def skeletonize(packages,
output_dir=".",
version=None,
git_tag=None,
cran_url="https://cran.r-project.org/",
recursive=False,
archive=True,
version_compare=False,
update_outdated=False,
config=None):
if not config:
config = Config()
if len(packages) > 1 and version_compare:
raise ValueError(
"--version-compare only works with one package at a time")
if not update_outdated and not packages:
raise ValueError("At least one package must be supplied")
package_dicts = {}
cran_metadata = get_cran_metadata(cran_url, output_dir)
if update_outdated:
packages = get_outdated(output_dir, cran_metadata, packages)
for pkg in packages:
rm_rf(join(output_dir[0], 'r-' + pkg))
while packages:
package = packages.pop()
is_github_url = 'github.com' in package
url = package
if is_github_url:
rm_rf(config.work_dir)
m = metadata.MetaData.fromdict({'source': {
'git_url': package
}},
config=config)
source.git_source(m.get_section('source'), m.config.git_cache,
m.config.work_dir)
git_tag = git_tag[0] if git_tag else get_latest_git_tag(config)
p = subprocess.Popen(['git', 'checkout', 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(
"Error: 'git checkout %s' failed (%s).\nInvalid tag?" %
(git_tag, stderr.strip()))
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,
package.split('/')[-1],
"DESCRIPTION")
if isfile(sub_description_pkg):
DESCRIPTION = sub_description_pkg
elif isfile(sub_description_name):
DESCRIPTION = sub_description_name
else:
sys.exit(
"%s does not appear to be a valid R package "
"(no DESCRIPTION file in %s, %s)" %
(package, sub_description_pkg, sub_description_name))
with open(DESCRIPTION) as f:
description_text = clear_trailing_whitespace(f.read())
d = dict_from_cran_lines(
remove_package_line_continuations(
description_text.splitlines()))
d['orig_description'] = description_text
package = d['Package'].lower()
cran_metadata[package] = d
if package.startswith('r-'):
package = package[2:]
if package.endswith('/'):
package = package[:-1]
if package.lower() not in cran_metadata:
sys.exit("Package %s not found" % package)
# Make sure package is always uses the CRAN capitalization
package = cran_metadata[package.lower()]['Package']
if not is_github_url:
session = get_session(output_dir)
cran_metadata[package.lower()].update(
get_package_metadata(cran_url, package, session))
dir_path = join(output_dir, 'r-' + package.lower())
if exists(dir_path) and not version_compare:
raise RuntimeError("directory already exists: %s" % dir_path)
cran_package = cran_metadata[package.lower()]
d = package_dicts.setdefault(
package,
{
'cran_packagename': package,
'packagename': 'r-' + package.lower(),
'build_depends': '',
'run_depends': '',
# CRAN doesn't seem to have this metadata :(
'home_comment': '#',
'homeurl': '',
'summary_comment': '#',
'summary': '',
})
if is_github_url:
d['url_key'] = ''
d['fn_key'] = ''
d['git_url_key'] = 'git_url:'
d['git_tag_key'] = 'git_tag:'
d['hash_entry'] = '# You can add a hash for the file here, like md5, sha1 or sha256'
d['filename'] = ''
d['cranurl'] = ''
d['git_url'] = url
d['git_tag'] = git_tag
else:
d['url_key'] = 'url:'
d['fn_key'] = 'fn:'
d['git_url_key'] = ''
d['git_tag_key'] = ''
d['git_url'] = ''
d['git_tag'] = ''
d['hash_entry'] = ''
if version:
d['version'] = version
raise NotImplementedError(
"Package versions from CRAN are not yet implemented")
d['cran_version'] = cran_package['Version']
# Conda versions cannot have -. Conda (verlib) will treat _ as a .
d['conda_version'] = d['cran_version'].replace('-', '_')
if version_compare:
sys.exit(not version_compare(dir_path, d['conda_version']))
if not is_github_url:
filename = '{}_{}.tar.gz'
contrib_url = cran_url + 'src/contrib/'
package_url = contrib_url + filename.format(
package, d['cran_version'])
# calculate sha256 by downloading source
sha256 = hashlib.sha256()
print("Downloading source from {}".format(package_url))
sha256.update(urlopen(package_url).read())
d['hash_entry'] = 'sha256: {}'.format(sha256.hexdigest())
d['filename'] = filename.format(package, '{{ version }}')
if archive:
d['cranurl'] = (INDENT + contrib_url + d['filename'] + INDENT +
contrib_url + 'Archive/{}/'.format(package) +
d['filename'])
else:
d['cranurl'] = ' ' + cran_url + 'src/contrib/' + d['filename']
d['cran_metadata'] = '\n'.join(
['# %s' % l for l in cran_package['orig_lines'] if l])
# XXX: We should maybe normalize these
d['license'] = cran_package.get("License", "None")
d['license_family'] = guess_license_family(d['license'],
allowed_license_families)
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'] = ''
d['homeurl'] = ' https://CRAN.R-project.org/package={}'.format(
package)
if 'Description' in cran_package:
d['summary_comment'] = ''
d['summary'] = ' ' + yaml_quote_string(cran_package['Description'])
if "Suggests" in cran_package:
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 = {}
for s in set(chain(depends, imports, links)):
match = VERSION_DEPENDENCY_REGEX.match(s)
if not match:
sys.exit("Could not parse version from dependency of %s: %s" %
(package, s))
name = match.group('name')
archs = match.group('archs')
relop = match.group('relop') or ''
version = match.group('version') or ''
version = version.replace('-', '_')
# If there is a relop there should be a version
assert not relop or version
if archs:
sys.exit("Don't know how to handle archs from dependency of "
"package %s: %s" % (package, s))
dep_dict[name] = '{relop}{version}'.format(relop=relop,
version=version)
if 'R' not in dep_dict:
dep_dict['R'] = ''
for dep_type in ['build', 'run']:
deps = []
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-base' 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.
r_name = 'r-base'
# We don't include any R version restrictions because we
# always build R packages against an exact R version
deps.insert(
0, '{indent}{r_name}'.format(indent=INDENT,
r_name=r_name))
else:
conda_name = 'r-' + name.lower()
if dep_dict[name]:
deps.append('{indent}{name} {version}'.format(
name=conda_name,
version=dep_dict[name],
indent=INDENT))
else:
deps.append('{indent}{name}'.format(name=conda_name,
indent=INDENT))
if recursive:
if not exists(join(output_dir, conda_name)):
packages.append(name)
if cran_package.get("NeedsCompilation", 'no') == 'yes':
if dep_type == 'build':
deps.append('{indent}posix # [win]'.format(
indent=INDENT))
deps.append(
'{indent}{{{{native}}}}toolchain # [win]'.format(
indent=INDENT))
deps.append(
'{indent}gcc # [not win]'.format(
indent=INDENT))
elif dep_type == 'run':
deps.append(
'{indent}{{{{native}}}}gcc-libs # [win]'.format(
indent=INDENT))
deps.append(
'{indent}libgcc # [not win]'.format(
indent=INDENT))
d['%s_depends' % dep_type] = ''.join(deps)
for package in package_dicts:
d = package_dicts[package]
name = d['packagename']
# Normalize the metadata values
d = {
k: unicodedata.normalize("NFKD",
text_type(v)).encode('ascii',
'ignore').decode()
for k, v in iteritems(d)
}
makedirs(join(output_dir, name))
print("Writing recipe for %s" % package.lower())
with open(join(output_dir, name, 'meta.yaml'), 'w') as f:
f.write(clear_trailing_whitespace(CRAN_META.format(**d)))
with open(join(output_dir, name, 'build.sh'), 'w') as f:
f.write(CRAN_BUILD_SH.format(**d))
with open(join(output_dir, name, 'bld.bat'), 'w') as f:
f.write(CRAN_BLD_BAT.format(**d))
print("Done")
def main(args, parser):
if len(args.packages) > 1 and args.version_compare:
parser.error("--version-compare only works with one package at a time")
if not args.update_outdated and not args.packages:
parser.error("At least one package must be supplied")
package_dicts = {}
[output_dir] = args.output_dir
cran_metadata = get_cran_metadata(args.cran_url, output_dir)
if args.update_outdated:
args.packages = get_outdated(output_dir, cran_metadata, args.packages)
for pkg in args.packages:
rm_rf(join(args.output_dir, 'r-' + pkg))
while args.packages:
package = args.packages.pop()
is_github_url = 'github.com' in package
url = package
if is_github_url:
rm_rf(source.WORK_DIR)
source.git_source({'git_url': package}, '.')
