# Copyright (C) 2014 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
"""
Tools for converting Cran packages to conda recipes.
"""
from __future__ import annotations

import argparse
import copy
import hashlib
import re
import subprocess
import sys
import tarfile
import unicodedata
import zipfile
from itertools import chain
from os import environ, listdir, makedirs, sep
from os.path import (
    basename,
    commonprefix,
    exists,
    isabs,
    isdir,
    isfile,
    join,
    normpath,
    realpath,
    relpath,
)
from typing import Literal

import requests
import yaml

# try to import C dumper
try:
    from yaml import CSafeDumper as SafeDumper
except ImportError:
    from yaml import SafeDumper

from conda.common.io import dashlist

from .. import source
from ..conda_interface import TemporaryDirectory, cc_conda_build
from ..config import get_or_merge_config
from ..license_family import allowed_license_families, guess_license_family
from ..metadata import MetaData
from ..utils import ensure_list, rm_rf
from ..variants import DEFAULT_VARIANTS, get_package_variants

SOURCE_META = """\
  {archive_keys}
  {git_url_key} {git_url}
  {git_tag_key} {git_tag}
  {patches}
"""

BINARY_META = """\
  url: {cranurl}{sel}
  {hash_entry}{sel}
"""

VERSION_META = """\
{{% set version = '{cran_version}' %}}{sel}"""

CRAN_META = """\
{version_source}
{version_binary1}
{version_binary2}

{{% set posix = 'm2-' if win else '' %}}
{{% set native = 'm2w64-' if win else '' %}}

package:
  name: {packagename}
  version: {{{{ version|replace("-", "_") }}}}

source:
{source}
{binary1}
{binary2}

build:
  merge_build_host: True{sel_src_and_win}
  # If this is a new build for the same version, increment the build number.
  number: {build_number}
  {skip_os}
  {noarch_generic}

  # This is required to make R link correctly on Linux.
  rpaths:
    - lib/R/lib/
    - lib/
  {script_env}
{suggests}
requirements:
  build:{build_depends}

  host:{host_depends}

  run:{run_depends}

test:
  commands:
    # You can put additional test commands to be run here.
    - $R -e "library('{cran_packagename}')"           # [not win]
    - "\\"%R%\\" -e \\"library('{cran_packagename}')\\""  # [win]

  # You can also put a file called run_test.py, run_test.sh, or run_test.bat
  # in the recipe that will be run at test time.

  # requires:
    # Put any additional test requirements here.

about:
  {home_comment}home:{homeurl}
  license: {license}
  {summary_comment}summary:{summary}
  license_family: {license_family}
  {license_file}

{extra_recipe_maintainers}

# The original CRAN metadata for this package was:

{cran_metadata}

# See
# https://docs.conda.io/projects/conda-build for
# more information about meta.yaml

"""

CRAN_BUILD_SH_SOURCE = """\
#!/bin/bash

# 'Autobrew' is being used by more and more packages these days
# to grab static libraries from Homebrew bottles. These bottles
# are fetched via Homebrew's --force-bottle option which grabs
# a bottle for the build machine which may not be macOS 10.9.
# Also, we want to use conda packages (and shared libraries) for
# these 'system' dependencies. See:
# https://github.com/jeroen/autobrew/issues/3
export DISABLE_AUTOBREW=1

# R refuses to build packages that mark themselves as Priority: Recommended
mv DESCRIPTION DESCRIPTION.old
grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION
# shellcheck disable=SC2086
${{R}} CMD INSTALL --build . ${{R_ARGS}}

# Add more build steps here, if they are necessary.

# See
# https://docs.conda.io/projects/conda-build
# for a list of environment variables that are set during the build process.
"""

CRAN_BUILD_SH_MIXED = """\
#!/bin/bash

set -o errexit -o pipefail

if {source_pf_bash}; then
  export DISABLE_AUTOBREW=1
  mv DESCRIPTION DESCRIPTION.old
  grep -va '^Priority: ' DESCRIPTION.old > DESCRIPTION
  # shellcheck disable=SC2086
  ${{R}} CMD INSTALL --build . ${{R_ARGS}}
else
  mkdir -p "${{PREFIX}}"/lib/R/library/{cran_packagename}
  mv ./* "${{PREFIX}}"/lib/R/library/{cran_packagename}

  if [[ ${{target_platform}} == osx-64 ]]; then
    pushd "${{PREFIX}}"
      for libdir in lib/R/lib lib/R/modules lib/R/library lib/R/bin/exec sysroot/usr/lib; do
        pushd "${{libdir}}" || exit 1
          while IFS= read -r -d '' SHARED_LIB
          do
            echo "fixing SHARED_LIB ${{SHARED_LIB}}"
            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5.0-MRO/Resources/lib/libR.dylib "${{PREFIX}}"/lib/R/lib/libR.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib "${{PREFIX}}"/lib/R/lib/libR.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/local/clang4/lib/libomp.dylib "${{PREFIX}}"/lib/libomp.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/local/gfortran/lib/libgfortran.3.dylib "${{PREFIX}}"/lib/libgfortran.3.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib "${{PREFIX}}"/lib/libquadmath.0.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/local/gfortran/lib/libquadmath.0.dylib "${{PREFIX}}"/lib/libquadmath.0.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib "${{PREFIX}}"/lib/libgfortran.3.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/lib/libgcc_s.1.dylib "${{PREFIX}}"/lib/libgcc_s.1.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/lib/libiconv.2.dylib "${{PREFIX}}"/sysroot/usr/lib/libiconv.2.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/lib/libncurses.5.4.dylib "${{PREFIX}}"/sysroot/usr/lib/libncurses.5.4.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/lib/libicucore.A.dylib "${{PREFIX}}"/sysroot/usr/lib/libicucore.A.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/lib/libexpat.1.dylib "${{PREFIX}}"/lib/libexpat.1.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/lib/libcurl.4.dylib "${{PREFIX}}"/lib/libcurl.4.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /usr/lib/libc++.1.dylib "${{PREFIX}}"/lib/libc++.1.dylib "${{SHARED_LIB}}" || true
            install_name_tool -change /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libc++.1.dylib "${{PREFIX}}"/lib/libc++.1.dylib "${{SHARED_LIB}}" || true
          done <   <(find . \\( -type f -iname "*.dylib" -or -iname "*.so" -or -iname "R" \\) -print0)
        popd
      done
    popd
  fi
fi
"""  # noqa: E501

CRAN_BUILD_SH_BINARY = """\
#!/bin/bash

set -o errexit -o pipefail

mkdir -p "${{PREFIX}}"/lib/R/library/{cran_packagename}
mv ./* "${{PREFIX}}"/lib/R/library/{cran_packagename}
"""

CRAN_BLD_BAT_SOURCE = """\
"%R%" CMD INSTALL --build . %R_ARGS%
IF %ERRORLEVEL% NEQ 0 exit /B 1
"""

# We hardcode the fact that CRAN does not provide win32 binaries here.
CRAN_BLD_BAT_MIXED = """\
if "%target_platform%" == "win-64" goto skip_source_build
"%R%" CMD INSTALL --build . %R_ARGS%
IF %ERRORLEVEL% NEQ 0 exit /B 1
exit 0
:skip_source_build
mkdir %PREFIX%\\lib\\R\\library
robocopy /E . "%PREFIX%\\lib\\R\\library\\{cran_packagename}"
if %ERRORLEVEL% NEQ 1 exit /B 1
exit 0
"""

