friendliness. Advanced R users can already do everything covered
+       here, but with janitor they can do it faster and save their thinking
+       for the fun stuff."""
+
+    homepage = "https://github.com/sfirke/janitor"
+    url      = "https://cran.r-project.org/src/contrib/janitor_0.3.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/janitor"
+
+    version('0.3.0', '76036c54693b91aef19d468107ae066a')
+
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-jaspar2018/package.py b/var/spack/repos/builtin/packages/r-jaspar2018/package.py
new file mode 100644
index 0000000000..a2bd68de81
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-jaspar2018/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RJaspar2018(RPackage):
+    """Data package for JASPAR 2018. To search this databases,
+    please use the package TFBSTools (>= 1.15.6)."""
+
+    homepage = "http://jaspar.genereg.net/"
+    git      = "https://git.bioconductor.org/packages/JASPAR2018.git"
+
+    version('1.0.0', commit='4c84092b3737bb1c57ab56f4321f2f5e4b0efeaa')
+
+    depends_on('r@3.4.0:')
diff --git a/var/spack/repos/builtin/packages/r-jomo/package.py b/var/spack/repos/builtin/packages/r-jomo/package.py
new file mode 100644
index 0000000000..adc88c4ed5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-jomo/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RJomo(RPackage):
+    """Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel
+    joint modelling multiple imputation (Carpenter and Kenward, 2013)
+    <doi:10.1002/9781119942283>. Novel aspects of 'jomo' are the possibility of
+    handling binary and categorical data through latent normal variables, the
+    option to use cluster-specific covariance matrices and to impute compatibly
+    with the substantive model.
+    """
+
+    homepage = "https://cran.r-project.org/package=jomo"
+    url      = "https://cran.r-project.org/src/contrib/jomo_2.6-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/jomo"
+
+    version('2.6-2', 'eff4a6c1a971708959d65b3224c98a25')
+
+    depends_on('r-lme4', type=('build', 'run'))
+    depends_on('r-survival', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-jpeg/package.py b/var/spack/repos/builtin/packages/r-jpeg/package.py
index 5a11610fc9..e8c379ce8d 100644
--- a/var/spack/repos/builtin/packages/r-jpeg/package.py
+++ b/var/spack/repos/builtin/packages/r-jpeg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py
index 13f3bcd0e2..2403ec762a 100644
--- a/var/spack/repos/builtin/packages/r-jsonlite/package.py
+++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-kegg-db/package.py b/var/spack/repos/builtin/packages/r-kegg-db/package.py
index e205b1d42a..db4f1ff9e7 100644
--- a/var/spack/repos/builtin/packages/r-kegg-db/package.py
+++ b/var/spack/repos/builtin/packages/r-kegg-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-kegggraph/package.py b/var/spack/repos/builtin/packages/r-kegggraph/package.py
new file mode 100644
index 0000000000..424ceca845
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-kegggraph/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RKegggraph(RPackage):
+    """KEGGGraph is an interface between KEGG pathway and graph object as
+    well as a collection of tools to analyze, dissect and visualize these
+    graphs. It parses the regularly updated KGML (KEGG XML) files into graph
+    models maintaining all essential pathway attributes. The package offers
+    functionalities including parsing, graph operation, visualization and
+    etc."""
+
+    homepage = "https://www.bioconductor.org/packages/KEGGgraph/"
+    git      = "https://git.bioconductor.org/packages/KEGGgraph.git"
+
+    version('1.38.1', commit='dd31665beb36d5aad8ed09ed56c603633b6b2292')
+
+    depends_on('r-graph', type=('build', 'run'))
+    depends_on('r-xml', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.38.1')
diff --git a/var/spack/repos/builtin/packages/r-keggrest/package.py b/var/spack/repos/builtin/packages/r-keggrest/package.py
index b9a6e6a291..d19446e9a2 100644
--- a/var/spack/repos/builtin/packages/r-keggrest/package.py
+++ b/var/spack/repos/builtin/packages/r-keggrest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,11 +15,13 @@ class RKeggrest(RPackage):
        catalogue) are provided."""
 
     homepage = "http://bioconductor.org/packages/KEGGREST"
-    url      = "https://git.bioconductor.org/packages/KEGGREST"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/KEGGREST.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/KEGGREST', commit='ed48de0def57a909894e237fa4731c4a052d8849')
+    version('1.18.1', commit='f6e6f1987e4db9d977a75609fab0cb710be2e2e4')
+    version('1.2.0',  commit='ed48de0def57a909894e237fa4731c4a052d8849')
 
     depends_on('r-httr', type=('build', 'run'))
     depends_on('r-png', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.2.0')
+    depends_on('r@3.4.3:3.4.9', when='@1.18.1')
diff --git a/var/spack/repos/builtin/packages/r-kernlab/package.py b/var/spack/repos/builtin/packages/r-kernlab/package.py
index 9ff25832be..a2191441b0 100644
--- a/var/spack/repos/builtin/packages/r-kernlab/package.py
+++ b/var/spack/repos/builtin/packages/r-kernlab/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-kernsmooth/package.py b/var/spack/repos/builtin/packages/r-kernsmooth/package.py
index e6fd8512c2..c1ad34ec21 100644
--- a/var/spack/repos/builtin/packages/r-kernsmooth/package.py
+++ b/var/spack/repos/builtin/packages/r-kernsmooth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-kknn/package.py b/var/spack/repos/builtin/packages/r-kknn/package.py
index 86d67fb4d4..8d07faf285 100644
--- a/var/spack/repos/builtin/packages/r-kknn/package.py
+++ b/var/spack/repos/builtin/packages/r-kknn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-knitr/package.py b/var/spack/repos/builtin/packages/r-knitr/package.py
index 1e0e51a3f1..8b92234ce0 100644
--- a/var/spack/repos/builtin/packages/r-knitr/package.py
+++ b/var/spack/repos/builtin/packages/r-knitr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-ks/package.py b/var/spack/repos/builtin/packages/r-ks/package.py
new file mode 100644
index 0000000000..dca118bdf5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ks/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RKs(RPackage):
+    """Kernel smoothers for univariate and multivariate data."""
+
+    homepage = "https://cran.r-project.org/package=ks"
+    url      = "https://cran.r-project.org/src/contrib/Archive/ks/ks_1.11.2.tar.gz"
+
+    version('1.11.2', sha256='9dfd485096e1e67abc7dfcb7b76a83de110dd15bcfeffe5c899605b3a5592961')
+
+    depends_on('r@2.10:', type=('build', 'run'))
+
+    depends_on('r-fnn@1.1:', type=('build', 'run'))
+    depends_on('r-kernlab', type=('build', 'run'))
+    depends_on('r-mclust', type=('build', 'run'))
+    depends_on('r-multicool', type=('build', 'run'))
+    depends_on('r-mvtnorm@1.0:', type=('build', 'run'))
+    depends_on('r-kernsmooth@2.22:', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-labeling/package.py b/var/spack/repos/builtin/packages/r-labeling/package.py
index 02790fe88d..49c8c640dc 100644
--- a/var/spack/repos/builtin/packages/r-labeling/package.py
+++ b/var/spack/repos/builtin/packages/r-labeling/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lambda-r/package.py b/var/spack/repos/builtin/packages/r-lambda-r/package.py
index 914826af97..d6a2b56c1e 100644
--- a/var/spack/repos/builtin/packages/r-lambda-r/package.py
+++ b/var/spack/repos/builtin/packages/r-lambda-r/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,5 +13,6 @@ class RLambdaR(RPackage):
 
     homepage = "https://cran.rstudio.com/web/packages/lambda.r/index.html"
     url      = "https://cran.rstudio.com/src/contrib/lambda.r_1.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/lambda.r"
 
     version('1.2', 'bda49898b85ad5902880a31f43b432e2')
diff --git a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py
index 3af2665c3e..e255cb1e49 100644
--- a/var/spack/repos/builtin/packages/r-laplacesdemon/package.py
+++ b/var/spack/repos/builtin/packages/r-laplacesdemon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lars/package.py b/var/spack/repos/builtin/packages/r-lars/package.py
new file mode 100644
index 0000000000..8788aa715f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lars/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RLars(RPackage):
+    """Efficient procedures for fitting an entire lasso sequence with the cost
+    of a single least squares fit."""
+
+    homepage = "https://cran.r-project.org/web/packages/lars/index.html"
+    url      = "https://cran.r-project.org/src/contrib/lars_1.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/lars"
+
+    version('1.2',   '2571bae325f6cba1ad0202ea61695b8c')
+    version('1.1',   'e94f6902aade09b13ec25ba2381384e5')
+    version('0.9-8', 'e6f9fffab2d83898f6d3d811f04d177f')
+
+    depends_on('r@2.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-lattice/package.py b/var/spack/repos/builtin/packages/r-lattice/package.py
index 170e99aa9d..80450bee59 100644
--- a/var/spack/repos/builtin/packages/r-lattice/package.py
+++ b/var/spack/repos/builtin/packages/r-lattice/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-latticeextra/package.py b/var/spack/repos/builtin/packages/r-latticeextra/package.py
index 86c9d93ed7..a337e26ed5 100644
--- a/var/spack/repos/builtin/packages/r-latticeextra/package.py
+++ b/var/spack/repos/builtin/packages/r-latticeextra/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lava/package.py b/var/spack/repos/builtin/packages/r-lava/package.py
index ae4218e1db..deb37f9da7 100644
--- a/var/spack/repos/builtin/packages/r-lava/package.py
+++ b/var/spack/repos/builtin/packages/r-lava/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lazyeval/package.py b/var/spack/repos/builtin/packages/r-lazyeval/package.py
index 3746851d00..035661c0cc 100644
--- a/var/spack/repos/builtin/packages/r-lazyeval/package.py
+++ b/var/spack/repos/builtin/packages/r-lazyeval/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-leaflet/package.py b/var/spack/repos/builtin/packages/r-leaflet/package.py
index ef6debbdbb..fd418c4dc8 100644
--- a/var/spack/repos/builtin/packages/r-leaflet/package.py
+++ b/var/spack/repos/builtin/packages/r-leaflet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-leaps/package.py b/var/spack/repos/builtin/packages/r-leaps/package.py
index e27874ec27..056c84fea1 100644
--- a/var/spack/repos/builtin/packages/r-leaps/package.py
+++ b/var/spack/repos/builtin/packages/r-leaps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-learnbayes/package.py b/var/spack/repos/builtin/packages/r-learnbayes/package.py
index 71904b3d24..731f6488d1 100644
--- a/var/spack/repos/builtin/packages/r-learnbayes/package.py
+++ b/var/spack/repos/builtin/packages/r-learnbayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lhs/package.py b/var/spack/repos/builtin/packages/r-lhs/package.py
new file mode 100644
index 0000000000..c607d68124
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-lhs/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RLhs(RPackage):
+    """Provides a number of methods for creating and augmenting Latin Hypercube
+       Samples."""
+
+    homepage = "http://lhs.r-forge.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/lhs_0.16.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/lhs"
+
+    version('0.16', '088e593e5283414951e7e541a50ec2d1')
diff --git a/var/spack/repos/builtin/packages/r-limma/package.py b/var/spack/repos/builtin/packages/r-limma/package.py
index 8c4df2b059..7de1463b5f 100644
--- a/var/spack/repos/builtin/packages/r-limma/package.py
+++ b/var/spack/repos/builtin/packages/r-limma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,12 @@ class RLimma(RPackage):
     for microarray data."""
 
     homepage = "https://www.bioconductor.org/packages/limma/"
-    url      = "https://git.bioconductor.org/packages/limma"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/limma.git"
 
-    version('3.32.10', git='https://git.bioconductor.org/packages/limma', commit='593edf28e21fe054d64137ae271b8a52ab05bc60')
-    version('3.32.6', 'df5dc2b85189a24e939efa3a8e6abc41')
+    version('3.36.2',  commit='0cd5c13e22565182226bd2937ffcf8c59de1ca59')
+    version('3.34.9',  commit='6755278a929f942a49e2441fb002a3ed393e1139')
+    version('3.32.10', commit='593edf28e21fe054d64137ae271b8a52ab05bc60')
 
+    depends_on('r@3.5.0:3.5.9', when='@3.36.2')
+    depends_on('r@3.4.2:3.4.9', when='@3.34.9')
     depends_on('r@3.4.0:3.4.9', when='@3.32.10')
diff --git a/var/spack/repos/builtin/packages/r-lme4/package.py b/var/spack/repos/builtin/packages/r-lme4/package.py
index c7565e381e..8ba8e92a12 100644
--- a/var/spack/repos/builtin/packages/r-lme4/package.py
+++ b/var/spack/repos/builtin/packages/r-lme4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lmtest/package.py b/var/spack/repos/builtin/packages/r-lmtest/package.py
index 160fd3669b..ad8dbaf468 100644
--- a/var/spack/repos/builtin/packages/r-lmtest/package.py
+++ b/var/spack/repos/builtin/packages/r-lmtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-locfit/package.py b/var/spack/repos/builtin/packages/r-locfit/package.py
index 99b7af6fcf..f08811d14b 100644
--- a/var/spack/repos/builtin/packages/r-locfit/package.py
+++ b/var/spack/repos/builtin/packages/r-locfit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-log4r/package.py b/var/spack/repos/builtin/packages/r-log4r/package.py
index c6719cbe30..28cd6314e7 100644
--- a/var/spack/repos/builtin/packages/r-log4r/package.py
+++ b/var/spack/repos/builtin/packages/r-log4r/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lpsolve/package.py b/var/spack/repos/builtin/packages/r-lpsolve/package.py
index 996725f129..e3690b86f9 100644
--- a/var/spack/repos/builtin/packages/r-lpsolve/package.py
+++ b/var/spack/repos/builtin/packages/r-lpsolve/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lsei/package.py b/var/spack/repos/builtin/packages/r-lsei/package.py
index a2de608256..5d23d10991 100644
--- a/var/spack/repos/builtin/packages/r-lsei/package.py
+++ b/var/spack/repos/builtin/packages/r-lsei/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-lubridate/package.py b/var/spack/repos/builtin/packages/r-lubridate/package.py
index bdb314e673..d156d2c776 100644
--- a/var/spack/repos/builtin/packages/r-lubridate/package.py
+++ b/var/spack/repos/builtin/packages/r-lubridate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,11 @@ class RLubridate(RPackage):
     fun."""
 
     homepage = "https://cran.r-project.org/web/packages/lubridate/index.html"
-    url      = "https://cran.r-project.org/src/contrib/lubridate_1.5.6.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/lubridate_1.7.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/lubridate"
 
+    version('1.7.1', '17dcb4c6a95189941bbdcffecf61b83b')
     version('1.5.6', 'a5dc44817548ee219d26a10bae92e611')
 
+    depends_on('r-rcpp@0.11:', type=('build', 'run'))
     depends_on('r-stringr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py
index b6cd78be63..7365cfc3dd 100644
--- a/var/spack/repos/builtin/packages/r-magic/package.py
+++ b/var/spack/repos/builtin/packages/r-magic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-magrittr/package.py b/var/spack/repos/builtin/packages/r-magrittr/package.py
index 528fb7ff67..a52960890b 100644
--- a/var/spack/repos/builtin/packages/r-magrittr/package.py
+++ b/var/spack/repos/builtin/packages/r-magrittr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-makecdfenv/package.py b/var/spack/repos/builtin/packages/r-makecdfenv/package.py
index 8c74fc532b..fe307b5220 100644
--- a/var/spack/repos/builtin/packages/r-makecdfenv/package.py
+++ b/var/spack/repos/builtin/packages/r-makecdfenv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RMakecdfenv(RPackage):
     that environment."""
 
     homepage = "https://www.bioconductor.org/packages/makecdfenv/"
-    url      = "https://git.bioconductor.org/packages/makecdfenv"
+    git      = "https://git.bioconductor.org/packages/makecdfenv.git"
 
-    version('1.52.0', git='https://git.bioconductor.org/packages/makecdfenv', commit='b88a3e93e3b7feeeca69eda7c1fc5a0826c81120')
+    version('1.52.0', commit='b88a3e93e3b7feeeca69eda7c1fc5a0826c81120')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.0')
     depends_on('r-affyio', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-maldiquant/package.py b/var/spack/repos/builtin/packages/r-maldiquant/package.py
index ad1e1bb95f..69ad9033b5 100644
--- a/var/spack/repos/builtin/packages/r-maldiquant/package.py
+++ b/var/spack/repos/builtin/packages/r-maldiquant/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mapproj/package.py b/var/spack/repos/builtin/packages/r-mapproj/package.py
index d17ba5a8b3..689e175d67 100644
--- a/var/spack/repos/builtin/packages/r-mapproj/package.py
+++ b/var/spack/repos/builtin/packages/r-mapproj/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-maps/package.py b/var/spack/repos/builtin/packages/r-maps/package.py
index f9d6a487df..4895599fa0 100644
--- a/var/spack/repos/builtin/packages/r-maps/package.py
+++ b/var/spack/repos/builtin/packages/r-maps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-maptools/package.py b/var/spack/repos/builtin/packages/r-maptools/package.py
index e84fc2ef70..6a7487cc94 100644
--- a/var/spack/repos/builtin/packages/r-maptools/package.py
+++ b/var/spack/repos/builtin/packages/r-maptools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-markdown/package.py b/var/spack/repos/builtin/packages/r-markdown/package.py
index d58e56548c..ff9175ae97 100644
--- a/var/spack/repos/builtin/packages/r-markdown/package.py
+++ b/var/spack/repos/builtin/packages/r-markdown/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mass/package.py b/var/spack/repos/builtin/packages/r-mass/package.py
index 5767b10be1..9bcd7bf70b 100644
--- a/var/spack/repos/builtin/packages/r-mass/package.py
+++ b/var/spack/repos/builtin/packages/r-mass/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-matr/package.py b/var/spack/repos/builtin/packages/r-matr/package.py
new file mode 100644
index 0000000000..4f2c03d546
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-matr/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMatr(RPackage):
+    """Package matR (Metagenomics Analysis Tools for R) is an analysis
+    client for the MG-RAST metagenome annotation engine, part of the US
+    Department of Energy (DOE) Systems Biology Knowledge Base (KBase).
+    Customized analysis and visualization tools securely access remote
+    data and metadata within the popular open source R language and
+    environment for statistical computing."""
+
+    homepage = "https://github.com/MG-RAST/matR"
+    url      = "https://cran.r-project.org/src/contrib/matR_0.9.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/matR/matR_0.9.tar.gz"
+
+    version('0.9.1', sha256='554aeff37b27d0f17ddeb62b2e1004aa1f29190300e4946b1bec1d7c2bde82e3')
+    version('0.9', 'e2be8734009f5c5b9c1f6b677a77220a')
+
+    depends_on('r-mgraster', type=('build', 'run'))
+    depends_on('r-biom-utils', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-matrix/package.py b/var/spack/repos/builtin/packages/r-matrix/package.py
index c2911c4211..533cece9ff 100644
--- a/var/spack/repos/builtin/packages/r-matrix/package.py
+++ b/var/spack/repos/builtin/packages/r-matrix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,12 @@ class RMatrix(RPackage):
     using 'LAPACK' and 'SuiteSparse'."""
 
     homepage = "http://matrix.r-forge.r-project.org/"
-    url      = "https://cran.rstudio.com/src/contrib/Matrix_1.2-11.tar.gz"
+    url      = "https://cran.rstudio.com/src/contrib/Matrix_1.2-14.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/Matrix"
-    version('1.2-11', 'a8c1a893f36d7ea918ddbf8cb8d10b43')
+
+    version('1.2-14', 'b2babcf1515625196b75592c9b345bba')
+    version('1.2-12', '0ade6e374716f08650cc8b8da99a313c')
+    version('1.2-11', 'b7d2a639aa52228dfde7c3c3ee68b38e')
     version('1.2-8', '4a6406666bf97d3ec6b698eea5d9c0f5')
     version('1.2-6', 'f545307fb1284861e9266c4e9712c55e')
 
diff --git a/var/spack/repos/builtin/packages/r-matrixmodels/package.py b/var/spack/repos/builtin/packages/r-matrixmodels/package.py
index de309edbdd..02fc848414 100644
--- a/var/spack/repos/builtin/packages/r-matrixmodels/package.py
+++ b/var/spack/repos/builtin/packages/r-matrixmodels/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-matrixstats/package.py b/var/spack/repos/builtin/packages/r-matrixstats/package.py
index 177275267b..79001b6802 100644
--- a/var/spack/repos/builtin/packages/r-matrixstats/package.py
+++ b/var/spack/repos/builtin/packages/r-matrixstats/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mclust/package.py b/var/spack/repos/builtin/packages/r-mclust/package.py
index 30e1200da0..c198d9905c 100644
--- a/var/spack/repos/builtin/packages/r-mclust/package.py
+++ b/var/spack/repos/builtin/packages/r-mclust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py
index 19bd61f746..edf11d4c55 100644
--- a/var/spack/repos/builtin/packages/r-mcmcglmm/package.py
+++ b/var/spack/repos/builtin/packages/r-mcmcglmm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mco/package.py b/var/spack/repos/builtin/packages/r-mco/package.py
new file mode 100644
index 0000000000..eae3fe7a99
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mco/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMco(RPackage):
+    """Functions for multiple criteria optimization using genetic algorithms
+       and related test problems"""
+
+    homepage = "https://github.com/cran/mco"
+    url      = "https://cran.r-project.org/src/contrib/mco_1.0-15.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mco"
+
+    version('1.0-15.1', '1768dea61d0561d71be2bbc6ac3dccfa')
+    version('1.0-15', '0b444e085c59d919611224e86b5637f8')
diff --git a/var/spack/repos/builtin/packages/r-mda/package.py b/var/spack/repos/builtin/packages/r-mda/package.py
index 492cc4fe13..f59f09844e 100644
--- a/var/spack/repos/builtin/packages/r-mda/package.py
+++ b/var/spack/repos/builtin/packages/r-mda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-memoise/package.py b/var/spack/repos/builtin/packages/r-memoise/package.py
index 6bc766f0cd..e8a8b32e1b 100644
--- a/var/spack/repos/builtin/packages/r-memoise/package.py
+++ b/var/spack/repos/builtin/packages/r-memoise/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mergemaid/package.py b/var/spack/repos/builtin/packages/r-mergemaid/package.py
index ae6ef977c5..ff4ae551f3 100644
--- a/var/spack/repos/builtin/packages/r-mergemaid/package.py
+++ b/var/spack/repos/builtin/packages/r-mergemaid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,9 +19,9 @@ class RMergemaid(RPackage):
        cross-validate associations of gene expression data with survival."""
 
     homepage = "https://www.bioconductor.org/packages/MergeMaid/"
-    url      = "https://git.bioconductor.org/packages/MergeMaid"
+    git      = "https://git.bioconductor.org/packages/MergeMaid.git"
 
-    version('2.48.0', git='https://git.bioconductor.org/packages/MergeMaid', commit='aee89c523fcafff4c166ff3db4fff90df16a1ed4')
+    version('2.48.0', commit='aee89c523fcafff4c166ff3db4fff90df16a1ed4')
 
     depends_on('r-survival', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-methodss3/package.py b/var/spack/repos/builtin/packages/r-methodss3/package.py
index 2c1768a1b1..d5793a73a0 100644
--- a/var/spack/repos/builtin/packages/r-methodss3/package.py
+++ b/var/spack/repos/builtin/packages/r-methodss3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mgcv/package.py b/var/spack/repos/builtin/packages/r-mgcv/package.py
index 0bf7563df1..22296ac36d 100644
--- a/var/spack/repos/builtin/packages/r-mgcv/package.py
+++ b/var/spack/repos/builtin/packages/r-mgcv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,6 +16,12 @@ class RMgcv(RPackage):
     url      = "https://cran.r-project.org/src/contrib/mgcv_1.8-16.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/mgcv"
 
+    version('1.8-22', 'b42079b33b46de784f293a74c824b877')
+    version('1.8-21', 'aae8262a07c8698ca8d6213065c4983f')
+    version('1.8-20', '58eb94404aad7ff8a0cf11a2f098f8bf')
+    version('1.8-19', 'f9a4e29464f4d10b7b2cb9d0bec3fa9e')
+    version('1.8-18', 'c134fc2db253530233b95f2e36b56a2f')
+    version('1.8-17', '398582d0f999ac34749f4f5f1d103f75')
     version('1.8-16', '4c1d85e0f80b017bccb4b63395842911')
     version('1.8-13', '30607be3aaf44b13bd8c81fc32e8c984')
 
diff --git a/var/spack/repos/builtin/packages/r-mgraster/package.py b/var/spack/repos/builtin/packages/r-mgraster/package.py
new file mode 100644
index 0000000000..f3e3978860
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mgraster/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMgraster(RPackage):
+    """Convenience Functions for R Language Access to the v.1 API of the
+    MG-RAST Metagenome Annotation Server, part of the US Department of Energy
+    (DOE) Systems Biology Knowledge Base (KBase)."""
+
+    homepage = "https://github.com/braithwaite/MGRASTer/"
+    url      = "https://cran.r-project.org/src/contrib/MGRASTer_0.9.tar.gz"
+
+    version('0.9', '902c7ad4180b858d6b6428ea26d7652a')
+
+    depends_on('r@3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mice/package.py b/var/spack/repos/builtin/packages/r-mice/package.py
new file mode 100644
index 0000000000..e18a83c9a4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mice/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMice(RPackage):
+    """Multiple imputation using Fully Conditional Specification (FCS)
+    implemented by the MICE algorithm as described in Van Buuren and
+    Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>.
+
+    Each variable has its own imputation model. Built-in imputation models are
+    provided for continuous data (predictive mean matching, normal), binary
+    data (logistic regression), unordered categorical data (polytomous logistic
+    regression) and ordered categorical data (proportional odds). MICE can
+    also impute continuous two-level data (normal model, pan, second-level
+    variables). Passive imputation can be used to maintain consistency between
+    variables. Various diagnostic plots are available to inspect the quality
+    of the imputations."""
+
+    homepage = "https://cran.r-project.org/package=mice"
+    url      = "https://cran.r-project.org/src/contrib/mice_3.0.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mice"
+
+    version('3.0.0', 'fb54a29679536c474c756cca4538d7e3')
+
+    depends_on('r-broom', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-mitml', type=('build', 'run'))
+    depends_on('r-nnet', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'))
+    depends_on('r-rpart', type=('build', 'run'))
+    depends_on('r-survival', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py
index bb235270d7..4d0dd95015 100644
--- a/var/spack/repos/builtin/packages/r-mime/package.py
+++ b/var/spack/repos/builtin/packages/r-mime/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-minfi/package.py b/var/spack/repos/builtin/packages/r-minfi/package.py
index 3621743aaa..06cfff4cef 100644
--- a/var/spack/repos/builtin/packages/r-minfi/package.py
+++ b/var/spack/repos/builtin/packages/r-minfi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,9 @@ class RMinfi(RPackage):
     """Tools to analyze & visualize Illumina Infinium methylation arrays."""
 
     homepage = "https://bioconductor.org/packages/minfi/"
-    url      = "https://git.bioconductor.org/packages/minfi"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/minfi.git"
 
-    version('1.22.1', git='https://git.bioconductor.org/packages/minfi', commit='b2faf84bcbb291e32d470a0e029450093527545b')
+    version('1.22.1', commit='b2faf84bcbb291e32d470a0e029450093527545b')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-minqa/package.py b/var/spack/repos/builtin/packages/r-minqa/package.py
index 23fe7b5b5c..4b52bef0aa 100644
--- a/var/spack/repos/builtin/packages/r-minqa/package.py
+++ b/var/spack/repos/builtin/packages/r-minqa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-misc3d/package.py b/var/spack/repos/builtin/packages/r-misc3d/package.py
new file mode 100644
index 0000000000..838b8bf738
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-misc3d/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMisc3d(RPackage):
+    """A collection of miscellaneous 3d plots, including isosurfaces."""
+
+    homepage = "https://cran.r-project.org/web/packages/misc3d/index.html"
+    url      = "https://cran.r-project.org/src/contrib/misc3d_0.8-4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/misc3d"
+
+    version('0.8-4', 'aefa27e67a243c21a1046868540343fe')
diff --git a/var/spack/repos/builtin/packages/r-mitml/package.py b/var/spack/repos/builtin/packages/r-mitml/package.py
new file mode 100644
index 0000000000..4a0f91d65c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mitml/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMitml(RPackage):
+    """Provides tools for multiple imputation of missing data in multilevel
+    modeling. Includes a user-friendly interface to the packages 'pan' and
+    'jomo', and several functions for visualization, data management and the
+    analysis of multiply imputed data sets."""
+
+    homepage = "https://cran.r-project.org/package=mitml"
+    url      = "https://cran.r-project.org/src/contrib/mitml_0.3-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mitml"
+    version('0.3-5', '6f8659c33696915bf510241287b2a34d')
+
+    depends_on('r-pan', type=('build', 'run'))
+    depends_on('r-jomo', type=('build', 'run'))
+    depends_on('r-haven', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mixtools/package.py b/var/spack/repos/builtin/packages/r-mixtools/package.py
new file mode 100644
index 0000000000..3538113eb8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mixtools/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMixtools(RPackage):
+    """mixtools: Tools for Analyzing Finite Mixture Models
+
+    Analyzes finite mixture models for various parametric and semiparametric
+    settings."""
+
+    homepage = "https://cran.r-project.org/web/packages/mixtools/index.html"
+    url      = "https://cran.r-project.org/src/contrib/mixtools_1.1.0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/mixtools"
+
+    version('1.1.0', 'c7d59110dd42964d40593a05b98acd5f')
+    version('1.0.4', 'c0e6ec44d16ec8914797fb74a651d3e5')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-segmented', type=('build', 'run'))
+    depends_on('r-survival', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mlbench/package.py b/var/spack/repos/builtin/packages/r-mlbench/package.py
index 9d450ced9e..c2eec7e418 100644
--- a/var/spack/repos/builtin/packages/r-mlbench/package.py
+++ b/var/spack/repos/builtin/packages/r-mlbench/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
index 9c83563b8f..79ea6ba809 100644
--- a/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
+++ b/var/spack/repos/builtin/packages/r-mlinterfaces/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RMlinterfaces(RPackage):
     code for data in R and Bioconductor containers."""
 
     homepage = "https://www.bioconductor.org/packages/MLInterfaces/"
-    url      = "https://git.bioconductor.org/packages/MLInterfaces"
+    git      = "https://git.bioconductor.org/packages/MLInterfaces.git"
 
-    version('1.56.0', git='https://git.bioconductor.org/packages/MLInterfaces', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f')
+    version('1.56.0', commit='31fe6fb20d859fcb01d5552f42bca6bab16cc67f')
 
     depends_on('r@3.4.0:3.4.9', when='@1.56.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mlr/package.py b/var/spack/repos/builtin/packages/r-mlr/package.py
new file mode 100644
index 0000000000..120c7adaa9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mlr/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMlr(RPackage):
+    """Interface to a large number of classification and regression techniques,
+       including machine-readable parameter descriptions. There is also an
+       experimental extension for survival analysis, clustering and general,
+       example-specific cost-sensitive learning. Generic resampling,
+       including cross-validation, bootstrapping and subsampling.
+       Hyperparameter tuning with modern optimization techniques,
+       for single- and multi-objective problems. Filter and wrapper methods for
+       feature selection. Extension of basic learners with additional
+       operations common in machine learning, also allowing for easy nested
+       resampling. Most operations can be parallelized."""
+
+    homepage = "https://github.com/mlr-org/mlr/"
+    url      = "https://cran.r-project.org/src/contrib/mlr_2.12.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mlr"
+
+    version('2.12.1', 'abddfc9dfe95f290a233ecd97969a4ec')
+    version('2.12', '94ee7495aeafb432c8af5a8bdd26c25f')
+
+    depends_on('r-paramhelpers@1.10:', type=('build', 'run'))
+    depends_on('r-bbmisc@1.11:', type=('build', 'run'))
+    depends_on('r-backports@1.1.0:', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-stringi', type=('build', 'run'))
+    depends_on('r-checkmate@1.8.2:', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-parallelmap@1.3:', type=('build', 'run'))
+    depends_on('r-xml', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mlrmbo/package.py b/var/spack/repos/builtin/packages/r-mlrmbo/package.py
new file mode 100644
index 0000000000..3f789a869c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mlrmbo/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMlrmbo(RPackage):
+    """Flexible and comprehensive R toolbox for model-based optimization
+       ('MBO'), also known as Bayesian optimization. It is designed for both
+       single- and multi-objective optimization with mixed continuous,
+       categorical and conditional parameters. The machine learning toolbox
+       'mlr' provide dozens of regression learners to model the performance of
+       the target algorithm with respect to the parameter settings. It provides
+       many different infill criteria to guide the search process. Additional
+       features include multi-point batch proposal, parallel execution as well
+       as visualization and sophisticated logging mechanisms, which is
+       especially useful for teaching and understanding of algorithm behavior.
+       'mlrMBO' is implemented in a modular fashion, such that single
+       components can be easily replaced or adapted by the user for specific
+       use cases."""
+
+    homepage = "https://github.com/mlr-org/mlrMBO/"
+    url      = "https://cran.r-project.org/src/contrib/mlrMBO_1.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mlrMBO"
+
+    version('1.1.1', '9a35b41ceb8754111af294dee0ae76e0')
+    version('1.1.0', '9e27ff8498225d24863b8da758d2918e')
+
+    depends_on('r-mlr@2.10:', type=('build', 'run'))
+    depends_on('r-paramhelpers@1.10:', type=('build', 'run'))
+    depends_on('r-smoof@1.5.1:', type=('build', 'run'))
+    depends_on('r-backports@1.1.0:', type=('build', 'run'))
+    depends_on('r-bbmisc@1.11:', type=('build', 'run'))
+    depends_on('r-checkmate@1.8.2:', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-lhs', type=('build', 'run'))
+    depends_on('r-parallelmap@1.3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mmwrweek/package.py b/var/spack/repos/builtin/packages/r-mmwrweek/package.py
new file mode 100644
index 0000000000..f62bd6275c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mmwrweek/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMmwrweek(RPackage):
+    """The first day of any MMWR week is Sunday. MMWR week numbering is
+    sequential beginning with 1 and incrementing with each week to a maximum
+    of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year
+    that has at least four days in the calendar year. This package provides
+    functionality to convert Dates to MMWR day, week, and year and the
+    reverse."""
+
+    homepage = "https://cran.r-project.org/package=MMWRweek"
+    url      = "https://cran.r-project.org/src/contrib/MMWRweek_0.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/MMWRweek"
+
+    version('0.1.1', 'a1245025126f8a96c72be8f7b06b0499')
diff --git a/var/spack/repos/builtin/packages/r-mnormt/package.py b/var/spack/repos/builtin/packages/r-mnormt/package.py
new file mode 100644
index 0000000000..34c88cf85a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-mnormt/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMnormt(RPackage):
+    """Functions are provided for computing the density and the distribution
+       function of multivariate normal and "t" random variables, and for
+       generating random vectors sampled from these distributions.
+       Probabilities are computed via non-Monte Carlo methods; different
+       routines are used in the case d=1, d=2, d>2, if d denotes the number
+       of dimensions."""
+
+    homepage = "http://azzalini.stat.unipd.it/SW/Pkg-mnormt"
+    url      = "https://cran.r-project.org/src/contrib/mnormt_1.5-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/mnormt"
+
+    version('1.5-5', '19b5be2e9ed33b92d7a716bfcca6b2c7')
diff --git a/var/spack/repos/builtin/packages/r-modelmetrics/package.py b/var/spack/repos/builtin/packages/r-modelmetrics/package.py
index c3625e1e37..fd4648abd9 100644
--- a/var/spack/repos/builtin/packages/r-modelmetrics/package.py
+++ b/var/spack/repos/builtin/packages/r-modelmetrics/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-modelr/package.py b/var/spack/repos/builtin/packages/r-modelr/package.py
new file mode 100644
index 0000000000..2d9bf982ef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-modelr/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RModelr(RPackage):
+    """Functions for modelling that help you seamlessly integrate modelling
+       into a pipeline of data manipulation and visualisation."""
+
+    homepage = "https://github.com/hadley/modelr"
+    url      = "https://cran.r-project.org/src/contrib/modelr_0.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/modelr"
+
+    version('0.1.1', 'ce5fd088fb7850228ab1e34d241a975d')
+
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-lazyeval', type=('build', 'run'))
+    depends_on('r-tibble', type=('build', 'run'))
+    depends_on('r-broom', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-modeltools/package.py b/var/spack/repos/builtin/packages/r-modeltools/package.py
index 1c0873dfae..5f8b660029 100644
--- a/var/spack/repos/builtin/packages/r-modeltools/package.py
+++ b/var/spack/repos/builtin/packages/r-modeltools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mpm/package.py b/var/spack/repos/builtin/packages/r-mpm/package.py
index 78b21ab11b..7bf560cc8c 100644
--- a/var/spack/repos/builtin/packages/r-mpm/package.py
+++ b/var/spack/repos/builtin/packages/r-mpm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-msnbase/package.py b/var/spack/repos/builtin/packages/r-msnbase/package.py
index fddbffdcec..78f882ec53 100644
--- a/var/spack/repos/builtin/packages/r-msnbase/package.py
+++ b/var/spack/repos/builtin/packages/r-msnbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RMsnbase(RPackage):
        proteomics data."""
 
     homepage = "https://www.bioconductor.org/packages/MSnbase/"
-    url      = "https://git.bioconductor.org/packages/MSnbase"
+    git      = "https://git.bioconductor.org/packages/MSnbase.git"
 
-    version('2.2.0', git='https://git.bioconductor.org/packages/MSnbase', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197')
+    version('2.2.0', commit='d6e8fb7f106d05096fa9074da0f829ac8f02c197')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-multcomp/package.py b/var/spack/repos/builtin/packages/r-multcomp/package.py
index 8b5b6deff7..d8eb6b6d5c 100644
--- a/var/spack/repos/builtin/packages/r-multcomp/package.py
+++ b/var/spack/repos/builtin/packages/r-multcomp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-multicool/package.py b/var/spack/repos/builtin/packages/r-multicool/package.py
new file mode 100644
index 0000000000..3bb41ac560
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-multicool/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RMulticool(RPackage):
+    """Permutations of multisets in cool-lex order."""
+
+    homepage = "https://cran.r-project.org/package=multicool"
+    url      = "https://cran.r-project.org/src/contrib/Archive/multicool/multicool_0.1-9.tar.gz"
+
+    version('0.1-9', sha256='bdf92571cef1b649952d155395a92b8683099ee13114f73a9d41fc5d7d49d329')
+
+    depends_on('r-rcpp@0.11.2:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-multtest/package.py b/var/spack/repos/builtin/packages/r-multtest/package.py
index 04030423ee..aa5e5a34a0 100644
--- a/var/spack/repos/builtin/packages/r-multtest/package.py
+++ b/var/spack/repos/builtin/packages/r-multtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class RMulttest(RPackage):
     """Resampling-based multiple hypothesis testing"""
 
     homepage = "https://www.bioconductor.org/packages/multtest/"
-    url      = "https://git.bioconductor.org/packages/multtest"
+    git      = "https://git.bioconductor.org/packages/multtest.git"
 
-    version('2.32.0', git='https://git.bioconductor.org/packages/multtest', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a')
+    version('2.32.0', commit='c5e890dfbffcc3a3f107303a24b6085614312f4a')
 
     depends_on('r@3.4.0:3.4.9', when='@2.32.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-munsell/package.py b/var/spack/repos/builtin/packages/r-munsell/package.py
index de729c84ef..353e9ecd2c 100644
--- a/var/spack/repos/builtin/packages/r-munsell/package.py
+++ b/var/spack/repos/builtin/packages/r-munsell/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mvtnorm/package.py b/var/spack/repos/builtin/packages/r-mvtnorm/package.py
index 9806c21cb5..e341a2e76e 100644
--- a/var/spack/repos/builtin/packages/r-mvtnorm/package.py
+++ b/var/spack/repos/builtin/packages/r-mvtnorm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-mzid/package.py b/var/spack/repos/builtin/packages/r-mzid/package.py
index cb23814ea8..ea9778ffcb 100644
--- a/var/spack/repos/builtin/packages/r-mzid/package.py
+++ b/var/spack/repos/builtin/packages/r-mzid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class RMzid(RPackage):
        supply an mzIdentML file so the problems can be fixed quickly."""
 
     homepage = "https://www.bioconductor.org/packages/mzID/"
-    url      = "https://git.bioconductor.org/packages/mzID"
+    git      = "https://git.bioconductor.org/packages/mzID.git"
 
-    version('1.14.0', git='https://git.bioconductor.org/packages/mzID', commit='1c53aa6523ae61d3ebb13381381fc119d6cc6115')
+    version('1.14.0', commit='1c53aa6523ae61d3ebb13381381fc119d6cc6115')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-plyr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py
index 282962153b..19b5080037 100644
--- a/var/spack/repos/builtin/packages/r-mzr/package.py
+++ b/var/spack/repos/builtin/packages/r-mzr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,9 @@ class RMzr(RPackage):
        reading code has previously been used in XCMS."""
 
     homepage = "https://www.bioconductor.org/packages/mzR/"
-    url      = "https://git.bioconductor.org/packages/mzR"
+    git      = "https://git.bioconductor.org/packages/mzR.git"
 
-    version('2.10.0', git='https://git.bioconductor.org/packages/mzR', commit='a6168b68e48c281e88de9647254a8db1e21df388')
+    version('2.10.0', commit='a6168b68e48c281e88de9647254a8db1e21df388')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-nanotime/package.py b/var/spack/repos/builtin/packages/r-nanotime/package.py
new file mode 100644
index 0000000000..07c3d8830a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-nanotime/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RNanotime(RPackage):
+    """Full 64-bit resolution date and time support with resolution up to
+       nanosecond granularity is provided, with easy transition to and from
+       the standard 'POSIXct' type."""
+
+    homepage = "https://cran.r-project.org/package=nanotime"
+    url      = "https://cran.r-project.org/src/contrib/nanotime_0.2.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/nanotime"
+
+    version('0.2.0', '796b1f7d0bb43e2f3d98e3cc6f4b0657')
+
+    depends_on('r-bit64', type=('build', 'run'))
+    depends_on('r-rcppcctz', type=('build', 'run'))
+    depends_on('r-zoo', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ncbit/package.py b/var/spack/repos/builtin/packages/r-ncbit/package.py
index c9bc90654c..3d66e92009 100644
--- a/var/spack/repos/builtin/packages/r-ncbit/package.py
+++ b/var/spack/repos/builtin/packages/r-ncbit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py
index 8e24a0eba1..d38ba6d5b9 100644
--- a/var/spack/repos/builtin/packages/r-ncdf4/package.py
+++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-network/package.py b/var/spack/repos/builtin/packages/r-network/package.py
index 867fbf41f6..e586c6d030 100644
--- a/var/spack/repos/builtin/packages/r-network/package.py
+++ b/var/spack/repos/builtin/packages/r-network/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-networkd3/package.py b/var/spack/repos/builtin/packages/r-networkd3/package.py
index 4102dbefe4..45eada135f 100644
--- a/var/spack/repos/builtin/packages/r-networkd3/package.py
+++ b/var/spack/repos/builtin/packages/r-networkd3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nlme/package.py b/var/spack/repos/builtin/packages/r-nlme/package.py
index b50fa42c10..fac6a7c7f6 100644
--- a/var/spack/repos/builtin/packages/r-nlme/package.py
+++ b/var/spack/repos/builtin/packages/r-nlme/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nloptr/package.py b/var/spack/repos/builtin/packages/r-nloptr/package.py
index 613900c799..d77d18f17f 100644
--- a/var/spack/repos/builtin/packages/r-nloptr/package.py
+++ b/var/spack/repos/builtin/packages/r-nloptr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,3 +23,13 @@ class RNloptr(RPackage):
     version('1.0.4', 'f2775dfb4f7f5552d46937a04c062b0d')
 
     depends_on('r-testthat', type=('build', 'run'))
+    depends_on('nlopt')
+
+    def configure_args(self):
+        include_flags = self.spec['nlopt'].headers.include_flags
+        libs = self.spec['nlopt'].libs.libraries[0]
+        args = [
+            '--with-nlopt-cflags={0}'.format(include_flags),
+            '--with-nlopt-libs={0}'.format(libs)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py
index 8e2806efed..8be0914277 100644
--- a/var/spack/repos/builtin/packages/r-nmf/package.py
+++ b/var/spack/repos/builtin/packages/r-nmf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nnet/package.py b/var/spack/repos/builtin/packages/r-nnet/package.py
index 5298b38abe..1326221ceb 100644
--- a/var/spack/repos/builtin/packages/r-nnet/package.py
+++ b/var/spack/repos/builtin/packages/r-nnet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nnls/package.py b/var/spack/repos/builtin/packages/r-nnls/package.py
index 44ea8174c2..3da3e20b63 100644
--- a/var/spack/repos/builtin/packages/r-nnls/package.py
+++ b/var/spack/repos/builtin/packages/r-nnls/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-nor1mix/package.py b/var/spack/repos/builtin/packages/r-nor1mix/package.py
index f02a70cc9b..9e4f27007b 100644
--- a/var/spack/repos/builtin/packages/r-nor1mix/package.py
+++ b/var/spack/repos/builtin/packages/r-nor1mix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-np/package.py b/var/spack/repos/builtin/packages/r-np/package.py
index 6bb788e38d..1a32b6f71d 100644
--- a/var/spack/repos/builtin/packages/r-np/package.py
+++ b/var/spack/repos/builtin/packages/r-np/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-numderiv/package.py b/var/spack/repos/builtin/packages/r-numderiv/package.py
index 86887bb1a5..8e145d572f 100644
--- a/var/spack/repos/builtin/packages/r-numderiv/package.py
+++ b/var/spack/repos/builtin/packages/r-numderiv/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-oligoclasses/package.py b/var/spack/repos/builtin/packages/r-oligoclasses/package.py
index 85e221e275..86d72876fe 100644
--- a/var/spack/repos/builtin/packages/r-oligoclasses/package.py
+++ b/var/spack/repos/builtin/packages/r-oligoclasses/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class ROligoclasses(RPackage):
     crlmm packages."""
 
     homepage = "https://www.bioconductor.org/packages/oligoClasses/"
-    url      = "https://git.bioconductor.org/packages/oligoClasses"
+    git      = "https://git.bioconductor.org/packages/oligoClasses.git"
 
-    version('1.38.0', git='https://git.bioconductor.org/packages/oligoClasses', commit='fe2bb7f02c7ed3cbd338254c27ceba6ff829a962')
+    version('1.38.0', commit='fe2bb7f02c7ed3cbd338254c27ceba6ff829a962')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.0')
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-oo/package.py b/var/spack/repos/builtin/packages/r-oo/package.py
index 7f4a3e39d9..6cba9eb491 100644
--- a/var/spack/repos/builtin/packages/r-oo/package.py
+++ b/var/spack/repos/builtin/packages/r-oo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-openssl/package.py b/var/spack/repos/builtin/packages/r-openssl/package.py
index 4c038f29c9..4b228646ac 100644
--- a/var/spack/repos/builtin/packages/r-openssl/package.py
+++ b/var/spack/repos/builtin/packages/r-openssl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py
new file mode 100644
index 0000000000..893c6618f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-org-hs-eg-db/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class ROrgHsEgDb(RPackage):
+    """Genome wide annotation for Human, primarily based on mapping
+    using Entrez Gene identifiers."""
+
+    homepage = "https://bioconductor.org/packages/org.Hs.eg.db/"
+    url      = "https://www.bioconductor.org/packages/3.5/data/annotation/src/contrib/org.Hs.eg.db_3.4.1.tar.gz"
+
+    version('3.4.1', '0a987ef7d6167df70e91e6f48145e41c')
+
+    depends_on('r@3.4.0:3.4.9', when='@3.4.1')
+    depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-organismdbi/package.py b/var/spack/repos/builtin/packages/r-organismdbi/package.py
index b299c5919b..e9cd3d499b 100644
--- a/var/spack/repos/builtin/packages/r-organismdbi/package.py
+++ b/var/spack/repos/builtin/packages/r-organismdbi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class ROrganismdbi(RPackage):
        fact that each of these packages implements a select methods."""
 
     homepage = "https://bioconductor.org/packages/OrganismDbi/"
-    url      = "https://git.bioconductor.org/packages/OrganismDbi"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/OrganismDbi.git"
 
-    version('1.18.1', git='https://git.bioconductor.org/packages/OrganismDbi', commit='ba2d1237256805e935d9534a0c6f1ded07b42e95')
+    version('1.18.1', commit='ba2d1237256805e935d9534a0c6f1ded07b42e95')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-annotationdbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-packrat/package.py b/var/spack/repos/builtin/packages/r-packrat/package.py
index c87326cacb..7a8b002786 100644
--- a/var/spack/repos/builtin/packages/r-packrat/package.py
+++ b/var/spack/repos/builtin/packages/r-packrat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pacman/package.py b/var/spack/repos/builtin/packages/r-pacman/package.py
index c272904a2e..a419b520da 100644
--- a/var/spack/repos/builtin/packages/r-pacman/package.py
+++ b/var/spack/repos/builtin/packages/r-pacman/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pamr/package.py b/var/spack/repos/builtin/packages/r-pamr/package.py
index 9e3de93ad6..3be3f2e4c3 100644
--- a/var/spack/repos/builtin/packages/r-pamr/package.py
+++ b/var/spack/repos/builtin/packages/r-pamr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pan/package.py b/var/spack/repos/builtin/packages/r-pan/package.py
new file mode 100644
index 0000000000..db9bc7988d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pan/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPan(RPackage):
+    """Multiple imputation for multivariate panel or clustered data."""
+
+    homepage = "https://cran.r-project.org/package=pan"
+    url      = "https://cran.r-project.org/src/contrib/pan_1.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/pan"
+
+    version('1.4', 'cdead963110561fc42dc544a60ac44ed')
diff --git a/var/spack/repos/builtin/packages/r-parallelmap/package.py b/var/spack/repos/builtin/packages/r-parallelmap/package.py
new file mode 100644
index 0000000000..cb7c10a028
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-parallelmap/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RParallelmap(RPackage):
+    """Unified parallelization framework for multiple back-end, designed for
+       internal package and interactive usage. The main operation is a parallel
+       "map" over lists. Supports local, multicore, mpi and BatchJobs mode.
+       Allows "tagging" of the parallel operation with a level name that can be
+       later selected by the user to switch on parallel execution for exactly
+       this operation."""
+
+    homepage = "https://github.com/berndbischl/parallelMap"
+    url      = "https://cran.r-project.org/src/contrib/parallelMap_1.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/parallelMap"
+
+    version('1.3', 'dd62866b395847b0bd5b13bed98c0081')
+
+    depends_on('r-bbmisc@1.8:', type=('build', 'run'))
+    depends_on('r-checkmate@1.5.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-paramhelpers/package.py b/var/spack/repos/builtin/packages/r-paramhelpers/package.py
new file mode 100644
index 0000000000..2fabb7954a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-paramhelpers/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RParamhelpers(RPackage):
+    """Functions for parameter descriptions and operations in black-box
+       optimization, tuning and machine learning. Parameters can be described
+       (type, constraints, defaults, etc.), combined to parameter sets and can
+       in general be programmed on. A useful OptPath object (archive) to log
+       function evaluations is also provided."""
+
+    homepage = "https://github.com/berndbischl/ParamHelpers"
+    url      = "https://cran.r-project.org/src/contrib/ParamHelpers_1.10.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ParamHelpers"
+
+    version('1.10', '36e9060488ebd484d62cd991a4693332')
+
+    depends_on('r-bbmisc@1.10:', type=('build', 'run'))
+    depends_on('r-checkmate@1.8.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-party/package.py b/var/spack/repos/builtin/packages/r-party/package.py
index de9be7d79d..f0d5065d68 100644
--- a/var/spack/repos/builtin/packages/r-party/package.py
+++ b/var/spack/repos/builtin/packages/r-party/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-partykit/package.py b/var/spack/repos/builtin/packages/r-partykit/package.py
index 45ce019cad..680891ae0d 100644
--- a/var/spack/repos/builtin/packages/r-partykit/package.py
+++ b/var/spack/repos/builtin/packages/r-partykit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-pathview/package.py b/var/spack/repos/builtin/packages/r-pathview/package.py
new file mode 100644
index 0000000000..bedd4571f7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pathview/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPathview(RPackage):
+    """Pathview is a tool set for pathway based data integration and
+    visualization. It maps and renders a wide variety of biological data on
+    relevant pathway graphs. All users need is to supply their data and
+    specify the target pathway. Pathview automatically downloads the pathway
+    graph data, parses the data file, maps user data to the pathway, and
+    render pathway graph with the mapped data. In addition, Pathview also
+    seamlessly integrates with pathway and gene set (enrichment) analysis
+    tools for large-scale and fully automated analysis."""
+
+    homepage = "https://www.bioconductor.org/packages/pathview/"
+    git      = "https://git.bioconductor.org/packages/pathview.git"
+
+    version('1.16.7', commit='fc560ed15ef7393a73d35e714716cc24dc835339')
+
+    depends_on('r-keggrest', type=('build', 'run'))
+    depends_on('r-png', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-graph', type=('build', 'run'))
+    depends_on('r-rgraphviz', type=('build', 'run'))
+    depends_on('r-xml', type=('build', 'run'))
+    depends_on('r-kegggraph', type=('build', 'run'))
+    depends_on('r-org-hs-eg-db', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.16.7')
diff --git a/var/spack/repos/builtin/packages/r-pbapply/package.py b/var/spack/repos/builtin/packages/r-pbapply/package.py
new file mode 100644
index 0000000000..14d5d9a178
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pbapply/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPbapply(RPackage):
+    """A lightweight package that adds progress bar to vectorized R
+    apply functions."""
+
+    homepage = "https://cran.r-project.org/web/packages/pbapply/index.html"
+    url      = "https://cran.r-project.org/src/contrib/pbapply_1.3-3.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/pbapply"
+
+    version('1.3-3', '570db6795179a1439c174be881c77d18')
+    version('1.3-2', 'd72a777bfe4a28ba4e1585e31680f82e')
+    version('1.3-1', '13d64dead441426aa96a3bf3fde29daf')
+    version('1.3-0', 'a3f93cd05054657a01893a3817fa1f08')
+    version('1.2-2', '23e2bfe531c704b79308b0b5fbe1ace8')
+
+    depends_on('r@3.4.0:3.4.9')
diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py
index 82adce3430..5ff32c0487 100644
--- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py
+++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-pbkrtest/package.py b/var/spack/repos/builtin/packages/r-pbkrtest/package.py
index 4d6ae727cc..1bb9f75f0b 100644
--- a/var/spack/repos/builtin/packages/r-pbkrtest/package.py
+++ b/var/spack/repos/builtin/packages/r-pbkrtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pcamethods/package.py b/var/spack/repos/builtin/packages/r-pcamethods/package.py
index b43fac79d0..a0e9721e9d 100644
--- a/var/spack/repos/builtin/packages/r-pcamethods/package.py
+++ b/var/spack/repos/builtin/packages/r-pcamethods/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,9 +18,9 @@ class RPcamethods(RPackage):
        Physiology, Golm, Germany."""
 
     homepage = "http://bioconductor.org/packages/pcaMethods/"
-    url      = "https://git.bioconductor.org/packages/pcaMethods"
-    list_url = homepage
-    version('1.68.0', git='https://git.bioconductor.org/packages/pcaMethods', commit='c8d7c93dcaf7ef728f3d089ae5d55771b320bdab')
+    git      = "https://git.bioconductor.org/packages/pcaMethods.git"
+
+    version('1.68.0', commit='c8d7c93dcaf7ef728f3d089ae5d55771b320bdab')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-pcapp/package.py b/var/spack/repos/builtin/packages/r-pcapp/package.py
new file mode 100644
index 0000000000..3fe6f2d745
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-pcapp/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPcapp(RPackage):
+        """Provides functions for robust PCA by projection pursuit."""
+
+        homepage = "https://cran.r-project.org/web/packages/pcaPP/index.html"
+        url      = "https://cran.r-project.org/src/contrib/pcaPP_1.9-72.tar.gz"
+        list_url = "https://cran.rstudio.com/src/contrib/Archive/pcaPP"
+
+        version('1.9-72', '87c08f8ecab69311bba395c026bbc91c')
+        version('1.9-70', '3fcc809ec1cdc910f10e9ebf372888e8')
+        version('1.9-61', '1bd5bc3aff968b168493e8c523d726ea')
+        version('1.9-60', '23dd468abb9fedc11e40166446df1017')
+        version('1.9-50', 'be44f173404fd6e86ba0a5515711bfa3')
+
+        depends_on('r-mvtnorm', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-permute/package.py b/var/spack/repos/builtin/packages/r-permute/package.py
index 846028e0da..48f4197e5f 100644
--- a/var/spack/repos/builtin/packages/r-permute/package.py
+++ b/var/spack/repos/builtin/packages/r-permute/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pfam-db/package.py b/var/spack/repos/builtin/packages/r-pfam-db/package.py
index ef580a84bb..c29bdad99c 100644
--- a/var/spack/repos/builtin/packages/r-pfam-db/package.py
+++ b/var/spack/repos/builtin/packages/r-pfam-db/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-phangorn/package.py b/var/spack/repos/builtin/packages/r-phangorn/package.py
new file mode 100644
index 0000000000..c20fd50fe4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-phangorn/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPhangorn(RPackage):
+    """Package contains methods for estimation of phylogenetic trees and
+       networks using Maximum Likelihood, Maximum Parsimony, distance methods
+       and Hadamard conjugation. Allows to compare trees, models selection and
+       offers visualizations for trees and split networks."""
+
+    homepage = "https://cran.r-project.org/package=phangorn"
+    url      = "https://cran.r-project.org/src/contrib/phangorn_2.3.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/phangorn"
+
+    version('2.3.1', '85e7309900d061432508ab6f7e3e627e')
+
+    depends_on('r-ape@5.0:', type=('build', 'run'))
+    depends_on('r-quadprog', type=('build', 'run'))
+    depends_on('r-igraph@1.0:', type=('build', 'run'))
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-fastmatch', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py
new file mode 100644
index 0000000000..a40df310b9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPhantompeakqualtools(RPackage):
+    """Computes informative enrichment and quality measures for
+       ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. This is a modified version
+       of r-spp to be used in conjunction with the phantompeakqualtools
+       package."""
+
+    homepage = "https://github.com/kundajelab/phantompeakqualtools"
+    url      = "https://github.com/kundajelab/phantompeakqualtools/raw/master/spp_1.14.tar.gz"
+
+    version('1.14', '4de207d570999170c1bf45bcba8c6d2d')
+
+    depends_on('boost@1.41.0:')
+    depends_on('r-catools', type=('build', 'run'))
+    depends_on('r-snow', type=('build', 'run'))
+    depends_on('r-snowfall', type=('build', 'run'))
+    depends_on('r-bitops', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+
+    conflicts('%gcc@6:')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('BOOST_ROOT', self.spec['boost'].prefix)
diff --git a/var/spack/repos/builtin/packages/r-phyloseq/package.py b/var/spack/repos/builtin/packages/r-phyloseq/package.py
new file mode 100644
index 0000000000..c2323c4209
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-phyloseq/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPhyloseq(RPackage):
+    """phyloseq provides a set of classes and tools to facilitate the import,
+    storage, analysis, and graphical display of microbiome census data."""
+
+    homepage = "https://www.bioconductor.org/packages/phyloseq/"
+    git      = "https://git.bioconductor.org/packages/phyloseq.git"
+
+    version('1.20.0', commit='107d1d5e3437a6e33982c06a548d3cc91df2a7e0')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.20.0')
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-ade4', type=('build', 'run'))
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-biomformat', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-cluster', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-foreach', type=('build', 'run'))
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
+    depends_on('r-multtest', type=('build', 'run'))
+    depends_on('r-plyr', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-scales', type=('build', 'run'))
+    depends_on('r-vegan', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-picante/package.py b/var/spack/repos/builtin/packages/r-picante/package.py
new file mode 100644
index 0000000000..f967e5b19b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-picante/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPicante(RPackage):
+    """R tools for integrating phylogenies and ecology"""
+
+    homepage = "https://cran.r-project.org/package=picante"
+    url      = "https://cran.r-project.org/src/contrib/picante_1.6-2.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/picante"
+
+    version('1.6-2', 'e3eba6ef254068d2cfa9e96760bcd7a3')
+    version('1.6-1', '73d86b90eceda582654e995d47236d6e')
+
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'))
+    depends_on('r-vegan', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-pkgconfig/package.py b/var/spack/repos/builtin/packages/r-pkgconfig/package.py
index 56263cb210..b35d0e1383 100644
--- a/var/spack/repos/builtin/packages/r-pkgconfig/package.py
+++ b/var/spack/repos/builtin/packages/r-pkgconfig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py
index efb91262a4..8b0b1b7e1c 100644
--- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py
+++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-plogr/package.py b/var/spack/repos/builtin/packages/r-plogr/package.py
index 0f5e1319b7..e959c294a2 100644
--- a/var/spack/repos/builtin/packages/r-plogr/package.py
+++ b/var/spack/repos/builtin/packages/r-plogr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,9 @@ class RPlogr(RPackage):
     'LinkingTo: plogr' to 'DESCRIPTION', and '#include <plogr.h>'
     in your C++ modules to use it."""
 
-    homepage = "https://cran.r-project.org/web/packages/plogr/index.html"
-    url      = "https://cran.r-project.org/src/contrib/plogr_0.1-1.tar.gz"
+    homepage = "https://cran.r-project.org/package=plogr"
+    url      = "https://cran.r-project.org/src/contrib/plogr_0.2.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/plogr"
+
+    version('0.2.0', sha256='0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29')
     version('0.1-1', '5ee46ed21b5c571d02900219098517c0')
diff --git a/var/spack/repos/builtin/packages/r-plot3d/package.py b/var/spack/repos/builtin/packages/r-plot3d/package.py
new file mode 100644
index 0000000000..74883c1f2f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-plot3d/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPlot3d(RPackage):
+    """Functions for viewing 2-D and 3-D data, including perspective plots,
+       slice plots, surface plots, scatter plots, etc. Includes data sets from
+       oceanography."""
+
+    homepage = "https://CRAN.R-project.org/package=plot3D"
+    url      = "https://cran.r-project.org/src/contrib/plot3D_1.1.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/plot3D"
+
+    version('1.1.1', '5135aa1f3cf6106f2ded3f393a24e75d')
+
+    depends_on('r-misc3d', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-plotly/package.py b/var/spack/repos/builtin/packages/r-plotly/package.py
new file mode 100644
index 0000000000..414155d75b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-plotly/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPlotly(RPackage):
+    """Easily translate 'ggplot2' graphs to an interactive web-based version
+    and/or create custom web-based visualizations directly from R."""
+
+    homepage = "https://cran.r-project.org/web/packages/plotly/index.html"
+    url      = "https://cran.r-project.org/src/contrib/plotly_4.7.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/plotly"
+
+    version('4.7.1', '4799c8b429291d4c52fb904380806548')
+    version('4.7.0', '5bd52d515c01af7ff291c30a6cf23bec')
+    version('4.6.0', '27ff3de288bacfaad6e6694752ea2929')
+    version('4.5.6', 'e6e00177fa64dc6b1a199facfd73f585')
+    version('4.5.2', '7eb11b24a9faa9a572657fd89ed72fa5')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-httr', type=('build', 'run'))
+    depends_on('r-base64enc', type=('build', 'run'))
+    depends_on('r-htmltools', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-htmlwidgets', type=('build', 'run'))
+    depends_on('r-data-table', type=('build', 'run'))
+    depends_on('r-hexbin', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-crosstalk', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-plotrix/package.py b/var/spack/repos/builtin/packages/r-plotrix/package.py
index 018d68c498..0ab72642af 100644
--- a/var/spack/repos/builtin/packages/r-plotrix/package.py
+++ b/var/spack/repos/builtin/packages/r-plotrix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pls/package.py b/var/spack/repos/builtin/packages/r-pls/package.py
index b4d5c5c493..51c83e32a3 100644
--- a/var/spack/repos/builtin/packages/r-pls/package.py
+++ b/var/spack/repos/builtin/packages/r-pls/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-plyr/package.py b/var/spack/repos/builtin/packages/r-plyr/package.py
index 70a2659f95..bd2dc01429 100644
--- a/var/spack/repos/builtin/packages/r-plyr/package.py
+++ b/var/spack/repos/builtin/packages/r-plyr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pmcmr/package.py b/var/spack/repos/builtin/packages/r-pmcmr/package.py
index 11d8d3edfb..5a2c5593ce 100644
--- a/var/spack/repos/builtin/packages/r-pmcmr/package.py
+++ b/var/spack/repos/builtin/packages/r-pmcmr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-png/package.py b/var/spack/repos/builtin/packages/r-png/package.py
index 6d65cc6476..d0cc9c24db 100644
--- a/var/spack/repos/builtin/packages/r-png/package.py
+++ b/var/spack/repos/builtin/packages/r-png/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-powerlaw/package.py b/var/spack/repos/builtin/packages/r-powerlaw/package.py
new file mode 100644
index 0000000000..9666f8fd09
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-powerlaw/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPowerlaw(RPackage):
+    """An implementation of maximum likelihood estimators for a variety of
+       heavy tailed distributions, including both the discrete and continuous
+       power law distributions. Additionally, a goodness-of-fit based approach
+       is used to estimate the lower cut-off for the scaling region."""
+
+    homepage = "https://github.com/csgillespie/poweRlaw"
+    url      = "https://cran.rstudio.com/src/contrib/poweRlaw_0.70.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/poweRlaw"
+
+    version('0.70.1', '4117cb95c37f72441f320ea12f553065')
+
+    depends_on('r-vgam', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-prabclus/package.py b/var/spack/repos/builtin/packages/r-prabclus/package.py
index de5b5b7db9..688cd683cd 100644
--- a/var/spack/repos/builtin/packages/r-prabclus/package.py
+++ b/var/spack/repos/builtin/packages/r-prabclus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-praise/package.py b/var/spack/repos/builtin/packages/r-praise/package.py
index f58ba04b06..06ae033e60 100644
--- a/var/spack/repos/builtin/packages/r-praise/package.py
+++ b/var/spack/repos/builtin/packages/r-praise/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-preprocesscore/package.py b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
index 95ce33d8c3..d07e164a6d 100644
--- a/var/spack/repos/builtin/packages/r-preprocesscore/package.py
+++ b/var/spack/repos/builtin/packages/r-preprocesscore/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,8 @@ class RPreprocesscore(RPackage):
     """A library of core preprocessing routines"""
 
     homepage = "https://bioconductor.org/packages/preprocessCore/"
-    url      = "https://git.bioconductor.org/packages/preprocessCore"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/preprocessCore.git"
 
-    version('1.38.1', git='https://git.bioconductor.org/packages/preprocessCore', commit='c58cb4c720eda0f1c733b989b14912093a7c5fbc')
+    version('1.38.1', commit='c58cb4c720eda0f1c733b989b14912093a7c5fbc')
 
     depends_on('r@3.4.0:3.4.9', when='@1.38.1')
diff --git a/var/spack/repos/builtin/packages/r-prettyunits/package.py b/var/spack/repos/builtin/packages/r-prettyunits/package.py
index 0741d17411..fc5de8b0e1 100644
--- a/var/spack/repos/builtin/packages/r-prettyunits/package.py
+++ b/var/spack/repos/builtin/packages/r-prettyunits/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-processx/package.py b/var/spack/repos/builtin/packages/r-processx/package.py
new file mode 100644
index 0000000000..fec9bba0b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-processx/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RProcessx(RPackage):
+    """Tools to run system processes in the background"""
+
+    homepage = "https://github.com/r-lib/processx"
+    url      = "https://cran.r-project.org/src/contrib/processx_3.2.0.tar.gz"
+    list_url      = "https://cran.r-project.org/src/contrib/Archive/processx/processx_3.1.0.tar.gz"
+
+    version('3.2.0', sha256='c4ba602fcbdc032ae9d94701b3e6b83a2dab1b53d0b4f9937b07a84eae22fddf')
+    version('3.1.0',   sha256='11ac120ab4e4aa0e99c9b2eda87d07bc683bab735f1761e95e5ddacd311b5972')
+    version('3.0.3',   sha256='53781dba3c538605a02e28b3b577e7de79e2064bfc502025f7ec0e5945e302bf')
+    version('2.0.0.1', sha256='8f61b2952d0f2d13c74465bfba174ce11eee559475c2f7b9be6bcb9e2e1d827b')
+    version('2.0.0',   sha256='8325b56a60a276909228756281523cda9256bc754c5f3ca03b41c5c17cc398ad')
+
+    depends_on('r-assertthat', type=('build', 'run'))
+    depends_on('r-crayon', type=('build', 'run'))
+    depends_on('r-ps', type=('build', 'run'))
+    depends_on('r-r6', type=('build', 'run'))
+    depends_on('r-utils', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-prodlim/package.py b/var/spack/repos/builtin/packages/r-prodlim/package.py
index b9721174d6..8cb3523f6d 100644
--- a/var/spack/repos/builtin/packages/r-prodlim/package.py
+++ b/var/spack/repos/builtin/packages/r-prodlim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-progress/package.py b/var/spack/repos/builtin/packages/r-progress/package.py
index b5a909a73d..756b8cecff 100644
--- a/var/spack/repos/builtin/packages/r-progress/package.py
+++ b/var/spack/repos/builtin/packages/r-progress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-protgenerics/package.py b/var/spack/repos/builtin/packages/r-protgenerics/package.py
index 7ec8fa8537..2b14314b29 100644
--- a/var/spack/repos/builtin/packages/r-protgenerics/package.py
+++ b/var/spack/repos/builtin/packages/r-protgenerics/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,8 @@ class RProtgenerics(RPackage):
     """S4 generic functions needed by Bioconductor proteomics packages."""
 
     homepage = "https://bioconductor.org/packages/ProtGenerics/"
-    url      = "https://git.bioconductor.org/packages/ProtGenerics"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/ProtGenerics.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/ProtGenerics', commit='b2b3bb0938e20f58fca905f6870de7dbc9dfd7a3')
+    version('1.8.0', commit='b2b3bb0938e20f58fca905f6870de7dbc9dfd7a3')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
diff --git a/var/spack/repos/builtin/packages/r-proto/package.py b/var/spack/repos/builtin/packages/r-proto/package.py
index 412ad956e3..5fe325b834 100644
--- a/var/spack/repos/builtin/packages/r-proto/package.py
+++ b/var/spack/repos/builtin/packages/r-proto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,4 +14,5 @@ class RProto(RPackage):
     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('1.0.0', sha256='9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1')
     version('0.3-10', 'd5523943a5be6ca2f0ab557c900f8212')
diff --git a/var/spack/repos/builtin/packages/r-proxy/package.py b/var/spack/repos/builtin/packages/r-proxy/package.py
index 5f6057c769..963568491c 100644
--- a/var/spack/repos/builtin/packages/r-proxy/package.py
+++ b/var/spack/repos/builtin/packages/r-proxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-pryr/package.py b/var/spack/repos/builtin/packages/r-pryr/package.py
index b1e9ad4e9b..89142810ba 100644
--- a/var/spack/repos/builtin/packages/r-pryr/package.py
+++ b/var/spack/repos/builtin/packages/r-pryr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-ps/package.py b/var/spack/repos/builtin/packages/r-ps/package.py
new file mode 100644
index 0000000000..0973376a04
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ps/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPs(RPackage):
+    """Manipulate processes on Windows, Linux and MacOS"""
+
+    homepage = "https://github.com/r-lib/ps"
+    url      = "https://cran.r-project.org/src/contrib/ps_1.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/ps/ps_1.0.0.tar.gz"
+
+    version('1.1.0', sha256='5d5240d5bf1d48c721b3fdf47cfc9dbf878e388ea1f057b764db05bffdc4a9fe')
+    version('1.0.0', sha256='9bdaf64aaa44ae11866868402eb75bf56c2e3022100476d9b9dcd16ca784ffd8')
diff --git a/var/spack/repos/builtin/packages/r-psych/package.py b/var/spack/repos/builtin/packages/r-psych/package.py
new file mode 100644
index 0000000000..d000222e7a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-psych/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RPsych(RPackage):
+    """A general purpose toolbox for personality, psychometric theory and
+       experimental psychology. Functions are primarily for multivariate
+       analysis and scale construction using factor analysis, principal
+       component analysis, cluster analysis and reliability analysis, although
+       others provide basic descriptive statistics. Item Response Theory is
+       done using factor analysis of tetrachoric and polychoric correlations.
+       Functions for analyzing data at multiple levels include within and
+       between group statistics, including correlations and factor analysis.
+       Functions for simulating and testing particular item and test structures
+       are included. Several functions serve as a useful front end for
+       structural equation modeling. Graphical displays of path diagrams,
+       factor analysis and structural equation models are created using basic
+       graphics. Some of the functions are written to support a book on
+       psychometric theory as well as publications in personality research.
+       For more information, see the <http://personality-project.org/r> web
+       page."""
+
+    homepage = "http://personality-project.org/r/psych"
+    url      = "https://cran.r-project.org/src/contrib/psych_1.7.8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/psych"
+
+    version('1.7.8', 'db37f2f85ff5470ee40bbc0a58ebe22b')
+
+    depends_on('r-mnormt', type=('build', 'run'))
+    depends_on('r-foreign', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-nlme', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-ptw/package.py b/var/spack/repos/builtin/packages/r-ptw/package.py
index 38048bc2a7..dcb5fdedc0 100644
--- a/var/spack/repos/builtin/packages/r-ptw/package.py
+++ b/var/spack/repos/builtin/packages/r-ptw/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-purrr/package.py b/var/spack/repos/builtin/packages/r-purrr/package.py
index 4ef40d9480..73a422c0cb 100644
--- a/var/spack/repos/builtin/packages/r-purrr/package.py
+++ b/var/spack/repos/builtin/packages/r-purrr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-quadprog/package.py b/var/spack/repos/builtin/packages/r-quadprog/package.py
index dc35139a65..ad68a31a0d 100644
--- a/var/spack/repos/builtin/packages/r-quadprog/package.py
+++ b/var/spack/repos/builtin/packages/r-quadprog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-quantmod/package.py b/var/spack/repos/builtin/packages/r-quantmod/package.py
index 749558f894..b9f0e063e8 100644
--- a/var/spack/repos/builtin/packages/r-quantmod/package.py
+++ b/var/spack/repos/builtin/packages/r-quantmod/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-quantreg/package.py b/var/spack/repos/builtin/packages/r-quantreg/package.py
index 6b33827526..e882ece170 100644
--- a/var/spack/repos/builtin/packages/r-quantreg/package.py
+++ b/var/spack/repos/builtin/packages/r-quantreg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-quantro/package.py b/var/spack/repos/builtin/packages/r-quantro/package.py
index 05185abe8b..796685c40a 100644
--- a/var/spack/repos/builtin/packages/r-quantro/package.py
+++ b/var/spack/repos/builtin/packages/r-quantro/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,9 @@ class RQuantro(RPackage):
        user-defined groups."""
 
     homepage = "https://www.bioconductor.org/packages/quantro/"
-    url      = "https://git.bioconductor.org/packages/quantro"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/quantro.git"
 
-    version('1.10.0', git='https://git.bioconductor.org/packages/quantro', commit='111337c0aba052aa49c3d2e2d3042794b28858c9')
+    version('1.10.0', commit='111337c0aba052aa49c3d2e2d3042794b28858c9')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-minfi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-qvalue/package.py b/var/spack/repos/builtin/packages/r-qvalue/package.py
index f34f00c7e4..5deb42a748 100644
--- a/var/spack/repos/builtin/packages/r-qvalue/package.py
+++ b/var/spack/repos/builtin/packages/r-qvalue/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,10 +22,12 @@ class RQvalue(RPackage):
     and data mining."""
 
     homepage = "https://www.bioconductor.org/packages/qvalue/"
-    url      = "https://git.bioconductor.org/packages/qvalue"
+    git      = "https://git.bioconductor.org/packages/qvalue.git"
 
-    version('2.8.0', git='https://git.bioconductor.org/packages/qvalue', commit='c7bf3315619d42d800f57a36670c25a7495ded72')
+    version('2.12.0', commit='7df64ebfcbe69dcbf8b88cb6ef0068bf16979673')
+    version('2.8.0', commit='c7bf3315619d42d800f57a36670c25a7495ded72')
 
-    depends_on('r@3.4.0:3.4.9', when='@2.8.0')
     depends_on('r-ggplot2', type=('build', 'run'))
     depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@2.8.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@2.12.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-r6/package.py b/var/spack/repos/builtin/packages/r-r6/package.py
index f424b1c8e1..fad58e9517 100644
--- a/var/spack/repos/builtin/packages/r-r6/package.py
+++ b/var/spack/repos/builtin/packages/r-r6/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-randomforest/package.py b/var/spack/repos/builtin/packages/r-randomforest/package.py
index 3fbb2a3d1e..1125e26d22 100644
--- a/var/spack/repos/builtin/packages/r-randomforest/package.py
+++ b/var/spack/repos/builtin/packages/r-randomforest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-ranger/package.py b/var/spack/repos/builtin/packages/r-ranger/package.py
new file mode 100644
index 0000000000..0693fc0023
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-ranger/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRanger(RPackage):
+    """A fast implementation of Random Forests, particularly suited for high
+    dimensional data."""
+
+    homepage = "https://cran.r-project.org/web/packages/ranger/index.html"
+    url      = "https://cran.r-project.org/src/contrib/ranger_0.8.0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/ranger"
+
+    version('0.8.0', '1501380f418e784a6159bc1fb06fd32c')
+    version('0.7.0', 'c7fbcbab7c195bc8e65b1ceb3baeb87f')
+    version('0.6.0', '047ad26289c9b528b7476aa4811b4111')
+    version('0.5.0', 'd45001c8ff58d3078de7353971219927')
+    version('0.4.0', 'd404d8a9142372e3c77482b6b7dc469b')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-matrix', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-rcppeigen', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rappdirs/package.py b/var/spack/repos/builtin/packages/r-rappdirs/package.py
new file mode 100644
index 0000000000..b39a699690
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rappdirs/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRappdirs(RPackage):
+    """An easy way to determine which directories on the users computer
+    you should use to save data, caches and logs. A port of Python's
+    'Appdirs' to R."""
+
+    homepage = "https://cran.r-project.org/package=rappdirs"
+    url      = "https://cran.rstudio.com/src/contrib/rappdirs_0.3.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rappdirs"
+
+    version('0.3.1', 'fbbdceda2aa49374e61c7d387bf9ea21')
+
+    depends_on('r@2.14:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-raster/package.py b/var/spack/repos/builtin/packages/r-raster/package.py
index 917adfb7d6..0bcb424ea6 100644
--- a/var/spack/repos/builtin/packages/r-raster/package.py
+++ b/var/spack/repos/builtin/packages/r-raster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rbgl/package.py b/var/spack/repos/builtin/packages/r-rbgl/package.py
index 13cd4fb68e..87216adc55 100644
--- a/var/spack/repos/builtin/packages/r-rbgl/package.py
+++ b/var/spack/repos/builtin/packages/r-rbgl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RRbgl(RPackage):
     algorithms contained in the BOOST library."""
 
     homepage = "https://www.bioconductor.org/packages/RBGL/"
-    url      = "https://git.bioconductor.org/packages/RBGL"
+    git      = "https://git.bioconductor.org/packages/RBGL.git"
 
-    version('1.52.0', git='https://git.bioconductor.org/packages/RBGL', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0')
+    version('1.52.0', commit='93e8fcfafec8f1cd5638fe30dc0f9506d15b49c0')
 
     depends_on('r@3.4.0:3.4.9', when='@1.52.0')
     depends_on('r-graph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rbokeh/package.py b/var/spack/repos/builtin/packages/r-rbokeh/package.py
index ee254db179..22c421b16b 100644
--- a/var/spack/repos/builtin/packages/r-rbokeh/package.py
+++ b/var/spack/repos/builtin/packages/r-rbokeh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
index 6092e34163..7115d8b2b4 100644
--- a/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
+++ b/var/spack/repos/builtin/packages/r-rcolorbrewer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py
index b95626020a..933cd294fb 100644
--- a/var/spack/repos/builtin/packages/r-rcpp/package.py
+++ b/var/spack/repos/builtin/packages/r-rcpp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,6 +21,8 @@ class RRcpp(RPackage):
     url      = "https://cran.rstudio.com/src/contrib/Rcpp_0.12.13.tar.gz"
     list_url = "https://cran.rstudio.com/src/contrib/Archive/Rcpp"
 
+    version('0.12.16', 'ab5107766c63d66065ed1a92a4cab1b7')
+    version('0.12.15', 'bebac0782862c15c2944764343e55582')
     version('0.12.14', '89a3dbad0aa3e345b9d0b862fa1fc56a')
     version('0.12.13', '5186d119132bfe07f66da74c50b190a4')
     version('0.12.12', '97b36a3b567e3438067c4a7d0075fd90')
diff --git a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py
index dba1dfe93d..250e12ec2f 100644
--- a/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py
+++ b/var/spack/repos/builtin/packages/r-rcpparmadillo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rcppblaze/package.py b/var/spack/repos/builtin/packages/r-rcppblaze/package.py
new file mode 100644
index 0000000000..dfdcefa2b1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppblaze/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppblaze(RPackage):
+    """'Blaze' is an open-source, high-performance C++ math library for dense
+       and sparse arithmetic.
+
+       With its state-of-the-art Smart Expression Template implementation
+       'Blaze' combines the elegance and ease of use of a domain-specific
+       language with 'HPC'-grade performance, making it one of the most
+       intuitive and fastest C++ math libraries available. The 'Blaze'
+       library offers: - high performance through the integration of
+       'BLAS' libraries and manually tuned 'HPC' math kernels - vectorization
+       by 'SSE', 'SSE2', 'SSE3', 'SSSE3', 'SSE4', 'AVX', 'AVX2', 'AVX-512',
+       'FMA', and 'SVML' - parallel execution by 'OpenMP', C++11 threads and
+       'Boost' threads ('Boost' threads are disabled in 'RcppBlaze') - the
+       intuitive and easy to use API of a domain specific language - unified
+       arithmetic with dense and sparse vectors and matrices - thoroughly
+       tested matrix and vector arithmetic - completely portable, high quality
+       C++ source code. The 'RcppBlaze' package includes the header files from
+       the 'Blaze' library with disabling some functionalities related to link
+       to the thread and system libraries which make 'RcppBlaze' be a
+       header-only library. Therefore, users do not need to install 'Blaze'
+       and the dependency 'Boost'. 'Blaze' is licensed under the New (Revised)
+       BSD license, while 'RcppBlaze' (the 'Rcpp' bindings/bridge to 'Blaze')
+       is licensed under the GNU GPL version 2 or later, as is the rest of
+       'Rcpp'. Note that since 'Blaze' has committed to 'C++14' commit to
+       'C++14' which does not used by most R users from version 3.0, we will
+       use the version 2.6 of 'Blaze' which is 'C++98' compatible to support
+       the most compilers and system."""
+
+    homepage = "https://github.com/Chingchuan-chen/RcppBlaze"
+    url      = "https://cran.rstudio.com/src/contrib/RcppBlaze_0.2.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/RcppBlaze"
+
+    version('0.2.2', '22ecae73cf1bebce06ed6387d49f2c77')
+
+    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
+    depends_on('r-matrix@1.1-0:', type=('build', 'run'))
+    depends_on('r-bh@1.54.0-2:', type=('build', 'run'))
+    depends_on('r@3.0.2:')
diff --git a/var/spack/repos/builtin/packages/r-rcppcctz/package.py b/var/spack/repos/builtin/packages/r-rcppcctz/package.py
new file mode 100644
index 0000000000..5e454dd6dc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppcctz/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppcctz(RPackage):
+    """'Rcpp' Access to the 'CCTZ' timezone library is provided. 'CCTZ' is a
+       C++ library for translating between absolute and civil times using the
+       rules of a time zone. The 'CCTZ' source code, released under the
+       Apache 2.0 License, is included in this package. See
+       <https://github.com/google/cctz> for more details."""
+
+    homepage = "https://github.com/eddelbuettel/rcppcctz"
+    url      = "https://cran.r-project.org/src/contrib/RcppCCTZ_0.2.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RcppCCTZ"
+
+    version('0.2.3', '7635014a1cc696a3f00a7619fb5d7008')
+
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rcppcnpy/package.py b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py
new file mode 100644
index 0000000000..ace5876f48
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppcnpy/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppcnpy(RPackage):
+    """Rcpp bindings for NumPy files."""
+
+    homepage = "https://github.com/eddelbuettel/rcppcnpy"
+    url      = "https://cran.r-project.org/src/contrib/RcppCNPy_0.2.9.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/RcppCNPy"
+
+    version('0.2.9', '7f63354d15928b6716830c2975b3baf0')
+
+    depends_on('r@3.1.0:', type=('build', 'run'))
+    depends_on('cnpy')
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rcppeigen/package.py b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
index 47ce27e3f5..14d4e250ef 100644
--- a/var/spack/repos/builtin/packages/r-rcppeigen/package.py
+++ b/var/spack/repos/builtin/packages/r-rcppeigen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,6 +25,7 @@ class RRcppeigen(RPackage):
     url      = "https://cran.r-project.org/src/contrib/RcppEigen_0.3.2.9.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/RcppEigen"
 
+    version('0.3.3.3.1', '1a5ae17828813e40e6b3e7400e408a2b')
     version('0.3.2.9.0', '14a7786882a5d9862d53c4b2217df318')
     version('0.3.2.8.1', '4146e06e4fdf7f4d08db7839069d479f')
 
diff --git a/var/spack/repos/builtin/packages/r-rcppprogress/package.py b/var/spack/repos/builtin/packages/r-rcppprogress/package.py
new file mode 100644
index 0000000000..d56b33f757
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rcppprogress/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRcppprogress(RPackage):
+    """Allows to display a progress bar in the R console for long running
+    computations taking place in c++ code, and support for interrupting
+    those computations even in multithreaded code, typically using OpenMP."""
+
+    homepage = "https://cran.r-project.org/web/packages/RcppProgress/index.html"
+    url      = "https://cran.r-project.org/src/contrib/RcppProgress_0.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RcppProgress"
+
+    version('0.3',   '3cd527af84bc6fcb3c77422e0ff09dba')
+    version('0.2.1', 'c9cd69759ff457acfee0b52353f9af1b')
+    version('0.2',   '9522c962ecddd4895b5636e7a499bda5')
+    version('0.1',   '34afefe0580ca42b6353533fe758d5bf')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rcurl/package.py b/var/spack/repos/builtin/packages/r-rcurl/package.py
index a60499330c..031c69e842 100644
--- a/var/spack/repos/builtin/packages/r-rcurl/package.py
+++ b/var/spack/repos/builtin/packages/r-rcurl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rda/package.py b/var/spack/repos/builtin/packages/r-rda/package.py
index 614f6756ce..e8d455050a 100644
--- a/var/spack/repos/builtin/packages/r-rda/package.py
+++ b/var/spack/repos/builtin/packages/r-rda/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class RRda(RPackage):
     classification purpose in high dimensional data."""
 
     homepage = "https://cran.r-project.org/web/packages/rda/index.html"
-    url      = "https://cran.r-project.org/src/contrib/rda_1.0.2-2.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/rda_1.0.2-1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rda"
+
     version('1.0.2-1', '78060c5e054a63a2df4ae4002d7247bc')
diff --git a/var/spack/repos/builtin/packages/r-readr/package.py b/var/spack/repos/builtin/packages/r-readr/package.py
index bec64a6ebd..bb9b862ac9 100644
--- a/var/spack/repos/builtin/packages/r-readr/package.py
+++ b/var/spack/repos/builtin/packages/r-readr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-readxl/package.py b/var/spack/repos/builtin/packages/r-readxl/package.py
index c70750ea69..3d19f6808e 100644
--- a/var/spack/repos/builtin/packages/r-readxl/package.py
+++ b/var/spack/repos/builtin/packages/r-readxl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,8 +14,10 @@ class RReadxl(RPackage):
     without external dependencies."""
 
     homepage = "http://readxl.tidyverse.org/"
-    url      = "https://cran.r-project.org/src/contrib/readxl_1.0.0.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/readxl_1.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/readxl/readxl_1.0.0.tar.gz"
 
+    version('1.1.0', sha256='b63d21fc6510acb373e96deaec45e966a523ec75cbec75a089529297ed443116')
     version('1.0.0', '030c47ae1af5dd4168087160c29131e4')
 
     depends_on('r-tibble', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-registry/package.py b/var/spack/repos/builtin/packages/r-registry/package.py
index da252a9681..f83c78f0e0 100644
--- a/var/spack/repos/builtin/packages/r-registry/package.py
+++ b/var/spack/repos/builtin/packages/r-registry/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rematch/package.py b/var/spack/repos/builtin/packages/r-rematch/package.py
index 931f979c60..b4232fa1da 100644
--- a/var/spack/repos/builtin/packages/r-rematch/package.py
+++ b/var/spack/repos/builtin/packages/r-rematch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-reordercluster/package.py b/var/spack/repos/builtin/packages/r-reordercluster/package.py
index 49ab521967..cc4af49952 100644
--- a/var/spack/repos/builtin/packages/r-reordercluster/package.py
+++ b/var/spack/repos/builtin/packages/r-reordercluster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-reportingtools/package.py b/var/spack/repos/builtin/packages/r-reportingtools/package.py
index db5978248c..e093b019be 100644
--- a/var/spack/repos/builtin/packages/r-reportingtools/package.py
+++ b/var/spack/repos/builtin/packages/r-reportingtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,9 +21,9 @@ class RReportingtools(RPackage):
     site: http:// research-pub.gene.com/ReportingTools."""
 
     homepage = "https://bioconductor.org/packages/ReportingTools/"
-    url      = "https://git.bioconductor.org/packages/ReportingTools"
+    git      = "https://git.bioconductor.org/packages/ReportingTools.git"
 
-    version('2.16.0', git='https://git.bioconductor.org/packages/ReportingTools', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663')
+    version('2.16.0', commit='b1aa0ea302da7f2993ce8087b1d09c11ddf03663')
 
     depends_on('r@3.4.0:3.4.9', when='@2.16.0')
     depends_on('r-knitr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-repr/package.py b/var/spack/repos/builtin/packages/r-repr/package.py
index 056e19aedc..0396cd79bb 100644
--- a/var/spack/repos/builtin/packages/r-repr/package.py
+++ b/var/spack/repos/builtin/packages/r-repr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-reprex/package.py b/var/spack/repos/builtin/packages/r-reprex/package.py
index a4fa82ed16..e87e70367b 100644
--- a/var/spack/repos/builtin/packages/r-reprex/package.py
+++ b/var/spack/repos/builtin/packages/r-reprex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-reshape/package.py b/var/spack/repos/builtin/packages/r-reshape/package.py
index a4da7286ca..8364397fa2 100644
--- a/var/spack/repos/builtin/packages/r-reshape/package.py
+++ b/var/spack/repos/builtin/packages/r-reshape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-reshape2/package.py b/var/spack/repos/builtin/packages/r-reshape2/package.py
index 204ccdee8a..ac424cd4f3 100644
--- a/var/spack/repos/builtin/packages/r-reshape2/package.py
+++ b/var/spack/repos/builtin/packages/r-reshape2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rex/package.py b/var/spack/repos/builtin/packages/r-rex/package.py
index e39976644c..d8bb5841c2 100644
--- a/var/spack/repos/builtin/packages/r-rex/package.py
+++ b/var/spack/repos/builtin/packages/r-rex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rgdal/package.py b/var/spack/repos/builtin/packages/r-rgdal/package.py
new file mode 100644
index 0000000000..b2fbfee9dc
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rgdal/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRgdal(RPackage):
+    """Provides bindings to the 'Geospatial' Data Abstraction Library
+    ('GDAL') (>= 1.6.3) and access to projection/transformation operations
+    from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are
+    external to the package, and, when installing the package from source,
+    must be correctly installed first. Both 'GDAL' raster and 'OGR' vector
+    map data can be imported into R, and 'GDAL' raster data and 'OGR'
+    vector data exported. Use is made of classes defined in the 'sp' package.
+    Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and
+    'Expat') are provided on 'CRAN'."""
+
+    homepage = "https://cran.r-project.org/package=rgdal"
+    url      = "https://cran.rstudio.com/src/contrib/rgdal_1.2-16.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rgdal"
+
+    version('1.2-16', 'de83bf08519a53de68a7632ecb7f2dc9')
+
+    depends_on('r-sp', type=('build', 'run'))
+    depends_on('gdal')
+    depends_on('proj')
diff --git a/var/spack/repos/builtin/packages/r-rgenoud/package.py b/var/spack/repos/builtin/packages/r-rgenoud/package.py
new file mode 100644
index 0000000000..c2d7c517d4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rgenoud/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRgenoud(RPackage):
+    """A genetic algorithm plus derivative optimizer."""
+
+    homepage = "http://sekhon.berkeley.edu/rgenoud/"
+    url      = "https://cran.r-project.org/src/contrib/rgenoud_5.8-1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rgenoud"
+
+    version('5.8-1.0', '85801093d2f1e6789683b46ab4a7d70f')
diff --git a/var/spack/repos/builtin/packages/r-rgeos/package.py b/var/spack/repos/builtin/packages/r-rgeos/package.py
new file mode 100644
index 0000000000..2f55d523f6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rgeos/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRgeos(RPackage):
+    """Interface to Geometry Engine - Open Source ('GEOS') using the C
+    'API' for topology operations on geometries. The 'GEOS' library is
+    external to the package, and, when installing the package from source,
+    must be correctly installed first. Windows and Mac Intel OS X binaries
+    are provided on 'CRAN'."""
+
+    homepage = "https://cran.r-project.org/package=rgeos"
+    url      = "https://cran.rstudio.com/src/contrib/rgeos_0.3-26.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rgeos"
+
+    version('0.3-26', '7d10a28011b49f68c5817b6fbca132df')
+
+    depends_on('r-sp', type=('build', 'run'))
+    depends_on('geos')
diff --git a/var/spack/repos/builtin/packages/r-rgl/package.py b/var/spack/repos/builtin/packages/r-rgl/package.py
index 97f89ed092..261fbffa98 100644
--- a/var/spack/repos/builtin/packages/r-rgl/package.py
+++ b/var/spack/repos/builtin/packages/r-rgl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py
index e1665fd991..b246f8f63f 100644
--- a/var/spack/repos/builtin/packages/r-rgooglemaps/package.py
+++ b/var/spack/repos/builtin/packages/r-rgooglemaps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rgraphviz/package.py b/var/spack/repos/builtin/packages/r-rgraphviz/package.py
new file mode 100644
index 0000000000..1f341b24b9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rgraphviz/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRgraphviz(RPackage):
+    """Interfaces R with the AT and T graphviz library for plotting
+    R graph objects from the graph package."""
+
+    homepage = "http://bioconductor.org/packages/Rgraphviz/"
+    git      = "https://git.bioconductor.org/packages/Rgraphviz.git"
+
+    version('2.20.0', commit='eface6298150667bb22eac672f1a45e52fbf8c90')
+
+    depends_on('r@3.4.0:3.4.9', when='@2.20.0')
+    depends_on('r-graph', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rhdf5/package.py b/var/spack/repos/builtin/packages/r-rhdf5/package.py
new file mode 100644
index 0000000000..7c4a3a9987
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rhdf5/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRhdf5(RPackage):
+    """This R/Bioconductor package provides an interface between HDF5
+    and R. HDF5's main features are the ability to store and access very
+    large and/or complex datasets and a wide variety of metadata on mass
+    storage (disk) through a completely portable file format. The rhdf5
+    package is thus suited for the exchange of large and/or complex
+    datasets between R and other software package, and for letting R
+    applications work on datasets that are larger than the available RAM."""
+
+    homepage = "https://www.bioconductor.org/packages/rhdf5/"
+    git      = "https://git.bioconductor.org/packages/rhdf5.git"
+
+    version('2.20.0', commit='37b5165325062728bbec9167f89f5f4b794f30bc')
+
+    depends_on('r@3.4.0:3.4.9', when='@2.20.0')
+    depends_on('r-zlibbioc', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rhtslib/package.py b/var/spack/repos/builtin/packages/r-rhtslib/package.py
index 4af0093830..e87164b5aa 100644
--- a/var/spack/repos/builtin/packages/r-rhtslib/package.py
+++ b/var/spack/repos/builtin/packages/r-rhtslib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,10 @@ class RRhtslib(RPackage):
     are in the vignette, vignette(package="Rhtslib", "Rhtslib")."""
 
     homepage = "https://www.bioconductor.org/packages/Rhtslib/"
-    url      = "https://git.bioconductor.org/packages/Rhtslib"
+    git      = "https://git.bioconductor.org/packages/Rhtslib.git"
 
-    version('1.8.0', git='https://git.bioconductor.org/packages/Rhtslib', commit='3b5493473bed42958614091c58c739932ffcfa79')
+    version('1.8.0', commit='3b5493473bed42958614091c58c739932ffcfa79')
 
     depends_on('r@3.4.0:3.4.9', when='@1.8.0')
     depends_on('r-zlibbioc', type=('build', 'run'))
+    depends_on('autoconf@2.67:', type='build')
diff --git a/var/spack/repos/builtin/packages/r-rinside/package.py b/var/spack/repos/builtin/packages/r-rinside/package.py
index 1d744db01d..bc7d48745a 100644
--- a/var/spack/repos/builtin/packages/r-rinside/package.py
+++ b/var/spack/repos/builtin/packages/r-rinside/package.py
@@ -1,27 +1,7 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 from spack import *
 
@@ -43,9 +23,10 @@ class RRinside(RPackage):
     available at the 'RInside' website as well."""
 
     homepage = "http://dirk.eddelbuettel.com/code/rinside.html"
-    url      = "https://cran.r-project.org/src/contrib/RInside_0.2.13.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/RInside_0.2.14.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/RInside"
 
+    version('0.2.14', 'fc72761e22b1f597433eb53d6eb122ff')
     version('0.2.13', '2e3c35a7bd648e9bef98d0afcc02cf88')
 
-    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rjags/package.py b/var/spack/repos/builtin/packages/r-rjags/package.py
new file mode 100644
index 0000000000..1dae43af36
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rjags/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class RRjags(RPackage):
+    """Interface to the JAGS MCMC library.
+       Usage: $ spack load r-rjags """
+
+    homepage = "https://cran.r-project.org/web/packages/rjags/index.html"
+    url      = "https://cran.r-project.org/src/contrib/rjags_4-8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/rjags/"
+
+    version('4-8', sha256='1529827ab11493fb5f05552e239d700ae2f818995d86d3c9e4c92523f594b59f')
+    version('4-6', 'c26b7cc8e8ddcdb55e14cba28df39f4c')
+
+    depends_on('jags', type=('link'))
+    depends_on('r-coda', type=('build', 'run'))
+
+    def configure_args(self):
+        args = ['--with-jags-lib=%s' % self.spec['jags'].prefix.lib,
+                '--with-jags-include=%s' % self.spec['jags'].prefix.include,
+                '--with-jags-modules=%s/JAGS/modules-4'
+                % self.spec['jags'].prefix.lib]
+        return args
diff --git a/var/spack/repos/builtin/packages/r-rjava/package.py b/var/spack/repos/builtin/packages/r-rjava/package.py
index a1e8003343..fc8c3850aa 100644
--- a/var/spack/repos/builtin/packages/r-rjava/package.py
+++ b/var/spack/repos/builtin/packages/r-rjava/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rjson/package.py b/var/spack/repos/builtin/packages/r-rjson/package.py
index d22b7c780f..250c5171a8 100644
--- a/var/spack/repos/builtin/packages/r-rjson/package.py
+++ b/var/spack/repos/builtin/packages/r-rjson/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rjsonio/package.py b/var/spack/repos/builtin/packages/r-rjsonio/package.py
index 064a50aea8..a8134aa6d6 100644
--- a/var/spack/repos/builtin/packages/r-rjsonio/package.py
+++ b/var/spack/repos/builtin/packages/r-rjsonio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rlang/package.py b/var/spack/repos/builtin/packages/r-rlang/package.py
index 86eb205b7c..cd179fcf57 100644
--- a/var/spack/repos/builtin/packages/r-rlang/package.py
+++ b/var/spack/repos/builtin/packages/r-rlang/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,11 @@ class RRlang(RPackage):
     """A toolbox for working with base types, core R features like the
        condition system, and core 'Tidyverse' features like tidy evaluation."""
 