git_tag = args.git_tag[0] if args.git_tag else get_latest_git_tag()
p = subprocess.Popen(['git', 'checkout', git_tag], stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=source.WORK_DIR)
stdout, stderr = p.communicate()
stdout = stdout.decode('utf-8')
stderr = stderr.decode('utf-8')
if p.returncode:
sys.exit("Error: 'git checkout %s' failed (%s).\nInvalid tag?" % (git_tag, stderr.strip()))
if stdout:
print(stdout, file=sys.stdout)
if stderr:
print(stderr, file=sys.stderr)
DESCRIPTION = join(source.WORK_DIR, "DESCRIPTION")
if not isfile(DESCRIPTION):
sub_description_pkg = join(source.WORK_DIR, 'pkg', "DESCRIPTION")
sub_description_name = join(source.WORK_DIR, package.split('/')[-1], "DESCRIPTION")
if isfile(sub_description_pkg):
DESCRIPTION = sub_description_pkg
elif isfile(sub_description_name):
DESCRIPTION = sub_description_name
else:
sys.exit("%s does not appear to be a valid R package (no DESCRIPTION file)" % package)
with open(DESCRIPTION) as f:
description_text = clear_trailing_whitespace(f.read())
d = dict_from_cran_lines(remove_package_line_continuations(description_text.splitlines()))
d['orig_description'] = description_text
package = d['Package'].lower()
cran_metadata[package] = d
if package.startswith('r-'):
package = package[2:]
if package.endswith('/'):
package = package[:-1]
if package.lower() not in cran_metadata:
sys.exit("Package %s not found" % package)
# Make sure package is always uses the CRAN capitalization
package = cran_metadata[package.lower()]['Package']
if not is_github_url:
session = get_session(output_dir)
cran_metadata[package.lower()].update(get_package_metadata(args.cran_url,
package, session))
dir_path = join(output_dir, 'r-' + package.lower())
if exists(dir_path) and not args.version_compare:
raise RuntimeError("directory already exists: %s" % dir_path)
cran_package = cran_metadata[package.lower()]
d = package_dicts.setdefault(package,
{
'cran_packagename': package,
'packagename': 'r-' + package.lower(),
'build_depends': '',
'run_depends': '',
# CRAN doesn't seem to have this metadata :(
'home_comment': '#',
'homeurl': '',
'summary_comment': '#',
'summary': '',
})
if is_github_url:
d['url_key'] = ''
d['fn_key'] = ''
d['git_url_key'] = 'git_url:'
d['git_tag_key'] = 'git_tag:'
d['filename'] = ''
d['cranurl'] = ''
d['git_url'] = url
d['git_tag'] = git_tag
else:
d['url_key'] = 'url:'
d['fn_key'] = 'fn:'
d['git_url_key'] = ''
d['git_tag_key'] = ''
d['git_url'] = ''
d['git_tag'] = ''
if args.version:
raise NotImplementedError("Package versions from CRAN are not yet implemented")
[version] = args.version
d['version'] = version
d['cran_version'] = cran_package['Version']
# Conda versions cannot have -. Conda (verlib) will treat _ as a .
d['conda_version'] = d['cran_version'].replace('-', '_')
if args.version_compare:
sys.exit(not version_compare(dir_path, d['conda_version']))
if not is_github_url:
d['filename'] = "{cran_packagename}_{cran_version}.tar.gz".format(**d)
if args.archive:
d['cranurl'] = (INDENT + args.cran_url + 'src/contrib/' +
d['filename'] + INDENT + args.cran_url + 'src/contrib/' +
'Archive/' + d['cran_packagename'] + '/' + d['filename'])
else:
d['cranurl'] = ' ' + args.cran_url + 'src/contrib/' + d['filename']
d['cran_metadata'] = '\n'.join(['# %s' % l for l in
cran_package['orig_lines'] if l])
# XXX: We should maybe normalize these
d['license'] = cran_package.get("License", "None")
if 'License_is_FOSS' in cran_package:
d['license'] += ' (FOSS)'
if cran_package.get('License_restricts_use', None) == 'yes':
d['license'] += ' (Restricts use)'
if "URL" in cran_package:
d['home_comment'] = ''
d['homeurl'] = ' ' + yaml_quote_string(cran_package['URL'])
if 'Description' in cran_package:
d['summary_comment'] = ''
d['summary'] = ' ' + yaml_quote_string(cran_package['Description'])
if "Suggests" in cran_package:
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 = {}
for s in set(chain(depends, imports, links)):
match = VERSION_DEPENDENCY_REGEX.match(s)
if not match:
sys.exit("Could not parse version from dependency of %s: %s" %
(package, s))
name = match.group('name')
archs = match.group('archs')
relop = match.group('relop') or ''
version = match.group('version') or ''
version = version.replace('-', '_')
# If there is a relop there should be a version
assert not relop or version
if archs:
sys.exit("Don't know how to handle archs from dependency of "
"package %s: %s" % (package, s))
dep_dict[name] = '{relop}{version}'.format(relop=relop, version=version)
if 'R' not in dep_dict:
dep_dict['R'] = ''
for dep_type in ['build', 'run']:
deps = []
for name in sorted(dep_dict):
if name in R_BASE_PACKAGE_NAMES:
continue
if name == 'R':
# Put R first
if d['cran_packagename'] in R_RECOMMENDED_PACKAGE_NAMES and dep_type == 'build':
# On Linux and OS X, r is a metapackage depending on
# r-base and r-recommended. Recommended packages cannot
# build depend on r as they would then build depend on
# themselves and the built package would end up being
# empty (because conda would find no new files)
r_name = 'r-base'
else:
r_name = 'r'
# We don't include any R version restrictions because we
# always build R packages against an exact R version
deps.insert(0, '{indent}{r_name}'.format(indent=INDENT, r_name=r_name))
else:
conda_name = 'r-' + name.lower()
# The r package on Windows includes the recommended packages
if name in R_RECOMMENDED_PACKAGE_NAMES:
end = ' # [not win]'
else:
end = ''
if dep_dict[name]:
deps.append('{indent}{name} {version}{end}'.format(name=conda_name,
version=dep_dict[name], end=end, indent=INDENT))
else:
deps.append('{indent}{name}{end}'.format(name=conda_name,
indent=INDENT, end=end))
if args.recursive:
if not exists(join(output_dir, conda_name)):
args.packages.append(name)
if cran_package.get("NeedsCompilation", 'no') == 'yes':
if dep_type == 'build':
deps.append('{indent}gcc # [not win]'.format(indent=INDENT))
else:
deps.append('{indent}libgcc # [not win]'.format(indent=INDENT))
d['%s_depends' % dep_type] = ''.join(deps)
for package in package_dicts:
d = package_dicts[package]
name = d['packagename']
makedirs(join(output_dir, name))
print("Writing recipe for %s" % package.lower())
with open(join(output_dir, name, 'meta.yaml'), 'w') as f:
f.write(clear_trailing_whitespace(CRAN_META.format(**d)))
with open(join(output_dir, name, 'build.sh'), 'w') as f:
f.write(CRAN_BUILD_SH.format(**d))
with open(join(output_dir, name, 'bld.bat'), 'w') as f:
f.write(CRAN_BLD_BAT.format(**d))
print("Done")
def skeletonize(packages, output_dir=".", version=None, git_tag=None,
cran_url="https://cran.r-project.org/", recursive=False, archive=True,
version_compare=False, update_outdated=False, config=None):
if not config:
config = Config()
if len(packages) > 1 and version_compare:
raise ValueError("--version-compare only works with one package at a time")
if not update_outdated and not packages:
raise ValueError("At least one package must be supplied")
package_dicts = {}
cran_metadata = get_cran_metadata(cran_url, output_dir)
if update_outdated:
packages = get_outdated(output_dir, cran_metadata, packages)
for pkg in packages:
rm_rf(join(output_dir[0], 'r-' + pkg))
while packages:
package = packages.pop()
is_github_url = 'github.com' in package
url = package
if is_github_url:
rm_rf(config.work_dir)
m = metadata.MetaData.fromdict({'source': {'git_url': package}}, config=config)
source.git_source(m.get_section('source'), m.config.git_cache, m.config.work_dir)
git_tag = git_tag[0] if git_tag else get_latest_git_tag(config)
p = subprocess.Popen(['git', 'checkout', 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("Error: 'git checkout %s' failed (%s).\nInvalid tag?" %
(git_tag, stderr.strip()))
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, package.split('/')[-1], "DESCRIPTION")
if isfile(sub_description_pkg):
DESCRIPTION = sub_description_pkg
elif isfile(sub_description_name):
DESCRIPTION = sub_description_name
else:
sys.exit("%s does not appear to be a valid R package "
"(no DESCRIPTION file in %s, %s)"
% (package, sub_description_pkg, sub_description_name))
with open(DESCRIPTION) as f:
description_text = clear_trailing_whitespace(f.read())
d = dict_from_cran_lines(remove_package_line_continuations(
description_text.splitlines()))
d['orig_description'] = description_text
package = d['Package'].lower()
cran_metadata[package] = d
if package.startswith('r-'):
package = package[2:]
if package.endswith('/'):
package = package[:-1]
if package.lower() not in cran_metadata:
sys.exit("Package %s not found" % package)
# Make sure package is always uses the CRAN capitalization
package = cran_metadata[package.lower()]['Package']
if not is_github_url:
session = get_session(output_dir)
cran_metadata[package.lower()].update(get_package_metadata(cran_url,
package, session))
dir_path = join(output_dir, 'r-' + package.lower())
if exists(dir_path) and not version_compare:
raise RuntimeError("directory already exists: %s" % dir_path)
cran_package = cran_metadata[package.lower()]
d = package_dicts.setdefault(package,
{
'cran_packagename': package,
'packagename': 'r-' + package.lower(),
'build_depends': '',
'run_depends': '',
# CRAN doesn't seem to have this metadata :(
'home_comment': '#',
'homeurl': '',
'summary_comment': '#',
'summary': '',
})
if is_github_url:
d['url_key'] = ''
d['fn_key'] = ''
d['git_url_key'] = 'git_url:'
d['git_tag_key'] = 'git_tag:'
d['hash_entry'] = '# You can add a hash for the file here, like md5, sha1 or sha256'
d['filename'] = ''
d['cranurl'] = ''
d['git_url'] = url
d['git_tag'] = git_tag
else:
d['url_key'] = 'url:'
d['fn_key'] = 'fn:'
d['git_url_key'] = ''
d['git_tag_key'] = ''
d['git_url'] = ''
d['git_tag'] = ''
d['hash_entry'] = ''
if version:
d['version'] = version
raise NotImplementedError("Package versions from CRAN are not yet implemented")
d['cran_version'] = cran_package['Version']