INDENT = "\n    - "

CRAN_KEYS = [
    "Site",
    "Archs",
    "Depends",
    "Enhances",
    "Imports",
    "License",
    "License_is_FOSS",
    "License_restricts_use",
    "LinkingTo",
    "MD5sum",
    "NeedsCompilation",
    "OS_type",
    "Package",
    "Path",
    "Priority",
    "Suggests",
    "Version",
    "Title",
    "Author",
    "Maintainer",
]

# The following base/recommended package names are derived from R's source
# tree (R-3.0.2/share/make/vars.mk).  Hopefully they don't change too much
# between versions.
R_BASE_PACKAGE_NAMES = (
    "base",
    "compiler",
    "datasets",
    "graphics",
    "grDevices",
    "grid",
    "methods",
    "parallel",
    "splines",
    "stats",
    "stats4",
    "tcltk",
    "tools",
    "utils",
)

R_RECOMMENDED_PACKAGE_NAMES = (
    "MASS",
    "lattice",
    "Matrix",
    "nlme",
    "survival",
    "boot",
    "cluster",
    "codetools",
    "foreign",
    "KernSmooth",
    "rpart",
    "class",
    "nnet",
    "spatial",
    "mgcv",
)

# Stolen then tweaked from debian.deb822.PkgRelation.__dep_RE.
VERSION_DEPENDENCY_REGEX = re.compile(
    r"^\s*(?P<name>[a-zA-Z0-9.+\-]{1,})"
    r"(\s*\(\s*(?P<relop>[>=<]+)\s*"
    r"(?P<version>[0-9a-zA-Z:\-+~.]+)\s*\))"
    r"?(\s*\[(?P<archs>[\s!\w\-]+)\])?\s*$"
)

target_platform_bash_test_by_sel = {
    "linux": "=~ linux.*",
    "linux32": "== linux-32",
    "linux64": "== linux-64",
    "win32": "== win-32",
    "win64": "== win-64",
    "osx": "== osx-64",
}


def package_exists(package_name):
    # TODO: how can we get cran to spit out package presence?
    # available.packages() is probably a start, but no channels are working on mac right now?
    return True
    # install_output = subprocess.check_output([join(sys.prefix, "r"), "-e",
    #                     # ind=2 arbitrarily chooses some CRAN mirror to try.
    #                     "chooseCRANmirror(ind=2);install.packages('{}')".format(package_name)])


def add_parser(repos):
    # for loading default variant info
    cran = repos.add_parser(
        "cran",
        help="""
    Create recipe skeleton for packages hosted on the Comprehensive R Archive
    Network (CRAN) (cran.r-project.org).
        """,
        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
    )
    cran.add_argument(
        "packages",
        nargs="+",
        help="""CRAN packages to create recipe skeletons for.""",
    )
    cran.add_argument(
        "--output-dir",
        help="Directory to write recipes to (default: %(default)s).",
        default=".",
    )
    cran.add_argument(
        "--output-suffix",
        help="Suffix to add to recipe dir, can contain other dirs (eg: -feedstock/recipe).",
        default="",
    )
    cran.add_argument(
        "--add-maintainer",
        help="Add this github username as a maintainer if not already present.",
    )
    cran.add_argument(
        "--version",
        help="Version to use. Applies to all packages.",
    )
    cran.add_argument(
        "--git-tag",
        help="Git tag to use for GitHub recipes.",
    )
    cran.add_argument(
        "--all-urls",
        action="store_true",
        help="""Look at all URLs, not just source URLs. Use this if it can't
                find the right URL.""",
    )
    cran.add_argument(
        "--cran-url",
        help="URL to use for as source package repository",
    )
    cran.add_argument(
        "--r-interp",
        default="r-base",
        help="Declare R interpreter package",
    )
    cran.add_argument(
        "--use-binaries-ver",
        help=(
            "Repackage binaries from version provided by argument instead of building "
            "from source."
        ),
    )
    cran.add_argument(
        "--use-when-no-binary",
        choices=("src", "old", "src-old", "old-src", "error"),
        default="src",
        help="""Sometimes binaries are not available at the correct version for
                a given platform (macOS). You can use this flag to specify what
                fallback to take, either compiling from source or using an older
                binary or trying one then the other.""",
    )
    cran.add_argument(
        "--use-noarch-generic",
        action="store_true",
        dest="use_noarch_generic",
        help="Mark packages that do not need compilation as `noarch: generic`",
    )
    cran.add_argument(
        "--use-rtools-win",
        action="store_true",
        help="Use Rtools when building from source on Windows",
    )
    cran.add_argument(
        "--recursive",
        action="store_true",
        help="Create recipes for dependencies if they do not already exist.",
    )
    cran.add_argument(
        "--no-recursive",
        action="store_false",
        dest="recursive",
        help="Don't create recipes for dependencies if they do not already exist.",
    )
    cran.add_argument(
        "--no-archive",
        action="store_false",
        dest="archive",
        help="Don't include an Archive download url.",
    )
    cran.add_argument(
        "--allow-archived",
        action="store_true",
        dest="allow_archived",
        help="If the package has been archived, download the latest version.",
    )
    cran.add_argument(
        "--version-compare",
        action="store_true",
        help="""Compare the package version of the recipe with the one available
        on CRAN. Exits 1 if a newer version is available and 0 otherwise.""",
    )
    cran.add_argument(
        "--update-policy",
        action="store",
        choices=(
            "error",
            "skip-up-to-date",
            "skip-existing",
            "overwrite",
            "merge-keep-build-num",
            "merge-incr-build-num",
        ),
        default="error",
        help="""Dictates what to do when existing packages are encountered in the
        output directory (set by --output-dir). In the present implementation, the
        merge options avoid overwriting bld.bat and build.sh and only manage copying
        across patches, and the `build/{number,script_env}` fields. When the version
        changes, both merge options reset `build/number` to 0. When the version does
        not change they either keep the old `build/number` or else increase it by one.""",
    )
    cran.add_argument(
        "-m",
        "--variant-config-files",
        default=cc_conda_build.get("skeleton_config_yaml", None),
        help="""Variant config file to add.  These yaml files can contain
        keys such as `cran_mirror`.  Only one can be provided here.""",
    )
    cran.add_argument(
        "--add-cross-r-base",
        action="store_true",
        default=False,
        help="""Add cross-r-base to build requirements for cross compiling""",
    )
    cran.add_argument(
        "--no-comments",
        action="store_true",
        default=False,
        help="""Do not include instructional comments in recipe files""",
    )


def dict_from_cran_lines(lines):
    d = {}
    for line in lines:
        if not line:
            continue
        try:
            if ": " in line:
                (k, v) = line.split(": ", 1)
            else:
                # Sometimes fields are included but left blank, e.g.:
                #   - Enhances in data.tree
                #   - Suggests in corpcor
                (k, v) = line.split(":", 1)
        except ValueError:
            sys.exit("Error: Could not parse metadata (%s)" % line)
        d[k] = v
        # if k not in CRAN_KEYS:
        #     print("Warning: Unknown key %s" % k)
    d["orig_lines"] = lines
    return d


