Merge pull request #757 from glennpj/extend_r

Make R extendable

lib/spack/spack/cmd/create.py

@@ -124,10 +124,12 @@ def __call__(self, stage):
         autotools = "configure('--prefix=%s' % prefix)"
         cmake     = "cmake('.', *std_cmake_args)"
         python    = "python('setup.py', 'install', '--prefix=%s' % prefix)"
+        r         = "R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)"
 
         config_lines = ((r'/configure$',      'autotools', autotools),
                         (r'/CMakeLists.txt$', 'cmake',     cmake),
-                        (r'/setup.py$',       'python',    python))
+                        (r'/setup.py$',       'python',    python),
+                        (r'/NAMESPACE$',      'r',         r))
 
         # Peek inside the tarball.
         tar = which('tar')
@@ -272,6 +274,10 @@ def create(parser, args):
     if guesser.build_system == 'python':
         name = 'py-%s' % name
 
+    # Prepend 'r-' to R package names, by convention.
+    if guesser.build_system == 'r':
+        name = 'r-%s' % name
+
     # Create a directory for the new package.
     pkg_path = repo.filename_for_package_name(name)
     if os.path.exists(pkg_path) and not args.force:

lib/spack/spack/url.py

@@ -206,6 +206,9 @@ def parse_version_offset(path):
         # e.g. lame-398-1
         (r'-((\d)+-\d)', stem),
 
+        # e.g. foobar_1.2-3
+        (r'_((\d+\.)+\d+(-\d+)?[a-z]?)', stem),
+
         # e.g. foobar-4.5.1
         (r'-((\d+\.)*\d+)$', stem),
 

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

@@ -1,4 +1,14 @@
+import functools
+import glob
+import inspect
+import os
+import re
+from contextlib import closing
+
+import spack
+from llnl.util.lang import match_predicate
 from spack import *
+from spack.util.environment import *
 
 
 class R(Package):
@@ -10,6 +20,8 @@ class R(Package):
     homepage = "https://www.r-project.org"
     url = "http://cran.cnr.berkeley.edu/src/base/R-3/R-3.1.2.tar.gz"
     
+    extendable = True
+
     version('3.2.3', '1ba3dac113efab69e706902810cc2970')
     version('3.2.2', '57cef5c2e210a5454da1979562a10e5b')
     version('3.2.1', 'c2aac8b40f84e08e7f8c9068de9239a3')
@@ -38,12 +50,57 @@ class R(Package):
     depends_on('tk')
 
     def install(self, spec, prefix):
+        rlibdir = join_path(prefix, 'rlib')
         options = ['--prefix=%s' % prefix,
+                   '--libdir=%s' % rlibdir,
                    '--enable-R-shlib',
-                   '--enable-BLAS-shlib']
+                   '--enable-BLAS-shlib',
+                   '--enable-R-framework=no']
         if '+external-lapack' in spec:
             options.extend(['--with-blas', '--with-lapack'])
 
         configure(*options)
         make()
         make('install')
+
+    # ========================================================================
+    # Set up environment to make install easy for R extensions.
+    # ========================================================================
+
+    @property
+    def r_lib_dir(self):
+        return os.path.join('rlib', 'R', 'library')
+
+    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():
+            if d.package.extends(self.spec):
+                r_libs_path.append(os.path.join(d.prefix, self.r_lib_dir))
+
+        r_libs_path = ':'.join(r_libs_path)
+        spack_env.set('R_LIBS', r_libs_path)
+
+        # For run time environment set only the path for extension_spec and prepend it to R_LIBS
+        if extension_spec.package.extends(self.spec):
+            run_env.prepend_path('R_LIBS', os.path.join(extension_spec.prefix, self.r_lib_dir))
+
+
+    def setup_dependent_package(self, module, ext_spec):
+        """
+        Called before R modules' install() methods.
+
+        In most cases, extensions will only need to have one line::
+
+	R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)
+        """
+        # R extension builds can have a global R executable function
+        module.R = Executable(join_path(self.spec.prefix.bin, 'R'))
+
+        # Add variable for library directry
+        module.r_lib_dir = os.path.join(ext_spec.prefix, self.r_lib_dir)
+
+        # Make the site packages directory for extensions, if it does not exist already.
+        if ext_spec.package.is_extension:
+            mkdirp(module.r_lib_dir)

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

@@ -0,0 +1,14 @@
+from spack import *
+
+class RBiocgenerics(Package):
+    """S4 generic functions needed by many Bioconductor packages."""
+
+    homepage = 'https://www.bioconductor.org/packages/release/bioc/html/BiocGenerics.html'
+    url      = "https://www.bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.16.1.tar.gz"
+
+    version('0.16.1', 'c2148ffd86fc6f1f819c7f68eb2c744f', expand=False)
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)

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

@@ -0,0 +1,18 @@
+from spack import *
+
+class RAbind(Package):
+    """Combine multidimensional arrays into a single array. This is a
+    generalization of 'cbind' and 'rbind'. Works with vectors, matrices, and
+    higher-dimensional arrays. Also provides functions 'adrop', 'asub', and
+    'afill' for manipulating, extracting and replacing data in arrays."""
+
+    homepage = "https://cran.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/abind_1.4-3.tar.gz"
+
+    version('1.4-3', '10fcf80c677b991bf263d38be35a1fc5', expand=False)
+
+    extends('R')
+
+    def install(self, spec, prefix):
+
+        R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)

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

@@ -0,0 +1,22 @@
+from spack import *
+
+class RFilehash(Package):
+    """Implements a simple key-value style database where character string keys
+    are associated with data values that are stored on the disk. A simple
+    interface is provided for inserting, retrieving, and deleting data from the
+    database. Utilities are provided that allow 'filehash' databases to be
+    treated much like environments and lists are already used in R. These
+    utilities are provided to encourage interactive and exploratory analysis on
+    large datasets. Three different file formats for representing the database
+    are currently available and new formats can easily be incorporated by third
+    parties for use in the 'filehash' framework."""
+
+    homepage = 'https://cran.r-project.org/'
+    url      = "https://cran.r-project.org/src/contrib/filehash_2.3.tar.gz"
+
+    version('2.3', '01fffafe09b148ccadc9814c103bdc2f', expand=False)
+
+    extends('R')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)

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

@@ -0,0 +1,19 @@
+from spack import *
+
+class RMagic(Package):
+    """A collection of efficient, vectorized algorithms for the creation and
+    investigation of magic squares and hypercubes, including a variety of
+    functions for the manipulation and analysis of arbitrarily dimensioned
+    arrays."""
+
+    homepage = "https://cran.r-project.org/"
+    url      = "https://cran.r-project.org/src/contrib/magic_1.5-6.tar.gz"
+
+    version('1.5-6', 'a68e5ced253b2196af842e1fc84fd029', expand=False)
+
+    extends('R')
+
+    depends_on('r-abind')
+
+    def install(self, spec, prefix):
+        R('CMD', 'INSTALL', '--library=%s' % self.module.r_lib_dir, '%s' % self.stage.archive_file)