# Conda versions cannot have -. Conda (verlib) will treat _ as a .
d['conda_version'] = d['cran_version'].replace('-', '_')
if version_compare:
sys.exit(not version_compare(dir_path, d['conda_version']))
if not is_github_url:
filename = '{}_{}.tar.gz'
contrib_url = cran_url + 'src/contrib/'
package_url = contrib_url + filename.format(package, d['cran_version'])
# calculate sha256 by downloading source
sha256 = hashlib.sha256()
print("Downloading source from {}".format(package_url))
sha256.update(urlopen(package_url).read())
d['hash_entry'] = 'sha256: {}'.format(sha256.hexdigest())
d['filename'] = filename.format(package, '{{ version }}')
if archive:
d['cranurl'] = (INDENT + contrib_url +
d['filename'] + INDENT + contrib_url +
'Archive/{}/'.format(package) + d['filename'])
else:
d['cranurl'] = ' ' + cran_url + 'src/contrib/' + d['filename']
d['cran_metadata'] = '\n'.join(['# %s' % l for l in
cran_package['orig_lines'] if l])
# XXX: We should maybe normalize these
d['license'] = cran_package.get("License", "None")
d['license_family'] = guess_license_family(d['license'], allowed_license_families)
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'] = ''
d['homeurl'] = ' https://CRAN.R-project.org/package={}'.format(package)
if 'Description' in cran_package:
d['summary_comment'] = ''
d['summary'] = ' ' + yaml_quote_string(cran_package['Description'])
if "Suggests" in cran_package:
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 = {}
for s in set(chain(depends, imports, links)):
match = VERSION_DEPENDENCY_REGEX.match(s)
if not match:
sys.exit("Could not parse version from dependency of %s: %s" %
(package, s))
name = match.group('name')
archs = match.group('archs')
relop = match.group('relop') or ''
version = match.group('version') or ''
version = version.replace('-', '_')
# If there is a relop there should be a version
assert not relop or version
if archs:
sys.exit("Don't know how to handle archs from dependency of "
"package %s: %s" % (package, s))
dep_dict[name] = '{relop}{version}'.format(relop=relop, version=version)
if 'R' not in dep_dict:
dep_dict['R'] = ''
for dep_type in ['build', 'run']:
deps = []
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-base' 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.
r_name = 'r-base'
# We don't include any R version restrictions because we
# always build R packages against an exact R version
deps.insert(0, '{indent}{r_name}'.format(indent=INDENT, r_name=r_name))
else:
conda_name = 'r-' + name.lower()
if dep_dict[name]:
deps.append('{indent}{name} {version}'.format(name=conda_name,
version=dep_dict[name], indent=INDENT))
else:
deps.append('{indent}{name}'.format(name=conda_name,
indent=INDENT))
if recursive:
if not exists(join(output_dir, conda_name)):
packages.append(name)
if cran_package.get("NeedsCompilation", 'no') == 'yes':
if dep_type == 'build':
deps.append('{indent}posix # [win]'.format(indent=INDENT))
deps.append('{indent}{{{{native}}}}toolchain # [win]'.format(indent=INDENT))
deps.append('{indent}gcc # [not win]'.format(indent=INDENT))
elif dep_type == 'run':
deps.append('{indent}{{{{native}}}}gcc-libs # [win]'.format(indent=INDENT))
deps.append('{indent}libgcc # [not win]'.format(indent=INDENT))
d['%s_depends' % dep_type] = ''.join(deps)
for package in package_dicts:
d = package_dicts[package]
name = d['packagename']
# Normalize the metadata values
d = {k: unicodedata.normalize("NFKD", text_type(v)).encode('ascii', 'ignore')
.decode() for k, v in iteritems(d)}
makedirs(join(output_dir, name))
print("Writing recipe for %s" % package.lower())
with open(join(output_dir, name, 'meta.yaml'), 'w') as f:
f.write(clear_trailing_whitespace(CRAN_META.format(**d)))
with open(join(output_dir, name, 'build.sh'), 'w') as f:
f.write(CRAN_BUILD_SH.format(**d))
with open(join(output_dir, name, 'bld.bat'), 'w') as f:
f.write(CRAN_BLD_BAT.format(**d))
print("Done")
def skeletonize(in_packages, output_dir=".", output_suffix="", add_maintainer=None, version=None,
git_tag=None, cran_url="https://cran.r-project.org", recursive=False, archive=True,
version_compare=False, update_policy='', r_interp='r-base', use_binaries_ver=None,
use_noarch_generic=False, use_rtools_win=False, config=None):
output_dir = realpath(output_dir)
if not config:
config = Config()
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('/')
cran_metadata = get_cran_metadata(cran_url, output_dir)
# r_recipes_in_output_dir = []
# recipes = listdir(output_dir)
# for recipe in recipes:
# if not recipe.startswith('r-') or not isdir(recipe):
# continue
# r_recipes_in_output_dir.append(recipe)
for package in in_packages:
inputs_dict = package_to_inputs_dict(output_dir, output_suffix, git_tag, package)
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']
is_github_url = location and 'github.com' in location
is_tarfile = location and isfile(location) and tarfile.is_tarfile(location)
url = inputs['location']
dir_path = inputs['new-location']
print("Making/refreshing recipe for {}".format(pkg_name))
# Bodges GitHub packages into cran_metadata
if is_github_url or is_tarfile:
rm_rf(config.work_dir)
if is_github_url:
m = metadata.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("Error: 'git checkout %s' failed (%s).\nInvalid tag?" %
(new_git_tag, stderr.strip()))
if stdout:
print(stdout, file=sys.stdout)
if stderr:
print(stderr, file=sys.stderr)
else:
m = metadata.MetaData.fromdict({'source': {'url': location}}, config=config)
source.unpack(m.get_section('source'), m.config.work_dir, m.config.src_cache,
output_dir, m.config.work_dir)
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("%s does not appear to be a valid R package "
"(no DESCRIPTION file in %s, %s)"
% (location, sub_description_pkg, sub_description_name))
with open(DESCRIPTION) as f:
description_text = clear_whitespace(f.read())
d = dict_from_cran_lines(remove_package_line_continuations(
description_text.splitlines()))
d['orig_description'] = description_text
package = d['Package'].lower()
cran_metadata[package] = d
else:
package = pkg_name
if pkg_name not in cran_metadata:
sys.exit("Package %s not found" % pkg_name)
# Make sure package always uses the CRAN capitalization
package = cran_metadata[package.lower()]['Package']
if not is_github_url and not is_tarfile:
session = get_session(output_dir)
cran_metadata[package.lower()].update(get_package_metadata(cran_url,
package, session))
cran_package = cran_metadata[package.lower()]
package_dicts[package.lower()].update(
{
'cran_packagename': package,
'packagename': 'r-' + package.lower(),
'patches': '',
'build_number': 0,
'build_depends': '',
'host_depends': '',
'run_depends': '',
# CRAN doesn't seem to have this metadata :(
'home_comment': '#',
'homeurl': '',
'summary_comment': '#',
'summary': '',
})
d = package_dicts[package.lower()]
d['binary1'] = ''
d['binary2'] = ''
if version:
d['version'] = version
raise NotImplementedError("Package versions from CRAN are not yet implemented")
d['cran_version'] = cran_package['Version']