-    homepage = "https://cran.r-project.org/web/packages/rlang/index.html"
-    url      = "https://cran.r-project.org/src/contrib/rlang_0.1.2.tar.gz"
+    homepage = "https://cran.r-project.org/package=rlang"
+    url      = "https://cran.r-project.org/src/contrib/rlang_0.2.2.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rlang"
 
+    version('0.2.2', 'df2abf3a1936c503ed1edd4350ffb5f0')
+    version('0.1.4', 'daed5104d557c0cbfb4a654ec8ffb579')
     version('0.1.2', '170f8cf7b61898040643515a1746a53a')
     version('0.1.1', '38a51a0b8f8487eb52b4f3d986313682')
diff --git a/var/spack/repos/builtin/packages/r-rmarkdown/package.py b/var/spack/repos/builtin/packages/r-rmarkdown/package.py
index 1910aa043a..6258b03a6e 100644
--- a/var/spack/repos/builtin/packages/r-rmarkdown/package.py
+++ b/var/spack/repos/builtin/packages/r-rmarkdown/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -33,12 +14,17 @@ class RRmarkdown(RPackage):
     url      = "https://cran.r-project.org/src/contrib/rmarkdown_1.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rmarkdown"
 
+    version('1.7', '477c50840581ba7947b3d905c67a511b')
     version('1.0', '264aa6a59e9680109e38df8270e14c58')
 
-    depends_on('r-knitr', type=('build', 'run'))
-    depends_on('r-yaml', type=('build', 'run'))
-    depends_on('r-htmltools', type=('build', 'run'))
-    depends_on('r-catools', type=('build', 'run'))
-    depends_on('r-evaluate', type=('build', 'run'))
+    depends_on('r-knitr@1.14:', type=('build', 'run'))
+    depends_on('r-yaml@2.1.5:', type=('build', 'run'))
+    depends_on('r-htmltools@0.3.5:', type=('build', 'run'))
+    depends_on('r-evaluate@0.8:', type=('build', 'run'))
     depends_on('r-base64enc', type=('build', 'run'))
     depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-rprojroot', type=('build', 'run'))
+    depends_on('r-mime', type=('build', 'run'))
+    depends_on('r-stringr@1.2.0:', type=('build', 'run'))
+    depends_on('r-catools', type=('build', 'run'))
+    depends_on('r@3.0:')
diff --git a/var/spack/repos/builtin/packages/r-rminer/package.py b/var/spack/repos/builtin/packages/r-rminer/package.py
index 2bd9147afb..758ac03fbe 100644
--- a/var/spack/repos/builtin/packages/r-rminer/package.py
+++ b/var/spack/repos/builtin/packages/r-rminer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rmpfr/package.py b/var/spack/repos/builtin/packages/r-rmpfr/package.py
index 1c2e5aafe3..eb6eb23e18 100644
--- a/var/spack/repos/builtin/packages/r-rmpfr/package.py
+++ b/var/spack/repos/builtin/packages/r-rmpfr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rmpi/package.py b/var/spack/repos/builtin/packages/r-rmpi/package.py
index e7e2870975..c81e101f91 100644
--- a/var/spack/repos/builtin/packages/r-rmpi/package.py
+++ b/var/spack/repos/builtin/packages/r-rmpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -51,13 +32,13 @@ class RRmpi(RPackage):
         # The type of MPI. Supported values are:
         # OPENMPI, LAM, MPICH, MPICH2, or CRAY
         if mpi_name == 'openmpi':
-            Rmpi_type = 'OPENMPI'
+            rmpi_type = 'OPENMPI'
         elif mpi_name == 'mpich':
-            Rmpi_type = 'MPICH2'
+            rmpi_type = 'MPICH2'
         else:
             raise InstallError('Unsupported MPI type')
 
         return [
-            '--with-Rmpi-type={0}'.format(Rmpi_type),
+            '--with-Rmpi-type={0}'.format(rmpi_type),
             '--with-mpi={0}'.format(spec['mpi'].prefix),
         ]
diff --git a/var/spack/repos/builtin/packages/r-rmysql/package.py b/var/spack/repos/builtin/packages/r-rmysql/package.py
index e34677652c..dc14ddde16 100644
--- a/var/spack/repos/builtin/packages/r-rmysql/package.py
+++ b/var/spack/repos/builtin/packages/r-rmysql/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py
index a9b06161d7..6112485e4e 100644
--- a/var/spack/repos/builtin/packages/r-rngtools/package.py
+++ b/var/spack/repos/builtin/packages/r-rngtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-robustbase/package.py b/var/spack/repos/builtin/packages/r-robustbase/package.py
index 1361e289fb..719a0045c1 100644
--- a/var/spack/repos/builtin/packages/r-robustbase/package.py
+++ b/var/spack/repos/builtin/packages/r-robustbase/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rocr/package.py b/var/spack/repos/builtin/packages/r-rocr/package.py
index 9936d99dbf..1f2ca35c44 100644
--- a/var/spack/repos/builtin/packages/r-rocr/package.py
+++ b/var/spack/repos/builtin/packages/r-rocr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rodbc/package.py b/var/spack/repos/builtin/packages/r-rodbc/package.py
index f7364b16fc..4f70634b62 100644
--- a/var/spack/repos/builtin/packages/r-rodbc/package.py
+++ b/var/spack/repos/builtin/packages/r-rodbc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class RRodbc(RPackage):
 
     homepage = "https://cran.rstudio.com/web/packages/RODBC/"
     url      = "https://cran.rstudio.com/src/contrib/RODBC_1.3-13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/RODBC/"
 
     version('1.3-13', 'c52ef9139c2ed85adc53ad6effa7d68e')
 
diff --git a/var/spack/repos/builtin/packages/r-rots/package.py b/var/spack/repos/builtin/packages/r-rots/package.py
new file mode 100644
index 0000000000..3c19b4d325
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rots/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRots(RPackage):
+    """Calculates the Reproducibility-Optimized Test Statistic (ROTS)
+       for differential testing in omics data."""
+
+    homepage = "https://bioconductor.org/packages/release/bioc/html/ROTS.html"
+    git      = "https://git.bioconductor.org/packages/ROTS.git"
+
+    version('1.8.0', commit='02e3c6455bb1afe7c4cc59ad6d4d8bae7b01428b')
+
+    depends_on('r@3.5.0:3.5.9', when='@1.8.0:', type=('build', 'run'))
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-roxygen2/package.py b/var/spack/repos/builtin/packages/r-roxygen2/package.py
index 30e295fbad..60fd47687d 100644
--- a/var/spack/repos/builtin/packages/r-roxygen2/package.py
+++ b/var/spack/repos/builtin/packages/r-roxygen2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rpart-plot/package.py b/var/spack/repos/builtin/packages/r-rpart-plot/package.py
index e7c1a09519..b531df7e3d 100644
--- a/var/spack/repos/builtin/packages/r-rpart-plot/package.py
+++ b/var/spack/repos/builtin/packages/r-rpart-plot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rpart/package.py b/var/spack/repos/builtin/packages/r-rpart/package.py
index adfbf3fdef..2c2f926d55 100644
--- a/var/spack/repos/builtin/packages/r-rpart/package.py
+++ b/var/spack/repos/builtin/packages/r-rpart/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rpostgresql/package.py b/var/spack/repos/builtin/packages/r-rpostgresql/package.py
index 3c8d9f0798..9061ba3c1d 100644
--- a/var/spack/repos/builtin/packages/r-rpostgresql/package.py
+++ b/var/spack/repos/builtin/packages/r-rpostgresql/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rprojroot/package.py b/var/spack/repos/builtin/packages/r-rprojroot/package.py
new file mode 100644
index 0000000000..617646350c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rprojroot/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRprojroot(RPackage):
+    """Robust, reliable and flexible paths to files below a project root.
+    The 'root' of a project is defined as a directory that matches a
+    certain criterion, e.g., it contains a certain regular file."""
+
+    homepage = "https://cran.r-project.org/package=rprojroot"
+    url      = "https://cran.rstudio.com/src/contrib/rprojroot_1.2.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rprojroot"
+
+    version('1.2', 'c1a0574aaac2a43a72f804abbaea19c3')
+
+    depends_on('r-backports', type=('build', 'run'))
+    depends_on('r@3.0.0:')
diff --git a/var/spack/repos/builtin/packages/r-rsamtools/package.py b/var/spack/repos/builtin/packages/r-rsamtools/package.py
index 41b08a95c7..d8062cc89b 100644
--- a/var/spack/repos/builtin/packages/r-rsamtools/package.py
+++ b/var/spack/repos/builtin/packages/r-rsamtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,19 +13,27 @@ class RRsamtools(RPackage):
        indexed tab-delimited (tabix) files."""
 
     homepage = "https://bioconductor.org/packages/Rsamtools/"
-    url      = "https://git.bioconductor.org/packages/Rsamtools"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/Rsamtools.git"
 
-    version('1.28.0', git='https://git.bioconductor.org/packages/Rsamtools', commit='dfa5b6abef68175586f21add7927174786412472')
+    version('1.32.2', commit='2b3254ccdeb24dc6ad95a93c2eb527021631797e')
+    version('1.28.0', commit='dfa5b6abef68175586f21add7927174786412472')
 
     depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.1.3:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.8:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.12:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', when='@1.32.2', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-bitops', type=('build', 'run'))
     depends_on('r-biocparallel', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.28.0')
+    depends_on('r@3.4.0:3.4.9', when='@1.28.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.32.2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rsnns/package.py b/var/spack/repos/builtin/packages/r-rsnns/package.py
index 92b891bf1a..8de7a9b7a1 100644
--- a/var/spack/repos/builtin/packages/r-rsnns/package.py
+++ b/var/spack/repos/builtin/packages/r-rsnns/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-rsolnp/package.py b/var/spack/repos/builtin/packages/r-rsolnp/package.py
new file mode 100644
index 0000000000..db4ab24959
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rsolnp/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRsolnp(RPackage):
+    """General Non-linear Optimization Using Augmented Lagrange Multiplier
+    Method."""
+
+    homepage = "https://cran.r-project.org/package=Rsolnp"
+    url      = "https://cran.rstudio.com/src/contrib/Rsolnp_1.16.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/Rsolnp"
+
+    version('1.16', '507e1e1a64f5f1d32b7e4e12ed19599f')
+
+    depends_on('r-truncnorm', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rsqlite/package.py b/var/spack/repos/builtin/packages/r-rsqlite/package.py
index 50cd4df05d..61ba90e83c 100644
--- a/var/spack/repos/builtin/packages/r-rsqlite/package.py
+++ b/var/spack/repos/builtin/packages/r-rsqlite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class RRsqlite(RPackage):
     (version 3.8.6) is included."""
 
     homepage = "https://cran.rstudio.com/web/packages/RSQLite/index.html"
-    url      = "https://cran.r-project.org/src/contrib/RSQLite_1.0.0.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/RSQLite_2.0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/RSQLite"
+
     version('2.0', '63842410e78ccdfc52d4ee97992521d5')
 
     depends_on('r-dbi', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rstan/package.py b/var/spack/repos/builtin/packages/r-rstan/package.py
index 50c9dbb205..30b4166091 100644
--- a/var/spack/repos/builtin/packages/r-rstan/package.py
+++ b/var/spack/repos/builtin/packages/r-rstan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,6 +21,7 @@ class RRstan(RPackage):
     url      = "https://cran.r-project.org/src/contrib/rstan_2.10.1.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rstan"
 
+    version('2.17.2', '60f4a0284c58f5efc1b1cbf488d7edda')
     version('2.10.1', 'f5d212f6f8551bdb91fe713d05d4052a')
 
     depends_on('r-ggplot2', type=('build', 'run'))
@@ -48,4 +30,5 @@ class RRstan(RPackage):
     depends_on('r-gridextra', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
     depends_on('r-rcppeigen', type=('build', 'run'))
+    depends_on('r-rcppeigen@0.3.3.3.0:', type=('build', 'run'), when='@2.17.2:')
     depends_on('r-bh', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rstudioapi/package.py b/var/spack/repos/builtin/packages/r-rstudioapi/package.py
index a9d977f62e..5b51a050d8 100644
--- a/var/spack/repos/builtin/packages/r-rstudioapi/package.py
+++ b/var/spack/repos/builtin/packages/r-rstudioapi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class RRstudioapi(RPackage):
     messages when it's not."""
 
     homepage = "https://cran.r-project.org/web/packages/rstudioapi/index.html"
-    url      = "https://cran.r-project.org/src/contrib/rstudioapi_0.5.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/rstudioapi_0.7.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/rstudioapi"
 
+    version('0.7', 'ee4ab567a7a9fdfac1a6fd01fe38de4a')
     version('0.6', 'fdb13bf46aab02421557e713fceab66b')
     version('0.5', '6ce1191da74e7bcbf06b61339486b3ba')
diff --git a/var/spack/repos/builtin/packages/r-rtracklayer/package.py b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
index 11f604b72f..69a2d37c43 100644
--- a/var/spack/repos/builtin/packages/r-rtracklayer/package.py
+++ b/var/spack/repos/builtin/packages/r-rtracklayer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,20 +15,31 @@ class RRtracklayer(RPackage):
        current viewport."""
 
     homepage = "http://bioconductor.org/packages/rtracklayer/"
-    url      = "https://git.bioconductor.org/packages/rtracklayer"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/rtracklayer.git"
 
-    version('1.36.6', git='https://git.bioconductor.org/packages/rtracklayer', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131')
+    version('1.40.5', commit='4e5b06daccd0bca1ddcd93052deca896ade58fd6')
+    version('1.36.6', commit='8c0ac7230f94e0c5a981acbb178c8de70e968131')
 
     depends_on('r-xml', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.25.1:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.13:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-xvector', type=('build', 'run'))
+    depends_on('r-xvector@0.19.7:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.15.2:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-biostrings@2.47.6:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
     depends_on('r-rcurl', type=('build', 'run'))
     depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-rsamtools@1.31.2:', when='@1.40.5', type=('build', 'run'))
     depends_on('r-genomicalignments', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.36.6')
+    depends_on('r-genomicalignments@1.15.6:', when='@1.40.5', type=('build', 'run'))
+    depends_on('r-genomicranges@1.21.20:', when='@1.36.3', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.8:', when='@1.40.5', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.36.6', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.40.5', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rtsne/package.py b/var/spack/repos/builtin/packages/r-rtsne/package.py
new file mode 100644
index 0000000000..2ec641f5eb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rtsne/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRtsne(RPackage):
+    """An R wrapper around the fast T-distributed Stochastic Neighbor
+    Embedding implementation."""
+
+    homepage = "https://CRAN.R-project.org/package=Rtsne"
+    url      = "https://cran.r-project.org/src/contrib/Rtsne_0.13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/Rtsne"
+
+    version('0.13', 'ea1d2ef2bda16735bbf219ffda5b0661')
+    version('0.11', '9a1eaa9b71d67cc27a55780e6e9df733')
+    version('0.10', 'c587e1b76fdcea2629424f74c6e92340')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-rcpp', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-rvcheck/package.py b/var/spack/repos/builtin/packages/r-rvcheck/package.py
new file mode 100644
index 0000000000..25ba893d4f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-rvcheck/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RRvcheck(RPackage):
+    """Check latest release version of R and R package (both in 'CRAN',
+    'Bioconductor' or 'Github')."""
+
+    homepage = "https://cran.r-project.org/package=rvcheck"
+    url      = "https://cran.rstudio.com/src/contrib/rvcheck_0.0.9.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/rvcheck"
+
+    version('0.0.9', '7e9821de754577f94fdcbf7b02a20edc')
diff --git a/var/spack/repos/builtin/packages/r-rvest/package.py b/var/spack/repos/builtin/packages/r-rvest/package.py
index d35e14ace7..837dd81a05 100644
--- a/var/spack/repos/builtin/packages/r-rvest/package.py
+++ b/var/spack/repos/builtin/packages/r-rvest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py
index 18ef9e04f2..77f1420d04 100644
--- a/var/spack/repos/builtin/packages/r-rzmq/package.py
+++ b/var/spack/repos/builtin/packages/r-rzmq/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-s4vectors/package.py b/var/spack/repos/builtin/packages/r-s4vectors/package.py
index 84ee43cdfe..71eb0a588b 100644
--- a/var/spack/repos/builtin/packages/r-s4vectors/package.py
+++ b/var/spack/repos/builtin/packages/r-s4vectors/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,10 +17,13 @@ class RS4vectors(RPackage):
        package and in other Bioconductor infrastructure packages)."""
 
     homepage = "https://bioconductor.org/packages/S4Vectors/"
-    url      = "https://git.bioconductor.org/packages/S4Vectors"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/S4Vectors.git"
 
-    version('0.14.7', git='https://git.bioconductor.org/packages/S4Vectors', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23')
+    version('0.18.3', commit='d6804f94ad3663828440914920ac933b934aeff1')
+    version('0.16.0', commit='00fec03fcbcb7cff37917fab0da28d91fdf9dc3d')
+    version('0.14.7', commit='40af17fe0b8e93b6a72fc787540d2961773b8e23')
 
-    depends_on('r-biocgenerics', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@0.14.7')
+    depends_on('r-biocgenerics@0.21.1:', type=('build', 'run'), when='@0.14.7')
+    depends_on('r-biocgenerics@0.23.3:', type=('build', 'run'), when='@0.16.0:')
+    depends_on('r@3.4.0:3.4.9', when='@0.14.7', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@0.18.3', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-samr/package.py b/var/spack/repos/builtin/packages/r-samr/package.py
index da575143e8..f24a731bfc 100644
--- a/var/spack/repos/builtin/packages/r-samr/package.py
+++ b/var/spack/repos/builtin/packages/r-samr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sandwich/package.py b/var/spack/repos/builtin/packages/r-sandwich/package.py
index 5f7d66dd7a..5be31684c1 100644
--- a/var/spack/repos/builtin/packages/r-sandwich/package.py
+++ b/var/spack/repos/builtin/packages/r-sandwich/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-scales/package.py b/var/spack/repos/builtin/packages/r-scales/package.py
index ebe9798e86..eb1d75e7f4 100644
--- a/var/spack/repos/builtin/packages/r-scales/package.py
+++ b/var/spack/repos/builtin/packages/r-scales/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py
index eedd61cc6e..a4c5a41ca1 100644
--- a/var/spack/repos/builtin/packages/r-scatterplot3d/package.py
+++ b/var/spack/repos/builtin/packages/r-scatterplot3d/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sdmtools/package.py b/var/spack/repos/builtin/packages/r-sdmtools/package.py
new file mode 100644
index 0000000000..584a935eb4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sdmtools/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSdmtools(RPackage):
+    """Species Distribution Modelling Tools: Tools for processing data
+    associated with species distribution modelling exercises
+
+    This packages provides a set of tools for post processing the outcomes of
+    species distribution modeling exercises."""
+
+    homepage = "https://cran.r-project.org/web/packages/SDMTools/index.html"
+    url      = "https://cran.r-project.org/src/contrib/SDMTools_1.1-221.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/SDMTools"
+
+    version('1.1-221', '3604da1783d0c6081b62b29d35a32c3c')
+    version('1.1-20', '27cc8de63cfdd86d4ba9983012121c58')
+    version('1.1-13', '0d6a14d985988a81b9ff06c635675143')
+    version('1.1-12', 'a13d75e4024d908a57ea462112d8a437')
+    version('1.1-11', 'cb890ee06eb862f97141b73c7390a0a9')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-utils', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-segmented/package.py b/var/spack/repos/builtin/packages/r-segmented/package.py
index 784a9d55d5..bea89c1a27 100644
--- a/var/spack/repos/builtin/packages/r-segmented/package.py
+++ b/var/spack/repos/builtin/packages/r-segmented/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-selectr/package.py b/var/spack/repos/builtin/packages/r-selectr/package.py
index 321a7da099..601812dc19 100644
--- a/var/spack/repos/builtin/packages/r-selectr/package.py
+++ b/var/spack/repos/builtin/packages/r-selectr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-seqinr/package.py b/var/spack/repos/builtin/packages/r-seqinr/package.py
index a78e36ef74..8b7c566b87 100644
--- a/var/spack/repos/builtin/packages/r-seqinr/package.py
+++ b/var/spack/repos/builtin/packages/r-seqinr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-seqlogo/package.py b/var/spack/repos/builtin/packages/r-seqlogo/package.py
new file mode 100644
index 0000000000..b7864868c9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-seqlogo/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSeqlogo(RPackage):
+    """seqLogo takes the position weight matrix of a DNA sequence motif and
+       plots the corresponding sequence logo as introduced by Schneider and
+       Stephens (1990)."""
+
+    homepage = "https://bioconductor.org/packages/seqLogo/"
+    git      = "https://git.bioconductor.org/packages/seqLogo.git"
+
+    version('1.44.0', commit='4cac14ff29f413d6de1a9944eb5d21bfe5045fac')
+
+    depends_on('r@3.4.3:3.4.9', when='@1.44.0')
diff --git a/var/spack/repos/builtin/packages/r-seurat/package.py b/var/spack/repos/builtin/packages/r-seurat/package.py
new file mode 100644
index 0000000000..8d9b06758a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-seurat/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSeurat(RPackage):
+    """Seurat is an R package designed for QC, analysis, and exploration of
+    single cell RNA-seq data."""
+
+    homepage = "http://satijalab.org/seurat/"
+    url      = "https://cran.r-project.org/src/contrib/Seurat_2.1.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/Seurat"
+
+    version('2.1.0', '46427837bb739883f9b7addd08fccee5')
+    version('2.0.1', 'a77794891e93b9fa1ef41735fe8424ea')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-ggplot2', type=('build', 'run'))
+    depends_on('r-gplots', type=('build', 'run'))
+    depends_on('r-reshape2', type=('build', 'run'))
+    depends_on('r-ape', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-caret', type=('build', 'run'))
+    depends_on('r-gdata', type=('build', 'run'))
+    depends_on('r-glue', type=('build', 'run'))
+    depends_on('r-pkgconfig', type=('build', 'run'))
+    depends_on('r-plogr', type=('build', 'run'))
+    depends_on('r-gridextra', type=('build', 'run'))
+    depends_on('r-cowplot', type=('build', 'run'))
+    depends_on('r-rocr', type=('build', 'run'))
+    depends_on('r-hmisc', type=('build', 'run'))
+    depends_on('r-nmf', type=('build', 'run'))
+    depends_on('r-irlba', type=('build', 'run'))
+    depends_on('r-igraph', type=('build', 'run'))
+    depends_on('r-fpc', type=('build', 'run'))
+    depends_on('r-rcppprogress', type=('build', 'run'))
+    depends_on('r-lars', type=('build', 'run'))
+    depends_on('r-dtw', type=('build', 'run'))
+    depends_on('r-mixtools', type=('build', 'run'))
+    depends_on('r-ica', type=('build', 'run'))
+    depends_on('r-diffusionmap', type=('build', 'run'))
+    depends_on('r-tsne', type=('build', 'run'))
+    depends_on('r-rtsne', type=('build', 'run'))
+    depends_on('r-ranger', type=('build', 'run'))
+    depends_on('r-pbapply', type=('build', 'run'))
+    depends_on('r-ggjoy', type=('build', 'run'))
+    depends_on('r-plotly', type=('build', 'run'))
+    depends_on('r-sdmtools', type=('build', 'run'))
+    depends_on('r-tclust', type=('build', 'run'))
+    depends_on('r-fnn', type=('build', 'run'))
+    depends_on('r-vgam', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sf/package.py b/var/spack/repos/builtin/packages/r-sf/package.py
new file mode 100644
index 0000000000..019feb1b18
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sf/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSf(RPackage):
+    """Support for simple features, a standardized way to encode spatial
+       vector data. Binds to GDAL for reading and writing data, to GEOS for
+       geometrical operations, and to Proj.4 for projection conversions and
+       datum transformations."""
+
+    homepage = "https://github.com/r-spatial/sf/"
+    url      = "https://cran.r-project.org/src/contrib/sf_0.5-5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/sf"
+
+    version('0.5-5', '53ff32d0c9bf2844666c68ce7d75beb2')
+
+    depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-dbi@0.5:', type=('build', 'run'))
+    depends_on('r-units@0.4-6:', type=('build', 'run'))
+    depends_on('r-classint', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('gdal@2.0.0:')
+    depends_on('geos@3.3.0:')
+    depends_on('proj@4.8.0:')
diff --git a/var/spack/repos/builtin/packages/r-sfsmisc/package.py b/var/spack/repos/builtin/packages/r-sfsmisc/package.py
index d07abd3b44..c2bf1e540f 100644
--- a/var/spack/repos/builtin/packages/r-sfsmisc/package.py
+++ b/var/spack/repos/builtin/packages/r-sfsmisc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class RSfsmisc(RPackage):
     some were ported from S-plus."""
 
     homepage = "https://cran.r-project.org/web/packages/sfsmisc/index.html"
-    url      = "https://cran.r-project.org/src/contrib/sfsmisc_1.1-1.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/sfsmisc_1.1-0.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/sfsmisc"
+
     version('1.1-0', '1ba4303076e2bbf018f7eecc7d04e178')
diff --git a/var/spack/repos/builtin/packages/r-shape/package.py b/var/spack/repos/builtin/packages/r-shape/package.py
index 8f07f842e0..18ab11de62 100644
--- a/var/spack/repos/builtin/packages/r-shape/package.py
+++ b/var/spack/repos/builtin/packages/r-shape/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-shiny/package.py b/var/spack/repos/builtin/packages/r-shiny/package.py
index 1d42d8df23..7165cd7af6 100644
--- a/var/spack/repos/builtin/packages/r-shiny/package.py
+++ b/var/spack/repos/builtin/packages/r-shiny/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-shinydashboard/package.py b/var/spack/repos/builtin/packages/r-shinydashboard/package.py
new file mode 100644
index 0000000000..b9b6406f9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-shinydashboard/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RShinydashboard(RPackage):
+    """Create Dashboards with 'Shiny'"""
+
+    homepage = "https://cran.r-project.org/package=shinydashboard"
+    url      = "https://cran.r-project.org/src/contrib/shinydashboard_0.7.0.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/shinydashboard"
+
+    version('0.7.0', 'a572695884e3b45320b0ab5a7b364ffd')
+    version('0.6.1', '0f6ad0448237e10d53d4d27ade1c6863')
+
+    depends_on('r@3.3.0:', type=('build', 'run'))
+    depends_on('r-htmltools@0.2.6:', type=('build', 'run'))
+    depends_on('r-shiny@1.0.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-shortread/package.py b/var/spack/repos/builtin/packages/r-shortread/package.py
new file mode 100644
index 0000000000..81ed95b0b5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-shortread/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RShortread(RPackage):
+    """This package implements sampling, iteration, and input of FASTQ
+    files. The package includes functions for filtering and trimming
+    reads, and for generating a quality assessment report. Data are
+    represented as DNAStringSet-derived objects, and easily manipulated
+    for a diversity of purposes. The package also contains legacy support
+    for early single-end, ungapped alignment formats."""
+
+    homepage = "https://www.bioconductor.org/packages/ShortRead/"
+    git      = "https://git.bioconductor.org/packages/ShortRead.git"
+
+    version('1.34.2', commit='25daac63b301df66a8ef6e98cc2977522c6786cd')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.34.2')
+    depends_on('r-latticeextra', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-zlibbioc', type=('build', 'run'))
+    depends_on('r-hwriter', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-genomicalignments', type=('build', 'run'))
+    depends_on('r-rsamtools', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-siggenes/package.py b/var/spack/repos/builtin/packages/r-siggenes/package.py
index ec0809c9da..ec425f54bc 100644
--- a/var/spack/repos/builtin/packages/r-siggenes/package.py
+++ b/var/spack/repos/builtin/packages/r-siggenes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RSiggenes(RPackage):
        (EBAM)."""
 
     homepage = "http://bioconductor.org/packages/siggenes/"
-    url      = "https://git.bioconductor.org/packages/siggenes"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/siggenes.git"
 
-    version('1.50.0', git='https://git.bioconductor.org/packages/siggenes', commit='b1818f26e1449005ffd971df6bda8da0303080bc')
+    version('1.50.0', commit='b1818f26e1449005ffd971df6bda8da0303080bc')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-multtest', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-simpleaffy/package.py b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
index 36d616fa8c..c977569d5e 100644
--- a/var/spack/repos/builtin/packages/r-simpleaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-simpleaffy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,10 +14,9 @@ class RSimpleaffy(RPackage):
        for generating high resolution journal figures..."""
 
     homepage = "http://bioconductor.org/packages/simpleaffy/"
-    url      = "https://git.bioconductor.org/packages/simpleaffy"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/simpleaffy.git"
 
-    version('2.52.0', git='https://git.bioconductor.org/packages/simpleaffy', commit='f2b43fb9b8e6fa4c03fe28b4efb3144a0a42a385')
+    version('2.52.0', commit='f2b43fb9b8e6fa4c03fe28b4efb3144a0a42a385')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sm/package.py b/var/spack/repos/builtin/packages/r-sm/package.py
new file mode 100644
index 0000000000..e57ad8584b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sm/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSm(RPackage):
+    """This is software linked to the book 'Applied Smoothing Techniques for
+       Data Analysis - The Kernel Approach with S-Plus Illustrations'
+       Oxford University Press."""
+
+    homepage = "http://www.stats.gla.ac.uk/~adrian/sm"
+    url      = "https://cran.r-project.org/src/contrib/sm_2.2-5.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/sm"
+
+    version('2.2-5.5', sha256='43e212a14c364b98b10018b56fe0a619ccffe4bde1294e6c45b3eafe7caf82e7')
+
+    depends_on('r@3.1.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-smoof/package.py b/var/spack/repos/builtin/packages/r-smoof/package.py
new file mode 100644
index 0000000000..c980683109
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-smoof/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSmoof(RPackage):
+    """Provides generators for a high number of both single- and
+       multi- objective test functions which are frequently used for the
+       benchmarking of (numerical) optimization algorithms. Moreover, it offers
+       a set of convenient functions to generate, plot and work with objective
+       functions."""
+
+    homepage = "http://github.com/jakobbossek/smoof"
+    url      = "https://cran.r-project.org/src/contrib/smoof_1.5.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/smoof"
+
+    version('1.5.1', 'c3e3b5dafed34608f933ae255cf49054')
+    version('1.5', 'b371bde2724eade5a6d4d808fa3ad269')
+
+    depends_on('r-paramhelpers@1.8:', type=('build', 'run'))
+    depends_on('r-bbmisc@1.6:', type=('build', 'run'))
+    depends_on('r-checkmate@1.1:', type=('build', 'run'))
+    depends_on('r-ggplot2@2.2.1:', type=('build', 'run'))
+    depends_on('r-rcolorbrewer', type=('build', 'run'))
+    depends_on('r-plot3d', type=('build', 'run'))
+    depends_on('r-plotly', type=('build', 'run'))
+    depends_on('r-mco', type=('build', 'run'))
+    depends_on('r-rcpp@0.11.0:', type=('build', 'run'))
+    depends_on('r-rjsonio', type=('build', 'run'))
+    depends_on('r-rcpparmadillo', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sn/package.py b/var/spack/repos/builtin/packages/r-sn/package.py
new file mode 100644
index 0000000000..9dbfced26a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sn/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSn(RPackage):
+    """Build and manipulate probability distributions of the skew-normal
+    family and some related ones, notably the skew-t family, and provide
+    related statistical methods for data fitting and diagnostics, in the
+    univariate and the multivariate case."""
+
+    homepage = "https://cran.r-project.org/web/packages/sn/index.html"
+    url      = "https://cran.r-project.org/src/contrib/sn_1.5-0.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/sn"
+
+    version('1.5-0', 'a3349773be950199d7f4c17954be56d1')
+    version('1.4-0', 'cfa604317ea54224b06abd1cec179375')
+    version('1.3-0', '84d02ba2ab5ca6f3644626013e7ce36d')
+    version('1.2-4', 'bf3a47b05016326e910fdb4cc4967e4d')
+    version('1.2-3', '290ae511d974a6beb4c3c79c0106858f')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-mnormt', type=('build', 'run'))
+    depends_on('r-numderiv', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-snow/package.py b/var/spack/repos/builtin/packages/r-snow/package.py
index 7be7d36018..73bdd4bcf5 100644
--- a/var/spack/repos/builtin/packages/r-snow/package.py
+++ b/var/spack/repos/builtin/packages/r-snow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-snowfall/package.py b/var/spack/repos/builtin/packages/r-snowfall/package.py
new file mode 100644
index 0000000000..4ed0f934a6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-snowfall/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSnowfall(RPackage):
+    """Usability wrapper around snow for easier development of parallel R
+       programs. This package offers e.g. extended error checks, and additional
+       functions. All functions work in sequential mode, too, if no cluster is
+       present or wished. Package is also designed as connector to the cluster
+       management tool sfCluster, but can also used without it."""
+
+    homepage = "https://cran.r-project.org/web/packages/snowfall/index.html"
+    url      = "https://cran.r-project.org/src/contrib/snowfall_1.84-6.1.tar.gz"
+
+    version('1.84-6.1', '5ec38116aa9cac237d56f59ba5bd60e3')
+
+    depends_on('r-snow', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-snprelate/package.py b/var/spack/repos/builtin/packages/r-snprelate/package.py
new file mode 100644
index 0000000000..f7a0d04fa9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-snprelate/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSnprelate(RPackage):
+    """Genome-wide association studies (GWAS) are widely used to investigate
+       the genetic basis of diseases and traits, but they pose many
+       computational challenges. We developed an R package SNPRelate to
+       provide a binary format for single-nucleotide polymorphism (SNP) data
+       in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files.
+       The GDS format offers the efficient operations specifically designed
+       for integers with two bits, since a SNP could occupy only two bits.
+       SNPRelate is also designed to accelerate two key computations on SNP
+       data using parallel computing for multi-core symmetric multiprocessing
+       computer architectures: Principal Component Analysis (PCA) and
+       relatedness analysis using Identity-By-Descent measures. The SNP GDS
+       format is also used by the GWASTools package with the support of S4
+       classes and generic functions. The extended GDS format is implemented
+       in the SeqArray package to support the storage of single nucleotide
+       variations (SNVs), insertion/deletion polymorphism (indel) and
+       structural variation calls."""
+
+    homepage = "https://bioconductor.org/packages/SNPRelate"
+    git      = "https://git.bioconductor.org/packages/SNPRelate.git"
+
+    version('1.12.2', commit='dce2e2b6f36483a9f905bb5df6ae834a9f1136fe')
+
+    depends_on('r@3.4.0:3.4.9', when='@1.12.2')
+    depends_on('r-gdsfmt@1.8.3:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-som/package.py b/var/spack/repos/builtin/packages/r-som/package.py
new file mode 100644
index 0000000000..7a79e31f62
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-som/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSom(RPackage):
+    """Self-Organizing Map (with application in gene clustering)."""
+
+    homepage = "https://cran.r-project.org/web/packages/som/index.html"
+    url      = "https://cran.r-project.org/src/contrib/som_0.3-5.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/som"
+
+    version('0.3-5.1', '802a5a80902579354ce3420faeeeb756')
+    version('0.3-5', '72717499794c7aa945a768b742af8895')
+    version('0.3-4', '1e25572e446409f5e32c5da5f1af98e6')
+    version('0.3-3', 'd4ac444be24f71d08b99974c2f4b96e5')
+    version('0.3-2', '4ce28f46df68fbb73905711ba2416fac')
+
+    depends_on('r@2.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
index 004023fd25..36fdd5e78e 100644
--- a/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
+++ b/var/spack/repos/builtin/packages/r-somaticsignatures/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,9 @@ class RSomaticsignatures(RPackage):
        flexibility in the matrix decomposition algorithms."""
 
     homepage = "https://bioconductor.org/packages/SomaticSignatures/"
-    url      = "https://git.bioconductor.org/packages/SomaticSignatures"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/SomaticSignatures.git"
 
-    version('2.12.1', git='https://git.bioconductor.org/packages/SomaticSignatures', commit='932298c6877d076004de5541cec85a14e819517a')
+    version('2.12.1', commit='932298c6877d076004de5541cec85a14e819517a')
 
     depends_on('r-variantannotation', type=('build', 'run'))
     depends_on('r-genomicranges', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sourcetools/package.py b/var/spack/repos/builtin/packages/r-sourcetools/package.py
index 87f9dfc2c9..f0b08a0eef 100644
--- a/var/spack/repos/builtin/packages/r-sourcetools/package.py
+++ b/var/spack/repos/builtin/packages/r-sourcetools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sp/package.py b/var/spack/repos/builtin/packages/r-sp/package.py
index c085aa1521..0212bb028e 100644
--- a/var/spack/repos/builtin/packages/r-sp/package.py
+++ b/var/spack/repos/builtin/packages/r-sp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sparsem/package.py b/var/spack/repos/builtin/packages/r-sparsem/package.py
index 3aac221fd1..d5641178da 100644
--- a/var/spack/repos/builtin/packages/r-sparsem/package.py
+++ b/var/spack/repos/builtin/packages/r-sparsem/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-spdep/package.py b/var/spack/repos/builtin/packages/r-spdep/package.py
index f7b7a4671e..6fdd2e953b 100644
--- a/var/spack/repos/builtin/packages/r-spdep/package.py
+++ b/var/spack/repos/builtin/packages/r-spdep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-speedglm/package.py b/var/spack/repos/builtin/packages/r-speedglm/package.py
index f520965da5..c653323f27 100644
--- a/var/spack/repos/builtin/packages/r-speedglm/package.py
+++ b/var/spack/repos/builtin/packages/r-speedglm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-spem/package.py b/var/spack/repos/builtin/packages/r-spem/package.py
new file mode 100644
index 0000000000..ee4a1a794c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-spem/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSpem(RPackage):
+    """This package can optimize the parameter in S-system models given time
+    series data"""
+
+    homepage = "https://bioconductor.org/packages/SPEM/"
+    git      = "https://git.bioconductor.org/packages/SPEM.git"
+
+    version('1.18.0', commit='3ab425dd9889885eac328d26b73366a875cd250b')
+
+    depends_on('r-rsolnp', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.18.0')
diff --git a/var/spack/repos/builtin/packages/r-splitstackshape/package.py b/var/spack/repos/builtin/packages/r-splitstackshape/package.py
new file mode 100644
index 0000000000..3bff263624
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-splitstackshape/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSplitstackshape(RPackage):
+    """Stack and Reshape Datasets After Splitting Concatenated Values.
+
+    Online data collection tools like Google Forms often export
+    multiple-response questions with data concatenated in cells. The
+    concat.split (cSplit) family of functions splits such data into
+    separate cells. The package also includes functions to stack groups
+    of columns and to reshape wide data, even when the data are
+    "unbalanced" something which reshape (from base R) does not handle,
+    and which melt and dcast from reshape2 do not easily handle.
+    """
+
+    homepage = "http://github.com/mrdwab/splitstackshape"
+    url      = "https://cran.r-project.org/src/contrib/splitstackshape_1.4.4.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/splitstackshape"
+
+    version('1.4.4', '54d2554fe92dfc4670a000b45baacc28')
+
+    depends_on('r-data-table@1.9.4:', type=('build', 'run'))
+    depends_on('r@2.10:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-sqldf/package.py b/var/spack/repos/builtin/packages/r-sqldf/package.py
index c891891221..d0c90d4a14 100644
--- a/var/spack/repos/builtin/packages/r-sqldf/package.py
+++ b/var/spack/repos/builtin/packages/r-sqldf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-squash/package.py b/var/spack/repos/builtin/packages/r-squash/package.py
new file mode 100644
index 0000000000..e939b870e5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-squash/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSquash(RPackage):
+    """Color-Based Plots for Multivariate Visualization"""
+
+    homepage = "https://cran.r-project.org/package=squash"
+    url      = "https://cran.r-project.org/src/contrib/squash_1.0.8.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/squash"
+
+    version('1.0.8', '50d5743d306fa11cfa1a3c4daa75e508')
+    version('1.0.7', '4ac381b17d4d7b77bdaa6f824fbb03ab')
diff --git a/var/spack/repos/builtin/packages/r-stanheaders/package.py b/var/spack/repos/builtin/packages/r-stanheaders/package.py
index 383eb82580..62e787197f 100644
--- a/var/spack/repos/builtin/packages/r-stanheaders/package.py
+++ b/var/spack/repos/builtin/packages/r-stanheaders/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -46,4 +27,5 @@ class RStanheaders(RPackage):
     url      = "https://cran.r-project.org/src/contrib/StanHeaders_2.10.0-2.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/StanHeaders"
 
+    version('2.17.1', '11d8770277dd18e563852852633c6c25')
     version('2.10.0-2', '9d09b1e9278f08768f7a988ad9082d57')
diff --git a/var/spack/repos/builtin/packages/r-statmod/package.py b/var/spack/repos/builtin/packages/r-statmod/package.py
index 7eb095aa92..df2fbc70a5 100644
--- a/var/spack/repos/builtin/packages/r-statmod/package.py
+++ b/var/spack/repos/builtin/packages/r-statmod/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-statnet-common/package.py b/var/spack/repos/builtin/packages/r-statnet-common/package.py
index 2c61f23f2e..d8f8413200 100644
--- a/var/spack/repos/builtin/packages/r-statnet-common/package.py
+++ b/var/spack/repos/builtin/packages/r-statnet-common/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-stringi/package.py b/var/spack/repos/builtin/packages/r-stringi/package.py
index 55dd10e378..af49c8aca2 100644
--- a/var/spack/repos/builtin/packages/r-stringi/package.py
+++ b/var/spack/repos/builtin/packages/r-stringi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-stringr/package.py b/var/spack/repos/builtin/packages/r-stringr/package.py
index 64b291adc5..28497c97d8 100644
--- a/var/spack/repos/builtin/packages/r-stringr/package.py
+++ b/var/spack/repos/builtin/packages/r-stringr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-strucchange/package.py b/var/spack/repos/builtin/packages/r-strucchange/package.py
index 4f0a2bf28a..1b0ae07613 100644
--- a/var/spack/repos/builtin/packages/r-strucchange/package.py
+++ b/var/spack/repos/builtin/packages/r-strucchange/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-subplex/package.py b/var/spack/repos/builtin/packages/r-subplex/package.py
index 66df912a5f..3adb487f9d 100644
--- a/var/spack/repos/builtin/packages/r-subplex/package.py
+++ b/var/spack/repos/builtin/packages/r-subplex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
index 104a61cb8c..781db8fedc 100644
--- a/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
+++ b/var/spack/repos/builtin/packages/r-summarizedexperiment/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,16 +13,25 @@ class RSummarizedexperiment(RPackage):
        represent samples."""
 
     homepage = "https://bioconductor.org/packages/SummarizedExperiment/"
-    url      = "https://git.bioconductor.org/packages/SummarizedExperiment"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/SummarizedExperiment.git"
 
-    version('1.6.5', git='https://git.bioconductor.org/packages/SummarizedExperiment', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0')
+    version('1.10.0', commit='7ad2e991c8285bfc4b2e15b29d94cc86d07f8f2b')
+    version('1.8.1', commit='9d8a29aa9c78bbc7dcc6472537e13fc0d11dc1f7')
+    version('1.6.5', commit='ec69cd5cfbccaef148a9f6abdfb3e22e888695d0')
 
-    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-genomicranges@1.27.22:', when='@1.6.5', type=('build', 'run'))
+    depends_on('r-genomicranges@1.29.14:', when='@1.8.1', type=('build', 'run'))
+    depends_on('r-genomicranges@1.31.17:', when='@1.10.0', type=('build', 'run'))
     depends_on('r-biobase', type=('build', 'run'))
-    depends_on('r-delayedarray', type=('build', 'run'))
+    depends_on('r-delayedarray@0.1.9:', when='@1.6.5', type=('build', 'run'))
+    depends_on('r-delayedarray@0.3.20:', when='@1.8.1:', type=('build', 'run'))
     depends_on('r-matrix', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.25:', when='@1.10.0', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.16:', when='@1.10.0', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@1.6.5')
+    depends_on('r-genomeinfodb@1.13.1:', when='@1.10.0', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.15.3:', when='@1.6.5:', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.6.5:1.9.9', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.10.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-survey/package.py b/var/spack/repos/builtin/packages/r-survey/package.py
index 62d21bb00b..cf0c11d4b0 100644
--- a/var/spack/repos/builtin/packages/r-survey/package.py
+++ b/var/spack/repos/builtin/packages/r-survey/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-survival/package.py b/var/spack/repos/builtin/packages/r-survival/package.py
index c63c2eb864..f4f8b4eed3 100644
--- a/var/spack/repos/builtin/packages/r-survival/package.py
+++ b/var/spack/repos/builtin/packages/r-survival/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-sva/package.py b/var/spack/repos/builtin/packages/r-sva/package.py
new file mode 100644
index 0000000000..3510a46b2a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-sva/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RSva(RPackage):
+    """Surrogate Variable Analysis."""
+
+    homepage = "https://www.bioconductor.org/packages/sva/"
+    git      = "https://git.bioconductor.org/packages/sva.git"
+
+    version('3.24.4', commit='ed2ebb6e33374dc9ec50e6ea97cc1d9aef836c73')
+
+    depends_on('r@3.4.0:3.4.9', when='@3.24.4')
+    depends_on('r-mgcv', type=('build', 'run'))
+    depends_on('r-genefilter', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-matrixstats', type=('build', 'run'))
+    depends_on('r-limma', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tarifx/package.py b/var/spack/repos/builtin/packages/r-tarifx/package.py
index b58eb5194e..2fa7653d73 100644
--- a/var/spack/repos/builtin/packages/r-tarifx/package.py
+++ b/var/spack/repos/builtin/packages/r-tarifx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tclust/package.py b/var/spack/repos/builtin/packages/r-tclust/package.py
new file mode 100644
index 0000000000..0c07d18a56
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tclust/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTclust(RPackage):
+    """Provides functions for robust trimmed clustering."""
+
+    homepage = "https://cran.r-project.org/web/packages/tclust/index.html"
+    url      = "https://cran.r-project.org/src/contrib/tclust_1.3-1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/tclust"
+
+    version('1.3-1',  '5415d74682588d4a6fb8ce166fc75661')
+    version('1.2-7',  'e32cd02819682cc944c7baaac3b6f2b7')
+    version('1.2-3',  '922abc1abd8da4c6ac9830e1f2f71e84')
+    version('1.1-03', 'f1cc9278bdb068acce4623a9d98b7b62')
+    version('1.1-02', '6f206501b0341fb5623208d145984f5a')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-cluster', type=('build', 'run'))
+    depends_on('r-mclust', type=('build', 'run'))
+    depends_on('r-mvtnorm', type=('build', 'run'))
+    depends_on('r-sn', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tensora/package.py b/var/spack/repos/builtin/packages/r-tensora/package.py
index c19e3604fc..c999e3c759 100644
--- a/var/spack/repos/builtin/packages/r-tensora/package.py
+++ b/var/spack/repos/builtin/packages/r-tensora/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-testit/package.py b/var/spack/repos/builtin/packages/r-testit/package.py
index 7a5fb607e8..c349351975 100644
--- a/var/spack/repos/builtin/packages/r-testit/package.py
+++ b/var/spack/repos/builtin/packages/r-testit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-testthat/package.py b/var/spack/repos/builtin/packages/r-testthat/package.py
index 045f447df1..49d31da8c6 100644
--- a/var/spack/repos/builtin/packages/r-testthat/package.py
+++ b/var/spack/repos/builtin/packages/r-testthat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tfbstools/package.py b/var/spack/repos/builtin/packages/r-tfbstools/package.py
new file mode 100644
index 0000000000..1e4b224444
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tfbstools/package.py
@@ -0,0 +1,49 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTfbstools(RPackage):
+    """TFBSTools is a package for the analysis and manipulation of
+       transcription factor binding sites.
+
+       It includes matrices conversion between Position Frequency Matirx (PFM),
+       Position Weight Matirx (PWM) and Information Content Matrix (ICM). It
+       can also scan putative TFBS from sequence/alignment, query JASPAR
+       database and provides a wrapper of de novo motif discovery software.
+       TFBSTools is a package for the analysis and manipulation of
+       transcription factor binding sites. It includes matrices conversion
+       between Position Frequency Matirx (PFM), Position Weight Matirx (PWM)
+       and Information Content Matrix (ICM). It can also scan putative TFBS
+       from sequence/alignment, query JASPAR database and provides a wrapper
+       of de novo motif discovery software."""
+
+    homepage = "http://bioconductor.org/packages/TFBSTools/"
+    git      = "https://git.bioconductor.org/packages/TFBSTools.git"
+
+    version('1.16.0', commit='565436a5a674d4dea7279e796a20c5bd2034f65a')
+
+    depends_on('r-biobase@2.28:', type=('build', 'run'))
+    depends_on('r-biostrings@2.36.4:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.14.0:', type=('build', 'run'))
+    depends_on('r-biocparallel@1.2.21:', type=('build', 'run'))
+    depends_on('r-bsgenome@1.36.3:', type=('build', 'run'))
+    depends_on('r-catools@1.17.1:', type=('build', 'run'))
+    depends_on('r-cner@1.4.0:', type=('build', 'run'))
+    depends_on('r-dirichletmultinomial@1.10.0:', type=('build', 'run'))
+    depends_on('r-genomeinfodb@1.6.1:', type=('build', 'run'))
+    depends_on('r-genomicranges@1.20.6:', type=('build', 'run'))
+    depends_on('r-gtools@3.5.0:', type=('build', 'run'))
+    depends_on('r-iranges@2.2.7:', type=('build', 'run'))
+    depends_on('r-dbi@0.6:', type=('build', 'run'))
+    depends_on('r-rsqlite@1.0.0:', type=('build', 'run'))
+    depends_on('r-rtracklayer@1.28.10:', type=('build', 'run'))
+    depends_on('r-seqlogo@1.34.0:', type=('build', 'run'))
+    depends_on('r-s4vectors@0.9.25:', type=('build', 'run'))
+    depends_on('r-tfmpvalue@0.0.5:', type=('build', 'run'))
+    depends_on('r-xml@3.98-1.3:', type=('build', 'run'))
+    depends_on('r-xvector@0.8.0:', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.16.0')
diff --git a/var/spack/repos/builtin/packages/r-tfmpvalue/package.py b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py
new file mode 100644
index 0000000000..d3304686b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tfmpvalue/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTfmpvalue(RPackage):
+    """In putative Transcription Factor Binding Sites (TFBSs) identification
+       from sequence/alignments, we are interested in the significance of
+       certain match score. TFMPvalue provides the accurate calculation of
+       P-value with score threshold for Position Weight Matrices, or the score
+       with given P-value. This package is an interface to code originally
+       made available by Helene Touzet and Jean-Stephane Varre, 2007,
+       Algorithms Mol Biol:2, 15."""
+
+    homepage = "https://github.com/ge11232002/TFMPvalue"
+    url      = "https://cran.rstudio.com/src/contrib/TFMPvalue_0.0.6.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/TFMPvalue"
+
+    version('0.0.6', '69fdf4f9b9a0f408a5cee9ce34bea261')
+
+    depends_on('r-rcpp@0.11.1:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-th-data/package.py b/var/spack/repos/builtin/packages/r-th-data/package.py
index e5713ee9fc..ccbac55279 100644
--- a/var/spack/repos/builtin/packages/r-th-data/package.py
+++ b/var/spack/repos/builtin/packages/r-th-data/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-threejs/package.py b/var/spack/repos/builtin/packages/r-threejs/package.py
index f39ede0fb7..908cf9a283 100644
--- a/var/spack/repos/builtin/packages/r-threejs/package.py
+++ b/var/spack/repos/builtin/packages/r-threejs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tibble/package.py b/var/spack/repos/builtin/packages/r-tibble/package.py
index 66b9f9235a..af08f9b037 100644
--- a/var/spack/repos/builtin/packages/r-tibble/package.py
+++ b/var/spack/repos/builtin/packages/r-tibble/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tidycensus/package.py b/var/spack/repos/builtin/packages/r-tidycensus/package.py
new file mode 100644
index 0000000000..70c180eac0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tidycensus/package.py
@@ -0,0 +1,34 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTidycensus(RPackage):
+    """An integrated R interface to the decennial US Census and American
+    Community Survey APIs and the US Census Bureau's geographic boundary
+    files. Allows R users to return Census and ACS data as tidyverse-ready
+    data frames, and optionally returns a list-column with feature
+    geometry for many geographies."""
+
+    homepage = "https://cran.r-project.org/package=tidycensus"
+    url      = "https://cran.rstudio.com/src/contrib/tidycensus_0.3.1.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/tidycensus"
+
+    version('0.3.1', '420d046b5a408d321e775c3d410e7699')
+
+    depends_on('r-httr', type=('build', 'run'))
+    depends_on('r-sf', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-tigris', type=('build', 'run'))
+    depends_on('r-stringr', type=('build', 'run'))
+    depends_on('r-jsonlite', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-rvest', type=('build', 'run'))
+    depends_on('r-tidyr', type=('build', 'run'))
+    depends_on('r-rappdirs', type=('build', 'run'))
+    depends_on('r-readr', type=('build', 'run'))
+    depends_on('r-xml2', type=('build', 'run'))
+    depends_on('r-units', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tidyr/package.py b/var/spack/repos/builtin/packages/r-tidyr/package.py
index 0e6973fd13..1897495eb2 100644
--- a/var/spack/repos/builtin/packages/r-tidyr/package.py
+++ b/var/spack/repos/builtin/packages/r-tidyr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,14 +12,18 @@ class RTidyr(RPackage):
     pipelines."""
 
     homepage = "https://github.com/hadley/tidyr"
-    url      = "https://cran.r-project.org/src/contrib/tidyr_0.5.1.tar.gz"
+    url      = "https://cran.r-project.org/src/contrib/tidyr_0.7.2.tar.gz"
     list_url = "https://cran.r-project.org/src/contrib/Archive/tidyr"
 
+    version('0.7.2', '42d723bf04c5c1c59e27a8be14f3a6b6')
     version('0.5.1', '3cadc869510c054ed93d374ab44120bd')
 
     depends_on('r-tibble', type=('build', 'run'))
-    depends_on('r-dplyr', type=('build', 'run'))
+    depends_on('r-dplyr@0.7.0:', type=('build', 'run'))
     depends_on('r-stringi', type=('build', 'run'))
-    depends_on('r-lazyeval', type=('build', 'run'))
     depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-glue', type=('build', 'run'))
     depends_on('r-rcpp', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-tidyselect', type=('build', 'run'))
+    depends_on('r-rlang', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tidyselect/package.py b/var/spack/repos/builtin/packages/r-tidyselect/package.py
new file mode 100644
index 0000000000..96ae53a11c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tidyselect/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTidyselect(RPackage):
+    """A backend for the selecting functions of the 'tidyverse'. It makes it
+       easy to implement select-like functions in your own packages in a way
+       that is consistent with other 'tidyverse' interfaces for selection."""
+
+    homepage = "https://cran.r-project.org/package=tidyselect"
+    url      = "https://cran.r-project.org/src/contrib/tidyselect_0.2.3.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/tidyselect"
+
+    version('0.2.3', 'c9dbd895ad7ce209bacfad6d19de91c9')
+
+    depends_on('r-glue', type=('build', 'run'))
+    depends_on('r-purrr', type=('build', 'run'))
+    depends_on('r-rlang@0.1:', type=('build', 'run'))
+    depends_on('r-rcpp@0.12.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tidyverse/package.py b/var/spack/repos/builtin/packages/r-tidyverse/package.py
new file mode 100644
index 0000000000..f12e708308
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tidyverse/package.py
@@ -0,0 +1,46 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTidyverse(RPackage):
+    """The 'tidyverse' is a set of packages that work in harmony because they
+       share common data representations and 'API' design. This package is
+       designed to make it easy to install and load multiple 'tidyverse'
+       packages in a single step."""
+
+    homepage = "http://tidyverse.tidyverse.org/"
+    url      = "https://cran.r-project.org/src/contrib/tidyverse_1.2.1.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/tidyverse"
+
+    version('1.2.1', '7e2ca0b72ab668342c02fd0f52c082e1')
+
+    depends_on('r-broom@0.4.2:', type=('build', 'run'))
+    depends_on('r-cli@1.0.0:', type=('build', 'run'))
+    depends_on('r-crayon@1.3.4:', type=('build', 'run'))
+    depends_on('r-dplyr@0.7.4:', type=('build', 'run'))
+    depends_on('r-dbplyr@1.1.0:', type=('build', 'run'))
+    depends_on('r-forcats@0.2.0:', type=('build', 'run'))
+    depends_on('r-ggplot2@2.2.1:', type=('build', 'run'))
+    depends_on('r-haven@1.1.0:', type=('build', 'run'))
+    depends_on('r-hms@0.3:', type=('build', 'run'))
+    depends_on('r-httr@1.3.1:', type=('build', 'run'))
+    depends_on('r-jsonlite@1.5:', type=('build', 'run'))
+    depends_on('r-lubridate@1.7.1:', type=('build', 'run'))
+    depends_on('r-magrittr@1.5:', type=('build', 'run'))
+    depends_on('r-modelr@0.1.1:', type=('build', 'run'))
+    depends_on('r-purrr@0.2.4:', type=('build', 'run'))
+    depends_on('r-readr@1.1.1:', type=('build', 'run'))
+    depends_on('r-readxl@1.0.0:', type=('build', 'run'))
+    depends_on('r-reprex@0.1.1:', type=('build', 'run'))
+    depends_on('r-rlang@0.1.4:', type=('build', 'run'))
+    depends_on('r-rstudioapi@0.7:', type=('build', 'run'))
+    depends_on('r-rvest@0.3.2:', type=('build', 'run'))
+    depends_on('r-stringr@1.2.0:', type=('build', 'run'))
+    depends_on('r-tibble@1.3.4:', type=('build', 'run'))
+    depends_on('r-tidyr@0.7.2:', type=('build', 'run'))
+    depends_on('r-xml2@1.1.1:', type=('build', 'run'))
+    depends_on('r-rlang@0.1.4:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-tiff/package.py b/var/spack/repos/builtin/packages/r-tiff/package.py
index c751cb04e2..8dafca0a35 100644
--- a/var/spack/repos/builtin/packages/r-tiff/package.py
+++ b/var/spack/repos/builtin/packages/r-tiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tigris/package.py b/var/spack/repos/builtin/packages/r-tigris/package.py
new file mode 100644
index 0000000000..a87409ac1e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tigris/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTigris(RPackage):
+    """Download TIGER/Line shapefiles from the United States Census Bureau
+    and load into R as 'SpatialDataFrame' or 'sf' objects."""
+
+    homepage = "https://cran.r-project.org/package=tigris"
+    url      = "https://cran.rstudio.com/src/contrib/tigris_0.5.3.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/tigris"
+
+    version('0.5.3', 'c11cb459bf134d3deb1a641a60c86413')
+
+    depends_on('r-stringr', type=('build', 'run'))
+    depends_on('r-magrittr', type=('build', 'run'))
+    depends_on('r-rgdal', type=('build', 'run'))
+    depends_on('r-rgeos', type=('build', 'run'))
+    depends_on('r-sp', type=('build', 'run'))
+    depends_on('r-rappdirs', type=('build', 'run'))
+    depends_on('r-maptools', type=('build', 'run'))
+    depends_on('r-httr', type=('build', 'run'))
+    depends_on('r-uuid', type=('build', 'run'))
+    depends_on('r-sf', type=('build', 'run'))
+    depends_on('r-dplyr', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-timedate/package.py b/var/spack/repos/builtin/packages/r-timedate/package.py
index d593b6c2bc..b55d61b881 100644
--- a/var/spack/repos/builtin/packages/r-timedate/package.py
+++ b/var/spack/repos/builtin/packages/r-timedate/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tmixclust/package.py b/var/spack/repos/builtin/packages/r-tmixclust/package.py
new file mode 100644
index 0000000000..cbd49587b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tmixclust/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTmixclust(RPackage):
+    """Implementation of a clustering method for time series gene expression
+    data based on mixed-effects models with Gaussian variables and
+    non-parametric cubic splines estimation. The method can robustly account
+    for the high levels of noise present in typical gene expression time
+    series datasets."""
+
+    homepage = "https://bioconductor.org/packages/TMixClust/"
+    git      = "https://git.bioconductor.org/packages/TMixClust.git"
+
+    version('1.0.1', commit='0ac800210e3eb9da911767a80fb5582ab33c0cad')
+
+    depends_on('r-gss', type=('build', 'run'))
+    depends_on('r-mvtnorm', type=('build', 'run'))
+    depends_on('r-zoo', type=('build', 'run'))
+    depends_on('r-cluster', type=('build', 'run'))
+    depends_on('r-biocparallel', type=('build', 'run'))
+    depends_on('r-flexclust', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r-spem', type=('build', 'run'))
+    depends_on('r@3.4.3:3.4.9', when='@1.0.1')
diff --git a/var/spack/repos/builtin/packages/r-topgo/package.py b/var/spack/repos/builtin/packages/r-topgo/package.py
new file mode 100644
index 0000000000..1997f407c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-topgo/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTopgo(RPackage):
+    """topGO package provides tools for testing GO terms while accounting
+    for the topology of the GO graph. Different test statistics and
+    different methods for eliminating local similarities and dependencies
+    between GO terms can be implemented and applied."""
+
+    homepage = "https://www.bioconductor.org/packages/topGO/"
+    git      = "https://git.bioconductor.org/packages/topGO.git"
+
+    version('2.30.1', commit='b1469ce1d198ccb73ef79ca22cab81659e16dbaa')
+    version('2.28.0', commit='066a975d460046cce33fb27e74e6a0ebc33fd716')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-matrixstats', type=('build', 'run'))
+    depends_on('r-lattice', type=('build', 'run'))
+    depends_on('r-sparsem@0.73:', type=('build', 'run'))
+    depends_on('r-annotationdbi@1.7.19:', type=('build', 'run'))
+    depends_on('r-go-db@2.3.0:', type=('build', 'run'))
+    depends_on('r-biobase@2.0.0:', type=('build', 'run'))
+    depends_on('r-graph@1.14.0:', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.13.6:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-trimcluster/package.py b/var/spack/repos/builtin/packages/r-trimcluster/package.py
index c7f6cdb179..e1ea58534d 100644
--- a/var/spack/repos/builtin/packages/r-trimcluster/package.py
+++ b/var/spack/repos/builtin/packages/r-trimcluster/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-truncnorm/package.py b/var/spack/repos/builtin/packages/r-truncnorm/package.py
new file mode 100644
index 0000000000..07cfb8716e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-truncnorm/package.py
@@ -0,0 +1,17 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTruncnorm(RPackage):
+    """Density, probability, quantile and random number generation functions
+    for the truncated normal distribution."""
+
+    homepage = "https://cran.r-project.org/package=truncnorm"
+    url      = "https://cran.rstudio.com/src/contrib/truncnorm_1.0-8.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/truncnorm"
+
+    version('1.0-8', 'c60cd6555be0dd2ea91e61757439282d')
diff --git a/var/spack/repos/builtin/packages/r-trust/package.py b/var/spack/repos/builtin/packages/r-trust/package.py
index e83d8ad2b3..e076cf5cfd 100644
--- a/var/spack/repos/builtin/packages/r-trust/package.py
+++ b/var/spack/repos/builtin/packages/r-trust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tseries/package.py b/var/spack/repos/builtin/packages/r-tseries/package.py
index e581a77596..8509b84944 100644
--- a/var/spack/repos/builtin/packages/r-tseries/package.py
+++ b/var/spack/repos/builtin/packages/r-tseries/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-tsne/package.py b/var/spack/repos/builtin/packages/r-tsne/package.py
new file mode 100644
index 0000000000..89dd259886
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-tsne/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RTsne(RPackage):
+    """A "pure R" implementation of the t-SNE algorithm."""
+
+    homepage = "https://cran.r-project.org/web/packages/tsne/index.html"
+    url      = "https://cran.r-project.org/src/contrib/tsne_0.1-3.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/tnse"
+
+    version('0.1-3', '00974d4b3fd5f1100d0ebd24e03b0af9')
+    version('0.1-2', 'd96d8dce6ffeda68e2b25ec1ff52ea61')
+    version('0.1-1', '8197e5c61dec916b7a31b74e658b632d')
+
+    depends_on('r@3.4.0:3.4.9')
diff --git a/var/spack/repos/builtin/packages/r-ttr/package.py b/var/spack/repos/builtin/packages/r-ttr/package.py
index abaac57c6f..8c30fe566b 100644
--- a/var/spack/repos/builtin/packages/r-ttr/package.py
+++ b/var/spack/repos/builtin/packages/r-ttr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-udunits2/package.py b/var/spack/repos/builtin/packages/r-udunits2/package.py
new file mode 100644
index 0000000000..23dd7d86a0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-udunits2/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RUdunits2(RPackage):
+    """Provides simple bindings to Unidata's udunits library."""
+
+    homepage = "https://github.com/pacificclimate/Rudunits2"
+    url      = "https://cran.r-project.org/src/contrib/udunits2_0.13.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/udunits2"
+
+    version('0.13', 'c8717808c740ef70eed7aea93c7c4c7d')
+
+    depends_on('udunits2')
diff --git a/var/spack/repos/builtin/packages/r-units/package.py b/var/spack/repos/builtin/packages/r-units/package.py
new file mode 100644
index 0000000000..9d3f41d0d8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-units/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RUnits(RPackage):
+    """Support for measurement units in R vectors, matrices and arrays:
+       automatic propagation, conversion, derivation and simplification of
+       units; raising errors in case of unit incompatibility. Compatible with
+       the POSIXct, Date and difftime classes. Uses the UNIDATA udunits
+       library and unit database for unit compatibility checking and
+       conversion."""
+
+    homepage = "https://github.com/edzer/units/"
+    url      = "https://cran.r-project.org/src/contrib/units_0.4-6.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/units"
+
+    version('0.4-6', '0bb90dde5dad7608fa6feb1599381bf2')
+
+    depends_on('r-udunits2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-utils/package.py b/var/spack/repos/builtin/packages/r-utils/package.py
index bb39da3e60..5ea5e2d63c 100644
--- a/var/spack/repos/builtin/packages/r-utils/package.py
+++ b/var/spack/repos/builtin/packages/r-utils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-uuid/package.py b/var/spack/repos/builtin/packages/r-uuid/package.py
index ff0c13cf10..461a11ff84 100644
--- a/var/spack/repos/builtin/packages/r-uuid/package.py
+++ b/var/spack/repos/builtin/packages/r-uuid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-variantannotation/package.py b/var/spack/repos/builtin/packages/r-variantannotation/package.py
index 1b8e3da4d5..3063836f5a 100644
--- a/var/spack/repos/builtin/packages/r-variantannotation/package.py
+++ b/var/spack/repos/builtin/packages/r-variantannotation/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class RVariantannotation(RPackage):
        outcomes."""
 
     homepage = "https://www.bioconductor.org/packages/VariantAnnotation/"
-    url      = "https://git.bioconductor.org/packages/VariantAnnotation"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/VariantAnnotation.git"
 
-    version('1.22.3', git='https://git.bioconductor.org/packages/VariantAnnotation', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee')
+    version('1.22.3', commit='3a91b6d4297aa416d5f056dec6f8925eb1a8eaee')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
     depends_on('r-genomeinfodb', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-varselrf/package.py b/var/spack/repos/builtin/packages/r-varselrf/package.py
index 7cfb3392cd..05a11ee0b9 100644
--- a/var/spack/repos/builtin/packages/r-varselrf/package.py
+++ b/var/spack/repos/builtin/packages/r-varselrf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-vcd/package.py b/var/spack/repos/builtin/packages/r-vcd/package.py
index c0ca50a605..07d7104686 100644
--- a/var/spack/repos/builtin/packages/r-vcd/package.py
+++ b/var/spack/repos/builtin/packages/r-vcd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-vegan/package.py b/var/spack/repos/builtin/packages/r-vegan/package.py
index 51591ec41d..c571615d92 100644
--- a/var/spack/repos/builtin/packages/r-vegan/package.py
+++ b/var/spack/repos/builtin/packages/r-vegan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-vgam/package.py b/var/spack/repos/builtin/packages/r-vgam/package.py
new file mode 100644
index 0000000000..f148239434
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-vgam/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RVgam(RPackage):
+    """An implementation of about 6 major classes of statistical regression
+    models."""
+
+    homepage = "https://cran.r-project.org/web/packages/VGAM/index.html"
+    url      = "https://cran.r-project.org/src/contrib/VGAM_1.0-4.tar.gz"
+    list_url = "https://cran.rstudio.com/src/contrib/Archive/VGAM"
+
+    version('1.0-4', '9d30736842db6d9dcec83df49f11d3c1')
+    version('1.0-3', 'a158cd0a6ff956b4bf21d610df361b18')
+    version('1.0-2', '813b303d5d956914cf8910db3fa1ba14')
+    version('1.0-1', '778182585c774036ac3d10240cf63b40')
+    version('1.0-0', '81da7b3a797b5e26b9e859dc2f373b7b')
+
+    depends_on('r@3.4.0:3.4.9')
+    depends_on('r-mass', type=('build', 'run'))
+    depends_on('r-mgcv', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-vipor/package.py b/var/spack/repos/builtin/packages/r-vipor/package.py
new file mode 100644
index 0000000000..79c1d0cfba
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-vipor/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RVipor(RPackage):
+    """Plot Categorical Data Using Quasirandom Noise and Density Estimates"""
+
+    homepage = "https://cran.r-project.org/package=vipor"
+    url      = "https://cran.r-project.org/src/contrib/vipor_0.4.5.tar.gz"
+    list_url = "https://cran.r-project.org/src/contrib/Archive/vipor"
+
+    version('0.4.5', 'd08bc95b3aaf1574bf41b7eb41b67ce4')
+    version('0.4.4', '834212e3971787809ba9737744d54dee')
+
+    depends_on('r@3.0.0:', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-viridis/package.py b/var/spack/repos/builtin/packages/r-viridis/package.py
index 627ba4ac39..d71d0654b0 100644
--- a/var/spack/repos/builtin/packages/r-viridis/package.py
+++ b/var/spack/repos/builtin/packages/r-viridis/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-viridislite/package.py b/var/spack/repos/builtin/packages/r-viridislite/package.py
index bfdd6c3bc5..d83c606dca 100644
--- a/var/spack/repos/builtin/packages/r-viridislite/package.py
+++ b/var/spack/repos/builtin/packages/r-viridislite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-visnetwork/package.py b/var/spack/repos/builtin/packages/r-visnetwork/package.py
index 5cbc427c17..decbaa0f7d 100644
--- a/var/spack/repos/builtin/packages/r-visnetwork/package.py
+++ b/var/spack/repos/builtin/packages/r-visnetwork/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-vsn/package.py b/var/spack/repos/builtin/packages/r-vsn/package.py
index 649f42ea5d..27e7026b65 100644
--- a/var/spack/repos/builtin/packages/r-vsn/package.py
+++ b/var/spack/repos/builtin/packages/r-vsn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,9 +21,9 @@ class RVsn(RPackage):
        differential transcription."""
 
     homepage = "https://www.bioconductor.org/packages/vsn/"
-    url      = "https://git.bioconductor.org/packages/vsn"
+    git      = "https://git.bioconductor.org/packages/vsn.git"
 
-    version('3.44.0', git='https://git.bioconductor.org/packages/vsn', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
+    version('3.44.0', commit='e54513fcdd07ccfb8094359e93cef145450f0ee0')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-affy', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-whisker/package.py b/var/spack/repos/builtin/packages/r-whisker/package.py
index d22b1a5209..f54c9b4529 100644
--- a/var/spack/repos/builtin/packages/r-whisker/package.py
+++ b/var/spack/repos/builtin/packages/r-whisker/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-withr/package.py b/var/spack/repos/builtin/packages/r-withr/package.py
index 67afc532ae..cd9888c431 100644
--- a/var/spack/repos/builtin/packages/r-withr/package.py
+++ b/var/spack/repos/builtin/packages/r-withr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xde/package.py b/var/spack/repos/builtin/packages/r-xde/package.py
index 5d4a686fb5..25598b44dc 100644
--- a/var/spack/repos/builtin/packages/r-xde/package.py
+++ b/var/spack/repos/builtin/packages/r-xde/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class RXde(RPackage):
        expression."""
 
     homepage = "https://www.bioconductor.org/packages/XDE/"
-    url      = "https://git.bioconductor.org/packages/XDE"
+    git      = "https://git.bioconductor.org/packages/XDE.git"
 
-    version('2.22.0', git='https://git.bioconductor.org/packages/XDE', commit='25bcec965ae42a410dd285a9db9be46d112d8e81')
+    version('2.22.0', commit='25bcec965ae42a410dd285a9db9be46d112d8e81')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biocgenerics', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-xgboost/package.py b/var/spack/repos/builtin/packages/r-xgboost/package.py
index 22f87b5c54..ad7aac9f0e 100644
--- a/var/spack/repos/builtin/packages/r-xgboost/package.py
+++ b/var/spack/repos/builtin/packages/r-xgboost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/r-xlconnect/package.py b/var/spack/repos/builtin/packages/r-xlconnect/package.py
index 6a388c14a5..49d468f539 100644
--- a/var/spack/repos/builtin/packages/r-xlconnect/package.py
+++ b/var/spack/repos/builtin/packages/r-xlconnect/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py
index fd7913a296..a8f128cda1 100644
--- a/var/spack/repos/builtin/packages/r-xlconnectjars/package.py
+++ b/var/spack/repos/builtin/packages/r-xlconnectjars/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py
index 988fa41157..82d36970be 100644
--- a/var/spack/repos/builtin/packages/r-xlsx/package.py
+++ b/var/spack/repos/builtin/packages/r-xlsx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xlsxjars/package.py b/var/spack/repos/builtin/packages/r-xlsxjars/package.py
index 8bd19f97c4..bb49a81b70 100644
--- a/var/spack/repos/builtin/packages/r-xlsxjars/package.py
+++ b/var/spack/repos/builtin/packages/r-xlsxjars/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xmapbridge/package.py b/var/spack/repos/builtin/packages/r-xmapbridge/package.py
index 0836eb3951..07b410fc7f 100644
--- a/var/spack/repos/builtin/packages/r-xmapbridge/package.py
+++ b/var/spack/repos/builtin/packages/r-xmapbridge/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,8 @@ class RXmapbridge(RPackage):
        exports plotting files in a suitable format."""
 
     homepage = "https://www.bioconductor.org/packages/xmapbridge/"
-    url      = "https://git.bioconductor.org/packages/xmapbridge"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/xmapbridge.git"
 
-    version('1.34.0', git='https://git.bioconductor.org/packages/xmapbridge', commit='f162e1f72ead5f5a1aede69032d5771a6572d965')
+    version('1.34.0', commit='f162e1f72ead5f5a1aede69032d5771a6572d965')
 
     depends_on('r@3.4.0:3.4.9', when='@1.34.0')
diff --git a/var/spack/repos/builtin/packages/r-xml/package.py b/var/spack/repos/builtin/packages/r-xml/package.py
index aca86eade4..9ce222a351 100644
--- a/var/spack/repos/builtin/packages/r-xml/package.py
+++ b/var/spack/repos/builtin/packages/r-xml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xml2/package.py b/var/spack/repos/builtin/packages/r-xml2/package.py
index ffbe0f626f..9d5cc6f56d 100644
--- a/var/spack/repos/builtin/packages/r-xml2/package.py
+++ b/var/spack/repos/builtin/packages/r-xml2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xtable/package.py b/var/spack/repos/builtin/packages/r-xtable/package.py
index 8f3cc65c0b..78a5833949 100644
--- a/var/spack/repos/builtin/packages/r-xtable/package.py
+++ b/var/spack/repos/builtin/packages/r-xtable/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xts/package.py b/var/spack/repos/builtin/packages/r-xts/package.py
index 1c1184428a..1efa347f1c 100644
--- a/var/spack/repos/builtin/packages/r-xts/package.py
+++ b/var/spack/repos/builtin/packages/r-xts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-xvector/package.py b/var/spack/repos/builtin/packages/r-xvector/package.py
index 4018422c18..bd9c8a7672 100644
--- a/var/spack/repos/builtin/packages/r-xvector/package.py
+++ b/var/spack/repos/builtin/packages/r-xvector/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,13 +11,17 @@ class RXvector(RPackage):
        an R external pointer, or on disk)."""
 
     homepage = "https://bioconductor.org/packages/XVector/"
-    url      = "https://git.bioconductor.org/packages/XVector"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/XVector.git"
 
-    version('0.16.0', git='https://git.bioconductor.org/packages/XVector', commit='54615888e1a559da4a81de33e934fc0f1c3ad99f')
+    version('0.20.0', commit='a83a7ea01f6a710f0ba7d9fb021cfa795b291cb4')
+    version('0.16.0', commit='54615888e1a559da4a81de33e934fc0f1c3ad99f')
 
     depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-biocgenerics@0.19.2:', when='@0.20.0', type=('build', 'run'))
     depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-s4vectors@0.17.24:', when='@0.20.0', type=('build', 'run'))
     depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-iranges@2.13.16:', when='@0.20.0', type=('build', 'run'))
     depends_on('r-zlibbioc', type=('build', 'run'))
-    depends_on('r@3.4.0:3.4.9', when='@0.16.0')
+    depends_on('r@3.4.0:3.4.9', when='@0.16.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@0.20.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-yaml/package.py b/var/spack/repos/builtin/packages/r-yaml/package.py
index 25e60cdd9a..4c582bee8f 100644
--- a/var/spack/repos/builtin/packages/r-yaml/package.py
+++ b/var/spack/repos/builtin/packages/r-yaml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r-yapsa/package.py b/var/spack/repos/builtin/packages/r-yapsa/package.py
index a69b745a7e..4e771bd199 100644
--- a/var/spack/repos/builtin/packages/r-yapsa/package.py
+++ b/var/spack/repos/builtin/packages/r-yapsa/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,9 @@ class RYapsa(RPackage):
        catalogue) are provided."""
 
     homepage = "http://bioconductor.org/packages/YAPSA/"
-    url      = "https://git.bioconductor.org/packages/YAPSA"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/YAPSA.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/YAPSA', commit='320809b69e470e30a777a383f8341f93064ec24d')
+    version('1.2.0', commit='320809b69e470e30a777a383f8341f93064ec24d')
 
     depends_on('r-genomicranges', type=('build', 'run'))
     depends_on('r-ggplot2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
index 1901990927..9ead0a9110 100644
--- a/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
+++ b/var/spack/repos/builtin/packages/r-yaqcaffy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,9 @@ class RYaqcaffy(RPackage):
        reference datasets."""
 
     homepage = "http://bioconductor.org/packages/yaqcaffy/"
-    url      = "https://git.bioconductor.org/packages/yaqcaffy"
-    list_url = homepage
+    git      = "https://git.bioconductor.org/packages/yaqcaffy.git"
 
-    version('1.36.0', git='https://git.bioconductor.org/packages/yaqcaffy', commit='4d46fe77b2c8de2230a77b0c07dd5dd726e3abd6')
+    version('1.36.0', commit='4d46fe77b2c8de2230a77b0c07dd5dd726e3abd6')
 
     depends_on('r-simpleaffy', type=('build', 'run'))
     depends_on('r@3.4.0:3.4.9', when='@1.36.0')
diff --git a/var/spack/repos/builtin/packages/r-yarn/package.py b/var/spack/repos/builtin/packages/r-yarn/package.py
index 5b0a76b476..bf181f5886 100644
--- a/var/spack/repos/builtin/packages/r-yarn/package.py
+++ b/var/spack/repos/builtin/packages/r-yarn/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,11 +14,10 @@ class RYarn(RPackage):
        and statistical techniques to account for the large heterogeneity and
        sparsity found in very large RNA-seq experiments."""
 
-    homepage = "http://www.example.co://www.bioconductor.org/packages/yarn/"
-    url      = "https://git.bioconductor.org/packages/yarn"
-    list_url = homepage
+    homepage = "https://bioconductor.org/packages/yarn/"
+    git      = "https://git.bioconductor.org/packages/yarn.git"
 
-    version('1.2.0', git='https://git.bioconductor.org/packages/yarn', commit='28af616ef8c27dcadf6568e276dea8465486a697')
+    version('1.2.0', commit='28af616ef8c27dcadf6568e276dea8465486a697')
 
     depends_on('r-biobase', type=('build', 'run'))
     depends_on('r-biomart', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-zlibbioc/package.py b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
index 280c7da3de..b493b2a66f 100644
--- a/var/spack/repos/builtin/packages/r-zlibbioc/package.py
+++ b/var/spack/repos/builtin/packages/r-zlibbioc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,11 @@ class RZlibbioc(RPackage):
        direct need for this package). See the vignette for instructions
        on use."""
 
-    homepage = "http://bioconductor.org/packages/release/bioc/html/Zlibbioc.html"
-    url      = "https://git.bioconductor.org/packages/zlibbioc"
-    list_url = homepage
+    homepage = "http://bioconductor.org/packages/release/bioc/html/zlibbioc.html"
+    git      = "https://git.bioconductor.org/packages/zlibbioc.git"
+
+    version('1.26.0', commit='2e3ab097caa09a5e3ddaa3469b13e19a7224da0d')
+    version('1.22.0', commit='30377f830af2bc1ff17bbf3fdd2cb6442015fea5')
 
-    version('1.22.0', git='https://git.bioconductor.org/packages/zlibbioc', commit='30377f830af2bc1ff17bbf3fdd2cb6442015fea5')
-    depends_on('r@3.4.0:3.4.9', when='@1.22.0')
+    depends_on('r@3.4.0:3.4.9', when='@1.22.0', type=('build', 'run'))
+    depends_on('r@3.5.0:3.5.9', when='@1.26.0', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/r-zoo/package.py b/var/spack/repos/builtin/packages/r-zoo/package.py
index 33fa5d3353..c746c297b6 100644
--- a/var/spack/repos/builtin/packages/r-zoo/package.py
+++ b/var/spack/repos/builtin/packages/r-zoo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py
index 603a372861..6430e5b33f 100644
--- a/var/spack/repos/builtin/packages/r/package.py
+++ b/var/spack/repos/builtin/packages/r/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 shutil
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
 from spack import *
 
 
@@ -34,16 +16,22 @@ class R(AutotoolsPackage):
     Please consult the R project homepage for further information."""
 
     homepage = "https://www.r-project.org"
-    url = "https://cloud.r-project.org/src/base/R-3/R-3.4.0.tar.gz"
+    url = "https://cloud.r-project.org/src/base/R-3/R-3.4.3.tar.gz"
 
     extendable = True
 
+    version('3.5.1', sha256='0463bff5eea0f3d93fa071f79c18d0993878fd4f2e18ae6cf22c1639d11457ed')
+    version('3.5.0', 'c0455dbfa76ca807e4dfa93d49dcc817')
+    version('3.4.4', '9d6f73be072531e95884c7965ff80cd8')
+    version('3.4.3', 'bc55db54f992fda9049201ca62d2a584')
+    version('3.4.2', '1cd6d37850188e7f190f1eb94a24ca1f')
     version('3.4.1', '3a79c01dc0527c62e80ffb1c489297ea')
     version('3.4.0', '75083c23d507b9c16d5c6afbd7a827e7')
     version('3.3.3', '0ac211ec15e813a24f8f4a5a634029a4')
     version('3.3.2', '2437014ef40641cdc9673e89c040b7a8')
     version('3.3.1', 'f50a659738b73036e2f5635adbd229c5')
     version('3.3.0', '5a7506c8813432d1621c9725e86baf7a')
+    version('3.2.5', '7b23ee70cfb383be3bd4360e3c71d8c3')
     version('3.2.3', '1ba3dac113efab69e706902810cc2970')
     version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
     version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
@@ -55,12 +43,14 @@ class R(AutotoolsPackage):
             description='Links to externally installed BLAS/LAPACK')
     variant('X', default=False,
             description='Enable X11 support (call configure --with-x)')
+    variant('memory_profiling', default=False,
+            description='Enable memory profiling')
 
     # Virtual dependencies
     depends_on('blas', when='+external-lapack')
     depends_on('lapack', when='+external-lapack')
 
-    # Concrete dependencies
+    # Concrete dependencies.
     depends_on('readline')
     depends_on('ncurses')
     depends_on('icu4c')
@@ -86,6 +76,10 @@ class R(AutotoolsPackage):
 
     patch('zlib.patch', when='@:3.3.2')
 
+    filter_compiler_wrappers(
+        'Makeconf', relative_root=os.path.join('rlib', 'R', 'etc')
+    )
+
     @property
     def etcdir(self):
         return join_path(prefix, 'rlib', 'R', 'etc')
@@ -94,16 +88,21 @@ class R(AutotoolsPackage):
         spec   = self.spec
         prefix = self.prefix
 
+        tcl_config_path = join_path(spec['tcl'].prefix.lib, 'tclConfig.sh')
+        tk_config_path = join_path(spec['tk'].prefix.lib, 'tkConfig.sh')
+
         config_args = [
             '--libdir={0}'.format(join_path(prefix, 'rlib')),
             '--enable-R-shlib',
             '--enable-BLAS-shlib',
-            '--enable-R-framework=no'
+            '--enable-R-framework=no',
+            '--with-tcl-config={0}'.format(tcl_config_path),
+            '--with-tk-config={0}'.format(tk_config_path),
         ]
 
         if '+external-lapack' in spec:
             config_args.extend([
-                '--with-blas',
+                '--with-blas={0}'.format(spec['blas'].libs),
                 '--with-lapack'
             ])
 
@@ -112,6 +111,9 @@ class R(AutotoolsPackage):
         else:
             config_args.append('--without-x')
 
+        if '+memory_profiling' in spec:
+            config_args.append('--enable-memory-profiling')
+
         return config_args
 
     @run_after('install')
@@ -120,27 +122,7 @@ class R(AutotoolsPackage):
         # dependencies in Spack.
         src_makeconf = join_path(self.etcdir, 'Makeconf')
         dst_makeconf = join_path(self.etcdir, 'Makeconf.spack')
-        shutil.copy(src_makeconf, dst_makeconf)
-
-    @run_after('install')
-    def filter_compilers(self):
-        """Run after install to tell the configuration files and Makefiles
-        to use the compilers that Spack built the package with.
-
-        If this isn't done, they'll have CC and CXX set to Spack's generic
-        cc and c++. We want them to be bound to whatever compiler
-        they were built with."""
-
-        kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
-
-        filter_file(env['CC'], self.compiler.cc,
-                    join_path(self.etcdir, 'Makeconf'), **kwargs)
-        filter_file(env['CXX'], self.compiler.cxx,
-                    join_path(self.etcdir, 'Makeconf'), **kwargs)
-        filter_file(env['F77'], self.compiler.f77,
-                    join_path(self.etcdir, 'Makeconf'), **kwargs)
-        filter_file(env['FC'], self.compiler.fc,
-                    join_path(self.etcdir, 'Makeconf'), **kwargs)
+        install(src_makeconf, dst_makeconf)
 
     # ========================================================================
     # Set up environment to make install easy for R extensions.
diff --git a/var/spack/repos/builtin/packages/racon/package.py b/var/spack/repos/builtin/packages/racon/package.py
new file mode 100644
index 0000000000..706d1f68c2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/racon/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Racon(CMakePackage):
+    """Ultrafast consensus module for raw de novo genome assembly of long
+     uncorrected reads."""
+
+    homepage = "https://github.com/isovic/racon"
+    url      = "https://github.com/isovic/racon/releases/download/1.2.1/racon-v1.2.1.tar.gz"
+
+    version('1.3.0', 'e00d61f391bce2af20ebd2a3aee1e05a')
+    version('1.2.1', '7bf273b965a5bd0f41342a9ffe5c7639')
+
+    depends_on('cmake@3.2:', type='build')
+    depends_on('python', type='build')
+
+    conflicts('%gcc@:4.7')
+    conflicts('%clang@:3.1')
+
+    def cmake_args(self):
+        args = ['-Dracon_build_wrapper=ON']
+        return args
+
+    def install(self, spec, prefix):
+        install_tree('spack-build/bin', prefix.bin)
+        install_tree('spack-build/lib', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/raft/package.py b/var/spack/repos/builtin/packages/raft/package.py
index a5cc1f0ced..44d4828b97 100644
--- a/var/spack/repos/builtin/packages/raft/package.py
+++ b/var/spack/repos/builtin/packages/raft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,10 +12,11 @@ class Raft(CMakePackage):
        Toolbox under development at Brazilian Synchrotron Light Source."""
 
     homepage = "https://bitbucket.org/gill_martinez/raft_aps"
-    url = "https://bitbucket.org/gill_martinez/raft_aps/get/1.2.3.tar.gz"
+    url      = "https://bitbucket.org/gill_martinez/raft_aps/get/1.2.3.tar.gz"
+    git      = "https://bitbucket.org/gill_martinez/raft_aps.git"
 
+    version('develop', branch='master')
     version('1.2.3', '4d1b106d9b3493e63dde96f7dd44b834')
-    version('develop', git='https://bitbucket.org/gill_martinez/raft_aps.git')
 
     depends_on('mpi')
     depends_on('cmake', type='build')
diff --git a/var/spack/repos/builtin/packages/ragel/package.py b/var/spack/repos/builtin/packages/ragel/package.py
new file mode 100644
index 0000000000..90056223e4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ragel/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ragel(AutotoolsPackage):
+    """Ragel State Machine Compiler
+    Ragel compiles executable finite state machines from regular
+    languages. Ragel targets C, C++ and ASM. Ragel state machines can
+    not only recognize byte sequences as regular expression machines
+    do, but can also execute code at arbitrary points in the
+    recognition of a regular language. Code embedding is done using
+    inline operators that do not disrupt the regular language syntax.
+    """
+    homepage = "http://www.colm.net/open-source/ragel"
+    git      = "git://colm.net/ragel.git"
+    url      = "http://www.colm.net/files/ragel/ragel-6.10.tar.gz"
+
+    version('6.10', '748cae8b50cffe9efcaa5acebc6abf0d')
+
+    depends_on('colm', type='build')
diff --git a/var/spack/repos/builtin/packages/raja/package.py b/var/spack/repos/builtin/packages/raja/package.py
index 18d2135991..eceaf277fc 100644
--- a/var/spack/repos/builtin/packages/raja/package.py
+++ b/var/spack/repos/builtin/packages/raja/package.py
@@ -1,34 +1,45 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Raja(CMakePackage):
     """RAJA Parallel Framework."""
+
     homepage = "http://software.llnl.gov/RAJA/"
+    git      = "https://github.com/LLNL/RAJA.git"
+
+    version('develop', branch='develop', submodules='True')
+    version('master',  branch='master',  submodules='True')
+    version('0.5.3', tag='v0.5.3', submodules="True")
+    version('0.5.2', tag='v0.5.2', submodules="True")
+    version('0.5.1', tag='v0.5.1', submodules="True")
+    version('0.5.0', tag='v0.5.0', submodules="True")
+    version('0.4.1', tag='v0.4.1', submodules="True")
+    version('0.4.0', tag='v0.4.0', submodules="True")
 
-    version('develop', git='https://github.com/LLNL/RAJA.git', branch="master", submodules="True")
+    variant('cuda', default=False, description='Build with CUDA backend')
+    variant('openmp', default=True, description='Build OpenMP backend')
+
+    depends_on('cuda', when='+cuda')
 
     depends_on('cmake@3.3:', type='build')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        if '+openmp' in spec:
+            options.extend([
+                '-DENABLE_OPENMP=On'])
+
+        if '+cuda' in spec:
+            options.extend([
+                '-DENABLE_CUDA=On',
+                '-DCUDA_TOOLKIT_ROOT_DIR=%s' % (spec['cuda'].prefix)])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/randfold/package.py b/var/spack/repos/builtin/packages/randfold/package.py
index 5160840332..12f6b0e2fa 100644
--- a/var/spack/repos/builtin/packages/randfold/package.py
+++ b/var/spack/repos/builtin/packages/randfold/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/random123/package.py b/var/spack/repos/builtin/packages/random123/package.py
index 978467b457..0274adcc5d 100644
--- a/var/spack/repos/builtin/packages/random123/package.py
+++ b/var/spack/repos/builtin/packages/random123/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/randrproto/package.py b/var/spack/repos/builtin/packages/randrproto/package.py
index 24f6aaed41..151ada479e 100644
--- a/var/spack/repos/builtin/packages/randrproto/package.py
+++ b/var/spack/repos/builtin/packages/randrproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Randrproto(AutotoolsPackage):
 
     version('1.5.0', '863d6ee3e0b2708f75d968470ed31eb9')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/range-v3/package.py b/var/spack/repos/builtin/packages/range-v3/package.py
new file mode 100644
index 0000000000..e3d226a741
--- /dev/null
+++ b/var/spack/repos/builtin/packages/range-v3/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RangeV3(CMakePackage):
+    """Range library for C++11/14/17"""
+
+    homepage = "https://github.com/ericniebler/range-v3"
+    url      = "https://github.com/ericniebler/range-v3/archive/0.3.6.tar.gz"
+    git      = "https://github.com/ericniebler/range-v3.git"
+
+    version('develop', branch='master')
+    version('0.3.6', sha256='ce6e80c6b018ca0e03df8c54a34e1fd04282ac1b068cd39e902e2e5201ac117f')
+    version('0.3.5', sha256='0a0094b450fe17e1454468bef5b6bf60e73ef100aebe1663daf6fbdf2c353836')
+    version('0.3.0', sha256='cc29fbed5b06b11e7f9a732f7e1211483ebbd3cfe29d86e40c93209014790d74')
+    version('0.2.6', sha256='b1b448ead59bd726248bcb607b4a47335a00bed1c74630e09d550da3ff72d02c')
+    version('0.2.5', sha256='4125089da83dec3f0ed676066f0cf583fe55dd9270bc62f1736907f57656ca7e')
+    version('0.2.4', sha256='6fc4f9e80ee8eb22302db45c5648c665817aeeeee7f99b7effdf6a38a1be9a75')
+    version('0.2.3', sha256='214a3f0ea70d479ca58f0af8938de49a9ed476564213431ab3b8e02a849b8098')
+    version('0.2.2', sha256='01a7bee222570a55a79c84a54b2997ed718dac06f43a82122ff0150a11477f9d')
+    version('0.2.1', sha256='25d5e3dad8052d668873e960bd78f068bebfba3bd28a278f805ea386f9438790')
+    version('0.2.0', sha256='49b1a62a7a36dab582521c8034d8e736a8922af664d007c1529d3162b1294331')
+
+    variant('cxxstd',
+            default='11',
+            values=('11', '14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
+
+    depends_on('cmake@3.6:', type='build')
+
+    def cmake_args(self):
+        args = [
+            '-DRANGES_CXX_STD={0}'.format(self.spec.variants['cxxstd'].value)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/rankstr/package.py b/var/spack/repos/builtin/packages/rankstr/package.py
new file mode 100644
index 0000000000..3334b8deeb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rankstr/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rankstr(CMakePackage):
+    """Assign one-to-one mapping of MPI ranks to strings"""
+
+    homepage = "https://github.com/ECP-VeloC/rankstr"
+    url      = "https://github.com/ECP-VeloC/rankstr/archive/v0.0.1.zip"
+    git      = "https://github.com/ecp-veloc/rankstr.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.0.2', sha256='c16d53aa9bb79934cbe2dcd8612e2db7d59de80be500c104e39e8623d4eacd8e')
+
+    depends_on('mpi')
+
+    def cmake_args(self):
+        args = []
+        args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DRANKSTR_LINK_STATIC=ON")
+        return args
diff --git a/var/spack/repos/builtin/packages/rapidjson/package.py b/var/spack/repos/builtin/packages/rapidjson/package.py
new file mode 100644
index 0000000000..33d616cb2a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rapidjson/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rapidjson(CMakePackage):
+    """A fast JSON parser/generator for C++ with both SAX/DOM style API"""
+
+    homepage = "http://rapidjson.org"
+    url      = "https://github.com/Tencent/rapidjson/archive/v1.1.0.tar.gz"
+
+    version('1.1.0', 'badd12c511e081fec6c89c43a7027bce')
+    version('1.0.2', '97cc60d01282a968474c97f60714828c')
+    version('1.0.1', '48cc188df49617b859d13d31344a50b8')
+    version('1.0.0', '08247fbfa464d7f15304285f04b4b228')
diff --git a/var/spack/repos/builtin/packages/ravel/package.py b/var/spack/repos/builtin/packages/ravel/package.py
index 3f03444f76..7a2f53ea4d 100644
--- a/var/spack/repos/builtin/packages/ravel/package.py
+++ b/var/spack/repos/builtin/packages/ravel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/raxml/package.py b/var/spack/repos/builtin/packages/raxml/package.py
index 96d6f7c95b..edb781eb80 100644
--- a/var/spack/repos/builtin/packages/raxml/package.py
+++ b/var/spack/repos/builtin/packages/raxml/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -51,6 +32,9 @@ class Raxml(Package):
     conflicts('%xl')
     conflicts('%xl_r')
 
+    # can't build multiple binaries in parallel without things breaking
+    parallel = False
+
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         files = glob.iglob("Makefile.*")
@@ -62,46 +46,45 @@ class Raxml(Package):
             make('-f', 'Makefile.AVX.HYBRID.gcc')
             install('raxmlHPC-HYBRID-AVX', prefix.bin)
 
-        elif '+mpi' and '+sse' and '+pthreads' in spec:
+        if '+mpi' and '+sse' and '+pthreads' in spec:
             make('-f', 'Makefile.SSE3.HYBRID.gcc')
             install('raxmlHPC-HYBRID-SSE3', prefix.bin)
 
-        elif '+mpi' and '+pthreads' in spec:
+        if '+mpi' and '+pthreads' in spec:
             make('-f', 'Makefile.HYBRID.gcc')
             install('raxmlHPC-HYBRID', prefix.bin)
 
-        elif '+mpi' and '+avx' in spec:
+        if '+mpi' and '+avx' in spec:
             make('-f', 'Makefile.AVX.MPI.gcc')
             install('raxmlHPC-MPI-AVX', prefix.bin)
 
-        elif '+mpi' and '+sse' in spec:
+        if '+mpi' and '+sse' in spec:
             make('-f', 'Makefile.SSE3.MPI.gcc')
             install('raxmlHPC-MPI-SSE3', prefix.bin)
 
-        elif '+mpi' in spec:
+        if '+mpi' in spec:
             make('-f', 'Makefile.MPI.gcc')
             install('raxmlHPC-MPI', prefix.bin)
 
-        elif '+pthreads' and '+avx' in spec:
+        if '+pthreads' and '+avx' in spec:
             make('-f', 'Makefile.AVX.PTHREADS.gcc')
             install('raxmlHPC-PTHREADS-AVX', prefix.bin)
 
-        elif '+pthreads' and '+sse' in spec:
+        if '+pthreads' and '+sse' in spec:
             make('-f', 'Makefile.SSE3.PTHREADS.gcc')
             install('raxmlHPC-PTHREADS-SSE3', prefix.bin)
 
-        elif '+pthreads' in spec:
+        if '+pthreads' in spec:
             make('-f', 'Makefile.PTHREADS.gcc')
             install('raxmlHPC-PTHREADS', prefix.bin)
 
-        elif '+sse' in spec:
+        if '+sse' in spec:
             make('-f', 'Makefile.SSE3.gcc')
             install('raxmlHPC-SSE3', prefix.bin)
 
-        elif '+avx' in spec:
+        if '+avx' in spec:
             make('-f', 'Makefile.AVX.gcc')
             install('raxmlHPC-AVX', prefix.bin)
 
-        else:
-            make('-f', 'Makefile.gcc')
-            install('raxmlHPC', prefix.bin)
+        make('-f', 'Makefile.gcc')
+        install('raxmlHPC', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/ray/package.py b/var/spack/repos/builtin/packages/ray/package.py
index 45e08c74ff..f8d3c0f1b1 100644
--- a/var/spack/repos/builtin/packages/ray/package.py
+++ b/var/spack/repos/builtin/packages/ray/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/rclone/package.py b/var/spack/repos/builtin/packages/rclone/package.py
new file mode 100644
index 0000000000..ae8a1d2c26
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rclone/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rclone(Package):
+    """Rclone is a command line program to sync files and directories
+       to and from various cloud storage providers"""
+
+    homepage = "http://rclone.org"
+    url      = "https://github.com/ncw/rclone/releases/download/v1.43/rclone-v1.43.tar.gz"
+
+    version('1.43', sha256='d30527b00cecb4e5e7188dddb78e5cec62d67cf2422dab82190db58512b5a4e3')
+
+    depends_on("go", type='build')
+
+    def install(self, spec, prefix):
+        go('build')
+        mkdirp(prefix.bin)
+        install('rclone', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/rdma-core/package.py b/var/spack/repos/builtin/packages/rdma-core/package.py
new file mode 100644
index 0000000000..37138e9203
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rdma-core/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RdmaCore(CMakePackage):
+    """RDMA core userspace libraries and daemons"""
+
+    homepage = "https://github.com/linux-rdma/rdma-core"
+    url      = "https://github.com/linux-rdma/rdma-core/releases/download/v17.1/rdma-core-17.1.tar.gz"
+
+    version('20', sha256='bc846989f807cd2b03643927d2b99fbf6f849cb1e766ab49bc9e81ce769d5421')
+    version('17.1', sha256='b47444b7c05d3906deb8771eec3e634984dd83f5e620d5e37d3a83f74f0cc1ba')
+    version('13', sha256='e5230fd7cda610753ad1252b40a28b1e9cf836423a10d8c2525b081527760d97')
+
+    depends_on('pkgconfig', type='build')
+    depends_on('libnl')
+    conflicts('platform=darwin', msg='rdma-core requires FreeBSD or Linux')
+    conflicts('%intel', msg='rdma-core cannot be built with intel (use gcc instead)')
+
+# NOTE: specify CMAKE_INSTALL_RUNDIR explicitly to prevent rdma-core from
+#       using the spack staging build dir (which may be a very long file
+#       system path) as a component in compile-time static strings such as
+#       IBACM_SERVER_PATH.
+    def cmake_args(self):
+        cmake_args = ["-DCMAKE_INSTALL_SYSCONFDIR=" +
+                      self.spec.prefix.etc,
+                      "-DCMAKE_INSTALL_RUNDIR=/var/run"]
+        return cmake_args
diff --git a/var/spack/repos/builtin/packages/rdp-classifier/package.py b/var/spack/repos/builtin/packages/rdp-classifier/package.py
index 637e490a17..b17e926066 100644
--- a/var/spack/repos/builtin/packages/rdp-classifier/package.py
+++ b/var/spack/repos/builtin/packages/rdp-classifier/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/re2c/package.py b/var/spack/repos/builtin/packages/re2c/package.py
new file mode 100644
index 0000000000..596c03cc29
--- /dev/null
+++ b/var/spack/repos/builtin/packages/re2c/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+
+
+class Re2c(AutotoolsPackage):
+    """re2c: a free and open-source lexer generator for C and C++"""
+
+    homepage = "http://re2c.org/index.html"
+    url      = "https://github.com/skvadrik/re2c/releases/download/1.0.3/re2c-1.0.3.tar.gz"
+
+    version('1.0.3', '8f575e2bf2efd3c685c87042f279ae4f')
+
+    def configure_args(self):
+        args = ['--disable-dependency-tracking']
+        return args
diff --git a/var/spack/repos/builtin/packages/readfq/package.py b/var/spack/repos/builtin/packages/readfq/package.py
new file mode 100644
index 0000000000..28ee9225aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/readfq/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Readfq(Package):
+    """Readfq is a collection of routines for parsing the FASTA/FASTQ format.
+    It seamlessly parses both FASTA and multi-line FASTQ with a simple
+    interface."""
+
+    homepage = "https://github.com/lh3/readfq"
+    git      = "https://github.com/lh3/readfq.git"
+
+    version('2013.04.10', commit='4fb766095d8f459e0f8025be70f9173673905d12')
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/readline/package.py b/var/spack/repos/builtin/packages/readline/package.py
index ccdea0aa0f..156a7d429b 100644
--- a/var/spack/repos/builtin/packages/readline/package.py
+++ b/var/spack/repos/builtin/packages/readline/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,7 +15,7 @@ class Readline(AutotoolsPackage):
     csh-like history expansion on previous commands."""
 
