Merge remote-tracking branch 'upstream/develop' into package-opencv

* upstream/develop: (126 commits)
  Fix indent/flake8 error.
  openexr : Add new package
  Set environment variables
  Added gnu packages datamash, parallel, and screen
  added package as argument to setup_platform_environment
  ilmbase : Add new IlmBase package
  Documented linker default
  fixed flake errors
  removed commented-out code
  Set default link type to dynamic on cray. Includes hooks for platform-based environment changes
  fixed flake errors
  fixed flake errors
  Improved cray_xc detection bug fix
  Improved cray_xc detection
  remove FIXMEs
  Ensure that per-4.4.1 NetCDF doesn't use HDF5 1.10
  Re-ignore licenses directory
  Add "default" configuration scope.
  Draft CDO
  Make frontend OS on Cray machines a proper linux distro.
  ...

var/spack/repos/builtin.mock/packages/cmake-client/package.py

@@ -38,7 +38,7 @@ class CmakeClient(Package):
 
     version('1.0', '4cb3ff35b2472aae70f542116d616e63')
 
-    depends_on('cmake')
+    depends_on('cmake', type='build')
 
 
     def setup_environment(self, spack_env, run_env):

var/spack/repos/builtin.mock/packages/dtbuild1/package.py

@@ -0,0 +1,18 @@
+from spack import *
+
+
+class Dtbuild1(Package):
+    """Package for use as a build tool for deptypes testing which has its own
+    deptree"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtbuild1-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    depends_on('dtbuild2', type='build')
+    depends_on('dtlink2')
+    depends_on('dtrun2', type='run')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtbuild2/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+
+class Dtbuild2(Package):
+    """Simple package which acts as a build dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtbuild2-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtbuild3/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+
+class Dtbuild3(Package):
+    """Simple package which acts as a build dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtbuild3-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtlink1/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+
+class Dtlink1(Package):
+    """Simple package which acts as a link dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtlink1-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    depends_on('dtlink3')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtlink2/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+
+class Dtlink2(Package):
+    """Simple package which acts as a link dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtlink2-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtlink3/package.py

@@ -0,0 +1,16 @@
+from spack import *
+
+
+class Dtlink3(Package):
+    """Simple package which acts as a link dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtlink3-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    depends_on('dtbuild2', type='build')
+    depends_on('dtlink4')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtlink4/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+
+class Dtlink4(Package):
+    """Simple package which acts as a link dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtlink4-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtlink5/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+
+class Dtlink5(Package):
+    """Simple package which acts as a link dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtlink5-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtrun1/package.py

@@ -0,0 +1,16 @@
+from spack import *
+
+
+class Dtrun1(Package):
+    """Simple package which acts as a run dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtrun1-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    depends_on('dtlink5')
+    depends_on('dtrun3', type='run')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtrun2/package.py

@@ -0,0 +1,13 @@
+from spack import *
+
+
+class Dtrun2(Package):
+    """Simple package which acts as a run dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtrun2-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtrun3/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+
+class Dtrun3(Package):
+    """Simple package which acts as a run dependency"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtrun3-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    depends_on('dtbuild3', type='build')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dttop/package.py

@@ -0,0 +1,17 @@
+from spack import *
+
+
+class Dttop(Package):
+    """Package with a complicated dependency tree"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dttop-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    depends_on('dtbuild1', type='build')
+    depends_on('dtlink1')
+    depends_on('dtrun1', type='run')
+
+    def install(self, spec, prefix):
+        pass

var/spack/repos/builtin.mock/packages/dtuse/package.py

@@ -0,0 +1,15 @@
+from spack import *
+
+
+class Dtuse(Package):
+    """Simple package which uses dttop"""
+
+    homepage = "http://www.example.com"
+    url = "http://www.example.com/dtuse-1.0.tar.gz"
+
+    version('1.0', '0123456789abcdef0123456789abcdef')
+
+    depends_on('dttop')
+
+    def install(self, spec, prefix):
+        pass

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

@@ -51,7 +51,7 @@ class Imagemagick(Package):
         url="http://sourceforge.net/projects/imagemagick/files/old-sources/6.x/6.8/ImageMagick-6.8.9-10.tar.gz/download")
 
     depends_on('jpeg')
-    depends_on('libtool')
+    depends_on('libtool', type='build')
     depends_on('libpng')
     depends_on('freetype')
     depends_on('fontconfig')

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

@@ -41,6 +41,7 @@ class Mitos(Package):
     depends_on('dyninst@8.2.1:')
     depends_on('hwloc')
     depends_on('mpi')
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):

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

@@ -123,7 +123,7 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         # Set R_LIBS to include the library dir for the
         # extension and any other R extensions it depends on.
         r_libs_path = []
-        for d in extension_spec.traverse():
+        for d in extension_spec.traverse(deptype=nolink, deptype_query='run'):
             if d.package.extends(self.spec):
                 r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir))
 
@@ -136,6 +136,14 @@ def setup_dependent_environment(self, spack_env, run_env, extension_spec):
             run_env.prepend_path('R_LIBS', os.path.join(
                 extension_spec.prefix, self.r_lib_dir))
 
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('LIBRARY_PATH',
+                             join_path(self.prefix, 'rlib', 'R', 'lib'))
+        run_env.prepend_path('LD_LIBRARY_PATH',
+                             join_path(self.prefix, 'rlib', 'R', 'lib'))
+        run_env.prepend_path('CPATH',
+                             join_path(self.prefix, 'rlib', 'R', 'include'))
+
     def setup_dependent_package(self, module, ext_spec):
         """Called before R modules' install() methods. In most cases,
         extensions will only need to have one line:

var/spack/repos/builtin/packages/adept-utils/package.py

@@ -35,6 +35,7 @@ class AdeptUtils(Package):
 
     depends_on("boost")
     depends_on("mpi")
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         cmake(*std_cmake_args)

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

@@ -12,9 +12,9 @@ class Adios(Package):
     """
 
     homepage = "http://www.olcf.ornl.gov/center-projects/adios/"
-    url = "http://users.nccs.gov/~pnorbert/adios-1.9.0.tar.gz"
+    url = "https://github.com/ornladios/ADIOS/archive/v1.9.0.tar.gz"
 