def remove_package_line_continuations(chunk):
    """
    >>> chunk = [
        'Package: A3',
        'Version: 0.9.2',
        'Depends: R (>= 2.15.0), xtable, pbapply',
        'Suggests: randomForest, e1071',
        'Imports: MASS, R.methodsS3 (>= 1.5.2), R.oo (>= 1.15.8), R.utils (>=',
        '        1.27.1), matrixStats (>= 0.8.12), R.filesets (>= 2.3.0), ',
        '        sampleSelection, scatterplot3d, strucchange, systemfit',
        'License: GPL (>= 2)',
        'NeedsCompilation: no']
    >>> remove_package_line_continuations(chunk)
    ['Package: A3',
     'Version: 0.9.2',
     'Depends: R (>= 2.15.0), xtable, pbapply',
     'Suggests: randomForest, e1071',
     'Imports: MASS, R.methodsS3 (>= 1.5.2), R.oo (>= 1.15.8), R.utils (>= 1.27.1), matrixStats (>= 0.8.12), R.filesets (>= 2.3.0), sampleSelection, scatterplot3d, strucchange, systemfit, rgl,'
     'License: GPL (>= 2)',
     'NeedsCompilation: no']
    """  # NOQA
    continuation = (" ", "\t")
    continued_ix = None
    continued_line = None
    had_continuation = False
    accumulating_continuations = False

    chunk.append("")

    for i, line in enumerate(chunk):
        if line.startswith(continuation):
            line = " " + line.lstrip()
            if accumulating_continuations:
                assert had_continuation
                continued_line += line
                chunk[i] = None
            else:
                accumulating_continuations = True
                continued_ix = i - 1
                continued_line = chunk[continued_ix] + line
                had_continuation = True
                chunk[i] = None
        else:
            if accumulating_continuations:
                assert had_continuation
                chunk[continued_ix] = continued_line
                accumulating_continuations = False
                continued_line = None
                continued_ix = None

    if had_continuation:
        # Remove the None(s).
        chunk = [c for c in chunk if c]

    chunk.append("")

    return chunk


def yaml_quote_string(string):
    """
    Quote a string for use in YAML.

    We can't just use yaml.dump because it adds ellipses to the end of the
    string, and it in general doesn't handle being placed inside an existing
    document very well.

    Note that this function is NOT general.
    """
    return (
        yaml.dump(string, indent=True, Dumper=SafeDumper)
        .replace("\n...\n", "")
        .replace("\n", "\n  ")
        .rstrip("\n ")
    )


# Due to how we render the metadata there can be significant areas of repeated newlines.
# This collapses them and also strips any trailing spaces.
def clear_whitespace(string):
    lines = []
    last_line = ""
    for line in string.splitlines():
        line = line.rstrip()
        if not (line == "" and last_line == ""):
            lines.append(line)
        last_line = line
    return "\n".join(lines)


def read_description_contents(fp):
    bytes = fp.read()
    text = bytes.decode("utf-8", errors="replace")
    text = clear_whitespace(text)
    lines = remove_package_line_continuations(text.splitlines())
    return dict_from_cran_lines(lines)


def get_archive_metadata(path, verbose=True):
    if verbose:
        print("Reading package metadata from %s" % path)
    if basename(path) == "DESCRIPTION":
        with open(path, "rb") as fp:
            return read_description_contents(fp)
    elif tarfile.is_tarfile(path):
        with tarfile.open(path, "r") as tf:
            for member in tf:
                if re.match(r"^[^/]+/DESCRIPTION$", member.name):
                    fp = tf.extractfile(member)
                    return read_description_contents(fp)
    elif path.endswith(".zip"):
        with zipfile.ZipFile(path, "r") as zf:
            for member in zf.infolist():
                if re.match(r"^[^/]+/DESCRIPTION$", member.filename):
                    fp = zf.open(member, "r")
                    return read_description_contents(fp)
    else:
        sys.exit("Cannot extract a DESCRIPTION from file %s" % path)
    sys.exit("%s does not seem to be a CRAN package (no DESCRIPTION) file" % path)


def get_latest_git_tag(config):
    # SO says to use taggerdate instead of committerdate, but that is invalid for lightweight tags.
    p = subprocess.Popen(
        [
            "git",
            "for-each-ref",
            "refs/tags",
            "--sort=-committerdate",
            "--format=%(refname:short)",
            "--count=1",
        ],
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE,
        cwd=config.work_dir,
    )

    stdout, stderr = p.communicate()
    stdout = stdout.decode("utf-8")
    stderr = stderr.decode("utf-8")
    if stderr or p.returncode:
        sys.exit("Error: git tag failed (%s)" % stderr)
    tags = stdout.strip().splitlines()
    if not tags:
        sys.exit("Error: no tags found")

    print("Using tag %s" % tags[-1])
    return tags[-1]


def _ssl_no_verify():
    """Gets whether the SSL_NO_VERIFY environment variable is set to 1 or True.

    This provides a workaround for users in some corporate environments where
    MITM style proxies make it difficult to fetch data over HTTPS.
    """
    return environ.get("SSL_NO_VERIFY", "").strip().lower() in ("1", "true")


def get_session(output_dir, verbose=True):
    session = requests.Session()
    session.verify = _ssl_no_verify()
    try:
        import cachecontrol
        import cachecontrol.caches
    except ImportError:
        if verbose:
            print(
                "Tip: install CacheControl and lockfile (conda packages) to cache the "
                "CRAN metadata"
            )
    else:
        session = cachecontrol.CacheControl(
            session, cache=cachecontrol.caches.FileCache(join(output_dir, ".web_cache"))
        )
    return session


def get_cran_archive_versions(cran_url, session, package, verbose=True):
    if verbose:
        print(f"Fetching archived versions for package {package} from {cran_url}")
    r = session.get(cran_url + "/src/contrib/Archive/" + package + "/")
    try:
        r.raise_for_status()
    except requests.exceptions.HTTPError as e:
        if e.response.status_code == 404:
            print("No archive directory for package %s" % package)
            return []
        raise
    versions = []
    for p, dt in re.findall(
        r'<td><a href="([^"]+)">\1</a></td>\s*<td[^>]*>([^<]*)</td>', r.text
    ):
        if p.endswith(".tar.gz") and "_" in p:
            name, version = p.rsplit(".", 2)[0].split("_", 1)
            versions.append((dt.strip(), version))
    return [v for dt, v in sorted(versions, reverse=True)]


def get_cran_index(cran_url, session, verbose=True):
    if verbose:
        print("Fetching main index from %s" % cran_url)
    r = session.get(cran_url + "/src/contrib/")
    r.raise_for_status()
    records = {}
    for p in re.findall(r'<td><a href="([^"]+)">\1</a></td>', r.text):
        if p.endswith(".tar.gz") and "_" in p:
            name, version = p.rsplit(".", 2)[0].split("_", 1)
            records[name.lower()] = (name, version)
    r = session.get(cran_url + "/src/contrib/Archive/")
    r.raise_for_status()
    for p in re.findall(r'<td><a href="([^"]+)/">\1/</a></td>', r.text):
        if re.match(r"^[A-Za-z]", p):
            records.setdefault(p.lower(), (p, None))
    return records


def make_array(m, key, allow_empty=False):
    result = []
    try:
        old_vals = m.get_value(key, [])
    except:
        old_vals = []
    if old_vals or allow_empty:
        result.append(key.split("/")[-1] + ":")
    for old_val in old_vals:
        result.append(f"{INDENT}{old_val}")
    return result


def existing_recipe_dir(output_dir, output_suffix, package, version):
    result = None
    if version:
        package = package + "-" + version.replace("-", "_")
    if exists(join(output_dir, package)):
        result = normpath(join(output_dir, package))
    elif exists(join(output_dir, package + output_suffix)):
        result = normpath(join(output_dir, package + output_suffix))
    elif exists(join(output_dir, "r-" + package + output_suffix)):
        result = normpath(join(output_dir, "r-" + package + output_suffix))
    return result


def strip_end(string, end):
    if string.endswith(end):
        return string[: -len(end)]
    return string


def package_to_inputs_dict(
    output_dir, output_suffix, git_tag, package: str, version=None
):
    """
    Converts `package` (*) into a tuple of:

    pkg_name (without leading 'r-')
    location (in a subdir of output_dir - may not exist - or at GitHub)
    old_git_rev (from existing metadata, so corresponds to the *old* version)
    metadata or None (if a recipe does *not* already exist)