     homepage = "http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html"
-    url      = "https://ftp.gnu.org/gnu/readline/readline-7.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/readline/readline-7.0.tar.gz"
 
     version('7.0', '205b03a87fc83dab653b628c59b9fc91')
     version('6.3', '33c8fb279e981274f485fd91da77e94a')
diff --git a/var/spack/repos/builtin/packages/recordproto/package.py b/var/spack/repos/builtin/packages/recordproto/package.py
index dcbc0326e8..737d6e3ffb 100644
--- a/var/spack/repos/builtin/packages/recordproto/package.py
+++ b/var/spack/repos/builtin/packages/recordproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Recordproto(AutotoolsPackage):
 
     version('1.14.2', '868235e1e150e68916d5a316ebc4ccc4')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/redset/package.py b/var/spack/repos/builtin/packages/redset/package.py
new file mode 100644
index 0000000000..3514a9bbf1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/redset/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Redset(CMakePackage):
+    """Create MPI communicators for disparate redundancy sets"""
+
+    homepage = "https://github.com/ECP-VeloC/redset"
+    url      = "https://github.com/ECP-VeloC/redset/archive/v0.0.2.zip"
+    git      = "https://github.com/ecp-veloc/redset.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.0.3', sha256='f110c9b42209d65f84a8478b919b27ebe2d566839cb0cd0c86ccbdb1f51598f4')
+
+    depends_on('mpi')
+    depends_on('rankstr')
+    depends_on('kvtree+mpi')
+
+    def cmake_args(self):
+        args = []
+        args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DREDSET_LINK_STATIC=ON")
+        args.append("-DWITH_KVTREE_PREFIX=%s" % self.spec['kvtree'].prefix)
+        args.append("-DWITH_RANKSTR_PREFIX=%s" % self.spec['rankstr'].prefix)
+        return args
diff --git a/var/spack/repos/builtin/packages/redundans/package.py b/var/spack/repos/builtin/packages/redundans/package.py
index 71f83f623a..17aed51ee1 100644
--- a/var/spack/repos/builtin/packages/redundans/package.py
+++ b/var/spack/repos/builtin/packages/redundans/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,16 +17,22 @@ class Redundans(Package):
     depends_on('python', type=('build', 'run'))
     depends_on('py-pyscaf', type=('build', 'run'))
     depends_on('py-fastaindex', type=('build', 'run'))
+    depends_on('py-numpy', type=('build', 'run'))
     depends_on('perl', type=('build', 'run'))
     depends_on('sspace-standard')
     depends_on('bwa')
     depends_on('last')
     depends_on('gapcloser')
     depends_on('parallel')
-    depends_on('snap-berkeley')
+    depends_on('snap-berkeley@1.0beta.18:', type=('build', 'run'))
 
     def install(self, spec, prefix):
+        sspace_location = join_path(spec['sspace-standard'].prefix,
+                                    'SSPACE_Standard_v3.0.pl')
         mkdirp(prefix.bin)
+        filter_file(r'sspacebin = os.path.join(.*)$',
+                    'sspacebin = \'' + sspace_location + '\'',
+                    'redundans.py')
         install('redundans.py', prefix.bin)
         with working_dir('bin'):
             install('fasta2homozygous.py', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/regcm/package.py b/var/spack/repos/builtin/packages/regcm/package.py
new file mode 100644
index 0000000000..32fde4885b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/regcm/package.py
@@ -0,0 +1,73 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Regcm(AutotoolsPackage):
+    """RegCM ICTP Regional Climate Model."""
+
+    homepage = 'https://gforge.ictp.it/gf/project/regcm/'
+
+    version('4.7.0', sha256='456631c10dcb83d70e51c3babda2f7a1aa41ed9e60cb4209deb3764655267519',
+            url='https://gforge.ictp.it/gf/download/frsrelease/259/1845/RegCM-4.7.0.tar.gz')
+
+    variant('debug', default=False,
+            description='Build RegCM using debug options.')
+    variant('profile', default=False,
+            description='Build RegCM using profiling options.')
+    variant('singleprecision', default=False,
+            description='Build RegCM using single precision float type.')
+
+    # On Intel and PGI compilers, multiple archs can be built at the same time,
+    # producing a so-called fat binary. Unfortunately, gcc builds only the last
+    # architecture provided (in the configure), so we allow a single arch.
+    extensions = ('knl', 'skl', 'bdw', 'nhl')
+    variant('extension', default=None, values=extensions, multi=True,
+            description='Build extensions for a specific Intel architecture.')
+
+    depends_on('netcdf')
+    depends_on('netcdf-fortran')
+    depends_on('hdf5')
+    depends_on('mpi')
+
+    # 'make' sometimes crashes when compiling with more than 10-12 cores.
+    # Moreover, parallel compile time is ~ 1m 30s, while serial is ~ 50s.
+    parallel = False
+
+    def flag_handler(self, name, flags):
+        if name == 'fflags' and self.compiler.fc.endswith('gfortran'):
+            flags.extend(['-Wall', '-Wextra', '-Warray-temporaries',
+                          '-Wconversion', '-fimplicit-none', '-fbacktrace',
+                          '-ffree-line-length-0', '-finit-real=nan',
+                          '-ffpe-trap=zero,overflow,underflow', '-fcheck=all'])
+
+        elif name == 'ldlibs':
+            flags.extend(['-lnetcdff', '-lnetcdf'])
+            if self.compiler.fc.endswith('gfortran'):
+                flags.extend(['-lm', '-ldl'])
+            else:
+                flags.extend(['-lhdf5_hl', '-lhdf5', '-lz'])
+
+        return (None, None, flags)
+
+    def configure_args(self):
+        args = ['--enable-shared']
+
+        for opt in ('debug', 'profile', 'singleprecision'):
+            if '+{0}'.format(opt) in self.spec:
+                args.append('--enable-' + opt)
+
+        for ext in self.extensions:
+            if 'extension={0}'.format(ext) in self.spec:
+                args.append('--enable-' + ext)
+                break
+
+        # RegCM complains when compiled with gfortran, and unfortunately FFLAGS
+        # is ignored by the configure, so we need to set the option in FCFLAGS.
+        if self.compiler.fc.endswith('gfortran'):
+            args.append('FCFLAGS=-fno-range-check')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/relion/package.py b/var/spack/repos/builtin/packages/relion/package.py
index ba006b9b43..eb092b6fa1 100644
--- a/var/spack/repos/builtin/packages/relion/package.py
+++ b/var/spack/repos/builtin/packages/relion/package.py
@@ -1,56 +1,59 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Relion(CMakePackage):
+class Relion(CMakePackage, CudaPackage):
     """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a
     stand-alone computer program that employs an empirical Bayesian approach to
     refinement of (multiple) 3D reconstructions or 2D class averages in
     electron cryo-microscopy (cryo-EM)."""
 
     homepage = "http://http://www2.mrc-lmb.cam.ac.uk/relion"
-    url      = "https://github.com/3dem/relion"
+    git      = "https://github.com/3dem/relion.git"
 
-    version('develop', git='https://github.com/3dem/relion.git')
+    version('3.0_beta',
+            git='https://bitbucket.org/scheres/relion-3.0_beta.git')
+    version('2.1', preferred='true', tag='2.1')
+    version('2.0.3', tag='2.0.3')
+    # relion has no develop branch though pulling from master
+    # should be considered the same as develop
+    version('develop', branch='master')
 
     variant('gui', default=True, description="build the gui")
-    variant('cuda', default=False, description="enable compute on gpu")
-    variant('double', default=False, description="double precision (cpu) code")
-    variant('double-gpu', default=False, description="double precision (gpu) code")
+    variant('cuda', default=True, description="enable compute on gpu")
+    variant('double', default=True, description="double precision (cpu) code")
+    variant('double-gpu', default=False, description="double precision gpu")
+    # if built with purpose=cluster then relion will link to gpfs libraries
+    # if that's not desirable then use purpose=desktop
+    variant('purpose', default='cluster', values=('cluster', 'desktop'),
+            description="build relion for use in cluster or desktop")
     variant('build_type', default='RelWithDebInfo',
             description='The build type to build',
             values=('Debug', 'Release', 'RelWithDebInfo',
                     'Profiling', 'Benchmarking'))
 
     depends_on('mpi')
+    # relion will not build with newer versions of cmake
+    # per https://github.com/3dem/relion/issues/380
+    depends_on('cmake@3:3.9.4', type='build')
     depends_on('fftw+float+double')
     depends_on('fltk', when='+gui')
-    depends_on('cuda@8.0:8.99', when='+cuda')
+    depends_on('libtiff')
+
+    # relion 3 supports cuda 9
+    # relion < 3 does not
+    depends_on('cuda', when='+cuda')
+    depends_on('cuda@9:', when='@3: +cuda')
+    depends_on('cuda@8.0:8.99', when='@:2 +cuda')
 
     def cmake_args(self):
+
+        carch = self.spec.variants['cuda_arch'].value[0]
+
         args = [
             '-DCMAKE_C_FLAGS=-g',
             '-DCMAKE_CXX_FLAGS=-g',
@@ -58,9 +61,18 @@ class Relion(CMakePackage):
             '-DDoublePrec_CPU=%s' % ('+double' in self.spec),
             '-DDoublePrec_GPU=%s' % ('+double-gpu' in self.spec),
         ]
+
         if '+cuda' in self.spec:
-            args += [
-                '-DCUDA=on',
-                '-DCUFFT=on',
-            ]
+            # relion+cuda requires selecting cuda_arch
+            if not carch:
+                raise ValueError("select cuda_arch when building with +cuda")
+            else:
+                args += ['-DCUDA=ON', '-DCudaTexture=ON',
+                         '-DCUDA_ARCH=%s' % (carch)]
+
+        # these new values were added in relion 3
+        # do not seem to cause problems with < 3
+        else:
+            args += ['-DMKLFFT=ON', '-DFORCE_OWN_TBB=ON', '-DALTCPU=ON']
+
         return args
diff --git a/var/spack/repos/builtin/packages/rempi/package.py b/var/spack/repos/builtin/packages/rempi/package.py
index f6e2a2f3e5..d3559fe6a0 100644
--- a/var/spack/repos/builtin/packages/rempi/package.py
+++ b/var/spack/repos/builtin/packages/rempi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Rempi(AutotoolsPackage):
     homepage = "https://github.com/PRUNERS/ReMPI"
     url      = "https://github.com/PRUNERS/ReMPI/releases/download/v1.0.0/ReMPI-1.0.0.tar.gz"
 
+    version("1.1.0", "05b872a6f3e2f49a2fc6112a844c7f43")
     version("1.0.0", "32c780a6a74627b5796bea161d4c4733")
 
     depends_on("mpi")
diff --git a/var/spack/repos/builtin/packages/rename/package.py b/var/spack/repos/builtin/packages/rename/package.py
index 01bc35f073..dfdaa31027 100644
--- a/var/spack/repos/builtin/packages/rename/package.py
+++ b/var/spack/repos/builtin/packages/rename/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/rendercheck/package.py b/var/spack/repos/builtin/packages/rendercheck/package.py
index 65fcc7a312..ea66f66c0b 100644
--- a/var/spack/repos/builtin/packages/rendercheck/package.py
+++ b/var/spack/repos/builtin/packages/rendercheck/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Rendercheck(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/renderproto/package.py b/var/spack/repos/builtin/packages/renderproto/package.py
index a6c91ab06b..ded178b5bb 100644
--- a/var/spack/repos/builtin/packages/renderproto/package.py
+++ b/var/spack/repos/builtin/packages/renderproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Renderproto(AutotoolsPackage):
 
     version('0.11.1', '9b103359123e375bb7760f7dbae3dece')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py
index c9713c7892..63d680c2e1 100644
--- a/var/spack/repos/builtin/packages/repeatmasker/package.py
+++ b/var/spack/repos/builtin/packages/repeatmasker/package.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import inspect
-import distutils.dir_util
 
 
 class Repeatmasker(Package):
@@ -37,6 +17,7 @@ class Repeatmasker(Package):
     version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6')
 
     depends_on('perl', type=('build', 'run'))
+    depends_on('perl-text-soundex', type=('build', 'run'))
     depends_on('hmmer')
     depends_on('ncbi-rmblastn')
     depends_on('trf')
@@ -63,7 +44,7 @@ class Repeatmasker(Package):
         #    Repeatmasker? (Y/N)
         # Add a Search Engine: Done
 
-        config_answers = ['\n', '%s\n' % self.spec['perl'].prefix.bin.perl,
+        config_answers = ['\n', '%s\n' % self.spec['perl'].command.path,
                           '%s\n' % self.stage.source_path,
                           '%s\n' % self.spec['trf'].prefix.bin.trf, '2\n',
                           '%s\n' % self.spec['ncbi-rmblastn'].prefix.bin,
@@ -77,4 +58,4 @@ class Repeatmasker(Package):
         with open(config_answers_filename, 'r') as f:
             inspect.getmodule(self).perl('configure', input=f)
 
-        distutils.dir_util.copy_tree(".", prefix)
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/resourceproto/package.py b/var/spack/repos/builtin/packages/resourceproto/package.py
index 4e58ae7f00..98f126f5d9 100644
--- a/var/spack/repos/builtin/packages/resourceproto/package.py
+++ b/var/spack/repos/builtin/packages/resourceproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Resourceproto(AutotoolsPackage):
 
     version('1.2.0', '33091d5358ec32dd7562a1aa225a70aa')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/revbayes/package.py b/var/spack/repos/builtin/packages/revbayes/package.py
index 1ebbec534b..9eb3674b39 100644
--- a/var/spack/repos/builtin/packages/revbayes/package.py
+++ b/var/spack/repos/builtin/packages/revbayes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/rgb/package.py b/var/spack/repos/builtin/packages/rgb/package.py
index 2b09a2c4a5..f0aa44b75c 100644
--- a/var/spack/repos/builtin/packages/rgb/package.py
+++ b/var/spack/repos/builtin/packages/rgb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/rhash/package.py b/var/spack/repos/builtin/packages/rhash/package.py
index c2191f1f07..6ea3a56a0b 100644
--- a/var/spack/repos/builtin/packages/rhash/package.py
+++ b/var/spack/repos/builtin/packages/rhash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import glob
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/rlwrap/package.py b/var/spack/repos/builtin/packages/rlwrap/package.py
new file mode 100644
index 0000000000..6378e6b45d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rlwrap/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rlwrap(AutotoolsPackage):
+    """rlwrap is a 'readline wrapper', a small utility that uses the GNU
+    readline library to allow the editing of keyboard input for any command."""
+
+    homepage = "https://github.com/hanslub42/rlwrap"
+    url      = "https://github.com/hanslub42/rlwrap/releases/download/v0.43/rlwrap-0.43.tar.gz"
+
+    version('0.43', 'b993e83d3a292464de70719b32f83a34')
+
+    depends_on('readline@4.2:')
diff --git a/var/spack/repos/builtin/packages/rmats/package.py b/var/spack/repos/builtin/packages/rmats/package.py
new file mode 100644
index 0000000000..990d5a8f77
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rmats/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+from os import symlink
+
+
+class Rmats(Package):
+    """MATS is a computational tool to detect differential alternative
+       splicing events from RNA-Seq data."""
+
+    homepage = "https://rnaseq-mats.sourceforge.net/index.html"
+    url      = "https://downloads.sourceforge.net/project/rnaseq-mats/MATS/rMATS.4.0.2.tgz"
+
+    version('4.0.2', sha256='afab002a9ae836d396909aede96318f6dab6e5818078246419dd563624bf26d1')
+
+    depends_on('python@2.7:', type='run')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('openblas')
+
+    def install(self, spec, prefix):
+        # since the tool is a python script we install it to /usr/lib
+        install_tree('rMATS-turbo-Linux-UCS4', join_path(prefix.lib, 'rmats'))
+
+        # the script has an appropriate shebang so a quick symlink will do
+        set_executable(join_path(prefix.lib, 'rmats/rmats.py'))
+        mkdirp(prefix.bin)
+        symlink(join_path(prefix.lib, 'rmats/rmats.py'),
+                join_path(prefix.bin, 'rmats'))
diff --git a/var/spack/repos/builtin/packages/rmlab/package.py b/var/spack/repos/builtin/packages/rmlab/package.py
new file mode 100644
index 0000000000..5304bf0d09
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rmlab/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rmlab(CMakePackage):
+    """C++ File API for the reMarkable tablet"""
+
+    homepage = "https://github.com/ax3l/lines-are-beautiful"
+    git      = "https://github.com/ax3l/lines-are-beautiful.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='develop')
+
+    variant('png', default=True,
+            description='Enable PNG conversion support')
+
+    # modern CMake
+    depends_on('cmake@3.7.0:', type='build')
+    # C++11
+    conflicts('%gcc@:4.7')
+    conflicts('%intel@:15')
+    conflicts('%pgi@:14')
+
+    depends_on('pngwriter@0.6.0:', when='+png')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        args = [
+            '-DRmlab_USE_PNG={0}'.format(
+                'ON' if '+png' in spec else 'OFF')
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/rna-seqc/package.py b/var/spack/repos/builtin/packages/rna-seqc/package.py
new file mode 100644
index 0000000000..38fbf7c474
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rna-seqc/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class RnaSeqc(Package):
+    """RNA-SeQC is a java program which computes a series of quality control
+    metrics for RNA-seq data."""
+
+    homepage = "http://archive.broadinstitute.org/cancer/cga/rna-seqc"
+    url      = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar"
+
+    version('1.1.8', '71d7b5d3b3dcc1893cdc7f6819185d41', expand=False)
+    version('1.1.7', '2d0b8ecac955af2f9bc1b185fdfb6b45', expand=False)
+    version('1.1.6', 'fa9c9885081ae2e47f285c7c0f596a14', expand=False)
+    version('1.1.5', '4b875671e906f708cbb8fd9bcf0e958d', expand=False)
+    version('1.1.4', 'b04d06947c48cb2dc1b0ba29c8232db5', expand=False)
+
+    depends_on('jdk@8:', type='run')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        jar_file = 'RNA-SeQC_v{0}.jar'.format(self.version.dotted)
+        install(jar_file, prefix.bin)
+
+        # Set up a helper script to call java on the jar file,
+        # explicitly codes the path for java and the jar file.
+        script_sh = join_path(os.path.dirname(__file__), "rna-seqc.sh")
+        script = join_path(prefix.bin, "rna-seqc")
+        install(script_sh, script)
+        set_executable(script)
+
+        # Munge the helper script to explicitly point to java and the
+        # jar file.
+        java = self.spec['jdk'].prefix.bin.java
+        kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
+        filter_file('^java', java, script, **kwargs)
+        filter_file('RNA-SeQC_v{0}.jar', join_path(prefix.bin, jar_file),
+                    script, **kwargs)
diff --git a/var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh b/var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh
new file mode 100644
index 0000000000..c1d8d7c2e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rna-seqc/rna-seqc.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the rna-seqc jar file
+java $JAVA_ARGS $JAVA_OPTS -jar RNA-SeQC_v{}.jar "$@"
diff --git a/var/spack/repos/builtin/packages/rngstreams/package.py b/var/spack/repos/builtin/packages/rngstreams/package.py
new file mode 100644
index 0000000000..7168d0c400
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rngstreams/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Rngstreams(AutotoolsPackage):
+    """Multiple independent streams of pseudo-random numbers."""
+
+    homepage = "http://statmath.wu.ac.at/software/RngStreams"
+    url      = "http://statmath.wu.ac.at/software/RngStreams/rngstreams-1.0.1.tar.gz"
+
+    version('1.0.1', '6d9d842247cd1d4e9e60440406858a69')
diff --git a/var/spack/repos/builtin/packages/rockstar/package.py b/var/spack/repos/builtin/packages/rockstar/package.py
index 2f8bfdc804..fc9a0fa76d 100644
--- a/var/spack/repos/builtin/packages/rockstar/package.py
+++ b/var/spack/repos/builtin/packages/rockstar/package.py
@@ -1,38 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
 import os
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Rockstar(MakefilePackage):
     """The Rockstar Halo Finder"""
 
     homepage = "https://bitbucket.org/gfcstanford/rockstar"
-    url      = "https://bitbucket.org/gfcstanford/rockstar"
 
     version('develop', git='https://bitbucket.org/gfcstanford/rockstar.git')
     version('yt', hg='https://bitbucket.org/MatthewTurk/rockstar')
@@ -60,7 +38,7 @@ class Rockstar(MakefilePackage):
 
     def install(self, spec, prefix):
         # Install all files and directories
-        copy_tree(".", prefix)
+        install_tree('.', prefix)
 
         mkdir(prefix.bin)
         mkdir(prefix.lib)
diff --git a/var/spack/repos/builtin/packages/root/package.py b/var/spack/repos/builtin/packages/root/package.py
index a003d3d5e2..91da3fc582 100644
--- a/var/spack/repos/builtin/packages/root/package.py
+++ b/var/spack/repos/builtin/packages/root/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import sys
@@ -53,7 +34,7 @@ class Root(CMakePackage):
     variant('graphviz', default=False, description='Enable graphviz support')
 
     depends_on('cmake@3.4.3:', type='build')
-    depends_on('pkg-config',   type='build')
+    depends_on('pkgconfig',   type='build')
 
     depends_on('binutils')
     depends_on('zlib')
diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py
index 8a7f22cf97..537c30f2d4 100644
--- a/var/spack/repos/builtin/packages/rose/package.py
+++ b/var/spack/repos/builtin/packages/rose/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 # -----------------------------------------------------------------------------
 # Author: Justin Too <too1@llnl.gov>
 # -----------------------------------------------------------------------------
@@ -35,11 +16,11 @@ class Rose(Package):
        (Developed at Lawrence Livermore National Lab)"""
 
     homepage = "http://rosecompiler.org/"
-    url = "https://github.com/rose-compiler/rose/archive/v0.9.7.tar.gz"
+    url      = "https://github.com/rose-compiler/rose/archive/v0.9.7.tar.gz"
+    git      = "https://github.com/rose-compiler/rose.git"
 
+    version('master', branch='master')
     version('0.9.7', 'e14ce5250078df4b09f4f40559d46c75')
-    version('master', branch='master',
-            git='https://github.com/rose-compiler/rose.git')
 
     patch('add_spack_compiler_recognition.patch')
 
diff --git a/var/spack/repos/builtin/packages/ross/package.py b/var/spack/repos/builtin/packages/ross/package.py
new file mode 100644
index 0000000000..95b2f6a571
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ross/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ross(CMakePackage):
+    """Rensselaer Optimistic Simulation System"""
+
+    homepage = "http://carothersc.github.io/ROSS/"
+    git      = "https://github.com/carothersc/ROSS.git"
+
+    version('develop', branch='master')
+    version('7.0.0', tag='v7.0.0')
+
+    depends_on('mpi')
+
+    def cmake_args(self):
+        if 'x86_64' not in self.spec.architecture:
+            raise InstallError(
+                'This package currently only builds on x86_64 architectures')
+
+        args = ["-DBUILD_SHARED_LIBS=ON",
+                "-DARCH=x86_64",
+                "-DCMAKE_C_COMPILER=%s" % self.spec['mpi'].mpicc,
+                "-DCMAKE_CXX_COMPILER=%s" % self.spec['mpi'].mpicxx]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/rr/package.py b/var/spack/repos/builtin/packages/rr/package.py
index 245744a6fa..2c5ed168a0 100644
--- a/var/spack/repos/builtin/packages/rr/package.py
+++ b/var/spack/repos/builtin/packages/rr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,8 +20,8 @@ class Rr(CMakePackage):
     depends_on('zlib')
     # depends_on('capnproto', when='@4.6:')  # not yet in spack
     # depends_on('libcapnp')    # needed for future releases
-    depends_on('pkg-config', type='build')
-    depends_on('py-pexpect', type='build')  # actually tests
+    depends_on('pkgconfig', type='build')
+    depends_on('py-pexpect', type='test')
 
     # rr needs architecture Nehalem and beyond, how can spack
     # test this?
diff --git a/var/spack/repos/builtin/packages/rsbench/package.py b/var/spack/repos/builtin/packages/rsbench/package.py
index 91c8d6f71b..6f1595c02b 100644
--- a/var/spack/repos/builtin/packages/rsbench/package.py
+++ b/var/spack/repos/builtin/packages/rsbench/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/rsem/package.py b/var/spack/repos/builtin/packages/rsem/package.py
index 2d29610b20..8212c11427 100644
--- a/var/spack/repos/builtin/packages/rsem/package.py
+++ b/var/spack/repos/builtin/packages/rsem/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Rsem(MakefilePackage):
     homepage = "http://deweylab.github.io/RSEM/"
     url      = "https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz"
 
-    version('1.3.0', '9728161625d339d022130e2428604bf5')
+    version('1.3.0', '273fd755e23d349cc38a079b81bb03b6')
 
     depends_on('r', type=('build', 'run'))
     depends_on('perl', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/rstart/package.py b/var/spack/repos/builtin/packages/rstart/package.py
index 2a0cf59e81..d819274a9c 100644
--- a/var/spack/repos/builtin/packages/rstart/package.py
+++ b/var/spack/repos/builtin/packages/rstart/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Rstart(AutotoolsPackage):
     version('1.0.5', '32db3625cb5e841e17d6bc696f21edfb')
 
     depends_on('xproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/rsync/package.py b/var/spack/repos/builtin/packages/rsync/package.py
index 642f702ac0..d1f4384b6a 100644
--- a/var/spack/repos/builtin/packages/rsync/package.py
+++ b/var/spack/repos/builtin/packages/rsync/package.py
@@ -1,34 +1,16 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Rsync(AutotoolsPackage):
     """An open source utility that provides fast incremental file transfer."""
     homepage = "https://rsync.samba.org"
-    url      = "https://download.samba.org/pub/rsync/rsync-3.1.1.tar.gz"
+    url      = "https://download.samba.org/pub/rsync/src/rsync-3.1.2.tar.gz"
 
+    version('3.1.3', '1581a588fde9d89f6bc6201e8129afaf')
     version('3.1.2', '0f758d7e000c0f7f7d3792610fad70cb')
     version('3.1.1', '43bd6676f0b404326eee2d63be3cdcfe')
diff --git a/var/spack/repos/builtin/packages/rtags/package.py b/var/spack/repos/builtin/packages/rtags/package.py
index 8e1a962209..d7d9b313dd 100644
--- a/var/spack/repos/builtin/packages/rtags/package.py
+++ b/var/spack/repos/builtin/packages/rtags/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,16 +10,17 @@ class Rtags(CMakePackage):
     """RTags is a client/server application that indexes C/C++ code"""
 
     homepage = "https://github.com/Andersbakken/rtags/"
-    url      = "https://andersbakken.github.io/rtags-releases/rtags-2.12.tar.gz"
+    url      = "https://andersbakken.github.io/rtags-releases/rtags-2.17.tar.gz"
 
-    version('2.12', '84988aaff27915a79d4b4b57299f9a51')
+    version('2.17', '95b24d7729678645a027d83be114d624')
+    # version('2.12', '84988aaff27915a79d4b4b57299f9a51')  # no available
 
     depends_on("llvm@3.3: +clang")
     depends_on("zlib")
     depends_on("openssl")
     depends_on("lua@5.3:")
     depends_on("bash-completion")
-    depends_on("pkg-config", type='build')
+    depends_on("pkgconfig", type='build')
 
     patch("add_string_iterator_erase_compile_check.patch", when='@2.12')
 
diff --git a/var/spack/repos/builtin/packages/rtax/package.py b/var/spack/repos/builtin/packages/rtax/package.py
index 3e359d7346..ead8371499 100644
--- a/var/spack/repos/builtin/packages/rtax/package.py
+++ b/var/spack/repos/builtin/packages/rtax/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ruby-gnuplot/package.py b/var/spack/repos/builtin/packages/ruby-gnuplot/package.py
new file mode 100644
index 0000000000..a947c001aa
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-gnuplot/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyGnuplot(Package):
+    """Utility library to aid in interacting with gnuplot from ruby"""
+
+    homepage = "https://rubygems.org/gems/gnuplot/versions/2.6.2"
+    url      = "https://rubygems.org/downloads/gnuplot-2.6.2.gem"
+
+    version('2.6.2', 'ff36a37cf71b9cd6273fcd14bbfd82df', expand=False)
+
+    depends_on('gnuplot+X')
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('install', 'gnuplot-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-narray/package.py b/var/spack/repos/builtin/packages/ruby-narray/package.py
new file mode 100644
index 0000000000..52f1db091f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-narray/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyNarray(Package):
+    """Numo::NArray is an Numerical N-dimensional Array class for fast
+       processing and easy manipulation of multi-dimensional numerical data,
+       similar to numpy.ndaray."""
+
+    homepage = "https://rubygems.org/gems/narray"
+    git      = "https://github.com/ruby-numo/narray.git"
+
+    version('0.9.0.9', commit='9cadbbccf1e01b6d1bc143c19d598cad1c420869')
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('build', 'numo-narray.gemspec')
+        gem('install', 'numo-narray-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-ronn/package.py b/var/spack/repos/builtin/packages/ruby-ronn/package.py
new file mode 100644
index 0000000000..2637bcfc6a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-ronn/package.py
@@ -0,0 +1,23 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyRonn(Package):
+    """Ronn builds manuals. It converts simple, human readable textfiles to
+    roff for terminal display, and also to HTML for the web."""
+
+    homepage = "https://rubygems.org/gems/ronn"
+    url      = "https://github.com/rtomayko/ronn/archive/0.7.3.tar.gz"
+
+    version('0.7.3', '90cdedb42920c8c2a74e2d177e9535b6')
+    version('0.7.0', '34ad78510a75e46904629631f5335e06')
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('build', 'ronn.gemspec')
+        gem('install', 'ronn-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-rubyinline/package.py b/var/spack/repos/builtin/packages/ruby-rubyinline/package.py
new file mode 100644
index 0000000000..f3ab0cd49b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-rubyinline/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyRubyinline(Package):
+    """Inline allows you to write foreign code within your ruby code."""
+
+    homepage = "https://rubygems.org/gems/RubyInline"
+    url      = "https://rubygems.org/downloads/RubyInline-3.12.4.gem"
+
+    version('3.12.4', '3058f4c48e62baef811b127f4925ee70', expand=False)
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('install', 'RubyInline-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-svn2git/package.py b/var/spack/repos/builtin/packages/ruby-svn2git/package.py
new file mode 100644
index 0000000000..6373247051
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-svn2git/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubySvn2git(Package):
+    """svn2git is a tiny utility for migrating projects from Subversion to Git
+    while keeping the trunk, branches and tags where they should be. It uses
+    git-svn to clone an svn repository and does some clean-up to make sure
+    branches and tags are imported in a meaningful way, and that the code
+    checked into master ends up being what's currently in your svn trunk rather
+    than whichever svn branch your last commit was in."""
+
+    homepage = "https://github.com/nirvdrum/svn2git/"
+    url      = "https://github.com/nirvdrum/svn2git/archive/v2.4.0.tar.gz"
+
+    version('2.4.0', 'f19ac6eb0634aa1fed31a1e40a2aeaa2')
+
+    depends_on('git')
+    depends_on('subversion+perl')
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('build', 'svn2git.gemspec')
+        gem('install', 'svn2git-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby-terminal-table/package.py b/var/spack/repos/builtin/packages/ruby-terminal-table/package.py
new file mode 100644
index 0000000000..083e20bb5c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby-terminal-table/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class RubyTerminalTable(Package):
+    """Simple, feature rich ascii table generation library"""
+
+    homepage = "https://rubygems.org/gems/terminal-table"
+    url      = "https://rubygems.org/downloads/terminal-table-1.8.0.gem"
+
+    version('1.8.0', 'd78db9d71f70aaadd7e689641078e7e7', expand=False)
+
+    extends('ruby')
+
+    def install(self, spec, prefix):
+        gem('install', 'terminal-table-{0}.gem'.format(self.version))
diff --git a/var/spack/repos/builtin/packages/ruby/package.py b/var/spack/repos/builtin/packages/ruby/package.py
index 1e3934df76..f1ae31f177 100644
--- a/var/spack/repos/builtin/packages/ruby/package.py
+++ b/var/spack/repos/builtin/packages/ruby/package.py
@@ -1,56 +1,64 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Ruby(Package):
+class Ruby(AutotoolsPackage):
     """A dynamic, open source programming language with a focus on
     simplicity and productivity."""
 
     homepage = "https://www.ruby-lang.org/"
     url      = "http://cache.ruby-lang.org/pub/ruby/2.2/ruby-2.2.0.tar.gz"
+    list_url = "http://cache.ruby-lang.org/pub/ruby/"
+    list_depth = 1
+
+    version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852')
+
+    variant('openssl', default=True, description="Enable OpenSSL support")
+    variant('readline', default=False, description="Enable Readline support")
 
     extendable = True
 
-    version('2.2.0', 'cd03b28fd0b555970f5c4fd481700852')
+    depends_on('pkgconfig', type=('build'))
     depends_on('libffi')
     depends_on('zlib')
-    variant('openssl', default=False, description="Enable OpenSSL support")
+    depends_on('libx11')
+    depends_on('tcl')
+    depends_on('tk')
     depends_on('openssl', when='+openssl')
-    variant('readline', default=False, description="Enable Readline support")
     depends_on('readline', when='+readline')
 
-    def install(self, spec, prefix):
-        options = ["--prefix=%s" % prefix]
-        if '+openssl' in spec:
-            options.append("--with-openssl-dir=%s" % spec['openssl'].prefix)
-        if '+readline' in spec:
-            options.append("--with-readline-dir=%s" % spec['readline'].prefix)
-        configure(*options)
-        make()
-        make("install")
+    # gcc-7-based build requires patches (cf. https://bugs.ruby-lang.org/issues/13150)
+    patch('ruby_23_gcc7.patch', level=0, when='@2.2.0:2.2.999 %gcc@7:')
+    patch('ruby_23_gcc7.patch', level=0, when='@2.3.0:2.3.4 %gcc@7:')
+    patch('ruby_24_gcc7.patch', level=1, when='@2.4.0 %gcc@7:')
+
+    resource(
+        name='rubygems-updated-ssl-cert',
+        url='https://raw.githubusercontent.com/rubygems/rubygems/master/lib/rubygems/ssl_certs/index.rubygems.org/GlobalSignRootCA.pem',
+        sha256='df68841998b7fd098a9517fe971e97890be0fc93bbe1b2a1ef63ebdea3111c80',
+        when='+openssl',
+        destination='',
+        placement='rubygems-updated-ssl-cert',
+        expand=False
+    )
+
+    def url_for_version(self, version):
+        url = "http://cache.ruby-lang.org/pub/ruby/{0}/ruby-{1}.tar.gz"
+        return url.format(version.up_to(2), version)
+
+    def configure_args(self):
+        args = []
+        if '+openssl' in self.spec:
+            args.append("--with-openssl-dir=%s" % self.spec['openssl'].prefix)
+        if '+readline' in self.spec:
+            args.append("--with-readline-dir=%s"
+                        % self.spec['readline'].prefix)
+        args.append('--with-tk=%s' % self.spec['tk'].prefix)
+        return args
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         # TODO: do this only for actual extensions.
@@ -76,3 +84,21 @@ class Ruby(Package):
         # Ruby extension builds have global ruby and gem functions
         module.ruby = Executable(join_path(self.spec.prefix.bin, 'ruby'))
         module.gem = Executable(join_path(self.spec.prefix.bin, 'gem'))
+
+    @run_after('install')
+    def post_install(self):
+        """ RubyGems updated their SSL certificates at some point, so
+        new certificates must be installed after Ruby is installed
+        in order to download gems; see
+        http://guides.rubygems.org/ssl-certificate-update/
+        for details.
+        """
+        rubygems_updated_cert_path = join_path(self.stage.source_path,
+                                               'rubygems-updated-ssl-cert',
+                                               'GlobalSignRootCA.pem')
+        rubygems_certs_path = join_path(self.spec.prefix.lib,
+                                        'ruby',
+                                        '{0}'.format(self.spec.version.dotted),
+                                        'rubygems',
+                                        'ssl_certs')
+        install(rubygems_updated_cert_path, rubygems_certs_path)
diff --git a/var/spack/repos/builtin/packages/ruby/ruby_23_gcc7.patch b/var/spack/repos/builtin/packages/ruby/ruby_23_gcc7.patch
new file mode 100644
index 0000000000..b7fdd530b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby/ruby_23_gcc7.patch
@@ -0,0 +1,98 @@
+diff --git include/ruby/ruby.h include/ruby/ruby.h
+index 60cfb1174e..dccfdc763a 100644
+--- include/ruby/ruby.h
++++ include/ruby/ruby.h
+@@ -551,27 +551,23 @@ static inline int rb_type(VALUE obj);
+ 	((type) == RUBY_T_FLOAT) ? RB_FLOAT_TYPE_P(obj) : \
+ 	(!RB_SPECIAL_CONST_P(obj) && RB_BUILTIN_TYPE(obj) == (type)))
+ 
+-/* RB_GC_GUARD_PTR() is an intermediate macro, and has no effect by
+- * itself.  don't use it directly */
+ #ifdef __GNUC__
+-#define RB_GC_GUARD_PTR(ptr) \
+-    __extension__ ({volatile VALUE *rb_gc_guarded_ptr = (ptr); rb_gc_guarded_ptr;})
+-#else
+-#ifdef _MSC_VER
++#define RB_GC_GUARD(v) \
++    (*__extension__ ({ \
++	volatile VALUE *rb_gc_guarded_ptr = &(v); \
++	__asm__("" : : "m"(rb_gc_guarded_ptr)); \
++	rb_gc_guarded_ptr; \
++    }))
++#elif defined _MSC_VER
+ #pragma optimize("", off)
+ static inline volatile VALUE *rb_gc_guarded_ptr(volatile VALUE *ptr) {return ptr;}
+ #pragma optimize("", on)
++#define RB_GC_GUARD(v) (*rb_gc_guarded_ptr(&(v)))
+ #else
+ volatile VALUE *rb_gc_guarded_ptr_val(volatile VALUE *ptr, VALUE val);
+ #define HAVE_RB_GC_GUARDED_PTR_VAL 1
+ #define RB_GC_GUARD(v) (*rb_gc_guarded_ptr_val(&(v),(v)))
+ #endif
+-#define RB_GC_GUARD_PTR(ptr) rb_gc_guarded_ptr(ptr)
+-#endif
+-
+-#ifndef RB_GC_GUARD
+-#define RB_GC_GUARD(v) (*RB_GC_GUARD_PTR(&(v)))
+-#endif
+ 
+ #ifdef __GNUC__
+ #define RB_UNUSED_VAR(x) x __attribute__ ((unused))
+diff --git marshal.c marshal.c
+index c56de4af8d..b7274bf3c4 100644
+--- marshal.c
++++ marshal.c
+@@ -1022,7 +1022,7 @@ VALUE
+ rb_marshal_dump_limited(VALUE obj, VALUE port, int limit)
+ {
+     struct dump_arg *arg;
+-    VALUE wrapper; /* used to avoid memory leak in case of exception */
++    volatile VALUE wrapper; /* used to avoid memory leak in case of exception */
+ 
+     wrapper = TypedData_Make_Struct(rb_cData, struct dump_arg, &dump_arg_data, arg);
+     arg->dest = 0;
+@@ -1051,8 +1051,8 @@ rb_marshal_dump_limited(VALUE obj, VALUE port, int limit)
+ 	rb_io_write(arg->dest, arg->str);
+ 	rb_str_resize(arg->str, 0);
+     }
+-    clear_dump_arg(arg);
+-    RB_GC_GUARD(wrapper);
++    free_dump_arg(arg);
++    rb_gc_force_recycle(wrapper);
+ 
+     return port;
+ }
+@@ -2044,7 +2044,7 @@ rb_marshal_load_with_proc(VALUE port, VALUE proc)
+ {
+     int major, minor, infection = 0;
+     VALUE v;
+-    VALUE wrapper; /* used to avoid memory leak in case of exception */
++    volatile VALUE wrapper; /* used to avoid memory leak in case of exception */
+     struct load_arg *arg;
+ 
+     v = rb_check_string_type(port);
+@@ -2090,8 +2090,8 @@ rb_marshal_load_with_proc(VALUE port, VALUE proc)
+ 
+     if (!NIL_P(proc)) arg->proc = proc;
+     v = r_object(arg);
+-    clear_load_arg(arg);
+-    RB_GC_GUARD(wrapper);
++    free_load_arg(arg);
++    rb_gc_force_recycle(wrapper);
+ 
+     return v;
+ }
+diff --git test/ruby/test_marshal.rb test/ruby/test_marshal.rb
+index 6ac5c29991..dc2b8b30dc 100644
+--- test/ruby/test_marshal.rb
++++ test/ruby/test_marshal.rb
+@@ -645,6 +645,9 @@ def test_continuation
+     c = Bug9523.new
+     assert_raise_with_message(RuntimeError, /Marshal\.dump reentered at marshal_dump/) do
+       Marshal.dump(c)
++      GC.start
++      1000.times {"x"*1000}
++      GC.start
+       c.cc.call
+     end
+   end
diff --git a/var/spack/repos/builtin/packages/ruby/ruby_24_gcc7.patch b/var/spack/repos/builtin/packages/ruby/ruby_24_gcc7.patch
new file mode 100644
index 0000000000..4be26af7d6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ruby/ruby_24_gcc7.patch
@@ -0,0 +1,66 @@
+diff --git a/include/ruby/ruby.h b/include/ruby/ruby.h
+index 6144c672346d..4aa388849ba4 100644
+--- a/include/ruby/ruby.h
++++ b/include/ruby/ruby.h
+@@ -536,7 +536,11 @@ static inline int rb_type(VALUE obj);
+ 
+ #ifdef __GNUC__
+ #define RB_GC_GUARD(v) \
+-    (*__extension__ ({volatile VALUE *rb_gc_guarded_ptr = &(v); rb_gc_guarded_ptr;}))
++    (*__extension__ ({ \
++	volatile VALUE *rb_gc_guarded_ptr = &(v); \
++	__asm__("" : : "m"(rb_gc_guarded_ptr)); \
++	rb_gc_guarded_ptr; \
++    }))
+ #elif defined _MSC_VER
+ #pragma optimize("", off)
+ static inline volatile VALUE *rb_gc_guarded_ptr(volatile VALUE *ptr) {return ptr;}
+diff --git a/marshal.c b/marshal.c
+index a9926acf564e..7e16d0b024c4 100644
+--- a/marshal.c
++++ b/marshal.c
+@@ -1026,7 +1026,7 @@ rb_marshal_dump_limited(VALUE obj, VALUE port, int limit)
+     struct dump_arg *arg;
+     VALUE wrapper; /* used to avoid memory leak in case of exception */
+ 
+-    wrapper = TypedData_Make_Struct(rb_cData, struct dump_arg, &dump_arg_data, arg);
++    wrapper = TypedData_Make_Struct(0, struct dump_arg, &dump_arg_data, arg);
+     arg->dest = 0;
+     arg->symbols = st_init_numtable();
+     arg->data    = rb_init_identtable();
+@@ -2053,7 +2053,7 @@ rb_marshal_load_with_proc(VALUE port, VALUE proc)
+     else {
+ 	io_needed();
+     }
+-    wrapper = TypedData_Make_Struct(rb_cData, struct load_arg, &load_arg_data, arg);
++    wrapper = TypedData_Make_Struct(0, struct load_arg, &load_arg_data, arg);
+     arg->infection = infection;
+     arg->src = port;
+     arg->offset = 0;
+diff --git a/test/ruby/test_marshal.rb b/test/ruby/test_marshal.rb
+index bc22b5fd3ab8..bfc3f6df256f 100644
+--- a/test/ruby/test_marshal.rb
++++ b/test/ruby/test_marshal.rb
+@@ -644,6 +644,9 @@ def test_continuation
+     c = Bug9523.new
+     assert_raise_with_message(RuntimeError, /Marshal\.dump reentered at marshal_dump/) do
+       Marshal.dump(c)
++      GC.start
++      1000.times {"x"*1000}
++      GC.start
+       c.cc.call
+     end
+   end
+diff --git a/version.h b/version.h
+index 0a845df84416..39214c474439 100644
+--- a/version.h
++++ b/version.h
+@@ -1,6 +1,6 @@
+ #define RUBY_VERSION "2.4.0"
+ #define RUBY_RELEASE_DATE "2017-03-13"
+-#define RUBY_PATCHLEVEL 99
++#define RUBY_PATCHLEVEL 100
+ 
+ #define RUBY_RELEASE_YEAR 2017
+ #define RUBY_RELEASE_MONTH 3
+
diff --git a/var/spack/repos/builtin/packages/rust-bindgen/package.py b/var/spack/repos/builtin/packages/rust-bindgen/package.py
index 3c7e42ca8a..de0eda3fee 100644
--- a/var/spack/repos/builtin/packages/rust-bindgen/package.py
+++ b/var/spack/repos/builtin/packages/rust-bindgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/rust/package.py b/var/spack/repos/builtin/packages/rust/package.py
index 219c82fa83..8c86ae4696 100644
--- a/var/spack/repos/builtin/packages/rust/package.py
+++ b/var/spack/repos/builtin/packages/rust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -33,10 +14,11 @@ def get_submodules():
 
 class Rust(Package):
     """The rust programming language toolchain"""
+
     homepage = "http://www.rust-lang.org"
-    url = "https://github.com/rust-lang/rust"
+    git      = "https://github.com/rust-lang/rust.git"
 
-    version('1.8.0', tag='1.8.0', git="https://github.com/rust-lang/rust")
+    version('1.8.0', tag='1.8.0')
 
     resource(name='cargo',
              git="https://github.com/rust-lang/cargo.git",
diff --git a/var/spack/repos/builtin/packages/sabre/package.py b/var/spack/repos/builtin/packages/sabre/package.py
index b93b07be51..b1c7c8b81d 100644
--- a/var/spack/repos/builtin/packages/sabre/package.py
+++ b/var/spack/repos/builtin/packages/sabre/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -37,9 +18,9 @@ class Sabre(MakefilePackage):
     """
 
     homepage = "https://github.com/najoshi/sabre"
-    url = "https://github.com/najoshi/sabre"
+    git      = "https://github.com/najoshi/sabre.git"
 
-    version('2013-09-27', git='https://github.com/najoshi/sabre.git', commit='039a55e500ba07b7e6432ea6ec2ddcfb3471d949')
+    version('2013-09-27', commit='039a55e500ba07b7e6432ea6ec2ddcfb3471d949')
 
     depends_on('zlib')
 
diff --git a/var/spack/repos/builtin/packages/sailfish/package.py b/var/spack/repos/builtin/packages/sailfish/package.py
new file mode 100644
index 0000000000..1db70a05f5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sailfish/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sailfish(CMakePackage):
+    """Sailfish is a tool for transcript quantification from RNA-seq data."""
+
+    homepage = "http://www.cs.cmu.edu/~ckingsf/software/sailfish"
+    url      = "https://github.com/kingsfordgroup/sailfish/archive/v0.10.1.tar.gz"
+
+    version('0.10.1', 'e6dab4cf3a39f346df7c28f40eb58cad')
+
+    depends_on('boost@1.55:')
+    depends_on('tbb')
diff --git a/var/spack/repos/builtin/packages/salmon/package.py b/var/spack/repos/builtin/packages/salmon/package.py
index a323aa1dab..06bfd70324 100644
--- a/var/spack/repos/builtin/packages/salmon/package.py
+++ b/var/spack/repos/builtin/packages/salmon/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,9 +13,15 @@ class Salmon(CMakePackage):
     homepage = "http://combine-lab.github.io/salmon/"
     url      = "https://github.com/COMBINE-lab/salmon/archive/v0.8.2.tar.gz"
 
+    version('0.9.1', '1277b8ed65d2c6982ed176a496a2a1e3')
     version('0.8.2', 'ee512697bc44b13661a16d4e14cf0a00')
 
-    depends_on('boost')
+    depends_on('tbb')
+    depends_on('boost@:1.66.0')
+
+    def patch(self):
+        # remove static linking to libstdc++
+        filter_file('-static-libstdc++', '', 'CMakeLists.txt', string=True)
 
     def cmake_args(self):
         args = ['-DBOOST_ROOT=%s' % self.spec['boost'].prefix]
diff --git a/var/spack/repos/builtin/packages/sambamba/package.py b/var/spack/repos/builtin/packages/sambamba/package.py
index ad8c68547c..69ed5fd676 100644
--- a/var/spack/repos/builtin/packages/sambamba/package.py
+++ b/var/spack/repos/builtin/packages/sambamba/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Sambamba(Package):
     """Sambamba: process your BAM data faster (bioinformatics)"""
 
     homepage = "http://lomereiter.github.io/sambamba/"
+    git      = "https://github.com/lomereiter/sambamba.git"
 
-    version('0.6.6', git='https://github.com/lomereiter/sambamba.git',
-            tag='v0.6.6', submodules=True)
+    version('0.6.6', tag='v0.6.6', submodules=True)
 
     depends_on('ldc~shared', type=('build', 'link'))
     depends_on('python', type='build')
diff --git a/var/spack/repos/builtin/packages/samblaster/package.py b/var/spack/repos/builtin/packages/samblaster/package.py
new file mode 100644
index 0000000000..d463fbea55
--- /dev/null
+++ b/var/spack/repos/builtin/packages/samblaster/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Samblaster(MakefilePackage):
+    """A tool to mark duplicates and extract discordant and split reads from
+    sam files."""
+
+    homepage = "https://github.com/GregoryFaust/samblaster"
+    url      = "https://github.com/GregoryFaust/samblaster/archive/v.0.1.24.tar.gz"
+
+    version('0.1.24', '885d5782cc277865dfb086fc0a20243e')
+    version('0.1.23', '95d33b6fcceaa38a9bd79014446b4545')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('samblaster', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/samrai/package.py b/var/spack/repos/builtin/packages/samrai/package.py
index 78b674213d..468531da1b 100644
--- a/var/spack/repos/builtin/packages/samrai/package.py
+++ b/var/spack/repos/builtin/packages/samrai/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,12 @@ class Samrai(AutotoolsPackage):
     url      = "https://computation.llnl.gov/projects/samrai/download/SAMRAI-v3.11.2.tar.gz"
     list_url = homepage
 
+    version('3.12.0',     '07364f6e209284e45ac0e9caf1d610f6')
+    version('3.11.5',     '4359a03145c03501b230777f92b62104')
+    version('3.11.4',     '473d6796772f5926b1c0d1cf8f3f8c99')
+    # Version 3.11.3 permissions don't allow downloading
     version('3.11.2',     'd5f59f8efd755b23b797e46349428206')
+    version('3.11.1',     '19a2398a7448ec0f0f0c5e8fc6f80478')
     version('3.10.0',     'ff5f5b8b4a35b52a1b7e37a74166c65a')
     version('3.9.1',      '232d04d0c995f5abf20d94350befd0b2')
     version('3.8.0',      'c18fcffa706346bfa5828b36787ce5fe')
@@ -55,15 +41,23 @@ class Samrai(AutotoolsPackage):
     # and more print statements
     variant('debug', default=False,
             description='Compile with reduced optimization and debugging on')
+    variant('silo', default=False,
+            description='Compile with support for silo')
 
     depends_on('mpi')
     depends_on('zlib')
     depends_on('hdf5+mpi')
-    depends_on('boost')
     depends_on('m4', type='build')
+    depends_on('boost@:1.64.0', when='@3.0.0:3.11.99', type='build')
+    depends_on('silo+mpi', when='+silo')
 
-    # don't build tools with gcc
-    patch('no-tool-build.patch', when='%gcc')
+    # don't build SAMRAI 3+ with tools with gcc
+    patch('no-tool-build.patch', when='@3.0.0:%gcc')
+
+    # 2.4.4 needs a lot of patches to fix ADL and performance problems
+    patch('https://github.com/IBAMR/IBAMR/releases/download/v0.3.0/ibamr-samrai-fixes.patch',
+          sha256='1d088b6cca41377747fa0ae8970440c20cb68988bbc34f9032d5a4e6aceede47',
+          when='@2.4.4')
 
     def configure_args(self):
         options = []
@@ -74,13 +68,16 @@ class Samrai(AutotoolsPackage):
             '--with-F77=%s' % self.spec['mpi'].mpifc,
             '--with-M4=%s' % self.spec['m4'].prefix,
             '--with-hdf5=%s' % self.spec['hdf5'].prefix,
-            '--with-boost=%s' % self.spec['boost'].prefix,
             '--with-zlib=%s' % self.spec['zlib'].prefix,
             '--without-blas',
             '--without-lapack',
             '--with-hypre=no',
             '--with-petsc=no'])
 
+        # SAMRAI 2 used templates; enable implicit instantiation
+        if self.spec.satisfies('@:3'):
+            options.append('--enable-implicit-template-instantiation')
+
         if '+debug' in self.spec:
             options.extend([
                 '--disable-opt',
@@ -90,4 +87,14 @@ class Samrai(AutotoolsPackage):
                 '--enable-opt',
                 '--disable-debug'])
 
+        if '+silo' in self.spec:
+            options.append('--with-silo=%s' % self.spec['silo'].prefix)
+
+        if self.spec.satisfies('@3.0:3.11.99'):
+            options.append('--with-boost=%s' % self.spec['boost'].prefix)
+
         return options
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        if self.spec.satisfies('@3.12:'):
+            spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag)
diff --git a/var/spack/repos/builtin/packages/samtools/package.py b/var/spack/repos/builtin/packages/samtools/package.py
index ae0acdde47..95949a86c6 100644
--- a/var/spack/repos/builtin/packages/samtools/package.py
+++ b/var/spack/repos/builtin/packages/samtools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,9 @@ class Samtools(Package):
     homepage = "www.htslib.org"
     url = "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2"
 
+    version('1.9', 'cca9a40d9b91b007af2ff905cb8b5924')
+    version('1.8', 'c6e981c92ca00a44656a708c4b52aba3')
+    version('1.7', '2240175242b5183bfa6baf1483f68023')
     version('1.6', 'b756f05fd5d1a7042074417edb8c9aea')
     version('1.4', '8cbd7d2a0ec16d834babcd6c6d85d691')
     version('1.3.1', 'a7471aa5a1eb7fc9cc4c6491d73c2d88')
@@ -40,9 +24,14 @@ class Samtools(Package):
 
     depends_on('ncurses')
     # htslib became standalone @1.3.1, must use corresponding version
+    depends_on('htslib@1.9',   when='@1.9')
+    depends_on('htslib@1.8',   when='@1.8')
+    depends_on('htslib@1.7',   when='@1.7')
     depends_on('htslib@1.6',   when='@1.6')
     depends_on('htslib@1.4',   when='@1.4')
     depends_on('htslib@1.3.1', when='@1.3.1')
+    depends_on('zlib', when='@1.7:')
+    depends_on('bzip2', when='@1.7:')
 
     def install(self, spec, prefix):
         if self.spec.version >= Version('1.3.1'):
@@ -53,3 +42,9 @@ class Samtools(Package):
         else:
             make("prefix=%s" % prefix)
             make("prefix=%s" % prefix, "install")
+        # Install dev headers and libs for legacy apps depending on them
+        mkdir(prefix.include)
+        mkdir(prefix.lib)
+        install('sam.h', prefix.include)
+        install('bam.h', prefix.include)
+        install('libbam.a', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/sandbox/package.py b/var/spack/repos/builtin/packages/sandbox/package.py
index 58c6696243..d86222b0d9 100644
--- a/var/spack/repos/builtin/packages/sandbox/package.py
+++ b/var/spack/repos/builtin/packages/sandbox/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sas/package.py b/var/spack/repos/builtin/packages/sas/package.py
index f6a1cf4101..d2d07bff0a 100644
--- a/var/spack/repos/builtin/packages/sas/package.py
+++ b/var/spack/repos/builtin/packages/sas/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/satsuma2/package.py b/var/spack/repos/builtin/packages/satsuma2/package.py
index 4859c97c0e..82dae616e4 100644
--- a/var/spack/repos/builtin/packages/satsuma2/package.py
+++ b/var/spack/repos/builtin/packages/satsuma2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,9 +14,9 @@ class Satsuma2(CMakePackage):
     """
 
     homepage = "https://github.com/bioinfologics/satsuma2"
-    url      = "https://github.com/bioinfologics/satsuma2"
+    git      = "https://github.com/bioinfologics/satsuma2.git"
 
-    version('2016-11-22', git='https://github.com/bioinfologics/satsuma2.git', commit='da694aeecf352e344b790bea4a7aaa529f5b69e6')
+    version('2016-11-22', commit='da694aeecf352e344b790bea4a7aaa529f5b69e6')
 
     def install(self, spec, prefix):
         install_tree(join_path('spack-build', 'bin'), prefix.bin)
diff --git a/var/spack/repos/builtin/packages/savanna/package.py b/var/spack/repos/builtin/packages/savanna/package.py
index af2cdf9ed8..5e49428f0c 100644
--- a/var/spack/repos/builtin/packages/savanna/package.py
+++ b/var/spack/repos/builtin/packages/savanna/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Savanna(MakefilePackage):
@@ -32,12 +12,10 @@ class Savanna(MakefilePackage):
     """
 
     homepage = "https://github.com/CODARcode/savanna"
-    url = "https://github.com/CODARcode/savanna/archive/v0.5.tar.gz"
+    git      = "https://github.com/CODARcode/savanna.git"
 
-    version('develop', git='https://github.com/CODARcode/savanna.git',
-            branch='master', submodules=True)
-    version('0.5', git='https://github.com/CODARcode/savanna.git',
-            tag='0.5', submodules=True)
+    version('develop', branch='master', submodules=True)
+    version('0.5', tag='0.5', submodules=True)
 
     variant('tau', default=False, description='Enable TAU profiling support')
 
@@ -48,4 +26,4 @@ class Savanna(MakefilePackage):
     depends_on('tau', when='+tau')
 
     def install(self, spec, prefix):
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/saws/package.py b/var/spack/repos/builtin/packages/saws/package.py
index bda54644c6..359258a1dd 100644
--- a/var/spack/repos/builtin/packages/saws/package.py
+++ b/var/spack/repos/builtin/packages/saws/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,9 @@ class Saws(AutotoolsPackage):
        scientific or engineering application code into a webserver,
        allowing one to examine (and even modify) the state of the
        simulation with any browser from anywhere."""
+
     homepage = "https://bitbucket.org/saws/saws/wiki/Home"
+    git      = "https://bitbucket.org/saws/saws.git"
 
-    version('develop', git='https://bitbucket.org/saws/saws.git', tag='master')
-    version('0.1.0', git='https://bitbucket.org/saws/saws.git', tag='v0.1.0')
+    version('develop', tag='master')
+    version('0.1.0', tag='v0.1.0')
diff --git a/var/spack/repos/builtin/packages/sbt/package.py b/var/spack/repos/builtin/packages/sbt/package.py
index baa93fa93a..791d316ef2 100644
--- a/var/spack/repos/builtin/packages/sbt/package.py
+++ b/var/spack/repos/builtin/packages/sbt/package.py
@@ -1,41 +1,24 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import shutil
 
 
 class Sbt(Package):
     """Scala Build Tool"""
 
-    homepage = "http://www.scala-sbt.org"
-    url      = "https://dl.bintray.com/sbt/native-packages/sbt/0.13.12/sbt-0.13.12.tgz"
+    homepage = 'http://www.scala-sbt.org'
+    url      = "https://github.com/sbt/sbt/releases/download/v1.1.4/sbt-1.1.4.tgz"
 
-    version('0.13.12', 'cec3071d46ef13334c8097cc3467ff28')
+    version('1.1.6', 'd307b131ed041c783ac5ed7bbb4768dc')
+    version('1.1.5', 'b771480feb07f98fa8cd6d787c8d4485')
+    version('1.1.4', 'c71e5fa846164d14d4cd450520d66c6a')
+    version('0.13.17', 'c52c6152cc7aadfd1f0736a1a5d0a5b8')
 
     depends_on('java')
 
     def install(self, spec, prefix):
-        shutil.copytree('bin', join_path(prefix, 'bin'), symlinks=True)
-        shutil.copytree('conf', join_path(prefix, 'conf'), symlinks=True)
+        install_tree('bin',  prefix.bin)
+        install_tree('conf', prefix.conf)
diff --git a/var/spack/repos/builtin/packages/scala/package.py b/var/spack/repos/builtin/packages/scala/package.py
index 8c36f9e981..263a62b956 100644
--- a/var/spack/repos/builtin/packages/scala/package.py
+++ b/var/spack/repos/builtin/packages/scala/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -36,9 +17,10 @@ class Scala(Package):
     homepage = "https://www.scala-lang.org/"
     url = "https://downloads.lightbend.com/scala/2.12.1/scala-2.12.1.tgz"
 
+    version('2.12.5', '25cf4989d061c585bd0a3fa357ccf0a6')
     version('2.12.1', '3eaecbce019b0fa3067503846e292b32')
     version('2.11.11', '3f5b76001f60cbc31111ddb81de5ea07')
-    version('2.20.6', 'd79dc9fdc627b73289306bdaec81ca98')
+    version('2.10.6', 'd79dc9fdc627b73289306bdaec81ca98')
 
     depends_on('java')
 
diff --git a/var/spack/repos/builtin/packages/scalasca/package.py b/var/spack/repos/builtin/packages/scalasca/package.py
index 21f50cf1fe..b2f68c5b81 100644
--- a/var/spack/repos/builtin/packages/scalasca/package.py
+++ b/var/spack/repos/builtin/packages/scalasca/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -38,14 +19,18 @@ class Scalasca(AutotoolsPackage):
     homepage = "http://www.scalasca.org"
     url = "http://apps.fz-juelich.de/scalasca/releases/scalasca/2.1/dist/scalasca-2.1.tar.gz"
 
+    version('2.4',   '4a895868258030f700a635eac93d36764f60c8c63673c7db419ea4bcc6b0b760')
     version('2.3.1', 'a83ced912b9d2330004cb6b9cefa7585')
     version('2.2.2', '2bafce988b0522d18072f7771e491ab9')
     version('2.1',   'bab9c2b021e51e2ba187feec442b96e6')
 
     depends_on("mpi")
 
+    # version 2.4
+    depends_on('cubew@4.4:', when='@2.4:')
+
     # version 2.3
-    depends_on('cube@4.3:', when='@2.3:')
+    depends_on('cube@4.3', when='@2.3:2.3.99')
     depends_on('otf2@2:', when='@2.3:')
 
     # version 2.1+
@@ -60,7 +45,11 @@ class Scalasca(AutotoolsPackage):
 
         config_args = ["--enable-shared"]
 
-        config_args.append("--with-cube=%s" % spec['cube'].prefix.bin)
+        if spec.satisfies('@2.4:'):
+            config_args.append("--with-cube=%s" % spec['cubew'].prefix.bin)
+        else:
+            config_args.append("--with-cube=%s" % spec['cube'].prefix.bin)
+
         config_args.append("--with-otf2=%s" % spec['otf2'].prefix.bin)
 
         if self.spec['mpi'].name == 'openmpi':
diff --git a/var/spack/repos/builtin/packages/scalpel/package.py b/var/spack/repos/builtin/packages/scalpel/package.py
index f7d2834732..a44106cb68 100644
--- a/var/spack/repos/builtin/packages/scalpel/package.py
+++ b/var/spack/repos/builtin/packages/scalpel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/scan-for-matches/package.py b/var/spack/repos/builtin/packages/scan-for-matches/package.py
new file mode 100644
index 0000000000..54d5e285ec
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scan-for-matches/package.py
@@ -0,0 +1,22 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class ScanForMatches(Package):
+    """scan_for_matches is a utility written in C for locating patterns in DNA
+       or protein FASTA files."""
+
+    homepage = "http://blog.theseed.org/servers/2010/07/scan-for-matches.html"
+    url      = "http://www.theseed.org/servers/downloads/scan_for_matches.tgz"
+
+    version('2010-7-16', 'f64c9cfb385984ded2a7ad9ad2253d83')
+
+    def install(self, spec, prefix):
+        cc = Executable(self.compiler.cc)
+        cc('-O', '-o', 'scan_for_matches', 'ggpunit.c', 'scan_for_matches.c')
+        mkdirp(prefix.bin)
+        install('scan_for_matches', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/scons/package.py b/var/spack/repos/builtin/packages/scons/package.py
index 8bf6ceddcc..7dcae8c960 100644
--- a/var/spack/repos/builtin/packages/scons/package.py
+++ b/var/spack/repos/builtin/packages/scons/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,10 +10,14 @@ class Scons(PythonPackage):
     """SCons is a software construction tool"""
 
     homepage = "http://scons.org"
-    url      = "https://pypi.io/packages/source/s/scons/scons-2.5.1.tar.gz"
+    url      = "https://pypi.io/packages/source/s/scons/scons-3.0.1.tar.gz"
 
-    version('2.5.1', '3eac81e5e8206304a9b4683c57665aa4')
-    version('2.5.0', 'bda5530a70a41a7831d83c8b191c021e')
+    version('3.0.1', 'b6a292e251b34b82c203b56cfa3968b3',
+            url="https://pypi.python.org/packages/c1/0a/520a3c86ce5cff36e81af5e91d4dcd741ebc189c2f0f42d54cc12a8a7519/scons-3.0.1.tar.gz")
+    version('2.5.1', '3eac81e5e8206304a9b4683c57665aa4',
+            url="https://pypi.python.org/packages/2c/ee/a9601b958c94e93410e635a5d67ed95300998ffdc36127b16d322b054ff0/scons-2.5.1.tar.gz")
+    version('2.5.0', 'bda5530a70a41a7831d83c8b191c021e',
+            url="https://pypi.python.org/packages/17/f0/60464796a3fd16899a2cf54e22615c38bbe8124386cf3763c17ff367c2af/scons-2.5.0.tar.gz")
 
-    # Python 3 is not supported
-    depends_on('python@:2.8', type=('build', 'run'))
+    # Python 3 support was added in SCons 3.0.0
+    depends_on('python@:2', when='@:2', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/scorec-core/package.py b/var/spack/repos/builtin/packages/scorec-core/package.py
index e629a63ebe..ad6b5c1876 100644
--- a/var/spack/repos/builtin/packages/scorec-core/package.py
+++ b/var/spack/repos/builtin/packages/scorec-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,9 +12,9 @@ class ScorecCore(CMakePackage):
     """
 
     homepage = 'https://www.scorec.rpi.edu/'
-    url = 'https://github.com/SCOREC/core.git'
+    git      = 'https://github.com/SCOREC/core.git'
 
-    version('develop', git=url)
+    version('develop')
 
     depends_on('mpi')
     depends_on('zoltan')
diff --git a/var/spack/repos/builtin/packages/scorep/package.py b/var/spack/repos/builtin/packages/scorep/package.py
index fd7da69442..b5a1fa73cd 100644
--- a/var/spack/repos/builtin/packages/scorep/package.py
+++ b/var/spack/repos/builtin/packages/scorep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,21 +15,34 @@ class Scorep(AutotoolsPackage):
     homepage = "http://www.vi-hps.org/projects/score-p"
     url      = "http://www.vi-hps.org/upload/packages/scorep/scorep-2.0.2.tar.gz"
 
+    version('4.1',   '7bb6c1eecdd699b4a3207caf202866778ee01f15ff39a9ec198fcd872578fe63')
+    version('4.0',   'f04478e0407d67eeb8c49c3c51d91e12')
     version('3.1',   '065bf8eb08398e8146c895718ddb9145')
     version('3.0',   '44da8beaa3f71436a5f6fe51938aab2f')
     version('2.0.2', '8f00e79e1b5b96e511c5ebecd10b2888')
     version('1.4.2', '3b9a042b13bdd5836452354e6567f71e')
     version('1.3',   '9db6f957b7f51fa01377a9537867a55c')
 
-    patch('gcc7.patch')
+    patch('gcc7.patch', when='@:3')
+
+    variant('mpi', default=True, description="Enable MPI support")
+    variant('papi', default=True, description="Enable PAPI")
+    variant('pdt', default=False, description="Enable PDT")
+    variant('shmem', default=False, description='Enable shmem tracing')
 
-    ##########
     # Dependencies for SCORE-P are quite tight. See the homepage for more
-    # information.
+    # information. Starting with scorep 4.0 / cube 4.4, Score-P only depends on
+    # two components of cube -- cubew and cubelib.
+
+    # SCOREP 4
+    depends_on('otf2@2.1:', when='@4:')
+    depends_on('opari2@2.0:', when='@4:')
+    depends_on('cubew@4.4:', when='@4:')
+    depends_on('cubelib@4.4:', when='@4:')
     # SCOREP 3
-    depends_on('otf2@2:', when='@3:')
-    depends_on('opari2@2:', when='@3:')
-    depends_on('cube@4.3:', when='@3:')
+    depends_on('otf2@2:', when='@3:3.99')
+    depends_on('opari2@2:', when='@3:3.99')
+    depends_on('cube@4.3:', when='@3:3.99')
     # SCOREP 2.0.2
     depends_on('otf2@2.0', when='@2.0.2')
     depends_on('opari2@2.0', when='@2.0.2')
@@ -61,13 +55,10 @@ class Scorep(AutotoolsPackage):
     depends_on("otf2@1.4", when='@1.3')
     depends_on("opari2@1.1.4", when='@1.3')
     depends_on("cube@4.2.3", when='@1.3')
-    ##########
 
-    depends_on("mpi")
-    depends_on("papi")
-    depends_on('pdt')
-
-    variant('shmem', default=False, description='Enable shmem tracing')
+    depends_on('mpi', when="+mpi")
+    depends_on('papi', when="+papi")
+    depends_on('pdt', when="+pdt")
 
     # Score-P requires a case-sensitive file system, and therefore
     # does not work on macOS
@@ -80,15 +71,29 @@ class Scorep(AutotoolsPackage):
         config_args = [
             "--with-otf2=%s" % spec['otf2'].prefix.bin,
             "--with-opari2=%s" % spec['opari2'].prefix.bin,
-            "--with-cube=%s" % spec['cube'].prefix.bin,
-            "--with-papi-header=%s" % spec['papi'].prefix.include,
-            "--with-papi-lib=%s" % spec['papi'].prefix.lib,
-            "--with-pdt=%s" % spec['pdt'].prefix.bin,
             "--enable-shared"]
 
         cname = spec.compiler.name
         config_args.append('--with-nocross-compiler-suite={0}'.format(cname))
 
+        if self.version >= Version('4.0'):
+            config_args.append("--with-cubew=%s" % spec['cubew'].prefix.bin)
+            config_args.append("--with-cubelib=%s" %
+                               spec['cubelib'].prefix.bin)
+        else:
+            config_args.append("--with-cube=%s" % spec['cube'].prefix.bin)
+
+        if "+papi" in spec:
+            config_args.append("--with-papi-header=%s" %
+                               spec['papi'].prefix.include)
+            config_args.append("--with-papi-lib=%s" % spec['papi'].prefix.lib)
+
+        if "+pdt" in spec:
+            config_args.append("--with-pdt=%s" % spec['pdt'].prefix.bin)
+
+        config_args += self.with_or_without('shmem')
+        config_args += self.with_or_without('mpi')
+
         if spec.satisfies('^intel-mpi'):
             config_args.append('--with-mpi=intel3')
         elif spec.satisfies('^mpich') or spec.satisfies('^mvapich2'):
@@ -96,16 +101,17 @@ class Scorep(AutotoolsPackage):
         elif spec.satisfies('^openmpi'):
             config_args.append('--with-mpi=openmpi')
 
-        if '~shmem' in spec:
-            config_args.append("--without-shmem")
-
         config_args.extend([
             'CFLAGS={0}'.format(self.compiler.pic_flag),
-            'CXXFLAGS={0}'.format(self.compiler.pic_flag),
-            'MPICC={0}'.format(spec['mpi'].mpicc),
-            'MPICXX={0}'.format(spec['mpi'].mpicxx),
-            'MPIF77={0}'.format(spec['mpi'].mpif77),
-            'MPIFC={0}'.format(spec['mpi'].mpifc)
+            'CXXFLAGS={0}'.format(self.compiler.pic_flag)
         ])
 
+        if "+mpi" in spec:
+            config_args.extend([
+                'MPICC={0}'.format(spec['mpi'].mpicc),
+                'MPICXX={0}'.format(spec['mpi'].mpicxx),
+                'MPIF77={0}'.format(spec['mpi'].mpif77),
+                'MPIFC={0}'.format(spec['mpi'].mpifc)
+            ])
+
         return config_args
diff --git a/var/spack/repos/builtin/packages/scotch/libscotchmetis-return-6.0.5a.patch b/var/spack/repos/builtin/packages/scotch/libscotchmetis-return-6.0.5a.patch
new file mode 100644
index 0000000000..7e124c6aac
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scotch/libscotchmetis-return-6.0.5a.patch
@@ -0,0 +1,10 @@
+--- a/src/libscotchmetis/metis_graph_part.c	2018-07-13 14:25:50.000000000 -0500
++++ b/src/libscotchmetis/metis_graph_part.c	2018-07-13 14:21:08.000000000 -0500
+@@ -298,7 +298,7 @@
+
+     edgenbr = xadj[vertnbr] - baseval;
+     if ((edlotax = memAlloc (edgenbr * sizeof (SCOTCH_Num))) == NULL)
+-      return;
++      return (METIS_ERROR);
+     edlotax -= baseval;                           /* Base access to edlotax */
+     vsiztax  = vsize2 - baseval;
diff --git a/var/spack/repos/builtin/packages/scotch/metis-headers-6.0.4.patch b/var/spack/repos/builtin/packages/scotch/metis-headers-6.0.4.patch
new file mode 100644
index 0000000000..9c902a62b8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/scotch/metis-headers-6.0.4.patch
@@ -0,0 +1,634 @@
+--- A/src/libscotch/Makefile	2014-09-23 21:28:28.000000000 +0200
++++ B/src/libscotch/Makefile	2015-07-24 12:51:31.357132922 +0200
+@@ -60,7 +60,7 @@ scotch				:
+ 					libscotcherrexit$(LIB)
+ 
+ ptscotch			:	scotch
+-					$(MAKE) CFLAGS="$(CFLAGS) -DSCOTCH_PTSCOTCH" CC="$(CCP)"	\
++					$(MAKE) CFLAGS="$(CFLAGS) -DSCOTCH_PTSCOTCH" CC="$(CCP)" CCD="$(CCP)"	\
+ 					ptscotch.h							\
+ 					ptscotchf.h							\
+ 					libptscotch$(LIB)						\
+--- A/src/libscotchmetis/Makefile	2011-09-06 18:46:48.000000000 +0200
++++ B/src/libscotchmetis/Makefile	2015-08-25 13:37:31.424467916 +0200
+@@ -54,10 +54,12 @@ include ../Makefile.inc
+ 
+ scotch				:
+ 					$(MAKE) CC="$(CCS)" SCOTCHLIB=ptscotch						\
++					metis.h                                                                         \
+ 					libscotchmetis$(LIB)
+ 
+ ptscotch			:
+ 					$(MAKE) CFLAGS="$(CFLAGS) -DSCOTCH_PTSCOTCH" CC="$(CCP)" SCOTCHLIB=ptscotch	\
++					parmetis.h									\
+ 					libptscotchparmetis$(LIB)
+ 
+ install				:	scotch
+@@ -69,7 +71,7 @@ ptinstall			:	ptscotch
+ 					-$(CP) libptscotchparmetis$(LIB) $(libdir)
+ 
+ clean				:
+-					-$(RM) *~ *$(OBJ) lib*$(LIB)
++					-$(RM) *~ *$(OBJ) lib*$(LIB) metis.h parmetis.h
+ 
+ realclean			:	clean
+ 
+@@ -138,3 +140,10 @@ libscotchmetis$(LIB)		:	metis_graph_orde
+ 					metis_graph_part_f$(OBJ)
+ 					$(AR) $(ARFLAGS) $(@) $(^)
+ 					-$(RANLIB) $(@)
++metis.h				:	metis_skeleton.h			\
++					../libscotch/dummysizes
++					../libscotch/dummysizes metis_skeleton.h metis.h
++
++parmetis.h				:	parmetis_skeleton.h		\
++					../libscotch/dummysizes
++					../libscotch/dummysizes parmetis_skeleton.h parmetis.h
+--- A/src/libscotchmetis/metis.h	2012-09-13 17:43:52.000000000 +0200
++++ B/src/libscotchmetis/metis.h	1970-01-01 01:00:00.000000000 +0100
+@@ -1,97 +0,0 @@
+-/*********************************************************
+-**                                                      **
+-**  WARNING: THIS IS NOT THE ORIGINAL INCLUDE FILE OF   **
+-**  THE MeTiS SOFTWARE PACKAGE.                         **
+-**  This file is a compatibility include file provided  **
+-**  as part of the Scotch software distribution.        **
+-**  Preferably use the original MeTiS include file to   **
+-**  keep definitions of routines not overloaded by      **
+-**  the libScotchMeTiS library.                         **
+-**                                                      **
+-*********************************************************/
+-/* Copyright 2007,2010,2012 IPB, Universite de Bordeaux, INRIA & CNRS
+-**
+-** This file is part of the Scotch software package for static mapping,
+-** graph partitioning and sparse matrix ordering.
+-**
+-** This software is governed by the CeCILL-C license under French law
+-** and abiding by the rules of distribution of free software. You can
+-** use, modify and/or redistribute the software under the terms of the
+-** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
+-** URL: "http://www.cecill.info".
+-** 
+-** As a counterpart to the access to the source code and rights to copy,
+-** modify and redistribute granted by the license, users are provided
+-** only with a limited warranty and the software's author, the holder of
+-** the economic rights, and the successive licensors have only limited
+-** liability.
+-** 
+-** In this respect, the user's attention is drawn to the risks associated
+-** with loading, using, modifying and/or developing or reproducing the
+-** software by the user in light of its specific status of free software,
+-** that may mean that it is complicated to manipulate, and that also
+-** therefore means that it is reserved for developers and experienced
+-** professionals having in-depth computer knowledge. Users are therefore
+-** encouraged to load and test the software's suitability as regards
+-** their requirements in conditions enabling the security of their
+-** systems and/or data to be ensured and, more generally, to use and
+-** operate it in the same conditions as regards security.
+-** 
+-** The fact that you are presently reading this means that you have had
+-** knowledge of the CeCILL-C license and that you accept its terms.
+-*/
+-/************************************************************/
+-/**                                                        **/
+-/**   NAME       : metis.h                                 **/
+-/**                                                        **/
+-/**   AUTHOR     : Francois PELLEGRINI                     **/
+-/**                                                        **/
+-/**   FUNCTION   : Compatibility declaration file for the  **/
+-/**                MeTiS interface routines provided by    **/
+-/**                the Scotch project.                     **/
+-/**                                                        **/
+-/**   DATES      : # Version 5.0  : from : 08 sep 2006     **/
+-/**                                 to     07 jun 2007     **/
+-/**                # Version 5.1  : from : 30 jun 2010     **/
+-/**                                 to     30 jun 2010     **/
+-/**                # Version 6.0  : from : 13 sep 2012     **/
+-/**                                 to     13 sep 2012     **/
+-/**                                                        **/
+-/************************************************************/
+-
+-/*
+-**  The defines.
+-*/
+-
+-#ifdef SCOTCH_METIS_PREFIX
+-#define SCOTCH_METIS_PREFIXL        scotch_
+-#define SCOTCH_METIS_PREFIXU        SCOTCH_
+-#endif /* SCOTCH_METIS_PREFIX */
+-
+-#ifndef SCOTCH_METIS_PREFIXL
+-#define SCOTCH_METIS_PREFIXL
+-#endif /* SCOTCH_METIS_PREFIXL */
+-
+-#ifndef SCOTCH_METIS_PREFIXU
+-#define SCOTCH_METIS_PREFIXU
+-#endif /* SCOTCH_METIS_PREFIXU */
+-
+-#ifndef METISNAMEL
+-#define METISNAMEL(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXL),s)
+-#define METISNAMEU(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXU),s)
+-#define METISNAME2(p,s)             METISNAME4(p,s)
+-#define METISNAME3(s)               s
+-#define METISNAME4(p,s)             p##s
+-#endif /* METISNAMEL */
+-
+-/*
+-**  The function prototypes.
+-*/
+-
+-void                        METISNAMEU(METIS_EdgeND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-void                        METISNAMEU(METIS_NodeND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-void                        METISNAMEU(METIS_NodeWND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-
+-void                        METISNAMEU(METIS_PartGraphKway) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-void                        METISNAMEU(METIS_PartGraphRecursive) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+-void                        METISNAMEU(METIS_PartGraphVKway) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+--- A/src/libscotchmetis/metis_skeleton.h	1970-01-01 01:00:00.000000000 +0100
++++ B/src/libscotchmetis/metis_skeleton.h	2015-08-25 13:27:07.224497875 +0200
+@@ -0,0 +1,103 @@
++/*********************************************************
++**                                                      **
++**  WARNING: THIS IS NOT THE ORIGINAL INCLUDE FILE OF   **
++**  THE MeTiS SOFTWARE PACKAGE.                         **
++**  This file is a compatibility include file provided  **
++**  as part of the Scotch software distribution.        **
++**  Preferably use the original MeTiS include file to   **
++**  keep definitions of routines not overloaded by      **
++**  the libScotchMeTiS library.                         **
++**                                                      **
++*********************************************************/
++/* Copyright 2007,2010,2012 IPB, Universite de Bordeaux, INRIA & CNRS
++**
++** This file is part of the Scotch software package for static mapping,
++** graph partitioning and sparse matrix ordering.
++**
++** This software is governed by the CeCILL-C license under French law
++** and abiding by the rules of distribution of free software. You can
++** use, modify and/or redistribute the software under the terms of the
++** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
++** URL: "http://www.cecill.info".
++** 
++** As a counterpart to the access to the source code and rights to copy,
++** modify and redistribute granted by the license, users are provided
++** only with a limited warranty and the software's author, the holder of
++** the economic rights, and the successive licensors have only limited
++** liability.
++** 
++** In this respect, the user's attention is drawn to the risks associated
++** with loading, using, modifying and/or developing or reproducing the
++** software by the user in light of its specific status of free software,
++** that may mean that it is complicated to manipulate, and that also
++** therefore means that it is reserved for developers and experienced
++** professionals having in-depth computer knowledge. Users are therefore
++** encouraged to load and test the software's suitability as regards
++** their requirements in conditions enabling the security of their
++** systems and/or data to be ensured and, more generally, to use and
++** operate it in the same conditions as regards security.
++** 
++** The fact that you are presently reading this means that you have had
++** knowledge of the CeCILL-C license and that you accept its terms.
++*/
++/************************************************************/
++/**                                                        **/
++/**   NAME       : metis.h                                 **/
++/**                                                        **/
++/**   AUTHOR     : Francois PELLEGRINI                     **/
++/**                                                        **/
++/**   FUNCTION   : Compatibility declaration file for the  **/
++/**                MeTiS interface routines provided by    **/
++/**                the Scotch project.                     **/
++/**                                                        **/
++/**   DATES      : # Version 5.0  : from : 08 sep 2006     **/
++/**                                 to     07 jun 2007     **/
++/**                # Version 5.1  : from : 30 jun 2010     **/
++/**                                 to     30 jun 2010     **/
++/**                # Version 6.0  : from : 13 sep 2012     **/
++/**                                 to     13 sep 2012     **/
++/**                                                        **/
++/************************************************************/
++
++#include<stdint.h>
++
++/*
++**  The defines.
++*/
++
++#ifdef SCOTCH_METIS_PREFIX
++#define SCOTCH_METIS_PREFIXL        scotch_
++#define SCOTCH_METIS_PREFIXU        SCOTCH_
++#endif /* SCOTCH_METIS_PREFIX */
++
++#ifndef SCOTCH_METIS_PREFIXL
++#define SCOTCH_METIS_PREFIXL
++#endif /* SCOTCH_METIS_PREFIXL */
++
++#ifndef SCOTCH_METIS_PREFIXU
++#define SCOTCH_METIS_PREFIXU
++#endif /* SCOTCH_METIS_PREFIXU */
++
++#ifndef METISNAMEL
++#define METISNAMEL(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXL),s)
++#define METISNAMEU(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXU),s)
++#define METISNAME2(p,s)             METISNAME4(p,s)
++#define METISNAME3(s)               s
++#define METISNAME4(p,s)             p##s
++#endif /* METISNAMEL */
++
++/*+ Integer type. +*/
++
++typedef DUMMYINT SCOTCH_Num;
++
++/*
++**  The function prototypes.
++*/
++
++void                        METISNAMEU(METIS_EdgeND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++void                        METISNAMEU(METIS_NodeND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++void                        METISNAMEU(METIS_NodeWND) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++
++void                        METISNAMEU(METIS_PartGraphKway) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++void                        METISNAMEU(METIS_PartGraphRecursive) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
++void                        METISNAMEU(METIS_PartGraphVKway) (const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const);
+--- A/src/libscotchmetis/parmetis.h	2012-09-13 17:41:21.000000000 +0200
++++ B/src/libscotchmetis/parmetis.h	1970-01-01 01:00:00.000000000 +0100
+@@ -1,100 +0,0 @@
+-/*********************************************************
+-**                                                      **
+-**  WARNING: THIS IS NOT THE ORIGINAL INCLUDE FILE OF   **
+-**  THE ParMeTiS SOFTWARE PACKAGE.                      **
+-**  This file is a compatibility include file provided  **
+-**  as part of the Scotch software distribution.        **
+-**  Preferably use the original ParMeTiS include file   **
+-**  to keep definitions of routines not overloaded by   **
+-**  the libPTScotchMeTiS library.                       **
+-**                                                      **
+-*********************************************************/
+-/* Copyright 2007,2008,2010,2012 IPB, Universite de Bordeaux, INRIA & CNRS
+-**
+-** This file is part of the Scotch software package for static mapping,
+-** graph partitioning and sparse matrix ordering.
+-**
+-** This software is governed by the CeCILL-C license under French law
+-** and abiding by the rules of distribution of free software. You can
+-** use, modify and/or redistribute the software under the terms of the
+-** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
+-** URL: "http://www.cecill.info".
+-** 
+-** As a counterpart to the access to the source code and rights to copy,
+-** modify and redistribute granted by the license, users are provided
+-** only with a limited warranty and the software's author, the holder of
+-** the economic rights, and the successive licensors have only limited
+-** liability.
+-** 
+-** In this respect, the user's attention is drawn to the risks associated
+-** with loading, using, modifying and/or developing or reproducing the
+-** software by the user in light of its specific status of free software,
+-** that may mean that it is complicated to manipulate, and that also
+-** therefore means that it is reserved for developers and experienced
+-** professionals having in-depth computer knowledge. Users are therefore
+-** encouraged to load and test the software's suitability as regards
+-** their requirements in conditions enabling the security of their
+-** systems and/or data to be ensured and, more generally, to use and
+-** operate it in the same conditions as regards security.
+-** 
+-** The fact that you are presently reading this means that you have had
+-** knowledge of the CeCILL-C license and that you accept its terms.
+-*/
+-/************************************************************/
+-/**                                                        **/
+-/**   NAME       : parmetis.h                              **/
+-/**                                                        **/
+-/**   AUTHOR     : Francois PELLEGRINI                     **/
+-/**                                                        **/
+-/**   FUNCTION   : Compatibility declaration file for the  **/
+-/**                MeTiS interface routines provided by    **/
+-/**                the Scotch project.                     **/
+-/**                                                        **/
+-/**   DATES      : # Version 5.0  : from : 17 oct 2007     **/
+-/**                                 to     18 oct 2007     **/
+-/**                # Version 5.1  : from : 19 jun 2008     **/
+-/**                                 to     30 jun 2010     **/
+-/**                # Version 6.0  : from : 13 sep 2012     **/
+-/**                                 to     13 sep 2012     **/
+-/**                                                        **/
+-/************************************************************/
+-
+-/*
+-**  The defines and includes.
+-*/
+-
+-#ifndef __parmetis_h__
+-#define __parmetis_h__
+-
+-#include <mpi.h>                                  /* Since ParMeTiS does it, do it too */
+-
+-#endif /* __parmetis_h__ */
+-
+-#ifdef SCOTCH_METIS_PREFIX
+-#define SCOTCH_METIS_PREFIXL        scotch_
+-#define SCOTCH_METIS_PREFIXU        SCOTCH_
+-#endif /* SCOTCH_METIS_PREFIX */
+-
+-#ifndef SCOTCH_METIS_PREFIXL
+-#define SCOTCH_METIS_PREFIXL
+-#endif /* SCOTCH_METIS_PREFIXL */
+-
+-#ifndef SCOTCH_METIS_PREFIXU
+-#define SCOTCH_METIS_PREFIXU
+-#endif /* SCOTCH_METIS_PREFIXU */
+-
+-#ifndef METISNAMEL
+-#define METISNAMEL(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXL),s)
+-#define METISNAMEU(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXU),s)
+-#define METISNAME2(p,s)             METISNAME4(p,s)
+-#define METISNAME3(s)               s
+-#define METISNAME4(p,s)             p##s
+-#endif /* METISNAMEL */
+-
+-/*
+-**  The function prototypes.
+-*/
+-
+-void                        METISNAMEU(ParMETIS_V3_NodeND) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
+-void                        METISNAMEU(ParMETIS_V3_PartGeomKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
+-void                        METISNAMEU(ParMETIS_V3_PartKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
+--- A/src/libscotchmetis/parmetis_skeleton.h	1970-01-01 01:00:00.000000000 +0100
++++ B/src/libscotchmetis/parmetis_skeleton.h	2015-08-25 13:42:17.972454163 +0200
+@@ -0,0 +1,105 @@
++/*********************************************************
++**                                                      **
++**  WARNING: THIS IS NOT THE ORIGINAL INCLUDE FILE OF   **
++**  THE ParMeTiS SOFTWARE PACKAGE.                      **
++**  This file is a compatibility include file provided  **
++**  as part of the Scotch software distribution.        **
++**  Preferably use the original ParMeTiS include file   **
++**  to keep definitions of routines not overloaded by   **
++**  the libPTScotchMeTiS library.                       **
++**                                                      **
++*********************************************************/
++/* Copyright 2007,2008,2010,2012 IPB, Universite de Bordeaux, INRIA & CNRS
++**
++** This file is part of the Scotch software package for static mapping,
++** graph partitioning and sparse matrix ordering.
++**
++** This software is governed by the CeCILL-C license under French law
++** and abiding by the rules of distribution of free software. You can
++** use, modify and/or redistribute the software under the terms of the
++** CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
++** URL: "http://www.cecill.info".
++** 
++** As a counterpart to the access to the source code and rights to copy,
++** modify and redistribute granted by the license, users are provided
++** only with a limited warranty and the software's author, the holder of
++** the economic rights, and the successive licensors have only limited
++** liability.
++** 
++** In this respect, the user's attention is drawn to the risks associated
++** with loading, using, modifying and/or developing or reproducing the
++** software by the user in light of its specific status of free software,
++** that may mean that it is complicated to manipulate, and that also
++** therefore means that it is reserved for developers and experienced
++** professionals having in-depth computer knowledge. Users are therefore
++** encouraged to load and test the software's suitability as regards
++** their requirements in conditions enabling the security of their
++** systems and/or data to be ensured and, more generally, to use and
++** operate it in the same conditions as regards security.
++** 
++** The fact that you are presently reading this means that you have had
++** knowledge of the CeCILL-C license and that you accept its terms.
++*/
++/************************************************************/
++/**                                                        **/
++/**   NAME       : parmetis.h                              **/
++/**                                                        **/
++/**   AUTHOR     : Francois PELLEGRINI                     **/
++/**                                                        **/
++/**   FUNCTION   : Compatibility declaration file for the  **/
++/**                MeTiS interface routines provided by    **/
++/**                the Scotch project.                     **/
++/**                                                        **/
++/**   DATES      : # Version 5.0  : from : 17 oct 2007     **/
++/**                                 to     18 oct 2007     **/
++/**                # Version 5.1  : from : 19 jun 2008     **/
++/**                                 to     30 jun 2010     **/
++/**                # Version 6.0  : from : 13 sep 2012     **/
++/**                                 to     13 sep 2012     **/
++/**                                                        **/
++/************************************************************/
++
++/*
++**  The defines and includes.
++*/
++
++#ifndef __parmetis_h__
++#define __parmetis_h__
++
++#include<stdint.h>
++#include <mpi.h>                                  /* Since ParMeTiS does it, do it too */
++
++#endif /* __parmetis_h__ */
++
++#ifdef SCOTCH_METIS_PREFIX
++#define SCOTCH_METIS_PREFIXL        scotch_
++#define SCOTCH_METIS_PREFIXU        SCOTCH_
++#endif /* SCOTCH_METIS_PREFIX */
++
++#ifndef SCOTCH_METIS_PREFIXL
++#define SCOTCH_METIS_PREFIXL
++#endif /* SCOTCH_METIS_PREFIXL */
++
++#ifndef SCOTCH_METIS_PREFIXU
++#define SCOTCH_METIS_PREFIXU
++#endif /* SCOTCH_METIS_PREFIXU */
++
++#ifndef METISNAMEL
++#define METISNAMEL(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXL),s)
++#define METISNAMEU(s)               METISNAME2(METISNAME3(SCOTCH_METIS_PREFIXU),s)
++#define METISNAME2(p,s)             METISNAME4(p,s)
++#define METISNAME3(s)               s
++#define METISNAME4(p,s)             p##s
++#endif /* METISNAMEL */
++
++/*+ Integer type. +*/
++
++typedef DUMMYINT SCOTCH_Num;
++
++/*
++**  The function prototypes.
++*/
++
++void                        METISNAMEU(ParMETIS_V3_NodeND) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
++void                        METISNAMEU(ParMETIS_V3_PartGeomKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
++void                        METISNAMEU(ParMETIS_V3_PartKway) (const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const SCOTCH_Num * const, const float * const, const float * const, const SCOTCH_Num * const, SCOTCH_Num * const, SCOTCH_Num * const, MPI_Comm * const);
+--- A/src/Makefile	2014-10-02 17:31:36.000000000 +0200
++++ B/src/Makefile	2015-08-25 13:00:50.288573562 +0200
+@@ -115,6 +115,7 @@ install				:	required	$(bindir)	$(includ
+ 					-$(CP) -f ../bin/[agm]*$(EXE) $(bindir)
+ 					-$(CP) -f ../bin/d[agm]*$(EXE) $(bindir)
+ 					-$(CP) -f ../include/*scotch*.h $(includedir)
++					-$(CP) -f ../include/*metis*.h $(includedir)
+ 					-$(CP) -f ../lib/*scotch*$(LIB) $(libdir)
+ 					-$(CP) -Rf ../man/* $(mandir)
+ 
+--- A/src/Makefile~	1970-01-01 01:00:00.000000000 +0100
++++ B/src/Makefile~	2014-10-02 17:31:36.000000000 +0200
+@@ -0,0 +1,134 @@
++## Copyright 2004,2007,2008,2010-2012,2014 IPB, Universite de Bordeaux, INRIA & CNRS
++##
++## This file is part of the Scotch software package for static mapping,
++## graph partitioning and sparse matrix ordering.
++##
++## This software is governed by the CeCILL-C license under French law
++## and abiding by the rules of distribution of free software. You can
++## use, modify and/or redistribute the software under the terms of the
++## CeCILL-C license as circulated by CEA, CNRS and INRIA at the following
++## URL: "http://www.cecill.info".
++## 
++## As a counterpart to the access to the source code and rights to copy,
++## modify and redistribute granted by the license, users are provided
++## only with a limited warranty and the software's author, the holder of
++## the economic rights, and the successive licensors have only limited
++## liability.
++## 
++## In this respect, the user's attention is drawn to the risks associated
++## with loading, using, modifying and/or developing or reproducing the
++## software by the user in light of its specific status of free software,
++## that may mean that it is complicated to manipulate, and that also
++## therefore means that it is reserved for developers and experienced
++## professionals having in-depth computer knowledge. Users are therefore
++## encouraged to load and test the software's suitability as regards
++## their requirements in conditions enabling the security of their
++## systems and/or data to be ensured and, more generally, to use and
++## operate it in the same conditions as regards security.
++## 
++## The fact that you are presently reading this means that you have had
++## knowledge of the CeCILL-C license and that you accept its terms.
++##
++
++VERSION	= 6
++RELEASE = 0
++PATCHLEVEL = 4
++
++.PHONY				:	clean	default	install	ptscotch	realclean	required	scotch
++
++default				:	scotch
++
++required			:	Makefile.inc	../bin	../include	../lib
++
++Makefile.inc			:
++					@echo "#####################################################################"
++			        	@echo "BEFORE COMPILING Scotch OR PT-Scotch, YOU SHOULD HAVE AN APPROPRIATE"
++					@echo "Makefile.inc FILE IN THIS DIRECTORY. PLEASE LOOK INTO DIRECTORY"
++	        			@echo " ./Make.inc FOR AN EXISTING Makefile.inc FILE THAT FITS YOUR NEED, OR"
++		        		@echo "USE THEM AS MODELS IN CASE YOU NEED TO BUILD A NEW ONE FOR YOUR"
++		        		@echo "PARTICULAR PLATFORM."
++			        	@echo "#####################################################################"
++			        	@echo "Then, type \"make scotch\" (default) for the sequential library"
++			        	@echo "and software, or \"make ptscotch\" for the parallel library and"
++			        	@echo "software."
++					@exit 1
++
++include Makefile.inc
++
++prefix		?= /usr/local
++bindir		?= $(prefix)/bin
++includedir	?= $(prefix)/include
++libdir		?= $(prefix)/lib
++datarootdir	?= $(prefix)/share
++mandir		?= $(datarootdir)/man
++
++../bin				:
++					-$(MKDIR) ../bin
++
++../include			:
++					-$(MKDIR) ../include
++
++../lib				:
++					-$(MKDIR) ../lib
++
++$(bindir)			:
++					-$(MKDIR) $(bindir)
++
++$(datarootdir)			:
++					-$(MKDIR) $(datarootdir)
++
++$(includedir)			:
++					-$(MKDIR) $(includedir)
++
++$(libdir)			:
++					-$(MKDIR) $(libdir)
++
++$(mandir)			:	$(datarootdir)
++					-$(MKDIR) $(mandir)
++
++$(mandir)/man1			:	$(mandir)
++					-$(MKDIR) $(mandir)/man1
++
++scotch				:	required
++					(cd libscotch ;      $(MAKE) VERSION=$(VERSION) RELEASE=$(RELEASE) PATCHLEVEL=$(PATCHLEVEL) scotch && $(MAKE) install)
++					(cd scotch ;         $(MAKE) VERSION=$(VERSION) RELEASE=$(RELEASE) PATCHLEVEL=$(PATCHLEVEL) scotch && $(MAKE) install)
++					(cd libscotchmetis ; $(MAKE)                                                                scotch && $(MAKE) install)
++
++ptscotch			:	required
++					(cd libscotch ;      $(MAKE) VERSION=$(VERSION) RELEASE=$(RELEASE) PATCHLEVEL=$(PATCHLEVEL) ptscotch && $(MAKE) ptinstall)
++					(cd scotch ;         $(MAKE) VERSION=$(VERSION) RELEASE=$(RELEASE) PATCHLEVEL=$(PATCHLEVEL) ptscotch && $(MAKE) ptinstall)
++					(cd libscotchmetis ; $(MAKE)                                                                ptscotch && $(MAKE) ptinstall)
++
++check				:	scotch
++					(cd check ; $(MAKE) check)
++
++ptcheck				:	ptscotch
++					(cd check ; $(MAKE) ptcheck)
++
++esmumps				:	scotch
++					(cd esmumps ; $(MAKE) scotch && $(MAKE) install)
++
++ptesmumps			:	ptscotch
++					(cd esmumps ; $(MAKE) ptscotch && $(MAKE) ptinstall)
++
++install				:	required	$(bindir)	$(includedir)	$(libdir)	$(mandir)/man1
++					-$(CP) -f ../bin/[agm]*$(EXE) $(bindir)
++					-$(CP) -f ../bin/d[agm]*$(EXE) $(bindir)
++					-$(CP) -f ../include/*scotch*.h $(includedir)
++					-$(CP) -f ../lib/*scotch*$(LIB) $(libdir)
++					-$(CP) -Rf ../man/* $(mandir)
++
++clean				:	required
++					(cd libscotch ;      $(MAKE) clean)
++					(cd scotch ;         $(MAKE) clean)
++					(cd libscotchmetis ; $(MAKE) clean)
++					(cd check ;          $(MAKE) clean)
++					(cd esmumps ;        $(MAKE) clean)
++
++realclean			:	required
++					(cd libscotch ;      $(MAKE) realclean)
++					(cd scotch ;         $(MAKE) realclean)
++					(cd libscotchmetis ; $(MAKE) realclean)
++					(cd check ;          $(MAKE) realclean)
++					(cd esmumps ;        $(MAKE) realclean)
++					-$(RM) ../bin/* ../include/* ../lib/*
+--- A/src/Make.inc/Makefile.inc.x86-64_pc_linux2~	1970-01-01 01:00:00.000000000 +0100
++++ B/src/Make.inc/Makefile.inc.x86-64_pc_linux2~	2015-08-25 13:09:33.984548426 +0200
+@@ -0,0 +1,21 @@
++EXE		=
++LIB		= .a
++OBJ		= .o
++
++MAKE		= make
++AR		= ar
++ARFLAGS		= -ruv
++CAT		= cat
++CCS		= gcc
++CCP		= mpicc
++CCD		= gcc
++CFLAGS		= -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_PTHREAD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_PTHREAD -Drestrict=__restrict -DIDXSIZE64 -DINT=int64_t
++CLIBFLAGS	=
++LDFLAGS		= -lz -lm -lrt -pthread
++CP		= cp
++LEX		= flex -Pscotchyy -olex.yy.c
++LN		= ln
++MKDIR		= mkdir
++MV		= mv
++RANLIB		= ranlib
++YACC		= bison -pscotchyy -y -b y
diff --git a/var/spack/repos/builtin/packages/scotch/package.py b/var/spack/repos/builtin/packages/scotch/package.py
index 48ae1490c8..e15696b54b 100644
--- a/var/spack/repos/builtin/packages/scotch/package.py
+++ b/var/spack/repos/builtin/packages/scotch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,8 @@ class Scotch(Package):
     url      = "http://gforge.inria.fr/frs/download.php/latestfile/298/scotch_6.0.4.tar.gz"
     list_url = "http://gforge.inria.fr/frs/?group_id=248"
 
+    version('6.0.6', 'ef676a3118b5590c416176e402fac248')
+    version('6.0.5a', '8430dff7175a1dfd5a3258e75260cf71')
     version('6.0.4', 'd58b825eb95e1db77efe8c6ff42d329f')
     version('6.0.3', '10b0cc0f184de2de99859eafaca83cfc')
     version('6.0.0', 'c50d6187462ba801f9a82133ee666e8e')
@@ -60,6 +43,9 @@ class Scotch(Package):
     # Version-specific patches
     patch('nonthreaded-6.0.4.patch', when='@6.0.4')
     patch('esmumps-ldflags-6.0.4.patch', when='@6.0.4')
+    patch('metis-headers-6.0.4.patch', when='@6.0.4')
+
+    patch('libscotchmetis-return-6.0.5a.patch', when='@6.0.5a')
 
     # NOTE: In cross-compiling environment parallel build
     # produces weird linker errors.
@@ -91,7 +77,7 @@ class Scotch(Package):
             libraries = ['libesmumps'] + libraries
 
         scotchlibs = find_libraries(
-            libraries, root=self.prefix, recurse=True, shared=shared
+            libraries, root=self.prefix, recursive=True, shared=shared
         )
         if '+compression' in self.spec:
             zlibs = self.spec['zlib'].libs
@@ -159,7 +145,7 @@ class Scotch(Package):
         if self.compiler.name == 'gcc':
             cflags.append('-Drestrict=__restrict')
         elif self.compiler.name == 'intel':
-            cflags.append('-restrict')
+            cflags.append('-Drestrict=')
 
         mpicc_path = self.spec['mpi'].mpicc if '+mpi' in self.spec else 'mpicc'
         makefile_inc.append('CCS       = $(CC)')
diff --git a/var/spack/repos/builtin/packages/scr/package.py b/var/spack/repos/builtin/packages/scr/package.py
index 1f49f34969..cffbcd8a12 100644
--- a/var/spack/repos/builtin/packages/scr/package.py
+++ b/var/spack/repos/builtin/packages/scr/package.py
@@ -1,31 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 import os
-import shutil
 
 
 class Scr(CMakePackage):
@@ -34,13 +14,16 @@ class Scr(CMakePackage):
        capability for MPI codes"""
 
     homepage = "http://computation.llnl.gov/projects/scalable-checkpoint-restart-for-mpi"
+    url      = "https://github.com/LLNL/scr/archive/v1.2.0.tar.gz"
+    git      = "https://github.com/llnl/scr.git"
 
     # NOTE: scr-v1.1.8 is built with autotools and is not properly build here.
     # scr-v1.1.8 will be deprecated with the upcoming release of v1.2.0
     # url      = "https://github.com/LLNL/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz"
     # version('1.1.8', '6a0f11ad18e27fcfc00a271ff587b06e')
 
-    version('master', git='https://github.com/llnl/scr.git', branch='master')
+    version('master', branch='master')
+    version('1.2.0', '060e9e9c7604c1765f3991f9cd6e9d2d')
 
     depends_on('pdsh+static_modules', type=('build', 'run'))
     depends_on('zlib')
@@ -89,6 +72,8 @@ class Scr(CMakePackage):
     variant('cntl_base', default='/tmp',
             description='Compile time default location for control directory.')
 
