diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index f0cd50b8df6957..e3a31806ab82b7 100644 --- a/lib/spack/spack/cmd/create.py +++ b/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$', 'r', r)) # Peek inside the tarball. tar = which('tar') @@ -272,6 +274,10 @@ def create(parser, args): if guesser.build_system == 'python': name = 'py-%s' % name + # Prepend 'r-' to R package names, by convention. + if guesser.build_system == 'r': + name = 'r-%s' % name + # Create a directory for the new package. pkg_path = repo.filename_for_package_name(name) if os.path.exists(pkg_path) and not args.force: diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py index f51f05cad7d27b..ad51da9d47fae4 100644 --- a/lib/spack/spack/url.py +++ b/lib/spack/spack/url.py @@ -206,6 +206,9 @@ def parse_version_offset(path): # e.g. lame-398-1 (r'-((\d)+-\d)', stem), + # e.g. foobar_1.2-3 + (r'_((\d+\.)+\d+(-\d+)?[a-z]?)', stem), + # e.g. foobar-4.5.1 (r'-((\d+\.)*\d+)$', stem), diff --git a/var/spack/repos/builtin/packages/R/package.py b/var/spack/repos/builtin/packages/R/package.py index 2471dff09b6d24..7c4aa3520c827a 100644 --- a/var/spack/repos/builtin/packages/R/package.py +++ b/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): @@ -9,6 +19,8 @@ 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') @@ -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) diff --git a/var/spack/repos/builtin/packages/r-BiocGenerics/package.py b/var/spack/repos/builtin/packages/r-BiocGenerics/package.py new file mode 100644 index 00000000000000..2d92c1c4d88929 --- /dev/null +++ b/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) diff --git a/var/spack/repos/builtin/packages/r-abind/package.py b/var/spack/repos/builtin/packages/r-abind/package.py new file mode 100644 index 00000000000000..d06c7e9240aa8c --- /dev/null +++ b/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) diff --git a/var/spack/repos/builtin/packages/r-filehash/package.py b/var/spack/repos/builtin/packages/r-filehash/package.py new file mode 100644 index 00000000000000..4911c636b4df73 --- /dev/null +++ b/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) diff --git a/var/spack/repos/builtin/packages/r-magic/package.py b/var/spack/repos/builtin/packages/r-magic/package.py new file mode 100644 index 00000000000000..e900cdb216e241 --- /dev/null +++ b/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)