# Conda versions cannot have -. Conda (verlib) will treat _ as a .
d['conda_version'] = d['cran_version'].replace('-', '_')
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 = int(m.get_value('build/number', 0))
build_number += 1 if update_policy == 'merge-incr-build-num' else 0
if add_maintainer:
new_maintainer = "{indent}{add_maintainer}".format(indent=INDENT,
add_maintainer=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 = {'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': 'bin/windows/contrib/{}/'.format(use_binaries_ver),
'ext': '.zip',
'use_this': True if use_binaries_ver else False},
'osx-64': {'selector': 'osx',
'dir': 'bin/macosx/el-capitan/contrib/{}/'.format(
use_binaries_ver),
'ext': '.tgz',
'use_this': True if use_binaries_ver else False}}
available = {}
for archive_type, archive_details in iteritems(cran_layout):
contrib_url = ''
if archive_details['use_this']:
if is_tarfile:
filename = basename(location)
contrib_url = relpath(location, dir_path)
contrib_url_rendered = package_url = contrib_url
sha256 = hashlib.sha256()
cached_path = location
elif not is_github_url:
filename = '{}_{}'.format(package, d['cran_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
sha256 = hashlib.sha256()
print("Downloading {} from {}".format(archive_type, package_url))
# We may need to inspect the file later to determine which compilers are needed.
cached_path, _ = source.download_to_cache(config.src_cache, '',
dict({'url': package_url,
'fn': archive_type + '-' + filename}))
available_details = {}
available_details['selector'] = archive_details['selector']
if cached_path:
sha256.update(open(cached_path, 'rb').read())
available_details['filename'] = filename
available_details['contrib_url'] = contrib_url
available_details['contrib_url_rendered'] = contrib_url_rendered
available_details['package_url'] = package_url
available_details['hash_entry'] = 'sha256: {}'.format(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['fn_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['fn_key'] = 'fn:'
available_details['git_url_key'] = ''
available_details['git_tag_key'] = ''
available_details['cranurl'] = ' ' + contrib_url + filename
available_details['git_url'] = ''
available_details['git_tag'] = ''
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 iteritems(available):
if archive_type != 'source':
sel = archive_details['selector']
from_source.remove(sel)
binary_id += 1
else:
for k, v in iteritems(archive_details):
d[k] = v
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')) + ']'
d['sel_src'] = sel_src
d['sel_src_and_win'] = sel_src_and_win
d['sel_src_not_win'] = sel_src_not_win
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)
else:
available_details['cranurl'] = (INDENT + contrib_url +
filename + sel_src + INDENT + contrib_url +
'Archive/{}/'.format(package) + filename + sel_src)
else:
available_details['cranurl'] = ' ' + contrib_url + filename + sel_src
if not is_github_url:
available_details['archive_keys'] = '{fn_key} {filename}{sel}\n' \
' {url_key}{sel}' \
' {cranurl}\n' \
' {hash_entry}{sel}'.format(
**available_details)
d['cran_metadata'] = '\n'.join(['# %s' % l for l in
cran_package['orig_lines'] if l])
# Render the source and binaryN keys
binary_id = 1
for archive_type, archive_details in iteritems(available):
if archive_type == 'source':
d['source'] = SOURCE_META.format(**archive_details)
else:
archive_details['sel'] = ' # [' + archive_details['selector'] + ']'
d['binary' + str(binary_id)] = BINARY_META.format(**archive_details)
binary_id += 1
# XXX: We should maybe normalize these
d['license'] = cran_package.get("License", "None")
d['license_family'] = guess_license_family(d['license'], allowed_license_families)
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'] = ' {}'.format(location)
else:
d['homeurl'] = ' https://CRAN.R-project.org/package={}'.format(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:
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("Could not parse version from dependency of %s: %s" %
(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 "
"package %s: %s" % (package, s))
dep_dict[name] = '{relop}{version}'.format(relop=relop, version=ver)
if 'R' not in dep_dict:
dep_dict['R'] = ''
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')) 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("{indent}{{{{ compiler('c') }}}} {sel}".format(
indent=INDENT, sel=sel_src_not_win))
if need_cxx:
deps.append("{indent}{{{{ compiler('cxx') }}}} {sel}".format(
indent=INDENT, sel=sel_src_not_win))
if need_f:
deps.append("{indent}{{{{ compiler('fortran') }}}} {sel}".format(
indent=INDENT, sel=sel_src_not_win))
if use_rtools_win:
need_c = need_cxx = need_f = need_autotools = need_make = False
deps.append("{indent}{{{{native}}}}rtools {sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{native}}}}extsoft {sel}".format(
indent=INDENT, sel=sel_src_and_win))
if need_c or need_cxx or need_f:
deps.append("{indent}{{{{native}}}}toolchain {sel}".format(
indent=INDENT, sel=sel_src_and_win))
if need_autotools or need_make or need_git:
deps.append("{indent}{{{{posix}}}}filesystem {sel}".format(
indent=INDENT, sel=sel_src_and_win))
if need_git:
deps.append("{indent}{{{{posix}}}}git".format(indent=INDENT))
if need_autotools:
deps.append("{indent}{{{{posix}}}}sed {sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{posix}}}}grep {sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{posix}}}}autoconf {sel}".format(
indent=INDENT, sel=sel_src))
deps.append("{indent}{{{{posix}}}}automake-wrapper {sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{posix}}}}automake {sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{posix}}}}pkg-config".format(indent=INDENT))
if need_make:
deps.append("{indent}{{{{posix}}}}make {sel}".format(
indent=INDENT, sel=sel_src))
elif dep_type == 'run':
if need_c or need_cxx or need_f:
deps.append("{indent}{{{{native}}}}gcc-libs {sel}".format(
indent=INDENT, sel=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, '{indent}{r_name}'.format(indent=INDENT, r_name=r_interp))
else:
conda_name = 'r-' + name.lower()
if dep_dict[name]:
deps.append('{indent}{name} {version}'.format(name=conda_name,
version=dep_dict[name], indent=INDENT))
else:
deps.append('{indent}{name}'.format(name=conda_name,
indent=INDENT))
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)
assert lower_name == inputs_dict['pkg-name'], \
"name %s != inputs_dict['pkg-name'] %s" % (
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)
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' and up_to_date(cran_metadata,
d['inputs']['old-metadata']):
continue
elif update_policy == 'skip-existing' and d['inputs']['old-metadata']:
continue
# Normalize the metadata values
d = {k: unicodedata.normalize("NFKD", text_type(v)).encode('ascii', 'ignore')
.decode() for k, v in iteritems(d)}
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'), 'w') as f:
if from_source == all:
f.write(CRAN_BUILD_SH_SOURCE.format(**d))
elif from_source == []:
f.write(CRAN_BUILD_SH_BINARY.format(**d))
else:
tpbt = [target_platform_bash_test_by_sel[t] for t in from_source]
d['source_pf_bash'] = ' || '.join(['[[ $target_platform ' + s + ' ]]'
for s in tpbt])
f.write(CRAN_BUILD_SH_MIXED.format(**d))
if not exists(join(dir_path, 'bld.bat')) or update_policy == 'overwrite':
with open(join(dir_path, 'bld.bat'), 'w') as f:
if len([fs for fs in from_source if fs.startswith('win')]) == 2:
f.write(CRAN_BLD_BAT_SOURCE.format(**d))
else:
f.write(CRAN_BLD_BAT_MIXED.format(**d))
def main(args, parser):
package_dicts = {}
[output_dir] = args.output_dir
session = requests.Session()
try:
import cachecontrol
import cachecontrol.caches
except ImportError:
print("Tip: install CacheControl to cache the CRAN metadata")
else:
session = cachecontrol.CacheControl(session,
cache=cachecontrol.caches.FileCache(join(output_dir,
'.web_cache')))
print("Fetching metadata from %s" % args.cran_url)
r = session.get(args.cran_url + "src/contrib/PACKAGES")
r.raise_for_status()
PACKAGES = r.text
package_list = [remove_package_line_continuations(i.splitlines()) for i in PACKAGES.split('\n\n')]
cran_metadata = {d['Package'].lower(): d for d in map(dict_from_cran_lines,
package_list)}
while args.packages:
package = args.packages.pop()
is_github_url = 'github.com' in package
url = package
if is_github_url:
rm_rf(source.WORK_DIR)
source.git_source({'git_url': package}, '.')