+    conflicts('platform=bgq')
+
     def get_abs_path_rel_prefix(self, path):
         # Return path if absolute, otherwise prepend prefix
         if os.path.isabs(path):
@@ -100,6 +85,9 @@ class Scr(CMakePackage):
         spec = self.spec
         args = []
 
+        if 'platform=cray' in spec:
+            args.append('-DSCR_LINK_STATIC=ON')
+
         args.append('-DENABLE_FORTRAN={0}'.format('+fortran' in spec))
 
         conf_path = self.get_abs_path_rel_prefix(
@@ -143,4 +131,4 @@ class Scr(CMakePackage):
         if spec.variants['copy_config'].value:
             dest_path = self.get_abs_path_rel_prefix(
                 spec.variants['scr_config'].value)
-            shutil.copyfile(spec.variants['copy_config'].value, dest_path)
+            install(spec.variants['copy_config'].value, dest_path)
diff --git a/var/spack/repos/builtin/packages/screen/package.py b/var/spack/repos/builtin/packages/screen/package.py
index 34bc952ec6..5094b34971 100644
--- a/var/spack/repos/builtin/packages/screen/package.py
+++ b/var/spack/repos/builtin/packages/screen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Screen(AutotoolsPackage):
     """
 
     homepage = "https://www.gnu.org/software/screen/"
-    url      = "http://ftp.gnu.org/gnu/screen/screen-4.3.1.tar.gz"
+    url      = "https://ftpmirror.gnu.org/screen/screen-4.3.1.tar.gz"
 
+    version('4.6.2', 'a0f529d3333b128dfaa324d978ba73a8')
     version('4.3.1', '5bb3b0ff2674e29378c31ad3411170ad')
     version('4.3.0', 'f76d28eadc4caaf6cdff00685ae6ad46')
     version('4.2.1', '419a0594e2b25039239af8b90eda7d92')
diff --git a/var/spack/repos/builtin/packages/scripts/package.py b/var/spack/repos/builtin/packages/scripts/package.py
index ddd184b44f..5589169cc8 100644
--- a/var/spack/repos/builtin/packages/scripts/package.py
+++ b/var/spack/repos/builtin/packages/scripts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Scripts(AutotoolsPackage):
 
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/scrnsaverproto/package.py b/var/spack/repos/builtin/packages/scrnsaverproto/package.py
index 71fe86abbc..6647763b6a 100644
--- a/var/spack/repos/builtin/packages/scrnsaverproto/package.py
+++ b/var/spack/repos/builtin/packages/scrnsaverproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Scrnsaverproto(AutotoolsPackage):
 
     version('1.2.2', '21704f1bad472d94abd22fea5704bb48')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/sctk/package.py b/var/spack/repos/builtin/packages/sctk/package.py
index e64d2c79aa..33fbb76d70 100644
--- a/var/spack/repos/builtin/packages/sctk/package.py
+++ b/var/spack/repos/builtin/packages/sctk/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class Sctk(Package):
@@ -49,5 +29,4 @@ class Sctk(Package):
         make('config')
         make('all')
         make('install')
-        mkdirp(prefix.bin)
-        copy_tree('bin', prefix.bin)
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/sdl2-image/package.py b/var/spack/repos/builtin/packages/sdl2-image/package.py
index 3986c59c1e..6a28c37d40 100644
--- a/var/spack/repos/builtin/packages/sdl2-image/package.py
+++ b/var/spack/repos/builtin/packages/sdl2-image/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sdl2/package.py b/var/spack/repos/builtin/packages/sdl2/package.py
index 272261f54c..5e831ebba3 100644
--- a/var/spack/repos/builtin/packages/sdl2/package.py
+++ b/var/spack/repos/builtin/packages/sdl2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sed/package.py b/var/spack/repos/builtin/packages/sed/package.py
index 84c5c94ed9..19fd8b7c59 100644
--- a/var/spack/repos/builtin/packages/sed/package.py
+++ b/var/spack/repos/builtin/packages/sed/package.py
@@ -1,33 +1,14 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Sed(AutotoolsPackage):
     """GNU implementation of the famous stream editor."""
     homepage = "http://www.gnu.org/software/sed/"
-    url      = "http://ftpmirror.gnu.org/sed/sed-4.2.2.tar.bz2"
+    url      = "https://ftpmirror.gnu.org/sed/sed-4.2.2.tar.bz2"
 
     version('4.2.2', '7ffe1c7cdc3233e1e0c4b502df253974')
diff --git a/var/spack/repos/builtin/packages/sentieon-genomics/package.py b/var/spack/repos/builtin/packages/sentieon-genomics/package.py
new file mode 100644
index 0000000000..e860a76bef
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sentieon-genomics/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os.path
+from spack import *
+
+
+class SentieonGenomics(Package):
+    """Sentieon provides complete solutions for secondary DNA analysis.
+    Our software improves upon BWA, GATK, Mutect, and Mutect2 based pipelines.
+    The Sentieon tools are deployable on any CPU-based computing system.
+    Please set the path to the sentieon license server with:
+
+    export SENTIEON_LICENSE=[FQDN]:[PORT]
+
+    Note: A manual download is required.
+    Spack will search your current directory for the download file.
+    Alternatively, add this file to a mirror so that Spack can find it.
+    For instructions on how to set up a mirror, see
+    http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://www.sentieon.com/"
+    url      = "file://{0}/sentieon-genomics-201808.01.tar.gz".format(os.getcwd())
+
+    version('201808.01', sha256='6d77bcd5a35539549b28eccae07b19a3b353d027720536e68f46dcf4b980d5f7')
+
+    # Licensing.
+    license_require = True
+    license_vars = ['SENTIEON_LICENSE']
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('doc', prefix.doc)
+        install_tree('etc', prefix.etc)
+        install_tree('lib', prefix.lib)
+        install_tree('libexec', prefix.libexec)
+        install_tree('share', prefix.share)
diff --git a/var/spack/repos/builtin/packages/seqan/package.py b/var/spack/repos/builtin/packages/seqan/package.py
new file mode 100644
index 0000000000..a13ed6d3b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/seqan/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Seqan(CMakePackage):
+    """SeqAn is an open source C++ library of efficient algorithms and data
+    structures for the analysis of sequences with the focus on biological data.
+    Our library applies a unique generic design that guarantees high
+    performance, generality, extensibility, and integration with other
+    libraries. SeqAn is easy to use and simplifies the development of new
+    software tools with a minimal loss of performance"""
+
+    homepage = "https://www.seqan.de"
+    url      = "https://github.com/seqan/seqan/archive/seqan-v2.4.0.tar.gz"
+
+    version('2.4.0', 'd899821e295fed0a22e08099f40cbc17')
+
+    depends_on('cmake@3.4.0:', type='build')
+    depends_on('python@2.7.0:', type='build')
+    depends_on('py-nose', type='build')
+    depends_on('py-sphinx', type='build')
+    depends_on('boost', type=('build', 'link'))
+    depends_on('zlib', type=('build', 'link'))
+    depends_on('bzip2', type=('build', 'link'))
+
+    conflicts('%intel@:16.0.4')
+    conflicts('%gcc@:4.9.4')
+    conflicts('%llvm@:3.5.1')
diff --git a/var/spack/repos/builtin/packages/seqprep/package.py b/var/spack/repos/builtin/packages/seqprep/package.py
index d4c75cc5fa..793c8e5985 100644
--- a/var/spack/repos/builtin/packages/seqprep/package.py
+++ b/var/spack/repos/builtin/packages/seqprep/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/seqtk/package.py b/var/spack/repos/builtin/packages/seqtk/package.py
index 6393d3e587..addaee78a3 100644
--- a/var/spack/repos/builtin/packages/seqtk/package.py
+++ b/var/spack/repos/builtin/packages/seqtk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/serf/package.py b/var/spack/repos/builtin/packages/serf/package.py
index 5604b8b166..6135a4ecfa 100644
--- a/var/spack/repos/builtin/packages/serf/package.py
+++ b/var/spack/repos/builtin/packages/serf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -54,6 +35,19 @@ class Serf(SConsPackage):
             'ZLIB={0}'.format(spec['zlib'].prefix),
         ]
 
+        # ZLIB variable is ignored on non-Windows platforms before and
+        # including the version 1.3.9:
+        # https://www.mail-archive.com/dev@serf.apache.org/msg01359.html
+        # The issue is fixed in the trunk. Hopefully, the next stable version
+        # will work properly.
+        if '@:1.3.9' in self.spec:
+            zlib_spec = self.spec['zlib']
+            link_flags = [zlib_spec.libs.search_flags]
+            link_flags.extend([self.compiler.cc_rpath_arg + d
+                               for d in zlib_spec.libs.directories])
+            args.append('LINKFLAGS=' + ' '.join(link_flags))
+            args.append('CPPFLAGS=' + zlib_spec.headers.cpp_flags)
+
         if '+debug' in spec:
             args.append('DEBUG=yes')
         else:
diff --git a/var/spack/repos/builtin/packages/sessreg/package.py b/var/spack/repos/builtin/packages/sessreg/package.py
index af3f001e70..a93604ef09 100644
--- a/var/spack/repos/builtin/packages/sessreg/package.py
+++ b/var/spack/repos/builtin/packages/sessreg/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class Sessreg(AutotoolsPackage):
     version('1.1.0', '5d7eb499043c7fdd8d53c5ba43660312')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def patch(self):
diff --git a/var/spack/repos/builtin/packages/setxkbmap/package.py b/var/spack/repos/builtin/packages/setxkbmap/package.py
index 5a8a5ea345..1ed7903c8e 100644
--- a/var/spack/repos/builtin/packages/setxkbmap/package.py
+++ b/var/spack/repos/builtin/packages/setxkbmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Setxkbmap(AutotoolsPackage):
     depends_on('libxkbfile')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/sga/package.py b/var/spack/repos/builtin/packages/sga/package.py
index 2c38244675..0349d86c13 100644
--- a/var/spack/repos/builtin/packages/sga/package.py
+++ b/var/spack/repos/builtin/packages/sga/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/shapeit/package.py b/var/spack/repos/builtin/packages/shapeit/package.py
index 4f0295cca1..0cb36d4cf6 100644
--- a/var/spack/repos/builtin/packages/shapeit/package.py
+++ b/var/spack/repos/builtin/packages/shapeit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/shared-mime-info/package.py b/var/spack/repos/builtin/packages/shared-mime-info/package.py
index 80880eebc1..e63f7b048b 100644
--- a/var/spack/repos/builtin/packages/shared-mime-info/package.py
+++ b/var/spack/repos/builtin/packages/shared-mime-info/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
@@ -32,6 +13,7 @@ class SharedMimeInfo(AutotoolsPackage):
     homepage = "https://freedesktop.org/wiki/Software/shared-mime-info"
     url      = "http://freedesktop.org/~hadess/shared-mime-info-1.8.tar.xz"
 
+    version('1.9', '45103889b91242850aa47f09325e798b')
     version('1.8', 'f6dcadce764605552fc956563efa058c')
 
     parallel = False
@@ -40,7 +22,7 @@ class SharedMimeInfo(AutotoolsPackage):
     depends_on('libxml2')
     depends_on('intltool', type='build')
     depends_on('gettext', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         spack_env.prepend_path("XDG_DATA_DIRS",
diff --git a/var/spack/repos/builtin/packages/shiny-server/package.py b/var/spack/repos/builtin/packages/shiny-server/package.py
index 2edd966825..af306b0d98 100644
--- a/var/spack/repos/builtin/packages/shiny-server/package.py
+++ b/var/spack/repos/builtin/packages/shiny-server/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/shocklibs/package.py b/var/spack/repos/builtin/packages/shocklibs/package.py
new file mode 100644
index 0000000000..7cd90918cf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shocklibs/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Shocklibs(Package):
+    """The lib for shock: An object store for scientific data."""
+
+    homepage = "https://github.com/MG-RAST/Shock"
+    url      = "https://github.com/MG-RAST/Shock/archive/v0.9.24.tar.gz"
+
+    version('0.9.24', '98b2e91e2726c7165f75afaf0ca51a5b')
+
+    def install(self, spec, prefix):
+        install_tree('libs', prefix.libs)
diff --git a/var/spack/repos/builtin/packages/shoremap/package.py b/var/spack/repos/builtin/packages/shoremap/package.py
new file mode 100644
index 0000000000..cd4623ecaf
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shoremap/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Shoremap(MakefilePackage):
+    """SHOREmap is a computational tool implementing a method that enables
+       simple and straightforward mapping-by-sequencing analysis.
+
+       Whole genome resequencing of pools of recombinant mutant genomes allows
+       directly linking phenotypic traits to causal mutations. Such an
+       analysis, called mapping-by-sequencing, combines classical genetic
+       mapping and next generation sequencing by relying on selection-induced
+       patterns within genome-wide allele frequency in pooled genomes."""
+
+    homepage = "http://bioinfo.mpipz.mpg.de/shoremap/"
+    url      = "http://bioinfo.mpipz.mpg.de/shoremap/SHOREmap_v3.6.tar.gz"
+
+    version('3.6', 'ccc9331189705a139d50f2c161178cb1')
+
+    depends_on('dislin')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('makefile')
+        makefile.filter(r'-L/usr/lib/',
+                        self.spec['libxt'].libs.search_flags)
+        makefile.filter(r'-L\./dislin.* -ldislin_d',
+                        self.spec['dislin:d'].libs.ld_flags)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('SHOREmap', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/shortbred/package.py b/var/spack/repos/builtin/packages/shortbred/package.py
new file mode 100644
index 0000000000..6105e4e8f0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shortbred/package.py
@@ -0,0 +1,32 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Shortbred(Package):
+    """ShortBRED is a system for profiling protein families of interest at
+    very high specificity in shotgun meta'omic sequencing data."""
+
+    homepage = "https://huttenhower.sph.harvard.edu/shortbred"
+    url      = "https://bitbucket.org/biobakery/shortbred/get/0.9.4.tar.gz"
+
+    version('0.9.4', 'ad3dff344cbea3713e78b384afad28fd')
+
+    depends_on('blast-plus@2.2.28:')
+    depends_on('cdhit@4.6:')
+    depends_on('muscle@3.8.31:')
+    depends_on('python@2.7.9:')
+    depends_on('py-biopython')
+    depends_on('usearch@6.0.307:')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('shortbred_identify.py', prefix.bin)
+        install('shortbred_quantify.py', prefix.bin)
+        install_tree('src', prefix.src)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PYTHONPATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/shortstack/package.py b/var/spack/repos/builtin/packages/shortstack/package.py
index 75d363e185..5f55022ec6 100644
--- a/var/spack/repos/builtin/packages/shortstack/package.py
+++ b/var/spack/repos/builtin/packages/shortstack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/showfont/package.py b/var/spack/repos/builtin/packages/showfont/package.py
index 769c77f076..71c8b138d3 100644
--- a/var/spack/repos/builtin/packages/showfont/package.py
+++ b/var/spack/repos/builtin/packages/showfont/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Showfont(AutotoolsPackage):
 
     depends_on('libfs')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/shuffile/package.py b/var/spack/repos/builtin/packages/shuffile/package.py
new file mode 100644
index 0000000000..2bc1c28ca5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/shuffile/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Shuffile(CMakePackage):
+    """Shuffle files between MPI ranks"""
+
+    homepage = "https://github.com/ECP-VeloC/shuffile"
+    url      = "https://github.com/ECP-VeloC/shuffile/archive/v0.0.2.zip"
+    git      = "https://github.com/ecp-veloc/shuffile.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('0.0.3', sha256='6debdd9d6e6f1c4ec31015d7956e8b556acd61ce31f757e4d1fa5002029c75e2')
+
+    depends_on('mpi')
+    depends_on('kvtree')
+
+    def cmake_args(self):
+        args = []
+        args.append("-DMPI_C_COMPILER=%s" % self.spec['mpi'].mpicc)
+        if self.spec.satisfies('platform=cray'):
+            args.append("-DSHUFFILE_LINK_STATIC=ON")
+        args.append("-DWITH_KVTREE_PREFIX=%s" % self.spec['kvtree'].prefix)
+        return args
diff --git a/var/spack/repos/builtin/packages/sickle/package.py b/var/spack/repos/builtin/packages/sickle/package.py
index 248f1ef3b9..9b0a14ba3f 100644
--- a/var/spack/repos/builtin/packages/sickle/package.py
+++ b/var/spack/repos/builtin/packages/sickle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/siesta/configure.patch b/var/spack/repos/builtin/packages/siesta/configure.patch
new file mode 100644
index 0000000000..577c77f529
--- /dev/null
+++ b/var/spack/repos/builtin/packages/siesta/configure.patch
@@ -0,0 +1,53 @@
+--- a/Src/configure	2017-11-23 12:42:40.909339915 +0100
++++ b/Src/configure	2017-11-23 12:42:59.911416449 +0100
+@@ -6000,7 +6000,7 @@
+   withval="$with_netcdf"
+ 
+ fi;
+-if test x$with_netcdf != xno; then
++if test "x$with_netcdf" != xno; then
+ 
+ tw_netcdf_ok=no
+ ac_ext=${FC_SRCEXT-f}
+@@ -6069,7 +6069,7 @@
+   LIBS="$save_LIBS"
+ fi
+ if test $tw_netcdf_ok = yes; then
+-  DEFS="$DEFS CDF";NETCDF_INTERFACE="libnetcdf_f90.a"
++  DEFS="$DEFS CDF";
+ else
+   NETCDF_LIBS="";tw_netcdf_ok=no;if test ! -z "$with_netcdf"; then { { echo "$as_me:$LINENO: error: Could not find NetCDF library." >&5
+ echo "$as_me: error: Could not find NetCDF library." >&2;}
+--- a/Util/TBTrans_rep/Makefile	2017-12-08 09:49:02.307877000 +0100
++++ b/Util/TBTrans_rep/Makefile	2017-12-08 09:49:44.385288000 +0100
+@@ -14,7 +14,7 @@
+ # Please see note about Linear-Algebra libraries below
+ #
+ 
+-default: what tbtrans 
++default: what tbtrans_rep 
+ 
+ VPATH:=$(shell pwd)/../../Src
+ OBJDIR=Obj
+@@ -91,16 +91,16 @@
+                           "ARCH_MAKE=../$(ARCH_MAKE)" \
+                           "INCFLAGS=$(LINALG_INCFLAGS)" "FFLAGS=$(FFLAGS:$(IPO_FLAG)=)" $(LINALG))
+ 
+-tbtrans: FPPFLAGS+=$(DEFS_PREFIX) -DTBTRANS
+-tbtrans: DEFS+=$(DEFS_PREFIX) -DTBTRANS
+-tbtrans: $(MPI_INTERFACE) $(FDF) $(TBTOBJS) $(SYSOBJ) $(LINALG)
+-	$(FC) $(FFLAGS) $(LDFLAGS) -o tbtrans \
++tbtrans_rep: FPPFLAGS+=$(DEFS_PREFIX) -DTBTRANS
++tbtrans_rep: DEFS+=$(DEFS_PREFIX) -DTBTRANS
++tbtrans_rep: $(MPI_INTERFACE) $(FDF) $(TBTOBJS) $(SYSOBJ) $(LINALG)
++	$(FC) $(FFLAGS) $(LDFLAGS) -o tbtrans_rep \
+               $(TBTOBJS) $(MPI_INTERFACE)  \
+               $(FDF) $(LIBS) $(LINALG)  || echo "***Please see top of Makefile"
+ 
+ clean: 
+ 	@echo "==> Cleaning object, library, and executable files"
+-	rm -f tbtrans *.o *.a *.mod
++	rm -f tbtrans_rep *.o *.a *.mod
+ 	rm -rf ./fdf
+ 	rm -rf ./MPI
+ 	rm -rf ./Libs
diff --git a/var/spack/repos/builtin/packages/siesta/package.py b/var/spack/repos/builtin/packages/siesta/package.py
new file mode 100644
index 0000000000..ec35aa9160
--- /dev/null
+++ b/var/spack/repos/builtin/packages/siesta/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+import os
+
+
+class Siesta(Package):
+    """SIESTA performs electronic structure calculations and ab initio molecular
+       dynamics simulations of molecules and solids."""
+
+    homepage = "https://departments.icmab.es/leem/siesta/"
+
+    version('4.0.1', '5cb60ce068f2f6e84fa9184ffca94c08', url='https://launchpad.net/siesta/4.0/4.0.1/+download/siesta-4.0.1.tar.gz')
+    version('3.2-pl-5', '27a300c65eb2a25d107d910d26aaf81a', url='http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz')
+
+    patch('configure.patch', when='@:4.0')
+
+    depends_on('mpi')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('scalapack')
+    depends_on('netcdf')
+    depends_on('netcdf-fortran')
+
+    phases = ['configure', 'build', 'install']
+
+    def configure(self, spec, prefix):
+        sh = which('sh')
+        configure_args = ['--enable-mpi',
+                          '--with-blas=%s' % spec['blas'].libs,
+                          '--with-lapack=%s' % spec['lapack'].libs,
+                          # need to include BLAS below because Intel MKL's
+                          # BLACS depends on BLAS, otherwise the compiler
+                          # test fails
+                          '--with-blacs=%s' % (spec['scalapack'].libs +
+                                               spec['blas'].libs),
+                          '--with-scalapack=%s' % spec['scalapack'].libs,
+                          '--with-netcdf=%s' % (spec['netcdf-fortran'].libs +
+                                                spec['netcdf'].libs),
+                          # need to specify MPIFC explicitly below, otherwise
+                          # Intel's mpiifort is not found
+                          'MPIFC=%s' % spec['mpi'].mpifc
+                          ]
+        for d in ['Obj', 'Obj_trans']:
+            with working_dir(d, create=True):
+                sh('../Src/configure', *configure_args)
+                if spec.satisfies('@:4.0%intel'):
+                    with open('arch.make', 'a') as f:
+                        f.write('\natom.o: atom.F\n')
+                        f.write('\t$(FC) -c $(FFLAGS) -O1')
+                        f.write('$(INCFLAGS) $(FPPFLAGS) $<')
+                sh('../Src/obj_setup.sh')
+
+    def build(self, spec, prefix):
+        with working_dir('Obj'):
+            make(parallel=False)
+        with working_dir('Obj_trans'):
+            make('transiesta', parallel=False)
+        with working_dir('Util'):
+            sh = which('sh')
+            sh('build_all.sh')
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        with working_dir('Obj'):
+            install('siesta', prefix.bin)
+        with working_dir('Obj_trans'):
+            install('transiesta', prefix.bin)
+        for root, _, files in os.walk('Util'):
+            for fname in files:
+                fname = join_path(root, fname)
+                if os.access(fname, os.X_OK):
+                    install(fname, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/signalp/package.py b/var/spack/repos/builtin/packages/signalp/package.py
index 95197badfc..cbb5126884 100644
--- a/var/spack/repos/builtin/packages/signalp/package.py
+++ b/var/spack/repos/builtin/packages/signalp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/signify/package.py b/var/spack/repos/builtin/packages/signify/package.py
new file mode 100755
index 0000000000..7c98977c88
--- /dev/null
+++ b/var/spack/repos/builtin/packages/signify/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Signify(MakefilePackage):
+    """OpenBSD tool to signs and verify signatures on files."""
+
+    homepage = "https://github.com/aperezdc/signify"
+    url      = "https://github.com/aperezdc/signify/archive/v23.tar.gz"
+
+    version('23', '0552295572a172740ae8427eb018ede8')
+
+    depends_on('libbsd@0.8:')
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.set('PREFIX', self.prefix)
diff --git a/var/spack/repos/builtin/packages/silo/package.py b/var/spack/repos/builtin/packages/silo/package.py
index 763fc66383..fed4ea223e 100644
--- a/var/spack/repos/builtin/packages/silo/package.py
+++ b/var/spack/repos/builtin/packages/silo/package.py
@@ -1,38 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Silo(Package):
+class Silo(AutotoolsPackage):
     """Silo is a library for reading and writing a wide variety of scientific
        data to binary, disk files."""
 
     homepage = "http://wci.llnl.gov/simulation/computer-codes/silo"
     url      = "https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.10.2/silo-4.10.2.tar.gz"
 
-    version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8')
+    version('4.10.2', '9ceac777a2f2469ac8cef40f4fab49c8', preferred=True)
+    version('4.10.2-bsd', '60fef9ce373daf1e9cc8320cfa509bc5',
+            url="https://wci.llnl.gov/content/assets/docs/simulation/computer-codes/silo/silo-4.10.2/silo-4.10.2-bsd.tar.gz")
     version('4.9', 'a83eda4f06761a86726e918fc55e782a')
     version('4.8', 'b1cbc0e7ec435eb656dc4b53a23663c9')
 
@@ -42,14 +25,30 @@ class Silo(Package):
             description='Builds Silex, a GUI for viewing Silo files')
     variant('pic', default=True,
             description='Produce position-independent code (for shared libs)')
+    variant('mpi', default=True,
+            description='Compile with MPI Compatibility')
 
-    depends_on('hdf5')
+    depends_on('hdf5~mpi', when='~mpi')
+    depends_on('mpi', when='+mpi')
+    depends_on('hdf5+mpi', when='+mpi')
     depends_on('qt', when='+silex')
+    depends_on('zlib')
 
     patch('remove-mpiposix.patch', when='@4.8:4.10.2')
 
-    def install(self, spec, prefix):
+    def flag_handler(self, name, flags):
+        if name == 'ldflags' and self.spec['hdf5'].satisfies('~shared'):
+            flags.append('-ldl')
+        return (flags, None, None)
+
+    def configure_args(self):
+        spec = self.spec
         config_args = [
+            '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include,
+                                   spec['hdf5'].prefix.lib),
+            '--with-zlib=%s,%s' % (spec['zlib'].prefix.include,
+                                   spec['zlib'].prefix.lib),
+            '--enable-install-lite-headers',
             '--enable-fortran' if '+fortran' in spec else '--disable-fortran',
             '--enable-silex' if '+silex' in spec else '--disable-silex',
             '--enable-shared' if '+shared' in spec else '--disable-shared',
@@ -64,14 +63,9 @@ class Silo(Package):
                 'CXXFLAGS={0}'.format(self.compiler.pic_flag),
                 'FCFLAGS={0}'.format(self.compiler.pic_flag)]
 
-        configure(
-            '--prefix=%s' % prefix,
-            '--with-hdf5=%s,%s' % (spec['hdf5'].prefix.include,
-                                   spec['hdf5'].prefix.lib),
-            '--with-zlib=%s,%s' % (spec['zlib'].prefix.include,
-                                   spec['zlib'].prefix.lib),
-            '--enable-install-lite-headers',
-            *config_args)
+        if '+mpi' in spec:
+            config_args.append('CC=%s' % spec['mpi'].mpicc)
+            config_args.append('CXX=%s' % spec['mpi'].mpicxx)
+            config_args.append('FC=%s' % spec['mpi'].mpifc)
 
-        make()
-        make('install')
+        return config_args
diff --git a/var/spack/repos/builtin/packages/simplemoc/package.py b/var/spack/repos/builtin/packages/simplemoc/package.py
index 8f6759b019..49f91dc605 100644
--- a/var/spack/repos/builtin/packages/simplemoc/package.py
+++ b/var/spack/repos/builtin/packages/simplemoc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -33,9 +14,9 @@ class Simplemoc(MakefilePackage):
         light water reactor simulation."""
 
     homepage = "https://github.com/ANL-CESAR/SimpleMOC/"
-    url = "https://github.com/ANL-CESAR/SimpleMOC/archive/master.tar.gz"
+    url = "https://github.com/ANL-CESAR/SimpleMOC/archive/v4.tar.gz"
 
-    version('1.0', 'd8827221a4ae76e9766a32e16d143e60')
+    version('4', sha256='a39906014fdb234c43bf26e1919bdc8a13097788812e0b353a492b8e568816a6')
 
     tags = ['proxy-app']
 
diff --git a/var/spack/repos/builtin/packages/simul/package.py b/var/spack/repos/builtin/packages/simul/package.py
index 7ef8720dc9..e01f2d81da 100644
--- a/var/spack/repos/builtin/packages/simul/package.py
+++ b/var/spack/repos/builtin/packages/simul/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/simulationio/package.py b/var/spack/repos/builtin/packages/simulationio/package.py
index b027f49584..42d945dac0 100644
--- a/var/spack/repos/builtin/packages/simulationio/package.py
+++ b/var/spack/repos/builtin/packages/simulationio/package.py
@@ -1,40 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
 
 class Simulationio(CMakePackage):
     """SimulationIO: Efficient and convenient I/O for large PDE simulations"""
+
     homepage = "https://github.com/eschnett/SimulationIO"
     url      = "https://github.com/eschnett/SimulationIO/archive/version/0.1.0.tar.gz"
+    git      = "https://github.com/eschnett/SimulationIO.git"
 
+    version('develop', branch='master')
     version('1.0.0', '5cbf1d0084eb436d861ffcdd297eaa08')
     version('0.1.0', '00f7dabc08ed1ab77858785ce0809f50')
-    version('develop',
-            git='https://github.com/eschnett/SimulationIO.git', branch='master')
 
     variant('julia', default=False)
     variant('python', default=True)
diff --git a/var/spack/repos/builtin/packages/singularity/package.py b/var/spack/repos/builtin/packages/singularity/package.py
index 810a811d39..838cfe6f3e 100644
--- a/var/spack/repos/builtin/packages/singularity/package.py
+++ b/var/spack/repos/builtin/packages/singularity/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,13 +10,23 @@ class Singularity(AutotoolsPackage):
     """Singularity is a container platform focused on supporting 'Mobility of
        Compute'"""
 
-    homepage = "http://singularity.lbl.gov/"
-    url      = "https://github.com/singularityware/singularity/archive/2.4.tar.gz"
+    homepage = "https://www.sylabs.io/singularity/"
+    url      = "https://github.com/singularityware/singularity/releases/download/2.5.2/singularity-2.5.2.tar.gz"
+    git      = "https://github.com/singularityware/singularity.git"
+
+    # Versions before 2.5.2 suffer from a serious security problem.
+    # https://nvd.nist.gov/vuln/detail/CVE-2018-12021
+    version('develop', branch='master')
+    version('2.6.0', sha256='7c425211a099f6fa6f74037e6e17be58fb5923b0bd11aea745e48ef83c488b49')
+    version('2.5.2', '2edc1a8ac9a4d7d26fba6244f1c5fd95')
 
-    version('2.4', 'd357ce68ef2f8149edd84155731531465dbe74148c37719f87f168fc39384377')
-    version('2.3.1', '292ff7fe3db09c854b8accf42f763f62')
+    depends_on('libarchive', when='@2.5.2:')
+    # these are only needed if we're grabbing the unreleased tree
+    depends_on('m4',       type='build', when='@develop')
+    depends_on('autoconf', type='build', when='@develop')
+    depends_on('automake', type='build', when='@develop')
+    depends_on('libtool',  type='build', when='@develop')
 
-    depends_on('m4',       type='build')
-    depends_on('autoconf', type='build')
-    depends_on('automake', type='build')
-    depends_on('libtool',  type='build')
+    # When installing as root, the copy has to run before chmod runs
+    def install(self, spec, prefix):
+        make('install', parallel=False)
diff --git a/var/spack/repos/builtin/packages/skilion-onedrive/package.py b/var/spack/repos/builtin/packages/skilion-onedrive/package.py
new file mode 100644
index 0000000000..a78d2c8ce5
--- /dev/null
+++ b/var/spack/repos/builtin/packages/skilion-onedrive/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SkilionOnedrive(MakefilePackage):
+    """A complete tool to interact with OneDrive on Linux,
+    developed by Skilion, following the UNIX philosophy."""
+
+    homepage = "https://github.com/skilion/onedrive"
+    url      = "https://github.com/skilion/onedrive/archive/v1.1.1.tar.gz"
+
+    version('1.1.1', sha256='fb51c81ec95c28f3fe3b29e3b7f915e30161bd5f4b14bb53ae5c2233cc1e92e9')
+
+    depends_on('dmd')
+    depends_on('curl')
+    depends_on('sqlite')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        # Generate the version file
+        makefile.filter('.git/HEAD .git/index', '', string=True)
+        makefile.filter('$(shell git describe --tags)',
+                        '{0}'.format(spec.version),
+                        string=True)
+        # Patch sqlite.d https://github.com/skilion/onedrive/issues/392
+        sqlited = FileFilter('src/sqlite.d')
+        sqlited.filter('std.c.stdlib', 'core.stdc.stdlib', String=True)
+
+    def build(self, spec, prefix):
+        make('onedrive', 'DESTDIR={0}'.format(prefix), 'PREFIX=/')
+
+    def install(self, spec, prefix):
+        make('install', 'DESTDIR={0}'.format(prefix), 'PREFIX=/')
diff --git a/var/spack/repos/builtin/packages/sleef/package.py b/var/spack/repos/builtin/packages/sleef/package.py
new file mode 100644
index 0000000000..2375766582
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sleef/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sleef(CMakePackage):
+    """SIMD Library for Evaluating Elementary Functions,
+    vectorized libm and DFT."""
+
+    homepage = "http://sleef.org"
+    url      = "https://github.com/shibatch/sleef/archive/3.2.tar.gz"
+
+    version('3.2', '459215058f2c8d55cd2b644d56c8c4f0')
diff --git a/var/spack/repos/builtin/packages/slepc/package.py b/var/spack/repos/builtin/packages/slepc/package.py
index ac8df77d50..cb79b37acf 100644
--- a/var/spack/repos/builtin/packages/slepc/package.py
+++ b/var/spack/repos/builtin/packages/slepc/package.py
@@ -1,53 +1,43 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
+import sys
 from spack import *
 
 
 class Slepc(Package):
-    """
-    Scalable Library for Eigenvalue Problem Computations.
-    """
+    """Scalable Library for Eigenvalue Problem Computations."""
 
     homepage = "http://www.grycap.upv.es/slepc"
-    url = "http://slepc.upv.es/download/distrib/slepc-3.6.2.tar.gz"
+    url      = "http://slepc.upv.es/download/distrib/slepc-3.6.2.tar.gz"
+    git      = "https://bitbucket.org/slepc/slepc.git"
 
+    version('develop', branch='master')
+    version('3.10.1', 'f64787c8c2ab3d2f6db3c67d2bfe6ee84f741ce3dfde1d2f8221e131820a12a1')
+    version('3.10.0', '069d7a579995e0be1567c5bc869251e29c00044369a786933ca3040149d0412a')
+    version('3.9.2', '247585b3f8c10bf50b9464cb8ef7b5f22bead6f96524384897a37ec4146eb03e')
+    version('3.9.1', 'e174ea7c127d9161eef976b0288f0c56d443a58d6ab2dc8af1e8bd66f156ce17')
+    version('3.9.0', '1f3930db56b4065aaf214ea758ddff1a70bf19d45544cbdfd19d2787db4bfe0b')
+    version('3.8.2', '1e7d20d20eb26da307d36017461fe4a55f40e947e232739179dbe6412e22ed13')
     version('3.8.0', 'c58ccc4e852d1da01112466c48efa41f0839649f3a265925788237d76cd3d963')
     version('3.7.4', '2fb782844e3bc265a8d181c3c3e2632a4ca073111c874c654f1365d33ca2eb8a')
     version('3.7.3', '3ef9bcc645a10c1779d56b3500472ceb66df692e389d635087d30e7c46424df9')
     version('3.7.1', '670216f263e3074b21e0623c01bc0f562fdc0bffcd7bd42dd5d8edbe73a532c2')
     version('3.6.3', '384939d009546db37bc05ed81260c8b5ba451093bf891391d32eb7109ccff876')
     version('3.6.2', '2ab4311bed26ccf7771818665991b2ea3a9b15f97e29fd13911ab1293e8e65df')
-    version('develop', git='https://bitbucket.org/slepc/slepc.git')
 
     variant('arpack', default=True, description='Enables Arpack wrappers')
+    variant('blopex', default=False, description='Enables BLOPEX wrappers')
 
     # NOTE: make sure PETSc and SLEPc use the same python.
     depends_on('python@2.6:2.8', type='build')
     # Cannot mix release and development versions of SLEPc and PETSc:
     depends_on('petsc@develop', when='@develop')
+    depends_on('petsc@3.10:3.10.99', when='@3.10:3.10.99')
+    depends_on('petsc@3.9:3.9.99', when='@3.9:3.9.99')
     depends_on('petsc@3.8:3.8.99', when='@3.8:3.8.99')
     depends_on('petsc@3.7:3.7.7', when='@3.7.1:3.7.4')
     depends_on('petsc@3.6.3:3.6.4', when='@3.6.2:3.6.3')
@@ -59,6 +49,13 @@ class Slepc(Package):
     # Arpack can not be used with 64bit integers.
     conflicts('+arpack', when='^petsc+int64')
 
+    resource(name='blopex',
+             url='http://slepc.upv.es/download/external/blopex-1.1.2.tar.gz',
+             sha256='0081ee4c4242e635a8113b32f655910ada057c59043f29af4b613508a762f3ac',
+             destination=join_path('installed-arch-' + sys.platform + '-c-opt',
+                                   'externalpackages'),
+             when='+blopex')
+
     def install(self, spec, prefix):
         # set SLEPC_DIR for installation
         # Note that one should set the current (temporary) directory instead
@@ -80,6 +77,11 @@ class Slepc(Package):
                     '--with-arpack-flags=-lparpack,-larpack'
                 ])
 
+        # It isn't possible to install BLOPEX separately and link to it;
+        # BLOPEX has to be downloaded with SLEPc at configure time
+        if '+blopex' in spec:
+            options.append('--download-blopex')
+
         configure('--prefix=%s' % prefix, *options)
 
         make('MAKE_NP=%s' % make_jobs, parallel=False)
diff --git a/var/spack/repos/builtin/packages/slurm/package.py b/var/spack/repos/builtin/packages/slurm/package.py
index ac0d6f2610..afa3fc27db 100644
--- a/var/spack/repos/builtin/packages/slurm/package.py
+++ b/var/spack/repos/builtin/packages/slurm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -43,6 +24,8 @@ class Slurm(AutotoolsPackage):
     homepage = 'https://slurm.schedmd.com'
     url = 'https://github.com/SchedMD/slurm/archive/slurm-17-02-6-1.tar.gz'
 
+    version('18-08-0-1', sha256='62129d0f2949bc8a68ef86fe6f12e0715cbbf42f05b8da6ef7c3e7e7240b50d9')
+    version('17-11-9-2', sha256='6e34328ed68262e776f524f59cca79ac75bcd18030951d45ea545a7ba4c45906')
     version('17-02-6-1', '8edbb9ad41819464350d9de013367020')
 
     variant('gtk', default=False, description='Enable GTK+ support')
@@ -64,11 +47,11 @@ class Slurm(AutotoolsPackage):
     depends_on('lz4')
     depends_on('munge')
     depends_on('openssl')
-    depends_on('pkg-config', type='build')
-    depends_on('readline')
+    depends_on('pkgconfig', type='build')
+    depends_on('readline', when='+readline')
     depends_on('zlib')
 
-    depends_on('gtkplus+X', when='+gtk')
+    depends_on('gtkplus', when='+gtk')
     depends_on('hdf5', when='+hdf5')
     depends_on('hwloc', when='+hwloc')
     depends_on('mariadb', when='+mariadb')
@@ -89,9 +72,7 @@ class Slurm(AutotoolsPackage):
         if '~gtk' in spec:
             args.append('--disable-gtktest')
 
-        if '+readline' in spec:
-            args.append('--with-readline={0}'.format(spec['readline'].prefix))
-        else:
+        if '~readline' in spec:
             args.append('--without-readline')
 
         if '+hdf5' in spec:
diff --git a/var/spack/repos/builtin/packages/smalt/package.py b/var/spack/repos/builtin/packages/smalt/package.py
index 4c65afe20d..23466e0fd1 100644
--- a/var/spack/repos/builtin/packages/smalt/package.py
+++ b/var/spack/repos/builtin/packages/smalt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/smc/package.py b/var/spack/repos/builtin/packages/smc/package.py
deleted file mode 100644
index 353e5f46b9..0000000000
--- a/var/spack/repos/builtin/packages/smc/package.py
+++ /dev/null
@@ -1,83 +0,0 @@
-##############################################################################
-# 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/spack/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 glob
-
-
-class Smc(MakefilePackage):
-    """A minimalist high-order finite difference algorithm
-    for combustion problems. It includes core discretizations
-    for advection, diffusive transport and chemical kinetics.
-    The models for computing diffusive transport coefficients
-    have been replaced by a simplified approximation
-    but the full structure of the discretization of
-    the diffusive terms have been preserved."""
-
-    homepage = "https://ccse.lbl.gov/ExaCT/index.html"
-    url      = "https://ccse.lbl.gov/ExaCT/SMC.tar.gz"
-    tags     = ['proxy-app']
-
-    version('master', '94a4ea94abbc5e61397c2a4d1fb56ed6')
-
-    variant(
-        'mpi', default=True,
-        description='Build with MPI support')
-    variant(
-        'openmp', default=True,
-        description='Build with OpenMP support')
-    variant(
-        'debug', default=False,
-        description='Build with debugging')
-#   variant(
-#       'mic', default=False,
-#       description='Compile for Intel Xeon Phi')
-    variant(
-        'k_use_automatic', default=True,
-        description='Some arrays in kernels.F90 will be automatic')
-
-    depends_on('mpi', when='+mpi')
-    depends_on('gmake', type='build')
-
-    def edit(self, spec, prefix):
-        makefile = FileFilter('GNUmakefile')
-        if '~mpi' in spec:
-            makefile.filter('MPI := t', '#')
-        if '~openmp' in spec:
-            makefile.filter('OMP := t', '#')
-        if '+debug' in spec:
-            makefile.filter('NDEBUG :=', '#')
-        if '~k_use_automatic' in spec:
-            makefile.filter('K_U.*:= t', '#')
-        if self.compiler.name == 'intel':
-            makefile.filter('COMP := .*', 'COMP := Intel')
-
-    def install(self, spec, prefix):
-        mkdirp(prefix.bin)
-        files = glob.glob(join_path(self.build_directory, '*.exe'))
-        for f in files:
-            install(f, prefix.bin)
-        install('inputs_SMC', prefix.bin)
-        install('README', prefix)
-        install('BoxLib.license.txt', prefix)
diff --git a/var/spack/repos/builtin/packages/smproxy/package.py b/var/spack/repos/builtin/packages/smproxy/package.py
index 571b25d4b6..bc4f943244 100644
--- a/var/spack/repos/builtin/packages/smproxy/package.py
+++ b/var/spack/repos/builtin/packages/smproxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Smproxy(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxmu')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/snakemake/package.py b/var/spack/repos/builtin/packages/snakemake/package.py
index d97dc47442..3c55b55ec6 100644
--- a/var/spack/repos/builtin/packages/snakemake/package.py
+++ b/var/spack/repos/builtin/packages/snakemake/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/snap-berkeley/package.py b/var/spack/repos/builtin/packages/snap-berkeley/package.py
index a6b1e08c47..4f7865ceca 100644
--- a/var/spack/repos/builtin/packages/snap-berkeley/package.py
+++ b/var/spack/repos/builtin/packages/snap-berkeley/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/snap-korf/package.py b/var/spack/repos/builtin/packages/snap-korf/package.py
index 68fb4c61ae..840d2ccefb 100644
--- a/var/spack/repos/builtin/packages/snap-korf/package.py
+++ b/var/spack/repos/builtin/packages/snap-korf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
diff --git a/var/spack/repos/builtin/packages/snap/package.py b/var/spack/repos/builtin/packages/snap/package.py
index 7bc88b812f..8695a9efbf 100644
--- a/var/spack/repos/builtin/packages/snap/package.py
+++ b/var/spack/repos/builtin/packages/snap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,10 +15,11 @@ class Snap(MakefilePackage):
     It is modeled off the Los Alamos National Laboratory code PARTISN."""
 
     homepage = "https://github.com/lanl/SNAP"
-    url      = ""
-    tags     = ['proxy-app']
+    git      = "https://github.com/lanl/SNAP.git"
+
+    tags = ['proxy-app']
 
-    version('master', git='https://github.com/lanl/SNAP.git')
+    version('master')
 
     variant('openmp', default=False, description='Build with OpenMP support')
     variant('opt', default=True, description='Build with debugging')
diff --git a/var/spack/repos/builtin/packages/snappy/link_gtest.patch b/var/spack/repos/builtin/packages/snappy/link_gtest.patch
new file mode 100644
index 0000000000..7a95b77036
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snappy/link_gtest.patch
@@ -0,0 +1,11 @@
+--- a/CMakeLists.txt	2018-09-03 14:25:32.390110709 +0200
++++ b/CMakeLists.txt	2018-09-03 14:24:16.198182317 +0200
+@@ -118,7 +118,7 @@
+       "${PROJECT_SOURCE_DIR}/snappy-test.cc"
+   )
+   target_compile_definitions(snappy_unittest PRIVATE -DHAVE_CONFIG_H)
+-  target_link_libraries(snappy_unittest snappy ${GFLAGS_LIBRARIES})
++  target_link_libraries(snappy_unittest snappy ${GFLAGS_LIBRARIES} ${GTEST_LIBRARIES})
+ 
+   if(HAVE_LIBZ)
+     target_link_libraries(snappy_unittest z)
diff --git a/var/spack/repos/builtin/packages/snappy/package.py b/var/spack/repos/builtin/packages/snappy/package.py
index a023b2ee95..23845a4079 100644
--- a/var/spack/repos/builtin/packages/snappy/package.py
+++ b/var/spack/repos/builtin/packages/snappy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,6 +15,11 @@ class Snappy(CMakePackage):
     version('1.1.7', 'ee9086291c9ae8deb4dac5e0b85bf54a')
 
     variant('shared', default=True, description='Build shared libraries')
+    variant('pic', default=True, description='Build position independent code')
+
+    depends_on('googletest', type='test')
+
+    patch('link_gtest.patch')
 
     def cmake_args(self):
         spec = self.spec
@@ -42,11 +28,19 @@ class Snappy(CMakePackage):
             '-DCMAKE_INSTALL_LIBDIR:PATH={0}'.format(
                 self.prefix.lib),
             '-DBUILD_SHARED_LIBS:BOOL={0}'.format(
-                'ON' if '+shared' in spec else 'OFF')
+                'ON' if '+shared' in spec else 'OFF'),
+            '-DSNAPPY_BUILD_TESTS:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF')
         ]
 
         return args
 
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if '+pic' in self.spec and name in ('cflags', 'cxxflags'):
+            flags.append(self.compiler.pic_flag)
+        return (None, None, flags)
+
     @run_after('install')
     def install_pkgconfig(self):
         mkdirp(self.prefix.lib.pkgconfig)
diff --git a/var/spack/repos/builtin/packages/snbone/package.py b/var/spack/repos/builtin/packages/snbone/package.py
index eb493d9a16..8e112ebdba 100644
--- a/var/spack/repos/builtin/packages/snbone/package.py
+++ b/var/spack/repos/builtin/packages/snbone/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,9 +12,9 @@ class Snbone(MakefilePackage):
        continuous finite element based transport equation solver."""
 
     homepage = "https://github.com/ANL-CESAR/"
-    url = "https://github.com/ANL-CESAR/SNbone.git"
+    git      = "https://github.com/ANL-CESAR/SNbone.git"
 
-    version('develop', git='https://github.com/ANL-CESAR/SNbone.git')
+    version('develop')
 
     tags = ['proxy-app']
 
@@ -50,7 +31,9 @@ class Snbone(MakefilePackage):
                 elif self.compiler.name == 'intel':
                     make('COMPILER=intel', 'LDFLAGS=-lm')
                 else:
-                    make('COMPILER=gfortran', 'LDFLAGS=-lm')
+                    # older gcc need link libs after objs, but
+                    # LDFLAGS is in the front, so use IBMLIB instead
+                    make('COMPILER=gfortran', 'IBMLIB=-lm')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin.C)
diff --git a/var/spack/repos/builtin/packages/sniffles/package.py b/var/spack/repos/builtin/packages/sniffles/package.py
index caa6591a5e..0d498be646 100644
--- a/var/spack/repos/builtin/packages/sniffles/package.py
+++ b/var/spack/repos/builtin/packages/sniffles/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,7 @@ class Sniffles(CMakePackage):
     homepage = "https://github.com/fritzsedlazeck/Sniffles/wiki"
     url      = "https://github.com/fritzsedlazeck/Sniffles/archive/v1.0.5.tar.gz"
 
+    version('1.0.7', '83bd93c5ab5dad3a6dc776f11d3a880e')
     version('1.0.5', 'c2f2350d00418ba4d82c074e7f0b1832')
 
     # the build process doesn't actually install anything, do it by hand
diff --git a/var/spack/repos/builtin/packages/snpeff/SnpSift.sh b/var/spack/repos/builtin/packages/snpeff/SnpSift.sh
new file mode 100644
index 0000000000..3422a77914
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snpeff/SnpSift.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the SnpSift jar file
+java -jar SnpSift.jar "$@"
diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py
new file mode 100644
index 0000000000..81e7147d20
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snpeff/package.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os.path
+
+
+class Snpeff(Package):
+    """SnpEff is a variant annotation and effect prediction tool. It
+    annotates and predicts the effects of genetic variants (such as
+    amino acid changes)."""
+
+    homepage = "http://snpeff.sourceforge.net/"
+    url      = "https://kent.dl.sourceforge.net/project/snpeff/snpEff_latest_core.zip"
+
+    version('2017-11-24', '1fa84a703580a423e27f1e14a945901c')
+
+    depends_on('jdk', type=('build', 'run'))
+
+    def install(self, spec, prefix):
+        install_tree('snpEff', prefix.bin)
+
+        # Set up a helper script to call java on the jar files,
+        # explicitly codes the path for java and the jar files.
+        scripts = ['snpEff', 'SnpSift']
+
+        for script in scripts:
+            script_sh = join_path(os.path.dirname(__file__), script + ".sh")
+            script_path = join_path(prefix.bin, script)
+            install(script_sh, script_path)
+            set_executable(script_path)
+
+            # Munge the helper script to explicitly point to java and the
+            # jar file.
+            java = self.spec['java'].prefix.bin.java
+            kwargs = {'backup': False}
+            filter_file('^java', java, script_path, **kwargs)
+            filter_file(script + '.jar',
+                        join_path(prefix.bin, script + '.jar'),
+                        script_path, **kwargs)
diff --git a/var/spack/repos/builtin/packages/snpeff/snpEff.sh b/var/spack/repos/builtin/packages/snpeff/snpEff.sh
new file mode 100644
index 0000000000..7bee480e2e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snpeff/snpEff.sh
@@ -0,0 +1,3 @@
+#!/bin/sh
+# convenience wrapper for the snpEff jar file
+java -jar snpEff.jar "$@"
diff --git a/var/spack/repos/builtin/packages/snphylo/package.py b/var/spack/repos/builtin/packages/snphylo/package.py
new file mode 100644
index 0000000000..d249af2e65
--- /dev/null
+++ b/var/spack/repos/builtin/packages/snphylo/package.py
@@ -0,0 +1,37 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Snphylo(Package):
+    """A pipeline to generate a phylogenetic tree from huge SNP data"""
+
+    homepage = "http://chibba.pgml.uga.edu/snphylo/"
+    url      = "http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz"
+
+    version('2016-02-04', '467660814965bc9bed6c020c05c0d3a6')
+
+    depends_on('python', type=('build', 'run'))
+    depends_on('r', type=('build', 'run'))
+    depends_on('r-phangorn', type=('build', 'run'))
+    depends_on('r-gdsfmt', type=('build', 'run'))
+    depends_on('r-snprelate', type=('build', 'run'))
+    depends_on('r-getopt', type=('build', 'run'))
+    depends_on('muscle')
+    depends_on('phylip')
+
+    def install(self, spec, prefix):
+        install_answer = ['y', 'y', 'y', 'y']
+        install_answer_input = 'spack-config.in'
+        with open(install_answer_input, 'w') as f:
+            f.writelines(install_answer)
+        with open(install_answer_input, 'r') as f:
+            bash = which('bash')
+            bash('./setup.sh', input=f)
+            install_tree('.', prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.spec.prefix)
diff --git a/var/spack/repos/builtin/packages/snptest/package.py b/var/spack/repos/builtin/packages/snptest/package.py
index 57a49c5bec..a348c9fefd 100644
--- a/var/spack/repos/builtin/packages/snptest/package.py
+++ b/var/spack/repos/builtin/packages/snptest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/soap2/package.py b/var/spack/repos/builtin/packages/soap2/package.py
index 9b34e35320..20b71eb57e 100644
--- a/var/spack/repos/builtin/packages/soap2/package.py
+++ b/var/spack/repos/builtin/packages/soap2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/soapdenovo-trans/package.py b/var/spack/repos/builtin/packages/soapdenovo-trans/package.py
new file mode 100644
index 0000000000..f837ce94ea
--- /dev/null
+++ b/var/spack/repos/builtin/packages/soapdenovo-trans/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SoapdenovoTrans(MakefilePackage):
+    """SOAPdenovo-Trans is a de novo transcriptome assembler basing on the
+       SOAPdenovo framework, adapt to alternative splicing and different
+       expression level among transcripts."""
+
+    homepage = "http://soap.genomics.org.cn/SOAPdenovo-Trans.html"
+    url      = "https://github.com/aquaskyline/SOAPdenovo-Trans/archive/1.0.4.tar.gz"
+
+    version('1.0.4', 'a3b00b0f743b96141c4d5f1b49f2918c')
+
+    build_directory = 'src'
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            makefile = FileFilter('Makefile')
+            makefile.filter('CFLAGS=         -O3 -fomit-frame-pointer -static',
+                            'CFLAGS=         -O3 -fomit-frame-pointer')
+
+    def build(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make()
+            make('127mer=1', parallel=False)
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/soapdenovo2/package.py b/var/spack/repos/builtin/packages/soapdenovo2/package.py
new file mode 100644
index 0000000000..d64116e359
--- /dev/null
+++ b/var/spack/repos/builtin/packages/soapdenovo2/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Soapdenovo2(MakefilePackage):
+    """SOAPdenovo is a novel short-read assembly method that can build a de
+       novo draft assembly for the human-sized genomes. The program is
+       specially designed to assemble Illumina GA short reads. It creates
+       new opportunities for building reference sequences and carrying out
+       accurate analyses of unexplored genomes in a cost effective way."""
+
+    homepage = "https://github.com/aquaskyline/SOAPdenovo2"
+    url      = "https://github.com/aquaskyline/SOAPdenovo2/archive/r240.tar.gz"
+
+    version('240', '3bc6b63edf87bb47874bb6f126e43cd4')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('SOAPdenovo-63mer', prefix.bin)
+        install('SOAPdenovo-127mer', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/soapindel/package.py b/var/spack/repos/builtin/packages/soapindel/package.py
index 1a6bd4ff8d..56dafc5c12 100644
--- a/var/spack/repos/builtin/packages/soapindel/package.py
+++ b/var/spack/repos/builtin/packages/soapindel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/soapsnp/package.py b/var/spack/repos/builtin/packages/soapsnp/package.py
index 34c56eebb2..6908ba491a 100644
--- a/var/spack/repos/builtin/packages/soapsnp/package.py
+++ b/var/spack/repos/builtin/packages/soapsnp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sofa-c/package.py b/var/spack/repos/builtin/packages/sofa-c/package.py
new file mode 100644
index 0000000000..ec5d52c29b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sofa-c/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SofaC(MakefilePackage):
+    "Standards of Fundamental Astronomy (SOFA) library for ANSI C."
+
+    homepage = "http://www.iausofa.org/current_C.html"
+    url      = "http://www.iausofa.org/2018_0130_C/sofa_c-20180130.tar.gz"
+
+    version('20180130', '9d6903c7690e84a788b622fba6f10146')
+
+    @property
+    def build_directory(self):
+        return join_path(self.version, 'c', 'src')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter(join_path(self.build_directory, 'makefile'))
+        makefile.filter('CCOMPC = gcc', 'CCOMPC = {0}'.format(spack_cc))
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            mkdir(prefix.include)
+            install('sofa.h', prefix.include)
+            install('sofam.h', prefix.include)
+            mkdir(prefix.lib)
+            install('libsofa_c.a', prefix.lib)
diff --git a/var/spack/repos/builtin/packages/somatic-sniper/package.py b/var/spack/repos/builtin/packages/somatic-sniper/package.py
index 40c66af214..23c542bc52 100644
--- a/var/spack/repos/builtin/packages/somatic-sniper/package.py
+++ b/var/spack/repos/builtin/packages/somatic-sniper/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sortmerna/package.py b/var/spack/repos/builtin/packages/sortmerna/package.py
index bd3136162b..a24d92eba8 100644
--- a/var/spack/repos/builtin/packages/sortmerna/package.py
+++ b/var/spack/repos/builtin/packages/sortmerna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,9 +11,9 @@ class Sortmerna(CMakePackage):
        reads in metatranscriptomic and metagenomic data"""
 
     homepage = "https://github.com/biocore/sortmerna"
-    url      = "https://github.com/biocore/sortmerna"
+    git      = "https://github.com/biocore/sortmerna.git"
 
-    version('2017-07-13', git='https://github.com/biocore/sortmerna.git', commit='8bde6fa113a5d99a23ae81b48eeea6760e966094')
+    version('2017-07-13', commit='8bde6fa113a5d99a23ae81b48eeea6760e966094')
 
     depends_on('zlib')
 
diff --git a/var/spack/repos/builtin/packages/sosflow/package.py b/var/spack/repos/builtin/packages/sosflow/package.py
index c3b99fd479..1100794493 100644
--- a/var/spack/repos/builtin/packages/sosflow/package.py
+++ b/var/spack/repos/builtin/packages/sosflow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,12 +12,14 @@ class Sosflow(CMakePackage):
     observation, introspection, feedback, and control of HPC applications."""
 
     homepage = "https://github.com/cdwdirect/sos_flow/wiki"
-    url      = "https://github.com/cdwdirect/sos_flow.git"
+    git      = "https://github.com/cdwdirect/sos_flow.git"
 
-    version('spack', git='https://github.com/cdwdirect/sos_flow.git', tag='spack-build-v0.9901')
+    version('spack', tag='spack-build-v0.9901')
 
     depends_on('libevpath')
     depends_on('sqlite@3:')
+    depends_on('pkgconfig')
+    depends_on('mpi')
 
     def setup_environment(self, spack_env, run_env):
         spack_env.set('SOS_HOST_KNOWN_AS', 'SPACK-SOS-BUILD')
diff --git a/var/spack/repos/builtin/packages/sowing/package.py b/var/spack/repos/builtin/packages/sowing/package.py
index 668038255b..59ae89b841 100644
--- a/var/spack/repos/builtin/packages/sowing/package.py
+++ b/var/spack/repos/builtin/packages/sowing/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,6 +15,7 @@ class Sowing(AutotoolsPackage):
     homepage = "http://www.mcs.anl.gov/petsc/index.html"
     url = "http://ftp.mcs.anl.gov/pub/petsc/externalpackages/sowing-1.1.23-p1.tar.gz"
 
+    version('1.1.25-p1', 'fc5e5664b80e606ad71ba9b85f4c86b9')
     version('1.1.23-p1', '65aaf3ae2a4c0f30d532fec291702e16')
 
     def build(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/sox/package.py b/var/spack/repos/builtin/packages/sox/package.py
index 64c9803d52..d36222e23c 100644
--- a/var/spack/repos/builtin/packages/sox/package.py
+++ b/var/spack/repos/builtin/packages/sox/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spades/package.py b/var/spack/repos/builtin/packages/spades/package.py
index 0748ef0618..ee96794523 100644
--- a/var/spack/repos/builtin/packages/spades/package.py
+++ b/var/spack/repos/builtin/packages/spades/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,12 +13,17 @@ class Spades(CMakePackage):
     homepage = "http://cab.spbu.ru/software/spades/"
     url      = "http://cab.spbu.ru/files/release3.10.1/SPAdes-3.10.1.tar.gz"
 
+    version('3.12.0', '15b48a3bcbbe6a8ad58fd04ba5d3f1015990fbfd9bdf4913042803b171853ac7')
+    version('3.11.1', '478677b560e2f98db025e8efd5245cdf')
     version('3.10.1', 'dcab7d145af81b59cc867562f27536c3')
 
     depends_on('python', type=('build', 'run'))
     depends_on('zlib')
     depends_on('bzip2')
 
-    conflicts('%gcc@7.1.0:')
+    # SPAdes will explicitly not compile with gcc < 5.3.0
+    conflicts('%gcc@:5.2.9')
+
+    conflicts('%gcc@7.1.0:', when='@:3.10.1')
 
     root_cmakelists_dir = 'src'
diff --git a/var/spack/repos/builtin/packages/span-lite/package.py b/var/spack/repos/builtin/packages/span-lite/package.py
new file mode 100644
index 0000000000..2ec1ede756
--- /dev/null
+++ b/var/spack/repos/builtin/packages/span-lite/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from shutil import copytree
+
+
+class SpanLite(Package):
+    """
+    A single-file header-only version of a C++20-like span for C++98, C++11 and
+    later
+    """
+
+    homepage = "https://github.com/martinmoene/span-lite"
+    url      = "https://github.com/martinmoene/span-lite/archive/v0.3.0.tar.gz"
+
+    version('0.3.0', sha256='e083f368167fe632f866956edaa2c7a7d57a33ffb0d8def9b9f1a9daa47834bb')
+    version('0.2.0', sha256='6e3305fe868442410a00962a39fc59ed494cecc4f99fe2aff187e33932f06e46')
+    version('0.1.0', sha256='0a84b9369f86beba326e2160b683fd0922f416ce136437751a9ed70afcc67a1c')
+
+    def install(self, spec, prefix):
+        copytree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py
index 9d7f793803..4ccfbbf4cb 100644
--- a/var/spack/repos/builtin/packages/spark/package.py
+++ b/var/spack/repos/builtin/packages/spark/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import re
-import shutil
 
 from spack import *
 
@@ -42,6 +22,7 @@ class Spark(Package):
     depends_on('java', type=('build', 'run'))
     depends_on('hadoop', when='+hadoop', type=('build', 'run'))
 
+    version('2.3.0', 'db21021b8e877b219ab886097ef42344')
     version('2.1.0', '21d4471e78250775b1fa7c0e6c3a1326')
     version('2.0.2', '32110c1bb8f081359738742bd26bced1')
     version('2.0.0', '8a5307d973da6949a385aefb6ff747bb')
@@ -63,15 +44,12 @@ class Spark(Package):
         install_dir('yarn')
 
         # required for spark to recognize binary distribution
-        shutil.copy('RELEASE', prefix)
+        install('RELEASE', prefix)
 
     @when('+hadoop')
     def setup_environment(self, spack_env, run_env):
-
-        env['JAVA_HOME'] = self.spec['java'].prefix
-        # spack_env.set('JAVA_HOME', self.spec['jdk'].prefix)
-
         hadoop = self.spec['hadoop'].command
+        hadoop.add_default_env('JAVA_HOME', self.spec['java'].home)
         hadoop_classpath = hadoop('classpath', output=str)
 
         # Remove whitespaces, as they can compromise syntax in
diff --git a/var/spack/repos/builtin/packages/sparsehash/package.py b/var/spack/repos/builtin/packages/sparsehash/package.py
index 1d8b870bd5..6093db83b7 100644
--- a/var/spack/repos/builtin/packages/sparsehash/package.py
+++ b/var/spack/repos/builtin/packages/sparsehash/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sparta/package.py b/var/spack/repos/builtin/packages/sparta/package.py
index cfe6658f3b..1b3bbfe55b 100644
--- a/var/spack/repos/builtin/packages/sparta/package.py
+++ b/var/spack/repos/builtin/packages/sparta/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spdlog/package.py b/var/spack/repos/builtin/packages/spdlog/package.py
index 9d952728db..c669d99257 100644
--- a/var/spack/repos/builtin/packages/spdlog/package.py
+++ b/var/spack/repos/builtin/packages/spdlog/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,6 +12,20 @@ class Spdlog(CMakePackage):
     homepage = "https://github.com/gabime/spdlog"
     url = "https://github.com/gabime/spdlog/archive/v0.9.0.tar.gz"
 
+    version('1.2.1', sha256='867a4b7cedf9805e6f76d3ca41889679054f7e5a3b67722fe6d0eae41852a767')
+    version('1.2.0', sha256='0ba31b9e7f8e43a7be328ab0236d57810e5d4fc8a1a7842df665ae22d5cbd128')
+    version('1.1.0',  sha256='3dbcbfd8c07e25f5e0d662b194d3a7772ef214358c49ada23c044c4747ce8b19')
+    version('1.0.0',  sha256='90d5365121bcd2c41ce94dfe6a460e89507a2dfef6133fe5fad5bb35ac4ef0a1')
+    version('0.17.0', sha256='94f74fd1b3344733d1db3de2ec22e6cbeb769f93a8baa0d4a22b1f62dc7369f8')
+    version('0.16.3', sha256='b88d7be261d9089c817fc8cee6c000d69f349b357828e4c7f66985bc5d5360b8')
+    version('0.16.2', sha256='2081e5df5e87402398847431e16b87c71dd5c4d632314bb976ace8161f4d32de')
+    version('0.16.1', sha256='733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae')
+    version('0.16.0', sha256='9e64e3b10c2a3c54dfff63aa056057cf1db8a5fd506b3d9cf77207511820baac')
+    version('0.14.0', sha256='eb5beb4e53f4bfff5b32eb4db8588484bdc15a17b90eeefef3a9fc74fec1d83d')
+    version('0.13.0', sha256='d798a6ca19165f0a18a43938859359269f5a07fd8e0eb83ab8674739c9e8f361')
+    version('0.12.0', sha256='5cfd6a0b3182a88e1eb35bcb65a7ef9035140d7c73b16ba6095939dbf07325b9')
     version('0.11.0', '08232203f18a6f9ff47e083cc7a141a050805d3b')
     version('0.10.0', '57b471ef97a23cc29c38b62e00e89a411a87ea7f')
     version('0.9.0', 'dda741ef8e12d57d91f778d85e95a27d84a82ac4')
+
+    depends_on('cmake@3.1:', type='build')
diff --git a/var/spack/repos/builtin/packages/spectrum-mpi/package.py b/var/spack/repos/builtin/packages/spectrum-mpi/package.py
index c2b08c0086..c700f67285 100644
--- a/var/spack/repos/builtin/packages/spectrum-mpi/package.py
+++ b/var/spack/repos/builtin/packages/spectrum-mpi/package.py
@@ -1,38 +1,15 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at International Business Machines Corporation
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# This file is part of Spack.
-# Created by Serban Maerean, serban@us.ibm.gov, All rights reserved.
-# LLNL-CODE-647188
-#
-# For details, see https://github.com/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class SpectrumMpi(Package):
-    """
-    IBM MPI implementation from Spectrum MPI.
-
-    """
+    """IBM MPI implementation from Spectrum MPI."""
 
     homepage = "http://www-03.ibm.com/systems/spectrum-computing/products/mpi"
-    url = "http://www-03.ibm.com/systems/spectrum-computing/products/mpi"
 
     provides('mpi')
 
@@ -46,6 +23,11 @@ class SpectrumMpi(Package):
             self.spec.mpicxx = join_path(self.prefix.bin, 'mpixlC')
             self.spec.mpif77 = join_path(self.prefix.bin, 'mpixlf')
             self.spec.mpifc = join_path(self.prefix.bin, 'mpixlf')
+        elif '%pgi' in dependent_spec:
+            self.spec.mpicc = join_path(self.prefix.bin, 'mpipgicc')
+            self.spec.mpicxx = join_path(self.prefix.bin, 'mpipgic++')
+            self.spec.mpif77 = join_path(self.prefix.bin, 'mpipgifort')
+            self.spec.mpifc = join_path(self.prefix.bin, 'mpipgifort')
         else:
             self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
             self.spec.mpicxx = join_path(self.prefix.bin, 'mpicxx')
@@ -58,6 +40,11 @@ class SpectrumMpi(Package):
             spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpixlC'))
             spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpixlf'))
             spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpixlf'))
+        elif '%pgi' in dependent_spec:
+            spack_env.set('MPICC', join_path(self.prefix.bin, 'mpipgicc'))
+            spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpipgic++'))
+            spack_env.set('MPIF77', join_path(self.prefix.bin, 'mpipgifort'))
+            spack_env.set('MPIF90', join_path(self.prefix.bin, 'mpipgifort'))
         else:
             spack_env.set('MPICC', join_path(self.prefix.bin, 'mpicc'))
             spack_env.set('MPICXX', join_path(self.prefix.bin, 'mpic++'))
@@ -68,3 +55,5 @@ class SpectrumMpi(Package):
         spack_env.set('OMPI_CXX', spack_cxx)
         spack_env.set('OMPI_FC', spack_fc)
         spack_env.set('OMPI_F77', spack_f77)
+
+        spack_env.prepend_path('LD_LIBRARY_PATH', self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/speex/package.py b/var/spack/repos/builtin/packages/speex/package.py
index 6e0f50feec..51816e337a 100644
--- a/var/spack/repos/builtin/packages/speex/package.py
+++ b/var/spack/repos/builtin/packages/speex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spglib/fix_cmake_install.patch b/var/spack/repos/builtin/packages/spglib/fix_cmake_install.patch
new file mode 100644
index 0000000000..d7451460db
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spglib/fix_cmake_install.patch
@@ -0,0 +1,25 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 3296d91..d18d26c 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -47,17 +47,17 @@ set(SOURCES ${PROJECT_SOURCE_DIR}/src/arithmetic.c
+ add_library(symspg SHARED ${SOURCES})
+ set_property(TARGET symspg PROPERTY VERSION ${serial})
+ set_property(TARGET symspg PROPERTY SOVERSION ${soserial})
+-install(TARGETS symspg LIBRARY DESTINATION ${PROJECT_SOURCE_DIR}/lib)
++install(TARGETS symspg LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
+ 
+ # Static link library
+ add_library(symspg_static STATIC ${SOURCES})
+ set_property(TARGET symspg_static PROPERTY VERSION ${serial})
+ set_property(TARGET symspg_static PROPERTY SOVERSION ${soserial})
+ set_property(TARGET symspg_static PROPERTY OUTPUT_NAME symspg)
+-install(TARGETS symspg_static ARCHIVE DESTINATION ${PROJECT_SOURCE_DIR}/lib)
++install(TARGETS symspg_static ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib)
+ 
+ # Header file
+-install(FILES ${PROJECT_SOURCE_DIR}/src/spglib.h DESTINATION ${PROJECT_SOURCE_DIR}/include)
++install(FILES ${PROJECT_SOURCE_DIR}/src/spglib.h DESTINATION ${CMAKE_INSTALL_PREFIX}/include)
+ 
+ # make check
+ enable_testing()
diff --git a/var/spack/repos/builtin/packages/spglib/fix_cpp.patch b/var/spack/repos/builtin/packages/spglib/fix_cpp.patch
new file mode 100644
index 0000000000..9ab4c9bffe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spglib/fix_cpp.patch
@@ -0,0 +1,34 @@
+From a91ea68d6771ed7d6b03bcbffd891489dc77e574 Mon Sep 17 00:00:00 2001
+From: Krishnendu Ghosh
+Date: Thu, 22 Feb 2018 14:24:14 -0500
+Subject: [PATCH] added extern "C"
+
+---
+ src/spglib.h | 6 ++++++
+ 1 file changed, 6 insertions(+)
+
+diff --git a/src/spglib.h b/src/spglib.h
+index e1746b1..530dfa4 100644
+--- a/src/spglib.h
++++ b/src/spglib.h
+@@ -35,6 +35,9 @@
+ #ifndef __spglib_H__
+ #define __spglib_H__
+ 
++#ifdef __cplusplus
++extern "C" {
++#endif
+ /* SPGCONST is used instead of 'const' so to avoid gcc warning. */
+ /* However there should be better way than this way.... */
+ #ifndef SPGCONST
+@@ -481,4 +484,7 @@ void spg_get_neighboring_grid_points(int relative_grid_points[],
+ /* Return 0 if failed */
+ int spg_niggli_reduce(double lattice[3][3], const double symprec);
+ 
++#ifdef __cplusplus
++}
++#endif
+ #endif
+-- 
+2.7.4.1.g5468f9e
+
diff --git a/var/spack/repos/builtin/packages/spglib/package.py b/var/spack/repos/builtin/packages/spglib/package.py
new file mode 100644
index 0000000000..d68243c4b7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/spglib/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Spglib(CMakePackage):
+    """C library for finding and handling crystal symmetries."""
+
+    homepage = "https://atztogo.github.io/spglib/"
+    url      = "https://github.com/atztogo/spglib/archive/v1.10.3.tar.gz"
+
+    patch('fix_cmake_install.patch', when='@:1.10.3')
+    # patch by Krishnendu Ghosh
+    patch('fix_cpp.patch', when='@:1.10.3')
+
+    version('1.10.3', 'f6ef0554fa528ffa49d8eaee18a2b7b9')
+    version('1.10.0', '0ad9330ae8a511d25e2e26cb9bf02808')
diff --git a/var/spack/repos/builtin/packages/sph2pipe/package.py b/var/spack/repos/builtin/packages/sph2pipe/package.py
index 471461249a..f3e2e991e3 100644
--- a/var/spack/repos/builtin/packages/sph2pipe/package.py
+++ b/var/spack/repos/builtin/packages/sph2pipe/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spherepack/package.py b/var/spack/repos/builtin/packages/spherepack/package.py
index 792853b51d..eabd1731ef 100644
--- a/var/spack/repos/builtin/packages/spherepack/package.py
+++ b/var/spack/repos/builtin/packages/spherepack/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/spindle/package.py b/var/spack/repos/builtin/packages/spindle/package.py
index 1b863689c3..905ef33cf2 100644
--- a/var/spack/repos/builtin/packages/spindle/package.py
+++ b/var/spack/repos/builtin/packages/spindle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/spot/package.py b/var/spack/repos/builtin/packages/spot/package.py
index cd045dae68..1e74a0b2da 100644
--- a/var/spack/repos/builtin/packages/spot/package.py
+++ b/var/spack/repos/builtin/packages/spot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sqlite/package.py b/var/spack/repos/builtin/packages/sqlite/package.py
index de949df998..dc14a7b088 100644
--- a/var/spack/repos/builtin/packages/sqlite/package.py
+++ b/var/spack/repos/builtin/packages/sqlite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 from spack import architecture
 
@@ -33,6 +14,12 @@ class Sqlite(AutotoolsPackage):
     """
     homepage = "www.sqlite.org"
 
+    version('3.23.1', '0edbfd75ececb95e8e6448d6ff33df82774c9646',
+            url='https://www.sqlite.org/2018/sqlite-autoconf-3230100.tar.gz')
+    version('3.22.0', '2fb24ec12001926d5209d2da90d252b9825366ac',
+            url='https://www.sqlite.org/2018/sqlite-autoconf-3220000.tar.gz')
+    version('3.21.0', '7913de4c3126ba3c24689cb7a199ea31',
+            url='https://www.sqlite.org/2017/sqlite-autoconf-3210000.tar.gz')
     version('3.20.0', 'e262a28b73cc330e7e83520c8ce14e4d',
             url='https://www.sqlite.org/2017/sqlite-autoconf-3200000.tar.gz')
     version('3.18.0', 'a6687a8ae1f66abc8df739aeadecfd0c',
@@ -48,7 +35,31 @@ class Sqlite(AutotoolsPackage):
     # defines a macro B0. Sqlite has a shell.c source file that declares a
     # variable named B0 and will fail to compile when the macro is found. The
     # following patch undefines the macro in shell.c
-    patch('sqlite_b0.patch', when='@3.18.0')
+    patch('sqlite_b0.patch', when='@3.18.0:3.21.0')
+
+    # Starting version 3.17.0, SQLite uses compiler built-ins
+    # __builtin_sub_overflow(), __builtin_add_overflow(), and
+    # __builtin_mul_overflow(), which are not supported by Intel compiler.
+    # Starting version 3.21.0 SQLite doesn't use the built-ins if Intel
+    # compiler is used.
+    patch('remove_overflow_builtins.patch', when='@3.17.0:3.20%intel')
+
+    variant('functions', default=False,
+            description='Provide mathematical and string extension functions '
+                        'for SQL queries using the loadable extensions '
+                        'mechanism.')
+
+    resource(name='extension-functions',
+             url='https://sqlite.org/contrib/download/extension-functions.c/download/extension-functions.c?get=25',
+             md5='3a32bfeace0d718505af571861724a43',
+             expand=False,
+             placement={'extension-functions.c?get=25':
+                        'extension-functions.c'},
+             when='+functions')
+
+    @property
+    def libs(self):
+        return find_libraries('libsqlite3', root=self.prefix.lib)
 
     def get_arch(self):
         arch = architecture.Arch()
@@ -62,3 +73,12 @@ class Sqlite(AutotoolsPackage):
             args.append('--build=powerpc64le-redhat-linux-gnu')
 
         return args
+
+    @run_after('install')
+    def build_libsqlitefunctions(self):
+        if '+functions' in self.spec:
+            libraryname = 'libsqlitefunctions.' + dso_suffix
+            cc = Executable(spack_cc)
+            cc(self.compiler.pic_flag, '-lm', '-shared',
+                'extension-functions.c', '-o', libraryname)
+            install(libraryname, self.prefix.lib)
diff --git a/var/spack/repos/builtin/packages/sqlite/remove_overflow_builtins.patch b/var/spack/repos/builtin/packages/sqlite/remove_overflow_builtins.patch
new file mode 100644
index 0000000000..a0a5d2e3da
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sqlite/remove_overflow_builtins.patch
@@ -0,0 +1,48 @@
+diff --git a/sqlite3.c b/sqlite3.c
+index 4ec1271..8615169 100644
+--- a/sqlite3.c
++++ b/sqlite3.c
+@@ -29466,9 +29466,6 @@ SQLITE_PRIVATE int sqlite3SafetyCheckSickOrOk(sqlite3 *db){
+ ** overflow, leave *pA unchanged and return 1.
+ */
+ SQLITE_PRIVATE int sqlite3AddInt64(i64 *pA, i64 iB){
+-#if GCC_VERSION>=5004000
+-  return __builtin_add_overflow(*pA, iB, pA);
+-#else
+   i64 iA = *pA;
+   testcase( iA==0 ); testcase( iA==1 );
+   testcase( iB==-1 ); testcase( iB==0 );
+@@ -29483,12 +29480,8 @@ SQLITE_PRIVATE int sqlite3AddInt64(i64 *pA, i64 iB){
+   }
+   *pA += iB;
+   return 0; 
+-#endif
+ }
+ SQLITE_PRIVATE int sqlite3SubInt64(i64 *pA, i64 iB){
+-#if GCC_VERSION>=5004000
+-  return __builtin_sub_overflow(*pA, iB, pA);
+-#else
+   testcase( iB==SMALLEST_INT64+1 );
+   if( iB==SMALLEST_INT64 ){
+     testcase( (*pA)==(-1) ); testcase( (*pA)==0 );
+@@ -29498,12 +29491,8 @@ SQLITE_PRIVATE int sqlite3SubInt64(i64 *pA, i64 iB){
+   }else{
+     return sqlite3AddInt64(pA, -iB);
+   }
+-#endif
+ }
+ SQLITE_PRIVATE int sqlite3MulInt64(i64 *pA, i64 iB){
+-#if GCC_VERSION>=5004000
+-  return __builtin_mul_overflow(*pA, iB, pA);
+-#else
+   i64 iA = *pA;
+   if( iB>0 ){
+     if( iA>LARGEST_INT64/iB ) return 1;
+@@ -29519,7 +29508,6 @@ SQLITE_PRIVATE int sqlite3MulInt64(i64 *pA, i64 iB){
+   }
+   *pA = iA*iB;
+   return 0;
+-#endif
+ }
+ 
+ /*
diff --git a/var/spack/repos/builtin/packages/sqlitebrowser/package.py b/var/spack/repos/builtin/packages/sqlitebrowser/package.py
new file mode 100644
index 0000000000..5ec2d47707
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sqlitebrowser/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Sqlitebrowser(CMakePackage):
+    """DB Browser for SQLite (DB4S) is a high quality, visual,
+    open source tool to create, design, and edit database files
+    compatible with SQLite."""
+
+    homepage = "https://sqlitebrowser.org"
+    url      = "https://github.com/sqlitebrowser/sqlitebrowser/archive/v3.10.1.tar.gz"
+
+    version('3.10.1', '66cbe41f9da5be80067942ed3816576c')
+
+    msg = 'sqlitebrowser requires C++11 support'
+    conflicts('%gcc@:4.8.0', msg=msg)
+    conflicts('%clang@:3.2', msg=msg)
+    conflicts('%intel@:12',  msg=msg)
+    conflicts('%xl@:13.0',   msg=msg)
+    conflicts('%xl_r@:13.0', msg=msg)
+
+    depends_on('sqlite@3:+functions')
+    depends_on('qt@5.5:')
diff --git a/var/spack/repos/builtin/packages/squid/package.py b/var/spack/repos/builtin/packages/squid/package.py
index 379aff577c..13a6bd32f4 100644
--- a/var/spack/repos/builtin/packages/squid/package.py
+++ b/var/spack/repos/builtin/packages/squid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sra-toolkit/package.py b/var/spack/repos/builtin/packages/sra-toolkit/package.py
index e1d5b54300..0726883afd 100644
--- a/var/spack/repos/builtin/packages/sra-toolkit/package.py
+++ b/var/spack/repos/builtin/packages/sra-toolkit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,13 +14,14 @@ class SraToolkit(Package):
     homepage = "https://trace.ncbi.nlm.nih.gov/Traces/sra"
     url      = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2-1/sratoolkit.2.8.2-1-centos_linux64.tar.gz"
 
-    version('2.8.2-1', '3a2910754aea71aba5662804efff2a68')
+    version('2.9.2', sha256='17dbe13aa1ed7955d31e1e76e8b62786e80a77e9ed9d396631162dc3ad8b716d')
+    version('2.8.2-1', sha256='b053061aae7c6d00162fe0f514be4128a60365b4b2b5b36e7f4798b348b55cf5')
 
     def url_for_version(self, version):
         url = 'https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/{0}/sratoolkit.{0}-centos_linux64.tar.gz'
         return url.format(version)
 
     def install(self, spec, prefix):
-        install_tree('bin', prefix.bin)
+        install_tree('bin', prefix.bin, symlinks=True)
         install_tree('example', prefix.example)
         install_tree('schema', prefix.schema)
diff --git a/var/spack/repos/builtin/packages/ssht/package.py b/var/spack/repos/builtin/packages/ssht/package.py
new file mode 100644
index 0000000000..54d1d9684d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ssht/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ssht(Package):
+    """The SSHT code provides functionality to perform fast and exact
+    spin spherical harmonic transforms."""
+
+    homepage = "https://astro-informatics.github.io/ssht/"
+    git      = "https://github.com/astro-informatics/ssht.git"
+
+    version('1.2b1', commit='7378ce8853897cbd1b08adebf7ec088c1e40f860')
+
+    depends_on('fftw')
+
+    def install(self, spec, prefix):
+        make('default')
+        install_tree('include/c', join_path(prefix, 'include'))
+        install_tree('doc/c', join_path(prefix, 'doc'))
+        install_tree('lib/c', join_path(prefix, 'lib'))
diff --git a/var/spack/repos/builtin/packages/sspace-longread/package.py b/var/spack/repos/builtin/packages/sspace-longread/package.py
index 4eac8cf177..bb6c05b112 100644
--- a/var/spack/repos/builtin/packages/sspace-longread/package.py
+++ b/var/spack/repos/builtin/packages/sspace-longread/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/sspace-standard/package.py b/var/spack/repos/builtin/packages/sspace-standard/package.py
index 2724c1022f..9275b200ea 100644
--- a/var/spack/repos/builtin/packages/sspace-standard/package.py
+++ b/var/spack/repos/builtin/packages/sspace-standard/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
+import glob
 
 
 class SspaceStandard(Package):
@@ -41,15 +23,29 @@ class SspaceStandard(Package):
 
     version('3.0', '7e171b4861b9d514e80aafc3d9cdf554')
 
-    depends_on('perl', type=('build', 'run'))
+    depends_on('perl+threads', type=('build', 'run'))
+    depends_on('perl-perl4-corelibs', type=('build', 'run'))
 
     def install(self, spec, prefix):
+        rootscript = 'SSPACE_Standard_v{0}.pl'.format(self.version)
+
+        scripts = [rootscript]
+        scripts.extend(glob.glob('tools/*.pl'))
+        scripts.extend(glob.glob('bwa/*.pl'))
+
+        for s in scripts:
+            filter_file('/usr/bin/perl', '/usr/bin/env perl',
+                        s, string=True)
+            filter_file('require "getopts.pl";', 'use Getopt::Std;',
+                        s, string=True)
+            filter_file('&Getopts(', 'getopts(', s, string=True)
+
         install_tree('bin', prefix.bin)
         install_tree('bowtie', prefix.bowtie)
         install_tree('bwa', prefix.bwa)
         install_tree('dotlib', prefix.dotlib)
         install_tree('tools', prefix.tools)
-        install('SSPACE_Standard_v{0}.pl'.format(self.version), prefix)
+        install(rootscript, prefix)
 
     def setup_environment(self, spack_env, run_env):
         run_env.set('SSPACE_HOME', prefix)
diff --git a/var/spack/repos/builtin/packages/sst-core/package.py b/var/spack/repos/builtin/packages/sst-core/package.py
new file mode 100644
index 0000000000..a64bc40753
--- /dev/null
+++ b/var/spack/repos/builtin/packages/sst-core/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SstCore(AutotoolsPackage):
+    """The Structural Simulation Toolkit (SST) was developed to explore
+    innovations in highly concurrent systems where the ISA, microarchitecture,
+    and memory interact with the programming model and communications system"""
+
+    homepage = "http://sst-simulator.org/"
+    url      = "https://github.com/sstsimulator/sst-core/releases/download/v8.0.0_Final/sstcore-8.0.0.tar.gz"
+    git      = "https://github.com/sstsimulator/sst-core.git"
+
+    version('develop', branch='devel')
+    version('8.0.0', sha256='34a62425c3209cf80b6bca99cb0dcc328b67fb84ed92d5e6d6c975ad9319ba8a')
+
+    variant('mpi', default=True, description='Support multi-node simulations using MPI')
+    variant('boost', default=False, description='Use boost')
+
+    depends_on('autoconf@1.68:', type='build', when='@develop')
+    depends_on('automake@1.11.1:', type='build', when='@develop')
+    depends_on('libtool@1.2.4:', type='build', when='@develop')
+    depends_on('m4', type='build', when='@develop')
+
+    depends_on('python@:2')
+    depends_on('zlib', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('boost@1.56.0:', type='build', when='+boost')
+
+    def configure_args(self):
+        args = []
+        spec = self.spec
+
+        if '~mpi' in spec:
+            args.append('--disable-mpi')
+
+        if '+boost' in spec:
+            args.append('--with-boost=%s' % spec['boost'].prefix)
+
+        return args
diff --git a/var/spack/repos/builtin/packages/sst-dumpi/package.py b/var/spack/repos/builtin/packages/sst-dumpi/package.py
index 6422013871..96bbd6e3c7 100644
--- a/var/spack/repos/builtin/packages/sst-dumpi/package.py
+++ b/var/spack/repos/builtin/packages/sst-dumpi/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 # Author: Samuel Knight <sknigh@sandia.gov>
 # Date: Feb 3, 2017
@@ -39,14 +20,12 @@ class SstDumpi(AutotoolsPackage):
 
     homepage = "http://sst.sandia.gov/about_dumpi.html"
     url      = "https://github.com/sstsimulator/sst-dumpi/archive/6.1.0.tar.gz"
+    git      = "https://github.com/sstsimulator/sst-dumpi.git"
+
+    version('master', branch='master')
+    version('6.1.0', '31c3f40a697dc85bf23dd34270982319')
 
     depends_on('autoconf@1.68:', type='build')
     depends_on('automake@1.11.1:', type='build')
     depends_on('libtool@1.2.4:', type='build')
     depends_on('m4', type='build')
-
-    version('master',
-          git='https://github.com/sstsimulator/sst-dumpi.git',
-          branch='master')
-
-    version('6.1.0', '31c3f40a697dc85bf23dd34270982319')
diff --git a/var/spack/repos/builtin/packages/sst-macro/package.py b/var/spack/repos/builtin/packages/sst-macro/package.py
index 3fade2694f..65c0e613e0 100644
--- a/var/spack/repos/builtin/packages/sst-macro/package.py
+++ b/var/spack/repos/builtin/packages/sst-macro/package.py
@@ -1,64 +1,87 @@
-##############################################################################
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
-#
-# Author: Samuel Knight <sknigh@sandia.gov>
-# Date: Feb 3, 2017
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class SstMacro(AutotoolsPackage):
-    """The SST/macro software package provides a simulator for large-scale
-    parallel computer architectures for the coarse-grained study of
-    distributed-memory applications. The simulator is driven from either a
+    """The Structural Simulation Toolkit Macroscale Element Library simulates
+    large-scale parallel computer architectures for the coarse-grained study
+    of distributed-memory applications. The simulator is driven from either a
     trace file or skeleton application. SST/macro's modular architecture can
-    be extended with additional network models, trace file formats,
-    software services, and processor models.
+    be extended with additional network models, trace file formats, software
+    services, and processor models.
     """
 
     homepage = "http://sst.sandia.gov/about_sstmacro.html"
     url      = "https://github.com/sstsimulator/sst-macro/releases/download/v6.1.0_Final/sstmacro-6.1.0.tar.gz"
+    git      = "https://github.com/sstsimulator/sst-macro.git"
+
+    version('develop', branch='devel')
+    version('8.0.0', sha256='8618a259e98ede9a1a2ce854edd4930628c7c5a770c3915858fa840556c1861f')
+    version('6.1.0', '98b737be6326b8bd711de832ccd94d14')
 
-    depends_on('boost@1.59:')
-    depends_on('autoconf@1.68:', type='build', when='@master')
-    depends_on('automake@1.11.1:', type='build', when='@master')
-    depends_on('libtool@1.2.4:', type='build', when='@master')
-    depends_on('m4', type='build', when='@master')
+    depends_on('boost@1.59:', when='@:6.1.0')
 
-    version('master',
-          git='https://github.com/sstsimulator/sst-macro.git',
-          branch='master')
+    depends_on('autoconf@1.68:', type='build', when='@develop')
+    depends_on('automake@1.11.1:', type='build', when='@develop')
+    depends_on('libtool@1.2.4:', type='build', when='@develop')
+    depends_on('m4', type='build', when='@develop')
 
-    version('6.1.0', '98b737be6326b8bd711de832ccd94d14',
-          url='https://github.com/sstsimulator/sst-macro/releases/download/v6.1.0_Final/sstmacro-6.1.0.tar.gz')
+    depends_on('binutils', type='build')
+    depends_on('zlib', type=('build', 'link'))
+    depends_on('otf2', when='+otf2')
+    depends_on('llvm+clang@:5.99.99', when='+skeletonizer')
+    depends_on('mpi', when='+mpi')
+    depends_on('sst-core@8.0.0', when='@8.0.0 +core')
+    depends_on('sst-core@develop', when='@develop +core')
+
+    variant('core', default=False, description='Use SST Core for PDES')
+    variant('mpi', default=True, description='Enable distributed PDES simulation')
+    variant('otf2', default=False, description='Enable OTF2 trace emission and replay support')
+    variant('shared', default=True, description='Build shared libraries')
+    variant('skeletonizer', default=False, description='Enable Clang source-to-source autoskeletonization')
+    variant('static', default=True, description='Build static libraries')
+    variant('threaded', default=False, description='Enable thread-parallel PDES simulation')
 
     @run_before('autoreconf')
     def bootstrap(self):
-        if '@master' in self.spec:
+        if '@develop' in self.spec:
             Executable('./bootstrap.sh')()
 
     def configure_args(self):
         args = ['--disable-regex']
+
+        # Set CFLAGS and CXXFLAGS so they won't automatically insert '-g'
+        env['CFLAGS'] = '-O2'
+        env['CXXFLAGS'] = '-O2'
+
+        spec = self.spec
+        args.append(
+            '--enable-static=%s' % ('yes' if '+static' in spec else 'no'))
+        args.append(
+            '--enable-shared=%s' % ('yes' if '+shared' in spec else 'no'))
+
+        if spec.satisfies("@8.0.0:"):
+            args.extend([
+                '--%sable-otf2' % ('en' if '+otf2' in spec else 'dis'),
+                '--%sable-multithread' % (
+                    'en' if '+threaded' in spec else 'dis')
+            ])
+
+            if '+skeletonizer' in spec:
+                args.append('--with-clang=' + spec['llvm'].prefix)
+
+        if '+core' in spec:
+            args.append('--with-sst-core=%s' % spec['sst-core'].prefix)
+
+        # Optional MPI support
+        if '+mpi' in spec:
+            env['CC'] = spec['mpi'].mpicc
+            env['CXX'] = spec['mpi'].mpicxx
+            env['F77'] = spec['mpi'].mpif77
+            env['FC'] = spec['mpi'].mpifc
+
         return args
diff --git a/var/spack/repos/builtin/packages/stacks/package.py b/var/spack/repos/builtin/packages/stacks/package.py
index 975e1c88b6..d156ec9f30 100644
--- a/var/spack/repos/builtin/packages/stacks/package.py
+++ b/var/spack/repos/builtin/packages/stacks/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/staden-io-lib/package.py b/var/spack/repos/builtin/packages/staden-io-lib/package.py
index 3cb82061aa..9ecb46fbbe 100644
--- a/var/spack/repos/builtin/packages/staden-io-lib/package.py
+++ b/var/spack/repos/builtin/packages/staden-io-lib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/star-ccm-plus/package.py b/var/spack/repos/builtin/packages/star-ccm-plus/package.py
index cc230fe028..59d043fe65 100644
--- a/var/spack/repos/builtin/packages/star-ccm-plus/package.py
+++ b/var/spack/repos/builtin/packages/star-ccm-plus/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
@@ -35,7 +16,7 @@ class StarCcmPlus(Package):
 
     version('11.06.010_02', 'd349c6ac8293d8e6e7a53533d695588f')
 
-    variant('docs', default=False, description='Install the documentation')
+    variant('doc', default=False, description='Install the documentation')
 
     # Licensing
     license_required = True
diff --git a/var/spack/repos/builtin/packages/star/package.py b/var/spack/repos/builtin/packages/star/package.py
index 3a21e5806e..9f6d51c219 100644
--- a/var/spack/repos/builtin/packages/star/package.py
+++ b/var/spack/repos/builtin/packages/star/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,12 +10,21 @@ 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"
+    url      = "https://github.com/alexdobin/STAR/archive/2.6.1b.tar.gz"
+
+    version('2.6.1b', sha256='1bba5b26c1e6e9a7aca8473a99dbf37bad1dbdd0a589402448e278553bb6b3da')
+    version('2.6.1a', sha256='dc87357211432c05123ce49966aae712dec590cbe27c1fd0193c3aeb8d4abe4b')
+    version('2.6.0c', sha256='bebba6cc72da302429c44c20f3b07bdde6b0ddf33e538a99e297f1d342070387')
+    version('2.6.0b', sha256='1ebbecbb698a3de95990b35fe386189a2c00b07cd9d2d4e017ab8234e7dc042e')
+    version('2.6.0a', sha256='a6b0dd1918e1961eebec71e6c7c3c8e632f66d10e0620aa09c0710e2ab279179')
+    version('2.5.4b', sha256='bfa6ccd3b7b3878155a077a9c15eec5490dffad8e077ac93abe6f9bfa75bb2b4')
+    version('2.5.4a', sha256='17b02703cdd580c9fd426a14f20712ea252d32a4ded804eef759029b600e3afb')
+    version('2.5.3a', sha256='2a258e77cda103aa293e528f8597f25dc760cba188d0a7bc7c9452f4698e7c04')
+    version('2.5.2b', sha256='f88b992740807ab10f2ac3b83781bf56951617f210001fab523f6480d0b546d9')
+    version('2.5.2a', sha256='2a372d9bcab1dac8d35cbbed3f0ab58291e4fbe99d6c1842b094ba7449d55476')
+    version('2.4.2a', '8b9345f2685a5ec30731e0868e86d506', url='https://github.com/alexdobin/STAR/archive/STAR_2.4.2a.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')
+    depends_on('zlib')
 
     def install(self, spec, prefix):
         with working_dir('source'):
diff --git a/var/spack/repos/builtin/packages/startup-notification/package.py b/var/spack/repos/builtin/packages/startup-notification/package.py
new file mode 100644
index 0000000000..e10736253b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/startup-notification/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class StartupNotification(AutotoolsPackage):
+    """startup-notification contains a reference implementation of the
+    freedesktop startup notification protocol."""
+
+    homepage = "https://www.freedesktop.org/wiki/Software/startup-notification/"
+    url      = "http://www.freedesktop.org/software/startup-notification/releases/startup-notification-0.12.tar.gz"
+
+    version('0.12', '2cd77326d4dcaed9a5a23a1232fb38e9')
+
+    depends_on('libx11')
+    depends_on('libxcb')
+    depends_on('xcb-util')
diff --git a/var/spack/repos/builtin/packages/stat/package.py b/var/spack/repos/builtin/packages/stat/package.py
index f2733f8f61..3df3d04a61 100644
--- a/var/spack/repos/builtin/packages/stat/package.py
+++ b/var/spack/repos/builtin/packages/stat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,8 +10,14 @@ class Stat(AutotoolsPackage):
     """Library to create, manipulate, and export graphs Graphlib."""
 
     homepage = "http://paradyn.org/STAT/STAT.html"
-    url      = "https://github.com/lee218llnl/stat/archive/v2.0.0.tar.gz"
+    url      = "https://github.com/LLNL/STAT/archive/v2.0.0.tar.gz"
+    git      = "https://github.com/llnl/stat.git"
 
+    version('develop', branch='develop')
+    version('4.0.1', '3e21b48e7932d9a4a9efb300f0b97fa2',
+            url='https://github.com/LLNL/STAT/files/2489327/stat-4.0.1.tar.gz')
+    version('4.0.0', 'b357160662ced251bc55cb1b884c3407',
+            url='https://github.com/LLNL/STAT/releases/download/v4.0.0/stat-4.0.0.tar.gz')
     version('3.0.1', 'dac6f23c3639a0b21f923dc6219ba385',
             url='https://github.com/LLNL/STAT/files/911503/stat-3.0.1.zip')
     version('3.0.0', 'a97cb235c266371c4a26329112de48a2',
@@ -42,20 +29,23 @@ class Stat(AutotoolsPackage):
     # TODO: dysect requires Dyninst patch for version 3.0.0b
     variant('dysect', default=False, description="enable DySectAPI")
     variant('examples', default=False, description="enable examples")
+    variant('fgfs', default=True, description="enable file broadcasting")
 
     depends_on('autoconf', type='build')
     depends_on('automake', type='build')
     depends_on('libtool', type='build')
-    depends_on('libdwarf')
     depends_on('dyninst', when='~dysect')
     depends_on('dyninst@8.2.1+stat_dysect', when='+dysect')
+    depends_on('fast-global-file-status', when='+fgfs')
     depends_on('graphlib@2.0.0', when='@2.0.0:2.2.0')
     depends_on('graphlib@3.0.0', when='@3:')
     depends_on('graphviz', type=('build', 'link', 'run'))
     depends_on('launchmon')
     depends_on('mrnet')
-    depends_on('python@:2.8')
-    depends_on('py-pygtk', type=('build', 'run'))
+    depends_on('python@:2.8', when='@:4.0.0')
+    depends_on('py-pygtk', type=('build', 'run'), when='@:4.0.0')
+    depends_on('py-enum34', type=('run'), when='@:4.0.0')
+    depends_on('py-xdot', when='@4.0.1:')
     depends_on('swig')
     depends_on('mpi', when='+examples')
 
@@ -68,9 +58,11 @@ class Stat(AutotoolsPackage):
             "--with-mrnet=%s"       % spec['mrnet'].prefix,
             "--with-graphlib=%s"    % spec['graphlib'].prefix,
             "--with-stackwalker=%s" % spec['dyninst'].prefix,
-            "--with-libdwarf=%s"    % spec['libdwarf'].prefix,
             "--with-python=%s"      % spec['python'].command.path,
         ]
+        if '+fgfs' in spec:
+            args.append('--with-fgfs=%s'
+                        % spec['fast-global-file-status'].prefix)
         if '+dysect' in spec:
             args.append('--enable-dysectapi')
         if '~examples' in spec:
diff --git a/var/spack/repos/builtin/packages/stc/package.py b/var/spack/repos/builtin/packages/stc/package.py
index 7a55b73873..7332d4843d 100644
--- a/var/spack/repos/builtin/packages/stc/package.py
+++ b/var/spack/repos/builtin/packages/stc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,13 +11,14 @@ class Stc(AutotoolsPackage):
     """STC: The Swift-Turbine Compiler"""
 
     homepage = 'http://swift-lang.org/Swift-T'
-    url      = 'http://swift-lang.github.io/swift-t-downloads/stc-0.7.3.tar.gz'
+    url      = 'http://swift-lang.github.io/swift-t-downloads/spack/stc-0.0.0.tar.gz'
 
-    version('0.7.3', '6bf769f406f6c33d1c134521373718d3')
+    version('0.8.2', '883b0657f1aac9b81158ef0a8989be4c')
 