    (*) `package` could be:
    1. A package name beginning (or not) with 'r-'
    2. A GitHub URL
    3. A file:// URL to a tarball
    4. A relative path to a recipe from output_dir
    5. An absolute path to a recipe (fatal unless in the output_dir hierarchy)
    6. Any of the above ending (or not) in sep or '/'

    So this function cleans all that up:

    Some packages may be from GitHub but we'd like the user not to have to worry
    about that on the command-line (for pre-existing recipes). Also, we may want
    to get version information from them (or existing metadata to merge) so lets
    load *all* existing recipes (later we will add or replace this metadata with
    any that we create).
    """
    if isfile(package):
        return None
    print("Parsing input package %s:" % package)
    package = strip_end(package, "/")
    package = strip_end(package, sep)
    if "github.com" in package:
        package = strip_end(package, ".git")
    pkg_name = basename(package).lower()
    pkg_name = strip_end(pkg_name, "-feedstock")
    if output_suffix:
        pkg_name = strip_end(pkg_name, output_suffix)
    if pkg_name.startswith("r-"):
        pkg_name = pkg_name[2:]
    if package.startswith("file://"):
        location = package.replace("file://", "")
        pkg_filename = basename(location)
        pkg_name = re.match(r"(.*)_(.*)", pkg_filename).group(1).lower()
        existing_location = existing_recipe_dir(
            output_dir, output_suffix, "r-" + pkg_name, version
        )
    elif isabs(package):
        commp = commonprefix((package, output_dir))
        if commp != output_dir:
            raise RuntimeError(
                f"package {package} specified with abs path outside of output-dir {output_dir}"
            )
        location = package
        existing_location = existing_recipe_dir(
            output_dir, output_suffix, "r-" + pkg_name, version
        )
    elif "github.com" in package:
        location = package
        existing_location = existing_recipe_dir(
            output_dir, output_suffix, "r-" + pkg_name, version
        )
    else:
        location = existing_location = existing_recipe_dir(
            output_dir, output_suffix, package, version
        )
    m: MetaData | None
    if existing_location:
        try:
            m = MetaData(existing_location)
        except:
            # Happens when the folder exists but contains no recipe.
            m = None
    else:
        m = None

    # It can still be the case that a package without 'github.com' in the location does really
    # come from there, for that we need to inspect the existing metadata's source/git_url.
    old_git_rev = git_tag
    if location and m and "github.com" not in location:
        git_url = m.get_value("source/git_url", "")
        if "github.com" in git_url:
            location = git_url
            old_git_rev = m.get_value("source/git_rev", None)

    vstr = "-" + version.replace("-", "_") if version else ""
    new_location = join(output_dir, "r-" + pkg_name + vstr + output_suffix)
    print(f".. name: {pkg_name} location: {location} new_location: {new_location}")

    return {
        "pkg-name": pkg_name,
        "location": location,
        "old-git-rev": old_git_rev,
        "old-metadata": m,
        "new-location": new_location,
        "version": version,
    }


def get_available_binaries(cran_url, details):
    url = cran_url + "/" + details["dir"]
    response = requests.get(url)
    response.raise_for_status()
    ext = details["ext"]
    for filename in re.findall(r'<a href="([^"]*)">\1</a>', response.text):
        if filename.endswith(ext):
            pkg, _, ver = filename.rpartition("_")
            ver, _, _ = ver.rpartition(ext)
            details["binaries"].setdefault(pkg, []).append((ver, url + filename))


def remove_comments(template):
    re_comment = re.compile(r"^\s*#\s")
    lines = template.split("\n")
    lines_no_comments = [line for line in lines if not re_comment.match(line)]
    return "\n".join(lines_no_comments)


def skeletonize(
    in_packages,
    output_dir=".",
    output_suffix="",
    add_maintainer=None,
    version=None,
    git_tag=None,
    cran_url=None,
    recursive=False,
    archive=True,
    version_compare=False,
    update_policy="",
    r_interp="r-base",
    use_binaries_ver=None,
    use_noarch_generic=False,
    use_when_no_binary: Literal["error" | "src" | "old" | "old-src"] = "src",
    use_rtools_win=False,
    config=None,
    variant_config_files=None,
    allow_archived=False,
    add_cross_r_base=False,
    no_comments=False,
):
    if (
        use_when_no_binary != "error"
        and use_when_no_binary != "src"
        and use_when_no_binary != "old"
        and use_when_no_binary != "old-src"
    ):
        print(f"ERROR: --use_when_no_binary={use_when_no_binary} not yet implemented")
        sys.exit(1)

    m: MetaData

    output_dir = realpath(output_dir)
    config = get_or_merge_config(config, variant_config_files=variant_config_files)

    if allow_archived and not archive:
        print("ERROR: --no-archive and --allow-archived conflict")
        sys.exit(1)

    if not cran_url:
        with TemporaryDirectory() as t:
            _variant = get_package_variants(t, config)[0]
        cran_url = ensure_list(
            _variant.get("cran_mirror", DEFAULT_VARIANTS["cran_mirror"])
        )[0]

    if len(in_packages) > 1 and version_compare:
        raise ValueError("--version-compare only works with one package at a time")
    if update_policy == "error" and not in_packages:
        raise ValueError("At least one package must be supplied")

    package_dicts = {}
    package_list = []

    cran_url = cran_url.rstrip("/")

    # Get cran index lazily so we don't have to go to CRAN
    # for a github repo or a local tarball
    cran_index = None

    cran_layout_template = {
        "source": {
            "selector": "{others}",
            "dir": "src/contrib/",
            "ext": ".tar.gz",
            # If we had platform filters we would change this to:
            # build_for_linux or is_github_url or is_tarfile
            "use_this": True,
        },
        "win-64": {
            "selector": "win64",
            "dir": f"bin/windows/contrib/{use_binaries_ver}/",
            "ext": ".zip",
            "use_this": True if use_binaries_ver else False,
        },
        "osx-64": {
            "selector": "osx",
            "dir": f"bin/macosx/el-capitan/contrib/{use_binaries_ver}/",
            "ext": ".tgz",
            "use_this": True if use_binaries_ver else False,
        },
    }