DESCRIPTION = join(source.WORK_DIR, "DESCRIPTION")
if not isfile(DESCRIPTION):
sys.exit("%s does not appear to be a valid R package (no DESCRIPTION file)" % package)
with open(DESCRIPTION) as f:
description_text = f.read()
d = dict_from_cran_lines(remove_package_line_continuations(description_text.splitlines()))
d['orig_description'] = description_text
package = d['Package'].lower()
cran_metadata[package] = d
if package.startswith('r-'):
package = package[2:]
if package.lower() not in cran_metadata:
sys.exit("Package %s not found" % package)
# Make sure package is always uses the CRAN capitalization
package = cran_metadata[package.lower()]['Package']
if not is_github_url:
cran_metadata[package.lower()].update(get_package_metadata(args.cran_url,
package, session))
dir_path = join(output_dir, 'r-' + package.lower())
if exists(dir_path):
raise RuntimeError("directory already exists: %s" % dir_path)
cran_package = cran_metadata[package.lower()]
d = package_dicts.setdefault(package,
{
'cran_packagename': package,
'packagename': 'r-' + package.lower(),
'build_depends': '',
'run_depends': '',
# CRAN doesn't seem to have this metadata :(
'home_comment': '#',
'homeurl': '',
'summary_comment': '#',
'summary': '',
})
if is_github_url:
d['url_key'] = ''
d['fn_key'] = ''
d['git_url_key'] = 'git_url:'
d['git_tag_key'] = 'git_tag:'
d['filename'] = ''
d['cranurl'] = ''
d['git_url'] = url
d['git_tag'] = get_latest_git_tag()
else:
d['url_key'] = 'url:'
d['fn_key'] = 'fn:'
d['git_url_key'] = ''
d['git_tag_key'] = ''
d['git_url'] = ''
d['git_tag'] = ''
if args.version:
raise NotImplementedError("Package versions from CRAN are not yet implemented")
[version] = args.version
d['version'] = version
d['cran_version'] = cran_package['Version']
# Conda versions cannot have -. Conda (verlib) will treat _ as a .
d['conda_version'] = d['cran_version'].replace('-', '_')
if not is_github_url:
d['filename'] = "{cran_packagename}_{cran_version}.tar.gz".format(**d)
if args.archive:
d['cranurl'] = (INDENT + args.cran_url + 'src/contrib/' +
d['filename'] + INDENT + args.cran_url + 'src/contrib/' +
'Archive/' + d['cran_packagename'] + '/' + d['filename'])
else:
d['cranurl'] = ' ' + args.cran_url + 'src/contrib/' + d['filename']
d['cran_metadata'] = '\n'.join(['# %s' % l for l in
cran_package['orig_lines'] if l])
# XXX: We should maybe normalize these
d['license'] = cran_package.get("License", "None")
if 'License_is_FOSS' in cran_package:
d['license'] += ' (FOSS)'
if cran_package.get('License_restricts_use', None) == 'yes':
d['license'] += ' (Restricts use)'
if "URL" in cran_package:
d['home_comment'] = ''
d['homeurl'] = ' ' + yaml_quote_string(cran_package['URL'])
if 'Description' in cran_package:
d['summary_comment'] = ''
d['summary'] = ' ' + yaml_quote_string(cran_package['Description'])
if "Suggests" in cran_package:
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 = {}
for s in set(chain(depends, imports, links)):
match = VERSION_DEPENDENCY_REGEX.match(s)
if not match:
sys.exit("Could not parse version from dependency of %s: %s" %
(package, s))
name = match.group('name')
archs = match.group('archs')
relop = match.group('relop') or ''
version = match.group('version') or ''
version = version.replace('-', '_')
# If there is a relop there should be a version
assert not relop or version
if archs:
sys.exit("Don't know how to handle archs from dependency of "
"package %s: %s" % (package, s))
dep_dict[name] = '{relop}{version}'.format(relop=relop, version=version)
if 'R' not in dep_dict:
dep_dict['R'] = ''
for dep_type in ['build', 'run']:
deps = []
for name in sorted(dep_dict):
if name in R_BASE_PACKAGE_NAMES:
continue
if name == 'R':
# Put R first
if d['cran_packagename'] in R_RECOMMENDED_PACKAGE_NAMES and dep_type == 'build':
# On Linux and OS X, r is a metapackage depending on
# r-base and r-recommended. Recommended packages cannot
# build depend on r as they would then build depend on
# themselves and the built package would end up being
# empty (because conda would find no new files)
r_name = 'r-base'
else:
r_name = 'r'
# We don't include any R version restrictions because we
# always build R packages against an exact R version
deps.insert(0, '{indent}{r_name}'.format(indent=INDENT, r_name=r_name))
else:
conda_name = 'r-' + name.lower()
# The r package on Windows includes the recommended packages
if name in R_RECOMMENDED_PACKAGE_NAMES:
end = ' # [not win]'
else:
end = ''
if dep_dict[name]:
deps.append('{indent}{name} {version}{end}'.format(name=conda_name,
version=dep_dict[name], end=end, indent=INDENT))
else:
deps.append('{indent}{name}{end}'.format(name=conda_name,
indent=INDENT, end=end))
if args.recursive:
if not exists(join(output_dir, conda_name)):
args.packages.append(name)
d['%s_depends' % dep_type] = ''.join(deps)
for package in package_dicts:
d = package_dicts[package]
name = d['packagename']
makedirs(join(output_dir, name))
print("Writing recipe for %s" % package.lower())
with open(join(output_dir, name, 'meta.yaml'), 'w') as f:
f.write(clear_trailing_whitespace(CRAN_META.format(**d)))
with open(join(output_dir, name, 'build.sh'), 'w') as f:
f.write(CRAN_BUILD_SH.format(**d))
with open(join(output_dir, name, 'bld.bat'), 'w') as f:
f.write(CRAN_BLD_BAT.format(**d))
print("Done")
def main(args, parser):
if len(args.packages) > 1 and args.version_compare:
parser.error("--version-compare only works with one package at a time")
if not args.update_outdated and not args.packages:
parser.error("At least one package must be supplied")
package_dicts = {}
[output_dir] = args.output_dir
cran_metadata = get_cran_metadata(args.cran_url, output_dir)
if args.update_outdated:
args.packages = get_outdated(output_dir, cran_metadata, args.packages)
for pkg in args.packages:
rm_rf(join(args.output_dir, 'r-' + pkg))
while args.packages:
package = args.packages.pop()
is_github_url = 'github.com' in package
url = package
if is_github_url:
rm_rf(source.WORK_DIR)
source.git_source({'git_url': package}, '.')