-    depends_on('java')
-    depends_on('ant')
-    depends_on('turbine')
+    depends_on('java', type=('build', 'run'))
+    depends_on('ant', type='build')
+    depends_on('turbine', type=('build', 'run'))
+    depends_on('zsh', type=('build', 'run'))
 
     def configure_args(self):
         args = ['--with-turbine=' + self.spec['turbine'].prefix]
diff --git a/var/spack/repos/builtin/packages/steps/package.py b/var/spack/repos/builtin/packages/steps/package.py
new file mode 100644
index 0000000000..0831852f3c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/steps/package.py
@@ -0,0 +1,61 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Steps(CMakePackage):
+    """STochastic Engine for Pathway Simulation"""
+
+    homepage = "https://groups.oist.jp/cnu/software"
+    git      = "https://github.com/CNS-OIST/STEPS.git"
+
+    version("3.3.0", submodules=True)
+    version("3.2.0", submodules=True)
+    version("develop", branch="master", submodules=True)
+
+    variant("native", default=True, description="Generate non-portable arch-specific code")
+    variant("lapack", default=False, description="Use new BDSystem/Lapack code for E-Field solver")
+    variant("petsc", default=False, description="Use PETSc library for parallel E-Field solver")
+    variant("mpi", default=True, description="Use MPI for parallel solvers")
+
+    depends_on("blas")
+    depends_on("lapack", when="+lapack")
+    depends_on("mpi", when="+mpi")
+    depends_on("petsc~debug+int64", when="+petsc")
+    depends_on("python")
+    depends_on("py-cython")
+
+    def cmake_args(self):
+        args = []
+        spec = self.spec
+
+        if "+native" in spec:
+            args.append("-DTARGET_NATIVE_ARCH:BOOL=True")
+        else:
+            args.append("-DTARGET_NATIVE_ARCH:BOOL=False")
+
+        if "+lapack" in spec:
+            args.append("-DUSE_BDSYSTEM_LAPACK:BOOL=True")
+        else:
+            args.append("-DUSE_BDSYSTEM_LAPACK:BOOL=False")
+
+        if "+petsc" in spec:
+            args.append("-DUSE_PETSC:BOOL=True")
+        else:
+            args.append("-DUSE_PETSC:BOOL=False")
+
+        if "+mpi" in spec:
+            args.append("-DUSE_MPI:BOOL=True")
+        else:
+            args.append("-DUSE_MPI:BOOL=False")
+
+        args.append('-DBLAS_LIBRARIES=' + spec['blas'].libs.joined(";"))
+        return args
+
+    def setup_environment(self, spack_env, run_env):
+        # This recipe exposes a Python package from a C++ CMake project.
+        # This hook is required to reproduce what Spack PythonPackage does.
+        run_env.prepend_path('PYTHONPATH', self.prefix)
diff --git a/var/spack/repos/builtin/packages/stow/package.py b/var/spack/repos/builtin/packages/stow/package.py
new file mode 100644
index 0000000000..5861351441
--- /dev/null
+++ b/var/spack/repos/builtin/packages/stow/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Stow(AutotoolsPackage):
+    """GNU Stow: a symlink farm manager
+
+       GNU Stow is a symlink farm manager which takes distinct
+       packages of software and/or data located in separate
+       directories on the filesystem, and makes them appear to be
+       installed in the same place."""
+
+    homepage = "https://www.gnu.org/software/stow/"
+    url      = "https://ftpmirror.gnu.org/stow/stow-2.2.2.tar.bz2"
+
+    version('2.2.2', 'af1e1de9d973c835bee80c745b5ee849')
+    version('2.2.0', '5bb56592eff9aaf9dfb6c975b3004240')
+    version('2.1.3', '533651c25b29c3630f01d0be33849a7c')
+    version('2.1.2', '0b8154a2165e4004ddc9579e3499af98')
+    version('2.1.1', '882d2490d05723b4b78029c2973775d3')
+    version('2.1.0', 'aa3a2389b6cbf3bd555e15c80a0be6ab')
+
+    depends_on('perl@5.6.1:')
diff --git a/var/spack/repos/builtin/packages/strace/package.py b/var/spack/repos/builtin/packages/strace/package.py
new file mode 100644
index 0000000000..b43e2c4ef4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/strace/package.py
@@ -0,0 +1,20 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Strace(AutotoolsPackage):
+    """Strace is a diagnostic, debugging and instructional userspace
+    utility for Linux. It is used to monitor and tamper with interactions
+    between processes and the Linux kernel, which include system calls,
+    signal deliveries, and changes of process state."""
+
+    homepage = "https://strace.io"
+    url      = "https://strace.io/files/4.21/strace-4.21.tar.xz"
+
+    conflicts('platform=darwin', msg='strace runs only on Linux.')
+
+    version('4.21', '785b679a75e9758ebeb66816f315b9fe')
diff --git a/var/spack/repos/builtin/packages/stream/package.py b/var/spack/repos/builtin/packages/stream/package.py
index 69ddfe5b07..45aad6da05 100644
--- a/var/spack/repos/builtin/packages/stream/package.py
+++ b/var/spack/repos/builtin/packages/stream/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,8 +12,9 @@ class Stream(MakefilePackage):
     computation rate for simple vector kernels."""
 
     homepage = "https://www.cs.virginia.edu/stream/ref.html"
+    git      = "https://github.com/jeffhammond/STREAM.git"
 
-    version('5.10', git='https://github.com/jeffhammond/STREAM.git')
+    version('5.10')
 
     variant('openmp', default=False, description='Build with OpenMP support')
 
diff --git a/var/spack/repos/builtin/packages/strelka/package.py b/var/spack/repos/builtin/packages/strelka/package.py
index 19c5de7dc8..fdd4b67434 100644
--- a/var/spack/repos/builtin/packages/strelka/package.py
+++ b/var/spack/repos/builtin/packages/strelka/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/stress/package.py b/var/spack/repos/builtin/packages/stress/package.py
index 497853f73b..0588cc36a2 100644
--- a/var/spack/repos/builtin/packages/stress/package.py
+++ b/var/spack/repos/builtin/packages/stress/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/string-view-lite/package.py b/var/spack/repos/builtin/packages/string-view-lite/package.py
new file mode 100644
index 0000000000..ab564b4880
--- /dev/null
+++ b/var/spack/repos/builtin/packages/string-view-lite/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from shutil import copytree
+
+
+class StringViewLite(Package):
+    """
+    A single-file header-only version of a C++17-like string_view for C++98,
+    C++11 and later
+    """
+
+    homepage = "https://github.com/martinmoene/string-view-lite"
+    url      = "https://github.com/martinmoene/string-view-lite/archive/v1.0.0.tar.gz"
+
+    version('1.0.0', sha256='44e30dedd6f4777e646da26528f9d2d5cc96fd0fa79e2e5c0adc14817d048d63')
+    version('0.2.0', sha256='c8ae699dfd2ccd15c5835e9b1d246834135bbb91b82f7fc4211b8ac366bffd34')
+    version('0.1.0', sha256='7de87d6595230a6085655dab6145340bc423f2cf206263ef73c9b78f7b153340')
+
+    def install(self, spec, prefix):
+        copytree('include', prefix.include)
diff --git a/var/spack/repos/builtin/packages/stringtie/package.py b/var/spack/repos/builtin/packages/stringtie/package.py
index 9e5a690a5d..cb01647651 100644
--- a/var/spack/repos/builtin/packages/stringtie/package.py
+++ b/var/spack/repos/builtin/packages/stringtie/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,6 +13,7 @@ class Stringtie(MakefilePackage):
     homepage = "https://ccb.jhu.edu/software/stringtie"
     url      = "https://github.com/gpertea/stringtie/archive/v1.3.3b.tar.gz"
 
+    version('1.3.4a', '2a191ef6512242a3a5778cf7718bb6af')
     version('1.3.3b', '11a43260b18e4272182380e922445d88')
 
     depends_on('samtools')
diff --git a/var/spack/repos/builtin/packages/structure/package.py b/var/spack/repos/builtin/packages/structure/package.py
index cbfc1e9850..f0d04676be 100644
--- a/var/spack/repos/builtin/packages/structure/package.py
+++ b/var/spack/repos/builtin/packages/structure/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/strumpack/package.py b/var/spack/repos/builtin/packages/strumpack/package.py
new file mode 100644
index 0000000000..4bd4dac459
--- /dev/null
+++ b/var/spack/repos/builtin/packages/strumpack/package.py
@@ -0,0 +1,96 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Strumpack(CMakePackage):
+    """STRUMPACK -- STRUctured Matrix PACKage - provides linear solvers
+    for sparse matrices and for dense rank-structured matrices, i.e.,
+    matrices that exhibit some kind of low-rank property. It provides a
+    distributed memory fully algebraic sparse solver and
+    preconditioner. The preconditioner is mostly aimed at large sparse
+    linear systems which result from the discretization of a partial
+    differential equation, but is not limited to any particular type of
+    problem. STRUMPACK also provides preconditioned GMRES and BiCGStab
+    iterative solvers."""
+
+    homepage = "http://portal.nersc.gov/project/sparse/strumpack"
+    url      = "https://github.com/pghysels/STRUMPACK/archive/v3.0.3.tar.gz"
+    git      = "https://github.com/pghysels/STRUMPACK.git"
+
+    version('master', branch='master')
+    version('3.1.1', sha256='c1c3446ee023f7b24baa97b24907735e89ce4ae9f5ef516645dfe390165d1778')
+    version('3.1.0', sha256='b4f91b7d433955518b04538be1c726afc5de4bffb163e982ef8844d391b26fa7')
+    version('3.0.3', sha256='2bd2a40d9585b769ae4ba461de02c6e36433bf2b21827f824a50f2fdf73389f7')
+    version('3.0.2', sha256='828e5ec59019b2c74e008745b04ceebbb7ef1313fb4e3ac01fa8ff350799df38')
+    version('3.0.1', sha256='b4a4d870c589937e22e77a6c4b52a96fd808f0b564e363f826ae5ffc94b9d000')
+    version('3.0.0', sha256='7acd9b4653b8b11380de733c80b164348ca00f9226904f5dc166a8e3db88cd20')
+    version('2.2.0', sha256='8fe73875cbbb29ed1faf714e3bf13ad538eb062e39d7d5e73cb9c4aafb571e24')
+
+    variant('mpi', default=True, description='Use MPI')
+    variant('openmp', default=True,
+            description='Enable thread parallellism via tasking with OpenMP')
+    variant('parmetis', default=False,
+            description='Enable use of ParMetis')
+    variant('scotch', default=False,
+            description='Enable use of Scotch')
+    variant('c_interface', default=True,
+            description='Enable C interface')
+    variant('count_flops', default=False,
+            description='Build with flop counters')
+    variant('task_timers', default=False,
+            description='Build with timers for internal routines')
+    variant('build_dev_tests', default=False,
+            description='Build developer test routines')
+    variant('build_tests', default=False,
+            description='Build test routines')
+
+    depends_on('cmake@3.2:', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('scalapack', when='+mpi')
+    depends_on('metis')
+    depends_on('parmetis', when='+parmetis')
+    depends_on('scotch~metis', when='+scotch')
+    depends_on('scotch~metis+mpi', when='+scotch+mpi')
+
+    conflicts('+parmetis', when='~mpi')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        def on_off(varstr):
+            return 'ON' if varstr in spec else 'OFF'
+
+        if '+mpi' in spec:
+            args = ['-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+                    '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+                    '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+                    '-DSTRUMPACK_USE_MPI=ON']
+        else:
+            args = ['-DSTRUMPACK_USE_MPI=OFF']
+
+        args.extend([
+            '-DSTRUMPACK_USE_OPENMP=%s' % on_off('+openmp'),
+            '-DSTRUMPACK_C_INTERFACE=%s' % on_off('+c_interface'),
+            '-DSTRUMPACK_COUNT_FLOPS=%s' % on_off('+count_flops'),
+            '-DSTRUMPACK_TASK_TIMERS=%s' % on_off('+task_timers'),
+            '-DSTRUMPACK_DEV_TESTING=%s' % on_off('+build_dev_tests'),
+            '-DSTRUMPACK_BUILD_TESTS=%s' % on_off('+build_tests')
+        ])
+
+        if spec.satisfies('@3.0.4:'):
+            args.extend([
+                '-DTPL_ENABLE_PARMETIS=%s' % on_off('+parmetis'),
+                '-DTPL_ENABLE_SCOTCH=%s' % on_off('+scotch')
+            ])
+        else:
+            args.extend([
+                '-DSTRUMPACK_USE_PARMETIS=%s' % on_off('+parmetis'),
+                '-DSTRUMPACK_USE_SCOTCH=%s' % on_off('+scotch')
+            ])
+        return args
diff --git a/var/spack/repos/builtin/packages/sublime-text/package.py b/var/spack/repos/builtin/packages/sublime-text/package.py
index e28aa04c94..403d5c42a8 100644
--- a/var/spack/repos/builtin/packages/sublime-text/package.py
+++ b/var/spack/repos/builtin/packages/sublime-text/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
 
 
 class SublimeText(Package):
@@ -31,8 +11,9 @@ class SublimeText(Package):
     prose."""
 
     homepage = "http://www.sublimetext.com/"
-    url      = "https://download.sublimetext.com/sublime_text_3_build_3126_x64.tar.bz2"
+    url      = "https://download.sublimetext.com/sublime_text_3_build_3176_x64.tar.bz2"
 
+    version('3_build_3176', '7d4c8c5167224888d901e8cbafb6ec7f')
     version('3_build_3126', 'acc34252b0ea7dff1f581c5db1564dcb')
     version('2.0.2',        '699cd26d7fe0bada29eb1b2cd7b50e4b')
 
@@ -52,8 +33,8 @@ class SublimeText(Package):
         if version[0] == 2:
             return "https://download.sublimetext.com/Sublime%20Text%20{0}%20x64.tar.bz2".format(version)
         else:
-            return "https://download.sublimetext.com/sublime_text_3_build_{0}_x64.tar.bz2".format(version)
+            return "https://download.sublimetext.com/sublime_text_{0}_x64.tar.bz2".format(version)
 
     def install(self, spec, prefix):
         # Sublime text comes as a pre-compiled binary.
-        copy_tree('.', prefix)
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/subread/package.py b/var/spack/repos/builtin/packages/subread/package.py
index 86c5efe42e..b6af49d745 100644
--- a/var/spack/repos/builtin/packages/subread/package.py
+++ b/var/spack/repos/builtin/packages/subread/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -33,6 +14,8 @@ class Subread(MakefilePackage):
     homepage = "http://subread.sourceforge.net/"
     url      = "https://downloads.sourceforge.net/project/subread/subread-1.5.2/subread-1.5.2-source.tar.gz"
 
+    version('1.6.2', '70125531737fe9ba2be83622ca236e5e')
+    version('1.6.0', 'ed7e32c56bda1e769703e0a4db5a89a7')
     version('1.5.2', '817d2a46d87fcef885c8832475b8b247')
 
     depends_on('zlib')
@@ -41,6 +24,11 @@ class Subread(MakefilePackage):
         plat = sys.platform
         with working_dir('src'):
             if plat.startswith('linux'):
+                filter_file(
+                    'CC_EXEC = gcc',
+                    'CC_EXEC = {0}'.format(spack_cc),
+                    'Makefile.Linux'
+                )
                 make('-f', 'Makefile.Linux')
             elif plat.startswith('darwin'):
                 make('-f', 'Makefile.MacOS')
diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py
index 5d4b998b32..8a041451b2 100644
--- a/var/spack/repos/builtin/packages/subversion/package.py
+++ b/var/spack/repos/builtin/packages/subversion/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,8 @@ class Subversion(Package):
     homepage = 'https://subversion.apache.org/'
     url = 'http://archive.apache.org/dist/subversion/subversion-1.8.13.tar.gz'
 
+    version('1.9.7',     '1a5f48acf9d0faa60e8c7aea96a9b29ab1d4dcac')
+    version('1.9.6',     '89e1b3f9d79422c094ccb95769360d5fe7df2bb1')
     version('1.9.5',     'ac9f8ee235f1b667dd6506864af8035aaedfc2d9')
     version('1.9.3',     'a92bcfaec4e5038f82c74a7b5bbd2f46')
     version('1.8.17',    'd1f8d45f97168d6271c58c5b25421cc32954c81b')
diff --git a/var/spack/repos/builtin/packages/suite-sparse/graphblas_libm_dep.patch b/var/spack/repos/builtin/packages/suite-sparse/graphblas_libm_dep.patch
new file mode 100644
index 0000000000..441b0eff87
--- /dev/null
+++ b/var/spack/repos/builtin/packages/suite-sparse/graphblas_libm_dep.patch
@@ -0,0 +1,10 @@
+--- a/GraphBLAS/CMakeLists.txt
++++ b/GraphBLAS/CMakeLists.txt
+@@ -87,6 +87,7 @@
+     C_STANDARD_REQUIRED 11
+     PUBLIC_HEADER "Include/GraphBLAS.h" )
+ set_property ( TARGET graphblas PROPERTY C_STANDARD 11 )
++target_link_libraries ( graphblas m )
+
+ # create the static graphblas library.  Requires ANSI C11
+ add_library ( graphblas_static STATIC ${GRAPHBLAS_SOURCES} )
diff --git a/var/spack/repos/builtin/packages/suite-sparse/package.py b/var/spack/repos/builtin/packages/suite-sparse/package.py
index 429a7f0706..3ab4f06068 100644
--- a/var/spack/repos/builtin/packages/suite-sparse/package.py
+++ b/var/spack/repos/builtin/packages/suite-sparse/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,11 @@ class SuiteSparse(Package):
     SuiteSparse is a suite of sparse matrix algorithms
     """
     homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html'
-    url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.5.1.tar.gz'
+    url = 'http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-5.2.0.tar.gz'
 
+    version('5.3.0', sha256='90e69713d8c454da5a95a839aea5d97d8d03d00cc1f667c4bdfca03f640f963d')
+    version('5.2.0', '8e625539dbeed061cc62fbdfed9be7cf')
+    version('5.1.0', '9c34d7c07ad5ce1624b8187faa132046')
     version('4.5.5', '0a5b38af0016f009409a9606d2f1b555')
     version('4.5.4', 'f6ab689442e64a1624a47aa220072d1b')
     version('4.5.3', '8ec57324585df3c6483ad7f556afccbd')
@@ -44,6 +28,7 @@ class SuiteSparse(Package):
 
     depends_on('blas')
     depends_on('lapack')
+    depends_on('cmake', when='@5.2.0:', type='build')
 
     depends_on('metis@5.1.0', when='@4.5.1:')
     # in @4.5.1. TBB support in SPQR seems to be broken as TBB-related linkng
@@ -57,6 +42,12 @@ class SuiteSparse(Package):
     # This patch removes unsupported flags for pgi compiler
     patch('pgi.patch', when='%pgi')
 
+    # This patch adds '-lm' when linking libgraphblas and when using clang.
+    # Fixes 'libgraphblas.so.2.0.1: undefined reference to `__fpclassify''
+    patch('graphblas_libm_dep.patch', when='@5.2.0:5.2.99%clang')
+
+    conflicts('%gcc@:4.8', when='@5.2.0:', msg='gcc version must be at least 4.9 for suite-sparse@5.2.0:')
+
     def install(self, spec, prefix):
         # The build system of SuiteSparse is quite old-fashioned.
         # It's basically a plain Makefile which include an header
@@ -94,10 +85,16 @@ class SuiteSparse(Package):
             # with the TCOV path of SparseSuite 4.5.1's Suitesparse_config.mk,
             # even though this fix is ugly
             'BLAS=%s' % (spec['blas'].libs.ld_flags + (
-                '-lstdc++' if '@4.5.1' in spec else '')),
+                ' -lstdc++' if '@4.5.1' in spec else '')),
             'LAPACK=%s' % spec['lapack'].libs.ld_flags,
         ]
 
+        # 64bit blas in UMFPACK:
+        if (spec.satisfies('^openblas+ilp64') or
+            spec.satisfies('^intel-mkl+ilp64') or
+            spec.satisfies('^intel-parallel-studio+mkl+ilp64')):
+            make_args.append('UMFPACK_CONFIG=-DLONGBLAS="long long"')
+
         # SuiteSparse defaults to using '-fno-common -fexceptions' in
         # CFLAGS, but not all compilers use the same flags for these
         # optimizations
@@ -107,7 +104,7 @@ class SuiteSparse(Package):
         elif '%pgi' in spec:
             make_args += ['CFLAGS+=--exceptions']
 
-        if '%xl' in spec or '%xl_r' in spec:
+        if spack_f77.endswith('xlf') or spack_f77.endswith('xlf_r'):
             make_args += ['CFLAGS+=-DBLAS_NO_UNDERSCORE']
 
         # Intel TBB in SuiteSparseQR
@@ -118,3 +115,22 @@ class SuiteSparse(Package):
             ]
 
         make('install', *make_args)
+
+    @property
+    def libs(self):
+        """Export the libraries of SuiteSparse.
+        Sample usage: spec['suite-sparse'].libs.ld_flags
+                      spec['suite-sparse:klu,btf'].libs.ld_flags
+        """
+        # Component libraries, ordered by dependency. Any missing components?
+        all_comps = ['klu', 'btf', 'umfpack', 'cholmod', 'colamd', 'amd',
+                     'camd', 'ccolamd', 'cxsparse', 'ldl', 'rbio', 'spqr',
+                     'suitesparseconfig']
+        query_parameters = self.spec.last_query.extra_parameters
+        comps = all_comps if not query_parameters else query_parameters
+        libs = find_libraries(['lib' + c for c in comps], root=self.prefix.lib,
+                              shared=True, recursive=False)
+        if not libs:
+            return None
+        libs += find_system_libraries('librt')
+        return libs
diff --git a/var/spack/repos/builtin/packages/sumaclust/package.py b/var/spack/repos/builtin/packages/sumaclust/package.py
index 923fb347b4..66f7820d59 100644
--- a/var/spack/repos/builtin/packages/sumaclust/package.py
+++ b/var/spack/repos/builtin/packages/sumaclust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/sundials/package.py b/var/spack/repos/builtin/packages/sundials/package.py
index 16cbcbe34f..0002b3e376 100644
--- a/var/spack/repos/builtin/packages/sundials/package.py
+++ b/var/spack/repos/builtin/packages/sundials/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import sys
@@ -33,16 +14,22 @@ class Sundials(CMakePackage):
 
     homepage = "https://computation.llnl.gov/projects/sundials"
     url = "https://computation.llnl.gov/projects/sundials/download/sundials-2.7.0.tar.gz"
-    maintainers = ['cswoodward', 'gardner48']
+    maintainers = ['cswoodward', 'gardner48', 'balos1']
 
     # ==========================================================================
     # Versions
     # ==========================================================================
-
-    version('3.1.0', '1a84ca41c7f71067e03d519ddbcd9dae')
-    version('3.0.0', '5163a44cedd7398bddda442ba00313b8')
-    version('2.7.0', 'c304631b9bc82877d7b0e9f4d4fd94d3')
-    version('2.6.2', '3deeb0ede9f514184c6bd83ecab77d95')
+    version('4.0.0-dev.2', sha256='124fc12f2a68d32210c20f5005510607e0833764afaef2a70b741bc922519984')
+    version('4.0.0-dev.1', sha256='6354e1d266b60c23766137b4ffa9bbde8bca97a562ccd94cab756b597ed753c1')
+    version('4.0.0-dev', sha256='50e526327461aebe463accf6ef56f9c6773df65025f3020b9ce68b83bbf5dd27')
+    version('3.2.1', sha256='47d94d977ab2382cdcdd02f72a25ebd4ba8ca2634bbb2f191fe1636e71c86808', preferred=True)
+    version('3.2.0', sha256='d2b690afecadf8b5a048bb27ab341de591d714605b98d3518985dfc2250e93f9')
+    version('3.1.2', sha256='a8985bb1e851d90e24260450667b134bc13d71f5c6effc9e1d7183bd874fe116')
+    version('3.1.1', sha256='a24d643d31ed1f31a25b102a1e1759508ce84b1e4739425ad0e18106ab471a24')
+    version('3.1.0', sha256='18d52f8f329626f77b99b8bf91e05b7d16b49fde2483d3a0ea55496ce4cdd43a')
+    version('3.0.0', sha256='28b8e07eecfdef66e2c0d0ea0cb1b91af6e4e94d71008abfe80c27bf39f63fde')
+    version('2.7.0', sha256='d39fcac7175d701398e4eb209f7e92a5b30a78358d4a0c0fcc23db23c11ba104')
+    version('2.6.2', sha256='d8ed0151509dd2b0f317b318a4175f8b95a174340fc3080b8c20617da8aa4d2f')
 
     # ==========================================================================
     # Variants
@@ -164,6 +151,9 @@ class Sundials(CMakePackage):
 
     # Build dependencies
     depends_on('cmake@2.8.1:', type='build')
+    depends_on('cmake@2.8.12:', type='build', when='@3.1.2')
+    depends_on('cmake@3.0.2:', type='build', when='@4.0.0-dev.1')
+    depends_on('cmake@3.1.3:', type='build', when='@3.2.0,4.0.0-dev.2')
 
     # MPI related dependencies
     depends_on('mpi', when='+mpi')
@@ -215,10 +205,10 @@ class Sundials(CMakePackage):
             return 'ON' if varstr in self.spec else 'OFF'
 
         fortran_flag = self.compiler.pic_flag
-        if spec.satisfies('%clang platform=darwin'):
-            mpif77 = Executable(self.spec['mpi'].mpif77)
-            libgfortran = LibraryList(mpif77('--print-file-name',
-                                             'libgfortran.a', output=str))
+        if (spec.satisfies('%clang platform=darwin')) and ('+fcmix' in spec):
+            f77 = Executable(self.compiler.f77)
+            libgfortran = LibraryList(f77('--print-file-name',
+                                          'libgfortran.a', output=str))
             fortran_flag += ' ' + libgfortran.ld_flags
 
         # List of CMake arguments
@@ -325,6 +315,12 @@ class Sundials(CMakePackage):
                 '-DPETSC_LIBRARY_DIR=%s' % spec['petsc'].prefix.lib
             ])
 
+        # Building with RAJA
+        if '+raja' in spec:
+            args.extend([
+                '-DRAJA_DIR=%s' % spec['raja'].prefix.share.raja.cmake
+            ])
+
         # Examples
         if spec.satisfies('@3.0.0:'):
             args.extend([
@@ -374,6 +370,8 @@ class Sundials(CMakePackage):
         Spack's generic cc and f77. We want them to be bound to
         whatever compiler they were built with."""
 
+        spec = self.spec
+
         kwargs = {'ignore_absent': True, 'backup': False, 'string': True}
         dirname = os.path.join(self.prefix, 'examples')
 
@@ -469,10 +467,46 @@ class Sundials(CMakePackage):
             filter_file(r'^CPP\s*=.*', self.compiler.cc,
                         os.path.join(dirname, filename), **kwargs)
 
-        for filename in f77_files:
-            filter_file(os.environ['F77'], self.compiler.f77,
-                        os.path.join(dirname, filename), **kwargs)
-
-        for filename in f90_files:
-            filter_file(os.environ['FC'], self.compiler.fc,
-                        os.path.join(dirname, filename), **kwargs)
+        if ('+fcmix' in spec) and ('+examples-f77' in spec):
+            for filename in f77_files:
+                filter_file(os.environ['F77'], self.compiler.f77,
+                            os.path.join(dirname, filename), **kwargs)
+
+        if ('+fcmix' in spec) and ('+examples-f90' in spec):
+            for filename in f90_files:
+                filter_file(os.environ['FC'], self.compiler.fc,
+                            os.path.join(dirname, filename), **kwargs)
+
+    @property
+    def headers(self):
+        """Export the headers and defines of SUNDIALS.
+           Sample usage: spec['sundials'].headers.cpp_flags
+        """
+        # SUNDIALS headers are inside subdirectories, so we use a fake header
+        # in the include directory.
+        hdr = find(self.prefix.include.nvector, 'nvector_serial.h',
+                   recursive=False)
+        return HeaderList(join_path(self.spec.prefix.include, 'fake.h')) \
+            if hdr else None
+
+    @property
+    def libs(self):
+        """Export the libraries of SUNDIALS.
+           Sample usage: spec['sundials'].libs.ld_flags
+                         spec['sundials:arkode,cvode'].libs.ld_flags
+        """
+        query_parameters = self.spec.last_query.extra_parameters
+        if not query_parameters:
+            sun_libs = 'libsundials_*[!0-9]'
+            # Q: should the result be ordered by dependency?
+        else:
+            sun_libs = ['libsundials_' + p for p in query_parameters]
+        search_paths = [[self.prefix.lib, False], [self.prefix.lib64, False],
+                        [self.prefix, True]]
+        is_shared = '+shared' in self.spec
+        for path, recursive in search_paths:
+            libs = find_libraries(sun_libs, root=path, shared=is_shared,
+                                  recursive=recursive)
+            if libs:
+                return libs
+        return None  # Raise an error
diff --git a/var/spack/repos/builtin/packages/superlu-dist/package.py b/var/spack/repos/builtin/packages/superlu-dist/package.py
index cc7058236a..122b706b42 100644
--- a/var/spack/repos/builtin/packages/superlu-dist/package.py
+++ b/var/spack/repos/builtin/packages/superlu-dist/package.py
@@ -1,54 +1,33 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 glob
-import os
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class SuperluDist(Package):
+class SuperluDist(CMakePackage):
     """A general purpose library for the direct solution of large, sparse,
     nonsymmetric systems of linear equations on high performance machines."""
+
     homepage = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
-    url = "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz"
+    url      = "https://github.com/xiaoyeli/superlu_dist/archive/v6.0.0.tar.gz"
+    git      = "https://github.com/xiaoyeli/superlu_dist.git"
 
-    version('develop', git='https://github.com/xiaoyeli/superlu_dist', tag='master')
-    version('xsdk-0.2.0', git='https://github.com/xiaoyeli/superlu_dist', tag='xsdk-0.2.0')
-    version('5.2.2', 'a685ef7fb7859b24c8c9d5d5f121a8a5')
-    version('5.2.1', 'af857778ffeb04aea02aa4843e6e8e1d')
-    version('5.1.3', '3a9e88a8469aa7f319f0364364b8da35')
-    version('5.1.1', '12638c631733a27dcbd87110e9f9cb1e')
-    version('5.1.0', '6bb86e630bd4bd8650243aed8fd92eb9')
-    version('5.0.0', '2b53baf1b0ddbd9fcf724992577f0670')
-    version('4.3', 'ee66c84e37b4f7cc557771ccc3dc43ae')
-    version('4.2', 'ae9fafae161f775fbac6eba11e530a65')
-    version('4.1', '4edee38cc29f687bd0c8eb361096a455')
-    version('4.0', 'c0b98b611df227ae050bc1635c6940e0')
-    version('3.3', 'f4805659157d93a962500902c219046b')
+    version('develop', branch='master')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
+    version('6.0.0', 'ff6cdfa0263d595708bbb6d11fb780915d8cfddab438db651e246ea292f37ee4')
+    version('5.4.0', '3ac238fe082106a2c4dbaf0c22af1ff1247308ffa8f053de9d78c3ec7dd0d801')
+    version('5.3.0', '49ed110bdef1e284a0181d6c7dd1fae3aa110cb45f67c6aa5cb791070304d670')
+    version('5.2.2', '65cfb9ace9a81f7affac4ad92b9571badf0f10155b3468531b0fffde3bd8e727')
+    version('5.2.1', '67cf3c46cbded4cee68e2a9d601c30ab13b08091c8cdad95b0a8e018b6d5d1f1')
+    version('5.1.3', '58e3dfdb4ae6f8e3f6f3d5ee5e851af59b967c4483cdb3b15ccd1dbdf38f44f9')
+    version('5.1.2', 'e34865ad6696ee6a6d178b4a01c8e19103a7d241ba9de043603970d63b0ee1e2')
+    version('5.1.0', '73f292ab748b590b6dd7469e6986aeb95d279b8b8b3da511c695a396bdbc996c')
+    version('5.0.0', '78d1d6460ff16b3f71e4bcd7306397574d54d421249553ccc26567f00a10bfc6')
 
-    variant('int64', default=False,
-            description="Use 64bit integers")
+    variant('int64', default=False, description='Build with 64 bit integers')
+    variant('shared', default=True, description='Build shared libraries')
 
     depends_on('mpi')
     depends_on('blas')
@@ -56,61 +35,35 @@ class SuperluDist(Package):
     depends_on('parmetis')
     depends_on('metis@5:')
 
-    def install(self, spec, prefix):
+    def cmake_args(self):
+        spec = self.spec
         lapack_blas = spec['lapack'].libs + spec['blas'].libs
-        makefile_inc = []
-        makefile_inc.extend([
-            'PLAT         = _mac_x',
-            'DSuperLUroot = %s' % self.stage.source_path,
-            'DSUPERLULIB  = $(DSuperLUroot)/lib/libsuperlu_dist.a',
-            'BLASDEF      = -DUSE_VENDOR_BLAS',
-            'BLASLIB      = %s' % lapack_blas.ld_flags,
-            'METISLIB     = %s' % spec['metis'].libs.ld_flags,
-            'PARMETISLIB  = %s' % spec['parmetis'].libs.ld_flags,
-            'FLIBS        =',
-            'LIBS         = $(DSUPERLULIB) $(BLASLIB) $(PARMETISLIB) $(METISLIB)',  # noqa
-            'ARCH         = ar',
-            'ARCHFLAGS    = cr',
-            'RANLIB       = true',
-            'CC           = {0}'.format(self.spec['mpi'].mpicc),
-            'CFLAGS       = %s %s -O2 %s %s %s' % (
-                self.compiler.pic_flag,
-                '' if '%pgi' in spec else '-std=c99',
-                spec['parmetis'].headers.cpp_flags,
-                spec['metis'].headers.cpp_flags,
-                '-D_LONGINT' if '+int64' in spec and not
-                self.spec.satisfies('@5.2.0:') else ''),
-            'XSDK_INDEX_SIZE = %s' % ('64' if '+int64' in spec else '32'),
-            'NOOPTS       = %s -std=c99' % (
-                self.compiler.pic_flag),
-            'FORTRAN      = {0}'.format(self.spec['mpi'].mpif77),
-            'F90FLAGS     = -O2',
-            'LOADER       = {0}'.format(self.spec['mpi'].mpif77),
-            'LOADOPTS     =',
-            'CDEFS        = %s' % ("-DNoChange"
-                                       if '%xl' in spec or '%xl_r' in spec
-                                       else "-DAdd_")
-        ])
-
-        with open('make.inc', 'w') as fh:
-            fh.write('\n'.join(makefile_inc))
-
-        mkdirp(os.path.join(self.stage.source_path, 'lib'))
-        make("lib", parallel=False)
-
-        # FIXME:
-        # cd "EXAMPLE" do
-        # system "make"
+        args = [
+            '-DCMAKE_C_COMPILER=%s' % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s' % spec['mpi'].mpicxx,
+            '-DCMAKE_INSTALL_LIBDIR:STRING=%s' % self.prefix.lib,
+            '-DTPL_BLAS_LIBRARIES=%s' % lapack_blas.ld_flags,
+            '-DUSE_XSDK_DEFAULTS=YES',
+            '-DTPL_PARMETIS_LIBRARIES=%s' % spec['parmetis'].libs.ld_flags +
+            ';' + spec['metis'].libs.ld_flags,
+            '-DTPL_PARMETIS_INCLUDE_DIRS=%s' % spec['parmetis'].prefix.include
+        ]
 
-        # need to install by hand
-        headers_location = self.prefix.include
-        mkdirp(headers_location)
-        mkdirp(prefix.lib)
+        if '+int64' in spec:
+            args.append('-DXSDK_INDEX_SIZE=64')
+        else:
+            args.append('-DXSDK_INDEX_SIZE=32')
 
-        headers = glob.glob(join_path(self.stage.source_path, 'SRC', '*.h'))
-        for h in headers:
-            install(h, headers_location)
+        if '+shared' in spec:
+            args.append('-DBUILD_SHARED_LIBS:BOOL=ON')
+        else:
+            args.append('-DBUILD_SHARED_LIBS:BOOL=OFF')
+        return args
 
-        superludist_lib = join_path(self.stage.source_path,
-                                    'lib/libsuperlu_dist.a')
-        install(superludist_lib, self.prefix.lib)
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if name == 'cxxflags':
+            flags.append(self.compiler.cxx11_flag)
+        if name == 'cflags' and '%pgi' not in self.spec:
+            flags.append('-std=c99')
+        return (None, None, flags)
diff --git a/var/spack/repos/builtin/packages/superlu-mt/package.py b/var/spack/repos/builtin/packages/superlu-mt/package.py
index 99ecdcc642..fa663b9395 100644
--- a/var/spack/repos/builtin/packages/superlu-mt/package.py
+++ b/var/spack/repos/builtin/packages/superlu-mt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py
index 72f13ffde7..bb657b780f 100644
--- a/var/spack/repos/builtin/packages/superlu/package.py
+++ b/var/spack/repos/builtin/packages/superlu/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/supernova/package.py b/var/spack/repos/builtin/packages/supernova/package.py
new file mode 100644
index 0000000000..ed7b85405d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/supernova/package.py
@@ -0,0 +1,45 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Supernova(Package):
+    """Supernova is a software package for de novo assembly from Chromium
+    Linked-Reads that are made from a single whole-genome library from an
+    individual DNA source.
+
+    A key feature of Supernova is that it creates diploid assemblies, thus
+    separately representing maternal and paternal chromosomes over very long
+    distances. Almost all other methods instead merge homologous chromosomes
+    into single incorrect 'consensus' sequences. Supernova is the only
+    practical method for creating diploid assemblies of large genomes.
+
+    To install this package, you will need to go to the supernova download
+    page of supernova, register with your email address and download
+    supernova yourself. Spack will search your current directory for the
+    download file. Alternatively, add this file yo a mirror so that Spack
+    can find it. For instructions on how to set up a mirror, see
+    http://spack.readthedocs.io/en/latest/mirrors.html"""
+
+    homepage = "https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome"
+
+    version('2.0.1', '3697ce043c798fcb672fe0a66c56d6f0')
+
+    depends_on('bcl2fastq2')
+
+    def url_for_version(self, version):
+        return "file://{0}/supernova-{1}.tar.gz".format(os.getcwd(), version)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix)
+
+    def install(self, spec, prefix):
+        rm = which('rm')
+        # remove the broken symlinks
+        rm('anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtcl.so',
+            'anaconda-cs/2.2.0-anaconda-cs-c7/lib/libtk.so')
+        install_tree('.', prefix)
diff --git a/var/spack/repos/builtin/packages/sw4lite/package.py b/var/spack/repos/builtin/packages/sw4lite/package.py
index 868fc88ec2..379eedd6bf 100644
--- a/var/spack/repos/builtin/packages/sw4lite/package.py
+++ b/var/spack/repos/builtin/packages/sw4lite/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -34,9 +15,10 @@ class Sw4lite(MakefilePackage):
 
     homepage = "https://geodynamics.org/cig/software/sw4"
     url      = "https://github.com/geodynamics/sw4lite/archive/v1.0.zip"
+    git      = "https://github.com/geodynamics/sw4lite.git"
 
-    version('develop', git='https://github.com/geodynamics/sw4lite',
-            branch='master')
+    version('develop', branch='master')
+    version('1.1', sha256='34b5f7b56f9e40474c14abebcaa024192de018de6beb6dafee53d3db5b07c6d3')
     version('1.0', '3d911165f4f2ff6d5f9c1bd56ab6723f')
 
     variant('openmp', default=True, description='Build with OpenMP support')
diff --git a/var/spack/repos/builtin/packages/swap-assembler/package.py b/var/spack/repos/builtin/packages/swap-assembler/package.py
new file mode 100644
index 0000000000..938bb4c71d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/swap-assembler/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class SwapAssembler(MakefilePackage):
+    """A scalable and fully parallelized genome assembler."""
+
+    homepage = "https://sourceforge.net/projects/swapassembler/"
+    url      = "https://sourceforge.net/projects/swapassembler/files/SWAP_Assembler-0.4.tar.bz2/download"
+
+    version('0.4', '944f2aeae4f451be81160bb625304fc3')
+
+    depends_on('mpich')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('$(CC) -O2', '$(CC) -pthread -O2', string=True)
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/swarm/package.py b/var/spack/repos/builtin/packages/swarm/package.py
index 0f52b9774e..277a10974f 100644
--- a/var/spack/repos/builtin/packages/swarm/package.py
+++ b/var/spack/repos/builtin/packages/swarm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/swfft/package.py b/var/spack/repos/builtin/packages/swfft/package.py
index aeb7e00293..4297933639 100644
--- a/var/spack/repos/builtin/packages/swfft/package.py
+++ b/var/spack/repos/builtin/packages/swfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,19 +11,29 @@ class Swfft(MakefilePackage):
     """A stand-alone version of HACC's distributed-memory, pencil-decomposed,
     parallel 3D FFT."""
 
-    homepage = 'https://xgitlab.cels.anl.gov/hacc/SWFFT'
-
-    url = "https://xgitlab.cels.anl.gov/hacc/SWFFT/repository/v1.0/archive.tar.gz"
+    homepage = "https://xgitlab.cels.anl.gov/hacc/SWFFT"
+    url      = "https://xgitlab.cels.anl.gov/api/v4/projects/hacc%2FSWFFT/repository/archive.tar.gz?sha=v1.0"
+    git      = "https://xgitlab.cels.anl.gov/hacc/SWFFT.git"
 
     version('1.0', '0fbc34544b97ba9c3fb19ef2d7a0f076')
-    version('develop', git='https://xgitlab.cels.anl.gov/hacc/SWFFT',
-            branch='master')
+    version('develop', branch='master')
 
     depends_on('mpi')
     depends_on('fftw')
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
+    @property
+    def build_targets(self):
+        targets = []
+        spec = self.spec
+
+        targets.append('DFFT_MPI_CC=%s' % spec['mpi'].mpicc)
+        targets.append('DFFT_MPI_CXX=%s' % spec['mpi'].mpicxx)
+        targets.append('DFFT_MPI_F90=%s' % spec['mpi'].mpifc)
+
+        return targets
+
     def install(self, spec, prefix):
         mkdir(prefix.bin)
         install('build/CheckDecomposition', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/swiftsim/package.py b/var/spack/repos/builtin/packages/swiftsim/package.py
index 4f094c561f..494d92c1d7 100644
--- a/var/spack/repos/builtin/packages/swiftsim/package.py
+++ b/var/spack/repos/builtin/packages/swiftsim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import llnl.util.tty as tty
 
@@ -33,10 +14,10 @@ class Swiftsim(AutotoolsPackage):
     """
 
     homepage = 'http://icc.dur.ac.uk/swift/'
-    url = 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'
+    url = 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'
 
-    version('0.3.0', git='https://gitlab.cosma.dur.ac.uk/swift/swiftsim.git',
-            commit='254cc1b563b2f88ddcf437b1f71da123bb9db733')
+    version('0.7.0', '1c703d7e20a31a3896e1c291bddd71ab')
+    version('0.3.0', '162ec2bdfdf44a31a08b3fcee23a886a')
 
     variant('mpi', default=True,
             description='Enable distributed memory parallelism')
diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py
index e9148333de..0d4c97a58f 100644
--- a/var/spack/repos/builtin/packages/swig/package.py
+++ b/var/spack/repos/builtin/packages/swig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 
 
diff --git a/var/spack/repos/builtin/packages/symengine/package.py b/var/spack/repos/builtin/packages/symengine/package.py
index 844e0c2e5e..b0bbd61e37 100644
--- a/var/spack/repos/builtin/packages/symengine/package.py
+++ b/var/spack/repos/builtin/packages/symengine/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -31,11 +12,12 @@ class Symengine(CMakePackage):
 
     homepage = "https://github.com/symengine/symengine"
     url      = "https://github.com/symengine/symengine/archive/v0.2.0.tar.gz"
+    git      = "https://github.com/symengine/symengine.git"
 
+    version('develop', branch='master')
     version('0.3.0', 'e61d7513cca4963cd062616891de54c6')
     version('0.2.0', '45401561add36a13c1f0b0c5f8d7422d')
     version('0.1.0', '41ad7daed61fc5a77c285eb6c7303425')
-    version('develop', git='https://github.com/symengine/symengine.git')
 
     variant('boostmp',      default=False,
             description='Compile with Boost multi-precision integer library')
diff --git a/var/spack/repos/builtin/packages/sympol/package.py b/var/spack/repos/builtin/packages/sympol/package.py
index 215c23ae98..ca69920323 100644
--- a/var/spack/repos/builtin/packages/sympol/package.py
+++ b/var/spack/repos/builtin/packages/sympol/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/sz/package.py b/var/spack/repos/builtin/packages/sz/package.py
index 5ff44d18b2..f9d1c0f2a6 100644
--- a/var/spack/repos/builtin/packages/sz/package.py
+++ b/var/spack/repos/builtin/packages/sz/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,10 +11,20 @@ class Sz(AutotoolsPackage):
     """Error-bounded Lossy Compressor for HPC Data."""
 
     homepage = "https://collab.cels.anl.gov/display/ESR/SZ"
-    url      = "https://github.com/disheng222/SZ/archive/v1.4.11.0.tar.gz"
+    url      = "https://github.com/disheng222/SZ/archive/v2.0.2.0.tar.gz"
+
+    git      = "https://github.com/disheng222/SZ.git"
 
-    version('develop', git='https://github.com/disheng222/SZ.git',
-            branch='master')
+    version('develop', branch='master')
+    version('2.0.2.0',  sha256='176c65b421bdec8e91010ffbc9c7bf7852c799972101d6b66d2a30d9702e59b0')
+    version('1.4.13.5', sha256='b5e37bf3c377833eed0a7ca0471333c96cd2a82863abfc73893561aaba5f18b9')
+    version('1.4.13.4', sha256='c99b95793c48469cac60e6cf82f921babf732ca8c50545a719e794886289432b')
+    version('1.4.13.3', sha256='9d80390f09816bf01b7a817e07339030d596026b00179275616af55ed3c1af98')
+    version('1.4.13.2', sha256='bc45329bf54876ed0f721998940855dbd5fda54379ef35dad8463325488ea4c6')
+    version('1.4.13.0', sha256='baaa7fa740a47e152c319b8d7b9a69fe96b4fea5360621cdc96cb250635f946f')
+    version('1.4.12.3', sha256='c1413e1c260fac7a48cb11c6dd705730525f134b9f9b244af59885d564ac7a6f')
+    version('1.4.12.1', sha256='98289d75481a6e407e4027b5e23013ae83b4aed88b3f150327ea711322cd54b6')
+    version('1.4.11.1', sha256='6cbc5b233a3663a166055f1874f17c96ba29aa5a496d352707ab508288baa65c')
     version('1.4.11.0', '10dee28b3503821579ce35a50e352cc6')
     version('1.4.10.0', '82e23dc5a51bcce1f70ba7e3b68a5965')
     version('1.4.9.2',  '028ce90165b7a4c4051d4c0189f193c0')
diff --git a/var/spack/repos/builtin/packages/tabix/package.py b/var/spack/repos/builtin/packages/tabix/package.py
index 85c1b03e59..c35d15c1e8 100644
--- a/var/spack/repos/builtin/packages/tabix/package.py
+++ b/var/spack/repos/builtin/packages/tabix/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Tabix(MakefilePackage):
     """Generic indexer for TAB-delimited genome position files"""
 
     homepage = "https://github.com/samtools/tabix"
-    url      = "https://github.com/samtools/tabix"
+    git      = "https://github.com/samtools/tabix.git"
 
-    version('2013-12-16', git='https://github.com/samtools/tabix.git', commit='1ae158ac79b459f5feeed7490c67519b14ce9f35')
+    version('2013-12-16', commit='1ae158ac79b459f5feeed7490c67519b14ce9f35')
 
     depends_on('perl', type=('build', 'run'))
     depends_on('python', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/talass/package.py b/var/spack/repos/builtin/packages/talass/package.py
new file mode 100644
index 0000000000..94e0a10b28
--- /dev/null
+++ b/var/spack/repos/builtin/packages/talass/package.py
@@ -0,0 +1,58 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Talass(CMakePackage):
+    """TALASS: Topological Analysis of Large-Scale Simulations
+    This package compiles the talass tool chain thar implements
+    various topological algorithms to analyze large scale data.
+    The package is organized hierarchical FileFormat < Statistics
+    < StreamingTopology and any of the subsets can be build stand-
+    alone."""
+
+    homepage = "http://www.cedmav.org/research/project/16-talass.html"
+    git      = "git@bitbucket.org:cedmav/talass.git"
+
+    version('2018-09-21', commit='bf7da9bb54a026d8cb575b5be28b9c88095cb307')
+
+    # The default precision and index space sizes
+    variant('precision', default='32', values=('32', '64'),
+            description='Precision of the function values')
+    variant('global', default='32', values=('16', '32', '64'),
+            description='Number of bits used for the global index space')
+    variant('local', default='32', values=('16', '32', '64'),
+            description='Number of bits used for the local index space')
+
+    root_cmakelists_dir = 'StreamingTopology'
+
+    def cmake_args(self):
+        variants = self.spec.variants
+
+        args = []
+
+        if int(variants['local'].value) > int(variants['global'].value):
+            raise InstallError('The global index space (%d bits) must be at least as large\
+ as the local index space (% bits)' % (variants['global'].value,
+                                       variants['local'].value))
+
+        if variants['precision'].value == '32':
+            args.append('-DFUNCTION_TYPE=float')
+        elif variants['precision'].value == '64':
+            args.append('-DFUNCTION_TYPE=double')
+
+        # Set global index space
+        args.append('-DGLOBAL_INDEX_TYPE=uint{0}_t'.format(
+            variants['global'].value))
+
+        # Set local index space
+        args.append('-DLOCAL_INDEX_TYPE=uint{0}_t'.format(
+            variants['local'].value))
+
+        # Deal with the PROJECT_INSTALL_PREFIX to enable Talass super builds
+        args.append('-DPROJECT_INSTALL_PREFIX=%s' % self.prefix)
+
+        return args
diff --git a/var/spack/repos/builtin/packages/talloc/package.py b/var/spack/repos/builtin/packages/talloc/package.py
index b2d7160a00..2fec8da46b 100644
--- a/var/spack/repos/builtin/packages/talloc/package.py
+++ b/var/spack/repos/builtin/packages/talloc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tantan/package.py b/var/spack/repos/builtin/packages/tantan/package.py
new file mode 100644
index 0000000000..df183d07d9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tantan/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tantan(MakefilePackage):
+    """tantan is a tool to mask simple regions (low complexity and
+    short-period tandem repeats) in DNA, RNA, and protein sequences."""
+
+    homepage = "http://cbrc3.cbrc.jp/~martin/tantan"
+    url      = "http://cbrc3.cbrc.jp/~martin/tantan/tantan-13.zip"
+
+    version('13', '90a30284a7d0cd04d797527d47bc8bd0')
+
+    def install(self, spec, prefix):
+        make('prefix={0}'.format(self.prefix), 'install')
diff --git a/var/spack/repos/builtin/packages/tar/package.py b/var/spack/repos/builtin/packages/tar/package.py
index d6b660016a..3f491a5cfc 100644
--- a/var/spack/repos/builtin/packages/tar/package.py
+++ b/var/spack/repos/builtin/packages/tar/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,8 +11,9 @@ class Tar(AutotoolsPackage):
     other kinds of manipulation."""
 
     homepage = "https://www.gnu.org/software/tar/"
-    url = "https://ftp.gnu.org/gnu/tar/tar-1.29.tar.gz"
+    url      = "https://ftpmirror.gnu.org/tar/tar-1.29.tar.gz"
 
+    version('1.30', 'e0c5ed59e4dd33d765d6c90caadd3c73')
     version('1.29', 'cae466e6e58c7292355e7080248f244db3a4cf755f33f4fa25ca7f9a7ed09af0')
     version('1.28', '6ea3dbea1f2b0409b234048e021a9fd7')
 
diff --git a/var/spack/repos/builtin/packages/targetp/package.py b/var/spack/repos/builtin/packages/targetp/package.py
index 5b7fde557c..8fa33e7b9d 100644
--- a/var/spack/repos/builtin/packages/targetp/package.py
+++ b/var/spack/repos/builtin/packages/targetp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/task/package.py b/var/spack/repos/builtin/packages/task/package.py
index b4fdd020de..93c58bc6eb 100644
--- a/var/spack/repos/builtin/packages/task/package.py
+++ b/var/spack/repos/builtin/packages/task/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Task(CMakePackage):
     homepage = "http://www.taskwarrior.org"
     url      = "http://taskwarrior.org/download/task-2.4.4.tar.gz"
 
+    version('2.5.1', 'bcd984a00d6d1eb6b40faf567419f784')
     version('2.4.4', '517450c4a23a5842df3e9905b38801b3')
 
     depends_on('cmake@2.8:', type='build')
diff --git a/var/spack/repos/builtin/packages/taskd/package.py b/var/spack/repos/builtin/packages/taskd/package.py
index 56adbf619f..43f6a8b7df 100644
--- a/var/spack/repos/builtin/packages/taskd/package.py
+++ b/var/spack/repos/builtin/packages/taskd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tasmanian/package.py b/var/spack/repos/builtin/packages/tasmanian/package.py
new file mode 100644
index 0000000000..908841bce9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tasmanian/package.py
@@ -0,0 +1,125 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tasmanian(CMakePackage):
+    """The Toolkit for Adaptive Stochastic Modeling and Non-Intrusive
+    ApproximatioN is a robust library for high dimensional integration and
+    interpolation as well as parameter calibration."""
+
+    homepage = 'http://tasmanian.ornl.gov'
+    url      = 'https://github.com/ORNL/TASMANIAN/archive/v6.0.tar.gz'
+    git      = 'https://github.com/ORNL/TASMANIAN.git'
+
+    version('develop', branch='master')
+
+    version('6.0', '43dcb1d2bcb2f2c829ad046d0e91e83d')  # use for xsdk-0.4.0
+    version('5.1', '5d904029a24470a6acf4a87d3339846e')
+
+    version('5.0', '4bf131841d786033863d271739be0f7a',
+            url='http://tasmanian.ornl.gov/documents/Tasmanian_v5.0.zip')
+
+    variant('xsdkflags', default=False,
+            description='enable XSDK defaults for Tasmanian')
+
+    variant('openmp', default=True,
+            description='add OpenMP support to Tasmanian')
+    # tested with OpenMP 3.1 (clang4) through 4.0-4.5 (gcc 5 - 8)
+
+    variant('blas', default=False,
+            description='add BLAS support to Tasmanian')
+
+    variant('mpi', default=False,
+            description='add MPI support to Tasmanian')
+
+    variant('cuda', default=False,
+            description='add CUDA support to Tasmanian')
+
+    variant('magma', default=False,
+            description='add UTK MAGMA support to Tasmanian')
+
+    variant('python', default=False,
+            description='add Python binding for Tasmanian')
+
+    variant('fortran', default=False,
+            description='add Fortran 90/95 interface to Tasmanian')
+
+    variant('build_type', default='Release',
+            description='CMake build type',
+            values=('Debug', 'Release'))
+
+    depends_on('cmake@3.5.1:', type='build')
+
+    depends_on('python@2.7:', when='+python', type=('build', 'run'))
+    depends_on('py-numpy', when='+python', type=('build', 'run'))
+
+    extends('python', when='+python', type=('build', 'run'))
+
+    depends_on('mpi', when="+mpi", type=('build', 'run'))  # openmpi 2 and 3 tested
+
+    depends_on('blas', when="+blas", type=('build', 'run'))  # openblas 0.2.18 or newer
+
+    depends_on('cuda@8.0.61:', when='+cuda', type=('build', 'run'))
+    depends_on('cuda@8.0.61:', when='+magma', type=('build', 'run'))
+
+    depends_on('magma@2.4.0:', when='+magma', type=('build', 'run'))
+
+    conflicts('-cuda', when='+magma')  # currently MAGMA only works with CUDA
+
+    # old versions
+    conflicts('+magma', when='@:5.1')  # magma does not work prior to 6.0
+    conflicts('+mpi', when='@:5.1')    # MPI is broken prior to 6.0
+    conflicts('+xsdkflags', when='@:5.1')  # 6.0 is the first version included in xSDK
+
+    def cmake_args(self):
+        spec = self.spec
+
+        if '+xsdkflags' in spec:
+            args = [
+                '-DUSE_XSDK_DEFAULTS:BOOL=ON',
+                '-DXSDK_ENABLE_PYTHON:BOOL={0}'.format(
+                    'ON' if '+python' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_MPI:BOOL={0}'.format(
+                    'ON' if '+mpi' in spec else 'OFF'),
+                '-DXSDK_ENABLE_OPENMP:BOOL={0}'.format(
+                    'ON' if '+openmp' in spec else 'OFF'),
+                '-DTPL_ENABLE_BLAS:BOOL={0}'.format(
+                    'ON' if '+blas' in spec else 'OFF'),
+                '-DXSDK_ENABLE_CUDA:BOOL={0}'.format(
+                    'ON' if '+cuda' in spec else 'OFF'),
+                '-DTPL_ENABLE_MAGMA:BOOL={0}'.format(
+                    'ON' if '+magma' in spec else 'OFF'),
+                '-DXSDK_ENABLE_FORTRAN:BOOL={0}'.format(
+                    'ON' if '+fortran' in spec else 'OFF'), ]
+        else:
+            args = [
+                '-DTasmanian_ENABLE_OPENMP:BOOL={0}'.format(
+                    'ON' if '+openmp' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_BLAS:BOOL={0}'.format(
+                    'ON' if '+blas' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_PYTHON:BOOL={0}'.format(
+                    'ON' if '+python' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_MPI:BOOL={0}'.format(
+                    'ON' if '+mpi' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_CUDA:BOOL={0}'.format(
+                    'ON' if '+cuda' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_MAGMA:BOOL={0}'.format(
+                    'ON' if '+magma' in spec else 'OFF'),
+                '-DTasmanian_ENABLE_FORTRAN:BOOL={0}'.format(
+                    'ON' if '+fortran' in spec else 'OFF'), ]
+
+        if spec.satisfies('+python'):
+            args.append('-DPYTHON_EXECUTABLE:FILEPATH={0}'.format(
+                self.spec['python'].command.path))
+
+        # _CUBLAS and _CUDA were separate options prior to 6.0
+        # skipping _CUBLAS leads to peformance regression
+        if spec.satisfies('@:5.1'):
+            args.append('-DTasmanian_ENABLE_CUBLAS={0}'.format(
+                        'ON' if '+cuda' in spec else 'OFF'))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/tassel/package.py b/var/spack/repos/builtin/packages/tassel/package.py
index eb48897e0e..5a568cc0f4 100644
--- a/var/spack/repos/builtin/packages/tassel/package.py
+++ b/var/spack/repos/builtin/packages/tassel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,10 +11,9 @@ class Tassel(Package):
        evolutionary patterns, and linkage disequilibrium."""
 
     homepage = "http://www.maizegenetics.net/tassel"
-    url      = "https://bitbucket.org/tasseladmin/tassel-5-source/get/master.tar.gz"
+    git      = "https://bitbucket.org/tasseladmin/tassel-5-standalone.git"
 
-    version('2017-07-22', git='https://bitbucket.org/tasseladmin/tassel-5-standalone.git',
-            commit='ae96ae75c3c9a9e8026140b6c775fa4685bdf531')
+    version('2017-07-22', commit='ae96ae75c3c9a9e8026140b6c775fa4685bdf531')
 
     depends_on('java', type=('build', 'run'))
     depends_on('perl', type=('build', 'run'))
diff --git a/var/spack/repos/builtin/packages/tau/package.py b/var/spack/repos/builtin/packages/tau/package.py
index 26b1e38b27..9aa29297e4 100644
--- a/var/spack/repos/builtin/packages/tau/package.py
+++ b/var/spack/repos/builtin/packages/tau/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import glob
@@ -37,6 +18,9 @@ class Tau(Package):
     homepage = "http://www.cs.uoregon.edu/research/tau"
     url      = "https://www.cs.uoregon.edu/research/tau/tau_releases/tau-2.25.tar.gz"
 
+    version('2.27.1', '4f98ff67ae5ab1ff2712f694bdec1fa9')
+    version('2.27',   '76602d35fc96f546b5b9dcaf09158651')
+    version('2.26.3', '4ec14e85b8f3560b58628512c7b49e17')
     version('2.25', '46cd48fa3f3c4ce0197017b3158a2b43')
     version('2.24.1', '6635ece6d1f08215b02f5d0b3c1e971b')
     version('2.24', '57ce33539c187f2e5ec68f0367c76db4')
diff --git a/var/spack/repos/builtin/packages/tcl-itcl/package.py b/var/spack/repos/builtin/packages/tcl-itcl/package.py
new file mode 100644
index 0000000000..0b0d842fe3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcl-itcl/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TclItcl(AutotoolsPackage):
+    """[incr Tcl] is the most widely used O-O system for Tcl. The name is a
+    play on C++, and [incr Tcl] provides a similar object model, including
+    multiple inheritence and public and private classes and variables."""
+
+    homepage = "https://sourceforge.net/projects/incrtcl/"
+    url      = "https://sourceforge.net/projects/incrtcl/files/%5Bincr%20Tcl_Tk%5D-4-source/itcl%204.0.4/itcl4.0.4.tar.gz"
+
+    version('4.0.4', 'c9c52afdd9435490e2db17c3c6c95ab4')
+
+    extends('tcl')
+
+    def configure_args(self):
+        args = [
+            '--enable-shared',
+            '--enable-threads',
+            '--with-tcl=' + self.spec['tcl'].tcl_lib_dir,
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/tcl-tcllib/package.py b/var/spack/repos/builtin/packages/tcl-tcllib/package.py
new file mode 100644
index 0000000000..46ec7b6d46
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcl-tcllib/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TclTcllib(AutotoolsPackage):
+    """Tcllib is a collection of utility modules for Tcl. These modules provide
+    a wide variety of functionality, from implementations of standard data
+    structures to implementations of common networking protocols. The intent is
+    to collect commonly used function into a single library, which users can
+    rely on to be available and stable."""
+
+    homepage   = "http://www.tcl.tk/software/tcllib"
+    url        = "https://sourceforge.net/projects/tcllib/files/tcllib/1.19/tcllib-1.19.tar.gz"
+    list_url   = "https://sourceforge.net/projects/tcllib/files/tcllib/"
+    list_depth = 1
+
+    version('1.19', '8d3990d01e3fb66480d441d18a7a7d0d')
+    version('1.18', '219361e6bdf9d9c0d79edbd1ab3e8080')
+    version('1.17', '4c75fbfbb518f8990fcd4686b976bd70')
+    version('1.16', 'e65e91f5ca188648019fdbe15fbfb9bf')
+    version('1.15', '7a0525912e8863f8d4360ab10e5450f8')
+    version('1.14', '55bac9afce54c3328f368918cc2d7a4b')
+
+    extends('tcl')
diff --git a/var/spack/repos/builtin/packages/tcl-tclxml/package.py b/var/spack/repos/builtin/packages/tcl-tclxml/package.py
new file mode 100644
index 0000000000..4f50a86809
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcl-tclxml/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TclTclxml(AutotoolsPackage):
+    """TclXML is an API for parsing XML documents using the Tcl scripting
+    language. It is also a package including a DOM implementation (TclDOM) and
+    XSL Transformations (TclXSLT). These allow Tcl scripts to read, manipulate
+    and write XML documents."""
+
+    homepage   = "http://tclxml.sourceforge.net/tclxml.html"
+    url        = "https://sourceforge.net/projects/tclxml/files/TclXML/3.2/tclxml-3.2.tar.gz"
+    list_url   = "https://sourceforge.net/projects/tclxml/files/TclXML/"
+    list_depth = 1
+
+    version('3.2', '9d1605246c899eff7db591bca3c23200')
+    version('3.1', '35de63a4ceba7a6fdb85dd1a62f2e881')
+
+    extends('tcl')
+
+    depends_on('tcl-tcllib')
+    depends_on('libxml2')
+    depends_on('libxslt')
+
+    def configure_args(self):
+        return [
+            '--exec-prefix={0}'.format(
+                self.prefix),
+            '--with-tcl={0}/lib'.format(
+                self.spec['tcl'].prefix),
+            '--with-xml2-config={0}/bin/xml2-config'.format(
+                self.spec['libxml2'].prefix),
+            '--with-xslt-config={0}/bin/xslt-config'.format(
+                self.spec['libxslt'].prefix),
+        ]
diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py
index 219c63e62b..7e2d57c764 100644
--- a/var/spack/repos/builtin/packages/tcl/package.py
+++ b/var/spack/repos/builtin/packages/tcl/package.py
@@ -1,27 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+
+from spack.util.environment import is_system_path
 from spack import *
 
 
@@ -36,12 +20,15 @@ class Tcl(AutotoolsPackage):
     homepage = "http://www.tcl.tk"
     url      = "http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz"
 
+    version('8.6.8', '81656d3367af032e0ae6157eff134f89')
     version('8.6.6', '5193aea8107839a79df8ac709552ecb7')
     version('8.6.5', '0e6426a4ca9401825fbc6ecf3d89a326')
     version('8.6.4', 'd7cbb91f1ded1919370a30edd1534304')
     version('8.6.3', 'db382feca91754b7f93da16dc4cdad1f')
     version('8.5.19', '0e6426a4ca9401825fbc6ecf3d89a326')
 
+    extendable = True
+
     depends_on('zlib')
 
     configure_directory = 'unix'
@@ -49,17 +36,103 @@ class Tcl(AutotoolsPackage):
     def setup_environment(self, spack_env, run_env):
         # When using Tkinter from within spack provided python+tk, python
         # will not be able to find Tcl/Tk unless TCL_LIBRARY is set.
-        run_env.set('TCL_LIBRARY', join_path(self.prefix.lib, 'tcl{0}'.format(
-            self.spec.version.up_to(2))))
+        run_env.set('TCL_LIBRARY', join_path(self.prefix, self.tcl_lib_dir))
 
     def install(self, spec, prefix):
         with working_dir(self.build_directory):
             make('install')
 
+            # http://wiki.tcl.tk/17463
+            if self.spec.satisfies('@8.6:'):
+                make('install-headers')
+
             # Some applications like Expect require private Tcl headers.
             make('install-private-headers')
 
+            # Copy source to install tree
+            # A user-provided install option might re-do this
+            # https://github.com/spack/spack/pull/4102/files
+            installed_src = join_path(
+                self.spec.prefix, 'share', self.name, 'src')
+            stage_src = os.path.realpath(self.stage.source_path)
+            install_tree(stage_src, installed_src)
+
+            # Replace stage dir -> installed src dir in tclConfig
+            filter_file(
+                stage_src, installed_src,
+                join_path(self.spec.prefix, 'lib', 'tclConfig.sh'))
+
+        # Don't install binaries in src/ tree
+        with working_dir(join_path(installed_src, self.configure_directory)):
+            make('clean')
+
     @run_after('install')
     def symlink_tclsh(self):
         with working_dir(self.prefix.bin):
             symlink('tclsh{0}'.format(self.version.up_to(2)), 'tclsh')
+
+    # ========================================================================
+    # Set up environment to make install easy for tcl extensions.
+    # ========================================================================
+
+    @property
+    def libs(self):
+        return LibraryList([])
+
+    @property
+    def command(self):
+        """Returns the tclsh command.
+
+        :returns: The tclsh command
+        :rtype: Executable
+        """
+        return Executable(os.path.realpath(self.prefix.bin.tclsh))
+
+    @property
+    def tcl_lib_dir(self):
+        """The Tcl version-specific library directory where all extensions are
+        installed."""
+        return 'lib'
+
+    @property
+    def tcl_builtin_lib_dir(self):
+        """The Tcl version-specific library directory where all builtin
+        extensions are installed."""
+        return join_path(self.tcl_lib_dir,
+                         'tcl{0}'.format(self.version.up_to(2)))
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        """Set TCLLIBPATH to include the tcl-shipped directory for
+        extensions and any other tcl extension it depends on.
+        For further info see: https://wiki.tcl.tk/1787"""
+
+        # If we set TCLLIBPATH, we must also ensure that the corresponding
+        # tcl is found in the build environment. This to prevent cases
+        # where a system provided tcl is run against the standard libraries
+        # of a Spack built tcl. See issue #7128 that relates to python but
+        # it boils down to the same situation we have here.
+        path = os.path.dirname(self.command.path)
+        if not is_system_path(path):
+            spack_env.prepend_path('PATH', path)
+
+        tcl_paths = [join_path(self.prefix, self.tcl_builtin_lib_dir)]
+
+        for d in dependent_spec.traverse(deptype=('build', 'run', 'test')):
+            if d.package.extends(self.spec):
+                tcl_paths.append(join_path(d.prefix, self.tcl_lib_dir))
+
+        # WARNING: paths in $TCLLIBPATH must be *space* separated,
+        # its value is meant to be a Tcl list, *not* an env list
+        # as explained here: https://wiki.tcl.tk/1787:
+        # "TCLLIBPATH is a Tcl list, not some platform-specific
+        # colon-separated or semi-colon separated format"
+        tcllibpath = ' '.join(tcl_paths)
+        spack_env.set('TCLLIBPATH', tcllibpath)
+
+        # For run time environment set only the path for
+        # dependent_spec and prepend it to TCLLIBPATH
+        if dependent_spec.package.extends(self.spec):
+            dependent_tcllibpath = join_path(dependent_spec.prefix,
+                                             self.tcl_lib_dir)
+            run_env.prepend_path('TCLLIBPATH', dependent_tcllibpath,
+                                 separator=' ')
diff --git a/var/spack/repos/builtin/packages/tclap/package.py b/var/spack/repos/builtin/packages/tclap/package.py
new file mode 100644
index 0000000000..ab067f4e3e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tclap/package.py
@@ -0,0 +1,16 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tclap(AutotoolsPackage):
+    """Templatized C++ Command Line Parser"""
+
+    homepage = "http://tclap.sourceforge.net"
+    url      = "https://downloads.sourceforge.net/project/tclap/tclap-1.2.2.tar.gz"
+
+    version('1.2.2', '6f35665814dca292eceda007d7e13bcb')
+    version('1.2.1', 'eb0521d029bf3b1cc0dcaa7e42abf82a')
diff --git a/var/spack/repos/builtin/packages/tcoffee/package.py b/var/spack/repos/builtin/packages/tcoffee/package.py
index 667f876dd9..2b2ed2d95e 100644
--- a/var/spack/repos/builtin/packages/tcoffee/package.py
+++ b/var/spack/repos/builtin/packages/tcoffee/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,9 +10,9 @@ class Tcoffee(MakefilePackage):
     """T-Coffee is a multiple sequence alignment program."""
 
     homepage = "http://www.tcoffee.org/"
-    url      = "https://github.com/cbcrg/tcoffee"
+    git      = "https://github.com/cbcrg/tcoffee.git"
 
-    version('2017-08-17', git='https://github.com/cbcrg/tcoffee.git', commit='f389b558e91d0f82e7db934d9a79ce285f853a71')
+    version('2017-08-17', commit='f389b558e91d0f82e7db934d9a79ce285f853a71')
 
     depends_on('perl', type=('build', 'run'))
     depends_on('blast-plus')
diff --git a/var/spack/repos/builtin/packages/tcptrace/package.py b/var/spack/repos/builtin/packages/tcptrace/package.py
new file mode 100644
index 0000000000..dcb7dcd7f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcptrace/package.py
@@ -0,0 +1,40 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+from os.path import join
+
+
+class Tcptrace(AutotoolsPackage):
+    """tcptrace is a tool written by Shawn Ostermann at Ohio University for
+       analysis of TCP dump files. It can take as input the files produced by
+       several popular packet-capture programs, including tcpdump, snoop,
+       etherpeek, HP Net Metrix, and WinDump."""
+
+    homepage = "http://www.tcptrace.org/"
+    url      = "http://www.tcptrace.org/download/tcptrace-6.6.7.tar.gz"
+
+    version('6.6.7', '68128dc1817b866475e2f048e158f5b9')
+
+    depends_on('bison', type='build')
+    depends_on('flex', type='build')
+    depends_on('libpcap')
+
+    # Fixes incorrect API access in libpcap.
+    # See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=545595
+    patch('tcpdump.patch')
+
+    @run_after('configure')
+    def patch_makefile(self):
+        # see https://github.com/blitz/tcptrace/blob/master/README.linux
+        makefile = FileFilter('Makefile')
+        makefile.filter(
+            "PCAP_LDLIBS = -lpcap",
+            "DEFINES += -D_BSD_SOURCE\nPCAP_LDLIBS = -lpcap")
+
+    def install(self, spec, prefix):
+        # The build system has trouble creating directories
+        mkdirp(prefix.bin)
+        install('tcptrace', join(prefix.bin, 'tcptrace'))
diff --git a/var/spack/repos/builtin/packages/tcptrace/tcpdump.patch b/var/spack/repos/builtin/packages/tcptrace/tcpdump.patch
new file mode 100644
index 0000000000..107d3a8af6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tcptrace/tcpdump.patch
@@ -0,0 +1,37 @@
+--- a/tcpdump.c
++++ b/tcpdump.c
+@@ -68,9 +68,6 @@
+ 
+ 
+ 
+-/* external ref, in case missing in older version */
+-extern int pcap_offline_read(void *, int, pcap_handler, u_char *);
+-
+ /* global pointer, the pcap info header */
+ static pcap_t *pcap;
+ 
+@@ -248,9 +245,12 @@
+     void		**pplast)
+ {
+     int ret;
++    struct pcap_pkthdr *pkt_header;
++    const u_char *pkt_data;
+ 
+     while (1) {
+-	if ((ret = pcap_offline_read(pcap,1,(pcap_handler)callback,0)) != 1) {
++       ret = pcap_next_ex(pcap, &pkt_header, &pkt_data);
++       if (ret != 1) {
+ 	    /* prob EOF */
+ 
+ 	    if (ret == -1) {
+@@ -265,6 +265,10 @@
+ 	    return(0);
+ 	}
+ 
++   if (callback(0, pkt_header, (char *)pkt_data)) {
++      continue;
++   }
++
+ 	/* at least one tcpdump implementation (AIX) seems to be */
+ 	/* storing NANOseconds in the usecs field of the timestamp. */
+ 	/* This confuses EVERYTHING.  Try to compensate. */
diff --git a/var/spack/repos/builtin/packages/tcsh/package.py b/var/spack/repos/builtin/packages/tcsh/package.py
index 84d0ed28b0..876957b150 100644
--- a/var/spack/repos/builtin/packages/tcsh/package.py
+++ b/var/spack/repos/builtin/packages/tcsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class Tcsh(AutotoolsPackage):
 
     version('6.20.00', '59d40ef40a68e790d95e182069431834')
 
-    def fedora_patch(commit, file, **kwargs):
+    def fedora_patch(commit, file, **kwargs):  # noqa
         prefix = 'https://src.fedoraproject.org/rpms/tcsh/raw/{0}/f/'.format(commit)
         patch('{0}{1}'.format(prefix, file), **kwargs)
 
diff --git a/var/spack/repos/builtin/packages/tealeaf/package.py b/var/spack/repos/builtin/packages/tealeaf/package.py
index c5031e9bd4..208d11ccc7 100644
--- a/var/spack/repos/builtin/packages/tealeaf/package.py
+++ b/var/spack/repos/builtin/packages/tealeaf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import glob
 
diff --git a/var/spack/repos/builtin/packages/templight-tools/package.py b/var/spack/repos/builtin/packages/templight-tools/package.py
new file mode 100644
index 0000000000..d15db66459
--- /dev/null
+++ b/var/spack/repos/builtin/packages/templight-tools/package.py
@@ -0,0 +1,18 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TemplightTools(CMakePackage):
+    """Supporting tools for the Templight Profiler"""
+
+    homepage = "https://github.com/mikael-s-persson/templight-tools"
+    git      = "https://github.com/mikael-s-persson/templight-tools.git"
+
+    version('develop', branch='master')
+
+    depends_on('cmake @2.8.7:', type='build')
+    depends_on('boost @1.48.1: +filesystem +graph +program_options +test')
diff --git a/var/spack/repos/builtin/packages/templight/develop-20180720.patch b/var/spack/repos/builtin/packages/templight/develop-20180720.patch
new file mode 100644
index 0000000000..986d6a7783
--- /dev/null
+++ b/var/spack/repos/builtin/packages/templight/develop-20180720.patch
@@ -0,0 +1,44 @@
+--- a/templight_driver.cpp	2018-07-20 17:32:51.064430826 +0200
++++ b/templight_driver.cpp	2018-07-20 17:33:58.476431081 +0200
+@@ -57,6 +57,9 @@
+ #include "llvm/Support/TargetSelect.h"
+ #include "llvm/Support/Timer.h"
+ #include "llvm/Support/raw_ostream.h"
++#ifdef _WIN32
++#include "Windows/WindowsSupport.h"
++#endif
+ 
+ #include "TemplightAction.h"
+ 
+@@ -475,7 +478,21 @@
+ 
+ }
+ 
+-
++// llvm::sys::Process::GetArgumentVector was renamed as of rL330216
++// https://reviews.llvm.org/rL330216
++// This aims to preserves compatibility, but the better way to do it would
++// be to let InitLLVM do the job
++std::error_code GetArgumentVector(
++    SmallVectorImpl<const char *> &ArgsOut, ArrayRef<const char *> ArgsIn,
++    SpecificBumpPtrAllocator<char> &ArgAllocator) {
++#ifdef _WIN32
++  return windows::GetCommandLineArguments(ArgsOut, ArgAllocator);
++#else
++  ArgsOut.append(ArgsIn.begin(), ArgsIn.end());
++  (void)ArgAllocator;
++  return std::error_code();
++#endif
++}
+ 
+ int main(int argc_, const char **argv_) {
+   llvm::sys::PrintStackTraceOnErrorSignal(argv_[0]);
+@@ -486,7 +503,7 @@
+ 
+   SmallVector<const char *, 256> argv;
+   llvm::SpecificBumpPtrAllocator<char> ArgAllocator;
+-  std::error_code EC = llvm::sys::Process::GetArgumentVector(
++  std::error_code EC = GetArgumentVector(
+       argv, llvm::makeArrayRef(argv_, argc_), ArgAllocator);
+   if (EC) {
+     llvm::errs() << "error: couldn't get arguments: " << EC.message() << '\n';
diff --git a/var/spack/repos/builtin/packages/templight/package.py b/var/spack/repos/builtin/packages/templight/package.py
new file mode 100644
index 0000000000..15264e6d22
--- /dev/null
+++ b/var/spack/repos/builtin/packages/templight/package.py
@@ -0,0 +1,147 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Templight(CMakePackage):
+    """Templight is a Clang-based tool to profile the time and memory
+       consumption of template instantiations and to perform interactive
+       debugging sessions to gain introspection into the template
+       instantiation process."""
+
+    homepage = "https://github.com/mikael-s-persson/templight"
+    git      = "https://github.com/mikael-s-persson/templight.git"
+    llvm_svn = "http://llvm.org/svn/llvm-project/{0}/trunk"
+
+    family = 'compiler'  # Used by lmod
+
+    # Templight is a patch to clang, so we have three versions to care about:
+    # - The one that will be used in Spack specifications
+    # - The git branch that we need to fetch from in the templight repo
+    # - The svn tag that we need to fetch from in the LLVM repos
+    version('develop', branch='master')
+    resource(name='llvm-trunk',
+             svn=llvm_svn.format('llvm'),
+             destination='.',
+             placement='llvm',
+             when='@develop')
+    resource(name='clang-trunk',
+             svn=llvm_svn.format('cfe'),
+             destination='llvm/tools',
+             placement='clang',
+             when='@develop')
+
+    # Templight has no stable release yet, and is supposed to be built against
+    # the LLVM trunk. As this is a brittle combination, I decided to
+    # artificially create a stable release based on what works today. Please
+    # feel free to remove this version once templight has stabilized.
+    version('2018.07.20', commit='91589f95427620dd0a2346bd69ba922f374aa42a')
+    resource(name='llvm-r337566',
+             svn=llvm_svn.format('llvm'),
+             revision=337566,
+             destination='.',
+             placement='llvm',
+             when='@2018.07.20')
+    resource(name='clang-r337566',
+             svn=llvm_svn.format('cfe'),
+             revision=337566,
+             destination='llvm/tools',
+             placement='clang',
+             when='@2018.07.20')
+    patch('develop-20180720.patch', when='@2018.07.20')
+
+    # Clang debug builds can be _huge_ (20+ GB), make sure you know what you
+    # are doing before switching to them
+    variant('build_type', default='Release',
+            description='CMake build type',
+            values=('Debug', 'Release', 'RelWithDebInfo', 'MinSizeRel'))
+
+    # NOTE: LLVM has many configurable tweaks and optional tools/extensions.
+    #       I did not think that  propagating all of these to a debugging and
+    #       performance analysis tool was worth the maintenance burden. But
+    #       if you disagree, the llvm package can be used for inspiration.
+
+    depends_on('cmake@3.4.3:', type='build')
+    depends_on('python')
+    depends_on('py-lit', type=('build', 'run'))
+
+    def patch(self):
+        # We start with the templight source tree and an "llvm" subdir.
+        # But we actually need an llvm source tree with a "templight" subdir.
+        # Let's flip the directory organization around
+        templight_files = os.listdir('.')
+        templight_files.remove('llvm')
+        templight_dir = 'llvm/tools/clang/tools/templight'
+        os.mkdir(templight_dir)
+        for name in templight_files:
+            os.rename(name, os.path.join(templight_dir, name))
+        for name in os.listdir('llvm'):
+            os.rename(os.path.join('llvm', name), name)
+        os.rmdir('llvm')
+
+        # Tell the clang build system that it needs to build templight
+        with open("tools/clang/tools/CMakeLists.txt", "a") as cmake_lists:
+            cmake_lists.write("add_clang_subdirectory(templight)")
+
+    def setup_environment(self, spack_env, run_env):
+        spack_env.append_flags('CXXFLAGS', self.compiler.cxx11_flag)
+        run_env.set('CC', join_path(self.spec.prefix.bin, 'templight'))
+        run_env.set('CXX', join_path(self.spec.prefix.bin, 'templight++'))
+
+    def cmake_args(self):
+        spec = self.spec
+
+        # Templight is a debugging tool, not a production compiler, so we only
+        # need a very bare-bones build of clang
+        #
+        # Minimal build config ideas were taken from the llvm package, with
+        # the templight-specific assumption that we will always be building
+        # for LLVM / Clang 5.0+ and can safely ignore older tricks.
+        #
+        cmake_args = [
+            '-DLLVM_REQUIRES_RTTI:BOOL=ON',
+            '-DCLANG_DEFAULT_OPENMP_RUNTIME:STRING=libomp',
+            '-DPYTHON_EXECUTABLE:PATH={0}'.format(spec['python'].command.path),
+            '-DLLVM_EXTERNAL_POLLY_BUILD:Bool=OFF',
+            '-DLLVM_TOOL_POLLY_BUILD:Bool=OFF',
+            '-DLLVM_POLLY_BUILD:Bool=OFF',
+            '-DLLVM_POLLY_LINK_INTO_TOOLS:Bool=OFF',
+            '-DLLVM_EXTERNAL_LLDB_BUILD:Bool=OFF',
+            '-DLLVM_TOOL_LLDB_BUILD:Bool=OFF',
+            '-DLLVM_TOOL_LLD_BUILD:Bool=OFF',
+            '-DLLVM_EXTERNAL_LIBUNWIND_BUILD:Bool=OFF',
+            '-DLLVM_EXTERNAL_LIBCXX_BUILD:Bool=OFF',
+            '-DLLVM_EXTERNAL_LIBCXXABI_BUILD:Bool=OFF',
+            '-DLLVM_EXTERNAL_COMPILER_RT_BUILD:Bool=OFF',
+        ]
+
+        targets = ['NVPTX', 'AMDGPU']
+
+        if 'x86' in spec.architecture.target.lower():
+            targets.append('X86')
+        elif 'arm' in spec.architecture.target.lower():
+            targets.append('ARM')
+        elif 'aarch64' in spec.architecture.target.lower():
+            targets.append('AArch64')
+        elif 'sparc' in spec.architecture.target.lower():
+            targets.append('Sparc')
+        elif ('ppc' in spec.architecture.target.lower() or
+              'power' in spec.architecture.target.lower()):
+            targets.append('PowerPC')
+
+        cmake_args.append(
+            '-DLLVM_TARGETS_TO_BUILD:Bool=' + ';'.join(targets))
+
+        if spec.satisfies('platform=linux'):
+            cmake_args.append('-DCMAKE_BUILD_WITH_INSTALL_RPATH=1')
+
+        return cmake_args
+
+    @run_after('install')
+    def post_install(self):
+        with working_dir(self.build_directory):
+            install_tree('bin', self.prefix.libexec.llvm)
diff --git a/var/spack/repos/builtin/packages/tetgen/package.py b/var/spack/repos/builtin/packages/tetgen/package.py
index b7091c097c..3a23ec2902 100644
--- a/var/spack/repos/builtin/packages/tetgen/package.py
+++ b/var/spack/repos/builtin/packages/tetgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import glob
diff --git a/var/spack/repos/builtin/packages/tethex/package.py b/var/spack/repos/builtin/packages/tethex/package.py
index 4ebe564522..75994e27e6 100644
--- a/var/spack/repos/builtin/packages/tethex/package.py
+++ b/var/spack/repos/builtin/packages/tethex/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,11 +15,12 @@ class Tethex(CMakePackage):
 
     homepage = "https://github.com/martemyev/tethex"
     url      = "https://github.com/martemyev/tethex/archive/v0.0.7.tar.gz"
+    git      = "https://github.com/martemyev/tethex.git"
 
     maintainers = ['davydden']
 
+    version('develop', branch='master')
     version('0.0.7', '6c9e4a18a6637deb4400c6d77ec03184')
-    version('develop', git='https://github.com/martemyev/tethex.git')
 
     variant('build_type', default='Release',
             description='The build type to build',
diff --git a/var/spack/repos/builtin/packages/texinfo/package.py b/var/spack/repos/builtin/packages/texinfo/package.py
index 47d65bcc80..b78f1e0b35 100644
--- a/var/spack/repos/builtin/packages/texinfo/package.py
+++ b/var/spack/repos/builtin/packages/texinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,10 +15,13 @@ class Texinfo(AutotoolsPackage):
     of the time. It is used by many non-GNU projects as well."""
 
     homepage = "https://www.gnu.org/software/texinfo/"
-    url      = "http://ftp.gnu.org/gnu/texinfo/texinfo-6.0.tar.gz"
+    url      = "https://ftpmirror.gnu.org/texinfo/texinfo-6.0.tar.gz"
 
+    version('6.5', '94e8f7149876793030e5518dd8d6e956')
     version('6.3', '9b08daca9bf8eccae9b0f884aba41f9e')
     version('6.0', 'e1a2ef5dce5018b53f0f6eed45b247a7')
     version('5.2', '1b8f98b80a8e6c50422125e07522e8db')
     version('5.1', '54e250014fe698fb4832016158747c03')
     version('5.0', '918432285abe6fe96c98355594c5656a')
+
+    depends_on('perl')
diff --git a/var/spack/repos/builtin/packages/texlive/package.py b/var/spack/repos/builtin/packages/texlive/package.py
index 3b26d2de94..4216be091e 100644
--- a/var/spack/repos/builtin/packages/texlive/package.py
+++ b/var/spack/repos/builtin/packages/texlive/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
+import platform
 
 
 class Texlive(Package):
@@ -44,8 +26,8 @@ class Texlive(Package):
     # itself is stable.  Don't let that fool you though, it's still
     # installing TeX **LIVE** from e.g. ctan.math.... below, which is
     # not reproducible.
-    version('live', '8f8fc301514c08a89a2e97197369c648',
-            url='ftp://tug.org/historic/systems/texlive/2017/install-tl-unx.tar.gz')
+    version('live', '946701aa28ca1f93e55e8310ce63fbf8',
+            url='ftp://tug.org/historic/systems/texlive/2018/install-tl-unx.tar.gz')
 
     # There does not seem to be a complete list of schemes.
     # Examples include:
@@ -65,6 +47,10 @@ class Texlive(Package):
 
     depends_on('perl', type='build')
 
+    def setup_environment(self, spack_env, run_env):
+        suffix = "%s-%s" % (platform.machine(), platform.system().lower())
+        run_env.prepend_path('PATH', join_path(self.prefix.bin, suffix))
+
     def install(self, spec, prefix):
         # Using texlive's mirror system leads to mysterious problems,
         # in lieu of being able to specify a repository as a variant, hardwire
diff --git a/var/spack/repos/builtin/packages/the-platinum-searcher/package.py b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py
index 212bc0d75e..e10c899600 100644
--- a/var/spack/repos/builtin/packages/the-platinum-searcher/package.py
+++ b/var/spack/repos/builtin/packages/the-platinum-searcher/package.py
@@ -1,45 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-import os
-import shutil
 
 
 class ThePlatinumSearcher(Package):
     """Fast parallel recursive grep alternative"""
-    homepage = "https://github.com/monochromegane/the_platinum_searcher"
-    url = "https://github.com/monochromegane/the_platinum_searcher"
 
-    package = 'github.com/monochromegane/the_platinum_searcher/...'
+    homepage = "https://github.com/monochromegane/the_platinum_searcher"
+    go       = "github.com/monochromegane/the_platinum_searcher/..."
 