-    version('1.9.0', 'dbf5cb10e32add2f04c9b4052b7ffa76')
+    version('1.9.0', '310ff02388bbaa2b1c1710ee970b5678')
 
     # Lots of setting up here for this package
     # module swap PrgEnv-intel PrgEnv-$COMP

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

@@ -33,7 +33,7 @@ class Apex(Package):
 
     depends_on("binutils+libiberty")
     depends_on("boost@1.54:")
-    depends_on("cmake@2.8.12:")
+    depends_on('cmake@2.8.12:', type='build')
     depends_on("activeharmony@4.5:")
     depends_on("ompt-openmp")
 

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

@@ -33,11 +33,13 @@ class Armadillo(Package):
     homepage = "http://arma.sourceforge.net/"
     url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
 
+    version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2')
     version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e')
 
     variant('hdf5', default=False, description='Include HDF5 support')
 
-    depends_on('arpack')
+    depends_on('cmake@2.8:', type='build')
+    depends_on('arpack-ng')  # old arpack causes undefined symbols
     depends_on('blas')
     depends_on('lapack')
     depends_on('superlu@5.2:')
@@ -46,8 +48,8 @@ class Armadillo(Package):
     def install(self, spec, prefix):
         cmake_args = [
             # ARPACK support
-            '-DARPACK_LIBRARY={0}/libarpack.a'.format(
-                spec['arpack'].prefix.lib),
+            '-DARPACK_LIBRARY={0}/libarpack.{1}'.format(
+                spec['arpack-ng'].prefix.lib, dso_suffix),
             # BLAS support
             '-DBLAS_LIBRARY={0}'.format(spec['blas'].blas_shared_lib),
             # LAPACK support

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

@@ -72,10 +72,10 @@ class ArpackNg(Package):
 
     depends_on('blas')
     depends_on('lapack')
-    depends_on('automake', when='@3.3.0')
-    depends_on('autoconf', when='@3.3.0')
-    depends_on('libtool@2.4.2:', when='@3.3.0')
-    depends_on('cmake@2.8.6:', when='@3.4.0:')
+    depends_on('automake', when='@3.3.0', type='build')
+    depends_on('autoconf', when='@3.3.0', type='build')
+    depends_on('libtool@2.4.2:', when='@3.3.0', type='build')
+    depends_on('cmake@2.8.6:', when='@3.4.0:', type='build')
 
     depends_on('mpi', when='+mpi')
 

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

@@ -35,7 +35,7 @@ class Autoconf(Package):
     version('2.69', '82d05e03b93e45f5a39b828dc9c6c29b')
     version('2.62', '6c1f3b3734999035d77da5024aab4fbd')
 
-    depends_on('m4')
+    depends_on('m4', type='build')
 
     def _make_executable(self, name):
         return Executable(join_path(self.prefix.bin, name))

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

@@ -44,6 +44,7 @@ class Automaded(Package):
     depends_on('mpi')
     depends_on('boost')
     depends_on('callpath')
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         cmake("-DSTATE_TRACKER_WITH_CALLPATH=ON", *std_cmake_args)

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

@@ -31,7 +31,7 @@ class Bear(Package):
 
     version('2.0.4', 'fd8afb5e8e18f8737ba06f90bd77d011')
 
-    depends_on("cmake")
+    depends_on('cmake', type='build')
     depends_on("python")
 
     def install(self, spec, prefix):

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

@@ -37,8 +37,8 @@ class Bertini(Package):
 
     variant('mpi', default=True, description='Compile in parallel')
 
-    depends_on('flex')
-    depends_on('bison')
+    depends_on('flex', type='build')
+    depends_on('bison', type='build')
     depends_on('gmp')
     depends_on('mpfr')
     depends_on('mpi', when='+mpi')

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

@@ -38,9 +38,9 @@ class Binutils(Package):
     version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e')
     version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764')
 
-    depends_on('m4')
-    depends_on('flex')
-    depends_on('bison')
+    depends_on('m4', type='build')
+    depends_on('flex', type='build')
+    depends_on('bison', type='build')
 
     # Add a patch that creates binutils libiberty_pic.a which is preferred by
     # OpenSpeedShop and cbtf-krell

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

@@ -34,7 +34,7 @@ class Bison(Package):
 
     version('3.0.4', 'a586e11cd4aff49c3ff6d3b6a4c9ccf8')
 
-    depends_on("m4")
+    depends_on("m4", type='build')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

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

@@ -35,6 +35,7 @@ class Boxlib(Package):
     version('master', git='https://ccse.lbl.gov/pub/Downloads/BoxLib.git')
 
     depends_on('mpi')
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         args = std_cmake_args

var/spack/repos/builtin/packages/bzip2/package.py

@@ -24,54 +24,59 @@
 ##############################################################################
 from spack import *
 
+
 class Bzip2(Package):
     """bzip2 is a freely available, patent free high-quality data
-       compressor. It typically compresses files to within 10% to 15%
-       of the best available techniques (the PPM family of statistical
-       compressors), whilst being around twice as fast at compression
-       and six times faster at decompression.
+    compressor. It typically compresses files to within 10% to 15%
+    of the best available techniques (the PPM family of statistical
+    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"
 
     version('1.0.6', '00b516f4704d4a7cb50a1d97e6e8e15b')
 
-
     def patch(self):
-        mf = FileFilter('Makefile-libbz2_so')
-        mf.filter(r'^CC=gcc', 'CC=cc')
+        # 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')
 
-        # Below stuff patches the link line to use RPATHs on Mac OS X.
+        # Patch the link line to use RPATHs on macOS
         if 'darwin' in self.spec.architecture:
             v = self.spec.version
-            v1, v2, v3 = (v.up_to(i) for i in (1,2,3))
+            v1, v2, v3 = (v.up_to(i) for i in (1, 2, 3))
 
-            mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3),
-                      '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), string=True)
+            kwargs = {'ignore_absent': False, 'backup': False, 'string': True}
 