git_tag = args.git_tag[0] if args.git_tag else get_latest_git_tag()
p = subprocess.Popen(['git', 'checkout', git_tag],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=source.WORK_DIR)
stdout, stderr = p.communicate()
stdout = stdout.decode('utf-8')
stderr = stderr.decode('utf-8')
if p.returncode:
sys.exit(
"Error: 'git checkout %s' failed (%s).\nInvalid tag?" %
(git_tag, stderr.strip()))
if stdout:
print(stdout, file=sys.stdout)
if stderr:
print(stderr, file=sys.stderr)
DESCRIPTION = join(source.WORK_DIR, "DESCRIPTION")
if not isfile(DESCRIPTION):
sub_description_pkg = join(source.WORK_DIR, 'pkg',
"DESCRIPTION")
sub_description_name = join(source.WORK_DIR,
package.split('/')[-1],
"DESCRIPTION")
if isfile(sub_description_pkg):
DESCRIPTION = sub_description_pkg
elif isfile(sub_description_name):
DESCRIPTION = sub_description_name
else:
sys.exit(
"%s does not appear to be a valid R package (no DESCRIPTION file)"
% package)
with open(DESCRIPTION) as f:
description_text = clear_trailing_whitespace(f.read())
d = dict_from_cran_lines(
remove_package_line_continuations(
description_text.splitlines()))
d['orig_description'] = description_text
package = d['Package'].lower()
cran_metadata[package] = d
if package.startswith('r-'):
package = package[2:]
if package.endswith('/'):
package = package[:-1]
if package.lower() not in cran_metadata:
sys.exit("Package %s not found" % package)
# Make sure package is always uses the CRAN capitalization
package = cran_metadata[package.lower()]['Package']
if not is_github_url:
session = get_session(output_dir)
cran_metadata[package.lower()].update(
get_package_metadata(args.cran_url, package, session))
dir_path = join(output_dir, 'r-' + package.lower())
if exists(dir_path) and not args.version_compare:
raise RuntimeError("directory already exists: %s" % dir_path)
cran_package = cran_metadata[package.lower()]
d = package_dicts.setdefault(
package,
{
'cran_packagename': package,
'packagename': 'r-' + package.lower(),
'build_depends': '',
'run_depends': '',
# CRAN doesn't seem to have this metadata :(
'home_comment': '#',
'homeurl': '',
'summary_comment': '#',
'summary': '',
})
if is_github_url:
d['url_key'] = ''
d['fn_key'] = ''
d['git_url_key'] = 'git_url:'
d['git_tag_key'] = 'git_tag:'
d['filename'] = ''
d['cranurl'] = ''
d['git_url'] = url
d['git_tag'] = git_tag
else:
d['url_key'] = 'url:'
d['fn_key'] = 'fn:'
d['git_url_key'] = ''
d['git_tag_key'] = ''
d['git_url'] = ''
d['git_tag'] = ''
if args.version:
raise NotImplementedError(
"Package versions from CRAN are not yet implemented")
[version] = args.version
d['version'] = version
d['cran_version'] = cran_package['Version']
# Conda versions cannot have -. Conda (verlib) will treat _ as a .
d['conda_version'] = d['cran_version'].replace('-', '_')
if args.version_compare:
sys.exit(not version_compare(dir_path, d['conda_version']))
if not is_github_url:
d['filename'] = "{cran_packagename}_{cran_version}.tar.gz".format(
**d)
if args.archive:
d['cranurl'] = (INDENT + args.cran_url + 'src/contrib/' +
d['filename'] + INDENT + args.cran_url +
'src/contrib/' + 'Archive/' +
d['cran_packagename'] + '/' + d['filename'])
else:
d['cranurl'] = ' ' + args.cran_url + 'src/contrib/' + d[
'filename']
d['cran_metadata'] = '\n'.join(
['# %s' % l for l in cran_package['orig_lines'] if l])
# XXX: We should maybe normalize these
d['license'] = cran_package.get("License", "None")
if 'License_is_FOSS' in cran_package:
d['license'] += ' (FOSS)'
if cran_package.get('License_restricts_use', None) == 'yes':
d['license'] += ' (Restricts use)'
if "URL" in cran_package:
d['home_comment'] = ''
d['homeurl'] = ' ' + yaml_quote_string(cran_package['URL'])
if 'Description' in cran_package:
d['summary_comment'] = ''
d['summary'] = ' ' + yaml_quote_string(cran_package['Description'])
if "Suggests" in cran_package:
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 = {}
for s in set(chain(depends, imports, links)):
match = VERSION_DEPENDENCY_REGEX.match(s)
if not match:
sys.exit("Could not parse version from dependency of %s: %s" %
(package, s))
name = match.group('name')
archs = match.group('archs')
relop = match.group('relop') or ''
version = match.group('version') or ''
version = version.replace('-', '_')
# If there is a relop there should be a version
assert not relop or version
if archs:
sys.exit("Don't know how to handle archs from dependency of "
"package %s: %s" % (package, s))
dep_dict[name] = '{relop}{version}'.format(relop=relop,
version=version)
if 'R' not in dep_dict:
dep_dict['R'] = ''
for dep_type in ['build', 'run']:
deps = []
for name in sorted(dep_dict):
if name in R_BASE_PACKAGE_NAMES:
continue
if name == 'R':
# Put R first
if d['cran_packagename'] in R_RECOMMENDED_PACKAGE_NAMES and dep_type == 'build':
# On Linux and OS X, r is a metapackage depending on
# r-base and r-recommended. Recommended packages cannot
# build depend on r as they would then build depend on
# themselves and the built package would end up being
# empty (because conda would find no new files)
r_name = 'r-base'
else:
r_name = 'r'
# We don't include any R version restrictions because we
# always build R packages against an exact R version
deps.insert(
0, '{indent}{r_name}'.format(indent=INDENT,
r_name=r_name))
else:
conda_name = 'r-' + name.lower()
# The r package on Windows includes the recommended packages
if name in R_RECOMMENDED_PACKAGE_NAMES:
end = ' # [not win]'
else:
end = ''
if dep_dict[name]:
deps.append('{indent}{name} {version}{end}'.format(
name=conda_name,
version=dep_dict[name],
end=end,
indent=INDENT))
else:
deps.append('{indent}{name}{end}'.format(
name=conda_name, indent=INDENT, end=end))
if args.recursive:
if not exists(join(output_dir, conda_name)):
args.packages.append(name)
if cran_package.get("NeedsCompilation", 'no') == 'yes':
if dep_type == 'build':
deps.append(
'{indent}gcc # [not win]'.format(indent=INDENT))
else:
deps.append(
'{indent}libgcc # [not win]'.format(indent=INDENT))
d['%s_depends' % dep_type] = ''.join(deps)
for package in package_dicts:
d = package_dicts[package]
name = d['packagename']
#Normalize the metadata values
d = {
k: unicodedata.normalize("NFKD", compat.text_type(v)).encode(
'ascii', 'ignore')
for k, v in d.iteritems()
}
makedirs(join(output_dir, name))
print("Writing recipe for %s" % package.lower())
with open(join(output_dir, name, 'meta.yaml'), 'w') as f:
f.write(clear_trailing_whitespace(CRAN_META.format(**d)))
with open(join(output_dir, name, 'build.sh'), 'w') as f:
f.write(CRAN_BUILD_SH.format(**d))
with open(join(output_dir, name, 'bld.bat'), 'w') as f:
f.write(CRAN_BLD_BAT.format(**d))
print("Done")
def skeletonize(in_packages,
output_dir=".",
output_suffix="",
add_maintainer=None,
version=None,
git_tag=None,
cran_url="https://cran.r-project.org/",
recursive=False,
archive=True,
version_compare=False,
update_policy='',
config=None):
output_dir = realpath(output_dir)
if not config:
config = Config()
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_metadata = get_cran_metadata(cran_url, output_dir)
# r_recipes_in_output_dir = []
# recipes = listdir(output_dir)
# for recipe in recipes:
# if not recipe.startswith('r-') or not isdir(recipe):
# continue
# r_recipes_in_output_dir.append(recipe)
for package in in_packages:
inputs_dict = package_to_inputs_dict(output_dir, output_suffix,
git_tag, package)
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']
is_github_url = location and 'github.com' in location
url = inputs['location']
dir_path = inputs['new-location']
print("Making/refreshing recipe for {}".format(pkg_name))
# Bodges GitHub packages into cran_metadata
if is_github_url:
rm_rf(config.work_dir)
m = metadata.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(
"Error: 'git checkout %s' failed (%s).\nInvalid tag?" %
(new_git_tag, stderr.strip()))
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(
"%s does not appear to be a valid R package "
"(no DESCRIPTION file in %s, %s)" %
(location, sub_description_pkg, sub_description_name))
with open(DESCRIPTION) as f:
description_text = clear_trailing_whitespace(f.read())
d = dict_from_cran_lines(
remove_package_line_continuations(
description_text.splitlines()))
d['orig_description'] = description_text
package = d['Package'].lower()
cran_metadata[package] = d
else:
package = pkg_name
if pkg_name not in cran_metadata:
sys.exit("Package %s not found" % pkg_name)
# Make sure package always uses the CRAN capitalization
package = cran_metadata[package.lower()]['Package']
if not is_github_url:
session = get_session(output_dir)
cran_metadata[package.lower()].update(
get_package_metadata(cran_url, package, session))
cran_package = cran_metadata[package.lower()]
package_dicts[package.lower()].update({
'cran_packagename':
package,
'packagename':
'r-' + package.lower(),
'patches':
'',
'build_number':
0,
'build_depends':
'',
'run_depends':
'',
# CRAN doesn't seem to have this metadata :(
'home_comment':
'#',
'homeurl':
'',
'summary_comment':
'#',
'summary':
'',
})
d = package_dicts[package.lower()]
if is_github_url:
d['url_key'] = ''
d['fn_key'] = ''
d['git_url_key'] = 'git_url:'
d['git_tag_key'] = 'git_tag:'
d['hash_entry'] = '# You can add a hash for the file here, like md5, sha1 or sha256'
d['filename'] = ''
d['cranurl'] = ''
d['git_url'] = url
d['git_tag'] = new_git_tag
else:
d['url_key'] = 'url:'
d['fn_key'] = 'fn:'
d['git_url_key'] = ''
d['git_tag_key'] = ''
d['git_url'] = ''
d['git_tag'] = ''
d['hash_entry'] = ''
if version:
d['version'] = version
raise NotImplementedError(
"Package versions from CRAN are not yet implemented")
d['cran_version'] = cran_package['Version']