-    version('head', go=package)
+    version('head')
 
     extends("go", deptypes='build')
 
     def install(self, spec, prefix):
-        env = os.environ
         env['GOPATH'] = self.stage.source_path + ':' + env['GOPATH']
         go('install', self.package, env=env)
-        shutil.copytree('bin', os.path.join(prefix, 'bin'))
+        install_tree('bin', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/the-silver-searcher/package.py b/var/spack/repos/builtin/packages/the-silver-searcher/package.py
index 31b269e286..e3ed85d41f 100644
--- a/var/spack/repos/builtin/packages/the-silver-searcher/package.py
+++ b/var/spack/repos/builtin/packages/the-silver-searcher/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,4 +19,4 @@ class TheSilverSearcher(AutotoolsPackage):
     depends_on('pcre')
     depends_on('xz')
     depends_on('zlib')
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/thornado-mini/package.py b/var/spack/repos/builtin/packages/thornado-mini/package.py
new file mode 100644
index 0000000000..dc96f2a4b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/thornado-mini/package.py
@@ -0,0 +1,77 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+import os
+
+
+class ThornadoMini(MakefilePackage):
+    """Code to solve the equation of radiative transfer in the
+    multi-group two-moment approximation"""
+
+    tags = ['proxy-app', 'ecp-proxy-app']
+
+    homepage = "https://sites.google.com/lbl.gov/exastar/home"
+    url      = "https://github.com/ECP-Astro/thornado_mini/archive/v1.0.tar.gz"
+    git      = "https://github.com/ECP-Astro/thornado_mini.git"
+
+    version('1.0', sha256='8a9f97acc823d374cce567831270cfcc50fa968949e49159c7e3442b93a2827d')
+
+    depends_on('mpi')
+    depends_on('hdf5+fortran')
+    depends_on('lapack')
+
+    parallel = False
+
+    def edit(self, spec, prefix):
+        os.environ['THORNADO_MACHINE'] = 'mymachine'
+        os.environ['THORNADO_DIR'] = os.getcwd()
+
+        file = open('Makefile', 'w')
+
+        file.write('FORTRAN_mymachine = %s %s\n' % (self.spec['mpi'].mpifc,
+                                                    self.compiler.openmp_flag))
+        file.write('FLINKER_mymachine = %s %s\n' % (self.spec['mpi'].mpifc,
+                                                    self.compiler.openmp_flag))
+        file.write('DEBUG_mymachine = -g -ffpe-trap=invalid,zero \
+        -fcheck=bounds\n')
+        file.write('OPTIMIZE_mymachine = -O2\n')
+        file.write('INCLUDE_HDF5_mymachine = \n')
+        file.write('INCLUDE_LAPACK_mymachine = \n')
+        file.write('LIBRARIES_HDF5_mymachine = \n')
+        file.write('LIBRARIES_LAPACK_mymachine = \n')
+        file.write('export FORTRAN_mymachine FLINKER_mymachine \
+        DEBUG_mymachine OPTIMIZE_mymachine\n')
+
+        file.write('all:\n')
+        file.write('\t@$(MAKE) -C $(THORNADO_DIR)/DeleptonizationProblem/Executables \
+        -f Makefile\n')
+
+        file.close()
+
+    @property
+    def build_targets(self):
+        targets = []
+
+        targets.append('INCLUDE_HDF5_mymachine = -I{0}'
+                       .format(self.spec['hdf5'].prefix.include))
+        targets.append('INCLUDE_LAPACK_mymachine = -I{0}'
+                       .format(self.spec['lapack'].prefix.include))
+        targets.append('LIBRARIES_HDF5_mymachine = {0} -lhdf5_fortran'
+                       .format(self.spec['hdf5'].libs.ld_flags))
+        targets.append('LIBRARIES_LAPACK_mymachine = {0}'
+                       .format(self.spec['lapack'].libs.ld_flags))
+
+        return targets
+
+    def install(self, spec, prefix):
+        install_tree('Documents', prefix.docs)
+        install('README.md', prefix.docs)
+
+        mkdirp(prefix.bin)
+        install('DeleptonizationProblem/Executables/'
+                'DeleptonizationProblem1D_%s' %
+                os.environ['THORNADO_MACHINE'], prefix.bin)
diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py
index 9e296123fd..35d3a897e9 100644
--- a/var/spack/repos/builtin/packages/thrift/package.py
+++ b/var/spack/repos/builtin/packages/thrift/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,6 +19,7 @@ class Thrift(Package):
     homepage = "http://thrift.apache.org"
     url      = "http://apache.mirrors.ionfish.org/thrift/0.9.2/thrift-0.9.2.tar.gz"
 
+    version('0.11.0', '0be59730ebce071eceaf6bfdb8d3a20e')
     version('0.10.0', '795c5dd192e310ffff38cfd9430d6b29')
     version('0.9.3', '88d667a8ae870d5adeca8cb7d6795442')
     version('0.9.2', '89f63cc4d0100912f4a1f8a9dee63678')
@@ -45,6 +27,8 @@ class Thrift(Package):
     # Currently only support for c-family and python
     variant('c', default=True,
             description="Build support for C-family languages")
+    variant('pic', default=True,
+            description='Build position independent code')
     variant('python', default=True,
             description="Build support for python")
 
@@ -63,9 +47,13 @@ class Thrift(Package):
     depends_on('zlib', when='+c')
     depends_on('libevent', when='+c')
 
+    def setup_environment(self, spack_env, run_env):
+        if '+pic' in self.spec:
+            spack_env.append_flags('CFLAGS', self.compiler.pic_flag)
+            spack_env.append_flags('CXXFLAGS', self.compiler.pic_flag)
+
     def install(self, spec, prefix):
         env['PY_PREFIX'] = prefix
-        env['JAVA_HOME'] = spec['java'].prefix
 
         # configure options
         options = ['--prefix=%s' % prefix]
@@ -73,6 +61,7 @@ class Thrift(Package):
         options.append('--with-boost=%s' % spec['boost'].prefix)
         options.append('--enable-tests=no')
 
+        options.append('--with-nodejs=no')
         options.append('--with-c=%s' % ('yes' if '+c' in spec else 'no'))
         options.append('--with-python=%s' %
                        ('yes' if '+python' in spec else 'no'))
diff --git a/var/spack/repos/builtin/packages/thrust/package.py b/var/spack/repos/builtin/packages/thrust/package.py
index c3d7c8dadb..4870f828be 100644
--- a/var/spack/repos/builtin/packages/thrust/package.py
+++ b/var/spack/repos/builtin/packages/thrust/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tig/package.py b/var/spack/repos/builtin/packages/tig/package.py
index 18c0597c46..58f07a011f 100644
--- a/var/spack/repos/builtin/packages/tig/package.py
+++ b/var/spack/repos/builtin/packages/tig/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tinyxml/CMakeLists.txt b/var/spack/repos/builtin/packages/tinyxml/CMakeLists.txt
index 93f124d716..32db119762 100644
--- a/var/spack/repos/builtin/packages/tinyxml/CMakeLists.txt
+++ b/var/spack/repos/builtin/packages/tinyxml/CMakeLists.txt
@@ -1,17 +1,21 @@
 cmake_minimum_required(VERSION 2.6)
 
 project(TinyXml)
+
 OPTION(TIXML_USE_STL "Use STL with TIXML" ON)
+OPTION(BUILD_SHARED_LIBS "build as shared library" ON)
+
 if(TIXML_USE_STL)
 	add_definitions(-DTIXML_USE_STL)
 endif(TIXML_USE_STL)
-add_library(
-	tinyxml
-	tinyxml.cpp
-	tinystr.cpp
-	tinyxmlerror.cpp
-	tinyxmlparser.cpp
-)
 
-INSTALL( FILES tinyxml.h tinystr.h DESTINATION include )
-INSTALL( TARGETS tinyxml ARCHIVE DESTINATION lib )
+if(BUILD_SHARED_LIBS)
+  add_library(tinyxml SHARED tinyxml.cpp tinystr.cpp tinyxmlerror.cpp tinyxmlparser.cpp)
+  install(TARGETS tinyxml LIBRARY DESTINATION lib)
+else()
+  add_library(tinyxml_static STATIC tinyxml.cpp tinystr.cpp tinyxmlerror.cpp tinyxmlparser.cpp)
+  set_target_properties(tinyxml_static PROPERTIES OUTPUT_NAME tinyxml)
+  install(TARGETS tinyxml_static ARCHIVE DESTINATION lib)
+endif(BUILD_SHARED_LIBS)
+
+install(FILES tinyxml.h tinystr.h DESTINATION include)
diff --git a/var/spack/repos/builtin/packages/tinyxml/package.py b/var/spack/repos/builtin/packages/tinyxml/package.py
index 46f3c32a75..a7962a1253 100644
--- a/var/spack/repos/builtin/packages/tinyxml/package.py
+++ b/var/spack/repos/builtin/packages/tinyxml/package.py
@@ -1,29 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from shutil import copyfile
 import os.path
 
 
@@ -35,10 +15,17 @@ class Tinyxml(CMakePackage):
 
     version('2.6.2', 'cba3f50dd657cb1434674a03b21394df9913d764')
 
+    variant('shared', default=True, description='Build a shared library')
+
     def url_for_version(self, version):
         url = "https://sourceforge.net/projects/tinyxml/files/tinyxml/{0}/tinyxml_{1}.tar.gz"
         return url.format(version.dotted, version.underscored)
 
     def patch(self):
-        copyfile(join_path(os.path.dirname(__file__),
-                           "CMakeLists.txt"), "CMakeLists.txt")
+        copy(join_path(os.path.dirname(__file__),
+             "CMakeLists.txt"), "CMakeLists.txt")
+
+    def cmake_args(self):
+        spec = self.spec
+        return [
+            '-DBUILD_SHARED_LIBS=%s' % ('YES' if '+shared' in spec else 'NO')]
diff --git a/var/spack/repos/builtin/packages/tinyxml2/package.py b/var/spack/repos/builtin/packages/tinyxml2/package.py
index d54418e099..06f2e7b673 100644
--- a/var/spack/repos/builtin/packages/tinyxml2/package.py
+++ b/var/spack/repos/builtin/packages/tinyxml2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tioga/package.py b/var/spack/repos/builtin/packages/tioga/package.py
new file mode 100644
index 0000000000..89ea1923e6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tioga/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tioga(CMakePackage):
+    """Topology Independent Overset Grid Assembly (TIOGA)"""
+
+    homepage = "https://github.com/jsitaraman/tioga"
+    git      = "https://github.com/jsitaraman/tioga.git"
+
+    # The master branch doesn't support CMake
+    version('develop', branch='nalu-api')
+
+    variant('shared', default=True,
+            description="Enable building shared libraries")
+    variant('pic', default=True,
+            description="Position independent code")
+
+    depends_on('mpi')
+
+    # Tioga has the fortran module file problem with parallel builds
+    parallel = False
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = [
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in spec else 'OFF'),
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % (
+                'ON' if '+pic' in spec else 'OFF'),
+            '-DMPI_CXX_COMPILER:PATH=%s' % spec['mpi'].mpicxx,
+            '-DMPI_C_COMPILER:PATH=%s' % spec['mpi'].mpicc,
+            '-DMPI_Fortran_COMPILER:PATH=%s' % spec['mpi'].mpifc
+        ]
+
+        return options
diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py
index b03d07013a..6b5c2cfbc1 100644
--- a/var/spack/repos/builtin/packages/tk/package.py
+++ b/var/spack/repos/builtin/packages/tk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,15 +16,22 @@ class Tk(AutotoolsPackage):
     homepage = "http://www.tcl.tk"
     url      = "http://prdownloads.sourceforge.net/tcl/tk8.6.5-src.tar.gz"
 
+    version('8.6.8', '5e0faecba458ee1386078fb228d008ba')
     version('8.6.6', 'dd7dbb3a6523c42d05f6ab6e86096e99')
     version('8.6.5', '11dbbd425c3e0201f20d6a51482ce6c4')
     version('8.6.3', '85ca4dbf4dcc19777fd456f6ee5d0221')
 
-    depends_on('tcl')
+    extends('tcl')
+
+    depends_on('tcl@8.6:')
     depends_on('libx11')
 
     configure_directory = 'unix'
 
+    @property
+    def libs(self):
+        return LibraryList([])
+
     def setup_environment(self, spack_env, run_env):
         # When using Tkinter from within spack provided python+tk, python
         # will not be able to find Tcl/Tk unless TK_LIBRARY is set.
diff --git a/var/spack/repos/builtin/packages/tldd/package.py b/var/spack/repos/builtin/packages/tldd/package.py
new file mode 100644
index 0000000000..7db26422e7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tldd/package.py
@@ -0,0 +1,28 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tldd(MakefilePackage):
+    """A program similar to ldd(1) but showing the output as a tree."""
+
+    homepage = "https://gitlab.com/miscripts/tldd"
+    git      = "https://gitlab.com/miscripts/tldd.git"
+
+    version('2018-10-05', commit='61cb512cc992ea6cbb7239e99ec7ac92ea072507')
+    version('master', branch='master')
+
+    depends_on('pstreams@0.8.0:')
+
+    def patch(self):
+        filter_file(
+            r'#include <pstreams/pstream.h>',
+            r'#include <pstream.h>',
+            'tldd.cc')
+
+    @property
+    def install_targets(self):
+        return ['install', 'PREFIX={0}'.format(self.prefix)]
diff --git a/var/spack/repos/builtin/packages/tmalign/package.py b/var/spack/repos/builtin/packages/tmalign/package.py
index ac7df4fb15..877caa929f 100644
--- a/var/spack/repos/builtin/packages/tmalign/package.py
+++ b/var/spack/repos/builtin/packages/tmalign/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tmhmm/package.py b/var/spack/repos/builtin/packages/tmhmm/package.py
index 2fe2517444..32a34ec0e8 100644
--- a/var/spack/repos/builtin/packages/tmhmm/package.py
+++ b/var/spack/repos/builtin/packages/tmhmm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/tmux/package.py b/var/spack/repos/builtin/packages/tmux/package.py
index 52c6c530d1..d2a39eab0e 100644
--- a/var/spack/repos/builtin/packages/tmux/package.py
+++ b/var/spack/repos/builtin/packages/tmux/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,8 +15,10 @@ class Tmux(AutotoolsPackage):
     """
 
     homepage = "http://tmux.github.io"
-    url = "https://github.com/tmux/tmux/releases/download/2.2/tmux-2.2.tar.gz"
+    url = "https://github.com/tmux/tmux/releases/download/2.6/tmux-2.6.tar.gz"
 
+    version('2.7', 'bcdfcf910c94c3e02ce6b1c035880306')
+    version('2.6', 'd541ff392249f94c4f3635793556f827')
     version('2.5', '4a5d73d96d8f11b0bdf9b6f15ab76d15')
     version('2.4', '6165d3aca811a3225ef8afbd1afcf1c5')
     version('2.3', 'fcfd1611d705d8b31df3c26ebc93bd3e')
diff --git a/var/spack/repos/builtin/packages/tmuxinator/package.py b/var/spack/repos/builtin/packages/tmuxinator/package.py
index 0f79d1f5bf..358d90965e 100644
--- a/var/spack/repos/builtin/packages/tmuxinator/package.py
+++ b/var/spack/repos/builtin/packages/tmuxinator/package.py
@@ -1,38 +1,18 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Tmuxinator(Package):
     """A session configuration creator and manager for tmux"""
+
     homepage = "https://github.com/tmuxinator/tmuxinator"
-    url      = "https://github.com/tmuxinator/tmuxinator"
+    git      = "https://github.com/tmuxinator/tmuxinator.git"
 
-    version('0.6.11',
-            git='https://github.com/tmuxinator/tmuxinator',
-            tag='v0.6.11')
+    version('0.6.11', tag='v0.6.11')
 
     extends('ruby')
 
diff --git a/var/spack/repos/builtin/packages/tophat/package.py b/var/spack/repos/builtin/packages/tophat/package.py
index 682e9581eb..3dcf571f87 100644
--- a/var/spack/repos/builtin/packages/tophat/package.py
+++ b/var/spack/repos/builtin/packages/tophat/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,10 +12,15 @@ class Tophat(AutotoolsPackage):
     homepage = "http://ccb.jhu.edu/software/tophat/index.shtml"
     url      = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"
 
+    version('2.1.2', 'db844fd7f53c519e716cd6222e6195b2')
     version('2.1.1', 'ffd18de2f893a95eb7e9d0c5283d241f')
 
     depends_on('autoconf', type='build')
-    depends_on('automake', type='build')
+    # 2.1.1 only builds with automake@1.15.1.  There's a patch here:
+    # https://github.com/spack/spack/pull/8244, which was incorporated
+    # upstream in 2.1.2, which is known to build with 1.16.1 and 1.15.1.
+    depends_on('automake',                        type='build')
+    depends_on('automake@1.15.1', when='@:2.1.1', type='build')
     depends_on('libtool',  type='build')
     depends_on('m4',       type='build')
 
diff --git a/var/spack/repos/builtin/packages/tppred/package.py b/var/spack/repos/builtin/packages/tppred/package.py
index 15bf756f7a..75f5209c9f 100644
--- a/var/spack/repos/builtin/packages/tppred/package.py
+++ b/var/spack/repos/builtin/packages/tppred/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tracer/package.py b/var/spack/repos/builtin/packages/tracer/package.py
new file mode 100644
index 0000000000..9fc7777596
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tracer/package.py
@@ -0,0 +1,39 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Tracer(MakefilePackage):
+    """Trace Replay and Network Simulation Framework"""
+
+    homepage = "https://tracer-codes.readthedocs.io"
+    git      = "https://github.com/LLNL/tracer.git"
+
+    maintainers = ['bhatele']
+
+    version('develop', branch='master')
+
+    variant('otf2', default=True, description='Use OTF2 traces for simulation')
+
+    depends_on('mpi')
+    depends_on('codes')
+    depends_on('otf2', when='+otf2')
+
+    build_directory = 'tracer'
+
+    @property
+    def build_targets(self):
+        targets = []
+
+        targets.append('CXX = {0}'.format(self.spec['mpi'].mpicxx))
+        if "+otf2" in self.spec:
+            targets.append('SELECT_TRACE = -DTRACER_OTF_TRACES=1')
+
+        return targets
+
+    def install(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make('PREFIX={0}'.format(prefix), 'install')
diff --git a/var/spack/repos/builtin/packages/transabyss/package.py b/var/spack/repos/builtin/packages/transabyss/package.py
index 32a266f9f2..c14bff0de7 100644
--- a/var/spack/repos/builtin/packages/transabyss/package.py
+++ b/var/spack/repos/builtin/packages/transabyss/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/transdecoder/package.py b/var/spack/repos/builtin/packages/transdecoder/package.py
index 022f205d67..76fa35a0f3 100644
--- a/var/spack/repos/builtin/packages/transdecoder/package.py
+++ b/var/spack/repos/builtin/packages/transdecoder/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,6 +18,7 @@ class Transdecoder(MakefilePackage):
     version('3.0.1', 'f62b86a15fcb78b1dada9f80cc25f300')
 
     depends_on('perl', type=('build', 'run'))
+    depends_on('perl-uri-escape', type='run')
 
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
diff --git a/var/spack/repos/builtin/packages/transposome/package.py b/var/spack/repos/builtin/packages/transposome/package.py
index 63e7d47f41..ad7e83d536 100644
--- a/var/spack/repos/builtin/packages/transposome/package.py
+++ b/var/spack/repos/builtin/packages/transposome/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/transset/package.py b/var/spack/repos/builtin/packages/transset/package.py
index 52f83c6edf..9b5693ed56 100644
--- a/var/spack/repos/builtin/packages/transset/package.py
+++ b/var/spack/repos/builtin/packages/transset/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Transset(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/trapproto/package.py b/var/spack/repos/builtin/packages/trapproto/package.py
index c7b2f3727d..8718e15b28 100644
--- a/var/spack/repos/builtin/packages/trapproto/package.py
+++ b/var/spack/repos/builtin/packages/trapproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/tree/package.py b/var/spack/repos/builtin/packages/tree/package.py
index 339ce2c139..978b3b5ae6 100644
--- a/var/spack/repos/builtin/packages/tree/package.py
+++ b/var/spack/repos/builtin/packages/tree/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
diff --git a/var/spack/repos/builtin/packages/treesub/package.py b/var/spack/repos/builtin/packages/treesub/package.py
new file mode 100644
index 0000000000..99feceddf8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/treesub/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Treesub(Package):
+    """A small program (which glues together other programs) that
+       allows a user to input a codon alignment in FASTA format and
+       produce an annotated phylogenetic tree showing which substitutions
+       occurred on a given branch. Originally written for colleagues at
+       the MRC NIMR."""
+
+    homepage = "https:/github.com/tamuri/treesub"
+    url      = "https://github.com/tamuri/treesub/archive/v0.2.tar.gz"
+
+    version('0.2', sha256='58b0d2638cf9ae1ad8705df26a57c32b52a69f50e7954debbd678c82772fdc56')
+    version('0.1', sha256='c083ecc5f7e9f11645a7e768f6a09fefcbb254b526212003527b4b8dd14723f1')
+
+    depends_on('jdk', type='run')
+    depends_on('ant', type='build')
+    depends_on('paml', type='run')
+    depends_on('raxml', type='run')
+    depends_on('figtree', type='run')
+
+    def install(self, spec, prefix):
+        ant = self.spec['ant'].command
+        ant('jar')
+
+        mkdirp(prefix.bin)
+        install_tree('dist', prefix.bin)
+
+        mkdirp(prefix.lib)
+        install_tree('lib', prefix.lib)
+
+        execscript = join_path(self.package_dir, 'treesub')
+        os.chmod(execscript, 0o775)
+        install(execscript, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/treesub/treesub b/var/spack/repos/builtin/packages/treesub/treesub
new file mode 100755
index 0000000000..8be7cb73e6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/treesub/treesub
@@ -0,0 +1,2 @@
+#!/bin/sh
+java -jar $(dirname $0)/treesub.jar
diff --git a/var/spack/repos/builtin/packages/trf/package.py b/var/spack/repos/builtin/packages/trf/package.py
index f02e30302d..c429ccc33d 100644
--- a/var/spack/repos/builtin/packages/trf/package.py
+++ b/var/spack/repos/builtin/packages/trf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -44,3 +25,5 @@ class Trf(Package):
     def install(self, spec, prefix):
         mkdirp(prefix.bin)
         install('trf409.linux64', prefix.bin.trf)
+        chmod = which('chmod')
+        chmod('+x', prefix.bin.trf)
diff --git a/var/spack/repos/builtin/packages/triangle/package.py b/var/spack/repos/builtin/packages/triangle/package.py
index 9e20a4d964..ad6a775116 100644
--- a/var/spack/repos/builtin/packages/triangle/package.py
+++ b/var/spack/repos/builtin/packages/triangle/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index db0b1b3ba6..2170bc4d6d 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -1,31 +1,12 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import os
 import sys
 from spack import *
-from spack.operating_systems.mac_os import macOS_version
+from spack.operating_systems.mac_os import macos_version
 
 # Trilinos is complicated to build, as an inspiration a couple of links to
 # other repositories which build it:
@@ -45,137 +26,215 @@ class Trilinos(CMakePackage):
     """
     homepage = "https://trilinos.org/"
     url      = "https://github.com/trilinos/Trilinos/archive/trilinos-release-12-12-1.tar.gz"
+    git      = "https://github.com/trilinos/Trilinos.git"
 
     maintainers = ['aprokop']
 
     # ###################### Versions ##########################
 
-    version('xsdk-0.2.0',
-            git='https://github.com/trilinos/Trilinos.git', tag='xsdk-0.2.0')
-    version('develop',
-            git='https://github.com/trilinos/Trilinos.git', tag='develop')
-    version('master',
-            git='https://github.com/trilinos/Trilinos.git', tag='master')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
+    version('develop', branch='develop')
+    version('master', branch='master')
     version('12.12.1', 'ecd4606fa332212433c98bf950a69cc7')
     version('12.10.1', '667333dbd7c0f031d47d7c5511fd0810')
-    version('12.8.1', '01c0026f1e2050842857db941060ecd5')
-    version('12.6.4', 'c2ea7b5aa0d10bcabdb9b9a6e3bac3ea')
-    version('12.6.3', '8de5cc00981a0ca0defea6199b2fe4c1')
-    version('12.6.2', 'dc7f9924872778798149ecadd81605a5')
-    version('12.6.1', '8aecea78546e7558f63ecc9a3b2949da')
-    version('12.4.2', '4c25a757d86bde3531090bd900a2cea8')
-    version('12.2.1', '85d011f7f99a776a9c6c2625e8cb721c')
-    version('12.0.1', 'bcb3fdefd14d05dd6aa65ba4c5b9aa0e')
-    version('11.14.3', 'dea62e57ebe51a886bee0b10a2176969')
-    version('11.14.2', 'e7c3cdbbfe3279a8a68838b873ad6d51')
-    version('11.14.1', 'b7760b142eef66c79ed13de7c9560f81')
+    version('12.8.1', '9f37f683ee2b427b5540db8a20ed6b15')
+    version('12.6.4', 'e11fff717d0e4565779f75a47feecbb2')
+    version('12.6.3', '9ce30b6ab956bfc41730479a9ef05d05')
+    version('12.6.2', '0237d32feedd979a6fbb139aa5df8500')
+    version('12.6.1', '14ab8f7e74b66c33d5731cbf68b8cb82')
+    version('12.4.2', '98880f414752220e60feaeb36b023f60')
+    version('12.2.1', '8b344a9e9e533126dfd96db58ce69dde')
+    version('12.0.1', 'b8263f7037f7c688091d0da19d169709')
+    version('11.14.3', 'ff31ad49d633ab28369c228784055c85')
+    version('11.14.2', '1fdf15a5b4494f832b414f9c447ab685')
+    version('11.14.1', '478d0438d935294a7c94347c94a7c8cb')
 
     # ###################### Variants ##########################
 
-    variant('alloptpkgs',   default=False,
-            description='Compile with all optional packages')
-    variant('xsdkflags',    default=False,
-            description='Compile using the default xSDK configuration')
-    variant('metis',        default=True,
-            description='Compile with METIS and ParMETIS')
-    variant('mumps',        default=True,
-            description='Compile with support for MUMPS solvers')
-    variant('superlu-dist', default=True,
-            description='Compile with SuperluDist solvers')
-    variant('superlu',      default=False,
-            description='Compile with SuperLU solvers')
-    variant('hypre',        default=True,
-            description='Compile with Hypre preconditioner')
-    variant('hdf5',         default=True,
-            description='Compile with HDF5')
-    variant('suite-sparse', default=True,
-            description='Compile with SuiteSparse solvers')
+    # Other
     # not everyone has py-numpy activated, keep it disabled by default to avoid
     # configure errors
     variant('python',       default=False,
             description='Build python wrappers')
+
+    # Build options
+    variant('complex', default=False,
+            description='Enable complex numbers in Trilinos')
+    variant('explicit_template_instantiation',  default=True,
+            description='Enable explicit template instantiation (ETI)')
+    variant('float', default=False,
+            description='Enable single precision (float) numbers in Trilinos')
+    variant('fortran',      default=True,
+            description='Compile with Fortran support')
+    variant('openmp',       default=False,
+            description='Enable OpenMP')
     variant('shared',       default=True,
             description='Enables the build of shared libraries')
+    variant('xsdkflags',    default=False,
+            description='Compile using the default xSDK configuration')
+
+    # TPLs (alphabet order)
     variant('boost',        default=True,
             description='Compile with Boost')
-    variant('tpetra',       default=True,
-            description='Compile with Tpetra')
-    variant('epetra',       default=True,
-            description='Compile with Epetra')
-    variant('epetraext',    default=True,
-            description='Compile with EpetraExt')
+    variant('cgns',         default=False,
+            description='Enable CGNS')
     variant('exodus',       default=True,
             description='Compile with Exodus from SEACAS')
+    variant('gtest',        default=True,
+            description='Compile with Gtest')
+    variant('hdf5',         default=True,
+            description='Compile with HDF5')
+    variant('hypre',        default=True,
+            description='Compile with Hypre preconditioner')
+    variant('metis',        default=True,
+            description='Compile with METIS and ParMETIS')
+    variant('mumps',        default=True,
+            description='Compile with support for MUMPS solvers')
     variant('pnetcdf',      default=False,
             description='Compile with parallel-netcdf')
+    variant('suite-sparse', default=True,
+            description='Compile with SuiteSparse solvers')
+    variant('superlu-dist', default=False,
+            description='Compile with SuperluDist solvers')
+    variant('superlu',      default=False,
+            description='Compile with SuperLU solvers')
+    variant('x11',          default=False,
+            description='Compile with X11')
     variant('zlib',         default=False,
             description='Compile with zlib')
-    variant('stk',          default=False,
-            description='Compile with STK')
-    variant('teuchos',      default=True,
-            description='Compile with Teuchos')
-    variant('belos',        default=True,
-            description='Compile with Belos')
-    variant('zoltan',       default=True,
-            description='Compile with Zoltan')
-    variant('zoltan2',      default=True,
-            description='Compile with Zoltan2')
+
+    # Package options (alphabet order)
+    variant('alloptpkgs',   default=False,
+            description='Compile with all optional packages')
     variant('amesos',       default=True,
             description='Compile with Amesos')
     variant('amesos2',      default=True,
             description='Compile with Amesos2')
-    variant('anasazi',       default=True,
+    variant('anasazi',      default=True,
             description='Compile with Anasazi')
+    variant('aztec',        default=True,
+            description='Compile with Aztec')
+    variant('belos',        default=True,
+            description='Compile with Belos')
+    variant('epetra',       default=True,
+            description='Compile with Epetra')
+    variant('epetraext',    default=True,
+            description='Compile with EpetraExt')
     variant('ifpack',       default=True,
             description='Compile with Ifpack')
     variant('ifpack2',      default=True,
             description='Compile with Ifpack2')
-    variant('muelu',        default=True,
-            description='Compile with Muelu')
-    variant('fortran',      default=True,
-            description='Compile with Fortran support')
+    variant('intrepid',     default=False,
+            description='Enable Intrepid')
+    variant('intrepid2',    default=False,
+            description='Enable Intrepid2')
+    variant('isorropia',    default=False,
+            description='Compile with Isorropia')
+    variant('kokkos',       default=True,
+            description='Compile with Kokkos')
     variant('ml',           default=True,
             description='Compile with ML')
-    variant('gtest',        default=True,
-            description='Compile with Gtest')
-    variant('aztec',        default=True,
-            description='Compile with Aztec')
+    variant('minitensor',   default=False,
+            description='Compile with MiniTensor')
+    variant('muelu',        default=True,
+            description='Compile with Muelu')
+    variant('nox',          default=False,
+            description='Compile with NOX')
+    variant('piro',         default=False,
+            description='Compile with Piro')
+    variant('phalanx',      default=False,
+            description='Compile with Phalanx')
+    variant('rol',          default=False,
+            description='Compile with ROL')
+    variant('rythmos',      default=False,
+            description='Compile with Rythmos')
     variant('sacado',       default=True,
             description='Compile with Sacado')
-    variant('x11',          default=False,
-            description='Compile with X11')
-    variant('instantiate',  default=True,
-            description='Compile with explicit instantiation')
-    variant('instantiate_cmplx', default=False,
-            description='Compile with explicit instantiation for complex')
+    variant('stk',          default=False,
+            description='Compile with STK')
+    variant('shards',       default=False,
+            description='Compile with Shards')
+    variant('teko',         default=False,
+            description='Compile with Teko')
+    variant('tempus',       default=False,
+            description='Compile with Tempus')
+    variant('teuchos',      default=True,
+            description='Compile with Teuchos')
+    variant('tpetra',       default=True,
+            description='Compile with Tpetra')
+    variant('zoltan',       default=True,
+            description='Compile with Zoltan')
+    variant('zoltan2',      default=True,
+            description='Compile with Zoltan2')
+
+    # External package options
     variant('dtk',          default=False,
             description='Enable DataTransferKit')
     variant('fortrilinos',  default=False,
             description='Enable ForTrilinos')
-    variant('openmp',       default=False,
-            description='Enable OpenMP')
-    variant('rol',          default=False,
-            description='Enable ROL')
-    variant('nox',          default=False,
-            description='Enable NOX')
-    variant('shards',       default=False,
-            description='Enable Shards')
-    variant('intrepid',     default=False,
-            description='Enable Intrepid')
-    variant('intrepid2',     default=False,
-            description='Enable Intrepid2')
 
     resource(name='dtk',
-             git='https://github.com/ornl-cees/DataTransferKit',
+             git='https://github.com/ornl-cees/DataTransferKit.git',
              tag='master',
              placement='DataTransferKit',
              when='+dtk')
     resource(name='fortrilinos',
-             git='https://github.com/trilinos/ForTrilinos',
+             git='https://github.com/trilinos/ForTrilinos.git',
              tag='develop',
              placement='packages/ForTrilinos',
              when='+fortrilinos')
 
+    conflicts('+amesos2', when='~teuchos')
+    conflicts('+amesos2', when='~tpetra')
+    conflicts('+amesos', when='~epetra')
+    conflicts('+amesos', when='~teuchos')
+    conflicts('+anasazi', when='~teuchos')
+    conflicts('+belos', when='~teuchos')
+    conflicts('+epetraext', when='~epetra')
+    conflicts('+epetraext', when='~teuchos')
+    conflicts('+ifpack2', when='~belos')
+    conflicts('+ifpack2', when='~teuchos')
+    conflicts('+ifpack2', when='~tpetra')
+    conflicts('+ifpack', when='~epetra')
+    conflicts('+ifpack', when='~teuchos')
+    conflicts('+intrepid2', when='~kokkos')
+    conflicts('+intrepid2', when='~shards')
+    conflicts('+intrepid2', when='~teuchos')
+    conflicts('+intrepid', when='~sacado')
+    conflicts('+intrepid', when='~shards')
+    conflicts('+intrepid', when='~teuchos')
+    conflicts('+isorropia', when='~epetra')
+    conflicts('+isorropia', when='~epetraext')
+    conflicts('+isorropia', when='~teuchos')
+    conflicts('+isorropia', when='~zoltan')
+    conflicts('+muelu', when='~teuchos')
+    conflicts('+muelu', when='~xpetra')
+    conflicts('+nox', when='~teuchos')
+    conflicts('+phalanx', when='~kokkos')
+    conflicts('+phalanx', when='~sacado')
+    conflicts('+phalanx', when='~teuchos')
+    conflicts('+piro', when='~teuchos')
+    conflicts('+rol', when='~teuchos')
+    conflicts('+rythmos', when='~teuchos')
+    conflicts('+teko', when='~amesos')
+    conflicts('+teko', when='~anasazi')
+    conflicts('+teko', when='~aztec')
+    conflicts('+teko', when='~ifpack')
+    conflicts('+teko', when='~ml')
+    conflicts('+teko', when='~teuchos')
+    conflicts('+teko', when='~tpetra')
+    conflicts('+tempus', when='~nox')
+    conflicts('+tempus', when='~teuchos')
+    conflicts('+tpetra', when='~kokkos')
+    conflicts('+tpetra', when='~teuchos')
+    conflicts('+zoltan2', when='~teuchos')
+    conflicts('+zoltan2', when='~tpetra')
+    conflicts('+zoltan2', when='~xpetra')
+    conflicts('+zoltan2', when='~zoltan')
+
+    conflicts('+dtk', when='~intrepid2')
+    conflicts('+dtk', when='~kokkos')
+    conflicts('+dtk', when='~teuchos')
     conflicts('+dtk', when='~tpetra')
     conflicts('+fortrilinos', when='~fortran')
     conflicts('+fortrilinos', when='@:99')
@@ -185,8 +244,21 @@ class Trilinos(CMakePackage):
     # For Trilinos v11 we need to force SuperLUDist=OFF, since only the
     # deprecated SuperLUDist v3.3 together with an Amesos patch is working.
     conflicts('+superlu-dist', when='@11.4.1:11.14.3')
+    # see https://github.com/trilinos/Trilinos/issues/3566
+    conflicts('+superlu-dist', when='+float+amesos2+explicit_template_instantiation^superlu-dist@5.3.0:')
+    # Amesos, conflicting types of double and complex SLU_D
+    # see
+    # https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
+    # and
+    # https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
+    conflicts('+superlu-dist', when='+complex+amesos2')
     # PnetCDF was only added after v12.10.1
     conflicts('+pnetcdf', when='@0:12.10.1')
+    # https://github.com/trilinos/Trilinos/issues/2994
+    conflicts(
+        '+shared', when='+stk platform=darwin',
+        msg='Cannot build Trilinos with STK as a shared library on Darwin.'
+    )
 
     # ###################### Dependencies ##########################
 
@@ -205,7 +277,9 @@ class Trilinos(CMakePackage):
     depends_on('mpi')
     depends_on('netcdf+mpi', when="~pnetcdf")
     depends_on('netcdf+mpi+parallel-netcdf', when="+pnetcdf@master,12.12.1:")
+    depends_on('parallel-netcdf', when="+pnetcdf@master,12.12.1:")
     depends_on('parmetis', when='+metis')
+    depends_on('cgns', when='+cgns')
     # Trilinos' Tribits config system is limited which makes it very tricky to
     # link Amesos with static MUMPS, see
     # https://trilinos.org/docs/dev/packages/amesos2/doc/html/classAmesos2_1_1MUMPS.html
@@ -217,6 +291,7 @@ class Trilinos(CMakePackage):
     depends_on('scalapack', when='+mumps')
     depends_on('superlu-dist', when='+superlu-dist')
     depends_on('superlu-dist@:4.3', when='@:12.6.1+superlu-dist')
+    depends_on('superlu-dist@4.4:5.3', when='@12.6.2:12.12.1+superlu-dist')
     depends_on('superlu-dist@develop', when='@develop+superlu-dist')
     depends_on('superlu-dist@xsdk-0.2.0', when='@xsdk-0.2.0+superlu-dist')
     depends_on('superlu+pic@4.3', when='+superlu')
@@ -224,15 +299,19 @@ class Trilinos(CMakePackage):
     depends_on('hypre~internal-superlu~int64', when='+hypre')
     depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0+hypre')
     depends_on('hypre@develop~internal-superlu', when='@develop+hypre')
-    # FIXME: concretizer bug? 'hl' req by netcdf is affecting this code.
+    # We need hdf5+hl to match with netcdf during concretization
     depends_on('hdf5+hl+mpi', when='+hdf5')
     depends_on('python', when='+python')
     depends_on('py-numpy', when='+python', type=('build', 'run'))
     depends_on('swig', when='+python')
 
     patch('umfpack_from_suitesparse.patch', when='@11.14.1:12.8.1')
-    patch('xlf_seacas.patch', when='@12.10.1%xl')
-    patch('xlf_seacas.patch', when='@12.10.1%xl_r')
+    patch('xlf_seacas.patch', when='@12.10.1:12.12.1 %xl')
+    patch('xlf_seacas.patch', when='@12.10.1:12.12.1 %xl_r')
+    patch('xlf_seacas.patch', when='@12.10.1:12.12.1 %clang')
+    patch('xlf_tpetra.patch', when='@12.12.1%xl')
+    patch('xlf_tpetra.patch', when='@12.12.1%xl_r')
+    patch('xlf_tpetra.patch', when='@12.12.1%clang')
 
     def url_for_version(self, version):
         url = "https://github.com/trilinos/Trilinos/archive/trilinos-release-{0}.tar.gz"
@@ -278,50 +357,66 @@ class Trilinos(CMakePackage):
         options.extend([
             '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=%s' % (
                 'ON' if '+alloptpkgs' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Tpetra:BOOL=%s' % (
-                'ON' if '+tpetra' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Epetra:BOOL=%s' % (
-                'ON' if '+epetra' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_EpetraExt:BOOL=%s' % (
-                'ON' if '+epetraext' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_ML:BOOL=%s' % (
-                'ON' if '+ml' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_AztecOO:BOOL=%s' % (
-                'ON' if '+aztec' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Sacado:BOOL=%s' % (
-                'ON' if '+sacado' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Belos:BOOL=%s' % (
-                'ON' if '+belos' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Zoltan:BOOL=%s' % (
-                'ON' if '+zoltan' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Zoltan2:BOOL=%s' % (
-                'ON' if '+zoltan2' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Amesos:BOOL=%s' % (
                 'ON' if '+amesos' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Amesos2:BOOL=%s' % (
                 'ON' if '+amesos2' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_MueLu:BOOL=%s' % (
-                'ON' if '+muelu' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Anasazi:BOOL=%s' % (
+                'ON' if '+anasazi' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_AztecOO:BOOL=%s' % (
+                'ON' if '+aztec' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Belos:BOOL=%s' % (
+                'ON' if '+belos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Epetra:BOOL=%s' % (
+                'ON' if '+epetra' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_EpetraExt:BOOL=%s' % (
+                'ON' if '+epetraext' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Ifpack:BOOL=%s' % (
                 'ON' if '+ifpack' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Ifpack2:BOOL=%s' % (
                 'ON' if '+ifpack2' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Gtest:BOOL=%s' % (
-                'ON' if '+gtest' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Teuchos:BOOL=%s' % (
-                'ON' if '+teuchos' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Anasazi:BOOL=%s' % (
-                'ON' if '+anasazi' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_ROL:BOOL=%s' % (
-                'ON' if '+rol' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_NOX:BOOL=%s' % (
-                'ON' if '+nox' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_Shards=%s' % (
-                'ON' if '+shards' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Intrepid=%s' % (
                 'ON' if '+intrepid' in spec else 'OFF'),
             '-DTrilinos_ENABLE_Intrepid2=%s' % (
                 'ON' if '+intrepid2' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Isorropia=%s' % (
+                'ON' if '+isorropia' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Kokkos:BOOL=%s' % (
+                'ON' if '+kokkos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_MiniTensor=%s' % (
+                'ON' if '+minitensor' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_ML:BOOL=%s' % (
+                'ON' if '+ml' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_MueLu:BOOL=%s' % (
+                'ON' if '+muelu' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_NOX:BOOL=%s' % (
+                'ON' if '+nox' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Piro:BOOL=%s' % (
+                'ON' if '+piro' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Phalanx=%s' % (
+                'ON' if '+phalanx' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_PyTrilinos:BOOL=%s' % (
+                'ON' if '+python' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_ROL:BOOL=%s' % (
+                'ON' if '+rol' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Rythmos=%s' % (
+                'ON' if '+rythmos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Sacado:BOOL=%s' % (
+                'ON' if '+sacado' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Shards=%s' % (
+                'ON' if '+shards' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Teko=%s' % (
+                'ON' if '+teko' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Tempus=%s' % (
+                'ON' if '+tempus' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Teuchos:BOOL=%s' % (
+                'ON' if '+teuchos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Tpetra:BOOL=%s' % (
+                'ON' if '+tpetra' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Zoltan:BOOL=%s' % (
+                'ON' if '+zoltan' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Zoltan2:BOOL=%s' % (
+                'ON' if '+zoltan2' in spec else 'OFF'),
         ])
 
         if '+xsdkflags' in spec:
@@ -332,6 +427,7 @@ class Trilinos(CMakePackage):
             # They can likely change when necessary in the future
             options.extend([
                 '-DTrilinos_ENABLE_STKMesh:BOOL=ON',
+                '-DTrilinos_ENABLE_STKNGP:BOOL=ON',
                 '-DTrilinos_ENABLE_STKSimd:BOOL=ON',
                 '-DTrilinos_ENABLE_STKIO:BOOL=ON',
                 '-DTrilinos_ENABLE_STKTransfer:BOOL=ON',
@@ -340,7 +436,8 @@ class Trilinos(CMakePackage):
                 '-DTrilinos_ENABLE_STKTopology:BOOL=ON',
                 '-DTrilinos_ENABLE_STKUnit_tests:BOOL=ON',
                 '-DTrilinos_ENABLE_STKUnit_test_utils:BOOL=ON',
-                '-DTrilinos_ENABLE_STKClassic:BOOL=OFF'
+                '-DTrilinos_ENABLE_STKClassic:BOOL=OFF',
+                '-DTrilinos_ENABLE_STKExprEval:BOOL=ON'
             ])
 
         if '+dtk' in spec:
@@ -384,8 +481,8 @@ class Trilinos(CMakePackage):
             '-DNetCDF_ROOT:PATH=%s' % spec['netcdf'].prefix,
             '-DTPL_ENABLE_X11:BOOL=%s' % (
                 'ON' if '+x11' in spec else 'OFF'),
-            '-DTrilinos_ENABLE_PyTrilinos:BOOL=%s' % (
-                'ON' if '+python' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Gtest:BOOL=%s' % (
+                'ON' if '+gtest' in spec else 'OFF'),
         ])
 
         if '+hypre' in spec:
@@ -447,8 +544,9 @@ class Trilinos(CMakePackage):
                 '-DParMETIS_LIBRARY_DIRS=%s;%s' % (
                     spec['parmetis'].prefix.lib, spec['metis'].prefix.lib),
                 '-DParMETIS_LIBRARY_NAMES=parmetis;metis',
-                '-DTPL_ParMETIS_INCLUDE_DIRS=%s' % (
-                    spec['parmetis'].prefix.include)
+                '-DTPL_ParMETIS_INCLUDE_DIRS=%s;%s' % (
+                    spec['parmetis'].prefix.include,
+                    spec['metis'].prefix.include)
             ])
         else:
             options.extend([
@@ -479,13 +577,7 @@ class Trilinos(CMakePackage):
             ])
 
         if '+superlu-dist' in spec:
-            # Amesos, conflicting types of double and complex SLU_D
-            # see
-            # https://trilinos.org/pipermail/trilinos-users/2015-March/004731.html
-            # and
-            # https://trilinos.org/pipermail/trilinos-users/2015-March/004802.html
             options.extend([
-                '-DTeuchos_ENABLE_COMPLEX:BOOL=OFF',
                 '-DKokkosTSQR_ENABLE_Complex:BOOL=OFF'
             ])
             options.extend([
@@ -539,6 +631,17 @@ class Trilinos(CMakePackage):
                 '-DTPL_ENABLE_Zlib:BOOL=OFF'
             ])
 
+        if '+cgns' in spec:
+            options.extend([
+                '-DTPL_ENABLE_CGNS:BOOL=ON',
+                '-DCGNS_INCLUDE_DIRS:PATH=%s' % spec['cgns'].prefix.include,
+                '-DCGNS_LIBRARY_DIRS:PATH=%s' % spec['cgns'].prefix.lib
+            ])
+        else:
+            options.extend([
+                '-DTPL_ENABLE_CGNS:BOOL=OFF'
+            ])
+
         # ################# Miscellaneous Stuff ######################
 
         # OpenMP
@@ -564,19 +667,34 @@ class Trilinos(CMakePackage):
                     '-DTrilinos_ENABLE_Fortran=ON'
                 ])
 
-        # Explicit instantiation
-        if '+instantiate' in spec:
+        float_s = 'ON' if '+float' in spec else 'OFF'
+        complex_s = 'ON' if '+complex' in spec else 'OFF'
+        complex_float_s = 'ON' if ('+complex' in spec and
+                                   '+float' in spec) else 'OFF'
+        if '+teuchos' in spec:
             options.extend([
-                '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON'
+                '-DTeuchos_ENABLE_COMPLEX=%s' % complex_s,
+                '-DTeuchos_ENABLE_FLOAT=%s' % float_s
+            ])
+
+        # Explicit Template Instantiation (ETI) in Tpetra
+        # NOTE: Trilinos will soon move to fixed std::uint64_t for GO and
+        # std::int32_t or std::int64_t for local.
+        options.append(
+            '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=%s' % (
+                'ON' if '+explicit_template_instantiation' in spec else 'OFF'
+            )
+        )
+
+        if '+explicit_template_instantiation' in spec and '+tpetra' in spec:
+            options.extend([
+                '-DTpetra_INST_DOUBLE:BOOL=ON',
+                '-DTpetra_INST_INT_LONG:BOOL=ON',
+                '-DTpetra_INST_COMPLEX_DOUBLE=%s' % complex_s,
+                '-DTpetra_INST_COMPLEX_FLOAT=%s' % complex_float_s,
+                '-DTpetra_INST_FLOAT=%s' % float_s,
+                '-DTpetra_INST_SERIAL=ON'
             ])
-            if '+tpetra' in spec:
-                options.extend([
-                    '-DTpetra_INST_DOUBLE:BOOL=ON',
-                    '-DTpetra_INST_INT_LONG:BOOL=ON'
-                    '-DTpetra_INST_COMPLEX_DOUBLE=%s' % (
-                        'ON' if '+instantiate_cmplx' in spec else 'OFF'
-                    )
-                ])
 
         # disable due to compiler / config errors:
         if spec.satisfies('%xl') or spec.satisfies('%xl_r'):
@@ -590,11 +708,12 @@ class Trilinos(CMakePackage):
                 '-DTrilinos_ENABLE_FEI=OFF'
             ])
 
-        if sys.platform == 'darwin' and macOS_version() >= Version('10.12'):
+        if sys.platform == 'darwin' and macos_version() >= Version('10.12'):
             # use @rpath on Sierra due to limit of dynamic loader
             options.append('-DCMAKE_MACOSX_RPATH=ON')
         else:
-            options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s' % prefix.lib)
+            options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s' %
+                           self.prefix.lib)
 
         if spec.satisfies('%intel') and spec.satisfies('@12.6.2'):
             # Panzer uses some std:chrono that is not recognized by Intel
diff --git a/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch b/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch
new file mode 100644
index 0000000000..364bd28cb0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trilinos/xlf_tpetra.patch
@@ -0,0 +1,289 @@
+--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
++++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.cpp
+@@ -108,19 +108,19 @@
+ namespace Impl {
+ 
+ void
+-cgemm (const char transA,
+-       const char transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const ::Kokkos::complex<float>& alpha,
+-       const ::Kokkos::complex<float> A[],
+-       const int lda,
+-       const ::Kokkos::complex<float> B[],
+-       const int ldb,
+-       const ::Kokkos::complex<float>& beta,
+-       ::Kokkos::complex<float> C[],
+-       const int ldc)
++cgemm_fwrap (const char transA,
++             const char transB,
++             const int m,
++             const int n,
++             const int k,
++             const ::Kokkos::complex<float>& alpha,
++             const ::Kokkos::complex<float> A[],
++             const int lda,
++             const ::Kokkos::complex<float> B[],
++             const int ldb,
++             const ::Kokkos::complex<float>& beta,
++             ::Kokkos::complex<float> C[],
++             const int ldc)
+ {
+ #ifdef HAVE_TPETRA_INST_COMPLEX_FLOAT
+   TPETRACORE_CGEMM (&transA, &transB, &m, &n, &k, &alpha, A, &lda, B, &ldb, &beta, C, &ldc);
+@@ -131,55 +131,55 @@
+ }
+ 
+ void
+-dgemm (const char transA,
+-       const char transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const double alpha,
+-       const double A[],
+-       const int lda,
+-       const double B[],
+-       const int ldb,
+-       const double beta,
+-       double C[],
+-       const int ldc)
++dgemm_fwrap (const char transA,
++             const char transB,
++             const int m,
++             const int n,
++             const int k,
++             const double alpha,
++             const double A[],
++             const int lda,
++             const double B[],
++             const int ldb,
++             const double beta,
++             double C[],
++             const int ldc)
+ {
+   TPETRACORE_DGEMM (&transA, &transB, &m, &n, &k, &alpha, A, &lda, B, &ldb, &beta, C, &ldc);
+ }
+ 
+ void
+-sgemm (const char transA,
+-       const char transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const float alpha,
+-       const float A[],
+-       const int lda,
+-       const float B[],
+-       const int ldb,
+-       const float beta,
+-       float C[],
+-       const int ldc)
++sgemm_fwrap (const char transA,
++             const char transB,
++             const int m,
++             const int n,
++             const int k,
++             const float alpha,
++             const float A[],
++             const int lda,
++             const float B[],
++             const int ldb,
++             const float beta,
++             float C[],
++             const int ldc)
+ {
+   TPETRACORE_SGEMM (&transA, &transB, &m, &n, &k, &alpha, A, &lda, B, &ldb, &beta, C, &ldc);
+ }
+ 
+ void
+-zgemm (const char transA,
+-       const char transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const ::Kokkos::complex<double>& alpha,
+-       const ::Kokkos::complex<double> A[],
+-       const int lda,
+-       const ::Kokkos::complex<double> B[],
+-       const int ldb,
+-       const ::Kokkos::complex<double>& beta,
+-       ::Kokkos::complex<double> C[],
+-       const int ldc)
++zgemm_fwrap (const char transA,
++             const char transB,
++             const int m,
++             const int n,
++             const int k,
++             const ::Kokkos::complex<double>& alpha,
++             const ::Kokkos::complex<double> A[],
++             const int lda,
++             const ::Kokkos::complex<double> B[],
++             const int ldb,
++             const ::Kokkos::complex<double>& beta,
++             ::Kokkos::complex<double> C[],
++             const int ldc)
+ {
+ #ifdef HAVE_TPETRA_INST_COMPLEX_DOUBLE
+   TPETRACORE_ZGEMM (&transA, &transB, &m, &n, &k, &alpha, A, &lda, B, &ldb, &beta, C, &ldc);
+ 
+--- a/packages/tpetra/core/src/Tpetra_Details_libGemm.hpp
++++ b/packages/tpetra/core/src/Tpetra_Details_libGemm.hpp
+@@ -99,67 +99,67 @@
+ 
+ /// \brief Wrapped version of the BLAS library's cgemm.
+ void
+-cgemm (const char char_transA,
+-       const char char_transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const ::Kokkos::complex<float>& alpha,
+-       const ::Kokkos::complex<float> A[],
+-       const int lda,
+-       const ::Kokkos::complex<float> B[],
+-       const int ldb,
+-       const ::Kokkos::complex<float>& beta,
+-       ::Kokkos::complex<float> C[],
+-       const int ldc);
++cgemm_fwrap (const char char_transA,
++             const char char_transB,
++             const int m,
++             const int n,
++             const int k,
++             const ::Kokkos::complex<float>& alpha,
++             const ::Kokkos::complex<float> A[],
++             const int lda,
++             const ::Kokkos::complex<float> B[],
++             const int ldb,
++             const ::Kokkos::complex<float>& beta,
++             ::Kokkos::complex<float> C[],
++             const int ldc);
+ 
+ /// \brief Wrapped version of the BLAS library's dgemm.
+ void
+-dgemm (const char char_transA,
+-       const char char_transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const double alpha,
+-       const double A[],
+-       const int lda,
+-       const double B[],
+-       const int ldb,
+-       const double beta,
+-       double C[],
+-       const int ldc);
++dgemm_fwrap (const char char_transA,
++             const char char_transB,
++             const int m,
++             const int n,
++             const int k,
++             const double alpha,
++             const double A[],
++             const int lda,
++             const double B[],
++             const int ldb,
++             const double beta,
++             double C[],
++             const int ldc);
+ 
+ /// \brief Wrapped version of the BLAS library's sgemm.
+ void
+-sgemm (const char char_transA,
+-       const char char_transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const float alpha,
+-       const float A[],
+-       const int lda,
+-       const float B[],
+-       const int ldb,
+-       const float beta,
+-       float C[],
+-       const int ldc);
++sgemm_fwrap (const char char_transA,
++             const char char_transB,
++             const int m,
++             const int n,
++             const int k,
++             const float alpha,
++             const float A[],
++             const int lda,
++             const float B[],
++             const int ldb,
++             const float beta,
++             float C[],
++             const int ldc);
+ 
+ /// \brief Wrapped version of the BLAS library's zgemm.
+ void
+-zgemm (const char char_transA,
+-       const char char_transB,
+-       const int m,
+-       const int n,
+-       const int k,
+-       const ::Kokkos::complex<double>& alpha,
+-       const ::Kokkos::complex<double> A[],
+-       const int lda,
+-       const ::Kokkos::complex<double> B[],
+-       const int ldb,
+-       const ::Kokkos::complex<double>& beta,
+-       ::Kokkos::complex<double> C[],
+-       const int ldc);
++zgemm_fwrap (const char char_transA,
++             const char char_transB,
++             const int m,
++             const int n,
++             const int k,
++             const ::Kokkos::complex<double>& alpha,
++             const ::Kokkos::complex<double> A[],
++             const int lda,
++             const ::Kokkos::complex<double> B[],
++             const int ldb,
++             const ::Kokkos::complex<double>& beta,
++             ::Kokkos::complex<double> C[],
++             const int ldc);
+ 
+ /// \brief Wrapper for the above wrappers, templated on scalar type
+ ///   (the type of each entry in the matrices).
+@@ -184,7 +184,7 @@
+         scalar_type C[],
+         const int ldc)
+   {
+-    return cgemm (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
++    return cgemm_fwrap (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
+   }
+ };
+ 
+@@ -207,7 +207,7 @@
+         scalar_type C[],
+         const int ldc)
+   {
+-    return dgemm (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
++    return dgemm_fwrap (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
+   }
+ };
+ 
+@@ -230,7 +230,7 @@
+         scalar_type C[],
+         const int ldc)
+   {
+-    return sgemm (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
++    return sgemm_fwrap (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
+   }
+ };
+ 
+@@ -253,7 +253,7 @@
+         scalar_type C[],
+         const int ldc)
+   {
+-    return zgemm (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
++    return zgemm_fwrap (transA, transB, m, n, k, alpha, A, lda, B, ldb, beta, C, ldc);
+   }
+ };
+ 
diff --git a/var/spack/repos/builtin/packages/trimal/package.py b/var/spack/repos/builtin/packages/trimal/package.py
new file mode 100644
index 0000000000..68d9efc6af
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trimal/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Trimal(MakefilePackage):
+    """A tool for automated alignment trimming in large-scale
+       phylogenetic analyses"""
+
+    homepage = "https://github.com/scapella/trimal"
+    url      = "https://github.com/scapella/trimal/archive/v1.4.1.tar.gz"
+
+    version('1.4.1', sha256='cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e')
+
+    build_directory = 'source'
+
+    def install(self, sinstall_treepec, prefix):
+        mkdirp(prefix.bin)
+        binaries = ['trimal', 'readal', 'statal']
+        with working_dir(self.build_directory):
+            for b in binaries:
+                install(b, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/trimgalore/package.py b/var/spack/repos/builtin/packages/trimgalore/package.py
index e1dca34f43..81cee833be 100644
--- a/var/spack/repos/builtin/packages/trimgalore/package.py
+++ b/var/spack/repos/builtin/packages/trimgalore/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,7 @@ class Trimgalore(Package):
     homepage = "https://github.com/FelixKrueger/TrimGalore"
     url      = "https://github.com/FelixKrueger/TrimGalore/archive/0.4.4.tar.gz"
 
+    version('0.4.5', 'c71756042b2a65c34d483533a29dc206')
     version('0.4.4', 'aae1b807b48e38bae7074470203997bb')
 
     depends_on('perl', type=('build', 'run'))
@@ -40,5 +22,7 @@ class Trimgalore(Package):
     depends_on('fastqc')
 
     def install(self, spec, prefix):
+        filter_file(r'#!/usr/bin/perl', '#!/usr/bin/env perl', 'trim_galore')
+
         mkdirp(prefix.bin)
         install('trim_galore', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/trimmomatic/package.py b/var/spack/repos/builtin/packages/trimmomatic/package.py
index da741d5017..0f04596cf8 100644
--- a/var/spack/repos/builtin/packages/trimmomatic/package.py
+++ b/var/spack/repos/builtin/packages/trimmomatic/package.py
@@ -1,30 +1,9 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
-from distutils.dir_util import copy_tree
-from shutil import copyfile
 import os.path
 
 
@@ -47,18 +26,18 @@ class Trimmomatic(Package):
         install(jar_file, prefix.bin)
 
         # Put the adapter files someplace sensible
-        copy_tree('adapters', join_path(self.prefix.share, 'adapters'))
+        install_tree('adapters', prefix.share.adapters)
 
         # Set up a helper script to call java on the jar file,
         # explicitly codes the path for java and the jar file.
         script_sh = join_path(os.path.dirname(__file__), "trimmomatic.sh")
-        script = join_path(prefix.bin, "trimmomatic")
-        copyfile(script_sh, script)
+        script = prefix.bin.trimmomatic
+        install(script_sh, script)
         set_executable(script)
 
         # Munge the helper script to explicitly point to java and the
         # jar file.
-        java = join_path(self.spec['java'].prefix, 'bin', 'java')
+        java = self.spec['java'].prefix.bin.java
         kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
         filter_file('^java', java, script, **kwargs)
         filter_file('trimmomatic.jar', join_path(prefix.bin, jar_file),
diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py
new file mode 100644
index 0000000000..8e198113d7
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trinity/package.py
@@ -0,0 +1,91 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Trinity(MakefilePackage):
+    """Trinity, developed at the Broad Institute and the Hebrew University of
+       Jerusalem, represents a novel method for the efficient and robust de
+       novo reconstruction of transcriptomes from RNA-seq data. Trinity
+       combines three independent software modules: Inchworm, Chrysalis, and
+       Butterfly, applied sequentially to process large volumes of RNA-seq
+       reads. Trinity partitions the sequence data into many individual de
+       Bruijn graphs, each representing the transcriptional complexity at a
+       given gene or locus, and then processes each graph independently to
+       extract full-length splicing isoforms and to tease apart transcripts
+       derived from paralogous genes.
+    """
+
+    homepage = "http://trinityrnaseq.github.io/"
+    url      = "https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.6.6.tar.gz"
+
+    version('2.6.6', 'b7472e98ab36655a6d9296d965471a56')
+
+    depends_on("java@8:", type=("build", "run"))
+    depends_on("bowtie2")
+    depends_on("jellyfish")
+    depends_on("salmon")
+    depends_on("perl+threads", type=("build", "run"))
+    depends_on("autoconf", type="build")
+    depends_on("automake", type="build")
+    depends_on("libtool", type="build")
+
+    # There is no documented list of these deps, but they're in the Dockerfile
+    #  and we have runtime errors without them
+    # https://github.com/trinityrnaseq/trinityrnaseq/blob/master/Docker/Dockerfile
+    depends_on("blast-plus", type="run")
+    depends_on("bowtie", type="run")
+    depends_on("r", type="run")
+    depends_on("r-tidyverse", type="run")
+    depends_on("r-edger", type="run")
+    depends_on("r-deseq2", type="run")
+    depends_on("r-ape", type="run")
+    depends_on("r-gplots", type="run")
+    depends_on("r-biobase", type="run")
+    depends_on("r-qvalue", type="run")
+    depends_on("rsem", type="run")
+    depends_on("kallisto", type="run")
+    depends_on("fastqc", type="run")
+    depends_on("samtools", type="run")
+    depends_on("py-numpy", type="run")
+    depends_on("express", type="run")
+    depends_on("perl-dbfile", type="run")
+    depends_on("perl-uri-escape", type="run")
+    depends_on("r-fastcluster", type="run")
+    depends_on("r-ctc", type="run")
+    depends_on("r-goseq", type="run")
+    depends_on("r-glimma", type="run")
+    depends_on("r-rots", type="run")
+    depends_on("r-goplot", type="run")
+    depends_on("r-argparse", type="run")
+    depends_on("r-sm", type="run")
+
+    def build(self, spec, prefix):
+        make()
+        make("trinity_essentials")
+        make("plugins")
+
+    def install(self, spec, prefix):
+        install_tree('.', prefix.bin)
+        force_remove(join_path(prefix.bin, '.gitmodules'))
+        force_remove(join_path(prefix.bin, 'Butterfly', '.err'))
+        force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.classpath'))
+        force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.err'))
+        force_remove(join_path(prefix.bin, 'Butterfly', 'src', '.project'))
+        remove_linked_tree(join_path(prefix.bin, 'Butterfly', 'src',
+                                     '.settings'))
+        remove_linked_tree(join_path(prefix.bin, 'Inchworm', 'src', '.deps'))
+        remove_linked_tree(join_path(prefix.bin, 'trinity-plugins',
+                                     'ParaFly-0.1.0', 'src', '.deps'))
+        force_remove(join_path(prefix.bin, 'trinity-plugins',
+                               'seqtk-trinity-0.0.2', '.gitignore'))
+        force_remove(join_path(prefix.bin, 'trinity-plugins', 'slclust', 'bin',
+                               '.hidden'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.set('TRINITY_HOME', self.prefix.bin)
+        run_env.prepend_path('PATH', self.prefix.bin.util)
+        spack_env.append_flags('CXXFLAGS', self.compiler.openmp_flag)
diff --git a/var/spack/repos/builtin/packages/trinotate/package.py b/var/spack/repos/builtin/packages/trinotate/package.py
new file mode 100644
index 0000000000..718a061ba8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trinotate/package.py
@@ -0,0 +1,42 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Trinotate(Package):
+    """Trinotate is a comprehensive annotation suite designed for
+       automatic functional annotation of transcriptomes, particularly
+       de novo assembled transcriptomes, from model or non-model organisms"""
+
+    homepage = "https://trinotate.github.io/"
+    url      = "https://github.com/Trinotate/Trinotate/archive/Trinotate-v3.1.1.tar.gz"
+
+    version('3.1.1', sha256='f8af0fa5dbeaaf5a085132cd4ac4f4206b05cc4630f0a17a672c586691f03843')
+
+    depends_on('trinity', type='run')
+    depends_on('transdecoder', type='run')
+    depends_on('sqlite', type='run')
+    depends_on('ncbi-rmblastn', type='run')
+    depends_on('hmmer', type='run')
+    depends_on('perl', type='run')
+    depends_on('lighttpd', type='run')
+    depends_on('perl-dbi', type='run')
+    depends_on('perl-dbd-mysql', type='run')
+    depends_on('perl-cgi', type='run')
+
+    def install(self, spec, prefix):
+        # most of the perl modules have local deps, install the whole tree
+        mkdirp(prefix.lib)
+        install_tree('.', join_path(prefix.lib, 'trinotate'))
+
+        mkdirp(prefix.bin)
+        os.symlink(join_path(prefix.lib, 'trinotate/Trinotate'),
+                   join_path(prefix.bin, 'Trinotate'))
+
+        os.symlink(join_path(prefix.lib,
+                             'trinotate/run_TrinotateWebserver.pl'),
+                   join_path(prefix.bin, 'run_TrinotateWebserver.pl'))
diff --git a/var/spack/repos/builtin/packages/trnascan-se/package.py b/var/spack/repos/builtin/packages/trnascan-se/package.py
new file mode 100644
index 0000000000..fcd2a3affd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/trnascan-se/package.py
@@ -0,0 +1,15 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class TrnascanSe(AutotoolsPackage):
+    """Seaching for tRNA genes in genomic sequence"""
+
+    homepage = "http://lowelab.ucsc.edu/tRNAscan-SE/"
+    url      = "http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz"
+
+    version('2.0.0',    '36d2b53bcb281efbae09e0305346e544')
diff --git a/var/spack/repos/builtin/packages/turbine/package.py b/var/spack/repos/builtin/packages/turbine/package.py
index d12fa0a41c..7c4a2d7172 100644
--- a/var/spack/repos/builtin/packages/turbine/package.py
+++ b/var/spack/repos/builtin/packages/turbine/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -30,17 +11,41 @@ class Turbine(AutotoolsPackage):
     """Turbine: The Swift/T runtime"""
 
     homepage = 'http://swift-lang.org/Swift-T'
-    url      = 'http://swift-lang.github.io/swift-t-downloads/turbine-1.0.0.tar.gz'
+    url      = 'http://swift-lang.github.io/swift-t-downloads/spack/turbine-0.0.0.tar.gz'
 
-    version('1.0.0', '7ed56d65d6db0bfe15a439d818b4259e')
+    version('1.2.3', 'f2e393c292c4248b4e77a19f8272ae88')
+    version('1.2.1', 'c8976b22849aafe02a8fb4259dfed434')
+    version('1.1.0', '9a347cf16df02707cb529f96c265a082')
 
+    variant('python', default=False,
+            description='Enable calling python')
+    variant('r', default=False,
+            description='Enable calling R')
+    depends_on('adlbx@:0.8.0', when='@:1.1.0')
+    depends_on('adlbx', when='@1.2.1:')
     depends_on('adlbx')
-    depends_on('tcl')
-    depends_on('zsh', type='run')
+    depends_on('tcl', type=('build', 'run'))
+    depends_on('zsh', type=('build', 'run'))
+    depends_on('swig', type='build')
+    depends_on('python', when='+python')
+    depends_on('r', when='+r')
+
+    def setup_environment(self, spack_env, run_env):
+        spec = self.spec
+
+        spack_env.set('CC', spec['mpi'].mpicc)
+        spack_env.set('CXX', spec['mpi'].mpicxx)
+        spack_env.set('CXXLD', spec['mpi'].mpicxx)
 
     def configure_args(self):
         args = ['--with-c-utils=' + self.spec['exmcutils'].prefix,
                 '--with-adlb='    + self.spec['adlbx'].prefix,
                 '--with-tcl='     + self.spec['tcl'].prefix,
                 '--with-mpi='     + self.spec['mpi'].prefix]
+        if '+python' in self.spec:
+            args.append('--with-python-exe={0}'.format(
+                        self.spec['python'].command.path))
+        if '+r' in self.spec:
+            args.append('--with-r={0}/rlib/R'.format(
+                        self.spec['r'].prefix))
         return args
diff --git a/var/spack/repos/builtin/packages/turbomole/package.py b/var/spack/repos/builtin/packages/turbomole/package.py
index 14af3e4bdf..dfa424055f 100644
--- a/var/spack/repos/builtin/packages/turbomole/package.py
+++ b/var/spack/repos/builtin/packages/turbomole/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 import subprocess
diff --git a/var/spack/repos/builtin/packages/tut/package.py b/var/spack/repos/builtin/packages/tut/package.py
index c0d2bbcc8f..f39d83807e 100644
--- a/var/spack/repos/builtin/packages/tut/package.py
+++ b/var/spack/repos/builtin/packages/tut/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,6 +14,8 @@ class Tut(WafPackage):
 
     version('2016-12-19', '8b1967fa295ae1ce4d4431c2f811e521')
 
+    patch('python3-octal.patch', when='@2016-12-19')
+
     def build_args(self):
         args = []
 
diff --git a/var/spack/repos/builtin/packages/tut/python3-octal.patch b/var/spack/repos/builtin/packages/tut/python3-octal.patch
new file mode 100644
index 0000000000..d6d9b14273
--- /dev/null
+++ b/var/spack/repos/builtin/packages/tut/python3-octal.patch
@@ -0,0 +1,11 @@
+--- a/waftools/gcov.py	2016-12-19 04:55:44.000000000 -0600
++++ b/waftools/gcov.py	2018-03-28 10:42:53.000000000 -0500
+@@ -13,7 +13,7 @@
+     wrapper = NamedTemporaryFile(delete=False)
+     wrapper.write(script)
+     wrapper.close()
+-    os.chmod(wrapper.name, 0777)
++    os.chmod(wrapper.name, 0o777)
+ 
+     yield wrapper.name
+ 
diff --git a/var/spack/repos/builtin/packages/twm/package.py b/var/spack/repos/builtin/packages/twm/package.py
index b467420c82..34facb6666 100644
--- a/var/spack/repos/builtin/packages/twm/package.py
+++ b/var/spack/repos/builtin/packages/twm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -46,5 +27,5 @@ class Twm(AutotoolsPackage):
     depends_on('xproto@7.0.17:', type='build')
     depends_on('bison', type='build')
     depends_on('flex', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/tycho2/package.py b/var/spack/repos/builtin/packages/tycho2/package.py
index 0f54c2e661..5ac7bc3bb7 100644
--- a/var/spack/repos/builtin/packages/tycho2/package.py
+++ b/var/spack/repos/builtin/packages/tycho2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -31,9 +12,9 @@ class Tycho2(MakefilePackage):
        on unstructured, 3D tetrahedral meshes.
     """
     homepage = "https://github.com/lanl/tycho2"
-    url      = "https://github.com/lanl/tycho2/tarball/v0.1"
+    git      = "https://github.com/lanl/tycho2.git"
 
-    version('develop', git='https://github.com/lanl/tycho2', branch='master')
+    version('develop', branch='master')
 
     depends_on("mpi")
 
diff --git a/var/spack/repos/builtin/packages/typhon/package.py b/var/spack/repos/builtin/packages/typhon/package.py
new file mode 100644
index 0000000000..3de1bf4344
--- /dev/null
+++ b/var/spack/repos/builtin/packages/typhon/package.py
@@ -0,0 +1,25 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Typhon(CMakePackage):
+    """
+    Typhon is a distributed communications library for unstructured mesh
+    applications.
+    """
+
+    homepage = "https://github.com/UK-MAC/Typhon"
+    url      = "https://github.com/UK-MAC/Typhon/archive/v3.0.tar.gz"
+    git      = "https://github.com/UK-MAC/Typhon.git"
+
+    version('develop', branch='develop')
+
+    version('3.0.2', sha256='28087eb07bf91d23792900214728b5eea61b5e81aa33df28c032dadd6d89b76e')
+    version('3.0.1', '89045decfba5fd468ef05ad4c924df8c')
+    version('3.0', 'ec67cd1aa585ce2410d4fa50514a916f')
+
+    depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/typhonio/package.py b/var/spack/repos/builtin/packages/typhonio/package.py
index 35fe269fd6..7b7285106f 100644
--- a/var/spack/repos/builtin/packages/typhonio/package.py
+++ b/var/spack/repos/builtin/packages/typhonio/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,19 +12,19 @@ class Typhonio(CMakePackage):
 
     homepage = "http://uk-mac.github.io/typhonio/"
     url      = "https://github.com/UK-MAC/typhonio/archive/v1.6_CMake.tar.gz"
+    git      = "https://github.com/UK-MAC/typhonio.git"
 
+    version('develop', branch='cmake_build')
     version('1.6_CMake', '8e8b2940a57874205e6d451856db5c2755884bf9')
-    version('develop', git='https://github.com/UK-MAC/typhonio.git',
-            branch='cmake_build')
 
     variant('build_type', default='Release', description='The build type to build',
         values=('Debug', 'Release'))
     variant('fortran', default=False, description='Enable Fortran support')
     variant('shared', default=False, description='Build shared libraries')
-    variant('docs', default=False, description='Build user guide and doxygen documentation')
+    variant('doc', default=False, description='Build user guide and doxygen documentation')
 
     depends_on('mpi')
-    depends_on('hdf5')
+    depends_on('hdf5+hl')
 
     def cmake_args(self):
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/uberftp/package.py b/var/spack/repos/builtin/packages/uberftp/package.py
index 040434f1b1..85a908c1df 100644
--- a/var/spack/repos/builtin/packages/uberftp/package.py
+++ b/var/spack/repos/builtin/packages/uberftp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ucx/package.py b/var/spack/repos/builtin/packages/ucx/package.py
new file mode 100644
index 0000000000..7e85b65194
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ucx/package.py
@@ -0,0 +1,24 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Ucx(AutotoolsPackage):
+    """a communication library implementing high-performance messaging for
+    MPI/PGAS frameworks"""
+
+    homepage = "http://www.openucx.org"
+    url      = "https://github.com/openucx/ucx/releases/download/v1.3.1/ucx-1.3.1.tar.gz"
+    # Current
+    version('1.3.1', '443ffdd64dc0e912b672a0ccb37ff666')
+
+    # Still supported
+    version('1.3.0', '2fdc3028eac3ef3ee1b1b523d170c071')
+    version('1.2.2', 'ff3fe65e4ebe78408fc3151a9ce5d286')
+    version('1.2.1', '697c2fd7912614fb5a1dadff3bfa485c')
+
+    depends_on('numactl')
+    depends_on('rdma-core')
diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits2/package.py
index 0e273f60ab..0b71b5f76c 100644
--- a/var/spack/repos/builtin/packages/udunits2/package.py
+++ b/var/spack/repos/builtin/packages/udunits2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/ufo-core/package.py b/var/spack/repos/builtin/packages/ufo-core/package.py
new file mode 100644
index 0000000000..eeaf19c473
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ufo-core/package.py
@@ -0,0 +1,21 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UfoCore(CMakePackage):
+    """The UFO data processing framework is a C library suited to build general
+    purpose streams data processing on heterogeneous architectures such as
+    CPUs, GPUs or clusters. This package contains the run-time system and
+    development files."""
+
+    homepage = "https://ufo.kit.edu"
+    url      = "https://github.com/ufo-kit/ufo-core/archive/v0.14.0.tar.gz"
+
+    version('0.14.0', '3bd94d10d0f589953aba11821a8295f3')
+
+    depends_on('glib')
+    depends_on('json-glib')
diff --git a/var/spack/repos/builtin/packages/ufo-filters/package.py b/var/spack/repos/builtin/packages/ufo-filters/package.py
new file mode 100644
index 0000000000..4cfd0c7527
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ufo-filters/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class UfoFilters(CMakePackage):
+    """The UFO data processing framework is a C library suited to build general
+    purpose streams data processing on heterogeneous architectures such as
+    CPUs, GPUs or clusters. This package contains filter plugins."""
+
+    homepage = "https://ufo.kit.edu"
+    url      = "https://github.com/ufo-kit/ufo-filters/archive/v0.14.1.tar.gz"
+
+    version('0.14.1', 'f2a81f5d38cfa71de58cbb5279782297')
+
+    depends_on('ufo-core')
diff --git a/var/spack/repos/builtin/packages/umpire/package.py b/var/spack/repos/builtin/packages/umpire/package.py
new file mode 100644
index 0000000000..d3d31f6cd6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/umpire/package.py
@@ -0,0 +1,43 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Umpire(CMakePackage):
+    """An application-focused API for memory management on NUMA & GPU
+    architectures"""
+
+    homepage = 'https://github.com/LLNL/Umpire'
+    git      = 'https://github.com/LLNL/Umpire.git'
+
+    version('develop', branch='develop', submodules='True')
+    version('master', branch='master', submodules='True')
+    version('0.1.4', tag='v0.1.4', submodules='True')
+    version('0.1.3', tag='v0.1.3', submodules='True')
+
+    variant('cuda', default=False, description='Build with CUDA support')
+    variant('fortran', default=False, description='Build C/Fortran API')
+
+    depends_on('cuda', when='+cuda')
+    depends_on('cmake@3.3:', type='build')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        options = []
+
+        if '+cuda' in spec:
+            options.extend([
+                '-DENABLE_CUDA=On',
+                '-DCUDA_TOOLKIT_ROOT_DIR=%s' % (spec['cuda'].prefix)])
+        else:
+            options.append('-DENABLE_CUDA=Off')
+
+        if '+fortran' in spec:
+            options.append('-DENABLE_FORTRAN=On')
+
+        return options
diff --git a/var/spack/repos/builtin/packages/unblur/package.py b/var/spack/repos/builtin/packages/unblur/package.py
new file mode 100644
index 0000000000..2ca644f658
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unblur/package.py
@@ -0,0 +1,53 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Unblur(AutotoolsPackage):
+    """Unblur is used to align the frames of movies recorded on an electron
+    microscope to reduce image blurring due to beam-induced motion."""
+
+    homepage = "http://grigoriefflab.janelia.org/unblur"
+    url      = "http://grigoriefflab.janelia.org/sites/default/files/unblur_1.0.2.tar.gz"
+
+    version('1.0.2', 'b6e367061cd0cef1b62a391a6289f681')
+
+    variant('openmp', default=True, description='Enable OpenMP support')
+    variant('shared', default=True, description='Dynamic linking')
+
+    depends_on('zlib')
+    depends_on('jpeg')
+    depends_on('libtiff')
+    depends_on('gsl')
+    depends_on('jbigkit')
+    depends_on('fftw@3:')
+    # Requires Intel Fortran compiler
+    conflicts('%gcc')
+    conflicts('%pgi')
+    conflicts('%clang')
+    conflicts('%cce')
+    conflicts('%xl')
+    conflicts('%xl_r')
+    conflicts('%nag')
+
+    configure_directory = 'src'
+
+    def patch(self):
+        filter_file(r'<<<<<<<.*', '', 'src/missing')
+
+    def configure_args(self):
+        spec = self.spec
+        return ['FC=ifort',
+                'F77=ifort',
+                '--enable-static={0}'
+                .format('yes' if '~shared' in spec else 'no'),
+                '--enable-openmp={0}'
+                .format('yes' if '+openmp' in spec else 'no'),
+                '--enable-optimisations=yes']
+
+    def build(self, spec, prefix):
+        with working_dir('src'):
+            make(parallel=False)
diff --git a/var/spack/repos/builtin/packages/uncrustify/package.py b/var/spack/repos/builtin/packages/uncrustify/package.py
index fdd7a49ec7..6222951641 100644
--- a/var/spack/repos/builtin/packages/uncrustify/package.py
+++ b/var/spack/repos/builtin/packages/uncrustify/package.py
@@ -1,34 +1,31 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
-class Uncrustify(AutotoolsPackage):
+class Uncrustify(Package):
     """Source Code Beautifier for C, C++, C#, ObjectiveC, Java, and others."""
 
     homepage = "http://uncrustify.sourceforge.net/"
     url      = "http://downloads.sourceforge.net/project/uncrustify/uncrustify/uncrustify-0.61/uncrustify-0.61.tar.gz"
 
+    version('0.67', '0c9a08366e5c97cd02ae766064e957de41827611')
     version('0.61', 'b6140106e74c64e831d0b1c4b6cf7727')
+
+    depends_on('cmake', type='build', when='@0.64:')
+
+    @when('@0.64:')
+    def install(self, spec, prefix):
+        with working_dir('spack-build', create=True):
+            cmake('..', *std_cmake_args)
+            make()
+            make('install')
+
+    @when('@:0.62')
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(self.prefix))
+        make()
+        make('install')
diff --git a/var/spack/repos/builtin/packages/unibilium/package.py b/var/spack/repos/builtin/packages/unibilium/package.py
index 74cea8c8e2..dd1d1514ed 100644
--- a/var/spack/repos/builtin/packages/unibilium/package.py
+++ b/var/spack/repos/builtin/packages/unibilium/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/unifycr/package.py b/var/spack/repos/builtin/packages/unifycr/package.py
new file mode 100644
index 0000000000..17feb65e7a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unifycr/package.py
@@ -0,0 +1,95 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack import *
+
+
+class Unifycr(AutotoolsPackage):
+    """User level file system that enables applications to use node-local
+    storage as burst buffers for shared files. Supports scalable and efficient
+    aggregation of I/O bandwidth from burst buffers while having the same life
+    cycle as a batch-submitted job.
+    UnifyCR is designed to support common I/O workloads, including
+    checkpoint/restart. While primarily designed for N-N write/read, UnifyCR
+    compliments its functionality with the support for N-1 write/read."""
+
+    homepage = "https://github.com/LLNL/UnifyCR"
+    git      = "https://github.com/LLNL/UnifyCR.git"
+
+    version('develop', branch='dev', preferred=True)
+    version('0.1.1', tag='v0.1.1')
+
+    variant('debug', default='False', description='Enable debug build options')
+    variant('hdf5', default='False', description='Build with parallel HDF5 (install with `^hdf5~mpi` for serial)')
+    variant('numa', default='False', description='Build with NUMA')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    # Required dependencies
+    # Latest version of GOTCHA has API changes that break UnifyCR.
+    # Updates to UnifyCR are coming in order to fix this.
+    depends_on('gotcha@0.0.2')
+    depends_on('leveldb')
+    depends_on('mpi')
+    depends_on('pkg-config@0.9.0:')
+
+    # Optional dependencies
+
+    # UnifyCR's integration with HDF5 is still a WIP and is currently
+    # configured for serial only. HDF5 is parallel by default.
+    #
+    # To build with serial HDF5, use `spack install unifycr+hdf5 ^hdf5~mpi`
+    #
+    # Once UnifyCR is compatible with parallel HDF5, excluding `^hdf5~mpi` from
+    # the install line will build UnifyCR with parallel HDF5.
+
+    # v0.1.1 not HDF5 compatible; can change when v0.1.1 is no longer supported
+    depends_on('hdf5', when='@0.1.2: +hdf5')
+    depends_on('numactl',  when='+numa')
+
+    # we depend on numactl, which does't currently build on darwin
+    conflicts('platform=darwin', when='+numa')
+    conflicts('+hdf5', when='@:0.1.1')
+
+    # Parallel disabled to prevent tests from being run out-of-order when
+    # installed with the --test={root, all} option. Can potentially change if
+    # we add a +test configure option and variant.
+    parallel = False
+    build_directory = 'spack-build'
+
+    def configure_args(self):
+        spec = self.spec
+        args = []
+
+        if spec.satisfies('@0.1.1'):
+            env['CC'] = spec['mpi'].mpicc
+
+        # UnifyCR's configure requires the exact path for HDF5
+        def hdf5_compiler_path(name):
+            if '~mpi' in spec[name]:  # serial HDF5
+                return spec[name].prefix.bin.h5cc
+            else:  # parallel HDF5
+                return spec[name].prefix.bin.h5pcc
+
+        args.extend(self.with_or_without('numa',
+                                         lambda x: spec['numactl'].prefix))
+        args.extend(self.with_or_without('hdf5', hdf5_compiler_path))
+
+        if '+debug' in spec:
+            args.append('--enable-debug')
+
+        if spack.config.get('config:debug'):
+            args.append('--disable-silent-rules')
+        else:
+            args.append('--enable-silent-rules')
+
+        return args
+
+#    @when('@develop') TODO: uncomment when we `make dist` a stable release
+    def autoreconf(self, spec, prefix):
+        bash = which('bash')
+        bash('./autogen.sh')
diff --git a/var/spack/repos/builtin/packages/unison/package.py b/var/spack/repos/builtin/packages/unison/package.py
index 3d94ca7f49..55977a23c6 100644
--- a/var/spack/repos/builtin/packages/unison/package.py
+++ b/var/spack/repos/builtin/packages/unison/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/units/package.py b/var/spack/repos/builtin/packages/units/package.py
index 502dc999b7..f9e85f98a7 100644
--- a/var/spack/repos/builtin/packages/units/package.py
+++ b/var/spack/repos/builtin/packages/units/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -29,7 +10,7 @@ class Units(AutotoolsPackage):
     """GNU units converts between different systems of units"""
 
     homepage = "https://www.gnu.org/software/units/"
-    url      = "https://ftp.gnu.org/gnu/units/units-2.13.tar.gz"
+    url      = "https://ftpmirror.gnu.org/units/units-2.13.tar.gz"
 
     version('2.13', '5cbf2a6af76e94ba0ac55fc8d99d5a3e')
 
diff --git a/var/spack/repos/builtin/packages/unixodbc/package.py b/var/spack/repos/builtin/packages/unixodbc/package.py
index 30a771cdf2..488c91b553 100644
--- a/var/spack/repos/builtin/packages/unixodbc/package.py
+++ b/var/spack/repos/builtin/packages/unixodbc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/unuran/package.py b/var/spack/repos/builtin/packages/unuran/package.py
new file mode 100644
index 0000000000..2708882c6e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unuran/package.py
@@ -0,0 +1,41 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Unuran(AutotoolsPackage):
+    """Universal Non-Uniform Random number generator."""
+
+    homepage = "http://statmath.wu.ac.at/unuran"
+    url      = "http://statmath.wu.ac.at/unuran/unuran-1.8.1.tar.gz"
+
+    version('1.8.1', 'a5885baab53a2608c1d85517bf5d06a5')
+
+    variant('shared', default=True,
+        description="Enable the build of shared libraries")
+    variant('rngstreams', default=True,
+        description="Use RNGSTREAM library for uniform random generation")
+    variant('gsl',      default=False,
+        description="Use random number generators from GNU Scientific Library")
+
+    depends_on('gsl',        when="+gsl")
+    depends_on('rngstreams', when="+rngstreams")
+
+    def configure_args(self):
+
+        spec = self.spec
+
+        args = [
+            '--%s-shared' % ('enable' if '+shared' in spec else 'disable'),
+            '--with-urgn-default=%s' % (
+                'rngstream' if '+rngstreams' in spec else 'builtin'),
+            '--%s-urng-gsl' % (
+                'with' if '+gsl' in spec else 'without'),
+            '--%s-urng-rngstreams' % (
+                'with' if '+rngstreams' in spec else 'without')
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/unzip/package.py b/var/spack/repos/builtin/packages/unzip/package.py
new file mode 100644
index 0000000000..de9cc39c2e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/unzip/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Unzip(MakefilePackage):
+    """Unzip is a compression and file packaging/archive utility."""
+
+    homepage = 'http://www.info-zip.org/Zip.html'
+    url      = 'http://downloads.sourceforge.net/infozip/unzip60.tar.gz'
+
+    version('6.0', '62b490407489521db863b523a7f86375')
+
+    conflicts('platform=cray', msg='Unzip does not currently build on Cray')
+
+    make_args = ['-f', 'unix/Makefile']
+    build_targets = make_args + ['generic']
+
+    def url_for_version(self, version):
+        return 'http://downloads.sourceforge.net/infozip/unzip{0}.tar.gz'.format(version.joined)
+
+    @property
+    def install_targets(self):
+        return self.make_args + ['prefix={0}'.format(self.prefix), 'install']
diff --git a/var/spack/repos/builtin/packages/usearch/package.py b/var/spack/repos/builtin/packages/usearch/package.py
index b426376404..9ff833b907 100644
--- a/var/spack/repos/builtin/packages/usearch/package.py
+++ b/var/spack/repos/builtin/packages/usearch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/util-linux/package.py b/var/spack/repos/builtin/packages/util-linux/package.py
index f013737347..58b26abd5e 100644
--- a/var/spack/repos/builtin/packages/util-linux/package.py
+++ b/var/spack/repos/builtin/packages/util-linux/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/util-macros/package.py b/var/spack/repos/builtin/packages/util-macros/package.py
index e49987a57f..2ab1899ce1 100644
--- a/var/spack/repos/builtin/packages/util-macros/package.py
+++ b/var/spack/repos/builtin/packages/util-macros/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/uuid/package.py b/var/spack/repos/builtin/packages/uuid/package.py
index 5ad2e75341..0c6757e6c1 100644
--- a/var/spack/repos/builtin/packages/uuid/package.py
+++ b/var/spack/repos/builtin/packages/uuid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/valgrind/package.py b/var/spack/repos/builtin/packages/valgrind/package.py
index b950e1cffd..3f9b7f39eb 100644
--- a/var/spack/repos/builtin/packages/valgrind/package.py
+++ b/var/spack/repos/builtin/packages/valgrind/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -35,22 +16,34 @@ class Valgrind(AutotoolsPackage):
 
     Valgrind is Open Source / Free Software, and is freely available
     under the GNU General Public License, version 2.
-
     """
     homepage = "http://valgrind.org/"
-    url = "http://valgrind.org/downloads/valgrind-3.11.0.tar.bz2"
+    url      = "https://sourceware.org/pub/valgrind/valgrind-3.13.0.tar.bz2"
+    git      = "git://sourceware.org/git/valgrind.git"
 
+    version('develop', branch='master')
+    version('3.14.0', '74175426afa280184b62591b58c671b3')
+    version('3.13.0', '817dd08f1e8a66336b9ff206400a5369')
     version('3.12.0', '6eb03c0c10ea917013a7622e483d61bb')
     version('3.11.0', '4ea62074da73ae82e0162d6550d3f129')
     version('3.10.1', '60ddae962bc79e7c95cfc4667245707f')
     version('3.10.0', '7c311a72a20388aceced1aa5573ce970')
-    version('develop', svn='svn://svn.valgrind.org/valgrind/trunk')
 
     variant('mpi', default=True,
             description='Activates MPI support for valgrind')
     variant('boost', default=True,
             description='Activates boost support for valgrind')
+    variant('only64bit', default=True,
+            description='Sets --enable-only64bit option for valgrind')
+    variant('ubsan', default=True,
+            description='Activates ubsan support for valgrind')
 
+    conflicts('+ubsan', when='platform=darwin %clang',
+              msg="""
+Cannot build libubsan with clang on macOS.
+Otherwise with (Apple's) clang there is a linker error:
+clang: error: unknown argument: '-static-libubsan'
+""")
     depends_on('mpi', when='+mpi')
     depends_on('boost', when='+boost')
 
@@ -65,14 +58,11 @@ class Valgrind(AutotoolsPackage):
     def configure_args(self):
         spec = self.spec
         options = []
-        if not (spec.satisfies('%clang') and sys.platform == 'darwin'):
-            # Otherwise with (Apple's) clang there is a linker error:
-            # clang: error: unknown argument: '-static-libubsan'
+        if spec.satisfies('+ubsan'):
             options.append('--enable-ubsan')
+        if spec.satisfies('+only64bit'):
+            options.append('--enable-only64bit')
 
         if sys.platform == 'darwin':
-            options.extend([
-                '--build=amd64-darwin',
-                '--enable-only64bit'
-            ])
+            options.append('--build=amd64-darwin')
         return options
diff --git a/var/spack/repos/builtin/packages/vampirtrace/package.py b/var/spack/repos/builtin/packages/vampirtrace/package.py
index bc53cc6008..19d37118fd 100644
--- a/var/spack/repos/builtin/packages/vampirtrace/package.py
+++ b/var/spack/repos/builtin/packages/vampirtrace/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/vardictjava/package.py b/var/spack/repos/builtin/packages/vardictjava/package.py
index 66745a6a58..0168e7921c 100644
--- a/var/spack/repos/builtin/packages/vardictjava/package.py
+++ b/var/spack/repos/builtin/packages/vardictjava/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 
@@ -34,6 +15,7 @@ class Vardictjava(Package):
     url      = "https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.5.1/VarDict-1.5.1.tar"
 
     version('1.5.1', '8c0387bcc1f7dc696b04e926c48b27e6')
+    version('1.4.4', '6b2d7e1e5502b875760fc9938a0fe5e0')
 
     depends_on('java@8:', type='run')
 
diff --git a/var/spack/repos/builtin/packages/varscan/package.py b/var/spack/repos/builtin/packages/varscan/package.py
index 0ce5c6b634..4793c15fe3 100644
--- a/var/spack/repos/builtin/packages/varscan/package.py
+++ b/var/spack/repos/builtin/packages/varscan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os.path
 
diff --git a/var/spack/repos/builtin/packages/vc/package.py b/var/spack/repos/builtin/packages/vc/package.py
index 048955205b..49b4add8e2 100644
--- a/var/spack/repos/builtin/packages/vc/package.py
+++ b/var/spack/repos/builtin/packages/vc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/vcftools/package.py b/var/spack/repos/builtin/packages/vcftools/package.py
index f62702a0eb..09ac1cb37b 100644
--- a/var/spack/repos/builtin/packages/vcftools/package.py
+++ b/var/spack/repos/builtin/packages/vcftools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -55,8 +36,7 @@ class Vcftools(AutotoolsPackage):
 
         with working_dir('src/perl'):
             match = '^#!/usr/bin/env perl'
-            perl = join_path(self.spec['perl'].prefix.bin, 'perl')
-            substitute = "#!{perl}".format(perl=perl)
+            substitute = "#!{perl}".format(perl=self.spec['perl'].command.path)
             # tab-to-vcf added in 0.1.15
             files = ['fill-aa', 'fill-an-ac', 'fill-fs',
                      'fill-ref-md5', 'tab-to-vcf', 'vcf-annotate',
diff --git a/var/spack/repos/builtin/packages/vcsh/package.py b/var/spack/repos/builtin/packages/vcsh/package.py
index 76cdaf3b7b..bcc21caa66 100644
--- a/var/spack/repos/builtin/packages/vcsh/package.py
+++ b/var/spack/repos/builtin/packages/vcsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/vdt/package.py b/var/spack/repos/builtin/packages/vdt/package.py
index 1ff2d014e3..7c2fc4eebd 100644
--- a/var/spack/repos/builtin/packages/vdt/package.py
+++ b/var/spack/repos/builtin/packages/vdt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/vecgeom/package.py b/var/spack/repos/builtin/packages/vecgeom/package.py
index 05c1519220..c4ba864f8b 100644
--- a/var/spack/repos/builtin/packages/vecgeom/package.py
+++ b/var/spack/repos/builtin/packages/vecgeom/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import platform
@@ -32,9 +13,22 @@ class Vecgeom(CMakePackage):
     (toolkits)."""
 
     homepage = "https://gitlab.cern.ch/VecGeom/VecGeom"
-
-    version('0.3.rc', git='https://gitlab.cern.ch/VecGeom/VecGeom.git',
-            tag='v0.3.rc')
+    url = "https://gitlab.cern.ch/api/v4/projects/VecGeom%2FVecGeom/repository/archive.tar.gz?sha=v0.3.rc"
+
+    version('01.00.00', git='https://gitlab.cern.ch/VecGeom/VecGeom.git', tag='v01.00.00')
+    version('00.05.00', git='https://gitlab.cern.ch/VecGeom/VecGeom.git', tag='v00.05.00', preferred=True)
+    version('0.3.rc', 'c1f5d620f655f3c0610a44e7735203b5')
+
+    variant('cxxstd',
+            default='17',
+            values=('14', '17'),
+            multi=False,
+            description='Use the specified C++ standard when building.')
+    variant('vector',
+             default='native',
+             values=('sse3', 'sse4.2', 'native'),
+             multi=False,
+             description='Specify the instruction set for vectorization.')
 
     depends_on('cmake@3.5:', type='build')
 
@@ -43,12 +37,16 @@ class Vecgeom(CMakePackage):
             '-DBACKEND=Scalar',
             '-DGEANT4=OFF',
             '-DUSOLIDS=ON',
-            '-DUSOLIDS_VECGEOM=ON'
-        ]
-
+            '-DUSOLIDS_VECGEOM=ON',
+            '-DROOT=OFF',
+            '-DNO_SPECIALIZATION=ON',
+            '-DCMAKE_VERBOSE_MAKEFILE=TRUE']
+        options.append('-DCMAKE_CXX_STANDARD={0}'.
+                       format(self.spec.variants['cxxstd'].value))
         arch = platform.machine()
         if arch == 'x86_64':
-            options.append('-DVECGEOM_VECTOR=sse4.2')
+            options.append('-DVECGEOM_VECTOR={0}'.
+                           format(self.spec.variants['vector'].value))
         else:
             options.append('-DVECGEOM_VECTOR=' + arch)
         return options
diff --git a/var/spack/repos/builtin/packages/veclibfort/package.py b/var/spack/repos/builtin/packages/veclibfort/package.py
index e57384fd2c..988e59adf3 100644
--- a/var/spack/repos/builtin/packages/veclibfort/package.py
+++ b/var/spack/repos/builtin/packages/veclibfort/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -33,9 +14,10 @@ class Veclibfort(Package):
 
     homepage = "https://github.com/mcg1969/vecLibFort"
     url      = "https://github.com/mcg1969/vecLibFort/archive/0.4.2.tar.gz"
+    git      = "https://github.com/mcg1969/vecLibFort.git"
 
+    version('develop', branch='master')
     version('0.4.2', '83395ffcbe8a2122c3f726a5c3a7cf93')
-    version('develop', git='https://github.com/mcg1969/vecLibFort.git')
 
     variant('shared', default=True,
             description="Build shared libraries as well as static libs.")
@@ -48,7 +30,7 @@ class Veclibfort(Package):
     def libs(self):
         shared = True if '+shared' in self.spec else False
         return find_libraries(
-            'libvecLibFort', root=self.prefix, shared=shared, recurse=True
+            'libvecLibFort', root=self.prefix, shared=shared, recursive=True
         )
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/vegas2/package.py b/var/spack/repos/builtin/packages/vegas2/package.py
index ad452b3384..d6d4e7f6cf 100644
--- a/var/spack/repos/builtin/packages/vegas2/package.py
+++ b/var/spack/repos/builtin/packages/vegas2/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/veloc/package.py b/var/spack/repos/builtin/packages/veloc/package.py
new file mode 100644
index 0000000000..72b1ff746e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/veloc/package.py
@@ -0,0 +1,51 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Veloc(CMakePackage):
+    """Very-Low Overhead Checkpointing System. VELOC is a multi-level
+    checkpoint-restart runtime for HPC supercomputing infrastructures"""
+
+    homepage = "https://github.com/ECP-VeloC/VELOC"
+    url      = "https://github.com/ECP-VeloC/VELOC/archive/veloc-1.0rc1.zip"
+    git      = "https://github.com/ecp-veloc/veloc.git"
+
+    tags = ['ecp']
+
+    version('master', branch='master')
+    version('1.0',    '98fe2d9abd2a1b53d7a52267dab91fae', preferred=True)
+    version('1.0rc1', 'c6db0de56b5b865183b1fa719ac74c1d')
+
+    depends_on('boost~atomic~chrono~clanglibcpp~date_time~debug~exception'
+               '~filesystem~graph~icu~iostreams~locale~log~math~mpi'
+               '~multithreaded~numpy~program_options~python~random~regex'
+               '~serialization~shared~signals~singlethreaded~system'
+               '~taggedlayout~test~thread~timer~versionedlayout~wave')
+    depends_on('libpthread-stubs')
+    depends_on('mpi')
+    depends_on('er')
+    depends_on('axl')
+    depends_on('cmake@3.9:', type='build')
+
+    conflicts('%gcc@:4.9.3')
+
+    # requires C++11
+    def flag_handler(self, name, flags):
+        flags = list(flags)
+        if name == 'cxxflags':
+            flags.append(self.compiler.cxx11_flag)
+        return (None, None, flags)
+
+    def cmake_args(self):
+        args = [
+            "-DWITH_AXL_PREFIX=%s" % self.spec['axl'].prefix,
+            "-DWITH_ER_PREFIX=%s" % self.spec['er'].prefix,
+            "-DBOOST_ROOT=%s" % self.spec['boost'].prefix,
+            "-DMPI_CXX_COMPILER=%s" % self.spec['mpi'].mpicxx
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/velvet/package.py b/var/spack/repos/builtin/packages/velvet/package.py
index 45e10f4ce2..8813cfe16c 100644
--- a/var/spack/repos/builtin/packages/velvet/package.py
+++ b/var/spack/repos/builtin/packages/velvet/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/verilator/package.py b/var/spack/repos/builtin/packages/verilator/package.py
new file mode 100644
index 0000000000..b993071266
--- /dev/null
+++ b/var/spack/repos/builtin/packages/verilator/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Verilator(AutotoolsPackage):
+    """Verilator is the fastest free Verilog HDL simulator.
+
+    It compiles synthesizable Verilog (not test-bench code!), plus some PSL,
+    SystemVerilog and Synthesis assertions into C++ or SystemC code. It is
+    designed for large projects where fast simulation performance is of primary
+    concern, and is especially well suited to generate executable models of
+    CPUs for embedded software design teams.
+
+    Please do not download this program if you are expecting a full featured
+    replacement for NC-Verilog, VCS or another commercial Verilog simulator
+    or Verilog compiler for a little project! (Try Icarus instead.) However, if
+    you are looking for a path to migrate synthesizable Verilog to C++ or
+    SystemC, and writing just a touch of C code and Makefiles doesn't scare you
+    off, this is the free Verilog compiler for you.
+
+    Verilator supports the synthesis subset of Verilog, plus initial
+    statements, proper blocking/non-blocking assignments, functions, tasks,
+    multi-dimensional arrays, and signed numbers. It also supports very simple
+    forms of SystemVerilog assertions and coverage analysis. Verilator supports
+    the more important Verilog 2005 constructs, and some SystemVerilog
+    features, with additional constructs being added as users request them.
+
+    Verilator has been used to simulate many very large multi-million gate
+    designs with thousands of modules."""
+
+    homepage = "https://www.veripool.org/projects/verilator"
+    url      = "https://www.veripool.org/ftp/verilator-3.920.tgz"
+
+    version('3.920', '71de7b9ddb27a72e96ed2a04e5ccf933')
+    version('3.904', '7d4dc8e61d5e0e564c3016a06f0b9d07')
+
+    depends_on('bison', type='build')
+    depends_on('flex',  type='build')
+    depends_on('perl',  type=('build', 'run'))
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('VERILATOR_ROOT', self.prefix)
+
+    # verilator requires access to its shipped scripts (bin) and include
+    # but the standard make doesn't put it in the correct places
+    @run_before('install')
+    def install_include(self):
+        install_tree('include', prefix.include)
+        install_tree('bin', prefix.bin)
+
+    # we need to fix the CXX and LINK paths, as they point to the spack
+    # wrapper scripts which aren't usable without spack
+    @run_after('install')
+    def patch_cxx(self):
+        filter_file(r'^CXX\s*=.*', 'CXX = {0}'.format(self.compiler.cxx),
+                    join_path(self.prefix.include, 'verilated.mk'))
+        filter_file(r'^LINK\s*=.*', 'LINK = {0}'.format(self.compiler.cxx),
+                    join_path(self.prefix.include, 'verilated.mk'))
diff --git a/var/spack/repos/builtin/packages/verrou/package.py b/var/spack/repos/builtin/packages/verrou/package.py
new file mode 100644
index 0000000000..d0cde05339
--- /dev/null
+++ b/var/spack/repos/builtin/packages/verrou/package.py
@@ -0,0 +1,86 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os
+import sys
+
+
+class Verrou(AutotoolsPackage):
+    """A floating-point error checker.
+
+    Verrou helps you look for floating-point round-off errors in programs. It
+    implements a stochastic floating-point arithmetic based on random rounding:
+    all floating-point operations are perturbed by randomly switching rounding
+    modes. This can be seen as an asynchronous variant of the CESTAC method, or
+    a subset of Monte Carlo Arithmetic, performing only output randomization
+    through random rounding.
+    """
+
+    homepage = "https://github.com/edf-hpc/verrou"
+    url      = "https://github.com/edf-hpc/verrou/archive/v2.0.0.tar.gz"
+    git      = "https://github.com/edf-hpc/verrou.git"
+
+    version('develop', branch='master')
+    version('2.0.0', '388d493df3f253c9b049ce0ceae55fd6')
+    version('1.1.0', '9752d776fb534890e5e29f9721ee6125')
+
+    resource(name='valgrind-3.13.0',
+             url='https://sourceware.org/pub/valgrind/valgrind-3.13.0.tar.bz2',
+             sha256='d76680ef03f00cd5e970bbdcd4e57fb1f6df7d2e2c071635ef2be74790190c3b',
+             when='@1.1.0:')
+
+    variant('fma', default=True,
+            description='Activates fused multiply-add support for Verrou')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
+    depends_on('m4', type='build')
+
+    def patch(self):
+        # We start with the verrou source tree and a "valgrind-x.y.z" subdir.
+        # But we actually need a valgrind source tree with a "verrou" subdir.
+        # First, let's locate the valgrind sources...
+        valgrind_dirs = glob.glob('valgrind-*')
+        assert len(valgrind_dirs) == 1
+        valgrind_dir = valgrind_dirs[0]
+
+        # ...then we can flip the directory organization around
+        verrou_files = os.listdir('.')
+        verrou_files.remove(valgrind_dir)
+        os.mkdir('verrou')
+        for name in verrou_files:
+            os.rename(name, os.path.join('verrou', name))
+        for name in os.listdir(valgrind_dir):
+            os.rename(os.path.join(valgrind_dir, name), name)
+        os.rmdir(valgrind_dir)
+
+        # Once this is done, we can patch valgrind
+        which('patch')('-p0', '--input=verrou/valgrind.diff')
+
+        # Autogenerated perl path may be too long, need to fix this here
+        # because these files are used during the build.
+        for link_tool_in in glob.glob('coregrind/link_tool_exe_*.in'):
+            filter_file('^#! @PERL@',
+                        '#! /usr/bin/env perl',
+                        link_tool_in)
+
+    def autoreconf(self, spec, prefix):
+        # Needed because we patched valgrind
+        which("bash")("autogen.sh")
+
+    def configure_args(self):
+        spec = self.spec
+        options = [
+            '--enable-only64bit',
+            '--{0}able-verrou-fma'.format('en' if '+fma' in spec else 'dis')
+        ]
+
+        if sys.platform == 'darwin':
+            options.append('--build=amd64-darwin')
+
+        return options
diff --git a/var/spack/repos/builtin/packages/videoproto/package.py b/var/spack/repos/builtin/packages/videoproto/package.py
index 21a40f98ff..4f093034b5 100644
--- a/var/spack/repos/builtin/packages/videoproto/package.py
+++ b/var/spack/repos/builtin/packages/videoproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Videoproto(AutotoolsPackage):
 
     version('2.3.3', 'd984100603ee2420072f27bb491f4b7d')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/viennarna/package.py b/var/spack/repos/builtin/packages/viennarna/package.py
index c3fad661db..d96d32ec64 100644
--- a/var/spack/repos/builtin/packages/viennarna/package.py
+++ b/var/spack/repos/builtin/packages/viennarna/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,8 +13,9 @@ class Viennarna(AutotoolsPackage):
     """
 
     homepage = "https://www.tbi.univie.ac.at/RNA/"
-    url      = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/ViennaRNA-2.3.5.tar.gz"
+    url      = "https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.3.tar.gz"
 
+    version('2.4.3', '41be2fd36a5323a35ed50debfc7bd118')
     version('2.3.5', '4542120adae9b7abb605e2304c2a1326')
 
     variant('sse', default=True, description='Enable SSE in order to substantially speed up execution')
@@ -54,6 +36,8 @@ class Viennarna(AutotoolsPackage):
         args = self.enable_or_disable('sse')
         args += self.with_or_without('python')
         args += self.with_or_without('perl')
+        if self.spec.satisfies('@2.4.3:'):
+            args.append('--without-swig')
 
         if 'python@3:' in self.spec:
             args.append('--with-python3')
diff --git a/var/spack/repos/builtin/packages/viewres/package.py b/var/spack/repos/builtin/packages/viewres/package.py
index 0929dace52..06108c46ca 100644
--- a/var/spack/repos/builtin/packages/viewres/package.py
+++ b/var/spack/repos/builtin/packages/viewres/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Viewres(AutotoolsPackage):
     depends_on('libxmu')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/vim/package.py b/var/spack/repos/builtin/packages/vim/package.py
index d216cb0aed..84c6372ab9 100644
--- a/var/spack/repos/builtin/packages/vim/package.py
+++ b/var/spack/repos/builtin/packages/vim/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,8 +16,11 @@ class Vim(AutotoolsPackage):
     """
 
     homepage = "http://www.vim.org"
-    url      = "https://github.com/vim/vim/archive/v8.0.0134.tar.gz"
+    url      = "https://github.com/vim/vim/archive/v8.1.0338.tar.gz"
 
+    version('8.1.0338', '94191b4141245a5deb4955c4a80359bb')
+    version('8.1.0001', 'edb6f5c67cb3100ea9e3966a43b9c9da')
+    version('8.0.1376', '62855881a2d96d48956859d74cfb8a3b')
     version('8.0.0503', '82b77bd5cb38b70514bed47cfe033b8c')
     version('8.0.0454', '4030bf677bdfbd14efb588e4d9a24128')
     version('8.0.0134', 'c74668d25c2acc85d655430dd60886cd')
@@ -65,6 +49,11 @@ class Vim(AutotoolsPackage):
     # support for auto/no/gtk2/gnome2/gtk3/motif/athena/neXtaw/photon/carbon
     variant('gui', default=False, description="build with gui (gvim)")
     variant('x', default=False, description="use the X Window System")
+    depends_on('libx11', when="+x")
+    depends_on('libsm', when="+x")
+    depends_on('libxpm', when="+x")
+    depends_on('libxt', when="+x")
+    depends_on('libxtst', when="+x")
 
     depends_on('ncurses', when="@7.4:")
 
@@ -95,9 +84,14 @@ class Vim(AutotoolsPackage):
         configure_args.append("--with-features=" + feature_set)
 
         if '+python' in spec:
-            configure_args.append("--enable-pythoninterp=yes")
+            if 'python@3:' in self.spec:
+                configure_args.append("--enable-python3interp=yes")
+                configure_args.append("--enable-pythoninterp=no")
+            else:
+                configure_args.append("--enable-python3interp=no")
+                configure_args.append("--enable-pythoninterp=yes")
         else:
-            configure_args.append("--enable-pythoninterp=no")
+            configure_args.append("--enable-python3interp=no")
 
         if '+ruby' in spec:
             configure_args.append("--enable-rubyinterp=yes")
@@ -130,6 +124,10 @@ class Vim(AutotoolsPackage):
 
         return configure_args
 
+    # Tests must be run in serial
+    def check(self):
+        make('test', parallel=False)
+
     # Run the install phase with -j 1.  There seems to be a problem with
     # parallel builds that results in the creation of the links (e.g. view)
     # to the vim binary silently failing.
diff --git a/var/spack/repos/builtin/packages/virtualgl/package.py b/var/spack/repos/builtin/packages/virtualgl/package.py
index c80eea5345..9ccef35acb 100644
--- a/var/spack/repos/builtin/packages/virtualgl/package.py
+++ b/var/spack/repos/builtin/packages/virtualgl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 #
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/visit/package.py b/var/spack/repos/builtin/packages/visit/package.py
index 56dec99eec..47d93c3a7b 100644
--- a/var/spack/repos/builtin/packages/visit/package.py
+++ b/var/spack/repos/builtin/packages/visit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,31 +12,72 @@ class Visit(CMakePackage):
     homepage = "https://wci.llnl.gov/simulation/computer-codes/visit/"
     url = "http://portal.nersc.gov/project/visit/releases/2.10.1/visit2.10.1.tar.gz"
 
+    version('2.13.0', '716644b8e78a00ff82691619d4d1e7a914965b6535884890b667b97ba08d6a0f')
+    version('2.12.3', '2dd351a291ee3e79926bc00391ca89b202cfa4751331b0fdee1b960c7922161f')
     version('2.12.2', '355779b1dbf440cdd548526eecd77b60')
     version('2.10.3', 'a1082a6f6dab3e2dcb58993603456c2b')
     version('2.10.2', '253de0837a9d69fb689befc98ea4d068')
     version('2.10.1', '3cbca162fdb0249f17c4456605c4211e')
 
+    variant('gui',    default=True, description='Enable VisIt\'s GUI')
+    variant('hdf5',   default=True, description='Enable HDF5 file format')
+    variant('silo',   default=True, description='Enable Silo file format')
+    variant('python', default=True, description='Enable Python support')
+    variant('mpi',    default=True, description='Enable parallel engine')
+
     depends_on('cmake@3.0:', type='build')
-    depends_on('vtk@6.1.0~opengl2')
-    depends_on('qt@4.8.6')
-    depends_on('python')
-    depends_on('silo+shared')
-    depends_on('hdf5~mpi')
+    depends_on('vtk@6.1.0~opengl2~mpi')
+    depends_on('qt@4.8.6', when='+gui')
+    depends_on('qwt', when='+gui')
+    depends_on('python', when='+python')
+    depends_on('silo+shared', when='+silo')
+    depends_on('hdf5', when='+hdf5')
+    depends_on('mpi', when='+mpi')
+
+    conflicts('+hdf5', when='~gui')
+    conflicts('+silo', when='~gui')
 
     root_cmakelists_dir = 'src'
 
     def cmake_args(self):
         spec = self.spec
-        qt_bin = spec['qt'].prefix.bin
 
-        return [
+        args = [
             '-DVTK_MAJOR_VERSION={0}'.format(spec['vtk'].version[0]),
             '-DVTK_MINOR_VERSION={0}'.format(spec['vtk'].version[1]),
-            '-DVISIT_USE_GLEW=OFF',
-            '-DVISIT_LOC_QMAKE_EXE:FILEPATH={0}/qmake-qt4'.format(qt_bin),
-            '-DPYTHON_DIR:PATH={0}'.format(spec['python'].home),
-            '-DVISIT_SILO_DIR:PATH={0}'.format(spec['silo'].prefix),
-            '-DVISIT_HDF5_DIR:PATH={0}'.format(spec['hdf5'].prefix),
             '-DVISIT_VTK_DIR:PATH={0}'.format(spec['vtk'].prefix),
+            '-DVISIT_USE_GLEW=OFF',
+            '-DCMAKE_CXX_FLAGS=-fPIC',
+            '-DCMAKE_C_FLAGS=-fPIC'
         ]
+
+        if(spec.variants['python'].value):
+            args.append('-DPYTHON_DIR:PATH={0}'.format(spec['python'].home))
+
+        if(spec.variants['gui'].value):
+            qt_bin = spec['qt'].prefix.bin
+            args.append(
+                '-DVISIT_LOC_QMAKE_EXE:FILEPATH={0}/qmake-qt4'.format(qt_bin))
+            args.append('-DVISIT_QWT_DIR:PATH={0}'.format(spec['qwt'].prefix))
+        else:
+            args.append('-DVISIT_SERVER_COMPONENTS_ONLY=ON')
+            args.append('-DVISIT_ENGINE_ONLY=ON')
+
+        if(spec.variants['hdf5'].value):
+            args.append(
+                '-DVISIT_HDF5_DIR:PATH={0}'.format(spec['hdf5'].prefix))
+            if spec.satisfies('^hdf5+mpi', strict=True):
+                args.append('-DVISIT_HDF5_MPI_DIR:PATH={0}'.format(
+                    spec['hdf5'].prefix))
+
+        if(spec.variants['silo'].value):
+            args.append(
+                '-DVISIT_SILO_DIR:PATH={0}'.format(spec['silo'].prefix))
+
+        if(spec.variants['mpi'].value):
+            args.append('-DVISIT_PARALLEL=ON')
+            args.append('-DVISIT_C_COMPILER={0}'.format(spec['mpi'].mpicc))
+            args.append('-DVISIT_CXX_COMPILER={0}'.format(spec['mpi'].mpicxx))
+            args.append('-DVISIT_MPI_COMPILER={0}'.format(spec['mpi'].mpicxx))
+
+        return args
diff --git a/var/spack/repos/builtin/packages/vizglow/package.py b/var/spack/repos/builtin/packages/vizglow/package.py
index b35af35164..4a8db820e6 100644
--- a/var/spack/repos/builtin/packages/vizglow/package.py
+++ b/var/spack/repos/builtin/packages/vizglow/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import glob
 import os
diff --git a/var/spack/repos/builtin/packages/vmatch/package.py b/var/spack/repos/builtin/packages/vmatch/package.py
index e58f9fbb22..62b38a8667 100644
--- a/var/spack/repos/builtin/packages/vmatch/package.py
+++ b/var/spack/repos/builtin/packages/vmatch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/voropp/package.py b/var/spack/repos/builtin/packages/voropp/package.py
index e88c20d864..e0a63f6f8e 100644
--- a/var/spack/repos/builtin/packages/voropp/package.py
+++ b/var/spack/repos/builtin/packages/voropp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/votca-csg/package.py b/var/spack/repos/builtin/packages/votca-csg/package.py
index 5c827ad36d..ca2f1b39b3 100644
--- a/var/spack/repos/builtin/packages/votca-csg/package.py
+++ b/var/spack/repos/builtin/packages/votca-csg/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -35,8 +17,9 @@ class VotcaCsg(CMakePackage):
     """
     homepage = "http://www.votca.org"
     url      = "https://github.com/votca/csg/tarball/v1.4"
+    git      = "https://github.com/votca/csg.git"
 