-            mf.filter('$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3),
-                      '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'.format(v3), string=True)
+            mf = FileFilter('Makefile-libbz2_so')
+            mf.filter('$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)'.format(v2, v3),  # NOQA ignore=E501
+                      '$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib -current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)'.format(v1, v2, v3, v3), **kwargs)  # NOQA ignore=E501
+
+            mf.filter('$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}'.format(v3),  # NOQA ignore=E501
+                      '$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib'.format(v3), **kwargs)  # NOQA ignore=E501
             mf.filter('rm -f libbz2.so.{0}'.format(v2),
-                      'rm -f libbz2.{0}.dylib'.format(v2), string=True)
+                      'rm -f libbz2.{0}.dylib'.format(v2), **kwargs)
             mf.filter('ln -s libbz2.so.{0} libbz2.so.{1}'.format(v3, v2),
-                      'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), string=True)
-
+                      'ln -s libbz2.{0}.dylib libbz2.{1}.dylib'.format(v3, v2), **kwargs)  # NOQA ignore=E501
 
     def install(self, spec, prefix):
+        # Build the dynamic library first
         make('-f', 'Makefile-libbz2_so')
-        make('clean')
-        make("install", "PREFIX=%s" % prefix)
+        # Build the static library and everything else
+        make()
+        make('install', 'PREFIX={0}'.format(prefix))
 
         install('bzip2-shared', join_path(prefix.bin, 'bzip2'))
 
-        v1, v2, v3 = (self.spec.version.up_to(i) for i in (1,2,3))
+        v1, v2, v3 = (self.spec.version.up_to(i) for i in (1, 2, 3))
         if 'darwin' in self.spec.architecture:
             lib = 'libbz2.dylib'
-            lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) for v in (v1, v2, v3))
+            lib1, lib2, lib3 = ('libbz2.{0}.dylib'.format(v) for v in (v1, v2, v3))  # NOQA ignore=E501
         else:
             lib = 'libbz2.so'
-            lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) for v in (v1, v2, v3))
+            lib1, lib2, lib3 = ('libbz2.so.{0}'.format(v) for v in (v1, v2, v3))  # NOQA ignore=E501
 
         install(lib3, join_path(prefix.lib, lib3))
         with working_dir(prefix.lib):

var/spack/repos/builtin/packages/c-blosc/package.py

@@ -38,7 +38,7 @@ class CBlosc(Package):
     version('1.8.1', 'd73d5be01359cf271e9386c90dcf5b05')
     version('1.8.0', '5b92ecb287695ba20cc33d30bf221c4f')
 
-    depends_on("cmake")
+    depends_on("cmake", type='build')
     depends_on("snappy")
     depends_on("zlib")
 

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

@@ -41,6 +41,7 @@ class Caliper(Package):
     depends_on('libunwind')
     depends_on('papi')
     depends_on('mpi', when='+mpi')
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
       with working_dir('build', create=True):

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

@@ -39,6 +39,7 @@ class Callpath(Package):
     depends_on("dyninst")
     depends_on("adept-utils")
     depends_on("mpi")
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         # TODO: offer options for the walker used.

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

@@ -42,7 +42,7 @@ class Cantera(Package):
     variant('matlab',     default=False, description='Build the Cantera Matlab toolbox')
 
     # Required dependencies
-    depends_on('scons')
+    depends_on('scons', type='build')
 
     # Recommended dependencies
     depends_on('blas',      when='+lapack')
@@ -52,10 +52,10 @@ class Cantera(Package):
 
     # Python module dependencies
     extends('python', when='+python')
-    depends_on('py-numpy',  when='+python')
-    depends_on('py-scipy',  when='+python')
-    depends_on('py-cython', when='+python')
-    depends_on('py-3to2',   when='+python')
+    depends_on('py-numpy',  when='+python', type=nolink)
+    depends_on('py-scipy',  when='+python', type=nolink)
+    depends_on('py-cython', when='+python', type=nolink)
+    depends_on('py-3to2',   when='+python', type=nolink)
     # TODO: these "when" specs don't actually work
     # depends_on('py-unittest2',     when='+python^python@2.6')
     # depends_on('py-unittest2py3k', when='+python^python@3.1')

var/spack/repos/builtin/packages/cbtf-argonavis/package.py

@@ -53,7 +53,7 @@ class CbtfArgonavis(Package):
 
     version('1.6', branch='master', git='https://github.com/OpenSpeedShop/cbtf-argonavis.git')
 
-    depends_on("cmake@3.0.2")
+    depends_on("cmake@3.0.2", type='build')
     depends_on("boost@1.50.0:")
     depends_on("papi")
     depends_on("mrnet@5.0.1:+lwthreads+krellpatch")

var/spack/repos/builtin/packages/cbtf-krell/package.py

@@ -64,7 +64,7 @@ class CbtfKrell(Package):
     variant('mpich', default=False, description="Build mpi experiment collector for mpich MPI when this variant is enabled.")
 
     # Dependencies for cbtf-krell
-    depends_on("cmake@3.0.2")
+    depends_on("cmake@3.0.2", type='build')
 
     # For binutils service
     depends_on("binutils@2.24+krellpatch")

var/spack/repos/builtin/packages/cbtf-lanl/package.py

@@ -53,7 +53,7 @@ class CbtfLanl(Package):
 
     version('1.6', branch='master', git='http://git.code.sf.net/p/cbtf-lanl/cbtf-lanl')
 
-    depends_on("cmake@3.0.2")
+    depends_on("cmake@3.0.2", type='build')
     # Dependencies for cbtf-krell
     depends_on("mrnet@5.0.1:+lwthreads+krellpatch")
     depends_on("xerces-c@3.1.1:")

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

@@ -57,7 +57,7 @@ class Cbtf(Package):
 
     variant('runtime', default=False, description="build only the runtime libraries and collectors.")
 