# Conda versions cannot have -. Conda (verlib) will treat _ as a .
d['conda_version'] = d['cran_version'].replace('-', '_')
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 = int(m.get_value('build/number', 0))
build_number += 1 if update_policy == 'merge-incr-build-num' else 0
if not len(patches):
patches.append("# patches:\n")
patches.append(" # List any patch files here\n")
patches.append(" # - fix.patch")
if add_maintainer:
new_maintainer = "{indent}{add_maintainer}".format(
indent=INDENT, add_maintainer=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
if not is_github_url:
filename = '{}_{}.tar.gz'
contrib_url = cran_url + 'src/contrib/'
package_url = contrib_url + filename.format(
package, d['cran_version'])
# calculate sha256 by downloading source
sha256 = hashlib.sha256()
print("Downloading source from {}".format(package_url))
# We may need to inspect the file later to determine which compilers are needed.
cached_path, _ = source.download_to_cache(
config.src_cache, '', dict({'url': package_url}))
sha256.update(open(cached_path, 'rb').read())
d['hash_entry'] = 'sha256: {}'.format(sha256.hexdigest())
d['filename'] = filename.format(package, '{{ version }}')
if archive:
d['cranurl'] = (INDENT + contrib_url + d['filename'] + INDENT +
contrib_url + 'Archive/{}/'.format(package) +
d['filename'])
else:
d['cranurl'] = ' ' + cran_url + 'src/contrib/' + d['filename']
d['cran_metadata'] = '\n'.join(
['# %s' % l for l in cran_package['orig_lines'] if l])
# XXX: We should maybe normalize these
d['license'] = cran_package.get("License", "None")
d['license_family'] = guess_license_family(d['license'],
allowed_license_families)
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'] = ' {}'.format(location)
else:
d['homeurl'] = ' https://CRAN.R-project.org/package={}'.format(
package)
if 'Description' in cran_package:
d['summary_comment'] = ''
d['summary'] = ' ' + yaml_quote_string(cran_package['Description'])
if "Suggests" in cran_package:
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("Could not parse version from dependency of %s: %s" %
(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 "
"package %s: %s" % (package, s))
dep_dict[name] = '{relop}{version}'.format(relop=relop,
version=ver)
if 'R' not in dep_dict:
dep_dict['R'] = ''
need_git = is_github_url
if cran_package.get("NeedsCompilation", 'no') == 'yes':
with tarfile.open(cached_path) as tf:
need_f = any([
f.name.lower().endswith(('.f', '.f90', '.f77')) 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
for dep_type in ['build', 'run']:
deps = []
# Put non-R dependencies first.
if dep_type == 'build':
if need_c:
deps.append(
"{indent}{{{{ compiler('c') }}}} # [not win]".
format(indent=INDENT))
if need_cxx:
deps.append(
"{indent}{{{{ compiler('cxx') }}}} # [not win]".
format(indent=INDENT))
if need_f:
deps.append(
"{indent}{{{{ compiler('fortran') }}}} # [not win]".
format(indent=INDENT))
if need_c or need_cxx or need_f:
deps.append(
"{indent}{{{{native}}}}toolchain # [win]".
format(indent=INDENT))
if need_autotools or need_make or need_git:
deps.append(
"{indent}{{{{posix}}}}filesystem # [win]".
format(indent=INDENT))
if need_git:
deps.append(
"{indent}{{{{posix}}}}git".format(indent=INDENT))
if need_autotools:
deps.append(
"{indent}{{{{posix}}}}sed # [win]".
format(indent=INDENT))
deps.append(
"{indent}{{{{posix}}}}grep # [win]".
format(indent=INDENT))
deps.append(
"{indent}{{{{posix}}}}autoconf".format(indent=INDENT))
deps.append(
"{indent}{{{{posix}}}}automake".format(indent=INDENT))
deps.append("{indent}{{{{posix}}}}pkg-config".format(
indent=INDENT))
if need_make:
deps.append(
"{indent}{{{{posix}}}}make".format(indent=INDENT))
elif dep_type == 'run':
if need_c or need_cxx or need_f:
deps.append(
"{indent}{{{{native}}}}gcc-libs # [win]".
format(indent=INDENT))
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-base' 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.
r_name = 'r-base'
# We don't include any R version restrictions because we
# always build R packages against an exact R version
deps.insert(
0, '{indent}{r_name}'.format(indent=INDENT,
r_name=r_name))
else:
conda_name = 'r-' + name.lower()
if dep_dict[name]:
deps.append('{indent}{name} {version}'.format(
name=conda_name,
version=dep_dict[name],
indent=INDENT))
else:
deps.append('{indent}{name}'.format(name=conda_name,
indent=INDENT))
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)
assert lower_name == inputs_dict['pkg-name'], \
"name %s != inputs_dict['pkg-name'] %s" % (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)
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' and up_to_date(
cran_metadata, d['inputs']['old-metadata']):
continue
elif update_policy == 'skip-existing' and d['inputs']['old-metadata']:
continue
# Normalize the metadata values
d = {
k: unicodedata.normalize("NFKD",
text_type(v)).encode('ascii',
'ignore').decode()
for k, v in iteritems(d)
}
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_trailing_whitespace(CRAN_META.format(**d)))
if not exists(join(dir_path,
'build.sh')) or update_policy == 'overwrite':
with open(join(dir_path, 'build.sh'), 'w') as f:
f.write(CRAN_BUILD_SH.format(**d))
if not exists(join(dir_path,
'bld.bat')) or update_policy == 'overwrite':
with open(join(dir_path, 'bld.bat'), 'w') as f:
f.write(CRAN_BLD_BAT.format(**d))
def main(args, parser):
if len(args.packages) > 1 and args.version_compare:
parser.error("--version-compare only works with one package at a time")
if not args.update_outdated and not args.packages:
parser.error("At least one package must be supplied")
package_dicts = {}
[output_dir] = args.output_dir
cran_metadata = get_cran_metadata(args.cran_url, output_dir)
if args.update_outdated:
args.packages = get_outdated(output_dir, cran_metadata, args.packages)
for pkg in args.packages:
rm_rf(join(args.output_dir, "r-" + pkg))
while args.packages:
package = args.packages.pop()
is_github_url = "github.com" in package
url = package
if is_github_url:
rm_rf(source.WORK_DIR)
source.git_source({"git_url": package}, ".")
