Source code for spack.build_systems.r

# Copyright 2013-2024 Lawrence Livermore 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 inspect
from typing import Optional, Tuple

import llnl.util.lang as lang

from spack.directives import extends

from .generic import GenericBuilder, Package



[docs]
class RBuilder(GenericBuilder):
    """The R builder provides a single phase that can be overridden:

        1. :py:meth:`~.RBuilder.install`

    It has sensible defaults, and for many packages the only thing
    necessary will be to add dependencies.
    """

    #: Names associated with package methods in the old build-system format
    legacy_methods: Tuple[str, ...] = (
        "configure_args",
        "configure_vars",
    ) + GenericBuilder.legacy_methods


[docs]
    def configure_args(self):
        """Arguments to pass to install via ``--configure-args``."""
        return []



[docs]
    def configure_vars(self):
        """Arguments to pass to install via ``--configure-vars``."""
        return []



[docs]
    def install(self, pkg, spec, prefix):
        """Installs an R package."""

        config_args = self.configure_args()
        config_vars = self.configure_vars()

        args = ["--vanilla", "CMD", "INSTALL"]

        if config_args:
            args.append("--configure-args={0}".format(" ".join(config_args)))

        if config_vars:
            args.append("--configure-vars={0}".format(" ".join(config_vars)))

        args.extend(["--library={0}".format(self.pkg.module.r_lib_dir), self.stage.source_path])

        inspect.getmodule(self.pkg).R(*args)





[docs]
class RPackage(Package):
    """Specialized class for packages that are built using R.

    For more information on the R build system, see:
    https://stat.ethz.ch/R-manual/R-devel/library/utils/html/INSTALL.html
    """

    # package attributes that can be expanded to set the homepage, url,
    # list_url, and git values
    # For CRAN packages
    cran: Optional[str] = None

    # For Bioconductor packages
    bioc: Optional[str] = None

    GenericBuilder = RBuilder

    #: This attribute is used in UI queries that need to know the build
    #: system base class
    build_system_class = "RPackage"

    extends("r")

    @lang.classproperty
    def homepage(cls):
        if cls.cran:
            return "https://cloud.r-project.org/package=" + cls.cran
        elif cls.bioc:
            return "https://bioconductor.org/packages/" + cls.bioc

    @lang.classproperty
    def url(cls):
        if cls.cran:
            return (
                "https://cloud.r-project.org/src/contrib/"
                + cls.cran
                + "_"
                + str(list(cls.versions)[0])
                + ".tar.gz"
            )

    @lang.classproperty
    def list_url(cls):
        if cls.cran:
            return "https://cloud.r-project.org/src/contrib/Archive/" + cls.cran + "/"

    @property
    def git(self):
        if self.bioc:
            return "https://git.bioconductor.org/packages/" + self.bioc