-    depends_on("cmake@3.0.2")
+    depends_on("cmake@3.0.2", type='build')
     depends_on("boost@1.50.0:")
     depends_on("mrnet@5.0.1:+lwthreads+krellpatch")
     depends_on("xerces-c@3.1.1:")

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

@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Cdo(Package):
+    """CDO is a collection of command line Operators to manipulate and analyse
+    Climate and NWP model Data. """
+
+    homepage = "https://code.zmaw.de/projects/cdo"
+    url      = "https://code.zmaw.de/attachments/download/10198/cdo-1.6.9.tar.gz"
+
+    version('1.6.9', 'bf0997bf20e812f35e10188a930e24e2')
+
+    depends_on('netcdf')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')

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

@@ -40,7 +40,7 @@ class Cereal(Package):
 
     patch("Werror.patch")
 
-    depends_on("cmake @2.6.2:")
+    depends_on('cmake@2.6.2:', type='build')
 
     def install(self, spec, prefix):
         # Don't use -Werror

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

@@ -46,7 +46,7 @@ class Cgal(Package):
     depends_on('mpfr')
     depends_on('gmp')
     depends_on('zlib')
-    depends_on('cmake')
+    depends_on('cmake', type='build')
 
     # FIXME : Qt5 dependency missing (needs Qt5 and OpenGL)
     # FIXME : Optional third party libraries missing

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

@@ -40,6 +40,7 @@ class Cleverleaf(Package):
     depends_on("SAMRAI@3.8.0:")
     depends_on("hdf5+mpi")
     depends_on("boost")
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         cmake(*std_cmake_args)

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

@@ -30,6 +30,7 @@ class Cmake(Package):
     homepage  = 'https://www.cmake.org'
     url       = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz'
 
+    version('3.6.0',    'aa40fbecf49d99c083415c2411d12db9')
     version('3.5.2',    '701386a1b5ec95f8d1075ecf96383e02')
     version('3.5.1',    'ca051f4a66375c89d1a524e726da0296')
     version('3.5.0',    '33c5d09d4c33d4ffcc63578a6ba8777e')
@@ -47,8 +48,8 @@ class Cmake(Package):
     depends_on('ncurses', when='+ncurses')
     depends_on('openssl', when='+openssl')
     depends_on('qt', when='+qt')
-    depends_on('python@2.7.11:', when='+doc')
-    depends_on('py-sphinx', when='+doc')
+    depends_on('python@2.7.11:', when='+doc', type='build')
+    depends_on('py-sphinx', when='+doc', type='build')
 
     def url_for_version(self, version):
         """Handle CMake's version-based custom URLs."""

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

@@ -32,6 +32,8 @@ class Cmocka(Package):
     version('1.0.1', 'ed861e501a21a92b2af63e466df2015e')
     parallel = False
 
+    depends_on('cmake', type='build')
+
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
 	    cmake('..', *std_cmake_args)

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

@@ -33,6 +33,7 @@ class Cram(Package):
 
     extends('python')
     depends_on("mpi")
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         cmake(".", *std_cmake_args)

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

@@ -32,10 +32,10 @@ class Czmq(Package):
 
     version('3.0.2', '23e9885f7ee3ce88d99d0425f52e9be1', url='https://github.com/zeromq/czmq/archive/v3.0.2.tar.gz')
 
-    depends_on('libtool')
-    depends_on('automake')
-    depends_on('autoconf')
-    depends_on('pkg-config')
+    depends_on('libtool', type='build')
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('pkg-config', type='build')
     depends_on('zeromq')
 
     def install(self, spec, prefix):

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

@@ -55,6 +55,7 @@ class Dakota(Package):
 
     depends_on('python')
     depends_on('boost')
+    depends_on('cmake', type='build')
 
     def url_for_version(self, version):
         return Dakota._url_str.format(version=version)

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

@@ -31,6 +31,8 @@ class Damselfly(Package):
 
     version('1.0', '05cf7e2d8ece4408c0f2abb7ab63fd74c0d62895', git='https://github.com/llnl/damselfly.git', tag='v1.0')
 
+    depends_on('cmake', type='build')
+
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):
 	    cmake('-DCMAKE_BUILD_TYPE=release', '..', *std_cmake_args)

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

@@ -0,0 +1,45 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Datamash(Package):
+    """
+    GNU datamash is a command-line program which performs basic numeric,
+    textual and statistical operations on input textual data files.
+    """
+
+    homepage = "https://www.gnu.org/software/datamash/"
+    url      = "http://ftp.gnu.org/gnu/datamash/datamash-1.0.5.tar.gz"
+
+    version('1.1.0', '79a6affca08107a095e97e4237fc8775')
+    version('1.0.7', '9f317bab07454032ba9c068e7f17b04b')
+    version('1.0.6', 'ff26fdef0f343cb695cf1853e14a1a5b')
+    version('1.0.5', '9a29549dc7feca49fdc5fab696614e11')
+
+    def install(self, spec, prefix):
+        configure('--prefix=%s' % prefix)
+        make()
+        make("install")

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

@@ -60,7 +60,7 @@ class Dealii(Package):
     depends_on("boost@1.59.0:+thread+system+serialization+iostreams",     when='~mpi')  # NOQA: ignore=E501
     depends_on("boost@1.59.0:+mpi+thread+system+serialization+iostreams", when='+mpi')  # NOQA: ignore=E501
     depends_on("bzip2")
-    depends_on("cmake")
+    depends_on("cmake", type='build')
     depends_on("lapack")
     depends_on("muparser")
     depends_on("suite-sparse")

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

@@ -31,7 +31,7 @@ class Dia(Package):
 
     version('0.97.3',    '0e744a0f6a6c4cb6a089e4d955392c3c')
 
-    depends_on('intltool')
+    depends_on('intltool', type='build')
     depends_on('gtkplus@2.6.0:')
     depends_on('cairo')
     #depends_on('libart') # optional dependency, not yet supported by spack.

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

@@ -24,6 +24,8 @@
 ##############################################################################
 from spack import *
 
+import sys
+
 
 class Doxygen(Package):
     """Doxygen is the de facto standard tool for generating documentation
@@ -41,12 +43,12 @@ class Doxygen(Package):
     # graphviz appears to be a run-time optional dependency
     variant('graphviz', default=True, description='Build with dot command support from Graphviz.')  # NOQA: ignore=E501
 
-    depends_on("cmake@2.8.12:")
-    depends_on("flex")
-    depends_on("bison")
+    depends_on("cmake@2.8.12:", type='build')
+    depends_on("flex", type='build')
+    depends_on("bison", type='build')
 
     # optional dependencies
-    depends_on("graphviz", when="+graphviz")
+    depends_on("graphviz", when="+graphviz", type='run')
 
     def install(self, spec, prefix):
         cmake('.', *std_cmake_args)

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

@@ -43,6 +43,7 @@ class Dyninst(Package):
     depends_on("libelf")
     depends_on("libdwarf")
     depends_on("boost@1.42:")
+    depends_on('cmake', type='build')
 