-    version('develop', git='https://github.com/votca/csg', branch='master')
+    version('develop', branch='master')
     version('1.4', 'd009e761e5e3afd51eed89c420610a67')
     version('1.4.1', 'e4195d69db2036e9d76f22115ae31f81')
 
@@ -44,3 +27,4 @@ class VotcaCsg(CMakePackage):
     depends_on("votca-tools@1.4:1.4.999", when='@1.4:1.4.999')
     depends_on("votca-tools@develop", when='@develop')
     depends_on("gromacs~mpi@5.1:")
+    depends_on("hdf5~mpi")
diff --git a/var/spack/repos/builtin/packages/votca-ctp/package.py b/var/spack/repos/builtin/packages/votca-ctp/package.py
index f02c7eb564..3cbd2e0c9f 100644
--- a/var/spack/repos/builtin/packages/votca-ctp/package.py
+++ b/var/spack/repos/builtin/packages/votca-ctp/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,12 +16,11 @@ class VotcaCtp(CMakePackage):
        This package contains the VOTCA charge transport engine.
     """
     homepage = "http://www.votca.org"
-    # No release yet
-    # url      = "https://github.com/votca/ctp/tarball/v1.4"
+    git      = "https://github.com/votca/ctp.git"
 
-    version('develop', git='https://github.com/votca/ctp', branch='master')
+    version('develop', branch='master')
 
     depends_on("cmake@2.8:", type='build')
     depends_on("votca-tools@develop", when='@develop')
     depends_on("votca-csg@develop", when='@develop')
-    depends_on("votca-moo@develop", when='@develop')
+    depends_on("gsl")
diff --git a/var/spack/repos/builtin/packages/votca-moo/package.py b/var/spack/repos/builtin/packages/votca-moo/package.py
deleted file mode 100644
index 308d28aab1..0000000000
--- a/var/spack/repos/builtin/packages/votca-moo/package.py
+++ /dev/null
@@ -1,43 +0,0 @@
-#############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
-#
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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 VotcaMoo(CMakePackage):
-    """Versatile Object-oriented Toolkit for Coarse-graining
-       Applications (VOTCA) is a package intended to reduce the amount of
-       routine work when doing systematic coarse-graining of various
-       systems. The core is written in C++.
-
-       This package contains the VOTCA molecular orbital module.
-    """
-    homepage = "http://www.votca.org"
-    # No release yet
-    # url      = "https://github.com/votca/moo/tarball/v1.4"
-
-    version('develop', git='https://github.com/votca/moo', branch='master')
-
-    depends_on("cmake@2.8:", type='build')
-    depends_on("votca-tools@develop", when='@develop')
diff --git a/var/spack/repos/builtin/packages/votca-tools/package.py b/var/spack/repos/builtin/packages/votca-tools/package.py
index 9eb7fd147a..1f0a67ee3e 100644
--- a/var/spack/repos/builtin/packages/votca-tools/package.py
+++ b/var/spack/repos/builtin/packages/votca-tools/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -35,14 +17,22 @@ class VotcaTools(CMakePackage):
     """
     homepage = "http://www.votca.org"
     url      = "https://github.com/votca/tools/tarball/v1.4"
+    git      = "https://github.com/votca/tools.git"
 
-    version('develop', git='https://github.com/votca/tools', branch='master')
+    version('develop', branch='master')
     version('1.4', 'cd47868e9f28e2c7b9d01f95aa0185ca')
     version('1.4.1', '3176b72f8a41ec053cc740a5398e7dc4')
 
     depends_on("cmake@2.8:", type='build')
     depends_on("expat")
     depends_on("fftw")
-    depends_on("gsl")
+    depends_on("gsl", when="@:1.4.9999")
+    depends_on("eigen@3.3:", when="@1.5:")
     depends_on("boost")
     depends_on("sqlite")
+
+    def cmake_args(self):
+        args = [
+            '-DWITH_RC_FILES=OFF'
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/votca-xtp/package.py b/var/spack/repos/builtin/packages/votca-xtp/package.py
index e2b8ee059e..14a323de71 100644
--- a/var/spack/repos/builtin/packages/votca-xtp/package.py
+++ b/var/spack/repos/builtin/packages/votca-xtp/package.py
@@ -1,26 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, The VOTCA Development Team (http://www.votca.org)
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -34,9 +16,10 @@ class VotcaXtp(CMakePackage):
        This package contains the VOTCA exciton transport engine.
     """
     homepage = "http://www.votca.org"
-    url      = "https://github.com/votca/xtp/tarball/v1.4"
+    url      = "https://github.com/votca/xtp/tarball/v1.4.1"
+    git      = "https://github.com/votca/xtp.git"
 
-    version('develop', git='https://github.com/votca/xtp', branch='master')
+    version('develop', branch='master')
     version('1.4.1', '31a2dbd8bd48bf337bc88b20ab312050')
 
     depends_on("cmake@2.8:", type='build')
@@ -45,4 +28,5 @@ class VotcaXtp(CMakePackage):
     depends_on("votca-csg@develop", when='@develop')
     depends_on("votca-csg@1.4:1.4.999", when='@1.4:1.4.999')
     depends_on("votca-ctp@develop", when='@develop')
-    depends_on("votca-moo@develop", when='@develop')
+    depends_on("libxc", when='@1.5:')
+    depends_on("ceres-solver", when='@1.5:')
diff --git a/var/spack/repos/builtin/packages/vpfft/package.py b/var/spack/repos/builtin/packages/vpfft/package.py
index 1de6bdcfe4..0d58430d7d 100644
--- a/var/spack/repos/builtin/packages/vpfft/package.py
+++ b/var/spack/repos/builtin/packages/vpfft/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,10 +16,11 @@ class Vpfft(MakefilePackage):
     """
 
     homepage = "http://www.exmatex.org/vpfft.html"
-    url      = "https://github.com/exmatex/VPFFT/archive/master.tar.gz"
-    tag      = ['proxy-app']
+    git      = "https://github.com/exmatex/VPFFT.git"
+
+    tag = ['proxy-app']
 
-    version('develop', git='https://github.com/exmatex/VPFFT.git')
+    version('develop')
 
     depends_on('eigen')
     depends_on('fftw')
diff --git a/var/spack/repos/builtin/packages/vpic/package.py b/var/spack/repos/builtin/packages/vpic/package.py
index b5be3c6b82..5be359be28 100644
--- a/var/spack/repos/builtin/packages/vpic/package.py
+++ b/var/spack/repos/builtin/packages/vpic/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -36,9 +17,9 @@ class Vpic(CMakePackage):
        order finite-difference-time-domain (FDTD) solve.
     """
     homepage = "https://github.com/lanl/vpic"
-    url      = "https://github.com/lanl/vpic/tarball/v1.0"
+    git      = "https://github.com/lanl/vpic.git"
 
-    version('develop', git='https://github.com/lanl/vpic', branch='master', submodules=True)
+    version('develop', branch='master', submodules=True)
 
     depends_on("cmake@3.1:", type='build')
     depends_on('mpi')
diff --git a/var/spack/repos/builtin/packages/vsearch/package.py b/var/spack/repos/builtin/packages/vsearch/package.py
index 8a69123d17..892dcfb9ec 100644
--- a/var/spack/repos/builtin/packages/vsearch/package.py
+++ b/var/spack/repos/builtin/packages/vsearch/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/vt/package.py b/var/spack/repos/builtin/packages/vt/package.py
new file mode 100644
index 0000000000..b3b8305a9c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vt/package.py
@@ -0,0 +1,19 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Vt(MakefilePackage):
+    """A tool set for short variant discovery in genetic sequence data."""
+
+    homepage = "http://genome.sph.umich.edu/wiki/vt"
+    url      = "https://github.com/atks/vt/archive/0.577.tar.gz"
+
+    version('0.577',  '59807456022bcecf978314c93254fe15')
+
+    def install(self, spec, spack):
+        mkdirp(prefix.bin)
+        install('vt', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py
index 0ab9a1a131..9cc75f3a8b 100644
--- a/var/spack/repos/builtin/packages/vtk/package.py
+++ b/var/spack/repos/builtin/packages/vtk/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+
+import os
 from spack import *
 
 
@@ -32,74 +14,250 @@ class Vtk(CMakePackage):
     processing and visualization. """
 
     homepage = "http://www.vtk.org"
-    url      = "http://www.vtk.org/files/release/7.1/VTK-7.1.0.tar.gz"
+    url      = "http://www.vtk.org/files/release/8.0/VTK-8.0.1.tar.gz"
     list_url = "http://www.vtk.org/download/"
 
+    version('8.1.1', sha256='71a09b4340f0a9c58559fe946dc745ab68a866cf20636a41d97b6046cb736324')
+    version('8.0.1', '692d09ae8fadc97b59d35cab429b261a')
     version('7.1.0', 'a7e814c1db503d896af72458c2d0228f')
     version('7.0.0', '5fe35312db5fb2341139b8e4955c367d')
     version('6.3.0', '0231ca4840408e9dd60af48b314c5b6d')
     version('6.1.0', '25e4dfb3bad778722dcaec80cd5dab7d')
 
     # VTK7 defaults to OpenGL2 rendering backend
-    variant('opengl2', default=True, description='Build with OpenGL2 instead of OpenGL as rendering backend')
-    variant('python', default=False, description='Build the python modules')
+    variant('opengl2', default=True, description='Enable OpenGL2 backend')
+    variant('osmesa', default=False, description='Enable OSMesa support')
+    variant('python', default=False, description='Enable Python support')
+    variant('qt', default=False, description='Build with support for Qt')
+    variant('xdmf', default=False, description='Build XDMF file support')
+    variant('ffmpeg', default=False, description='Build with FFMPEG support')
+    variant('mpi', default=True, description='Enable MPI support')
+
+    # Haru causes trouble on Fedora and Ubuntu in v8.1.1
+    # See https://bugzilla.redhat.com/show_bug.cgi?id=1460059#c13
+    variant('haru', default=True, description='Enable libharu')
 
     patch('gcc.patch', when='@6.1.0')
 
-    depends_on('qt')
+    # At the moment, we cannot build with both osmesa and qt, but as of
+    # VTK 8.1, that should change
+    conflicts('+osmesa', when='+qt')
+
+    depends_on('python', when='+python')
+    depends_on('py-mpi4py', when='+mpi +python', type='run')
+    extends('python', when='+python')
+    # python3.7 compatibility patch backported from upstream
+    # https://gitlab.kitware.com/vtk/vtk/commit/706f1b397df09a27ab8981ab9464547028d0c322
+    patch('python3.7-const-char.patch', when='@:8.1.1 ^python@3.7:')
+
+    # The use of the OpenGL2 backend requires at least OpenGL Core Profile
+    # version 3.2 or higher.
+    depends_on('gl@3.2:', when='+opengl2')
+
+    # If you didn't ask for osmesa, then hw rendering using vendor-specific
+    # drivers is faster, but it must be done externally.
+    depends_on('opengl', when='~osmesa')
+
+    # Note: it is recommended to use mesa+llvm, if possible.
+    # mesa default is software rendering, llvm makes it faster
+    depends_on('mesa', when='+osmesa')
+
+    # VTK will need Qt5OpenGL, and qt needs '-opengl' for that
+    depends_on('qt+opengl', when='+qt')
+
+    depends_on('mpi', when='+mpi')
+
+    depends_on('libharu', when='+haru')
+
+    depends_on('boost', when='+xdmf')
+    depends_on('boost+mpi', when='+xdmf +mpi')
+
+    depends_on('mpi', when='+mpi')
+
+    depends_on('ffmpeg', when='+ffmpeg')
+
+    depends_on('expat')
+    depends_on('freetype')
+    depends_on('glew')
     depends_on('hdf5')
+    depends_on('libjpeg')
+    depends_on('jsoncpp')
+    depends_on('libxml2')
+    depends_on('lz4')
     depends_on('netcdf')
     depends_on('netcdf-cxx')
-
-    extends('python', when='+python')
+    depends_on('libpng')
+    depends_on('libtiff')
+    depends_on('zlib')
 
     def url_for_version(self, version):
         url = "http://www.vtk.org/files/release/{0}/VTK-{1}.tar.gz"
         return url.format(version.up_to(2), version)
 
+    def setup_environment(self, spack_env, run_env):
+        # VTK has some trouble finding freetype unless it is set in
+        # the environment
+        spack_env.set('FREETYPE_DIR', self.spec['freetype'].prefix)
+
     def cmake_args(self):
         spec = self.spec
 
         opengl_ver = 'OpenGL{0}'.format('2' if '+opengl2' in spec else '')
-        qt_ver = spec['qt'].version.up_to(1)
-        qt_bin = spec['qt'].prefix.bin
 
-        cmake_args = std_cmake_args[:]
-        cmake_args.extend([
+        cmake_args = [
             '-DBUILD_SHARED_LIBS=ON',
             '-DVTK_RENDERING_BACKEND:STRING={0}'.format(opengl_ver),
-            '-DVTK_USE_SYSTEM_HDF5=ON',
-            '-DVTK_USE_SYSTEM_NETCDF=ON',
+
+            '-DVTK_USE_SYSTEM_LIBHARU=%s' % (
+                'ON' if '+haru' in spec else 'OFF'),
+
+            # In general, we disable use of VTK "ThirdParty" libs, preferring
+            # spack-built versions whenever possible
+            '-DVTK_USE_SYSTEM_LIBRARIES:BOOL=ON',
+
+            # However, in a few cases we can't do without them yet
+            '-DVTK_USE_SYSTEM_GL2PS:BOOL=OFF',
+            '-DVTK_USE_SYSTEM_LIBPROJ4:BOOL=OFF',
+            '-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=OFF',
+
             '-DNETCDF_DIR={0}'.format(spec['netcdf'].prefix),
             '-DNETCDF_C_ROOT={0}'.format(spec['netcdf'].prefix),
             '-DNETCDF_CXX_ROOT={0}'.format(spec['netcdf-cxx'].prefix),
 
-            # Enable/Disable wrappers for Python.
-            '-DVTK_WRAP_PYTHON={0}'.format(
-                'ON' if '+python' in spec else 'OFF'),
-
             # Disable wrappers for other languages.
             '-DVTK_WRAP_JAVA=OFF',
             '-DVTK_WRAP_TCL=OFF',
+        ]
+
+        if '+mpi' in spec:
+            cmake_args.extend([
+                '-DVTK_Group_MPI:BOOL=ON',
+                '-DVTK_USE_SYSTEM_DIY2:BOOL=OFF',
+            ])
 
-            # Enable Qt support here.
-            '-DVTK_QT_VERSION:STRING={0}'.format(qt_ver),
-            '-DQT_QMAKE_EXECUTABLE:PATH={0}/qmake'.format(qt_bin),
-            '-DVTK_Group_Qt:BOOL=ON',
-        ])
+        if '+ffmpeg' in spec:
+            cmake_args.extend(['-DModule_vtkIOFFMPEG:BOOL=ON'])
 
-        # NOTE: The following definitions are required in order to allow
-        # VTK to build with qt~webkit versions (see the documentation for
-        # more info: http://www.vtk.org/Wiki/VTK/Tutorials/QtSetup).
-        if '~webkit' in spec['qt']:
+        # Enable/Disable wrappers for Python.
+        if '+python' in spec:
             cmake_args.extend([
-                '-DVTK_Group_Qt:BOOL=OFF',
-                '-DModule_vtkGUISupportQt:BOOL=ON',
-                '-DModule_vtkGUISupportQtOpenGL:BOOL=ON',
+                '-DVTK_WRAP_PYTHON=ON',
+                '-DPYTHON_EXECUTABLE={0}'.format(spec['python'].command.path),
+                '-DVTK_USE_SYSTEM_MPI4PY:BOOL=ON'
+            ])
+        else:
+            cmake_args.append('-DVTK_WRAP_PYTHON=OFF')
+
+        if 'darwin' in spec.architecture:
+            cmake_args.extend([
+                '-DCMAKE_MACOSX_RPATH=ON'
+            ])
+
+        if '+qt' in spec:
+            qt_ver = spec['qt'].version.up_to(1)
+            qt_bin = spec['qt'].prefix.bin
+            qmake_exe = os.path.join(qt_bin, 'qmake')
+
+            cmake_args.extend([
+                # Enable Qt support here.
+                '-DVTK_QT_VERSION:STRING={0}'.format(qt_ver),
+                '-DQT_QMAKE_EXECUTABLE:PATH={0}'.format(qmake_exe),
+                '-DVTK_Group_Qt:BOOL=ON',
+            ])
+
+            # NOTE: The following definitions are required in order to allow
+            # VTK to build with qt~webkit versions (see the documentation for
+            # more info: http://www.vtk.org/Wiki/VTK/Tutorials/QtSetup).
+            if '~webkit' in spec['qt']:
+                cmake_args.extend([
+                    '-DVTK_Group_Qt:BOOL=OFF',
+                    '-DModule_vtkGUISupportQt:BOOL=ON',
+                    '-DModule_vtkGUISupportQtOpenGL:BOOL=ON',
+                ])
+
+        if '+xdmf' in spec:
+            if spec.satisfies('^cmake@3.12:'):
+                # This policy exists only for CMake >= 3.12
+                cmake_args.extend(["-DCMAKE_POLICY_DEFAULT_CMP0074=NEW"])
+
+            cmake_args.extend([
+                # Enable XDMF Support here
+                "-DModule_vtkIOXdmf2:BOOL=ON",
+                "-DModule_vtkIOXdmf3:BOOL=ON",
+                "-DBOOST_ROOT={0}".format(spec['boost'].prefix),
+                "-DBOOST_LIBRARY_DIR={0}".format(spec['boost'].prefix.lib),
+                "-DBOOST_INCLUDE_DIR={0}".format(spec['boost'].prefix.include),
+                "-DBOOST_NO_SYSTEM_PATHS:BOOL=ON",
+                # This is needed because VTK has multiple FindBoost
+                # and they stick to system boost if there's a system boost
+                # installed with CMake
+                "-DBoost_NO_BOOST_CMAKE:BOOL=ON",
+                "-DHDF5_ROOT={0}".format(spec['hdf5'].prefix),
+                # The xdmf project does not export any CMake file...
+                "-DVTK_USE_SYSTEM_XDMF3:BOOL=OFF",
+                "-DVTK_USE_SYSTEM_XDMF2:BOOL=OFF"
+            ])
+
+            if '+mpi' in spec:
+                cmake_args.extend(["-DModule_vtkIOParallelXdmf3:BOOL=ON"])
+
+        if '+osmesa' in spec:
+            prefix = spec['mesa'].prefix
+            osmesa_include_dir = prefix.include
+            osmesa_library = os.path.join(prefix.lib, 'libOSMesa.so')
+
+            use_param = 'VTK_USE_X'
+            if 'darwin' in spec.architecture:
+                use_param = 'VTK_USE_COCOA'
+
+            cmake_args.extend([
+                '-D{0}:BOOL=OFF'.format(use_param),
+                '-DVTK_OPENGL_HAS_OSMESA:BOOL=ON',
+                '-DOSMESA_INCLUDE_DIR:PATH={0}'.format(osmesa_include_dir),
+                '-DOSMESA_LIBRARY:FILEPATH={0}'.format(osmesa_library),
+            ])
+        else:
+            prefix = spec['opengl'].prefix
+
+            opengl_include_dir = prefix.include
+            opengl_library = os.path.join(prefix.lib, 'libGL.so')
+            if 'darwin' in spec.architecture:
+                opengl_include_dir = prefix
+                opengl_library = prefix
+
+            cmake_args.extend([
+                '-DOPENGL_INCLUDE_DIR:PATH={0}'.format(opengl_include_dir),
+                '-DOPENGL_gl_LIBRARY:FILEPATH={0}'.format(opengl_library)
             ])
 
         if spec.satisfies('@:6.1.0'):
-            cmake_args.append('-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY')
-            cmake_args.append('-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY')
+            cmake_args.extend([
+                '-DCMAKE_C_FLAGS=-DGLX_GLXEXT_LEGACY',
+                '-DCMAKE_CXX_FLAGS=-DGLX_GLXEXT_LEGACY'
+            ])
+
+            # VTK 6.1.0 (and possibly earlier) does not use
+            # NETCDF_CXX_ROOT to detect NetCDF C++ bindings, so
+            # NETCDF_CXX_INCLUDE_DIR and NETCDF_CXX_LIBRARY must be
+            # used instead to detect these bindings
+            netcdf_cxx_lib = spec['netcdf-cxx'].libs.joined()
+            cmake_args.extend([
+                '-DNETCDF_CXX_INCLUDE_DIR={0}'.format(
+                    spec['netcdf-cxx'].prefix.include),
+                '-DNETCDF_CXX_LIBRARY={0}'.format(netcdf_cxx_lib),
+            ])
+
+            # Garbage collection is unsupported in Xcode starting with
+            # version 5.1; if the Apple clang version of the compiler
+            # is 5.1.0 or later, unset the required Objective-C flags
+            # to remove the garbage collection flags.  Versions of VTK
+            # after 6.1.0 set VTK_REQUIRED_OBJCXX_FLAGS to the empty
+            # string. This fix was recommended on the VTK mailing list
+            # in March 2014 (see
+            # https://public.kitware.com/pipermail/vtkusers/2014-March/083368.html)
+            if (self.spec.satisfies('%clang') and
+                self.compiler.is_apple and
+                self.compiler.version >= Version('5.1.0')):
+                cmake_args.extend(['-DVTK_REQUIRED_OBJCXX_FLAGS=""'])
 
         return cmake_args
diff --git a/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch b/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch
new file mode 100644
index 0000000000..80dbc78530
--- /dev/null
+++ b/var/spack/repos/builtin/packages/vtk/python3.7-const-char.patch
@@ -0,0 +1,27 @@
+diff --git a/Wrapping/PythonCore/vtkPythonArgs.cxx b/Wrapping/PythonCore/vtkPythonArgs.cxx
+index 1a82af0802..b733458975 100644
+--- a/Wrapping/PythonCore/vtkPythonArgs.cxx
++++ b/Wrapping/PythonCore/vtkPythonArgs.cxx
+@@ -95,13 +95,21 @@ bool vtkPythonGetStringValue(PyObject *o, T *&a, const char *exctext)
+ {
+   if (PyBytes_Check(o))
+   {
++#if PY_VERSION_HEX >= 0x03070000
++    a = const_cast<char *>(PyBytes_AS_STRING(o));
++    return true;
++#else
+     a = PyBytes_AS_STRING(o);
+     return true;
++#endif
+   }
+ #ifdef Py_USING_UNICODE
+   else if (PyUnicode_Check(o))
+   {
+-#if PY_VERSION_HEX >= 0x03030000
++#if PY_VERSION_HEX >= 0x03070000
++    a = const_cast<char *>(PyUnicode_AsUTF8(o));
++    return true;
++#elif PY_VERSION_HEX >= 0x03030000
+     a = PyUnicode_AsUTF8(o);
+     return true;
+ #else
diff --git a/var/spack/repos/builtin/packages/vtkh/package.py b/var/spack/repos/builtin/packages/vtkh/package.py
index 9073c1f6f3..f42322332a 100644
--- a/var/spack/repos/builtin/packages/vtkh/package.py
+++ b/var/spack/repos/builtin/packages/vtkh/package.py
@@ -1,29 +1,11 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
+import os
 
 
 class Vtkh(Package):
@@ -32,12 +14,9 @@ class Vtkh(Package):
     and DIY2 to provide a toolkit with hybrid parallel capabilities."""
 
     homepage = "https://github.com/Alpine-DAV/vtk-h"
-    url      = "https://github.com/Alpine-DAV/vtk-h"
+    git      = "https://github.com/Alpine-DAV/vtk-h.git"
 
-    version('master',
-            git='https://github.com/Alpine-DAV/vtk-h.git',
-            branch='master',
-            submodules=True)
+    version('master', branch='master', submodules=True)
 
     maintainers = ['cyrush']
 
@@ -67,7 +46,9 @@ class Vtkh(Package):
                 mpicxx = spec['mpi'].mpicxx
                 cmake_args.extend(["-DMPI_C_COMPILER={0}".format(mpicc),
                                    "-DMPI_CXX_COMPILER={0}".format(mpicxx)])
-
+                mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
+                if os.path.isfile(mpiexe_bin):
+                    cmake_args.append("-DMPIEXEC={0}".format(mpiexe_bin))
             # tbb support
             if "+tbb" in spec:
                 cmake_args.append("-DTBB_DIR={0}".format(spec["tbb"].prefix))
diff --git a/var/spack/repos/builtin/packages/vtkm/package.py b/var/spack/repos/builtin/packages/vtkm/package.py
index c1bc968f85..ded4a551ac 100644
--- a/var/spack/repos/builtin/packages/vtkm/package.py
+++ b/var/spack/repos/builtin/packages/vtkm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import os
@@ -36,14 +17,12 @@ class Vtkm(Package):
     architectures."""
 
     homepage = "https://m.vtk.org/"
-    url      = "https://gitlab.kitware.com/vtk/vtk-m/repository/v1.1.0/archive.tar.gz"
+    url      = "https://gitlab.kitware.com/api/v4/projects/vtk%2Fvtk-m/repository/archive.tar.gz?sha=v1.1.0"
+    git      = "https://gitlab.kitware.com/vtk/vtk-m.git"
 
+    version('master', branch='master')
     version('1.1.0', "6aab1c0885f6ffaaffcf07930873d0df")
 
-    version('master',
-            git='https://gitlab.kitware.com/vtk/vtk-m.git',
-            branch='master')
-
     variant("cuda", default=False, description="build cuda support")
     variant("tbb", default=True, description="build TBB support")
 
diff --git a/var/spack/repos/builtin/packages/wannier90/package.py b/var/spack/repos/builtin/packages/wannier90/package.py
index c940d6c171..ec8a47620c 100644
--- a/var/spack/repos/builtin/packages/wannier90/package.py
+++ b/var/spack/repos/builtin/packages/wannier90/package.py
@@ -1,30 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 import inspect
 import os.path
-import shutil
 
 from spack import *
 
@@ -77,7 +57,7 @@ class Wannier90(MakefilePackage):
             'make.sys'
         )
 
-        shutil.copy(template, self.makefile_name)
+        copy(template, self.makefile_name)
         for key, value in substitutions.items():
             filter_file(key, value, self.makefile_name)
 
diff --git a/var/spack/repos/builtin/packages/warpx/package.py b/var/spack/repos/builtin/packages/warpx/package.py
new file mode 100644
index 0000000000..bfbcd7fa3a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/warpx/package.py
@@ -0,0 +1,84 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Warpx(MakefilePackage):
+    """WarpX is an advanced electromagnetic Particle-In-Cell code. It supports
+    many features including Perfectly-Matched Layers (PML) and mesh refinement.
+    In addition, WarpX is a highly-parallel and highly-optimized code and
+    features hybrid OpenMP/MPI parallelization, advanced vectorization
+    techniques and load balancing capabilities.
+    """
+
+    homepage = "https://ecp-warpx.github.io/index.html"
+    url      = "https://github.com/ECP-WarpX/WarpX"
+
+    version('master', git='https://github.com/ECP-WarpX/WarpX.git', tag='master')
+    version('dev', git='https://github.com/ECP-WarpX/WarpX.git', tag='dev')
+
+    depends_on('mpi')
+
+    variant('dims',
+            default='3',
+            values=('1', '2', '3'),
+            multi=False,
+            description='Number of spatial dimensions')
+
+    variant('psatd', default=False, description='Enable PSATD solver')
+    variant('do_electrostatic', default=False, description='Include electrostatic solver')
+    variant('debug', default=False, description='Enable debugging features')
+    variant('tprof', default=False, description='Enable tiny profiling features')
+    variant('openmp', default=True, description='Enable OpenMP features')
+
+    resource(name='amrex',
+             git='https://github.com/AMReX-Codes/amrex.git',
+             tag='development',
+             destination='.')
+
+    resource(name='picsar',
+             git='https://bitbucket.org/berkeleylab/picsar.git',
+             tag='master',
+             destination='.')
+
+    def edit(self, spec, prefix):
+
+        comp = 'gcc'
+        vendors = {'%gcc': 'gcc', '%intel': 'intel'}
+        for key, value in vendors.items():
+            if self.spec.satisfies(key):
+                comp = value
+
+        def torf(s):
+            "Returns the string TRUE or FALSE"
+            return repr(s in spec).upper()
+
+        makefile = FileFilter('GNUmakefile')
+        makefile.filter('AMREX_HOME .*', 'AMREX_HOME = amrex')
+        makefile.filter('PICSAR_HOME .*', 'PICSAR_HOME = picsar')
+        makefile.filter('COMP .*', 'COMP = {0}'.format(comp))
+        makefile.filter('DIM .*',
+                        'DIM = {0}'.format(int(spec.variants['dims'].value)))
+        makefile.filter('USE_PSATD .*',
+                        'USE_PSATD = {0}'.format(torf('+psatd')))
+        makefile.filter('DO_ELECTROSTATIC .*',
+                        'DO_ELECTROSTATIC = %s' % torf('+do_electrostatic'))
+        makefile.filter('USE_OMP .*',
+                        'USE_OMP = {0}'.format(torf('+openmp')))
+        makefile.filter('DEBUG .*',
+                        'DEBUG = {0}'.format(torf('+debug')))
+        makefile.filter('TINY_PROFILE .*',
+                        'TINY_PROFILE = {0}'.format(torf('+tprof')))
+        makefile.filter('EBASE .*', 'EBASE = warpx')
+
+    def setup_environment(self, spack_env, run_env):
+        # --- Fool the compiler into using the "unknown" configuration.
+        # --- With this, it will use the spack provided mpi.
+        spack_env.set('HOSTNAME', 'unknown')
+        spack_env.set('NERSC_HOST', 'unknown')
+
+    def install(self, spec, prefix):
+        make('WarpxBinDir = {0}'.format(prefix.bin), 'all')
diff --git a/var/spack/repos/builtin/packages/wcslib/package.py b/var/spack/repos/builtin/packages/wcslib/package.py
new file mode 100644
index 0000000000..a3b5a56a68
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wcslib/package.py
@@ -0,0 +1,48 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Wcslib(AutotoolsPackage):
+    """WCSLIB a C implementation of the coordinate transformations
+    defined in the FITS WCS papers."""
+
+    homepage = "http://www.atnf.csiro.au/people/mcalabre/WCS/wcslib/"
+    url      = "ftp://ftp.atnf.csiro.au/pub/software/wcslib/wcslib-5.18.tar.bz2"
+
+    version('5.18', '67a78354be74eca4f17d3e0853d5685f')
+
+    variant('cfitsio', default=False, description='Include CFITSIO support')
+    variant('x',       default=False, description='Use the X Window System')
+
+    depends_on('gmake', type='build')
+    depends_on('flex@2.5.9:', type='build')
+    depends_on('cfitsio', when='+cfitsio')
+    depends_on('libx11', when='+x')
+
+    def configure_args(self):
+        spec = self.spec
+
+        # TODO: Add PGPLOT package
+        args = ['--without-pgplot']
+
+        if '+cfitsio' in spec:
+            args.extend([
+                '--with-cfitsio',
+                '--with-cfitsiolib={0}'.format(
+                    spec['cfitsio'].libs.directories[0]),
+                '--with-cfitsioinc={0}'.format(
+                    spec['cfitsio'].headers.directories[0]),
+            ])
+        else:
+            args.append('--without-cfitsio')
+
+        if '+x' in spec:
+            args.append('--with-x')
+        else:
+            args.append('--without-x')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py
index 03e0c86cf3..2ee6ea4171 100644
--- a/var/spack/repos/builtin/packages/wget/package.py
+++ b/var/spack/repos/builtin/packages/wget/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,7 +13,7 @@ class Wget(AutotoolsPackage):
     cron jobs, terminals without X-Windows support, etc."""
 
     homepage = "http://www.gnu.org/software/wget/"
-    url      = "http://ftp.gnu.org/gnu/wget/wget-1.19.1.tar.gz"
+    url      = "https://ftpmirror.gnu.org/wget/wget-1.19.1.tar.gz"
 
     version('1.19.1', '87cea36b7161fd43e3fd51a4e8b89689')
     version('1.17',   'c4c4727766f24ac716936275014a0536')
@@ -60,10 +41,9 @@ class Wget(AutotoolsPackage):
     depends_on('pcre', when='+pcre')
 
     depends_on('perl@5.12.0:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
-    # TODO: Add a 'test' deptype
-    # depends_on('valgrind', type='test')
+    depends_on('valgrind', type='test')
 
     build_directory = 'spack-build'
 
diff --git a/var/spack/repos/builtin/packages/wgsim/package.py b/var/spack/repos/builtin/packages/wgsim/package.py
new file mode 100644
index 0000000000..7caa098346
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wgsim/package.py
@@ -0,0 +1,29 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Wgsim(Package):
+    """Wgsim is a small tool for simulating sequence reads from a reference
+    genome.
+
+    It is able to simulate diploid genomes with SNPs and insertion/deletion
+    (INDEL) polymorphisms, and simulate reads with uniform substitution
+    sequencing errors. It does not generate INDEL sequencing errors, but this
+    can be partly compensated by simulating INDEL polymorphisms."""
+
+    homepage = "https://github.com/lh3/wgsim"
+    git      = "https://github.com/lh3/wgsim.git"
+
+    version('2011.10.17', commit='a12da3375ff3b51a5594d4b6fa35591173ecc229')
+
+    depends_on('zlib')
+
+    def install(self, spec, prefix):
+        cc = Executable(spack_cc)
+        cc('-g', '-O2', '-Wall', '-o', 'wgsim', 'wgsim.c', '-lz', '-lm')
+
+        install_tree(self.stage.source_path, prefix.bin)
diff --git a/var/spack/repos/builtin/packages/windowswmproto/package.py b/var/spack/repos/builtin/packages/windowswmproto/package.py
index 70f1aae995..d893604996 100644
--- a/var/spack/repos/builtin/packages/windowswmproto/package.py
+++ b/var/spack/repos/builtin/packages/windowswmproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/wireshark/package.py b/var/spack/repos/builtin/packages/wireshark/package.py
new file mode 100644
index 0000000000..73640dc246
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wireshark/package.py
@@ -0,0 +1,117 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+
+
+class Wireshark(CMakePackage):
+    """Graphical network analyzer and capture tool"""
+
+    homepage = "https://www.wireshark.org"
+    url      = "https://www.wireshark.org/download/src/all-versions/wireshark-2.6.0.tar.xz"
+
+    version('2.6.0', 'd9f9e206977da14427bfd66b582601ae')
+
+    variant('smi',      default=False, description='Build with libsmi')
+    variant('libssh',   default=False, description='Build with libssh')
+    variant('nghttp2',  default=False, description='Build with nghttp2')
+    variant('qt',       default=False, description='Build with qt')
+    variant('gtk3',     default=False, description='Build with gtk3')
+    variant('gtk',      default=False, description='Build with gtk')
+    variant('headers',  default=True, description='Install headers')
+
+    depends_on('bison',     type='build')
+    depends_on('cares')
+    depends_on('doxygen',   type='build')
+    depends_on('flex',      type='build')
+    depends_on('git',       type='build')
+    depends_on('glib')
+    depends_on('gnutls')
+    depends_on('libgcrypt@1.4.2:')
+    depends_on('libmaxminddb')
+    depends_on('libtool@2.2.2:', type='build')
+    depends_on('libpcap')
+    depends_on('lua@5.0.0:5.2.99')
+    depends_on('krb5')
+    depends_on('pkgconfig', type='build')
+    depends_on('libsmi',    when='+smi')
+    depends_on('libssh',    when='+libssh')
+    depends_on('nghttp2',   when='+nghttp2')
+    depends_on('portaudio', when='+gtk')
+    depends_on('portaudio', when='+gtk3')
+    depends_on('qt@4.8:',   when='+qt')
+    depends_on('gtkplus3',  when='+gtk3')
+    depends_on('gtkplus',   when='+gtk')
+    depends_on('adwaita-icon-theme', when='+gtk3')
+
+    def cmake_args(self):
+        args = ['-DENEABLE_CARES=ON',
+                '-DENABLE_GNUTLS=ON',
+                '-DENABLE_LUA=ON',
+                '-DENABLE_MAXMINDDB=ON',
+                '-DYACC_EXECUTABLE=' + self.spec['bison'].prefix.bin.yacc,
+                '-DGIT_EXECUTABLE=' + self.spec['git'].prefix.bin.git,
+                '-DPCAP_INCLUDE_DIR=' + self.spec['libpcap'].prefix.include,
+                '-DPCAP_LIB=' + str(self.spec['libpcap'].libs),
+                '-DLUA_INCLUDE_DIR=' + self.spec['lua'].prefix.include,
+                '-DLUA_LIBRARY=' + str(self.spec['lua'].libs)
+                ]
+        if self.spec.satisfies('+qt'):
+            args.append('-DBUILD_wireshark=ON')
+            args.append('-DENABLE_APPLICATION_BUNDLE=ON')
+            if self.spec['qt'].version >= Version(5):
+                args.append('-DENABLE_QT5=ON')
+            else:
+                args.append('-DENABLE_QT5=OFF')
+        else:
+            args.append('-DBUILD_wireshark=OFF')
+            args.append('-DENABLE_APPLICATION_BUNDLE=OFF')
+            args.append('-DENABLE_QT5=OFF')
+
+        if self.spec.satisfies('+gtk3') or self.spec.satisfies('+gtk'):
+            args.append('-DBUILD_wireshark_gtk=ON')
+            args.append('-DENABLE_PORTAUDIO=ON')
+        else:
+            args.append('-DBUILD_wireshark_gtk=OFF')
+            args.append('-DENABLE_PORTAUDIO=OFF')
+        if self.spec.satisfies('+gtk3'):
+            args.append('-DENABLE_GTK3=ON')
+
+        if self.spec.satisfies('+libssh'):
+            args.append('-DBUILD_sshdump=ON')
+            args.append('-DBUILD_ciscodump=ON')
+        else:
+            args.append('-DBUILD_sshdump=OFF')
+            args.append('-DBUILD_ciscodump=OFF')
+
+        if self.spec.satisfies('+smi'):
+            args.append('-DBUILD_SMI=ON')
+        else:
+            args.append('-DBUILD_SMI=OFF')
+
+        if self.spec.satisfies('+nghttp2'):
+            args.append('-DBUILD_NGHTTP2=ON')
+        else:
+            args.append('-DBUILD_NGHTTP2=OFF')
+
+        return args
+
+    @run_after('install')
+    def symlink(self):
+        if self.spec.satisfies('platform=darwin'):
+            link(join_path(self.prefix,
+                           'Wireshark.app/Contents/MacOS/Wireshark'),
+                 self.prefix.bin.wireshark)
+
+    @run_after('install')
+    def install_headers(self):
+        if self.spec.satisfies('+headers'):
+            folders = ['.', 'epan/crypt', 'epan/dfilter', 'epan/dissectors',
+                       'epan/ftypes', 'epan/wmem', 'wiretap', 'wsutil']
+            for folder in folders:
+                headers = glob.glob(join_path(folder, '*.h'))
+                for h in headers:
+                    install(h, join_path(prefix.include, 'wireshark', folder))
diff --git a/var/spack/repos/builtin/packages/workrave/add_time_header.patch b/var/spack/repos/builtin/packages/workrave/add_time_header.patch
new file mode 100644
index 0000000000..535b7356fe
--- /dev/null
+++ b/var/spack/repos/builtin/packages/workrave/add_time_header.patch
@@ -0,0 +1,12 @@
+diff --git a/backend/src/TimePred.hh b/backend/src/TimePred.hh
+index 187f0fc..99bf48c 100644
+--- a/backend/src/TimePred.hh
++++ b/backend/src/TimePred.hh
+@@ -26,6 +26,7 @@
+ #else
+ # if HAVE_SYS_TIME_H
+ #  include <sys/time.h>
++#  include <time.h>
+ # else
+ #  include <time.h>
+ # endif
diff --git a/var/spack/repos/builtin/packages/workrave/dont_get_widget.patch b/var/spack/repos/builtin/packages/workrave/dont_get_widget.patch
new file mode 100644
index 0000000000..de8076748c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/workrave/dont_get_widget.patch
@@ -0,0 +1,22 @@
+diff --git a/frontend/plugin/statistics/gtkmm/src/StatisticsDialog.cc b/frontend/plugin/statistics/gtkmm/src/StatisticsDialog.cc
+index ee7d56f..608fddb 100644
+--- a/frontend/plugin/statistics/gtkmm/src/StatisticsDialog.cc
++++ b/frontend/plugin/statistics/gtkmm/src/StatisticsDialog.cc
+@@ -604,7 +604,7 @@ StatisticsDialog::on_history_delete_all()
+         );
+     Gtk::MessageDialog mb_ask( *this, msg, true, Gtk::MESSAGE_WARNING, Gtk::BUTTONS_YES_NO, false );
+     mb_ask.set_title( _("Warning") );
+-    mb_ask.get_widget_for_response( Gtk::RESPONSE_NO )->grab_default();
++    //mb_ask.get_widget_for_response( Gtk::RESPONSE_NO )->grab_default();
+     if( mb_ask.run() == Gtk::RESPONSE_YES )
+     {
+         mb_ask.hide();
+@@ -630,7 +630,7 @@ StatisticsDialog::on_history_delete_all()
+                 );
+             Gtk::MessageDialog mb_error( *this, msg, true, Gtk::MESSAGE_ERROR, Gtk::BUTTONS_YES_NO, false );
+             mb_error.set_title( _("Error") );
+-            mb_error.get_widget_for_response( Gtk::RESPONSE_NO )->grab_default();
++            //mb_error.get_widget_for_response( Gtk::RESPONSE_NO )->grab_default();
+             if( mb_error.run() != Gtk::RESPONSE_YES )
+                 break;
+         }
diff --git a/var/spack/repos/builtin/packages/workrave/no_gettext.patch b/var/spack/repos/builtin/packages/workrave/no_gettext.patch
new file mode 100644
index 0000000000..ab440c0e11
--- /dev/null
+++ b/var/spack/repos/builtin/packages/workrave/no_gettext.patch
@@ -0,0 +1,29 @@
+diff --git a/configure.ac b/configure.ac
+index a8a437f..6128cd2 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -949,8 +949,8 @@ dnl
+ dnl Internationalization
+ dnl
+ 
+-AM_GNU_GETTEXT_VERSION([0.17])
+-AM_GNU_GETTEXT([external])
++dnl AM_GNU_GETTEXT_VERSION([0.17])
++dnl AM_GNU_GETTEXT([external])
+ 
+ dnl Hack because windows gettext package is SEVERELY broken...
+ if test "x$platform_os_win32" = "xyes"
+@@ -963,9 +963,10 @@ then
+         BUILD_INCLUDED_LIBINTL=no
+ fi
+ 
+-GETTEXT_PACKAGE=workrave
+-AC_SUBST(GETTEXT_PACKAGE)
+-AC_DEFINE_UNQUOTED(GETTEXT_PACKAGE, "$GETTEXT_PACKAGE", [Define to the gettext domain name.])
++dnl GETTEXT_PACKAGE=workrave
++dnl AC_SUBST(GETTEXT_PACKAGE)
++dnl AC_DEFINE_UNQUOTED(GETTEXT_PACKAGE, "$GETTEXT_PACKAGE", [Define to the gettext domain name.])
++AC_DEFINE_UNQUOTED(GETTEXT_PACKAGE,"$GETTEXT_PACKAGE", [Gettext package])
+ IT_PROG_INTLTOOL([0.40.0])
+ 
+ 
diff --git a/var/spack/repos/builtin/packages/workrave/package.py b/var/spack/repos/builtin/packages/workrave/package.py
new file mode 100644
index 0000000000..fdbc2607c1
--- /dev/null
+++ b/var/spack/repos/builtin/packages/workrave/package.py
@@ -0,0 +1,85 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Workrave(AutotoolsPackage):
+    """Workrave is a program that assists in the recovery and prevention of
+       Repetitive Strain Injury (RSI). The program frequently alerts you to
+       take micro-pauses, rest breaks and restricts you to your daily limit.
+       The program runs on GNU/Linux and Microsoft Windows.
+    """
+
+    homepage = "http://www.workrave.org/"
+    url      = "https://github.com/rcaelers/workrave/archive/v1_10_20.tar.gz"
+
+    version('1_10_20', '095567c10311bd2c1a52f98035cc8590')
+    version('1_10_19', 'a87ed53d5b321133e8b6b98fd715507b')
+    version('1_10_18', 'd36c2aba0485116b831d5b36a862f343')
+    version('1_10_17', 'ba829bb2c0ec999b3194b4d845549c39')
+    version('1_10_16', 'b9bf77bfe0c909fff56759e7dda40f9d')
+    version('1_10_15', '4a70c2e325503249d1a40fcc236d6802')
+    version('1_10_14', '67108d993719d9438a1b69f0cb8fc9b8')
+    version('1_10_13', 'd5e7110dfb0b0a31c909405913ac2a75')
+    version('1_10_12', '0bfbaa1dc35901ffa8f1a3676421a992')
+    version('1_10_10', 'cf827672c8a1ece074f8ddfcf73d0fe2')
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+
+    depends_on('libx11')
+    depends_on('py-cheetah')
+    depends_on('glib')
+    depends_on('glibmm')
+    depends_on('gtkplus')
+    depends_on('gtkmm@2.17.1')
+    depends_on('libsigcpp')
+
+    # adds #include <time.h> to a workrave test
+    patch('add_time_header.patch')
+
+    # removes call to missing gtkmm api function
+    patch('dont_get_widget.patch')
+
+    # removes gettext which canot be use with intltool
+    # https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=724555
+    # https://bugzilla.gnome.org/show_bug.cgi?id=708673#c4
+    patch('no_gettext.patch')
+
+    # add a couple m4 macros used during autoreconf
+    # https://github.com/rcaelers/workrave/issues/95
+    m4files = ['ax_cxx_compile_stdcxx_11', 'ax_cxx_compile_stdcxx']
+    resource(name=m4files[0],
+             url='http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m4/ax_cxx_compile_stdcxx_11.m4',
+             sha256='d75fc9fe4502eea02e8c5bfb61b88a04cd08aa6d5bd757fe66e9a9a1e4781b46',
+             expand=False,
+             destination='',
+             placement=m4files[0])
+    resource(name=m4files[1],
+             url='http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m4/ax_cxx_compile_stdcxx.m4',
+             sha256='0c08d2f64147f65eb7e255019102c1042ab695c60fd49add19793951a1279a1a',
+             expand=False,
+             destination='',
+             placement=m4files[1])
+
+    def setup_environment(self, build_env, run_env):
+        # unset PYTHONHOME to let system python script with explict
+        # system python sbangs like glib-mkenums work, see #6968
+        # Without this, we will get
+        # ImportError: No module named site
+        # during build phase when make runs glib-mkenums
+        build_env.unset('PYTHONHOME')
+
+    @run_before('autoreconf')
+    def extra_m4(self):
+        # move m4 macros, which we added with the resource() directive,
+        # to the m4 directory, where aclocal will pick them up
+        for fname in self.m4files:
+            src = '%s/%s/%s.m4' % (self.stage.source_path, fname, fname)
+            dest = '%s/m4/%s.m4' % (self.stage.source_path, fname)
+            copy(src, dest)
diff --git a/var/spack/repos/builtin/packages/wt/package.py b/var/spack/repos/builtin/packages/wt/package.py
index 36eefdf2c0..991a3fdc9f 100644
--- a/var/spack/repos/builtin/packages/wt/package.py
+++ b/var/spack/repos/builtin/packages/wt/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,11 +12,11 @@ class Wt(CMakePackage):
     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"
+    url      = "https://github.com/emweb/wt/archive/3.3.7.tar.gz"
+    git      = "https://github.com/emweb/wt.git"
 
+    version('master', branch='master')
     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
diff --git a/var/spack/repos/builtin/packages/wx/math_include.patch b/var/spack/repos/builtin/packages/wx/math_include.patch
new file mode 100644
index 0000000000..152f095d18
--- /dev/null
+++ b/var/spack/repos/builtin/packages/wx/math_include.patch
@@ -0,0 +1,12 @@
+diff --git a/src/stc/scintilla/src/Editor.cxx b/src/stc/scintilla/src/Editor.cxx
+index cd72953ae7..8c19154313 100644
+--- a/src/stc/scintilla/src/Editor.cxx
++++ b/src/stc/scintilla/src/Editor.cxx
+@@ -10,6 +10,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <assert.h>
++#include <math.h>
+
+ #include <string>
+ #include <vector>
diff --git a/var/spack/repos/builtin/packages/wx/package.py b/var/spack/repos/builtin/packages/wx/package.py
index fc42b5153f..284dab072c 100644
--- a/var/spack/repos/builtin/packages/wx/package.py
+++ b/var/spack/repos/builtin/packages/wx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import sys
 
@@ -35,16 +16,19 @@ class Wx(AutotoolsPackage):
        native look and feel because it uses the platform's native API
        rather than emulating the GUI. It's also extensive, free,
        open-source and mature."""
+
     homepage = "http://www.wxwidgets.org/"
     url      = "https://github.com/wxWidgets/wxWidgets/releases/download/v3.1.0/wxWidgets-3.1.0.tar.bz2"
+    git      = "https://github.com/wxWidgets/wxWidgets.git"
 
+    version('develop', branch='master')
     version('3.1.0', '2170839cfa9d9322e8ee8368b21a15a2497b4f11')
     version('3.0.2', '6461eab4428c0a8b9e41781b8787510484dea800')
     version('3.0.1', '73e58521d6871c9f4d1e7974c6e3a81629fddcf8')
 
-    version('develop', git='https://github.com/wxWidgets/wxWidgets.git', branch='master')
+    patch('math_include.patch', when='@3.0.1:3.0.2')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('gtkplus')
 
     @when('@:3.0.2')
diff --git a/var/spack/repos/builtin/packages/wxpropgrid/package.py b/var/spack/repos/builtin/packages/wxpropgrid/package.py
index 7df30895fc..090655f67a 100644
--- a/var/spack/repos/builtin/packages/wxpropgrid/package.py
+++ b/var/spack/repos/builtin/packages/wxpropgrid/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/x11perf/package.py b/var/spack/repos/builtin/packages/x11perf/package.py
index b5a2e9344b..a52dcfc90b 100644
--- a/var/spack/repos/builtin/packages/x11perf/package.py
+++ b/var/spack/repos/builtin/packages/x11perf/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class X11perf(AutotoolsPackage):
     depends_on('libxft')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xapian-core/package.py b/var/spack/repos/builtin/packages/xapian-core/package.py
index 8ea340a55a..c36e4e61fc 100644
--- a/var/spack/repos/builtin/packages/xapian-core/package.py
+++ b/var/spack/repos/builtin/packages/xapian-core/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xauth/package.py b/var/spack/repos/builtin/packages/xauth/package.py
index ac02ba48b9..d247edc968 100644
--- a/var/spack/repos/builtin/packages/xauth/package.py
+++ b/var/spack/repos/builtin/packages/xauth/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,7 +21,7 @@ class Xauth(AutotoolsPackage):
     depends_on('libxmu')
 
     depends_on('xproto@7.0.17:')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # TODO: add package for cmdtest test dependency
diff --git a/var/spack/repos/builtin/packages/xbacklight/package.py b/var/spack/repos/builtin/packages/xbacklight/package.py
index 2f4057ee80..e2cc57cb17 100644
--- a/var/spack/repos/builtin/packages/xbacklight/package.py
+++ b/var/spack/repos/builtin/packages/xbacklight/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xbacklight(AutotoolsPackage):
     depends_on('libxcb')
     depends_on('xcb-util')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xbiff/package.py b/var/spack/repos/builtin/packages/xbiff/package.py
index 7d85e59fbf..19315e792b 100644
--- a/var/spack/repos/builtin/packages/xbiff/package.py
+++ b/var/spack/repos/builtin/packages/xbiff/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Xbiff(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xbitmaps', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xbitmaps/package.py b/var/spack/repos/builtin/packages/xbitmaps/package.py
index 6282ce7041..86823338b7 100644
--- a/var/spack/repos/builtin/packages/xbitmaps/package.py
+++ b/var/spack/repos/builtin/packages/xbitmaps/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,5 +15,5 @@ class Xbitmaps(AutotoolsPackage):
 
     version('1.1.1', '288bbe310db67280a9e2e5ebc5602595')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xbraid/package.py b/var/spack/repos/builtin/packages/xbraid/package.py
new file mode 100644
index 0000000000..81d85c401a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xbraid/package.py
@@ -0,0 +1,54 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import glob
+import os.path
+
+
+class Xbraid(MakefilePackage):
+    """XBraid: Parallel time integration with Multigrid"""
+
+    homepage = "https://computation.llnl.gov/projects/parallel-time-integration-multigrid/software"
+    url      = "https://computation.llnl.gov/projects/parallel-time-integration-multigrid/download/braid_2.2.0.tar.gz"
+
+    version('2.2.0', '0a9c2fc3eb8f605f73cce78ab0d8a7d9')
+
+    depends_on('mpi')
+
+    def build(self, spec, prefix):
+        make('libbraid.a')
+
+    # XBraid doesn't have a real install target, so it has to be done
+    # manually
+    def install(self, spec, prefix):
+        # Install headers
+        mkdirp(prefix.include)
+        headers = glob.glob('*.h')
+        for f in headers:
+            install(f, join_path(prefix.include, os.path.basename(f)))
+
+        # Install library
+        mkdirp(prefix.lib)
+        library = 'libbraid.a'
+        install(library, join_path(prefix.lib, library))
+
+        # Install other material (e.g., examples, tests, docs)
+        mkdirp(prefix.share)
+        install('makefile.inc', prefix.share)
+        install_tree('examples', prefix.share.examples)
+        install_tree('drivers', prefix.share.drivers)
+
+        # TODO: Some of the scripts in 'test' are useful, even for
+        # users; some could be deleted from an installation because
+        # they're not useful to users
+        install_tree('test', prefix.share.test)
+        install_tree('user_utils', prefix.share.user_utils)
+        install_tree('docs', prefix.share.docs)
+
+    @property
+    def libs(self):
+        return find_libraries('libbraid', root=self.prefix,
+                              shared=False, recursive=True)
diff --git a/var/spack/repos/builtin/packages/xcalc/package.py b/var/spack/repos/builtin/packages/xcalc/package.py
index 5218ecac99..2ee66d7b98 100644
--- a/var/spack/repos/builtin/packages/xcalc/package.py
+++ b/var/spack/repos/builtin/packages/xcalc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xcalc(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-demo/package.py b/var/spack/repos/builtin/packages/xcb-demo/package.py
index 7a2c2f65f4..421d97dbb7 100644
--- a/var/spack/repos/builtin/packages/xcb-demo/package.py
+++ b/var/spack/repos/builtin/packages/xcb-demo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class XcbDemo(AutotoolsPackage):
     depends_on('xcb-util-image')
     depends_on('xcb-util-wm')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
 
     # FIXME: crashes with the following error message
     # X11/XCB/xcb.h: No such file or directory
diff --git a/var/spack/repos/builtin/packages/xcb-proto/package.py b/var/spack/repos/builtin/packages/xcb-proto/package.py
index 9cb2480b17..ed9667f7c1 100644
--- a/var/spack/repos/builtin/packages/xcb-proto/package.py
+++ b/var/spack/repos/builtin/packages/xcb-proto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,12 +11,14 @@ class XcbProto(AutotoolsPackage):
     generate the majority of its code and API."""
 
     homepage = "http://xcb.freedesktop.org/"
-    url      = "http://xcb.freedesktop.org/dist/xcb-proto-1.11.tar.gz"
+    url      = "http://xcb.freedesktop.org/dist/xcb-proto-1.13.tar.gz"
 
+    version('1.13', '0cc0294eb97e4af3a743e470e6a9d910')
     version('1.12', '5ee1ec124ea8d56bd9e83b8e9e0b84c4')
     version('1.11', 'c8c6cb72c84f58270f4db1f39607f66a')
 
     # TODO: uncomment once build deps can be resolved separately
+    # See #7646, #4145, #4063, and #2548 for details
     # extends('python')
 
     patch('xcb-proto-1.12-schema-1.patch', when='@1.12')
diff --git a/var/spack/repos/builtin/packages/xcb-util-cursor/package.py b/var/spack/repos/builtin/packages/xcb-util-cursor/package.py
index 64faa37207..2e79d358ac 100644
--- a/var/spack/repos/builtin/packages/xcb-util-cursor/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-cursor/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,4 +23,4 @@ class XcbUtilCursor(AutotoolsPackage):
     depends_on('xcb-util-renderutil')
     depends_on('xcb-util-image')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-errors/package.py b/var/spack/repos/builtin/packages/xcb-util-errors/package.py
index 07aa424ddc..ca2b68af00 100644
--- a/var/spack/repos/builtin/packages/xcb-util-errors/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-errors/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,4 +22,4 @@ class XcbUtilErrors(AutotoolsPackage):
     depends_on('libxcb@1.4:')
 
     depends_on('xcb-proto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-image/package.py b/var/spack/repos/builtin/packages/xcb-util-image/package.py
index a9f2f2263a..99eaea5d9b 100644
--- a/var/spack/repos/builtin/packages/xcb-util-image/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-image/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,4 +23,4 @@ class XcbUtilImage(AutotoolsPackage):
     depends_on('xcb-util')
 
     depends_on('xproto@7.0.8:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py b/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py
index 3901624e9a..11becf0611 100644
--- a/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-keysyms/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,4 +22,4 @@ class XcbUtilKeysyms(AutotoolsPackage):
     depends_on('libxcb@1.4:')
 
     depends_on('xproto@7.0.8:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py b/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py
index e9a325e83c..66500d4e6a 100644
--- a/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-renderutil/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,4 +21,4 @@ class XcbUtilRenderutil(AutotoolsPackage):
 
     depends_on('libxcb@1.4:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-wm/package.py b/var/spack/repos/builtin/packages/xcb-util-wm/package.py
index 5d9a5e3932..65e7a1de8a 100644
--- a/var/spack/repos/builtin/packages/xcb-util-wm/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util-wm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,4 +21,4 @@ class XcbUtilWm(AutotoolsPackage):
 
     depends_on('libxcb@1.4:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xcb-util-xrm/package.py b/var/spack/repos/builtin/packages/xcb-util-xrm/package.py
new file mode 100644
index 0000000000..ceb6aec837
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xcb-util-xrm/package.py
@@ -0,0 +1,26 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class XcbUtilXrm(AutotoolsPackage):
+    """XCB util-xrm module provides the 'xrm' library, i.e.  utility functions
+    for the X resource manager."""
+
+    homepage = "https://github.com/Airblader/xcb-util-xrm"
+    git      = "https://github.com/Airblader/xcb-util-xrm.git"
+
+    # This GitHub project includes some git submodules, which must be fetched
+    # in order to build it.
+    version('1.2', tag='v1.2', submodules=True)
+
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool',  type='build')
+    depends_on('m4',       type='build')
+    depends_on('pkgconfig', type='build')
+
+    depends_on('libxcb@1.4:')
diff --git a/var/spack/repos/builtin/packages/xcb-util/package.py b/var/spack/repos/builtin/packages/xcb-util/package.py
index c8ac0d40ab..e8526b962f 100644
--- a/var/spack/repos/builtin/packages/xcb-util/package.py
+++ b/var/spack/repos/builtin/packages/xcb-util/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,4 +21,4 @@ class XcbUtil(AutotoolsPackage):
 
     depends_on('libxcb@1.4:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xclip/package.py b/var/spack/repos/builtin/packages/xclip/package.py
index d685d1f07c..a18a8bf7ae 100644
--- a/var/spack/repos/builtin/packages/xclip/package.py
+++ b/var/spack/repos/builtin/packages/xclip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -34,9 +15,9 @@ class Xclip(AutotoolsPackage):
        which can then be redirected to a file or another program."""
 
     homepage = "https://github.com/astrand/xclip"
-    url      = "https://github.com/astrand/xclip"
+    git      = "https://github.com/astrand/xclip.git"
 
-    version('0.13', git='https://github.com/astrand/xclip', commit='9aa7090c3b8b437c6489edca32ae43d82e0c1281')
+    version('0.13', commit='9aa7090c3b8b437c6489edca32ae43d82e0c1281')
 
     depends_on('libxmu')
     depends_on('libx11')
diff --git a/var/spack/repos/builtin/packages/xclipboard/package.py b/var/spack/repos/builtin/packages/xclipboard/package.py
index bad81a9a96..a4917f3055 100644
--- a/var/spack/repos/builtin/packages/xclipboard/package.py
+++ b/var/spack/repos/builtin/packages/xclipboard/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xclipboard(AutotoolsPackage):
     depends_on('libxkbfile')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xclock/package.py b/var/spack/repos/builtin/packages/xclock/package.py
index 47614e50e1..15cbcc2ba4 100644
--- a/var/spack/repos/builtin/packages/xclock/package.py
+++ b/var/spack/repos/builtin/packages/xclock/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Xclock(AutotoolsPackage):
     depends_on('libxt')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcmiscproto/package.py b/var/spack/repos/builtin/packages/xcmiscproto/package.py
index 92c1b886a5..f478a2fe9f 100644
--- a/var/spack/repos/builtin/packages/xcmiscproto/package.py
+++ b/var/spack/repos/builtin/packages/xcmiscproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xcmiscproto(AutotoolsPackage):
 
     version('1.2.2', 'ded6cd23fb2800df93ebf2b3f3b01119')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcmsdb/package.py b/var/spack/repos/builtin/packages/xcmsdb/package.py
index b59a254262..0be4808cd8 100644
--- a/var/spack/repos/builtin/packages/xcmsdb/package.py
+++ b/var/spack/repos/builtin/packages/xcmsdb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xcmsdb(AutotoolsPackage):
 
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcompmgr/package.py b/var/spack/repos/builtin/packages/xcompmgr/package.py
index dc8aa398b1..3af77c565a 100644
--- a/var/spack/repos/builtin/packages/xcompmgr/package.py
+++ b/var/spack/repos/builtin/packages/xcompmgr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Xcompmgr(AutotoolsPackage):
     depends_on('libxrender')
     depends_on('libxext')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xconsole/package.py b/var/spack/repos/builtin/packages/xconsole/package.py
index 2c130091d3..519d7447b5 100644
--- a/var/spack/repos/builtin/packages/xconsole/package.py
+++ b/var/spack/repos/builtin/packages/xconsole/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xconsole(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xcursor-themes/package.py b/var/spack/repos/builtin/packages/xcursor-themes/package.py
index 112d63c274..4b0eaa7234 100644
--- a/var/spack/repos/builtin/packages/xcursor-themes/package.py
+++ b/var/spack/repos/builtin/packages/xcursor-themes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class XcursorThemes(Package):
     depends_on('libxcursor')
 
     depends_on('xcursorgen', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/xcursorgen/package.py b/var/spack/repos/builtin/packages/xcursorgen/package.py
index c2b808b0af..5751365007 100644
--- a/var/spack/repos/builtin/packages/xcursorgen/package.py
+++ b/var/spack/repos/builtin/packages/xcursorgen/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xcursorgen(AutotoolsPackage):
     depends_on('libxcursor')
     depends_on('libpng@1.2.0:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xdbedizzy/package.py b/var/spack/repos/builtin/packages/xdbedizzy/package.py
index 9e21e54ca6..053c7e9954 100644
--- a/var/spack/repos/builtin/packages/xdbedizzy/package.py
+++ b/var/spack/repos/builtin/packages/xdbedizzy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xdbedizzy(AutotoolsPackage):
     depends_on('libx11')
     depends_on('libxext')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xditview/package.py b/var/spack/repos/builtin/packages/xditview/package.py
index 5111de58af..c8c5294df1 100644
--- a/var/spack/repos/builtin/packages/xditview/package.py
+++ b/var/spack/repos/builtin/packages/xditview/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xditview(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xdm/package.py b/var/spack/repos/builtin/packages/xdm/package.py
index 8f1b544f6d..90cdaeb0a6 100644
--- a/var/spack/repos/builtin/packages/xdm/package.py
+++ b/var/spack/repos/builtin/packages/xdm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Xdm(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libxext')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xdpyinfo/package.py b/var/spack/repos/builtin/packages/xdpyinfo/package.py
index ab5935b474..bc4259a1ba 100644
--- a/var/spack/repos/builtin/packages/xdpyinfo/package.py
+++ b/var/spack/repos/builtin/packages/xdpyinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -47,5 +28,5 @@ class Xdpyinfo(AutotoolsPackage):
     depends_on('recordproto', type='build')
     depends_on('inputproto', type='build')
     depends_on('fixesproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xdriinfo/package.py b/var/spack/repos/builtin/packages/xdriinfo/package.py
index 86645072c0..ed58cdb505 100644
--- a/var/spack/repos/builtin/packages/xdriinfo/package.py
+++ b/var/spack/repos/builtin/packages/xdriinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Xdriinfo(AutotoolsPackage):
     depends_on('pcre')
 
     depends_on('glproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xedit/package.py b/var/spack/repos/builtin/packages/xedit/package.py
index 752fbf61d5..de2a345cfb 100644
--- a/var/spack/repos/builtin/packages/xedit/package.py
+++ b/var/spack/repos/builtin/packages/xedit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xedit(AutotoolsPackage):
     depends_on('libxt@1.0:')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py
index 3e832784f8..a316e14d30 100644
--- a/var/spack/repos/builtin/packages/xerces-c/package.py
+++ b/var/spack/repos/builtin/packages/xerces-c/package.py
@@ -1,28 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
+import sys
 
 
 class XercesC(AutotoolsPackage):
@@ -33,9 +15,58 @@ class XercesC(AutotoolsPackage):
     APIs."""
 
     homepage = "https://xerces.apache.org/xerces-c"
-    url      = "https://archive.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.4.tar.bz2"
+    url      = "https://archive.apache.org/dist/xerces/c/3/sources/xerces-c-3.2.1.tar.bz2"
 
+    version('3.2.2', '4c395216ecbef3c88a756ff4090e6f7e')
+    version('3.2.1', '8f98a81a3589bbc2dad9837452f7d319')
     version('3.1.4', 'd04ae9d8b2dee2157c6db95fa908abfd')
 
+    # It's best to be explicit about the transcoder or else xerces may
+    # choose another value.
+    if sys.platform == 'darwin':
+        default_transcoder = 'macos'
+    elif sys.platform.startswith('win') or sys.platform == 'cygwin':
+        default_transcoder = 'windows'
+    else:
+        default_transcoder = 'gnuiconv'
+
+    variant('transcoder', default=default_transcoder,
+            values=('gnuiconv', 'iconv', 'icu', 'macos', 'windows'),
+            multi=False,
+            description='Use the specified transcoder')
+
+    depends_on('libiconv', type='link', when='transcoder=gnuiconv')
+    depends_on('icu4c',    type='link', when='transcoder=icu')
+
+    # Pass flags to configure.  This is necessary for CXXFLAGS or else
+    # the xerces default will override the spack wrapper.
+    def flag_handler(self, name, flags):
+        spec = self.spec
+
+        # There is no --with-pkg for gnuiconv.
+        if name == 'ldflags' and 'transcoder=gnuiconv' in spec:
+            flags.append(spec['libiconv'].libs.ld_flags)
+
+        return (None, None, flags)
+
     def configure_args(self):
-        return ['--disable-network']
+        spec = self.spec
+        args = ['--disable-network']
+
+        if 'transcoder=gnuiconv' in spec:
+            args.append('--enable-transcoder-gnuiconv')
+
+        if 'transcoder=iconv' in spec:
+            args.append('--enable-transcoder-iconv')
+
+        if 'transcoder=icu' in spec:
+            args.append('--enable-transcoder-icu')
+            args.append('--with-icu=%s' % spec['icu4c'].prefix)
+
+        if 'transcoder=macos' in spec:
+            args.append('--enable-transcoder-macosunicodeconverter')
+
+        if 'transcoder=windows' in spec:
+            args.append('--enable-transcoder-windows')
+
+        return args
diff --git a/var/spack/repos/builtin/packages/xeus/cmake_find_cryptopp_and_check_cxx_compatibility.patch b/var/spack/repos/builtin/packages/xeus/cmake_find_cryptopp_and_check_cxx_compatibility.patch
new file mode 100644
index 0000000000..da19f84134
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xeus/cmake_find_cryptopp_and_check_cxx_compatibility.patch
@@ -0,0 +1,52 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 810d5d1..d6ba3e9 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -49,7 +49,33 @@ message(STATUS "xeus binary version: v${XEUS_BINARY_VERSION}")
+ find_package(nlohmann_json 3.2.0 REQUIRED)
+ find_package(xtl 0.4 REQUIRED)
+ find_package(cppzmq 4.3.0 REQUIRED)
+-find_package(cryptopp REQUIRED)
++
++# cryptopp isn't built with cmake, find it manually
++find_path(cryptopp_ROOT_DIR
++  NAMES include/cryptopp/cryptlib.h
++  PATHS ENV cryptopp_ROOT)
++
++find_path(cryptopp_INCLUDE_DIR
++  NAMES cryptopp/cryptlib.h
++  HINTS ${cryptopp_ROOT_DIR}
++  PATH_SUFFIXES include)
++
++find_library(cryptopp_STATIC_LIB
++  NAMES libcryptopp.a
++  HINTS ${cryptopp_ROOT_DIR}
++  PATH_SUFFIXES lib)
++
++if (NOT cryptopp_INCLUDE_DIR OR NOT cryptopp_STATIC_LIB)
++  message(FATAL_ERROR "cannot find cryptopp, missing include dir or static lib")
++else()
++  message("Found cryptopp: ${cryptopp_ROOT_DIR}")
++endif()
++
++add_library(cryptopp-static STATIC IMPORTED)
++set_target_properties(cryptopp-static
++  PROPERTIES
++    IMPORTED_LOCATION ${cryptopp_STATIC_LIB}
++    INTERFACE_INCLUDE_DIRECTORIES ${cryptopp_INCLUDE_DIR})
+ 
+ # On Unix platforms, ZeroMQ is built with autotools and pkg-config is
+ # required to locate it.
+@@ -157,10 +183,11 @@ get_target_property(cryptopp_INCLUDE_DIR cryptopp-static INTERFACE_INCLUDE_DIREC
+ get_target_property(cryptopp_LIBRARY cryptopp-static LOCATION)
+ set(CMAKE_REQUIRED_LIBRARIES ${cryptopp_LIBRARY})
+ set(CMAKE_REQUIRED_INCLUDES ${cryptopp_INCLUDE_DIR})
++set(CMAKE_REQUIRED_FLAGS "--std=c++11")
+ check_cxx_source_compiles("
+ #include \"cryptopp/config.h\"
+ int main(){
+-  [[maybe_unused]] CryptoPP::byte b = CryptoPP::byte{0x36};
++  CryptoPP::byte b = CryptoPP::byte{0x36};
+ }" HAVE_CRYPTOPP_BYTE_T)
+ 
+ cmake_pop_check_state()
diff --git a/var/spack/repos/builtin/packages/xeus/package.py b/var/spack/repos/builtin/packages/xeus/package.py
new file mode 100644
index 0000000000..1b1286666c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xeus/package.py
@@ -0,0 +1,44 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xeus(CMakePackage):
+    """QuantStack C++ implementation of Jupyter kernel protocol"""
+
+    homepage = "https://xeus.readthedocs.io/en/latest/"
+    url      = "https://github.com/QuantStack/xeus/archive/0.14.1.tar.gz"
+    git      = "https://github.com/QuantStack/xeus.git"
+
+    version('develop', branch='master')
+    version('0.15.0', sha256='bc99235b24d5757dc129f3ed531501fb0d0667913927ed39ee24281952649183')
+    version('0.14.1', sha256='a6815845d4522ec279f142d3b4e92ef52cd80847b512146a65f256a77e058cfe')
+
+    variant('examples', default=False, description="Build examples")
+
+    conflicts('%gcc@:4.8')
+    conflicts('%clang@:3.6')
+    conflicts('%intel@:17')
+
+    depends_on('zeromq@4.2.5:-libsodium')
+    depends_on('cppzmq@4.3.0:')
+    depends_on('cryptopp@7.0.0:')
+    depends_on('xtl@0.4.0:')
+    depends_on('nlohmann-json@3.2.0', when='@develop@0.15.0:')
+    depends_on('nlohmann-json@3.1.1', when='@0.14.1')
+    depends_on('libuuid')
+
+    # finds cryptopp not built with cmake, removes c++17 attribute
+    # in check_cxx_source_compiles
+    patch('cmake_find_cryptopp_and_check_cxx_compatibility.patch')
+
+    def cmake_args(self):
+        args = [
+            '-DBUILD_EXAMPLES:BOOL=%s' % (
+                'ON' if '+examples' in self.spec else 'OFF')
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/xev/package.py b/var/spack/repos/builtin/packages/xev/package.py
index fbccb0e103..94b7802885 100644
--- a/var/spack/repos/builtin/packages/xev/package.py
+++ b/var/spack/repos/builtin/packages/xev/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xev(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xextproto/package.py b/var/spack/repos/builtin/packages/xextproto/package.py
index d02c1935c2..dbb83e13dc 100644
--- a/var/spack/repos/builtin/packages/xextproto/package.py
+++ b/var/spack/repos/builtin/packages/xextproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -33,7 +14,7 @@ class Xextproto(AutotoolsPackage):
 
     version('7.3.0', '37b700baa8c8ea7964702d948dd13821')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     parallel = False
diff --git a/var/spack/repos/builtin/packages/xeyes/package.py b/var/spack/repos/builtin/packages/xeyes/package.py
index 232f46212b..2487ecf8df 100644
--- a/var/spack/repos/builtin/packages/xeyes/package.py
+++ b/var/spack/repos/builtin/packages/xeyes/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xeyes(AutotoolsPackage):
     depends_on('libxmu')
     depends_on('libxrender@0.4:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xf86bigfontproto/package.py b/var/spack/repos/builtin/packages/xf86bigfontproto/package.py
index 4a1315b617..212c8a9072 100644
--- a/var/spack/repos/builtin/packages/xf86bigfontproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86bigfontproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xf86dga/package.py b/var/spack/repos/builtin/packages/xf86dga/package.py
index 3768fced15..ec4ff65565 100644
--- a/var/spack/repos/builtin/packages/xf86dga/package.py
+++ b/var/spack/repos/builtin/packages/xf86dga/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xf86dga(AutotoolsPackage):
     depends_on('libx11')
     depends_on('libxxf86dga@1.1:')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xf86dgaproto/package.py b/var/spack/repos/builtin/packages/xf86dgaproto/package.py
index 88cd07c286..b42c3bdb8d 100644
--- a/var/spack/repos/builtin/packages/xf86dgaproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86dgaproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xf86driproto/package.py b/var/spack/repos/builtin/packages/xf86driproto/package.py
index 4877440649..16403e2b93 100644
--- a/var/spack/repos/builtin/packages/xf86driproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86driproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xf86driproto(AutotoolsPackage):
 
     version('2.1.1', '3ba16a48d8d9f9f746f9bd281ba8fb3f')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xf86miscproto/package.py b/var/spack/repos/builtin/packages/xf86miscproto/package.py
index 60e1db78bf..67c46f15f3 100644
--- a/var/spack/repos/builtin/packages/xf86miscproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86miscproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xf86rushproto/package.py b/var/spack/repos/builtin/packages/xf86rushproto/package.py
index 6b29e07c6a..3c9b0cf66c 100644
--- a/var/spack/repos/builtin/packages/xf86rushproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86rushproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py b/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py
index f8ce028474..993d203ecc 100644
--- a/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py
+++ b/var/spack/repos/builtin/packages/xf86vidmodeproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xf86vidmodeproto(AutotoolsPackage):
 
     version('2.3.1', '99016d0fe355bae0bb23ce00fb4d4a2c')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfd/package.py b/var/spack/repos/builtin/packages/xfd/package.py
index 024f8ce141..ddec96e7a7 100644
--- a/var/spack/repos/builtin/packages/xfd/package.py
+++ b/var/spack/repos/builtin/packages/xfd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -42,5 +23,5 @@ class Xfd(AutotoolsPackage):
     depends_on('libxt')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfindproxy/package.py b/var/spack/repos/builtin/packages/xfindproxy/package.py
index fc12753133..d01aaf633b 100644
--- a/var/spack/repos/builtin/packages/xfindproxy/package.py
+++ b/var/spack/repos/builtin/packages/xfindproxy/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xfindproxy(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xproxymanagementprotocol', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfontsel/package.py b/var/spack/repos/builtin/packages/xfontsel/package.py
index 2a615216d5..babdee0cf7 100644
--- a/var/spack/repos/builtin/packages/xfontsel/package.py
+++ b/var/spack/repos/builtin/packages/xfontsel/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xfontsel(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfs/package.py b/var/spack/repos/builtin/packages/xfs/package.py
index 6846c320e2..f831cdf2b4 100644
--- a/var/spack/repos/builtin/packages/xfs/package.py
+++ b/var/spack/repos/builtin/packages/xfs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xfs(AutotoolsPackage):
     depends_on('xproto@7.0.17:', type='build')
     depends_on('fontsproto', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfsinfo/package.py b/var/spack/repos/builtin/packages/xfsinfo/package.py
index 8f8ec13247..cf318828c2 100644
--- a/var/spack/repos/builtin/packages/xfsinfo/package.py
+++ b/var/spack/repos/builtin/packages/xfsinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xfsinfo(AutotoolsPackage):
     depends_on('libfs')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xfwp/package.py b/var/spack/repos/builtin/packages/xfwp/package.py
index b0c8fa9158..da418e6396 100644
--- a/var/spack/repos/builtin/packages/xfwp/package.py
+++ b/var/spack/repos/builtin/packages/xfwp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,7 @@ class Xfwp(AutotoolsPackage):
 
     depends_on('xproto', type='build')
     depends_on('xproxymanagementprotocol', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # FIXME: fails with the error message:
diff --git a/var/spack/repos/builtin/packages/xgamma/package.py b/var/spack/repos/builtin/packages/xgamma/package.py
index b417a47c1c..bb0bf65211 100644
--- a/var/spack/repos/builtin/packages/xgamma/package.py
+++ b/var/spack/repos/builtin/packages/xgamma/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xgamma(AutotoolsPackage):
     depends_on('libxxf86vm')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xgc/package.py b/var/spack/repos/builtin/packages/xgc/package.py
index 0b507332da..8c9dbdc084 100644
--- a/var/spack/repos/builtin/packages/xgc/package.py
+++ b/var/spack/repos/builtin/packages/xgc/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xgc(AutotoolsPackage):
 
     depends_on('flex', type='build')
     depends_on('bison', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xhmm/package.py b/var/spack/repos/builtin/packages/xhmm/package.py
new file mode 100644
index 0000000000..3538641da6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xhmm/package.py
@@ -0,0 +1,31 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xhmm(MakefilePackage):
+    """The XHMM C++ software suite was written to
+    call copy number variation (CNV) from next-generation
+    sequencing projects, where exome capture was used
+    (or targeted sequencing, more generally)."""
+
+    homepage = "http://atgu.mgh.harvard.edu/xhmm/index.shtml"
+    git      = "https://bitbucket.org/statgen/xhmm.git"
+
+    version('20160104', commit='cc14e528d90932f059ac4fe94e869e81221fd732')
+
+    depends_on('lapack')
+
+    def edit(self, spec, prefix):
+        filter_file('GCC', 'CC', 'sources/hmm++/config_rules.Makefile')
+        filter_file('GCC =gcc', '', 'sources/hmm++/config_defs.Makefile')
+
+    def build(self, spec, prefix):
+        make('LAPACK_LIBS=%s' % ''.join(spec['lapack'].libs.names))
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        install('xhmm', prefix.bin)
diff --git a/var/spack/repos/builtin/packages/xhost/package.py b/var/spack/repos/builtin/packages/xhost/package.py
index 072a5a29b1..5affa15df6 100644
--- a/var/spack/repos/builtin/packages/xhost/package.py
+++ b/var/spack/repos/builtin/packages/xhost/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xhost(AutotoolsPackage):
     depends_on('libxau')
 
     depends_on('xproto@7.0.22:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xineramaproto/package.py b/var/spack/repos/builtin/packages/xineramaproto/package.py
index b05e26254b..7a6e341bdd 100644
--- a/var/spack/repos/builtin/packages/xineramaproto/package.py
+++ b/var/spack/repos/builtin/packages/xineramaproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xineramaproto(AutotoolsPackage):
 
     version('1.2.1', 'e0e148b11739e144a546b8a051b17dde')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xinit/package.py b/var/spack/repos/builtin/packages/xinit/package.py
index 03487e44a2..66a61f33e0 100644
--- a/var/spack/repos/builtin/packages/xinit/package.py
+++ b/var/spack/repos/builtin/packages/xinit/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xinit(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xinput/package.py b/var/spack/repos/builtin/packages/xinput/package.py
index 2a441d545d..88adddf090 100644
--- a/var/spack/repos/builtin/packages/xinput/package.py
+++ b/var/spack/repos/builtin/packages/xinput/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xinput(AutotoolsPackage):
     depends_on('fixesproto', type='build')
     depends_on('randrproto', type='build')
     depends_on('xineramaproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch b/var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch
new file mode 100644
index 0000000000..cf2aeaaa4e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/bld_extern_1.0.patch
@@ -0,0 +1,27 @@
+--- a/bld.cfg	2017-12-23 11:41:14.000000000 +1100
++++ b/bld.cfg	2017-12-23 15:34:53.914024629 +1100
+@@ -24,9 +24,6 @@
+ 
+ search_src           true
+ src::zzz .
+-src::date $PWD/extern/boost/src/date_time
+-src::blitz $PWD/extern/blitz/src
+-src::netcdf $PWD/extern/netcdf4
+ bld::lib xios
+ bld::target libxios.a
+ #bld::target generate_fortran_interface.exe 
+@@ -37,11 +34,11 @@
+ bld::tool::fc        %FCOMPILER
+ bld::tool::fpp       %FPP
+ bld::tool::cpp       %CPP
+-bld::tool::cppflags  %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include 
+-bld::tool::fppflags  %BASE_INC -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include 
++bld::tool::cppflags  %CBASE_INC -I${PWD}/extern/rapidxml/include
++bld::tool::fppflags  %BASE_INC -I${PWD}/extern/rapidxml/include 
+ bld::tool::ld        %LINKER
+ bld::tool::ldflags   %LD_FLAGS 
+-bld::tool::cflags    %CFLAGS %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include 
++bld::tool::cflags    %CFLAGS %CBASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::fflags    %FFLAGS %FBASE_INC 
+ bld::tool::cppkeys   %CPP_KEY
+ bld::tool::fppkeys   %CPP_KEY
diff --git a/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch b/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch
new file mode 100644
index 0000000000..fe52da1192
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/bld_extern_1.x.patch
@@ -0,0 +1,27 @@
+--- a/bld.cfg	2017-12-23 15:21:01.458603785 +1100
++++ b/bld.cfg	2017-12-23 15:36:36.667684136 +1100
+@@ -24,9 +24,6 @@
+ 
+ search_src           true
+ src::zzz .
+-src::date $PWD/extern/boost/src/date_time
+-src::blitz $PWD/extern/blitz/src
+-src::netcdf $PWD/extern/netcdf4
+ src::remap $PWD/extern/remap/src
+ bld::lib xios
+ bld::target libxios.a 
+@@ -46,11 +43,11 @@
+ bld::tool::fc        %FCOMPILER
+ bld::tool::fpp       %FPP
+ bld::tool::cpp       %CPP
+-bld::tool::cppflags  %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include 
+-bld::tool::fppflags  %BASE_INC -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include 
++bld::tool::cppflags  %CBASE_INC -I${PWD}/extern/rapidxml/include
++bld::tool::fppflags  %BASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::ld        %LINKER
+ bld::tool::ldflags   %LD_FLAGS 
+-bld::tool::cflags    %CFLAGS %CBASE_INC -I${PWD}/extern/src_netcdf -I${PWD}/extern/boost/include -I${PWD}/extern/rapidxml/include -I${PWD}/extern/blitz/include 
++bld::tool::cflags    %CFLAGS %CBASE_INC -I${PWD}/extern/rapidxml/include
+ bld::tool::fflags    %FFLAGS %FBASE_INC 
+ bld::tool::cppkeys   %CPP_KEY
+ bld::tool::fppkeys   %CPP_KEY
diff --git a/var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch b/var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch
new file mode 100644
index 0000000000..9eb5c21950
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/llvm_bug_17782.patch
@@ -0,0 +1,11 @@
+--- a/src/duration.cpp	2017-12-28 10:45:09.000000000 +1100
++++ b/src/duration.cpp	2017-12-28 11:01:40.000000000 +1100
+@@ -43,7 +43,7 @@
+       StdIStream& operator>>(StdIStream& in , CDuration& duration)
+       {
+         duration = NoneDu;
+-        double v = 1.0;
++        int v = 1;
+         char   c = '/';
+         bool   invalidUnit = false;
+         CDuration sentinel = NoneDu;
diff --git a/var/spack/repos/builtin/packages/xios/package.py b/var/spack/repos/builtin/packages/xios/package.py
new file mode 100644
index 0000000000..90ea16b10e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xios/package.py
@@ -0,0 +1,204 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+#
+from spack import *
+import os
+
+
+class Xios(Package):
+    """XML-IO-SERVER library for IO management of climate models."""
+
+    homepage = "https://forge.ipsl.jussieu.fr/ioserver/wiki"
+
+    version('1.0', revision=910,
+            svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0')
+    version('develop', svn='http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk')
+
+    variant('mode', values=('debug', 'dev', 'prod'), default='dev',
+            description='Build for debugging, development or production')
+    # NOTE: oasis coupler could be supported with a variant
+
+    # Use spack versions of blitz and netcdf for compatibility
+    # with recent compilers and optimised platform libraries:
+    patch('bld_extern_1.0.patch', when='@:1.0')
+    patch('bld_extern_1.x.patch', when='@1.1:')
+
+    # Workaround bug #17782 in llvm, where reading a double
+    # followed by a character is broken (e.g. duration '1d'):
+    patch('llvm_bug_17782.patch', when='@1.1: %clang')
+
+    depends_on('netcdf+mpi')
+    depends_on('netcdf-fortran')
+    depends_on('hdf5+mpi')
+    depends_on('mpi')
+    depends_on('boost')
+    depends_on('blitz')
+    depends_on('perl', type='build')
+    depends_on('perl-uri-escape', type='build')
+    depends_on('gmake', type='build')
+
+    @when('%clang')
+    def patch(self):
+        """Fix type references that are ambiguous for clang."""
+        for dirpath, dirnames, filenames in os.walk('src'):
+            for filename in filenames:
+                filepath = os.path.join(dirpath, filename)
+                # Use boost definition of type shared_ptr:
+                filter_file(r'([^:/])shared_ptr<',
+                            r'\1boost::shared_ptr<', filepath)
+                # Use type long for position in output stream:
+                filter_file(r'oss.tellp\(\) *- *startPos',
+                            r'(long)oss.tellp() - startPos', filepath)
+
+    def xios_env(self):
+        file = join_path('arch', 'arch-SPACK.env')
+        touch(file)
+
+    def xios_path(self):
+        file = join_path('arch', 'arch-SPACK.path')
+        spec = self.spec
+        paths = {'NETCDF_INC_DIR': spec['netcdf'].prefix.include,
+                 'NETCDF_LIB_DIR': spec['netcdf'].prefix.lib,
+                 'HDF5_INC_DIR': spec['hdf5'].prefix.include,
+                 'HDF5_LIB_DIR': spec['hdf5'].prefix.lib}
+        text = r"""
+NETCDF_INCDIR="-I {NETCDF_INC_DIR}"
+NETCDF_LIBDIR="-L {NETCDF_LIB_DIR}"
+NETCDF_LIB="-lnetcdff -lnetcdf"
+
+MPI_INCDIR=""
+MPI_LIBDIR=""
+MPI_LIB=""
+
+HDF5_INCDIR="-I {HDF5_INC_DIR}"
+HDF5_LIBDIR="-L {HDF5_LIB_DIR}"
+HDF5_LIB="-lhdf5_hl -lhdf5"
+
+OASIS_INCDIR=""
+OASIS_LIBDIR=""
+OASIS_LIB=""
+"""
+        with open(file, 'w') as f:
+            f.write(text.format(**paths))
+
+    def xios_fcm(self):
+        file = join_path('arch', 'arch-SPACK.fcm')
+        spec = self.spec
+        param = dict()
+        param['MPICXX'] = spec['mpi'].mpicxx
+        param['MPIFC'] = spec['mpi'].mpifc
+        param['CC'] = self.compiler.cc
+        param['FC'] = self.compiler.fc
+        param['BOOST_INC_DIR'] = spec['boost'].prefix.include
+        param['BOOST_LIB_DIR'] = spec['boost'].prefix.lib
+        param['BLITZ_INC_DIR'] = spec['blitz'].prefix.include
+        param['BLITZ_LIB_DIR'] = spec['blitz'].prefix.lib
+        if spec.satisfies('%clang platform=darwin'):
+            param['LIBCXX'] = '-lc++'
+        else:
+            param['LIBCXX'] = '-lstdc++'
+
+        if any(map(spec.satisfies, ('%gcc', '%intel', '%clang'))):
+            text = r"""
+%CCOMPILER      {MPICXX}
+%FCOMPILER      {MPIFC}
+%LINKER         {MPIFC}
+
+%BASE_CFLAGS    -ansi -w -D_GLIBCXX_USE_CXX11_ABI=0 \
+                -I{BOOST_INC_DIR} -I{BLITZ_INC_DIR}
+%PROD_CFLAGS    -O3 -DBOOST_DISABLE_ASSERTS
+%DEV_CFLAGS     -g -O2
+%DEBUG_CFLAGS   -g
+
+%BASE_FFLAGS    -D__NONE__
+%PROD_FFLAGS    -O3
+%DEV_FFLAGS     -g -O2
+%DEBUG_FFLAGS   -g
+
+%BASE_INC       -D__NONE__
+%BASE_LD        -L{BOOST_LIB_DIR} -L{BLITZ_LIB_DIR} -lblitz {LIBCXX}
+
+%CPP            {CC} -E
+%FPP            {CC} -E -P -x c
+%MAKE           gmake
+""".format(**param)
+        elif spec.satisfies('%cce'):
+            # In the CC compiler prior to cce/8.3.7,
+            # optimisation must be reduced to avoid a bug,
+            # as reported by Mike Rezny at the UK Met Office:
+            if spec.satisfies('%cce@8.3.7:'):
+                param.update({'CC_OPT_DEV': '-O2', 'CC_OPT_PROD': '-O3'})
+            else:
+                param.update({'CC_OPT_DEV': '-O1', 'CC_OPT_PROD': '-O1'})
+
+            text = r"""
+%CCOMPILER      {MPICXX}
+%FCOMPILER      {MPIFC}
+%LINKER         {MPIFC}
+
+%BASE_CFLAGS    -DMPICH_SKIP_MPICXX -h msglevel_4 -h zero -h gnu \
+                -I{BOOST_INC_DIR} -I{BLITZ_INC_DIR}
+%PROD_CFLAGS    {CC_OPT_PROD} -DBOOST_DISABLE_ASSERTS
+%DEV_CFLAGS     {CC_OPT_DEV}
+%DEBUG_CFLAGS   -g
+
+%BASE_FFLAGS    -em -m 4 -e0 -eZ
+%PROD_FFLAGS    -O3
+%DEV_FFLAGS     -G2
+%DEBUG_FFLAGS   -g
+
+%BASE_INC       -D__NONE__
+%BASE_LD        -D__NONE__ -L{BOOST_LIB_DIR} -L{BLITZ_LIB_DIR} -lblitz
+
+%CPP            cpp
+%FPP            cpp -P -CC
+%MAKE           gmake
+""".format(**param)
+        else:
+            raise InstallError('Unsupported compiler.')
+
+        with open(file, 'w') as f:
+            f.write(text)
+
+    def install(self, spec, prefix):
+        env['CC'] = spec['mpi'].mpicc
+        env['CXX'] = spec['mpi'].mpicxx
+        env['F77'] = spec['mpi'].mpif77
+        env['FC'] = spec['mpi'].mpifc
+
+        options = ['--full',
+                   '--%s' % spec.variants['mode'].value,
+                   '--arch', 'SPACK',
+                   '--netcdf_lib', 'netcdf4_par',
+                   '--job', str(make_jobs)]
+
+        self.xios_env()
+        self.xios_path()
+        self.xios_fcm()
+
+        make_xios = Executable('./make_xios')
+        make_xios(*options)
+
+        mkdirp(spec.prefix)
+        install_tree('bin', spec.prefix.bin)
+        install_tree('lib', spec.prefix.lib)
+        install_tree('inc', spec.prefix.include)
+        install_tree('etc', spec.prefix.etc)
+        install_tree('cfg', spec.prefix.cfg)
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_build(self):
+        mpirun = os.getenv('MPIRUN')
+        if mpirun is None:
+            mpirun = 'mpiexec'
+        mpiexec = Executable(mpirun)
+        with working_dir('inputs'):
+            try:
+                mpiexec('-n', '2', join_path('..', 'bin', 'test_client.exe'))
+            except Exception:
+                raise InstallError(
+                    'Test failed; defining MPIRUN variable may help.')
diff --git a/var/spack/repos/builtin/packages/xkbcomp/package.py b/var/spack/repos/builtin/packages/xkbcomp/package.py
index 2385bb75e9..ee858b4427 100644
--- a/var/spack/repos/builtin/packages/xkbcomp/package.py
+++ b/var/spack/repos/builtin/packages/xkbcomp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xkbcomp(AutotoolsPackage):
 
     depends_on('xproto@7.0.17:', type='build')
     depends_on('bison', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xkbdata/package.py b/var/spack/repos/builtin/packages/xkbdata/package.py
index cb35f1ae3a..d937e91815 100644
--- a/var/spack/repos/builtin/packages/xkbdata/package.py
+++ b/var/spack/repos/builtin/packages/xkbdata/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xkbevd/package.py b/var/spack/repos/builtin/packages/xkbevd/package.py
index 8ca91494b1..a0bef99bad 100644
--- a/var/spack/repos/builtin/packages/xkbevd/package.py
+++ b/var/spack/repos/builtin/packages/xkbevd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xkbevd(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('bison', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xkbprint/package.py b/var/spack/repos/builtin/packages/xkbprint/package.py
index 8d5205843f..3af59469a2 100644
--- a/var/spack/repos/builtin/packages/xkbprint/package.py
+++ b/var/spack/repos/builtin/packages/xkbprint/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xkbprint(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xkbutils/package.py b/var/spack/repos/builtin/packages/xkbutils/package.py
index c4f604407a..ccf31b1512 100644
--- a/var/spack/repos/builtin/packages/xkbutils/package.py
+++ b/var/spack/repos/builtin/packages/xkbutils/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xkbutils(AutotoolsPackage):
 
     depends_on('xproto@7.0.17:', type='build')
     depends_on('inputproto', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xkeyboard-config/package.py b/var/spack/repos/builtin/packages/xkeyboard-config/package.py
index 5995a7eae7..3e572148d5 100644
--- a/var/spack/repos/builtin/packages/xkeyboard-config/package.py
+++ b/var/spack/repos/builtin/packages/xkeyboard-config/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class XkeyboardConfig(AutotoolsPackage):
     depends_on('libx11@1.4.3:')
 
     depends_on('libxslt', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('intltool@0.30:', type='build')
     depends_on('xproto@7.0.20:', type='build')
 
diff --git a/var/spack/repos/builtin/packages/xkill/package.py b/var/spack/repos/builtin/packages/xkill/package.py
index 37ee488071..562f88f578 100644
--- a/var/spack/repos/builtin/packages/xkill/package.py
+++ b/var/spack/repos/builtin/packages/xkill/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xkill(AutotoolsPackage):
     depends_on('libxmu')
 
     depends_on('xproto@7.0.22:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xload/package.py b/var/spack/repos/builtin/packages/xload/package.py
index cda2ab21a7..5326b9bd57 100644
--- a/var/spack/repos/builtin/packages/xload/package.py
+++ b/var/spack/repos/builtin/packages/xload/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xload(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xlogo/package.py b/var/spack/repos/builtin/packages/xlogo/package.py
index aca6a47df8..5b5401fcf1 100644
--- a/var/spack/repos/builtin/packages/xlogo/package.py
+++ b/var/spack/repos/builtin/packages/xlogo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -43,5 +24,5 @@ class Xlogo(AutotoolsPackage):
     depends_on('libxrender')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xlsatoms/package.py b/var/spack/repos/builtin/packages/xlsatoms/package.py
index b85fac8660..d27bc3e574 100644
--- a/var/spack/repos/builtin/packages/xlsatoms/package.py
+++ b/var/spack/repos/builtin/packages/xlsatoms/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xlsatoms(AutotoolsPackage):
     depends_on('libxcb', when='@1.1:')
     depends_on('libx11', when='@:1.0')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xlsclients/package.py b/var/spack/repos/builtin/packages/xlsclients/package.py
index 6deb2c88e8..bc99dc1352 100644
--- a/var/spack/repos/builtin/packages/xlsclients/package.py
+++ b/var/spack/repos/builtin/packages/xlsclients/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xlsclients(AutotoolsPackage):
     depends_on('libxcb@1.6:', when='@1.1:')
     depends_on('libx11', when='@:1.0')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xlsfonts/package.py b/var/spack/repos/builtin/packages/xlsfonts/package.py
index 15761e2d9f..177b434604 100644
--- a/var/spack/repos/builtin/packages/xlsfonts/package.py
+++ b/var/spack/repos/builtin/packages/xlsfonts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xlsfonts(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmag/package.py b/var/spack/repos/builtin/packages/xmag/package.py
index 5a8ae6e961..bdbf014494 100644
--- a/var/spack/repos/builtin/packages/xmag/package.py
+++ b/var/spack/repos/builtin/packages/xmag/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xmag(AutotoolsPackage):
     depends_on('libxt')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xman/package.py b/var/spack/repos/builtin/packages/xman/package.py
index df11504f69..484f3b75ae 100644
--- a/var/spack/repos/builtin/packages/xman/package.py
+++ b/var/spack/repos/builtin/packages/xman/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xman(AutotoolsPackage):
     depends_on('libxt')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmessage/package.py b/var/spack/repos/builtin/packages/xmessage/package.py
index dee5d86e21..48b1ce61c8 100644
--- a/var/spack/repos/builtin/packages/xmessage/package.py
+++ b/var/spack/repos/builtin/packages/xmessage/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xmessage(AutotoolsPackage):
     depends_on('libxaw')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmh/package.py b/var/spack/repos/builtin/packages/xmh/package.py
index 65873360c2..096c0b7cc8 100644
--- a/var/spack/repos/builtin/packages/xmh/package.py
+++ b/var/spack/repos/builtin/packages/xmh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,5 +22,5 @@ class Xmh(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xbitmaps@1.1.0:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmlf90/package.py b/var/spack/repos/builtin/packages/xmlf90/package.py
new file mode 100644
index 0000000000..09091adcfb
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xmlf90/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Xmlf90(AutotoolsPackage):
+    """xmlf90 is a suite of libraries to handle XML in Fortran."""
+
+    homepage = "https://launchpad.net/xmlf90"
+    url      = "https://launchpad.net/xmlf90/trunk/1.5/+download/xmlf90-1.5.2.tgz"
+
+    version('1.5.2', '324fdcba7dafce83db26e72aab9f6656')
+
+    depends_on('autoconf@2.69:', type='build')
+    depends_on('automake@1.14:', type='build')
+    depends_on('libtool@2.4.2:', type='build')
+    depends_on('m4',             type='build')
+
+    def autoreconf(self, spec, prefix):
+        sh = which('sh')
+        sh('autogen.sh')
+
+    def configure_args(self):
+        if self.spec.satisfies('%gcc'):
+            return ['FCFLAGS=-ffree-line-length-none']
+        return []
+
+    @run_after('install')
+    def fix_mk(self):
+        install(join_path(self.prefix, 'share', 'org.siesta-project',
+                          'xmlf90.mk'), prefix)
diff --git a/var/spack/repos/builtin/packages/xmlto/package.py b/var/spack/repos/builtin/packages/xmlto/package.py
index b1122d8ef6..af70c2f70d 100644
--- a/var/spack/repos/builtin/packages/xmlto/package.py
+++ b/var/spack/repos/builtin/packages/xmlto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xmodmap/package.py b/var/spack/repos/builtin/packages/xmodmap/package.py
index 62582df6f2..13a8527bb8 100644
--- a/var/spack/repos/builtin/packages/xmodmap/package.py
+++ b/var/spack/repos/builtin/packages/xmodmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xmodmap(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xmore/package.py b/var/spack/repos/builtin/packages/xmore/package.py
index 0b76828999..597d7c0e8b 100644
--- a/var/spack/repos/builtin/packages/xmore/package.py
+++ b/var/spack/repos/builtin/packages/xmore/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xmore(AutotoolsPackage):
     depends_on('libxaw')
     depends_on('libxt')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xorg-cf-files/package.py b/var/spack/repos/builtin/packages/xorg-cf-files/package.py
index edeba12f0e..ef1befcb4b 100644
--- a/var/spack/repos/builtin/packages/xorg-cf-files/package.py
+++ b/var/spack/repos/builtin/packages/xorg-cf-files/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,4 +17,4 @@ class XorgCfFiles(AutotoolsPackage):
 
     version('1.0.6', 'c0ce98377c70d95fb48e1bd856109bf8')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xorg-docs/package.py b/var/spack/repos/builtin/packages/xorg-docs/package.py
index bb67538f0a..0a0b94fc90 100644
--- a/var/spack/repos/builtin/packages/xorg-docs/package.py
+++ b/var/spack/repos/builtin/packages/xorg-docs/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,7 +17,7 @@ class XorgDocs(AutotoolsPackage):
 
     version('1.7.1', 'ca689ccbf8ebc362afbe5cc5792a4abd')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
     depends_on('xorg-sgml-doctools@1.8:', type='build')
     depends_on('xmlto', type='build')
diff --git a/var/spack/repos/builtin/packages/xorg-gtest/package.py b/var/spack/repos/builtin/packages/xorg-gtest/package.py
index 594ba2a3bd..49953792b6 100644
--- a/var/spack/repos/builtin/packages/xorg-gtest/package.py
+++ b/var/spack/repos/builtin/packages/xorg-gtest/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,7 +19,7 @@ class XorgGtest(AutotoolsPackage):
     depends_on('libxi')
     depends_on('xorg-server')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     # TODO: may be missing evemu package?
diff --git a/var/spack/repos/builtin/packages/xorg-server/package.py b/var/spack/repos/builtin/packages/xorg-server/package.py
index 6b616bfe43..14d885a997 100644
--- a/var/spack/repos/builtin/packages/xorg-server/package.py
+++ b/var/spack/repos/builtin/packages/xorg-server/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,7 +20,7 @@ class XorgServer(AutotoolsPackage):
     depends_on('libxshmfence@1.1:')
     depends_on('libdrm@2.3.0:')
     depends_on('libx11')
-    # depends_on('gl@9.2.0:')
+    depends_on('mesa+hwrender', type='build')
 
     depends_on('dri2proto@2.8:', type='build')
     depends_on('dri3proto@1.0:', type='build')
@@ -47,56 +28,33 @@ class XorgServer(AutotoolsPackage):
 
     depends_on('flex', type='build')
     depends_on('bison', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
-
-    # TODO: add missing dependencies
-    # $LIBSELINUX $REQUIRED_MODULES $REQUIRED_LIBS
-    # $LIBPCIACCESS $DGAPROTO $XORG_MODULES epoxy xdmcp xau xfixes x11-xcb
-    # xcb-aux xcb-image xcb-ewmh xcb-icccm $WINDOWSWMPROTO windowsdriproto
-    # khronos-opengl-registry
-    # $APPLEWMPROTO $LIBAPPLEWM xfixes $LIBDMX $LIBXEXT $LIBDMX xmu $LIBXEXT
-    # $LIBDMX $LIBXI $LIBXEXT $LIBXTST $LIBXEXT xres $LIBXEXT $LIBXEXT
-    # $XEPHYR_REQUIRED_LIBS
-
-    # VIDEOPROTO="videoproto"
-    # COMPOSITEPROTO="compositeproto >= 0.4"
-    # RECORDPROTO="recordproto >= 1.13.99.1"
-    # SCRNSAVERPROTO="scrnsaverproto >= 1.1"
-    # RESOURCEPROTO="resourceproto >= 1.2.0"
-    # DRIPROTO="xf86driproto >= 2.1.0"
-    # XINERAMAPROTO="xineramaproto"
-    # BIGFONTPROTO="xf86bigfontproto >= 1.2.0"
-    # DGAPROTO="xf86dgaproto >= 2.0.99.1"
-    # DMXPROTO="dmxproto >= 2.2.99.1"
-    # VIDMODEPROTO="xf86vidmodeproto >= 2.2.99.1"
-    # WINDOWSWMPROTO="windowswmproto"
-    # APPLEWMPROTO="applewmproto >= 1.4"
-
-    # XPROTO="xproto >= 7.0.28"
-    # RANDRPROTO="randrproto >= 1.5.0"
-    # RENDERPROTO="renderproto >= 0.11"
-    # XEXTPROTO="xextproto >= 7.2.99.901"
-    # INPUTPROTO="inputproto >= 2.3"
-    # KBPROTO="kbproto >= 1.0.3"
-    # FONTSPROTO="fontsproto >= 2.1.3"
-    # FIXESPROTO="fixesproto >= 5.0"
-    # DAMAGEPROTO="damageproto >= 1.1"
-    # XCMISCPROTO="xcmiscproto >= 1.2.0"
-    # BIGREQSPROTO="bigreqsproto >= 1.1.0"
-    # XTRANS="xtrans >= 1.3.5"
-    # PRESENTPROTO="presentproto >= 1.0"
-
-    # LIBAPPLEWM="applewm >= 1.4"
-    # LIBDMX="dmx >= 1.0.99.1"
-    # LIBDRI="dri >= 7.8.0"
-    # LIBEGL="egl"
-    # LIBGBM="gbm >= 10.2.0"
-    # LIBXEXT="xext >= 1.0.99.4"
-    # LIBXFONT="xfont2 >= 2.0.0"
-    # LIBXI="xi >= 1.2.99.1"
-    # LIBXTST="xtst >= 1.0.99.2"
-    # LIBPCIACCESS="pciaccess >= 0.12.901"
-    # LIBUDEV="libudev >= 143"
-    # LIBSELINUX="libselinux >= 2.0.86"
-    # LIBDBUS="dbus-1 >= 1.0"
+    depends_on('fixesproto@5.0:')
+    depends_on('damageproto@1.1:')
+    depends_on('xcmiscproto@1.2.0:')
+    depends_on('xtrans@1.3.5:')
+    depends_on('bigreqsproto@1.1.0:')
+    depends_on('xproto@7.0.28:')
+    depends_on('randrproto@1.5.0:')
+    depends_on('renderproto@0.11:')
+    depends_on('xextproto@7.2.99.901:')
+    depends_on('inputproto@2.3:')
+    depends_on('kbproto@1.0.3:')
+    depends_on('fontsproto@2.1.3:')
+    depends_on('pixman@0.27.2:')
+    depends_on('videoproto')
+    depends_on('compositeproto@0.4:')
+    depends_on('recordproto@1.13.99.1:')
+    depends_on('scrnsaverproto@1.1:')
+    depends_on('resourceproto@1.2.0:')
+    depends_on('xf86driproto@2.1.0:')
+    depends_on('glproto@1.4.17:')
+    depends_on('presentproto@1.0:')
+    depends_on('xineramaproto')
+    depends_on('libxkbfile')
+    depends_on('libxfont2')
+    depends_on('libxext')
+    depends_on('libxdamage')
+    depends_on('libxfixes')
+    depends_on('libepoxy')
diff --git a/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py b/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py
index 1adc06dc41..53f2425dc5 100644
--- a/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py
+++ b/var/spack/repos/builtin/packages/xorg-sgml-doctools/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class XorgSgmlDoctools(AutotoolsPackage):
 
     version('1.11', '51cf4c6b476e2b98a068fea6975b9b21')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xphelloworld/package.py b/var/spack/repos/builtin/packages/xphelloworld/package.py
index 10f9be36df..c6ac5d62ee 100644
--- a/var/spack/repos/builtin/packages/xphelloworld/package.py
+++ b/var/spack/repos/builtin/packages/xphelloworld/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -44,5 +25,5 @@ class Xphelloworld(AutotoolsPackage):
     # It looks like xprint support was removed from libxaw at some point.
     # But even the oldest version of libxaw doesn't build libxaw8.
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xplor-nih/package.py b/var/spack/repos/builtin/packages/xplor-nih/package.py
index 3be84ebf22..bdfd68b1b2 100644
--- a/var/spack/repos/builtin/packages/xplor-nih/package.py
+++ b/var/spack/repos/builtin/packages/xplor-nih/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
diff --git a/var/spack/repos/builtin/packages/xplsprinters/package.py b/var/spack/repos/builtin/packages/xplsprinters/package.py
index 0757de82ba..5347c9a9e9 100644
--- a/var/spack/repos/builtin/packages/xplsprinters/package.py
+++ b/var/spack/repos/builtin/packages/xplsprinters/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xplsprinters(AutotoolsPackage):
     depends_on('libxprintutil')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xpr/package.py b/var/spack/repos/builtin/packages/xpr/package.py
index 5d246e957a..a5de719915 100644
--- a/var/spack/repos/builtin/packages/xpr/package.py
+++ b/var/spack/repos/builtin/packages/xpr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xpr(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xprehashprinterlist/package.py b/var/spack/repos/builtin/packages/xprehashprinterlist/package.py
index 65701b180f..bc934a7391 100644
--- a/var/spack/repos/builtin/packages/xprehashprinterlist/package.py
+++ b/var/spack/repos/builtin/packages/xprehashprinterlist/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xprehashprinterlist(AutotoolsPackage):
     depends_on('libxp')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xprop/package.py b/var/spack/repos/builtin/packages/xprop/package.py
index 359ed6d6f1..6414b9784c 100644
--- a/var/spack/repos/builtin/packages/xprop/package.py
+++ b/var/spack/repos/builtin/packages/xprop/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xprop(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xproto/package.py b/var/spack/repos/builtin/packages/xproto/package.py
index 2396e2966f..bd45c4cf8a 100644
--- a/var/spack/repos/builtin/packages/xproto/package.py
+++ b/var/spack/repos/builtin/packages/xproto/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -41,7 +22,7 @@ class Xproto(AutotoolsPackage):
     version('7.0.31', '04b925bf9e472c80f9212615cd684f1e')
     version('7.0.29', '16a78dd2c5ad73011105c96235f6a0af')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
 
     def install(self, spec, prefix):
diff --git a/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py b/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py
index 2f70146e00..4a35b33993 100644
--- a/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py
+++ b/var/spack/repos/builtin/packages/xproxymanagementprotocol/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xqilla/package.py b/var/spack/repos/builtin/packages/xqilla/package.py
index 0c63fa6c3f..2949dcda73 100644
--- a/var/spack/repos/builtin/packages/xqilla/package.py
+++ b/var/spack/repos/builtin/packages/xqilla/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xrandr/package.py b/var/spack/repos/builtin/packages/xrandr/package.py
index 4aeb34d020..2a5544df8d 100644
--- a/var/spack/repos/builtin/packages/xrandr/package.py
+++ b/var/spack/repos/builtin/packages/xrandr/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,7 +18,8 @@ class Xrandr(AutotoolsPackage):
     depends_on('libxrandr@1.5:')
     depends_on('libxrender')
     depends_on('libx11')
+    depends_on('randrproto')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xrdb/package.py b/var/spack/repos/builtin/packages/xrdb/package.py
index 075e04e9dc..a3ae50cc95 100644
--- a/var/spack/repos/builtin/packages/xrdb/package.py
+++ b/var/spack/repos/builtin/packages/xrdb/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xrdb(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xrefresh/package.py b/var/spack/repos/builtin/packages/xrefresh/package.py
index 76a094779e..c4a97f718f 100644
--- a/var/spack/repos/builtin/packages/xrefresh/package.py
+++ b/var/spack/repos/builtin/packages/xrefresh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xrefresh(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xrootd/package.py b/var/spack/repos/builtin/packages/xrootd/package.py
index 94ee3eda46..8a14be9905 100644
--- a/var/spack/repos/builtin/packages/xrootd/package.py
+++ b/var/spack/repos/builtin/packages/xrootd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -32,10 +13,49 @@ class Xrootd(CMakePackage):
     homepage = "http://xrootd.org"
     url      = "http://xrootd.org/download/v4.6.0/xrootd-4.6.0.tar.gz"
 