    # Figure out what binaries are available once:
    for archive_type, archive_details in cran_layout_template.items():
        archive_details["binaries"] = dict()
        if archive_type != "source" and archive_details["use_this"]:
            get_available_binaries(cran_url, archive_details)

    for package in in_packages:
        inputs_dict = package_to_inputs_dict(
            output_dir, output_suffix, git_tag, package, version
        )
        if inputs_dict:
            package_dicts.update({inputs_dict["pkg-name"]: {"inputs": inputs_dict}})

    for package_name, package_dict in package_dicts.items():
        package_list.append(package_name)

    while package_list:
        inputs = package_dicts[package_list.pop()]["inputs"]
        location = inputs["location"]
        pkg_name = inputs["pkg-name"]
        version = inputs["version"]
        is_github_url = location and "github.com" in location
        is_tarfile = location and isfile(location) and tarfile.is_tarfile(location)
        is_archive = False
        url = inputs["location"]

        dir_path = inputs["new-location"]
        print(f"Making/refreshing recipe for {pkg_name}")

        # Bodges GitHub packages into cran_metadata
        if is_tarfile:
            cran_package = get_archive_metadata(location)

        elif is_github_url or is_tarfile:
            rm_rf(config.work_dir)
            m = MetaData.fromdict({"source": {"git_url": location}}, config=config)
            source.git_source(
                m.get_section("source"), m.config.git_cache, m.config.work_dir
            )
            new_git_tag = git_tag if git_tag else get_latest_git_tag(config)
            p = subprocess.Popen(
                ["git", "checkout", new_git_tag],
                stdout=subprocess.PIPE,
                stderr=subprocess.PIPE,
                cwd=config.work_dir,
            )
            stdout, stderr = p.communicate()
            stdout = stdout.decode("utf-8")
            stderr = stderr.decode("utf-8")
            if p.returncode:
                sys.exit(
                    f"Error: 'git checkout {new_git_tag}' failed ({stderr.strip()}).\n"
                    "Invalid tag?"
                )
            if stdout:
                print(stdout, file=sys.stdout)
            if stderr:
                print(stderr, file=sys.stderr)
            DESCRIPTION = join(config.work_dir, "DESCRIPTION")
            if not isfile(DESCRIPTION):
                sub_description_pkg = join(config.work_dir, "pkg", "DESCRIPTION")
                sub_description_name = join(
                    config.work_dir, location.split("/")[-1], "DESCRIPTION"
                )
                if isfile(sub_description_pkg):
                    DESCRIPTION = sub_description_pkg
                elif isfile(sub_description_name):
                    DESCRIPTION = sub_description_name
                else:
                    sys.exit(
                        f"{location} does not appear to be a valid R package "
                        f"(no DESCRIPTION file in {sub_description_pkg}, {sub_description_name})"
                    )
            cran_package = get_archive_metadata(DESCRIPTION)

        else:
            if cran_index is None:
                session = get_session(output_dir)
                cran_index = get_cran_index(cran_url, session)
            if pkg_name.lower() not in cran_index:
                sys.exit("Package %s not found" % pkg_name)
            package, cran_version = cran_index[pkg_name.lower()]
            if cran_version and (not version or version == cran_version):
                version = cran_version
            elif version and not archive:
                print(
                    f"ERROR: Version {version} of package {package} is archived, but --no-archive was selected"
                )
                sys.exit(1)
            elif not version and not cran_version and not allow_archived:
                print(
                    "ERROR: Package %s is archived; to build, use --allow-archived or a --version value"
                    % pkg_name
                )
                sys.exit(1)
            else:
                is_archive = True
                all_versions = get_cran_archive_versions(cran_url, session, package)
                if cran_version:
                    all_versions = [cran_version] + all_versions
                if not version:
                    version = all_versions[0]
                elif version not in all_versions:
                    msg = f"ERROR: Version {version} of package {package} not found.\n  Available versions: "
                    print(msg + ", ".join(all_versions))
                    sys.exit(1)
            cran_package = None

        if cran_package is not None:
            package = cran_package["Package"]
            version = cran_package["Version"]
        plower = package.lower()
        d = package_dicts[pkg_name]
        d.update(
            {
                "cran_packagename": package,
                "cran_version": version,
                "packagename": "r-" + plower,
                # Conda versions cannot have -. Conda (verlib) will treat _ as a .
                "conda_version": version.replace("-", "_"),
                "patches": "",
                "build_number": 0,
                "build_depends": "",
                "host_depends": "",
                "run_depends": "",
                # CRAN doesn't seem to have this metadata :(
                "home_comment": "#",
                "homeurl": "",
                "summary_comment": "#",
                "summary": "",
                "binary1": "",
                "binary2": "",
            }
        )

        if version_compare:
            sys.exit(not version_compare(dir_path, d["conda_version"]))

        patches = []
        script_env = []
        extra_recipe_maintainers = []
        build_number = 0
        if update_policy.startswith("merge") and inputs["old-metadata"]:
            m = inputs["old-metadata"]
            patches = make_array(m, "source/patches")
            script_env = make_array(m, "build/script_env")
            extra_recipe_maintainers = make_array(
                m, "extra/recipe-maintainers", add_maintainer
            )
            if m.version() == d["conda_version"]:
                build_number = m.build_number()
                build_number += 1 if update_policy == "merge-incr-build-num" else 0
        if add_maintainer:
            new_maintainer = f"{INDENT}{add_maintainer}"
            if new_maintainer not in extra_recipe_maintainers:
                if not len(extra_recipe_maintainers):
                    # We hit this case when there is no existing recipe.
                    extra_recipe_maintainers = make_array(
                        {}, "extra/recipe-maintainers", True
                    )
                extra_recipe_maintainers.append(new_maintainer)
        if len(extra_recipe_maintainers):
            extra_recipe_maintainers[1:].sort()
            extra_recipe_maintainers.insert(0, "extra:\n  ")
        d["extra_recipe_maintainers"] = "".join(extra_recipe_maintainers)
        d["patches"] = "".join(patches)
        d["script_env"] = "".join(script_env)
        d["build_number"] = build_number

        cached_path = None
        cran_layout = copy.deepcopy(cran_layout_template)
        available = {}