     # new version uses cmake
     def install(self, spec, prefix):

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

@@ -47,7 +47,7 @@ class Eigen(Package):
     variant('mpfr', default=True, description='Enables support for multi-precisions floating points via mpfr')
 
     # TODO : dependency on googlehash, superlu, adolc missing
-    depends_on('cmake')
+    depends_on('cmake', type='build')
     depends_on('metis@5:', when='+metis')
     depends_on('scotch', when='+scotch')
     depends_on('fftw', when='+fftw')

var/spack/repos/builtin/packages/environment-modules/package.py

@@ -35,7 +35,7 @@ class EnvironmentModules(Package):
     version('3.2.10', '8b097fdcb90c514d7540bb55a3cb90fb')
 
     # Dependencies:
-    depends_on('tcl')
+    depends_on('tcl', type=alldeps)
 
     def install(self, spec, prefix):
         tcl_spec = spec['tcl']

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

@@ -44,9 +44,7 @@ class Exodusii(Package):
 
     version('2016-02-08', git='https://github.com/gsjaardema/seacas.git', commit='dcf3529')
 
-    # TODO: Make this a build dependency once build dependencies are supported
-    # (see: https://github.com/LLNL/spack/pull/378).
-    depends_on('cmake@2.8.7:')
+    depends_on('cmake@2.8.7:', type='build')
     depends_on('hdf5~shared~mpi')
     depends_on('netcdf~mpi')
 

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

@@ -31,7 +31,7 @@ class Expat(Package):
 
     version('2.1.0', 'dd7dab7a5fea97d2a6a43f511449b7cd')
 
-    depends_on('cmake')
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
 

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

@@ -34,7 +34,8 @@ class Flex(Package):
     version('2.6.0', '5724bcffed4ebe39e9b55a9be80859ec')
     version('2.5.39', 'e133e9ead8ec0a58d81166b461244fde')
 
-    depends_on("bison")
+    depends_on("bison", type='build')
+    depends_on("m4", type='build')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

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

@@ -45,8 +45,8 @@ class Flux(Package):
     depends_on("py-cffi")
 
     # TODO: This provides a catalog, hacked with environment below for now
-    depends_on("docbook-xml")
-    depends_on("asciidoc")
+    depends_on("docbook-xml", type='build')
+    depends_on("asciidoc", type='build')
 
     def install(self, spec, prefix):
         # Bootstrap with autotools

var/spack/repos/builtin/packages/foam-extend/package.py

@@ -29,6 +29,7 @@ class FoamExtend(Package):
     depends_on('python')
     depends_on('flex@:2.5.99')
     depends_on('zlib')
+    depends_on('cmake', type='build')
 
     depends_on('scotch ~ metis', when='~ptscotch+scotch')
     depends_on('scotch ~ metis + mpi', when='+ptscotch')

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

@@ -62,7 +62,7 @@ class Gdal(Package):
     depends_on("libpng")
     depends_on("zlib")
     depends_on("proj")
-    depends_on("py-numpy")
+    depends_on("py-numpy", type=nolink)
 
     parallel = False
 

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

@@ -41,7 +41,7 @@ class Gdb(Package):
     version('7.9', '8f8ced422fe462a00e0135a643544f17')
     version('7.8.2', '8b0ea8b3559d3d90b3ff4952f0aeafbc')
 
-    depends_on('texinfo')
+    depends_on('texinfo', type='build')
 
     def install(self, spec, prefix):
         configure('--prefix=%s' % prefix)

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

@@ -37,6 +37,8 @@ class Gflags(Package):
 
     version('2.1.2', 'ac432de923f9de1e9780b5254884599f')
 
+    depends_on('cmake', type='build')
+
     def install(self, spec, prefix):
         cmake("-DCMAKE_INSTALL_PREFIX=" + prefix,
               "-DBUILD_SHARED_LIBS=ON")

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

@@ -49,7 +49,7 @@ class Git(Package):
 
 
     depends_on("openssl")
-    depends_on("autoconf")
+    depends_on("autoconf", type='build')
     depends_on("curl")
     depends_on("expat")
 

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

@@ -38,8 +38,8 @@ class Glib(Package):
 
     depends_on("libffi")
     depends_on("zlib")
-    depends_on("pkg-config")
-    depends_on('gettext', sys.platform == 'darwin')
+    depends_on("pkg-config", type='build')
+    depends_on('gettext', when=sys.platform == 'darwin')
 
     # The following patch is needed for gcc-6.1
     patch('g_date_strftime.patch')

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

@@ -35,8 +35,8 @@ class Glm(Package):
     url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz"
 
     version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8')
-    
-    depends_on ("cmake")
+
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         with working_dir('spack-build', create=True):

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

@@ -34,7 +34,7 @@ class Global(Package):
 
     version('6.5', 'dfec818b4f53d91721e247cf7b218078')
 
-    depends_on('exuberant-ctags')
+    depends_on('exuberant-ctags', type=nolink)
     depends_on('ncurses')
 
     def install(self, spec, prefix):

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

@@ -35,7 +35,7 @@ class Gmp(Package):
     version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470')
     version('6.0.0' , '6ef5869ae735db9995619135bd856b84')
 
-    depends_on("m4")
+    depends_on("m4", type='build')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

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

@@ -53,7 +53,7 @@ class Gmsh(Package):
 
     depends_on('blas')
     depends_on('lapack')
-    depends_on('cmake@2.8:')
+    depends_on('cmake@2.8:', type='build')
     depends_on('gmp')
     depends_on('mpi',  when='+mpi')
     # Assumes OpenGL with GLU is already provided by the system:

var/spack/repos/builtin/packages/gnu-prolog/package.py

@@ -0,0 +1,41 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+class GnuProlog(Package):
+    """A free Prolog compiler with constraint solving over finite domains."""
+    homepage = "http://www.gprolog.org/"
+    url      = "http://www.gprolog.org/gprolog-1.4.4.tar.gz"
+
+    version('1.4.4', '37009da471e5217ff637ad1c516448c8')
+
+    parallel = False
+
+    def install(self, spec, prefix):
+        with working_dir('src'):
+            configure('--with-install-dir=%s' % prefix,
+                      '--without-links-dir')
+            make()
+            make('install')