+    version('4.8.3', 'bb6302703ffc123f7f9141ddb589435e')
+    version('4.8.2', '531b632191b59c2cf76ab8d31af4a866')
+    version('4.8.1', 'a307973f7f43b0cc2688dfe502e17709')
+    version('4.8.0', '4349e7f664e686b72855e894b49063ad')
+    version('4.7.1', '4006422bcf99e0a19996ace4ebb99175')
+    version('4.7.0', '2a92ba483f574c6ba6a9ff061878af22')
+    version('4.6.1', '70c6f6e1f5f2b4eeb3c7d2c41a36bb2c')
     version('4.6.0', '5d60aade2d995b68fe0c46896bc4a5d1')
     version('4.5.0', 'd485df3d4a991e1c35efa4bf9ef663d7')
     version('4.4.1', '72b0842f802ccc94dede4ac5ab2a589e')
     version('4.4.0', '58f55e56801d3661d753ff5fd33dbcc9')
     version('4.3.0', '39c2fab9f632f35e12ff607ccaf9e16c')
 
+    variant('http', default=True,
+            description='Build with HTTP support')
+
+    variant('python', default=False,
+            description='Build pyxroot Python extension')
+
+    variant('readline', default=True,
+            description='Use readline')
+
+    depends_on('bzip2')
     depends_on('cmake@2.6:', type='build')
+    depends_on('libxml2', when='+http')
+    depends_on('openssl')
+    depends_on('python', when='+python')
+    depends_on('readline', when='+readline')
+    depends_on('xz')
+    depends_on('zlib')
+
+    extends('python', when='+python')
+    patch('python-support.patch', level=1, when='+python')
+
+    def cmake_args(self):
+        spec = self.spec
+        options = [
+            '-DENABLE_HTTP:BOOL={0}'.
+            format('ON' if '+http' in spec else 'OFF'),
+            '-DENABLE_PYTHON:BOOL={0}'.
+            format('ON' if '+python' in spec else 'OFF'),
+            '-DENABLE_READLINE:BOOL={0}'.
+            format('ON' if '+readline' in spec else 'OFF'),
+            '-DENABLE_CEPH:BOOL=OFF'
+        ]
+        return options
diff --git a/var/spack/repos/builtin/packages/xrootd/python-support.patch b/var/spack/repos/builtin/packages/xrootd/python-support.patch
new file mode 100644
index 0000000000..eef580641c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xrootd/python-support.patch
@@ -0,0 +1,30 @@
+diff -Naur xrootd-4.8.0/bindings/python/setup.py.in xrootd-4.8.0/bindings/python/setup.py.in
+--- xrootd-4.8.0/bindings/python/setup.py.in	2017-12-13 11:28:52.000000000 -0600
++++ xrootd-4.8.0/bindings/python/setup.py.in	2017-12-21 17:47:51.378701139 -0600
+@@ -16,6 +16,13 @@
+ py_cflags = cfg_vars["PY_CFLAGS"]
+ cfg_vars["PY_CFLAGS"] = " ".join( flag for flag in py_cflags.split() if flag not in ['-Wstrict-prototypes' ${CLANG_PROHIBITED} ] )
+ 
++ccl=cfg_vars["CC"].split()
++ccl[0]="${CMAKE_C_COMPILER}"
++cfg_vars["CC"] = " ".join(ccl)
++cxxl=cfg_vars["CXX"].split()
++cxxl[0]="${CMAKE_CXX_COMPILER}"
++cfg_vars["CXX"] = " ".join(cxxl)
++cfg_vars["PY_CXXFLAGS"] = "${CMAKE_CXX_FLAGS}"
+ 
+ sources = list()
+ depends = list()
+diff -Naur xrootd-4.8.0/cmake/XRootDFindLibs.cmake xrootd-4.8.0/cmake/XRootDFindLibs.cmake
+--- xrootd-4.8.0/cmake/XRootDFindLibs.cmake	2017-12-13 11:28:52.000000000 -0600
++++ xrootd-4.8.0/cmake/XRootDFindLibs.cmake	2017-12-21 17:47:51.379701131 -0600
+@@ -85,8 +85,8 @@
+ endif()
+ 
+ if( ENABLE_PYTHON AND (Linux OR APPLE) )
+-  find_package( PythonLibs ${XRD_PYTHON_REQ_VERSION} )
+   find_package( PythonInterp ${XRD_PYTHON_REQ_VERSION} )
++  find_package( PythonLibs ${XRD_PYTHON_REQ_VERSION} )
+   if( PYTHONINTERP_FOUND AND PYTHONLIBS_FOUND )
+     set( BUILD_PYTHON TRUE )
+     set( PYTHON_FOUND TRUE )
diff --git a/var/spack/repos/builtin/packages/xrx/package.py b/var/spack/repos/builtin/packages/xrx/package.py
index fba6a88df1..3b1a3f6a4f 100644
--- a/var/spack/repos/builtin/packages/xrx/package.py
+++ b/var/spack/repos/builtin/packages/xrx/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -47,5 +28,5 @@ class Xrx(AutotoolsPackage):
 
     depends_on('xtrans', type='build')
     depends_on('xproxymanagementprotocol', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsbench/package.py b/var/spack/repos/builtin/packages/xsbench/package.py
index 345d566bc0..e8010c135e 100644
--- a/var/spack/repos/builtin/packages/xsbench/package.py
+++ b/var/spack/repos/builtin/packages/xsbench/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
@@ -37,10 +18,12 @@ class Xsbench(MakefilePackage):
 
     tags = ['proxy-app', 'ecp-proxy-app']
 
+    version('18', sha256='a9a544eeacd1be8d687080d2df4eeb701c04eda31d3806e7c3ea1ff36c26f4b0')
     version('14', '94d5d28eb031fd4ef35507c9c1862169')
     version('13', '72a92232d2f5777fb52f5ea4082aff37')
 
-    variant('mpi', default=False, description='Build with MPI support')
+    variant('mpi', default=True, description='Build with MPI support')
+    variant('openmp', default=True, description='Build with OpenMP support')
 
     depends_on('mpi', when='+mpi')
 
@@ -54,8 +37,11 @@ class Xsbench(MakefilePackage):
         cflags = '-std=gnu99'
         if '+mpi' in self.spec:
             targets.append('CC={0}'.format(self.spec['mpi'].mpicc))
+        else:
+            targets.append('CC={0}'.format(self.compiler.cxx))
 
-        cflags += ' ' + self.compiler.openmp_flag
+        if '+openmp' in self.spec:
+            cflags += ' ' + self.compiler.openmp_flag
         targets.append('CFLAGS={0}'.format(cflags))
         targets.append('LDFLAGS=-lm')
 
diff --git a/var/spack/repos/builtin/packages/xscope/package.py b/var/spack/repos/builtin/packages/xscope/package.py
index c851fcf5f3..bea4a1d73f 100644
--- a/var/spack/repos/builtin/packages/xscope/package.py
+++ b/var/spack/repos/builtin/packages/xscope/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -35,5 +16,5 @@ class Xscope(AutotoolsPackage):
 
     depends_on('xproto@7.0.17:', type='build')
     depends_on('xtrans', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsd/package.py b/var/spack/repos/builtin/packages/xsd/package.py
new file mode 100644
index 0000000000..3fb1a74dcd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xsd/package.py
@@ -0,0 +1,33 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack import *
+
+
+class Xsd(MakefilePackage):
+    """CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema
+    to C++ data binding compiler. It support in-memory and event-driven XML
+    processing models and is available for a wide range of C++ compilers
+    and platforms."""
+
+    homepage = "https://www.codesynthesis.com"
+    url      = "https://www.codesynthesis.com/download/xsd/4.0/xsd-4.0.0+dep.tar.bz2"
+
+    version('4.0.0', 'ad3de699eb140e747a0a214462d95fc81a21b494')
+
+    depends_on('xerces-c')
+    depends_on('libtool', type='build')
+
+    def install(self, spec, prefix):
+        make('install', 'install_prefix=' + prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        xercesc_lib_flags = self.spec['xerces-c'].libs.search_flags
+        spack_env.append_flags('LDFLAGS', xercesc_lib_flags)
+
+    def url_for_version(self, version):
+        url = "https://www.codesynthesis.com/download/xsd/{0}/xsd-{1}+dep.tar.bz2"
+        return url.format(version.up_to(2), version)
diff --git a/var/spack/repos/builtin/packages/xsdk/package.py b/var/spack/repos/builtin/packages/xsdk/package.py
index 901613f77d..21f71b9abd 100644
--- a/var/spack/repos/builtin/packages/xsdk/package.py
+++ b/var/spack/repos/builtin/packages/xsdk/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 import os
 from spack import *
@@ -37,40 +18,75 @@ class Xsdk(Package):
 
     # Dummy url since Spack complains if I don't list something, will be
     # removed when metapackage is available
-    url      = 'https://bitbucket.org/saws/saws/get/master.tar.gz'
+    url      = 'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/xsdk.tar.gz'
 
     version('develop', 'a52dc710c744afa0b71429b8ec9425bc')
+    version('0.3.0', 'a52dc710c744afa0b71429b8ec9425bc', preferred=True)
     version('xsdk-0.2.0', 'a52dc710c744afa0b71429b8ec9425bc')
 
-    depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0')
+    variant('debug', default=False, description='Compile in debug mode')
+    variant('cuda', default=False, description='Enable CUDA dependent packages')
+
     depends_on('hypre@develop~internal-superlu', when='@develop')
+    depends_on('hypre@2.12.1~internal-superlu', when='@0.3.0')
+    depends_on('hypre@xsdk-0.2.0~internal-superlu', when='@xsdk-0.2.0')
+
+    depends_on('mfem@develop+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@develop')
+    depends_on('mfem@3.3.2+mpi+hypre+superlu-dist+petsc+sundials+examples+miniapps', when='@0.3.0')
 
-    depends_on('superlu-dist@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('superlu-dist@develop', when='@develop')
+    depends_on('superlu-dist@5.2.2', when='@0.3.0')
+    depends_on('superlu-dist@xsdk-0.2.0', when='@xsdk-0.2.0')
 
+    depends_on('trilinos@develop+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse+tpetra+nox+ifpack2+zoltan2+amesos2~exodus',
+               when='@develop')
+    depends_on('trilinos@12.12.1+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse~tpetra~ifpack2~zoltan2~amesos2~exodus',
+               when='@0.3.0')
     depends_on('trilinos@xsdk-0.2.0+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse~tpetra~ifpack2~zoltan2~amesos2~exodus',
                when='@xsdk-0.2.0')
-    depends_on('trilinos@develop+xsdkflags+hypre+superlu-dist+metis+hdf5~mumps+boost~suite-sparse~tpetra~ifpack2~zoltan2~amesos2~exodus',
-               when='@develop')
 
-    depends_on('petsc@xsdk-0.2.0+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps~boost+double~int64',
-               when='@xsdk-0.2.0')
-    depends_on('petsc@develop+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps~boost+double~int64',
+    depends_on('petsc@develop+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64',
                when='@develop')
+    depends_on('petsc@3.8.2+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64',
+               when='@0.3.0')
+    depends_on('petsc@xsdk-0.2.0+trilinos+mpi+hypre+superlu-dist+metis+hdf5~mumps+double~int64',
+               when='@xsdk-0.2.0')
+
+    depends_on('dealii@develop~assimp~python~doc~slepc~gmsh+petsc+mpi+trilinos~int64+hdf5~netcdf+metis', when='@develop')
 
-    depends_on('pflotran@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('pflotran@develop', when='@develop')
+    depends_on('pflotran@xsdk-0.3.0', when='@0.3.0')
+    depends_on('pflotran@xsdk-0.2.0', when='@xsdk-0.2.0')
 
-    depends_on('alquimia@xsdk-0.2.0', when='@xsdk-0.2.0')
     depends_on('alquimia@develop', when='@develop')
+    depends_on('alquimia@xsdk-0.3.0', when='@0.3.0')
+    depends_on('alquimia@xsdk-0.2.0', when='@xsdk-0.2.0')
+
+    depends_on('sundials@3.1.0~int64+hypre', when='@develop')
+    depends_on('sundials@3.1.0~int64+hypre', when='@0.3.0')
+
+    depends_on('plasma@17.2:', when='@develop %gcc@6.0:')
+
+    depends_on('magma@2.2.0', when='@develop +cuda')
+    depends_on('magma@2.2.0', when='@0.3.0 +cuda')
+
+    depends_on('amrex@develop', when='@develop %intel')
+    depends_on('amrex@develop', when='@develop %gcc')
+
+    depends_on('slepc@develop', when='@develop')
+
+    # the Fortran 2003 bindings of phist require python@3:, but this
+    # creates a conflict with other packages like petsc@develop. Actually
+    # these are type='build' dependencies, but spack reports a conflict anyway.
+    # This will be fixed once the new concretizer becomes available
+    # (says @adamjsteward)
+    depends_on('phist@develop kernel_lib=tpetra ~fortran ~scamac ~openmp', when='@develop')
 
     # xSDKTrilinos depends on the version of Trilinos built with
     # +tpetra which is turned off for faster xSDK
     # depends_on('xsdktrilinos@xsdk-0.2.0', when='@xsdk-0.2.0')
     # depends_on('xsdktrilinos@develop', when='@develop')
 
-    variant('debug', default=False, description='Compile in debug mode')
-
     # How do we propagate debug flag to all depends on packages ?
     # If I just do spack install xsdk+debug will that propogate it down?
 
diff --git a/var/spack/repos/builtin/packages/xsdktrilinos/package.py b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
index cc75589937..66de6cef0c 100644
--- a/var/spack/repos/builtin/packages/xsdktrilinos/package.py
+++ b/var/spack/repos/builtin/packages/xsdktrilinos/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
 
@@ -33,9 +14,10 @@ class Xsdktrilinos(CMakePackage):
     """
     homepage = "https://trilinos.org/"
     url      = "https://github.com/trilinos/xSDKTrilinos/archive/trilinos-release-12-8-1.tar.gz"
+    git      = "https://github.com/trilinos/xSDKTrilinos.git"
 
-    version('develop', git='https://github.com/trilinos/xSDKTrilinos.git', tag='master')
-    version('xsdk-0.2.0', git='https://github.com/trilinos/xSDKTrilinos.git', tag='xsdk-0.2.0')
+    version('develop', tag='master')
+    version('xsdk-0.2.0', tag='xsdk-0.2.0')
     version('12.8.1', '9cc338ded17d1e10ea6c0dc18b22dcd4')
     version('12.6.4', '44c4c54ccbac73bb8939f68797b9454a')
 
diff --git a/var/spack/repos/builtin/packages/xset/package.py b/var/spack/repos/builtin/packages/xset/package.py
index 8488ded70c..93260d65ec 100644
--- a/var/spack/repos/builtin/packages/xset/package.py
+++ b/var/spack/repos/builtin/packages/xset/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xset(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsetmode/package.py b/var/spack/repos/builtin/packages/xsetmode/package.py
index e4d9b1a6a0..e1eb7dc33d 100644
--- a/var/spack/repos/builtin/packages/xsetmode/package.py
+++ b/var/spack/repos/builtin/packages/xsetmode/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xsetmode(AutotoolsPackage):
     depends_on('libxi')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsetpointer/package.py b/var/spack/repos/builtin/packages/xsetpointer/package.py
index 296dae801b..66d91bbc04 100644
--- a/var/spack/repos/builtin/packages/xsetpointer/package.py
+++ b/var/spack/repos/builtin/packages/xsetpointer/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xsetpointer(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('inputproto@1.4:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsetroot/package.py b/var/spack/repos/builtin/packages/xsetroot/package.py
index 1468aa7e2e..43b61bd41c 100644
--- a/var/spack/repos/builtin/packages/xsetroot/package.py
+++ b/var/spack/repos/builtin/packages/xsetroot/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xsetroot(AutotoolsPackage):
 
     depends_on('xbitmaps', type='build')
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xsimd/package.py b/var/spack/repos/builtin/packages/xsimd/package.py
new file mode 100644
index 0000000000..a7d1f8474a
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xsimd/package.py
@@ -0,0 +1,36 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xsimd(CMakePackage):
+    """C++ wrappers for SIMD intrinsics"""
+
+    homepage = "http://quantstack.net/xsimd"
+    url      = "https://github.com/QuantStack/xsimd/archive/3.1.0.tar.gz"
+    git      = "https://github.com/QuantStack/xsimd.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('4.0.0', '4186ec94985daa3fc284d9d0d4aa03e8')
+    version('3.1.0', '29c1c525116cbda28f610e2bf24a827e')
+
+    depends_on('googletest', type='test')
+
+    # C++14 support
+    conflicts('%gcc@:4.8')
+    conflicts('%clang@:3.6')
+    # untested: conflicts('%intel@:15')
+    # untested: conflicts('%pgi@:14')
+
+    def cmake_args(self):
+        args = [
+            '-DBUILD_TESTS:BOOL={0}'.format(
+                'ON' if self.run_tests else 'OFF')
+        ]
+
+        return args
diff --git a/var/spack/repos/builtin/packages/xsm/package.py b/var/spack/repos/builtin/packages/xsm/package.py
index 0bbd3ec805..eb1a3417dc 100644
--- a/var/spack/repos/builtin/packages/xsm/package.py
+++ b/var/spack/repos/builtin/packages/xsm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -39,5 +20,5 @@ class Xsm(AutotoolsPackage):
     depends_on('libsm')
     depends_on('libxaw')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xstdcmap/package.py b/var/spack/repos/builtin/packages/xstdcmap/package.py
index 9b8d4a1641..3f9ae0960b 100644
--- a/var/spack/repos/builtin/packages/xstdcmap/package.py
+++ b/var/spack/repos/builtin/packages/xstdcmap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xstdcmap(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xtensor-python/package.py b/var/spack/repos/builtin/packages/xtensor-python/package.py
new file mode 100644
index 0000000000..5bf808ff5e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xtensor-python/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class XtensorPython(CMakePackage):
+    """Python bindings for the xtensor C++ multi-dimensional array library"""
+
+    homepage = "https://xtensor-python.readthedocs.io"
+    url      = "https://github.com/QuantStack/xtensor-python/archive/0.17.0.tar.gz"
+    git      = "https://github.com/QuantStack/xtensor-python.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('0.17.0', '51d22e42909a81201c3421d9e119eed0')
+
+    depends_on('xtensor@0.15.1:0.15.99', when='@0.17.0:')
+    depends_on('xtl@0.4.0:0.4.99', when='@0.17.0:')
+    depends_on('py-pybind11@2.2.1', when='@0.17.0:')
+
+    depends_on('py-numpy')
+    depends_on('python', type=('build', 'link', 'run'))
+
+    extends('python')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        python_exe = spec['python'].command.path
+
+        args = [
+            '-DPYTHON_EXECUTABLE={0}'.format(python_exe)
+        ]
+        return args
diff --git a/var/spack/repos/builtin/packages/xtensor/package.py b/var/spack/repos/builtin/packages/xtensor/package.py
new file mode 100644
index 0000000000..9ba3dcda16
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xtensor/package.py
@@ -0,0 +1,35 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xtensor(CMakePackage):
+    """Multi-dimensional arrays with broadcasting and lazy computing"""
+
+    homepage = "http://quantstack.net/xtensor"
+    url      = "https://github.com/QuantStack/xtensor/archive/0.13.1.tar.gz"
+    git      = "https://github.com/QuantStack/xtensor.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('0.15.1', 'c24ecc406003bd1ac22291f1f7cac29a')
+    version('0.13.1', '80e7e33f05066d17552bf0f8b582dcc5')
+
+    variant('xsimd', default=True,
+            description='Enable SIMD intrinsics')
+
+    depends_on('xtl')
+    depends_on('xtl@0.4.0:0.4.99', when='@0.15.1:')
+    depends_on('xtl@0.3.3:0.3.99', when='@0.13.1')
+    depends_on('xsimd@4.0.0', when='@0.15.1 +xsimd')
+    depends_on('xsimd@3.1.0', when='@0.13.1 +xsimd')
+
+    # C++14 support
+    conflicts('%gcc@:4.8')
+    conflicts('%clang@:3.5')
+    # untested: conflicts('%intel@:15')
+    # untested: conflicts('%pgi@:14')
diff --git a/var/spack/repos/builtin/packages/xterm/package.py b/var/spack/repos/builtin/packages/xterm/package.py
index 8c24931d7a..8ecd6eb64f 100644
--- a/var/spack/repos/builtin/packages/xterm/package.py
+++ b/var/spack/repos/builtin/packages/xterm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -31,7 +12,7 @@ class Xterm(AutotoolsPackage):
     that can't use the window system directly."""
 
     homepage = "http://invisible-island.net/xterm/"
-    url      = "http://invisible-island.net/xterm/xterm-327.tgz"
+    url      = "ftp://ftp.invisible-island.net/xterm/xterm-327.tgz"
 
     version('327', '3c32e931adcad44e64e57892e75d9e02')
 
@@ -52,4 +33,4 @@ class Xterm(AutotoolsPackage):
     depends_on('libxau')
     depends_on('bzip2')
 
-    depends_on('pkg-config', type='build')
+    depends_on('pkgconfig', type='build')
diff --git a/var/spack/repos/builtin/packages/xtl/package.py b/var/spack/repos/builtin/packages/xtl/package.py
new file mode 100644
index 0000000000..b73ec8fa10
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xtl/package.py
@@ -0,0 +1,27 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xtl(CMakePackage):
+    """QuantStack tools library"""
+
+    homepage = "https://github.com/QuantStack/xtl"
+    url      = "https://github.com/QuantStack/xtl/archive/0.3.4.tar.gz"
+    git      = "https://github.com/QuantStack/xtl.git"
+
+    maintainers = ['ax3l']
+
+    version('develop', branch='master')
+    version('0.4.0', '48c76b63ab12e497a53fb147c41ae747')
+    version('0.3.4', 'b76548a55f1e171a9c849e5ed543e8b3')
+    version('0.3.3', '09b6d9611e460d9280bf1156bcca20f5')
+
+    # C++14 support
+    conflicts('%gcc@:4.8')
+    conflicts('%clang@:3.6')
+    # untested: conflicts('%intel@:15')
+    # untested: conflicts('%pgi@:14')
diff --git a/var/spack/repos/builtin/packages/xtrans/package.py b/var/spack/repos/builtin/packages/xtrans/package.py
index 186e3587e6..508483c358 100644
--- a/var/spack/repos/builtin/packages/xtrans/package.py
+++ b/var/spack/repos/builtin/packages/xtrans/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xtrans(AutotoolsPackage):
 
     version('1.3.5', '6e4eac1b7c6591da0753052e1eccfb58')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xtrap/package.py b/var/spack/repos/builtin/packages/xtrap/package.py
index ef297e9e6d..e78aab7b66 100644
--- a/var/spack/repos/builtin/packages/xtrap/package.py
+++ b/var/spack/repos/builtin/packages/xtrap/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,5 @@ class Xtrap(AutotoolsPackage):
     depends_on('libx11')
     depends_on('libxtrap')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xts/package.py b/var/spack/repos/builtin/packages/xts/package.py
index 985a35bd5a..f8e6038d50 100644
--- a/var/spack/repos/builtin/packages/xts/package.py
+++ b/var/spack/repos/builtin/packages/xts/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/xvidtune/package.py b/var/spack/repos/builtin/packages/xvidtune/package.py
index 573c027627..37cbc8a1d5 100644
--- a/var/spack/repos/builtin/packages/xvidtune/package.py
+++ b/var/spack/repos/builtin/packages/xvidtune/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -40,5 +21,5 @@ class Xvidtune(AutotoolsPackage):
     depends_on('libxmu')
     depends_on('libx11')
 
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xvinfo/package.py b/var/spack/repos/builtin/packages/xvinfo/package.py
index 358573dcbe..7dd8670ce5 100644
--- a/var/spack/repos/builtin/packages/xvinfo/package.py
+++ b/var/spack/repos/builtin/packages/xvinfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xvinfo(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.25:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xwd/package.py b/var/spack/repos/builtin/packages/xwd/package.py
index 0b992365be..ba5b693fbf 100644
--- a/var/spack/repos/builtin/packages/xwd/package.py
+++ b/var/spack/repos/builtin/packages/xwd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xwd(AutotoolsPackage):
     depends_on('libxkbfile')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xwininfo/package.py b/var/spack/repos/builtin/packages/xwininfo/package.py
index bba7088166..86473d401c 100644
--- a/var/spack/repos/builtin/packages/xwininfo/package.py
+++ b/var/spack/repos/builtin/packages/xwininfo/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -38,5 +19,5 @@ class Xwininfo(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xwud/package.py b/var/spack/repos/builtin/packages/xwud/package.py
index b4b92cd214..dd13f44ced 100644
--- a/var/spack/repos/builtin/packages/xwud/package.py
+++ b/var/spack/repos/builtin/packages/xwud/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -37,5 +18,5 @@ class Xwud(AutotoolsPackage):
     depends_on('libx11')
 
     depends_on('xproto@7.0.17:', type='build')
-    depends_on('pkg-config@0.9.0:', type='build')
+    depends_on('pkgconfig', type='build')
     depends_on('util-macros', type='build')
diff --git a/var/spack/repos/builtin/packages/xxhash/package.py b/var/spack/repos/builtin/packages/xxhash/package.py
new file mode 100644
index 0000000000..990e6ed3e3
--- /dev/null
+++ b/var/spack/repos/builtin/packages/xxhash/package.py
@@ -0,0 +1,30 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Xxhash(MakefilePackage):
+    """xxHash is an Extremely fast Hash algorithm, running at RAM speed
+    limits. It successfully completes the SMHasher test suite which
+    evaluates collision, dispersion and randomness qualities of hash
+    functions. Code is highly portable, and hashes are identical on all
+    platforms (little / big endian).
+    """
+
+    homepage = "https://github.com/Cyan4973/xxHash"
+    url      = "https://github.com/Cyan4973/xxHash/archive/v0.6.5.tar.gz"
+
+    version('0.6.5', '6af3a964f3c2accebce66e54b44b6446')
+    version('0.6.4', '3c071c95e31bd601cca149cc354e6f19')
+    version('0.6.3', 'f2ec1497317c0eb89addd7f333c83228')
+    version('0.6.2', 'b2d12d99094b824e0a5f3ab63abc6c58')
+    version('0.6.1', 'f4ced3767aad8384b1ecb73bd5f992ca')
+    version('0.6.0', 'e0fd163b07ab0038f389a180dc263cf2')
+    version('0.5.1', '9417fd8a4d88204b680e21a60f0ccada')
+    version('0.5.0', '42e9a31a2cfc2f626fde17e84a0b6bb7')
+
+    def install(self, spec, prefix):
+        make('prefix={0}'.format(prefix), 'install')
diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py
index 04d91c76ac..9f2f9f9d83 100644
--- a/var/spack/repos/builtin/packages/xz/package.py
+++ b/var/spack/repos/builtin/packages/xz/package.py
@@ -1,39 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Xz(AutotoolsPackage):
     """XZ Utils is free general-purpose data compression software with
-       high compression ratio. XZ Utils were written for POSIX-like
-       systems, but also work on some not-so-POSIX systems. XZ Utils are
-       the successor to LZMA Utils."""
+    high compression ratio. XZ Utils were written for POSIX-like systems,
+    but also work on some not-so-POSIX systems. XZ Utils are the successor
+    to LZMA Utils."""
+
     homepage = "http://tukaani.org/xz/"
-    url      = "http://tukaani.org/xz/xz-5.2.0.tar.bz2"
+    url      = "http://tukaani.org/xz/xz-5.2.4.tar.bz2"
     list_url = "http://tukaani.org/xz/old.html"
 
+    version('5.2.4', 'b3264b15ab1db04c8c428dc81838d4eb')
     version('5.2.3', '1592e7ca3eece099b03b35f4d9179e7c')
     version('5.2.2', 'f90c9a0c8b259aee2234c4e0d7fd70af')
     version('5.2.0', '867cc8611760240ebf3440bd6e170bb9')
diff --git a/var/spack/repos/builtin/packages/yajl/package.py b/var/spack/repos/builtin/packages/yajl/package.py
index 604144c6e5..e26616bb05 100644
--- a/var/spack/repos/builtin/packages/yajl/package.py
+++ b/var/spack/repos/builtin/packages/yajl/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2017, Los Alamos National Security, LLC
-# Produced at the Los Alamos National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,6 +11,7 @@ class Yajl(CMakePackage):
 
     homepage = "http://lloyd.github.io/yajl/"
     url      = "https://github.com/lloyd/yajl/archive/2.1.0.zip"
+    git      = "https://github.com/lloyd/yajl.git"
 
-    version('develop', git='https://github.com/lloyd/yajl.git', branch='master')
+    version('develop', branch='master')
     version('2.1.0', '5eb9c16539bf354b937fcb20e263d1eb')
diff --git a/var/spack/repos/builtin/packages/yambo/package.py b/var/spack/repos/builtin/packages/yambo/package.py
new file mode 100644
index 0000000000..ddb5964233
--- /dev/null
+++ b/var/spack/repos/builtin/packages/yambo/package.py
@@ -0,0 +1,151 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Yambo(AutotoolsPackage):
+    """Yambo is a FORTRAN/C code for Many-Body calculations in solid
+    state and molecular physics.
+
+    Yambo relies on the Kohn-Sham wavefunctions generated by two DFT
+    public codes: abinit, and PWscf. The code was originally developed
+    in the Condensed Matter Theoretical Group of the Physics Department
+    at the University of Rome "Tor Vergata" by Andrea Marini. Previous
+    to its release under the GPL license, yambo was known as SELF.
+    """
+
+    homepage = "http://www.yambo-code.org/index.php"
+    url = "https://github.com/yambo-code/yambo/archive/4.2.2.tar.gz"
+
+    version('4.2.2', '97f3513bd726141be5e18072118b6fb5')
+    version('4.2.1', '99027014192c0f0f4b5d9b48414ad85d')
+    version('4.2.0', '0cbb4d7c9790596d163ebe872d95bd30')
+
+    variant('dp', default=False, description='Enable double precision')
+    variant(
+        'profile',
+        values=('time', 'memory'),
+        default='',
+        description='Activate profiling of specific sections',
+        multi=True
+    )
+
+    variant(
+        'io',
+        values=('iotk', 'etsf-io'),
+        default='',
+        description='Activate support for different io formats (requires network access)',  # noqa
+        multi=True
+    )
+
+    # MPI + OpenMP parallelism
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('openmp', default=False, description='Enable OpenMP support')
+
+    depends_on('blas')
+    depends_on('lapack')
+
+    # MPI dependencies are forced, until we have proper forwarding of variants
+    #
+    # Note that yambo is used as an application, and not linked as a library,
+    # thus there will be no case where another package pulls-in e.g. netcdf+mpi
+    # and wants to depend on yambo~mpi.
+    depends_on('mpi', when='+mpi')
+    depends_on('netcdf+mpi', when='+mpi')
+    depends_on('hdf5+mpi', when='+mpi')
+    depends_on('fftw+mpi', when='+mpi')
+    depends_on('scalapack', when='+mpi')
+
+    depends_on('netcdf~mpi', when='~mpi')
+    depends_on('hdf5~mpi', when='~mpi')
+    depends_on('fftw~mpi', when='~mpi')
+
+    depends_on('hdf5+fortran')
+    depends_on('netcdf')
+    depends_on('netcdf-fortran')
+    depends_on('libxc@2.0.3:')
+
+    build_targets = ['all']
+
+    parallel = False
+
+    # The configure in the package has the string 'cat config/report'
+    # hard-coded, which causes a failure at configure time due to the
+    # current working directory in Spack. Fix this by using the absolute
+    # path to the file.
+    @run_before('configure')
+    def filter_configure(self):
+        report_abspath = join_path(self.build_directory, 'config', 'report')
+        filter_file('config/report', report_abspath, 'configure')
+
+    def enable_or_disable_time(self, activated):
+        return '--enable-time-profile' if activated else '--disable-time-profile'  # noqa: E501
+
+    def enable_or_disable_memory(self, activated):
+        return '--enable-memory-profile' if activated else '--disable-memory-profile'  # noqa: E501
+
+    def enable_or_disable_openmp(self, activated):
+        return '--enable-open-mp' if activated else '--disable-open-mp'
+
+    def configure_args(self):
+
+        args = [
+            # As of version 4.2.1 there are hard-coded paths that make
+            # the build process fail if the target prefix is not the
+            # configure directory
+            '--prefix={0}'.format(self.stage.source_path),
+            '--disable-keep-objects',
+            '--with-editor=none'
+        ]
+        spec = self.spec
+
+        # Double precision
+        args.extend(self.enable_or_disable('dp'))
+
+        # Application profiling
+        args.extend(self.enable_or_disable('profile'))
+
+        # MPI + threading
+        args.extend(self.enable_or_disable('mpi'))
+        args.extend(self.enable_or_disable('openmp'))
+
+        # LAPACK
+        if '+mpi' in spec:
+            args.append('--with-scalapack-libs={0}'.format(
+                spec['scalapack'].libs +
+                spec['lapack'].libs +
+                spec['blas'].libs
+            ))
+
+        args.extend([
+            '--with-blas-libs={0}'.format(spec['blas'].libs),
+            '--with-lapack-libs={0}'.format(spec['lapack'].libs)
+        ])
+
+        # Netcdf
+        args.extend([
+            '--enable-netcdf-hdf5',
+            '--enable-hdf5-compression',
+            '--with-hdf5-libs={0}'.format(spec['hdf5'].libs),
+            '--with-netcdf-path={0}'.format(spec['netcdf'].prefix),
+            '--with-netcdff-path={0}'.format(spec['netcdf-fortran'].prefix)
+        ])
+
+        args.extend(self.enable_or_disable('io'))
+
+        # Other dependencies
+        args.append('--with-fft-path={0}'.format(spec['fftw'].prefix))
+        args.append('--with-libxc-path={0}'.format(spec['libxc'].prefix))
+
+        return args
+
+    def install(self, spec, prefix):
+        # As of version 4.2.1 an 'install' target is advertized,
+        # but not present
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
+        install_tree('include', prefix.include)
+        install_tree('driver', prefix.driver)
diff --git a/var/spack/repos/builtin/packages/yaml-cpp/package.py b/var/spack/repos/builtin/packages/yaml-cpp/package.py
index aaf6ab0a53..95df4da774 100644
--- a/var/spack/repos/builtin/packages/yaml-cpp/package.py
+++ b/var/spack/repos/builtin/packages/yaml-cpp/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,16 +11,27 @@ class YamlCpp(CMakePackage):
 
     homepage = "https://github.com/jbeder/yaml-cpp"
     url      = "https://github.com/jbeder/yaml-cpp/archive/yaml-cpp-0.5.3.tar.gz"
+    git      = "https://github.com/jbeder/yaml-cpp.git"
 
-    version('0.5.3', '4e47733d98266e46a1a73ae0a72954eb')
-    version('develop', git='https://github.com/jbeder/yaml-cpp', branch='master')
+    version('develop', branch='master')
+    version('0.6.2', '5b943e9af0060d0811148b037449ef82')
+    version('0.5.3', '2bba14e6a7f12c7272f87d044e4a7211')
 
     variant('shared', default=True,
             description='Enable build of shared libraries')
     variant('pic',   default=True,
             description='Build with position independent code')
 
-    depends_on('boost', when='@:0.5.3')
+    depends_on('boost@:1.66.99', when='@:0.5.3')
+
+    conflicts('%gcc@:4.7', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
+    conflicts('%clang@:3.3.0', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
+    # currently we can't check for apple-clang's version
+    # conflicts('%clang@:4.0.0-apple', when='@0.6.0:',
+    # msg="versions 0.6.0: require c++11 support")
+    conflicts('%intel@:11.1', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
+    conflicts('%xl@:13.1', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
+    conflicts('%xl_r@:13.1', when='@0.6.0:', msg="versions 0.6.0: require c++11 support")
 
     def cmake_args(self):
         spec = self.spec
diff --git a/var/spack/repos/builtin/packages/yasm/package.py b/var/spack/repos/builtin/packages/yasm/package.py
index 0d35e41e04..0f6bb70744 100644
--- a/var/spack/repos/builtin/packages/yasm/package.py
+++ b/var/spack/repos/builtin/packages/yasm/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -30,7 +11,15 @@ class Yasm(AutotoolsPackage):
        supports the x86 and AMD64 instruction sets, accepts NASM and
        GAS assembler syntaxes and outputs binary, ELF32 and ELF64
        object formats."""
+
     homepage = "http://yasm.tortall.net"
     url      = "http://www.tortall.net/projects/yasm/releases/yasm-1.3.0.tar.gz"
+    git      = "https://github.com/yasm/yasm.git"
 
+    version('develop', branch='master')
     version('1.3.0', 'fc9e586751ff789b34b1f21d572d96af')
+
+    depends_on('autoconf', when='@develop')
+    depends_on('automake', when='@develop')
+    depends_on('libtool', when='@develop')
+    depends_on('m4', when='@develop')
diff --git a/var/spack/repos/builtin/packages/yorick/package.py b/var/spack/repos/builtin/packages/yorick/package.py
index c30f9ca4ed..45f767a7ba 100644
--- a/var/spack/repos/builtin/packages/yorick/package.py
+++ b/var/spack/repos/builtin/packages/yorick/package.py
@@ -1,31 +1,10 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 import os
-import shutil
-import glob
 
 
 class Yorick(Package):
@@ -40,12 +19,11 @@ class Yorick(Package):
 
     homepage = "http://dhmunro.github.io/yorick-doc/"
     url      = "https://github.com/dhmunro/yorick/archive/y_2_2_04.tar.gz"
+    git      = "https://github.com/dhmunro/yorick.git"
 
+    version('master', branch='master')
     version('2.2.04', '1b5b0da6ad81b2d9dba64d991ec17939')
-    version('master', branch='master',
-            git='https://github.com/dhmunro/yorick.git')
-    version('f90-plugin', branch='f90-plugin',
-            git='https://github.com/trmwzm/yorick.git')
+    version('f90-plugin', branch='f90-plugin')
 
     variant('X', default=False, description='Enable X11 support')
 
@@ -75,13 +53,4 @@ class Yorick(Package):
         make()
         make("install")
 
-        try:
-            os.makedirs(prefix)
-        except OSError:
-            pass
-        os.chdir("relocate")
-        for f in glob.glob('*'):
-            if os.path.isdir(f):
-                shutil.copytree(f, os.path.join(prefix, f))
-            else:
-                shutil.copy2(f, os.path.join(prefix, f))
+        install_tree('relocate', prefix)
diff --git a/var/spack/repos/builtin/packages/z3/package.py b/var/spack/repos/builtin/packages/z3/package.py
index 2234b7e596..131ebba39a 100644
--- a/var/spack/repos/builtin/packages/z3/package.py
+++ b/var/spack/repos/builtin/packages/z3/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 
diff --git a/var/spack/repos/builtin/packages/zeromq/package.py b/var/spack/repos/builtin/packages/zeromq/package.py
index f48e868891..57ed8fd1fc 100644
--- a/var/spack/repos/builtin/packages/zeromq/package.py
+++ b/var/spack/repos/builtin/packages/zeromq/package.py
@@ -1,39 +1,22 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Zeromq(AutotoolsPackage):
-    """ The ZMQ networking/concurrency library and core API """
+    """The ZMQ networking/concurrency library and core API"""
+
     homepage = "http://zguide.zeromq.org/"
     url      = "http://download.zeromq.org/zeromq-4.1.2.tar.gz"
+    git      = "https://github.com/zeromq/libzmq.git"
 
-    version('develop', branch='master',
-            git='https://github.com/zeromq/libzmq.git')
-    version('4.2.2', '52499909b29604c1e47a86f1cb6a9115',
-            url='https://github.com/zeromq/libzmq/releases/download/v4.2.2/zeromq-4.2.2.tar.gz')
+    version('develop', branch='master')
+    version('4.2.5', 'a1c95b34384257e986842f4d006957b8',
+            url='https://github.com/zeromq/libzmq/releases/download/v4.2.5/zeromq-4.2.5.tar.gz')
+    version('4.2.2', '52499909b29604c1e47a86f1cb6a9115')
     version('4.1.4', 'a611ecc93fffeb6d058c0e6edf4ad4fb')
     version('4.1.2', '159c0c56a895472f02668e692d122685')
     version('4.1.1', '0a4b44aa085644f25c177f79dc13f253')
@@ -41,13 +24,17 @@ class Zeromq(AutotoolsPackage):
     version('4.0.6', 'd47dd09ed7ae6e7fd6f9a816d7f5fdf6')
     version('4.0.5', '73c39f5eb01b9d7eaf74a5d899f1d03d')
 
-    depends_on("libsodium")
-    depends_on("libsodium@:1.0.3", when='@:4.1.2')
+    variant("libsodium", default=True, description="Build with libsodium support")
+
+    depends_on("libsodium", when='+libsodium')
+    depends_on("libsodium@:1.0.3", when='+libsodium@:4.1.2')
 
     depends_on('autoconf', type='build', when='@develop')
     depends_on('automake', type='build', when='@develop')
     depends_on('libtool', type='build', when='@develop')
-    depends_on('pkg-config', type='build', when='@develop')
+    depends_on('pkgconfig', type='build')
+
+    conflicts('%gcc@8:', when='@:4.2.2')
 
     @when('@develop')
     def autoreconf(self, spec, prefix):
@@ -55,7 +42,9 @@ class Zeromq(AutotoolsPackage):
         bash('./autogen.sh')
 
     def configure_args(self):
-        config_args = ['--with-libsodium']
+        config_args = []
+        if '+libsodium' in self.spec:
+            config_args.append('--with-libsodium')
         if 'clang' in self.compiler.cc:
             config_args.append("CFLAGS=-Wno-gnu")
             config_args.append("CXXFLAGS=-Wno-gnu")
diff --git a/var/spack/repos/builtin/packages/zfp/package.py b/var/spack/repos/builtin/packages/zfp/package.py
index 704dc9dc72..447bbf4d2a 100644
--- a/var/spack/repos/builtin/packages/zfp/package.py
+++ b/var/spack/repos/builtin/packages/zfp/package.py
@@ -1,43 +1,21 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
 class Zfp(MakefilePackage):
-    """zfp is an open source C library for compressed floating-point arrays
-       that supports very high throughput read and write random acces,
-       target error bounds or bit rates.  Although bit-for-bit lossless
-       compression is not always possible, zfp is usually accurate to
-       within machine epsilon in near-lossless mode, and is often orders
-       of magnitude more accurate than other lossy compressors. Versions
-       of zfp 0.5.1 or newer also support compression of integer data.
+    """zfp is an open source C/C++ library for high-fidelity, high-throughput
+       lossy compression of floating-point and integer multi-dimensional
+       arrays.
     """
 
     homepage = 'http://computation.llnl.gov/projects/floating-point-compression'
-    url      = 'http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.1.tar.gz'
+    url      = 'http://computation.llnl.gov/projects/floating-point-compression/download/zfp-0.5.2.tar.gz'
 
+    version('0.5.2', '2f0a77aa34087219a6e10b8b7d031e77')
     version('0.5.1', '0ed7059a9b480635e0dd33745e213d17')
     version('0.5.0', '2ab29a852e65ad85aae38925c5003654')
 
diff --git a/var/spack/repos/builtin/packages/zip/package.py b/var/spack/repos/builtin/packages/zip/package.py
index 255f254dee..139e503c87 100644
--- a/var/spack/repos/builtin/packages/zip/package.py
+++ b/var/spack/repos/builtin/packages/zip/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
diff --git a/var/spack/repos/builtin/packages/zlib/package.py b/var/spack/repos/builtin/packages/zlib/package.py
index 4898bf2b77..eb34730906 100644
--- a/var/spack/repos/builtin/packages/zlib/package.py
+++ b/var/spack/repos/builtin/packages/zlib/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -54,7 +35,7 @@ class Zlib(Package):
     def libs(self):
         shared = '+shared' in self.spec
         return find_libraries(
-            ['libz'], root=self.prefix, recurse=True, shared=shared
+            ['libz'], root=self.prefix, recursive=True, shared=shared
         )
 
     def setup_environment(self, spack_env, run_env):
diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py
index eb393d3990..3fd29e17c3 100644
--- a/var/spack/repos/builtin/packages/zoltan/package.py
+++ b/var/spack/repos/builtin/packages/zoltan/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 
 from spack import *
 import re
@@ -33,7 +14,7 @@ class Zoltan(Package):
     """The Zoltan library is a toolkit of parallel combinatorial algorithms
        for parallel, unstructured, and/or adaptive scientific
        applications.  Zoltan's largest component is a suite of dynamic
-       load-balancing and paritioning algorithms that increase
+       load-balancing and partitioning algorithms that increase
        applications' parallel performance by reducing idle time.  Zoltan
        also has graph coloring and graph ordering algorithms, which are
        useful in task schedulers and parallel preconditioners.
@@ -53,9 +34,15 @@ class Zoltan(Package):
 
     variant('fortran', default=True, description='Enable Fortran support.')
     variant('mpi', default=True, description='Enable MPI support.')
+    variant('parmetis', default=False, description='Enable ParMETIS support.')
 
     depends_on('mpi', when='+mpi')
 
+    depends_on('parmetis@4:', when='+parmetis')
+    depends_on('metis', when='+parmetis')
+
+    conflicts('+parmetis', when='~mpi')
+
     def install(self, spec, prefix):
         # FIXME: The older Zoltan versions fail to compile the F90 MPI wrappers
         # because of some complicated generic type problem.
@@ -70,7 +57,7 @@ class Zoltan(Package):
         ]
         config_cflags = [
             '-O0' if '+debug' in spec else '-O3',
-            '-g' if '+debug' in spec else '-g0',
+            '-g' if '+debug' in spec else '',
         ]
 
         if '+shared' in spec:
@@ -78,7 +65,20 @@ class Zoltan(Package):
             config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o')
             config_cflags.append(self.compiler.pic_flag)
             if spec.satisfies('%gcc'):
-                config_args.append('--with-libs={0}'.format('-lgfortran'))
+                config_args.append('--with-libs=-lgfortran')
+            if spec.satisfies('%intel'):
+                config_args.append('--with-libs=-lifcore')
+
+        if '+parmetis' in spec:
+            config_args.append('--with-parmetis')
+            config_args.append('--with-parmetis-libdir={0}'
+                               .format(spec['parmetis'].prefix.lib))
+            config_args.append('--with-parmetis-incdir={0}'
+                               .format(spec['parmetis'].prefix.include))
+            config_args.append('--with-incdirs=-I{0}'
+                               .format(spec['metis'].prefix.include))
+            config_args.append('--with-ldflags=-L{0}'
+                               .format(spec['metis'].prefix.lib))
 
         if '+mpi' in spec:
             config_args.append('CC={0}'.format(spec['mpi'].mpicc))
diff --git a/var/spack/repos/builtin/packages/zsh/package.py b/var/spack/repos/builtin/packages/zsh/package.py
index 53b3c7d536..b03eb1f74e 100644
--- a/var/spack/repos/builtin/packages/zsh/package.py
+++ b/var/spack/repos/builtin/packages/zsh/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -32,10 +13,11 @@ class Zsh(AutotoolsPackage):
     """
 
     homepage = "http://www.zsh.org"
-    url = "http://downloads.sourceforge.net/project/zsh/zsh/5.1.1/zsh-5.1.1.tar.gz"
+    url = "http://downloads.sourceforge.net/project/zsh/zsh/5.4.2/zsh-5.4.2.tar.gz"
 
-    version('5.3.1', checksum='d583fbca0c2410bf9542ce8a651c26ca')
-    version('5.1.1', checksum='8ba28a9ef82e40c3a271602f18343b2f')
+    version('5.4.2', sha256='957bcdb2c57f64c02f673693ea5a7518ef24b6557aeb3a4ce222cefa6d74acc9')
+    version('5.3.1', sha256='3d94a590ff3c562ecf387da78ac356d6bea79b050a9ef81e3ecb9f8ee513040e')
+    version('5.1.1', sha256='94ed5b412023761bc8d2f03c173f13d625e06e5d6f0dff2c7a6e140c3fa55087')
 
     # Testing for terminal related things causes failures in e.g. Jenkins.
     # See e.g. https://www.zsh.org/mla/users/2003/msg00845.html,
diff --git a/var/spack/repos/builtin/packages/zstd/package.py b/var/spack/repos/builtin/packages/zstd/package.py
index 9387311fbb..1382aebb72 100644
--- a/var/spack/repos/builtin/packages/zstd/package.py
+++ b/var/spack/repos/builtin/packages/zstd/package.py
@@ -1,27 +1,8 @@
-##############################################################################
-# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
-# Produced at the Lawrence Livermore National Laboratory.
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
 #
-# 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/spack/spack
-# Please also see the NOTICE and LICENSE files 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
-##############################################################################
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
 from spack import *
 
 
@@ -36,5 +17,11 @@ class Zstd(MakefilePackage):
     version('1.3.0', '888660a850e33c2dcc7c4f9d0b04d347')
     version('1.1.2', '4c57a080d194bdaac83f2d3251fc7ffc')
 
+    variant('pic', default=True, description='Build position independent code')
+
+    def setup_environment(self, spack_env, run_env):
+        if '+pic' in self.spec:
+            spack_env.append_flags('CFLAGS', self.compiler.pic_flag)
+
     def install(self, spec, prefix):
         make('install', 'PREFIX={0}'.format(prefix))
diff --git a/var/spack/repos/tutorial/packages/armadillo/package.py b/var/spack/repos/tutorial/packages/armadillo/package.py
new file mode 100644
index 0000000000..d95a61f67d
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/armadillo/package.py
@@ -0,0 +1,62 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Armadillo(CMakePackage):
+    """Armadillo is a high quality linear algebra library (matrix maths)
+    for the C++ language, aiming towards a good balance between speed and
+    ease of use.
+    """
+
+    homepage = "http://arma.sourceforge.net/"
+    url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
+
+    version('8.100.1', 'd9762d6f097e0451d0cfadfbda295e7c')
+    version('7.950.1', 'c06eb38b12cae49cab0ce05f96147147')
+    version('7.900.1', '5ef71763bd429a3d481499878351f3be')
+    version('7.500.0', '7d316fdf3c3c7ea92b64704180ae315d')
+    version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2')
+    version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e')
+
+    variant('hdf5', default=False, description='Include HDF5 support')
+
+    depends_on('cmake@2.8.12:', type='build')
+    depends_on('arpack-ng')  # old arpack causes undefined symbols
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('superlu@5.2:')
+    depends_on('hdf5', when='+hdf5')
+
+    patch('undef_linux.patch', when='platform=linux')
+
+    def cmake_args(self):
+        spec = self.spec
+
+        # TUTORIAL: fix the lines below by adding the appropriate query to
+        # the right dependency. To ask a dependency, e.g. `blas`, for the
+        # list of libraries it provides it suffices to access its `libs`
+        # attribute:
+        #
+        #    blas_libs = spec['blas'].libs
+        #
+        # The CMake variables below require a semicolon separated list:
+        #
+        #    blas_libs.joined(';')
+
+        return [
+            # ARPACK support
+            '-DARPACK_LIBRARY={0}'.format('FIXME: arpack-ng'),
+            # BLAS support
+            '-DBLAS_LIBRARY={0}'.format('FIXME: blas'),
+            # LAPACK support
+            '-DLAPACK_LIBRARY={0}'.format('FIXME: lapack'),
+            # SuperLU support
+            '-DSuperLU_INCLUDE_DIR={0}'.format(spec['superlu'].prefix.include),
+            '-DSuperLU_LIBRARY={0}'.format('FIXME: superlu'),
+            # HDF5 support
+            '-DDETECT_HDF5={0}'.format('ON' if '+hdf5' in spec else 'OFF')
+        ]
diff --git a/var/spack/repos/tutorial/packages/armadillo/undef_linux.patch b/var/spack/repos/tutorial/packages/armadillo/undef_linux.patch
new file mode 100644
index 0000000000..68b434dca8
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/armadillo/undef_linux.patch
@@ -0,0 +1,4 @@
+--- a/include/armadillo_bits/compiler_setup.hpp
++++ b/include/armadillo_bits/compiler_setup.hpp
+@@ -0,0 +1 @@
++#undef linux
diff --git a/var/spack/repos/tutorial/packages/elpa/package.py b/var/spack/repos/tutorial/packages/elpa/package.py
new file mode 100644
index 0000000000..386295eea9
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/elpa/package.py
@@ -0,0 +1,78 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class Elpa(AutotoolsPackage):
+    """Eigenvalue solvers for Petaflop-Applications (ELPA)"""
+
+    homepage = 'http://elpa.mpcdf.mpg.de/'
+    url = 'http://elpa.mpcdf.mpg.de/elpa-2015.11.001.tar.gz'
+
+    version('2018.05.001.rc1', 'ccd77bd8036988ee624f43c04992bcdd')
+    version('2017.11.001', '4a437be40cc966efb07aaab84c20cd6e', preferred=True)
+    version('2017.05.003', '7c8e5e58cafab212badaf4216695700f')
+    version('2017.05.002', 'd0abc1ac1f493f93bf5e30ec8ab155dc')
+    version('2016.11.001.pre', '5656fd066cf0dcd071dbcaf20a639b37')
+    version('2016.05.004', 'c0dd3a53055536fc3a2a221e78d8b376')
+    version('2016.05.003', '88a9f3f3bfb63e16509dd1be089dcf2c')
+    version('2015.11.001', 'de0f35b7ee7c971fd0dca35c900b87e6')
+
+    variant('openmp', default=False, description='Activates OpenMP support')
+    variant('optflags', default=True, description='Build with optimization flags')
+
+    depends_on('mpi')
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('scalapack')
+
+    def url_for_version(self, version):
+        t = 'http://elpa.mpcdf.mpg.de/html/Releases/{0}/elpa-{0}.tar.gz'
+        if version < Version('2016.05.003'):
+            t = 'http://elpa.mpcdf.mpg.de/elpa-{0}.tar.gz'
+        return t.format(str(version))
+
+    @property
+    def libs(self):
+        libname = 'libelpa_openmp' if '+openmp' in self.spec else 'libelpa'
+        return find_libraries(
+            libname, root=self.prefix, shared=True, recursive=True
+        )
+
+    build_directory = 'spack-build'
+
+    def setup_environment(self, spack_env, run_env):
+        # TUTORIAL: set the following environment variables:
+        #
+        # CC=spec['mpi'].mpicc
+        # FC=spec['mpi'].mpifc
+        # CXX=spec['mpi'].mpicxx
+        # SCALAPACK_LDFLAGS=spec['scalapack'].libs.joined()
+        #
+        # and append the following flags:
+        #
+        # LDFLAGS -> spec['lapack'].libs.search_flags
+        # LIBS -> spec['lapack'].libs.link_flags
+        pass
+
+    def configure_args(self):
+        # TODO: set optimum flags for platform+compiler combo, see
+        # https://github.com/hfp/xconfigure/tree/master/elpa
+        # also see:
+        # https://src.fedoraproject.org/cgit/rpms/elpa.git/
+        # https://packages.qa.debian.org/e/elpa.html
+        options = []
+        # without -march=native there is configure error for 2017.05.02
+        # Could not compile test program, try with --disable-sse, or
+        # adjust the C compiler or CFLAGS
+        if '+optflags' in self.spec:
+            options.extend([
+                'FCFLAGS=-O2 -march=native -ffree-line-length-none',
+                'CFLAGS=-O2 -march=native'
+            ])
+        if '+openmp' in self.spec:
+            options.append('--enable-openmp')
+        return options
diff --git a/var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch b/var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch
new file mode 100644
index 0000000000..8bf5c142e9
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/hdf5/h5f90global-mult-obj-same-equivalence-same-common-block.patch
@@ -0,0 +1,16 @@
+diff --git a/fortran/src/H5f90global.F90 b/fortran/src/H5f90global.F90
+index dd2b171..629418a 100644
+--- a/fortran/src/H5f90global.F90
++++ b/fortran/src/H5f90global.F90
+@@ -142,10 +142,7 @@ MODULE H5GLOBAL
+
+   INTEGER(HID_T), DIMENSION(PREDEF_TYPES_LEN) :: predef_types
+   EQUIVALENCE (predef_types(1), H5T_NATIVE_INTEGER_KIND(1))
+-  EQUIVALENCE (predef_types(2), H5T_NATIVE_INTEGER_KIND(2))
+-  EQUIVALENCE (predef_types(3), H5T_NATIVE_INTEGER_KIND(3))
+-  EQUIVALENCE (predef_types(4), H5T_NATIVE_INTEGER_KIND(4))
+-  EQUIVALENCE (predef_types(5), H5T_NATIVE_INTEGER_KIND(5))
++  ! EQUIVALENCE predef_types(2:5) are unnecessary and violate the standard
+   EQUIVALENCE (predef_types(6), H5T_NATIVE_INTEGER)
+   EQUIVALENCE (predef_types(7), H5T_NATIVE_REAL)
+   EQUIVALENCE (predef_types(8), H5T_NATIVE_DOUBLE)
diff --git a/var/spack/repos/tutorial/packages/hdf5/package.py b/var/spack/repos/tutorial/packages/hdf5/package.py
new file mode 100644
index 0000000000..b879d81f1c
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/hdf5/package.py
@@ -0,0 +1,307 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import shutil
+import sys
+
+from spack import *
+
+
+class Hdf5(AutotoolsPackage):
+    """HDF5 is a data model, library, and file format for storing and managing
+    data. It supports an unlimited variety of datatypes, and is designed for
+    flexible and efficient I/O and for high volume and complex data.
+    """
+
+    homepage = "https://support.hdfgroup.org/HDF5/"
+    url      = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz"
+    list_url = "https://support.hdfgroup.org/ftp/HDF5/releases"
+    list_depth = 3
+
+    version('1.10.4', '8f60dc4dd6ab5fcd23c750d1dc5bca3d0453bdce5c8cdaf0a4a61a9d1122adb2')
+    version('1.10.3', 'b600d7c914cfa80ae127cd1a1539981213fee9994ac22ebec9e3845e951d9b39')
+    version('1.10.2', '8d4eae84e533efa57496638fd0dca8c3')
+    version('1.10.1', '43a2f9466702fb1db31df98ae6677f15')
+    version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295')
+    version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
+    version('1.8.19', '7f568e2464d4ab0a74d16b23956d900b')
+    version('1.8.18', 'dd2148b740713ca0295442ec683d7b1c')
+    version('1.8.17', '7d572f8f3b798a628b8245af0391a0ca')
+    version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
+    version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
+    version('1.8.14', 'a482686e733514a51cde12d6fe5c5d95')
+    version('1.8.13', 'c03426e9e77d7766944654280b467289')
+    version('1.8.12', 'd804802feb99b87fc668a90e6fa34411')
+    version('1.8.10', '710aa9fb61a51d61a7e2c09bf0052157')
+
+    variant('debug', default=False,
+            description='Builds a debug version of the library')
+    variant('shared', default=True,
+            description='Builds a shared version of the library')
+
+    variant('hl', default=False, description='Enable the high-level library')
+    variant('cxx', default=False, description='Enable C++ support')
+    variant('fortran', default=False, description='Enable Fortran support')
+    variant('threadsafe', default=False,
+            description='Enable thread-safe capabilities')
+
+    variant('mpi', default=True, description='Enable MPI support')
+    variant('szip', default=False, description='Enable szip support')
+    variant('pic', default=True,
+            description='Produce position-independent code (for shared libs)')
+
+    depends_on('mpi', when='+mpi')
+    # numactl does not currently build on darwin
+    if sys.platform != 'darwin':
+        depends_on('numactl', when='+mpi+fortran')
+    depends_on('szip', when='+szip')
+    depends_on('zlib@1.1.2:')
+
+    # There are several officially unsupported combinations of the features:
+    # 1. Thread safety is not guaranteed via high-level C-API but in some cases
+    #    it works.
+    # conflicts('+threadsafe+hl')
+
+    # 2. Thread safety is not guaranteed via Fortran (CXX) API, but it's
+    #    possible for a dependency tree to contain a package that uses Fortran
+    #    (CXX) API in a single thread and another one that uses low-level C-API
+    #    in multiple threads. To allow for such scenarios, we don't specify the
+    #    following conflicts.
+    # conflicts('+threadsafe+cxx')
+    # conflicts('+threadsafe+fortran')
+
+    # 3. Parallel features are not supported via CXX API, but for the reasons
+    #    described in #2 we allow for such combination.
+    # conflicts('+mpi+cxx')
+
+    # There are known build failures with intel@18.0.1. This issue is
+    # discussed and patch is provided at
+    # https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
+    patch('h5f90global-mult-obj-same-equivalence-same-common-block.patch',
+          when='@1.10.1%intel@18')
+
+    # Turn line comments into block comments to conform with pre-C99 language
+    # standards. Versions of hdf5 after 1.8.10 don't require this patch,
+    # either because they conform to pre-C99 or neglect to ask for pre-C99
+    # language standards from their compiler. The hdf5 build system adds
+    # the -ansi cflag (run 'man gcc' for info on -ansi) for some versions
+    # of some compilers (see hdf5-1.8.10/config/gnu-flags). The hdf5 build
+    # system does not provide an option to disable -ansi, but since the
+    # pre-C99 code is restricted to just five lines of line comments in
+    # three src files, this patch accomplishes the simple task of patching the
+    # three src files and leaves the hdf5 build system alone.
+    patch('pre-c99-comments.patch', when='@1.8.10')
+
+    # There are build errors with GCC 8, see
+    # https://forum.hdfgroup.org/t/1-10-2-h5detect-compile-error-gcc-8-1-0-on-centos-7-2-solved/4441
+    patch('https://salsa.debian.org/debian-gis-team/hdf5/raw/bf94804af5f80f662cad80a5527535b3c6537df6/debian/patches/gcc-8.patch', sha256='57cee5ff1992b4098eda079815c36fc2da9b10e00a9056df054f2384c4fc7523', when='@1.10.2%gcc@8:')
+
+    filter_compiler_wrappers('h5cc', 'h5c++', 'h5fc', relative_root='bin')
+
+    def url_for_version(self, version):
+        url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-{0}/hdf5-{1}/src/hdf5-{1}.tar.gz"
+        return url.format(version.up_to(2), version)
+
+    @property
+    def libs(self):
+        """HDF5 can be queried for the following parameters:
+
+        - "hl": high-level interface
+        - "cxx": C++ APIs
+        - "fortran": Fortran APIs
+
+        :return: list of matching libraries
+        """
+        # This map contains a translation from query_parameters
+        # to the libraries needed
+        query2libraries = {  # noqa: F841
+            tuple(): ['libhdf5'],
+            ('cxx', 'fortran', 'hl'): [
+                'libhdf5hl_fortran',
+                'libhdf5_hl_cpp',
+                'libhdf5_hl',
+                'libhdf5_fortran',
+                'libhdf5',
+            ],
+            ('cxx', 'hl'): [
+                'libhdf5_hl_cpp',
+                'libhdf5_hl',
+                'libhdf5',
+            ],
+            ('fortran', 'hl'): [
+                'libhdf5hl_fortran',
+                'libhdf5_hl',
+                'libhdf5_fortran',
+                'libhdf5',
+            ],
+            ('hl',): [
+                'libhdf5_hl',
+                'libhdf5',
+            ],
+            ('cxx', 'fortran'): [
+                'libhdf5_fortran',
+                'libhdf5_cpp',
+                'libhdf5',
+            ],
+            ('cxx',): [
+                'libhdf5_cpp',
+                'libhdf5',
+            ],
+            ('fortran',): [
+                'libhdf5_fortran',
+                'libhdf5',
+            ]
+        }
+
+        # TUTORIAL: you need to fix the implementation below, and
+        # return the correct list of libraries according to the
+        # query parameters your dependency has used.
+        #
+        # You can retrieve the query parameters by doing
+        #
+        # query_parameters = self.spec.last_query.extra_parameters
+        #
+        # and use the map above to query the list of libraries you need
+        # to search.
+        #
+        # Finally uncomment the lines below to return a LibraryList
+        #
+        # shared = '+shared' in self.spec
+        # return find_libraries(
+        #     libraries, root=self.prefix, shared=shared, recursive=True
+        # )
+        return []
+
+    @run_before('configure')
+    def fortran_check(self):
+        if '+fortran' in self.spec and not self.compiler.fc:
+            msg = 'cannot build a Fortran variant without a Fortran compiler'
+            raise RuntimeError(msg)
+
+    def configure_args(self):
+        # Always enable this option. This does not actually enable any
+        # features: it only *allows* the user to specify certain
+        # combinations of other arguments. Enabling it just skips a
+        # sanity check in configure, so this doesn't merit a variant.
+        extra_args = ['--enable-unsupported']
+        extra_args += self.enable_or_disable('threadsafe')
+        extra_args += self.enable_or_disable('cxx')
+        extra_args += self.enable_or_disable('hl')
+        extra_args += self.enable_or_disable('fortran')
+
+        if '+szip' in self.spec:
+            extra_args.append('--with-szlib=%s' % self.spec['szip'].prefix)
+        else:
+            extra_args.append('--without-szlib')
+
+        if self.spec.satisfies('@1.10:'):
+            if '+debug' in self.spec:
+                extra_args.append('--enable-build-mode=debug')
+            else:
+                extra_args.append('--enable-build-mode=production')
+        else:
+            if '+debug' in self.spec:
+                extra_args.append('--enable-debug=all')
+            else:
+                extra_args.append('--enable-production')
+
+            # '--enable-fortran2003' no longer exists as of version 1.10.0
+            if '+fortran' in self.spec:
+                extra_args.append('--enable-fortran2003')
+            else:
+                extra_args.append('--disable-fortran2003')
+
+        if '+shared' in self.spec:
+            extra_args.append('--enable-shared')
+        else:
+            extra_args.append('--disable-shared')
+            extra_args.append('--enable-static-exec')
+
+        if '+pic' in self.spec:
+            extra_args += ['%s=%s' % (f, self.compiler.pic_flag)
+                           for f in ['CFLAGS', 'CXXFLAGS', 'FCFLAGS']]
+
+        if '+mpi' in self.spec:
+            # The HDF5 configure script warns if cxx and mpi are enabled
+            # together. There doesn't seem to be a real reason for this, except
+            # that parts of the MPI interface are not accessible via the C++
+            # interface. Since they are still accessible via the C interface,
+            # this is not actually a problem.
+            extra_args += ['--enable-parallel',
+                           'CC=%s' % self.spec['mpi'].mpicc]
+
+            if '+cxx' in self.spec:
+                extra_args.append('CXX=%s' % self.spec['mpi'].mpicxx)
+
+            if '+fortran' in self.spec:
+                extra_args.append('FC=%s' % self.spec['mpi'].mpifc)
+
+        extra_args.append('--with-zlib=%s' % self.spec['zlib'].prefix)
+
+        return extra_args
+
+    @run_after('configure')
+    def patch_postdeps(self):
+        if '@:1.8.14' in self.spec:
+            # On Ubuntu14, HDF5 1.8.12 (and maybe other versions)
+            # mysteriously end up with "-l -l" in the postdeps in the
+            # libtool script.  Patch this by removing the spurious -l's.
+            filter_file(
+                r'postdeps="([^"]*)"',
+                lambda m: 'postdeps="%s"' % ' '.join(
+                    arg for arg in m.group(1).split(' ') if arg != '-l'),
+                'libtool')
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def check_install(self):
+        # Build and run a small program to test the installed HDF5 library
+        spec = self.spec
+        print("Checking HDF5 installation...")
+        checkdir = "spack-check"
+        with working_dir(checkdir, create=True):
+            source = r"""
+#include <hdf5.h>
+#include <assert.h>
+#include <stdio.h>
+int main(int argc, char **argv) {
+  unsigned majnum, minnum, relnum;
+  herr_t herr = H5get_libversion(&majnum, &minnum, &relnum);
+  assert(!herr);
+  printf("HDF5 version %d.%d.%d %u.%u.%u\n", H5_VERS_MAJOR, H5_VERS_MINOR,
+         H5_VERS_RELEASE, majnum, minnum, relnum);
+  return 0;
+}
+"""
+            expected = """\
+HDF5 version {version} {version}
+""".format(version=str(spec.version.up_to(3)))
+            with open("check.c", 'w') as f:
+                f.write(source)
+            if '+mpi' in spec:
+                cc = Executable(spec['mpi'].mpicc)
+            else:
+                cc = Executable(self.compiler.cc)
+            cc(*(['-c', "check.c"] + spec['hdf5'].headers.cpp_flags.split()))
+            cc(*(['-o', "check",
+                  "check.o"] + spec['hdf5'].libs.ld_flags.split()))
+            try:
+                check = Executable('./check')
+                output = check(output=str)
+            except ProcessError:
+                output = ""
+            success = output == expected
+            if not success:
+                print("Produced output does not match expected output.")
+                print("Expected output:")
+                print('-' * 80)
+                print(expected)
+                print('-' * 80)
+                print("Produced output:")
+                print('-' * 80)
+                print(output)
+                print('-' * 80)
+                raise RuntimeError("HDF5 install check failed")
+        shutil.rmtree(checkdir)
diff --git a/var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch b/var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch
new file mode 100644
index 0000000000..97743e8fa5
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/hdf5/pre-c99-comments.patch
@@ -0,0 +1,43 @@
+diff --git a/test/th5s.c b/test/th5s.c
+index 462bc36..8e18fad 100644
+--- a/test/th5s.c
++++ b/test/th5s.c
+@@ -730,8 +730,8 @@ test_h5s_zero_dim(void)
+         ret = H5Pset_chunk(plist_id, SPACE1_RANK, chunk_dims);
+         CHECK(ret, FAIL, "H5Pset_chunk");
+ 
+-        // ret = H5Pset_alloc_time(plist_id, alloc_time);
+-        // CHECK(ret, FAIL, "H5Pset_alloc_time");
++        /* ret = H5Pset_alloc_time(plist_id, alloc_time); */
++        /* CHECK(ret, FAIL, "H5Pset_alloc_time"); */
+ 
+         dset1 = H5Dcreate2(fid1, BASICDATASET1, H5T_NATIVE_INT, sid_chunk, H5P_DEFAULT, plist_id, H5P_DEFAULT);
+         CHECK(dset1, FAIL, "H5Dcreate2");
+diff --git a/tools/h5dump/h5dump_ddl.c b/tools/h5dump/h5dump_ddl.c
+index ee6de5e..3ed6045 100644
+--- a/tools/h5dump/h5dump_ddl.c
++++ b/tools/h5dump/h5dump_ddl.c
+@@ -1341,8 +1341,8 @@ handle_attributes(hid_t fid, const char *attr, void UNUSED * data, int UNUSED pe
+     string_dataformat.do_escape = display_escape;
+     outputformat = &string_dataformat;
+ 
+-    //attr_name = attr + j + 1;
+-	// need to replace escape characters
++    /* attr_name = attr + j + 1; */
++	/* need to replace escape characters */
+ 	attr_name = h5tools_str_replace(attr + j + 1, "\\/", "/");
+ 
+ 
+diff --git a/tools/lib/h5tools_str.c b/tools/lib/h5tools_str.c
+index 9ce3524..3b4e5e7 100644
+--- a/tools/lib/h5tools_str.c
++++ b/tools/lib/h5tools_str.c
+@@ -632,7 +632,7 @@ h5tools_str_indent(h5tools_str_t *str, const h5tool_format_t *info,
+         h5tools_str_append(str, "%s", OPT(info->line_indent, ""));
+     }
+ 
+-//    ctx->need_prefix = 0;
++/*    ctx->need_prefix = 0; */
+ }
+ 
+ /*-------------------------------------------------------------------------
diff --git a/var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch b/var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch
new file mode 100644
index 0000000000..01243072f7
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/mpich/mpich32_clang.patch
@@ -0,0 +1,13 @@
+diff --git a/src/include/mpiimpl.h b/src/include/mpiimpl.h
+index e705e5d..3bfcbee 100644
+--- a/src/include/mpiimpl.h
++++ b/src/include/mpiimpl.h
+@@ -1528,7 +1528,7 @@ typedef struct MPID_Request {
+ #ifdef MPID_DEV_REQUEST_DECL
+     MPID_DEV_REQUEST_DECL
+ #endif
+-} MPID_Request ATTRIBUTE((__aligned__(32)));
++} ATTRIBUTE((__aligned__(32))) MPID_Request;
+ 
+ extern MPIU_Object_alloc_t MPID_Request_mem;
+ /* Preallocated request objects */
diff --git a/var/spack/repos/tutorial/packages/mpich/package.py b/var/spack/repos/tutorial/packages/mpich/package.py
new file mode 100644
index 0000000000..c3e0b8a54b
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/mpich/package.py
@@ -0,0 +1,155 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+import os
+
+
+class Mpich(AutotoolsPackage):
+    """MPICH is a high performance and widely portable implementation of
+    the Message Passing Interface (MPI) standard."""
+
+    homepage = "http://www.mpich.org"
+    url      = "http://www.mpich.org/static/downloads/3.0.4/mpich-3.0.4.tar.gz"
+    git      = "https://github.com/pmodels/mpich.git"
+    list_url = "http://www.mpich.org/static/downloads/"
+    list_depth = 1
+
+    version('develop', submodules=True)
+    version('3.2.1', 'e175452f4d61646a52c73031683fc375')
+    version('3.2',   'f414cfa77099cd1fa1a5ae4e22db508a')
+    version('3.1.4', '2ab544607986486562e076b83937bba2')
+    version('3.1.3', '93cb17f91ac758cbf9174ecb03563778')
+    version('3.1.2', '7fbf4b81dcb74b07ae85939d1ceee7f1')
+    version('3.1.1', '40dc408b1e03cc36d80209baaa2d32b7')
+    version('3.1',   '5643dd176499bfb7d25079aaff25f2ec')
+    version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0')
+
+    variant('hydra', default=True,  description='Build the hydra process manager')
+    variant('pmi',   default=True,  description='Build with PMI support')
+    variant('romio', default=True,  description='Enable ROMIO MPI I/O implementation')
+    variant('verbs', default=False, description='Build support for OpenFabrics verbs.')
+    variant(
+        'device',
+        default='ch3',
+        description='''Abstract Device Interface (ADI)
+implementation. The ch4 device is currently in experimental state''',
+        values=('ch3', 'ch4'),
+        multi=False
+    )
+    variant(
+        'netmod',
+        default='tcp',
+        description='''Network module. Only single netmod builds are
+supported. For ch3 device configurations, this presumes the
+ch3:nemesis communication channel. ch3:sock is not supported by this
+spack package at this time.''',
+        values=('tcp', 'mxm', 'ofi', 'ucx'),
+        multi=False
+    )
+
+    provides('mpi')
+    provides('mpi@:3.0', when='@3:')
+    provides('mpi@:1.3', when='@1:')
+
+    filter_compiler_wrappers(
+        'mpicc', 'mpicxx', 'mpif77', 'mpif90', 'mpifort', relative_root='bin'
+    )
+
+    # fix MPI_Barrier segmentation fault
+    # see https://lists.mpich.org/pipermail/discuss/2016-May/004764.html
+    # and https://lists.mpich.org/pipermail/discuss/2016-June/004768.html
+    patch('mpich32_clang.patch', when='@3.2:3.2.0%clang')
+
+    depends_on('findutils', type='build')
+
+    depends_on('libfabric', when='netmod=ofi')
+
+    conflicts('device=ch4', when='@:3.2')
+    conflicts('netmod=ofi', when='@:3.1.4')
+    conflicts('netmod=ucx', when='device=ch3')
+    conflicts('netmod=mxm', when='device=ch4')
+    conflicts('netmod=mxm', when='@:3.1.3')
+    conflicts('netmod=tcp', when='device=ch4')
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        # TUTORIAL: set the following variables for dependents:
+        #
+        # MPICC=join_path(self.prefix.bin, 'mpicc')
+        # MPICXX=join_path(self.prefix.bin, 'mpic++')
+        # MPIF77=join_path(self.prefix.bin, 'mpif77')
+        # MPIF90=join_path(self.prefix.bin, 'mpif90')
+        # MPICH_CC=spack_cc
+        # MPICH_CXX=spack_cxx
+        # MPICH_F77=spack_f77
+        # MPICH_F90=spack_fc
+        # MPICH_FC=spack_fc
+        pass
+
+    def setup_dependent_package(self, module, dependent_spec):
+        if 'platform=cray' in self.spec:
+            self.spec.mpicc = spack_cc
+            self.spec.mpicxx = spack_cxx
+            self.spec.mpifc = spack_fc
+            self.spec.mpif77 = spack_f77
+        else:
+            self.spec.mpicc = join_path(self.prefix.bin, 'mpicc')
+            self.spec.mpicxx = join_path(self.prefix.bin, 'mpic++')
+            self.spec.mpifc = join_path(self.prefix.bin, 'mpif90')
+            self.spec.mpif77 = join_path(self.prefix.bin, 'mpif77')
+
+        self.spec.mpicxx_shared_libs = [
+            join_path(self.prefix.lib, 'libmpicxx.{0}'.format(dso_suffix)),
+            join_path(self.prefix.lib, 'libmpi.{0}'.format(dso_suffix))
+        ]
+
+    def autoreconf(self, spec, prefix):
+        """Not needed usually, configure should be already there"""
+        # If configure exists nothing needs to be done
+        if os.path.exists(self.configure_abs_path):
+            return
+        # Else bootstrap with autotools
+        bash = which('bash')
+        bash('./autogen.sh')
+
+    @run_before('autoreconf')
+    def die_without_fortran(self):
+        # Until we can pass variants such as +fortran through virtual
+        # dependencies depends_on('mpi'), require Fortran compiler to
+        # avoid delayed build errors in dependents.
+        if (self.compiler.f77 is None) or (self.compiler.fc is None):
+            raise InstallError(
+                'Mpich requires both C and Fortran compilers!'
+            )
+
+    def configure_args(self):
+        spec = self.spec
+        config_args = [
+            '--enable-shared',
+            '--with-pm={0}'.format('hydra' if '+hydra' in spec else 'no'),
+            '--with-pmi={0}'.format('yes' if '+pmi' in spec else 'no'),
+            '--{0}-romio'.format('enable' if '+romio' in spec else 'disable'),
+            '--{0}-ibverbs'.format('with' if '+verbs' in spec else 'without')
+        ]
+
+        # setup device configuration
+        device_config = ''
+        if 'device=ch4' in spec:
+            device_config = '--with-device=ch4:'
+        elif 'device=ch3' in spec:
+            device_config = '--with-device=ch3:nemesis:'
+
+        if 'netmod=ucx' in spec:
+            device_config += 'ucx'
+        elif 'netmod=ofi' in spec:
+            device_config += 'ofi'
+        elif 'netmod=mxm' in spec:
+            device_config += 'mxm'
+        elif 'netmod=tcp' in spec:
+            device_config += 'tcp'
+
+        config_args.append(device_config)
+
+        return config_args
diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/ibm-xl.patch b/var/spack/repos/tutorial/packages/netlib-lapack/ibm-xl.patch
new file mode 100644
index 0000000000..c6fba2a028
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/netlib-lapack/ibm-xl.patch
@@ -0,0 +1,42 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -62,7 +62,7 @@
+     set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fp-model strict")
+   endif()
+   if("${CMAKE_Fortran_COMPILER}" MATCHES "xlf")
+-    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict=none")
++    set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qnosave -qstrict")
+   endif()
+ # Delete libmtsk in linking sequence for Sun/Oracle Fortran Compiler.
+ # This library is not present in the Sun package SolarisStudio12.3-linux-x86-bin
+
+--- a/CMAKE/CheckLAPACKCompilerFlags.cmake
++++ b/CMAKE/CheckLAPACKCompilerFlags.cmake
+@@ -43,12 +43,6 @@
+   if( "${CMAKE_Fortran_FLAGS}" MATCHES "-qflttrap=[a-zA-Z:]:enable" )
+     set( FPE_EXIT TRUE )
+   endif()
+-
+-  if( NOT ("${CMAKE_Fortran_FLAGS}" MATCHES "-qfixed") )
+-    message( STATUS "Enabling fixed format F90/F95 with -qfixed" )
+-    set( CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -qfixed"
+-         CACHE STRING "Flags for Fortran compiler." FORCE )
+-  endif()
+ 
+ # HP Fortran
+ elseif( CMAKE_Fortran_COMPILER_ID STREQUAL "HP" )
+
+--- a/CBLAS/CMakeLists.txt
++++ b/CBLAS/CMakeLists.txt
+@@ -12,8 +12,8 @@
+                          SYMBOL_NAMESPACE "F77_")
+ if(NOT FortranCInterface_GLOBAL_FOUND OR NOT FortranCInterface_MODULE_FOUND)
+   message(WARNING "Reverting to pre-defined include/lapacke_mangling.h")
+-  configure_file(include/lapacke_mangling_with_flags.h.in
+-                 ${LAPACK_BINARY_DIR}/include/lapacke_mangling.h)
++  configure_file(include/cblas_mangling_with_flags.h.in
++                 ${LAPACK_BINARY_DIR}/include/cblas_mangling.h)
+ endif()
+ 
+ include_directories(include ${LAPACK_BINARY_DIR}/include)
+
diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/package.py b/var/spack/repos/tutorial/packages/netlib-lapack/package.py
new file mode 100644
index 0000000000..ef43b8a2e0
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/netlib-lapack/package.py
@@ -0,0 +1,186 @@
+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class NetlibLapack(CMakePackage):
+    """LAPACK version 3.X is a comprehensive FORTRAN library that does
+    linear algebra operations including matrix inversions, least squared
+    solutions to linear sets of equations, eigenvector analysis, singular
+    value decomposition, etc. It is a very comprehensive and reputable
+    package that has found extensive use in the scientific community.
+
+    """
+    homepage = "http://www.netlib.org/lapack/"
+    url = "http://www.netlib.org/lapack/lapack-3.5.0.tgz"
+
+    version('3.8.0', '96591affdbf58c450d45c1daa540dbd2',
+            url='http://www.netlib.org/lapack/lapack-3.8.0.tar.gz')
+    version('3.7.1', 'dcdeeed73de152c4643ccc5b1aeb453c')
+    version('3.7.0', '697bb8d67c7d336a0f339cc9dd0fa72f')
+    version('3.6.1', '421b2cb72e15f237e144428f9c460ee0')
+    version('3.6.0', 'f2f6c67134e851fe189bb3ca1fbb5101')
+    version('3.5.0', 'b1d3e3e425b2e44a06760ff173104bdf')
+    version('3.4.2', '61bf1a8a4469d4bdb7604f5897179478')
+    version('3.4.1', '44c3869c38c8335c2b9c2a8bb276eb55')
+    version('3.4.0', '02d5706ec03ba885fc246e5fa10d8c70')
+    version('3.3.1', 'd0d533ec9a5b74933c2a1e84eedc58b4')
+
+    variant('shared', default=True, description="Build shared library version")
+    variant('external-blas', default=False,
+            description='Build lapack with an external blas')
+
+    variant('lapacke', default=True,
+            description='Activates the build of the LAPACKE C interface')
+    variant('xblas', default=False,
+            description='Builds extended precision routines using XBLAS')
+
+    patch('ibm-xl.patch', when='@3.7: %xl')
+    patch('ibm-xl.patch', when='@3.7: %xl_r')
+
+    # https://github.com/Reference-LAPACK/lapack/issues/228
+    # TODO: update 'when' once the version of lapack
+    # containing the fix is released and added to Spack.
+    patch('undefined_declarations.patch', when='@3.8.0:')
+
+    # https://github.com/Reference-LAPACK/lapack/pull/268
+    # TODO: update 'when' once the version of lapack
+    # containing the fix is released and added to Spack.
+    patch('testing.patch', when='@3.7.0:')
+
+    # virtual dependency
+    provides('blas', when='~external-blas')
+    provides('lapack')
+
+    depends_on('blas', when='+external-blas')
+    depends_on('netlib-xblas+fortran+plain_blas', when='+xblas')
+    depends_on('python@2.7:', type='test')
+
+    # We need to run every phase twice in order to get static and shared
+    # versions of the libraries. When ~shared, we run the default
+    # implementations of the CMakePackage's phases and get only one building
+    # directory 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF (see
+    # implementations of self.build_directory and self.cmake_args() below).
+    # When +shared, we run the overridden methods for the phases, each
+    # running the default implementation twice with different values for
+    # self._building_shared. As a result, we get two building directories:
+    # 'spack-build-static' with -DBUILD_SHARED_LIBS:BOOL=OFF and
+    # 'spack-build-shared' with -DBUILD_SHARED_LIBS:BOOL=ON.
+    _building_shared = False
+
+    def patch(self):
+        # Fix cblas CMakeLists.txt -- has wrong case for subdirectory name.
+        if self.spec.satisfies('@3.6.0:'):
+            filter_file(
+                '${CMAKE_CURRENT_SOURCE_DIR}/CMAKE/',
+                '${CMAKE_CURRENT_SOURCE_DIR}/cmake/',
+                'CBLAS/CMakeLists.txt', string=True)
+
+    @property
+    def blas_libs(self):
+        shared = True if '+shared' in self.spec else False
+        query_parameters = self.spec.last_query.extra_parameters
+        query2libraries = {
+            tuple(): ['libblas'],
+            ('c', 'fortran'): [
+                'libcblas',
+                'libblas',
+            ],
+            ('c',): [
+                'libcblas',
+            ],
+            ('fortran',): [
+                'libblas',
+            ]
+        }
+        key = tuple(sorted(query_parameters))
+        libraries = query2libraries[key]
+        return find_libraries(
+            libraries, root=self.prefix, shared=shared, recursive=True
+        )
+
+    # TUTORIAL: add a proper `lapack_lib` property, along the lines
+    # of the `blas_lib` property above. The library that provides
+    # the lapack API is called `liblapack`.
+
+    @property
+    def headers(self):
+        include_dir = self.spec.prefix.include
+        cblas_h = join_path(include_dir, 'cblas.h')
+        lapacke_h = join_path(include_dir, 'lapacke.h')
+        return HeaderList([cblas_h, lapacke_h])
+
+    @property
+    def build_directory(self):
+        return join_path(self.stage.source_path,
+                         'spack-build-shared' if self._building_shared
+                         else 'spack-build-static')
+
+    def cmake_args(self):
+        args = ['-DBUILD_SHARED_LIBS:BOOL=' +
+                ('ON' if self._building_shared else 'OFF')]
+
+        if self.spec.satisfies('+lapacke'):
+            args.extend(['-DLAPACKE:BOOL=ON', '-DLAPACKE_WITH_TMG:BOOL=ON'])
+        else:
+            args.extend(['-DLAPACKE:BOOL=OFF', '-DLAPACKE_WITH_TMG:BOOL=OFF'])
+
+        if self.spec.satisfies('@3.6.0:'):
+            args.append('-DCBLAS=ON')  # always build CBLAS
+
+        if self.spec.satisfies('%intel'):
+            # Intel compiler finds serious syntax issues when trying to
+            # build CBLAS and LapackE
+            args.extend(['-DCBLAS=OFF', '-DLAPACKE:BOOL=OFF'])
+
+        if self.spec.satisfies('%xl') or self.spec.satisfies('%xl_r'):
+            # use F77 compiler if IBM XL
+            args.extend(['-DCMAKE_Fortran_COMPILER=' + self.compiler.f77,
+                         '-DCMAKE_Fortran_FLAGS=' +
+                         (' '.join(self.spec.compiler_flags['fflags'])) +
+                         " -O3 -qnohot"])
+
+        # deprecated routines are commonly needed by, for example, suitesparse
+        # Note that OpenBLAS spack is built with deprecated routines
+        args.append('-DBUILD_DEPRECATED:BOOL=ON')
+
+        if self.spec.satisfies('+external-blas'):
+            args.extend(['-DUSE_OPTIMIZED_BLAS:BOOL=ON',
+                         '-DBLAS_LIBRARIES:PATH=' +
+                         self.spec['blas'].libs.joined(';')])
+
+        if self.spec.satisfies('+xblas'):
+            args.extend(['-DXBLAS_INCLUDE_DIR=' +
+                         self.spec['netlib-xblas'].prefix.include,
+                         '-DXBLAS_LIBRARY=' +
+                         self.spec['netlib-xblas'].libs.joined(';')])
+
+        args.append('-DBUILD_TESTING:BOOL=' +
+                    ('ON' if self.run_tests else 'OFF'))
+
+        return args
+
+    # Build, install, and check both static and shared versions of the
+    # libraries when +shared
+    @when('+shared')
+    def cmake(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).cmake(spec, prefix)
+
+    @when('+shared')
+    def build(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).build(spec, prefix)
+
+    @when('+shared')
+    def install(self, spec, prefix):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).install(spec, prefix)
+
+    @when('+shared')
+    def check(self):
+        for self._building_shared in (False, True):
+            super(NetlibLapack, self).check()
diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/testing.patch b/var/spack/repos/tutorial/packages/netlib-lapack/testing.patch
new file mode 100644
index 0000000000..fce18548c4
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/netlib-lapack/testing.patch
@@ -0,0 +1,13 @@
+diff --git a/TESTING/LIN/alahd.f b/TESTING/LIN/alahd.f
+index 8f4cd58d..6a4946e0 100644
+--- a/TESTING/LIN/alahd.f
++++ b/TESTING/LIN/alahd.f
+@@ -1036,7 +1036,7 @@
+  9929 FORMAT( ' Test ratios (1-3: ', A1, 'TZRZF):' )
+  9920 FORMAT( 3X, ' 7-10: same as 3-6', 3X, ' 11-14: same as 3-6' )
+  9921 FORMAT( ' Test ratios:', / '    (1-2: ', A1, 'GELS, 3-6: ', A1,
+-     $      'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: '
++     $      'GELSY, 7-10: ', A1, 'GELSS, 11-14: ', A1, 'GELSD, 15-16: ',
+      $        A1, 'GETSLS)')
+  9928 FORMAT( 7X, 'where ALPHA = ( 1 + SQRT( 17 ) ) / 8' )
+  9927 FORMAT( 3X, I2, ': ABS( Largest element in L )', / 12X,
diff --git a/var/spack/repos/tutorial/packages/netlib-lapack/undefined_declarations.patch b/var/spack/repos/tutorial/packages/netlib-lapack/undefined_declarations.patch
new file mode 100644
index 0000000000..9dac2562f7
--- /dev/null
+++ b/var/spack/repos/tutorial/packages/netlib-lapack/undefined_declarations.patch
@@ -0,0 +1,26 @@
+diff --git a/SRC/dsytrf_aa_2stage.f b/SRC/dsytrf_aa_2stage.f
+index 2991305..f5f06cc 100644
+--- a/SRC/dsytrf_aa_2stage.f
++++ b/SRC/dsytrf_aa_2stage.f
+@@ -191,7 +191,7 @@
+       EXTERNAL           LSAME, ILAENV
+ *     ..
+ *     .. External Subroutines ..
+-      EXTERNAL           XERBLA, DCOPY, DLACGV, DLACPY,
++      EXTERNAL           XERBLA, DCOPY, DLACPY,
+      $                   DLASET, DGBTRF, DGEMM,  DGETRF, 
+      $                   DSYGST, DSWAP, DTRSM 
+ *     ..
+diff --git a/SRC/ssytrf_aa_2stage.f b/SRC/ssytrf_aa_2stage.f
+index be6809d..a929749 100644
+--- a/SRC/ssytrf_aa_2stage.f
++++ b/SRC/ssytrf_aa_2stage.f
+@@ -191,7 +191,7 @@
+       EXTERNAL           LSAME, ILAENV
+ *     ..
+ *     .. External Subroutines ..
+-      EXTERNAL           XERBLA, SCOPY, SLACGV, SLACPY,
++      EXTERNAL           XERBLA, SCOPY, SLACPY,
+      $                   SLASET, SGBTRF, SGEMM,  SGETRF, 
+      $                   SSYGST, SSWAP, STRSM 
+ *     ..
diff --git a/var/spack/repos/tutorial/repo.yaml b/var/spack/repos/tutorial/repo.yaml
new file mode 100644
index 0000000000..b43f511136
--- /dev/null
+++ b/var/spack/repos/tutorial/repo.yaml
@@ -0,0 +1,2 @@
+repo:
+  namespace: tutorial