        description_path = None
        for archive_type, archive_details in cran_layout.items():
            contrib_url = ""
            archive_details["cran_version"] = d["cran_version"]
            archive_details["conda_version"] = d["conda_version"]
            if is_archive and archive_type == "source":
                archive_details["dir"] += "Archive/" + package + "/"
            available_artefact = (
                True
                if archive_type == "source"
                else package in archive_details["binaries"]
                and any(
                    d["cran_version"] == v
                    for v, _ in archive_details["binaries"][package]
                )
            )
            if not available_artefact:
                if use_when_no_binary == "error":
                    print(
                        "ERROR: --use-when-no-binary is error (and there is no binary)"
                    )
                    sys.exit(1)
                elif use_when_no_binary.startswith("old"):
                    if package not in archive_details["binaries"]:
                        if use_when_no_binary.endswith("src"):
                            available_artefact = False
                            archive_details["use_this"] = False
                            continue
                        else:
                            print(
                                "ERROR: No binary nor old binary found "
                                "(maybe pass --use-when-no-binary=old-src to fallback to source?)"
                            )
                            sys.exit(1)
                    # Version needs to be stored in archive_details.
                    archive_details["cranurl"] = archive_details["binaries"][package][
                        -1
                    ][1]
                    archive_details["conda_version"] = archive_details["binaries"][
                        package
                    ][-1][0]
                    archive_details["cran_version"] = archive_details[
                        "conda_version"
                    ].replace("_", "-")
                    available_artefact = True
            # We may need to inspect the file later to determine which compilers are needed.
            cached_path = None
            sha256 = hashlib.sha256()
            if archive_details["use_this"] and available_artefact:
                if is_tarfile:
                    filename = basename(location)
                    contrib_url = relpath(location, dir_path)
                    contrib_url_rendered = package_url = contrib_url
                    cached_path = location
                elif not is_github_url or archive_type != "source":
                    filename_rendered = "{}_{}{}".format(
                        package, archive_details["cran_version"], archive_details["ext"]
                    )
                    filename = f"{package}_{{{{ version }}}}" + archive_details["ext"]
                    contrib_url = "{{{{ cran_mirror }}}}/{}".format(
                        archive_details["dir"]
                    )
                    contrib_url_rendered = cran_url + "/{}".format(
                        archive_details["dir"]
                    )
                    package_url = contrib_url_rendered + filename_rendered
                    print(f"Downloading {archive_type} from {package_url}")
                    try:
                        cached_path, _ = source.download_to_cache(
                            config.src_cache,
                            "",
                            {
                                "url": package_url,
                                "fn": archive_type + "-" + filename_rendered,
                            },
                        )
                    except:
                        print(
                            f"logic error, file {package_url} should exist, we found it in a dir listing earlier."
                        )
                        sys.exit(1)
                    if description_path is None or archive_type == "source":
                        description_path = cached_path
                available_details = {}
                available_details["selector"] = archive_details["selector"]
                available_details["cran_version"] = archive_details["cran_version"]
                available_details["conda_version"] = archive_details["conda_version"]
                if cached_path:
                    sha256.update(open(cached_path, "rb").read())
                    archive_details["cranurl"] = package_url
                    available_details["filename"] = filename
                    available_details["contrib_url"] = contrib_url
                    available_details["contrib_url_rendered"] = contrib_url_rendered
                    available_details["hash_entry"] = f"sha256: {sha256.hexdigest()}"
                    available_details["cached_path"] = cached_path
                # This is rubbish; d[] should be renamed global[] and should be
                #      merged into source and binaryN.
                if archive_type == "source":
                    if is_github_url:
                        available_details["url_key"] = ""
                        available_details["git_url_key"] = "git_url:"
                        available_details["git_tag_key"] = "git_tag:"
                        hash_msg = "# You can add a hash for the file here, (md5, sha1 or sha256)"
                        available_details["hash_entry"] = hash_msg
                        available_details["filename"] = ""
                        available_details["cranurl"] = ""
                        available_details["git_url"] = url
                        available_details["git_tag"] = new_git_tag
                        available_details["archive_keys"] = ""
                    else:
                        available_details["url_key"] = "url:"
                        available_details["git_url_key"] = ""
                        available_details["git_tag_key"] = ""
                        available_details["cranurl"] = " " + contrib_url + filename
                        available_details["git_url"] = ""
                        available_details["git_tag"] = ""
                else:
                    available_details["cranurl"] = archive_details["cranurl"]

                available_details["patches"] = d["patches"]
                available[archive_type] = available_details

        # Figure out the selectors according to what is available.
        _all = ["linux", "win32", "win64", "osx"]
        from_source = _all[:]
        binary_id = 1
        for archive_type, archive_details in available.items():
            if archive_type == "source":
                for k, v in archive_details.items():
                    d[k] = v
            else:
                sel = archive_details["selector"]
                # Does the file exist? If not we need to build from source.
                from_source.remove(sel)
                binary_id += 1
        if from_source == _all:
            sel_src = ""
            sel_src_and_win = "  # [win]"
            sel_src_not_win = "  # [not win]"
        else:
            sel_src = "  # [" + " or ".join(from_source) + "]"
            sel_src_and_win = (
                "  # ["
                + " or ".join(fs for fs in from_source if fs.startswith("win"))
                + "]"
            )
            sel_src_not_win = (
                "  # ["
                + " or ".join(fs for fs in from_source if not fs.startswith("win"))
                + "]"
            )
        sel_cross = "  # [build_platform != target_platform]"
        d["sel_src"] = sel_src
        d["sel_src_and_win"] = sel_src_and_win
        d["sel_src_not_win"] = sel_src_not_win
        d["from_source"] = from_source

        if "source" in available:
            available_details = available["source"]
            available_details["sel"] = sel_src
            filename = available_details["filename"]
            if "contrib_url" in available_details:
                contrib_url = available_details["contrib_url"]
                if archive:
                    if is_tarfile:
                        available_details["cranurl"] = INDENT + contrib_url
                    elif not is_archive:
                        available_details["cranurl"] = (
                            INDENT
                            + contrib_url
                            + filename
                            + sel_src
                            + INDENT
                            + contrib_url
                            + f"Archive/{package}/"
                            + filename
                            + sel_src
                        )
                else:
                    available_details["cranurl"] = (
                        " " + contrib_url + filename + sel_src
                    )
            if not is_github_url:
                available_details["archive_keys"] = (
                    "{url_key}{sel}    {cranurl}\n  {hash_entry}{sel}"
                ).format(**available_details)

        # Extract the DESCRIPTION data from the source
        if cran_package is None:
            cran_package = get_archive_metadata(description_path)
        d["cran_metadata"] = "\n".join(
            ["# %s" % line for line in cran_package["orig_lines"] if line]
        )

        # Render the source and binaryN keys
        binary_id = 1
        d["version_binary1"] = d["version_binary2"] = ""
        for archive_type, archive_details in available.items():
            if archive_type == "source":
                d["source"] = SOURCE_META.format(**archive_details)
                d["version_source"] = VERSION_META.format(**archive_details)
            else:
                archive_details["sel"] = "  # [" + archive_details["selector"] + "]"
                d["binary" + str(binary_id)] = BINARY_META.format(**archive_details)
                d["version_binary" + str(binary_id)] = VERSION_META.format(
                    **archive_details
                )
                binary_id += 1

        license_info = get_license_info(
            cran_package.get("License", "None"), allowed_license_families
        )
        d["license"], d["license_file"], d["license_family"] = license_info

        if "License_is_FOSS" in cran_package:
            d["license"] += " (FOSS)"
        if cran_package.get("License_restricts_use") == "yes":
            d["license"] += " (Restricts use)"

        if "URL" in cran_package:
            d["home_comment"] = ""
            d["homeurl"] = " " + yaml_quote_string(cran_package["URL"])
        else:
            # use CRAN page as homepage if nothing has been specified
            d["home_comment"] = ""
            if is_github_url:
                d["homeurl"] = f" {location}"
            else:
                d["homeurl"] = f" https://CRAN.R-project.org/package={package}"

        if (
            not use_noarch_generic
            or cran_package.get("NeedsCompilation", "no") == "yes"
        ):
            d["noarch_generic"] = ""
        else:
            d["noarch_generic"] = "noarch: generic"

        if "Description" in cran_package:
            d["summary_comment"] = ""
            d["summary"] = " " + yaml_quote_string(cran_package["Description"])

        if "Suggests" in cran_package and not no_comments:
            d["suggests"] = "# Suggests: %s" % cran_package["Suggests"]
        else:
            d["suggests"] = ""