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

@@ -24,7 +24,7 @@ class Go(Package):
 
     # to-do, make non-c self-hosting compilers feasible without backflips
     # should be a dep on external go compiler
-    depends_on('go-bootstrap')
+    depends_on('go-bootstrap', type='build')
     depends_on('git')
 
     def install(self, spec, prefix):

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

@@ -31,7 +31,7 @@ class Googletest(Package):
 
     version('1.7.0', '5eaf03ed925a47b37c8e1d559eb19bc4')
 
-    depends_on("cmake")
+    depends_on("cmake", type='build')
 
     def install(self, spec, prefix):
         which('cmake')('.', *std_cmake_args)

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

@@ -31,6 +31,8 @@ class Graphlib(Package):
 
     version('2.0.0', '43c6df84f1d38ba5a5dce0ae19371a70')
 
+    depends_on('cmake', type='build')
+
     def install(self, spec, prefix):
         cmake(".", *std_cmake_args)
 

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

@@ -44,7 +44,7 @@ class Graphviz(Package):
     depends_on("swig")
     depends_on("python")
     depends_on("ghostscript")
-    depends_on("pkg-config")
+    depends_on("pkg-config", type='build')
 
     def install(self, spec, prefix):
         options = ['--prefix=%s' % prefix]

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

@@ -50,6 +50,7 @@ class Gromacs(Package):
     depends_on('mpi', when='+mpi')
 
     depends_on('fftw')
+    depends_on('cmake', type='build')
 
     # TODO : add GPU support
 

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

@@ -0,0 +1,53 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Gts(Package):
+    """GTS stands for the GNU Triangulated Surface Library.
+
+    It is an Open Source Free Software Library intended to provide a set of
+    useful functions to deal with 3D surfaces meshed with interconnected
+    triangles. The source code is available free of charge under the Free
+    Software LGPL license.
+
+    The code is written entirely in C with an object-oriented approach
+    based mostly on the design of GTK+. Careful attention is paid to
+    performance related issues as the initial goal of GTS is to provide a
+    simple and efficient library to scientists dealing with 3D computational
+    surface meshes.
+    """
+
+    homepage = "http://gts.sourceforge.net/index.html"
+    url = "http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz"
+
+    version('121130', '023ebb6b13b8707534182a3ef0d12908')
+
+    depends_on('glib')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make()
+        make('install')

var/spack/repos/builtin/packages/hdf5-blosc/package.py

@@ -53,7 +53,7 @@ class Hdf5Blosc(Package):
 
     depends_on("c-blosc")
     depends_on("hdf5")
-    depends_on("libtool")
+    depends_on("libtool", type='build')
 
     parallel = False
 

var/spack/repos/builtin/packages/hdf5/package.py

@@ -40,7 +40,7 @@ class Hdf5(Package):
 
     version('1.10.0-patch1', '9180ff0ef8dc2ef3f61bd37a7404f295')
     version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199')
-    version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618', preferred=True)
+    version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618')
     version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24')
     version('1.8.13', 'c03426e9e77d7766944654280b467289')
 

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

@@ -0,0 +1,76 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Hmmer(Package):
+    """HMMER is used for searching sequence databases for sequence homologs,
+    and for making sequence alignments. It implements methods using
+    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'
+
+    version('3.1b2', 'c8c141018bc0ccd7fc37b33f2b945d5f')
+    version('3.0',   '4cf685f3bc524ba5b5cdaaa070a83588')
+    version('2.4i',  'dab234c87e026ac1de942450750acd20')
+    version('2.3.2', '5f073340c0cf761288f961a73821228a')
+    version('2.3.1', 'c724413e5761c630892506698a4716e2')
+
+    variant('mpi', default=True,  description='Compile with MPI')
+    variant('gsl', default=False, description='Compile with GSL')
+
+    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)
+        ]
+
+        if '+gsl' in self.spec:
+            configure_args.extend([
+                '--with-gsl',
+                'LIBS=-lgsl -lgslcblas'
+            ])
+
+        if '+mpi' in self.spec:
+            configure_args.append('--enable-mpi')
+
+        configure(*configure_args)
+        make()
+
+        if self.run_tests:
+            make('check')
+
+        make('install')

var/spack/repos/builtin/packages/hoomd-blue/package.py

@@ -45,12 +45,12 @@ class HoomdBlue(Package):
     variant('doc',  default=True, description='Generate documentation')
 
     extends('python')
-    depends_on('py-numpy')
+    depends_on('py-numpy', type=nolink)
     depends_on('boost+python')
-    depends_on('cmake')
+    depends_on('cmake', type='build')
     depends_on('mpi', when='+mpi')
     depends_on('cuda', when='+cuda')
-    depends_on('doxygen', when='+doc')
+    depends_on('doxygen', when='+doc', type='build')
 
     def install(self, spec, prefix):
 

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

@@ -23,7 +23,9 @@
 # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 ##############################################################################
 from spack import *
-import os, sys
+import os
+import sys
+
 
 class Hypre(Package):
     """Hypre is a library of high performance preconditioners that
@@ -37,7 +39,7 @@ class Hypre(Package):
     version('2.10.0b', '768be38793a35bb5d055905b271f5b8e')
 
     # hypre does not know how to build shared libraries on Darwin
-    variant('shared', default=sys.platform!='darwin', description="Build shared library version (disables static library)")
+    variant('shared', default=(sys.platform != 'darwin'), description="Build shared library version (disables static library)")
     # SuperluDist have conflicting headers with those in Hypre
     variant('internal-superlu', default=True, description="Use internal Superlu routines")
 
@@ -46,21 +48,26 @@ class Hypre(Package):
     depends_on("lapack")
 
     def install(self, spec, prefix):
-        blas_dir = spec['blas'].prefix
-        lapack_dir = spec['lapack'].prefix
-        mpi_dir = spec['mpi'].prefix
-
-        os.environ['CC'] = os.path.join(mpi_dir, 'bin', 'mpicc')
-        os.environ['CXX'] = os.path.join(mpi_dir, 'bin', 'mpicxx')
-        os.environ['F77'] = os.path.join(mpi_dir, 'bin', 'mpif77')
-
+        os.environ['CC'] = spec['mpi'].mpicc
+        os.environ['CXX'] = spec['mpi'].mpicxx
+        os.environ['F77'] = spec['mpi'].mpif77
 
+        # Since +shared does not build on macOS and also Atlas does not have
+        # a single static lib to build against, link against shared libs with
+        # a hope that --whole-archive linker option (or alike) was used
+        # to command the linker to include whole static libs' content into the
+        # shared lib
+        # Note: --with-(lapack|blas)_libs= needs space separated list of names
         configure_args = [
-                "--prefix=%s" % prefix,
-                "--with-lapack-libs=lapack",
-                "--with-lapack-lib-dirs=%s/lib" % lapack_dir,
-                "--with-blas-libs=blas",
-                "--with-blas-lib-dirs=%s/lib" % blas_dir]
+            '--prefix=%s' % prefix,
+            '--with-lapack-libs=%s' % to_lib_name(
+                spec['lapack'].lapack_shared_lib),
+            '--with-lapack-lib-dirs=%s/lib' % spec['lapack'].prefix,
+            '--with-blas-libs=%s' % to_lib_name(
+                spec['blas'].blas_shared_lib),
+            '--with-blas-lib-dirs=%s/lib' % spec['blas'].prefix
+        ]
+
         if '+shared' in self.spec:
             configure_args.append("--enable-shared")
 
@@ -76,4 +83,12 @@ def install(self, spec, prefix):
             configure(*configure_args)
 
             make()
+            if self.run_tests:
+                make("check")
+                make("test")
+                Executable(join_path('test', 'ij'))()
+                sstruct = Executable(join_path('test', 'struct'))
+                sstruct()
+                sstruct('-in', 'test/sstruct.in.default', '-solver', '40',
+                        '-rhsone')
             make("install")

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

@@ -26,13 +26,13 @@ class Ibmisc(CMakePackage):
     depends_on('netcdf-cxx4', when='+netcdf')
     depends_on('udunits2', when='+udunits2')
     depends_on('googletest', when='+googletest')
-    depends_on('py-cython', when='+python')
-    depends_on('py-numpy', when='+python')
+    depends_on('py-cython', when='+python', type=nolink)
+    depends_on('py-numpy', when='+python', type=nolink)
     depends_on('boost', when='+boost')
 
     # Build dependencies
-    depends_on('cmake')
-    depends_on('doxygen')
+    depends_on('cmake', type='build')
+    depends_on('doxygen', type='build')
 
     def configure_args(self):
         spec = self.spec

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

@@ -0,0 +1,42 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Ilmbase(Package):
+    """OpenEXR ILM Base libraries (high dynamic-range image file format)"""
+
+    homepage = "http://www.openexr.com/"
+    url      = "http://download.savannah.nongnu.org/releases/openexr/ilmbase-2.2.0.tar.gz"
+
+    version('2.2.0', 'b540db502c5fa42078249f43d18a4652')
+    version('2.1.0', 'af1115f4d759c574ce84efcde9845d29')
+    version('2.0.1', '74c0d0d2873960bd0dc1993f8e03f0ae')
+    version('1.0.2', '26c133ee8ca48e1196fbfb3ffe292ab4')
+    version('0.9.0', '4df45f8116cb7a013b286caf6da30a2e')
+
+    def install(self, spec, prefix):
+        configure('--prefix={0}'.format(prefix))
+        make('install')

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

@@ -38,7 +38,7 @@ class Ipopt(Package):
 
     depends_on("blas")
     depends_on("lapack")
-    depends_on("pkg-config")
+    depends_on("pkg-config", type='build')
     depends_on("mumps+double~mpi") 
     
     def install(self, spec, prefix):

var/spack/repos/builtin/packages/jasper/fix_alpha_channel_assert_fail.patch

@@ -0,0 +1,25 @@
+diff --git a/src/libjasper/jpc/jpc_dec.c b/src/libjasper/jpc/jpc_dec.c
+index fa72a0e..1f4845f 100644
+--- a/src/libjasper/jpc/jpc_dec.c
++++ b/src/libjasper/jpc/jpc_dec.c
+@@ -1069,12 +1069,18 @@ static int jpc_dec_tiledecode(jpc_dec_t *dec, jpc_dec_tile_t *tile)
+	/* Apply an inverse intercomponent transform if necessary. */
+	switch (tile->cp->mctid) {
+	case JPC_MCT_RCT:
+-		assert(dec->numcomps == 3);
++		if (dec->numcomps != 3 && dec->numcomps != 4) {
++			jas_eprintf("bad number of components (%d)\n", dec->numcomps);
++			return -1;
++		}
+		jpc_irct(tile->tcomps[0].data, tile->tcomps[1].data,
+		  tile->tcomps[2].data);
+		break;
+	case JPC_MCT_ICT:
+-		assert(dec->numcomps == 3);
++		if (dec->numcomps != 3 && dec->numcomps != 4) {
++			jas_eprintf("bad number of components (%d)\n", dec->numcomps);
++			return -1;
++		}
+		jpc_iict(tile->tcomps[0].data, tile->tcomps[1].data,
+		  tile->tcomps[2].data);
+		break;

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

@@ -0,0 +1,63 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class 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"
+
+    version('1.900.1', 'a342b2b4495b3e1394e161eb5d85d754')
+
+    variant('shared', default=True,
+            description='Builds shared versions of the libraries')
+    variant('debug', default=False,
+            description='Builds debug versions of the libraries')
+
+    depends_on('libjpeg-turbo')
+
+    # 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')
+
+    def install(self, spec, prefix):
+        configure_options = [
+            '--prefix={0}'.format(prefix),
+            '--mandir={0}'.format(spec.prefix.man),
+        ]
+
+        if '+shared' in spec:
+            configure_options.append('--enable-shared')
+
+        if '+debug' not in spec:
+            configure_options.append('--disable-debug')
+
+        configure(*configure_options)
+
+        make()
+        make('install')

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

@@ -44,16 +44,16 @@ class Julia(Package):
     patch('openblas.patch', when='@0.4:0.4.5')
 
     # Build-time dependencies:
-    # depends_on("awk")
-    # depends_on("m4")
-    # depends_on("pkg-config")
+    # depends_on("awk", type='build')
+    # depends_on("m4", type='build')
+    # depends_on("pkg-config", type='build')
 