        # Every package depends on at least R.
        # I'm not sure what the difference between depends and imports is.
        depends = [
            s.strip() for s in cran_package.get("Depends", "").split(",") if s.strip()
        ]
        imports = [
            s.strip() for s in cran_package.get("Imports", "").split(",") if s.strip()
        ]
        links = [
            s.strip() for s in cran_package.get("LinkingTo", "").split(",") if s.strip()
        ]

        dep_dict = {}

        seen = set()
        for s in list(chain(imports, depends, links)):
            match = VERSION_DEPENDENCY_REGEX.match(s)
            if not match:
                sys.exit(f"Could not parse version from dependency of {package}: {s}")
            name = match.group("name")
            if name in seen:
                continue
            seen.add(name)
            archs = match.group("archs")
            relop = match.group("relop") or ""
            ver = match.group("version") or ""
            ver = ver.replace("-", "_")
            # If there is a relop there should be a version
            assert not relop or ver

            if archs:
                sys.exit(
                    "Don't know how to handle archs from dependency of "
                    f"package {package}: {s}"
                )

            dep_dict[name] = f"{relop}{ver}"

        if "R" not in dep_dict:
            dep_dict["R"] = ""

        os_type = cran_package.get("OS_type", "")
        if os_type != "unix" and os_type != "windows" and os_type != "":
            print(f"Unknown OS_type: {os_type} in CRAN package")
            os_type = ""
        if os_type == "unix":
            d["skip_os"] = "skip: True  # [not unix]"
            d["noarch_generic"] = ""
        if os_type == "windows":
            d["skip_os"] = "skip: True  # [not win]"
            d["noarch_generic"] = ""
        if os_type == "" and no_comments:
            d["skip_os"] = ""
        elif os_type == "":
            d["skip_os"] = "# no skip"

        need_git = is_github_url
        if cran_package.get("NeedsCompilation", "no") == "yes":
            with tarfile.open(available["source"]["cached_path"]) as tf:
                need_f = any(
                    [
                        f.name.lower().endswith((".f", ".f90", ".f77", ".f95", ".f03"))
                        for f in tf
                    ]
                )
                # Fortran builds use CC to perform the link (they do not call the linker directly).
                need_c = (
                    True if need_f else any([f.name.lower().endswith(".c") for f in tf])
                )
                need_cxx = any(
                    [
                        f.name.lower().endswith((".cxx", ".cpp", ".cc", ".c++"))
                        for f in tf
                    ]
                )
                need_autotools = any(
                    [f.name.lower().endswith("/configure") for f in tf]
                )
                need_make = (
                    True
                    if any((need_autotools, need_f, need_cxx, need_c))
                    else any(
                        [
                            f.name.lower().endswith(("/makefile", "/makevars"))
                            for f in tf
                        ]
                    )
                )
        else:
            need_c = need_cxx = need_f = need_autotools = need_make = False

        if "Rcpp" in dep_dict or "RcppArmadillo" in dep_dict:
            need_cxx = True

        if need_cxx:
            need_c = True

        for dep_type in ["build", "host", "run"]:
            deps = []
            # Put non-R dependencies first.
            if dep_type == "build":
                if need_c:
                    deps.append(
                        f"{INDENT}{{{{ compiler('c') }}}}            {sel_src_not_win}"
                    )
                    deps.append(
                        f"{INDENT}{{{{ compiler('m2w64_c') }}}}      {sel_src_and_win}"
                    )
                if need_cxx:
                    deps.append(
                        f"{INDENT}{{{{ compiler('cxx') }}}}          {sel_src_not_win}"
                    )
                    deps.append(
                        f"{INDENT}{{{{ compiler('m2w64_cxx') }}}}    {sel_src_and_win}"
                    )
                if need_f:
                    deps.append(
                        f"{INDENT}{{{{ compiler('fortran') }}}}      {sel_src_not_win}"
                    )
                    deps.append(
                        f"{INDENT}{{{{ compiler('m2w64_fortran') }}}}{sel_src_and_win}"
                    )
                if use_rtools_win:
                    need_c = need_cxx = need_f = need_autotools = need_make = False
                    deps.append(f"{INDENT}rtools                   {sel_src_and_win}")
                    # extsoft is legacy. R packages will download rwinlib subprojects
                    # as necessary according to Jeroen Ooms. (may need to disable that
                    # for non-MRO builds or maybe switch to Jeroen's toolchain?)
                    # deps.append("{indent}{{{{native}}}}extsoft     {sel}".format(
                    #     indent=INDENT, sel=sel_src_and_win))
                if need_autotools or need_make or need_git:
                    deps.append(
                        f"{INDENT}{{{{ posix }}}}filesystem      {sel_src_and_win}"
                    )
                if need_git:
                    deps.append(f"{INDENT}{{{{ posix }}}}git")
                if need_autotools:
                    deps.append(
                        f"{INDENT}{{{{ posix }}}}sed             {sel_src_and_win}"
                    )
                    deps.append(
                        f"{INDENT}{{{{ posix }}}}grep            {sel_src_and_win}"
                    )
                    deps.append(f"{INDENT}{{{{ posix }}}}autoconf        {sel_src}")
                    deps.append(
                        f"{INDENT}{{{{ posix }}}}automake        {sel_src_not_win}"
                    )
                    deps.append(
                        f"{INDENT}{{{{ posix }}}}automake-wrapper{sel_src_and_win}"
                    )
                    deps.append(f"{INDENT}{{{{ posix }}}}pkg-config")
                if need_make:
                    deps.append(f"{INDENT}{{{{ posix }}}}make            {sel_src}")
                    if not need_autotools:
                        deps.append(
                            f"{INDENT}{{{{ posix }}}}sed             {sel_src_and_win}"
                        )
                    deps.append(
                        f"{INDENT}{{{{ posix }}}}coreutils       {sel_src_and_win}"
                    )
                deps.append(f"{INDENT}{{{{ posix }}}}zip             {sel_src_and_win}")
                if add_cross_r_base:
                    deps.append(f"{INDENT}cross-r-base {{{{ r_base }}}}  {sel_cross}")
            elif dep_type == "run":
                if need_c or need_cxx or need_f:
                    deps.append(
                        f"{INDENT}{{{{native}}}}gcc-libs       {sel_src_and_win}"
                    )

            if dep_type == "host" or dep_type == "run":
                for name in sorted(dep_dict):
                    if name in R_BASE_PACKAGE_NAMES:
                        continue
                    if name == "R":
                        # Put R first
                        # Regarless of build or run, and whether this is a
                        # recommended package or not, it can only depend on
                        # r_interp since anything else can and will cause
                        # cycles in the dependency graph. The cran metadata
                        # lists all dependencies anyway, even those packages
                        # that are in the recommended group.
                        # We don't include any R version restrictions because
                        # conda-build always pins r-base and mro-base version.
                        deps.insert(0, f"{INDENT}{r_interp}")
                    else:
                        conda_name = "r-" + name.lower()