     # Combined build-time and run-time dependencies:
-    depends_on("binutils")
-    depends_on("cmake @2.8:")
-    depends_on("git")
-    depends_on("openssl")
-    depends_on("python @2.7:2.999")
+    depends_on("binutils", type=nolink)
+    depends_on("cmake @2.8:", type=nolink)
+    depends_on("git", type=nolink)
+    depends_on("openssl", type=nolink)
+    depends_on("python @2.7:2.999", type=nolink)
 
     # I think that Julia requires the dependencies above, but it
     # builds fine (on my system) without these. We should enable them
@@ -93,8 +93,8 @@ class Julia(Package):
     # USE_SYSTEM_LIBGIT2=0
 
     # Run-time dependencies for Julia packages:
-    depends_on("hdf5")
-    depends_on("mpi")
+    depends_on("hdf5", type='run')
+    depends_on("mpi", type='run')
 
     def install(self, spec, prefix):
         # Explicitly setting CC, CXX, or FC breaks building libuv, one

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

@@ -33,9 +33,9 @@ class Launchmon(Package):
 
     version('1.0.2', '8d6ba77a0ec2eff2fde2c5cc8fa7ff7a')
 
-    depends_on('autoconf')
-    depends_on('automake')
-    depends_on('libtool')
+    depends_on('autoconf', type='build')
+    depends_on('automake', type='build')
+    depends_on('libtool', type='build')
 
     def install(self, spec, prefix):
         configure(

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

@@ -40,6 +40,7 @@ class Libgd(Package):
     version('2.1.1', 'e91a1a99903e460e7ba00a794e72cc1e')
 
     depends_on('libpng')
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
 

var/spack/repos/builtin/packages/libjpeg-turbo/package.py

@@ -35,8 +35,8 @@ class LibjpegTurbo(Package):
     version('1.3.1', '2c3a68129dac443a72815ff5bb374b05')
 
     # Can use either of these.
-    depends_on("yasm")
-    depends_on("nasm")
+    depends_on("yasm", type='build')
+    depends_on("nasm", type='build')
 
     def install(self, spec, prefix):
         configure("--prefix=%s" % prefix)

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

@@ -35,7 +35,7 @@ class Libtool(Package):
     version('2.4.6', 'addf44b646ddb4e3919805aa88fa7c5e')
     version('2.4.2', 'd2f3b7d4627e69e13514a40e72a24d50')
 
-    depends_on('m4')
+    depends_on('m4', type='build')
 
     def _make_executable(self, name):
         return Executable(join_path(self.prefix.bin, name))

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

@@ -31,9 +31,9 @@ class Libuv(Package):
 
     version('1.9.0', '14737f9c76123a19a290dabb7d1cd04c')
 
-    depends_on('automake')
-    depends_on('autoconf')
-    depends_on('libtool')
+    depends_on('automake', type='build')
+    depends_on('autoconf', type='build')
+    depends_on('libtool', type='build')
 
     def install(self, spec, prefix):
         bash = which("bash")

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

@@ -36,9 +36,9 @@ class Libxcb(Package):
     version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb')
     version('1.11.1', '118623c15a96b08622603a71d8789bf3')
 
-    depends_on("python")
+    depends_on("python", type='build')
     depends_on("xcb-proto")
-    depends_on("pkg-config")
+    depends_on("pkg-config", type='build')
     depends_on("libpthread-stubs")
     depends_on('libxau')
 

var/spack/repos/builtin/packages/llvm-lld/package.py

@@ -34,6 +34,8 @@ class LlvmLld(Package):
 
     version('3.4', '3b6a17e58c8416c869c14dd37682f78e')
 
+    depends_on('cmake', type='build')
+
     def install(self, spec, prefix):
         env['CXXFLAGS'] = self.compier.cxx11_flag
 

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

@@ -51,7 +51,7 @@ class Llvm(Package):
     variant('all_targets', default=True, description="Build all supported targets, default targets <current arch>,NVPTX,AMDGPU,CppBackend")
 
     # Build dependency
-    depends_on('cmake @2.8.12.2:')
+    depends_on('cmake@2.8.12.2:', type='build')
 
     # Universal dependency
     depends_on('python@2.7:2.8')  # Seems not to support python 3.X.Y

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

@@ -42,8 +42,8 @@ class Lmod(Package):
     version('6.0.1', '91abf52fe5033bd419ffe2842ebe7af9')
 
     depends_on('lua@5.2:')
-    depends_on('lua-luaposix')
-    depends_on('lua-luafilesystem')
+    depends_on('lua-luaposix', type=nolink)
+    depends_on('lua-luafilesystem', type=nolink)
 
     parallel = False
 

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

@@ -86,7 +86,7 @@ def append_paths(self, paths, cpaths, path):
 
     def setup_dependent_environment(self, spack_env, run_env, extension_spec):
         lua_paths = []
-        for d in extension_spec.traverse():
+        for d in extension_spec.traverse(deptypes=nolink, 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_share_dir))

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

@@ -37,7 +37,7 @@ class Mbedtls(Package):
     version('2.1.3' , '7eb4cf1dfa68578a2c8dbd0b6fa752dd')
     version('1.3.16', '4144d7320c691f721aeb9e67a1bc38e0')
 
-    depends_on('cmake')
+    depends_on('cmake', type='build')
 
     def install(self, spec, prefix):
         cmake('.', *std_cmake_args)

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

@@ -32,7 +32,7 @@ class Memaxes(Package):
     version('0.5', '5874f3fda9fd2d313c0ff9684f915ab5',
             url='https://github.com/llnl/MemAxes/archive/v0.5.tar.gz')
 
-    depends_on("cmake@2.8.9:")
+    depends_on('cmake@2.8.9:', type='build')
     depends_on("qt@5:")
 
     def install(self, spec, prefix):

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

@@ -44,8 +44,8 @@ class Mesa(Package):
 
     # mesa 10.x
     # depends_on("py-mako")
-    # depends_on("flex")
-    # depends_on("bison")
+    # depends_on("flex", type='build')
+    # depends_on("bison", type='build')
     # depends_on("dri2proto")
     # depends_on("libxcb")
     # depends_on("libxshmfence")