                        if dep_dict[name]:
                            deps.append(f"{INDENT}{conda_name} {dep_dict[name]}")
                        else:
                            deps.append(f"{INDENT}{conda_name}")
                        if recursive:
                            lower_name = name.lower()
                            if lower_name not in package_dicts:
                                inputs_dict = package_to_inputs_dict(
                                    output_dir, output_suffix, git_tag, lower_name, None
                                )
                                assert (
                                    lower_name == inputs_dict["pkg-name"]
                                ), "name {} != inputs_dict['pkg-name'] {}".format(
                                    name, inputs_dict["pkg-name"]
                                )
                                assert lower_name not in package_list
                                package_dicts.update(
                                    {lower_name: {"inputs": inputs_dict}}
                                )
                                package_list.append(lower_name)

            d["%s_depends" % dep_type] = "".join(deps)

    if no_comments:
        global CRAN_BUILD_SH_SOURCE, CRAN_META
        CRAN_BUILD_SH_SOURCE = remove_comments(CRAN_BUILD_SH_SOURCE)
        CRAN_META = remove_comments(CRAN_META)

    for package in package_dicts:
        d = package_dicts[package]
        dir_path = d["inputs"]["new-location"]
        if exists(dir_path) and not version_compare:
            if update_policy == "error":
                raise RuntimeError(
                    "directory already exists "
                    "(and --update-policy is 'error'): %s" % dir_path
                )
            elif update_policy == "overwrite":
                rm_rf(dir_path)
        elif update_policy == "skip-up-to-date":
            if cran_index is None:
                session = get_session(output_dir)
                cran_index = get_cran_index(cran_url, session)
            if up_to_date(cran_index, d["inputs"]["old-metadata"]):
                continue
        elif update_policy == "skip-existing" and d["inputs"]["old-metadata"]:
            continue

        from_sources = d["from_source"]
        # Normalize the metadata values
        d = {
            k: unicodedata.normalize("NFKD", str(v)).encode("ascii", "ignore").decode()
            for k, v in d.items()
        }
        try:
            makedirs(join(dir_path))
        except:
            pass
        print("Writing recipe for %s" % package.lower())
        with open(join(dir_path, "meta.yaml"), "w") as f:
            f.write(clear_whitespace(CRAN_META.format(**d)))
        if not exists(join(dir_path, "build.sh")) or update_policy == "overwrite":
            with open(join(dir_path, "build.sh"), "wb") as f:
                if from_sources == _all:
                    f.write(CRAN_BUILD_SH_SOURCE.format(**d).encode("utf-8"))
                elif from_sources == []:
                    f.write(CRAN_BUILD_SH_BINARY.format(**d).encode("utf-8"))
                else:
                    tpbt = [target_platform_bash_test_by_sel[t] for t in from_sources]
                    d["source_pf_bash"] = " || ".join(
                        ["[[ ${target_platform} " + s + " ]]" for s in tpbt]
                    )
                    f.write(CRAN_BUILD_SH_MIXED.format(**d).encode("utf-8"))

        if not exists(join(dir_path, "bld.bat")) or update_policy == "overwrite":
            with open(join(dir_path, "bld.bat"), "wb") as f:
                if len([fs for fs in from_sources if fs.startswith("win")]) == 2:
                    f.write(
                        CRAN_BLD_BAT_SOURCE.format(**d)
                        .replace("\n", "\r\n")
                        .encode("utf-8")
                    )
                else:
                    f.write(
                        CRAN_BLD_BAT_MIXED.format(**d)
                        .replace("\n", "\r\n")
                        .encode("utf-8")
                    )


def version_compare(recipe_dir: str, newest_conda_version):
    m = MetaData(recipe_dir)
    local_version = m.version()
    package = basename(recipe_dir)

    print(f"Local recipe for {package} has version {local_version}.")

    print(f"The version on CRAN for {package} is {newest_conda_version}.")

    return local_version == newest_conda_version


def get_outdated(output_dir, cran_index, packages=()):
    to_update = []
    recipes = listdir(output_dir)
    for recipe in recipes:
        if not recipe.startswith("r-") or not isdir(recipe):
            continue

        recipe_name = recipe[2:]

        if packages and not (recipe_name in packages or recipe in packages):
            continue

        if recipe_name not in cran_index:
            print("Skipping %s, not found on CRAN" % recipe)
            continue

        version_compare(
            join(output_dir, recipe), cran_index[recipe_name][1].replace("-", "_")
        )

        print("Updating %s" % recipe)
        to_update.append(recipe_name)

    return to_update


def get_existing(output_dir, cran_index, packages=()):
    existing = []
    recipes = listdir(output_dir)
    for recipe in recipes:
        if not recipe.startswith("r-") or not isdir(recipe):
            continue

        recipe_name = recipe[2:]

        if packages and not (recipe_name in packages or recipe in packages):
            continue

        existing.append(recipe_name)

    return existing


def up_to_date(cran_index, package):
    r_pkg_name, location, old_git_rev, m = package
    cran_pkg_name = r_pkg_name[2:]

    # Does not exist, so is not up to date.
    if not m:
        return False

    # For now. We can do better; need to collect *all* information upfront.
    if "github.com" in location:
        return False
    else:
        if cran_pkg_name not in cran_index:
            return False

    name, version = cran_index[cran_pkg_name]
    if version and m.version() != version:
        return False

    return True


def get_license_info(license_text, allowed_license_families):
    """
    Most R packages on CRAN do not include a license file. Instead, to avoid
    duplication, R base ships with common software licenses:

    complete: AGPL-3, Artistic-2.0, GPL-2, GPL-3, LGPL-2, LGPL-2.1, LGPL-3
    template: BSD_2_clause BSD_3_clause, MIT

    The complete licenses can be included in conda binaries by pointing to the
    license file shipped with R base. The template files are more complicated
    because they would need to be combined with the license information provided
    by the package authors. In this case, the template file and the license
    information file are both packaged. All optional ('|' seperated) licenses
    are included, if they are matching.

    This function returns the path to the license file for the unambiguous
    cases.
    """

    # The list order matters. The first element should be the name of the
    # license file shipped with r-base.
    d_license = {
        "agpl3": ["AGPL-3", "AGPL (>= 3)", "AGPL", "GNU Affero General Public License"],
        "artistic2": ["Artistic-2.0", "Artistic License 2.0"],
        "gpl2": ["GPL-2", "GPL (>= 2)", "GNU General Public License (>= 2)"],
        "gpl3": [
            "GPL-3",
            "GPL (>= 3)",
            "GNU General Public License (>= 3)",
            "GPL",
            "GNU General Public License",
        ],
        "lgpl2": ["LGPL-2", "LGPL (>= 2)"],
        "lgpl21": ["LGPL-2.1", "LGPL (>= 2.1)"],
        "lgpl3": ["LGPL-3", "LGPL (>= 3)", "LGPL", "GNU Lesser General Public License"],
        "bsd2": ["BSD_2_clause", "BSD_2_Clause", "BSD 2-clause License"],
        "bsd3": ["BSD_3_clause", "BSD_3_Clause", "BSD 3-clause License"],
        "mit": ["MIT"],
    }

    license_file_template = (
        "'{{{{ environ[\"PREFIX\"] }}}}/lib/R/share/licenses/{license_id}'"
    )

    license_texts = []
    license_files = []

    # split license_text by "|" and "+" into parts for further matching
    license_text_parts = [l_opt.strip() for l_opt in re.split(r"\||\+", license_text)]
    for l_opt in license_text_parts:
        # the file case
        if l_opt.startswith("file "):
            license_files.append(l_opt[5:])
            continue

        # license id string to match
        for license_id in d_license.keys():
            if l_opt in d_license[license_id]:
                l_opt_text = d_license[license_id][0]

                license_texts.append(l_opt_text)
                license_files.append(
                    license_file_template.format(license_id=l_opt_text)
                )
                break

    # Join or fallback to original license_text if matched license_texts is empty
    license_text = " | ".join(license_texts) or license_text

    # Build the license_file entry and ensure it is empty if no license file
    license_file = ""
    if license_files:
        license_file = f"license_file:{dashlist(license_files, indent=4)}\n"

    # Only one family is allowed, so guessing it once
    license_family = guess_license_family(license_text, allowed_license_families)

    return license_text, license_file, license_family