git_tag = args.git_tag[0] if args.git_tag else get_latest_git_tag()
p = subprocess.Popen(
["git", "checkout", git_tag], stdout=subprocess.PIPE, stderr=subprocess.PIPE, cwd=source.WORK_DIR
)
stdout, stderr = p.communicate()
stdout = stdout.decode("utf-8")
stderr = stderr.decode("utf-8")
if p.returncode:
sys.exit("Error: 'git checkout %s' failed (%s).\nInvalid tag?" % (git_tag, stderr.strip()))
if stdout:
print(stdout, file=sys.stdout)
if stderr:
print(stderr, file=sys.stderr)
DESCRIPTION = join(source.WORK_DIR, "DESCRIPTION")
if not isfile(DESCRIPTION):
sub_description_pkg = join(source.WORK_DIR, "pkg", "DESCRIPTION")
sub_description_name = join(source.WORK_DIR, package.split("/")[-1], "DESCRIPTION")
if isfile(sub_description_pkg):
DESCRIPTION = sub_description_pkg
elif isfile(sub_description_name):
DESCRIPTION = sub_description_name
else:
sys.exit("%s does not appear to be a valid R package (no DESCRIPTION file)" % package)
with open(DESCRIPTION) as f:
description_text = clear_trailing_whitespace(f.read())
d = dict_from_cran_lines(remove_package_line_continuations(description_text.splitlines()))
d["orig_description"] = description_text
package = d["Package"].lower()
cran_metadata[package] = d
if package.startswith("r-"):
package = package[2:]
if package.endswith("/"):
package = package[:-1]
if package.lower() not in cran_metadata:
sys.exit("Package %s not found" % package)
# Make sure package is always uses the CRAN capitalization
package = cran_metadata[package.lower()]["Package"]
if not is_github_url:
session = get_session(output_dir)
cran_metadata[package.lower()].update(get_package_metadata(args.cran_url, package, session))
dir_path = join(output_dir, "r-" + package.lower())
if exists(dir_path) and not args.version_compare:
raise RuntimeError("directory already exists: %s" % dir_path)
cran_package = cran_metadata[package.lower()]
d = package_dicts.setdefault(
package,
{
"cran_packagename": package,
"packagename": "r-" + package.lower(),
"build_depends": "",
"run_depends": "",
# CRAN doesn't seem to have this metadata :(
"home_comment": "#",
"homeurl": "",
"summary_comment": "#",
"summary": "",
},
)
if is_github_url:
d["url_key"] = ""
d["fn_key"] = ""
d["git_url_key"] = "git_url:"
d["git_tag_key"] = "git_tag:"
d["filename"] = ""
d["cranurl"] = ""
d["git_url"] = url
d["git_tag"] = git_tag
else:
d["url_key"] = "url:"
d["fn_key"] = "fn:"
d["git_url_key"] = ""
d["git_tag_key"] = ""
d["git_url"] = ""
d["git_tag"] = ""
if args.version:
raise NotImplementedError("Package versions from CRAN are not yet implemented")
[version] = args.version
d["version"] = version
d["cran_version"] = cran_package["Version"]
# Conda versions cannot have -. Conda (verlib) will treat _ as a .
d["conda_version"] = d["cran_version"].replace("-", "_")
if args.version_compare:
sys.exit(not version_compare(dir_path, d["conda_version"]))
if not is_github_url:
d["filename"] = "{cran_packagename}_{cran_version}.tar.gz".format(**d)
if args.archive:
d["cranurl"] = (
INDENT
+ args.cran_url
+ "src/contrib/"
+ d["filename"]
+ INDENT
+ args.cran_url
+ "src/contrib/"
+ "Archive/"
+ d["cran_packagename"]
+ "/"
+ d["filename"]
)
else:
d["cranurl"] = " " + args.cran_url + "src/contrib/" + d["filename"]
d["cran_metadata"] = "\n".join(["# %s" % l for l in cran_package["orig_lines"] if l])
# XXX: We should maybe normalize these
d["license"] = cran_package.get("License", "None")
if "License_is_FOSS" in cran_package:
d["license"] += " (FOSS)"
if cran_package.get("License_restricts_use", None) == "yes":
d["license"] += " (Restricts use)"
if "URL" in cran_package:
d["home_comment"] = ""
d["homeurl"] = " " + yaml_quote_string(cran_package["URL"])
if "Description" in cran_package:
d["summary_comment"] = ""
d["summary"] = " " + yaml_quote_string(cran_package["Description"])
if "Suggests" in cran_package:
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 = {}
for s in set(chain(depends, imports, links)):
match = VERSION_DEPENDENCY_REGEX.match(s)
if not match:
sys.exit("Could not parse version from dependency of %s: %s" % (package, s))
name = match.group("name")
archs = match.group("archs")
relop = match.group("relop") or ""
version = match.group("version") or ""
version = version.replace("-", "_")
# If there is a relop there should be a version
assert not relop or version
if archs:
sys.exit("Don't know how to handle archs from dependency of " "package %s: %s" % (package, s))
dep_dict[name] = "{relop}{version}".format(relop=relop, version=version)
if "R" not in dep_dict:
dep_dict["R"] = ""
for dep_type in ["build", "run"]:
deps = []
for name in sorted(dep_dict):
if name in R_BASE_PACKAGE_NAMES:
continue
if name == "R":
# Put R first
if d["cran_packagename"] in R_RECOMMENDED_PACKAGE_NAMES and dep_type == "build":
# On Linux and OS X, r is a metapackage depending on
# r-base and r-recommended. Recommended packages cannot
# build depend on r as they would then build depend on
# themselves and the built package would end up being
# empty (because conda would find no new files)
r_name = "r-base"
else:
r_name = "r"
# We don't include any R version restrictions because we
# always build R packages against an exact R version
deps.insert(0, "{indent}{r_name}".format(indent=INDENT, r_name=r_name))
else:
conda_name = "r-" + name.lower()
# The r package on Windows includes the recommended packages
if name in R_RECOMMENDED_PACKAGE_NAMES:
end = " # [not win]"
else:
end = ""
if dep_dict[name]:
deps.append(
"{indent}{name} {version}{end}".format(
name=conda_name, version=dep_dict[name], end=end, indent=INDENT
)
)
else:
deps.append("{indent}{name}{end}".format(name=conda_name, indent=INDENT, end=end))
if args.recursive:
if not exists(join(output_dir, conda_name)):
args.packages.append(name)
if cran_package.get("NeedsCompilation", "no") == "yes":
if dep_type == "build":
deps.append("{indent}gcc # [not win]".format(indent=INDENT))
else:
deps.append("{indent}libgcc # [not win]".format(indent=INDENT))
d["%s_depends" % dep_type] = "".join(deps)
for package in package_dicts:
d = package_dicts[package]
name = d["packagename"]
# Normalize the metadata values
d = {
k: unicodedata.normalize("NFKD", compat.text_type(v)).encode("ascii", "ignore").decode()
for k, v in compat.iteritems(d)
}
makedirs(join(output_dir, name))
print("Writing recipe for %s" % package.lower())
with open(join(output_dir, name, "meta.yaml"), "w") as f:
f.write(clear_trailing_whitespace(CRAN_META.format(**d)))
with open(join(output_dir, name, "build.sh"), "w") as f:
f.write(CRAN_BUILD_SH.format(**d))
with open(join(output_dir, name, "bld.bat"), "w") as f:
f.write(CRAN_BLD_BAT.format(**d))
print("Done")
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_rtools_win=False, config=None,
variant_config_files=None):
output_dir = realpath(output_dir)
config = get_or_merge_config(config, variant_config_files=variant_config_files)
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('/')
cran_metadata = get_cran_metadata(cran_url, output_dir)
# r_recipes_in_output_dir = []
# recipes = listdir(output_dir)
# for recipe in recipes:
# if not recipe.startswith('r-') or not isdir(recipe):
# continue
# r_recipes_in_output_dir.append(recipe)
for package in in_packages:
inputs_dict = package_to_inputs_dict(output_dir, output_suffix, git_tag, package)
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']
is_github_url = location and 'github.com' in location
is_tarfile = location and isfile(location) and tarfile.is_tarfile(location)
url = inputs['location']
dir_path = inputs['new-location']
print("Making/refreshing recipe for {}".format(pkg_name))
# Bodges GitHub packages into cran_metadata
if is_github_url or is_tarfile:
rm_rf(config.work_dir)
if is_github_url:
m = metadata.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("Error: 'git checkout %s' failed (%s).\nInvalid tag?" %
(new_git_tag, stderr.strip()))
if stdout:
print(stdout, file=sys.stdout)
if stderr:
print(stderr, file=sys.stderr)
else:
m = metadata.MetaData.fromdict({'source': {'url': location}}, config=config)
source.unpack(m.get_section('source'), m.config.work_dir, m.config.src_cache,
output_dir, m.config.work_dir)
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("%s does not appear to be a valid R package "
"(no DESCRIPTION file in %s, %s)"
% (location, sub_description_pkg, sub_description_name))
with open(DESCRIPTION) as f:
description_text = clear_whitespace(f.read())
d = dict_from_cran_lines(remove_package_line_continuations(
description_text.splitlines()))
d['orig_description'] = description_text
package = d['Package'].lower()
cran_metadata[package] = d
else:
package = pkg_name
if pkg_name not in cran_metadata:
sys.exit("Package %s not found" % pkg_name)
# Make sure package always uses the CRAN capitalization
package = cran_metadata[package.lower()]['Package']
if not is_github_url and not is_tarfile:
session = get_session(output_dir)
cran_metadata[package.lower()].update(get_package_metadata(cran_url,
package, session))
cran_package = cran_metadata[package.lower()]
package_dicts[package.lower()].update(
{
'cran_packagename': package,
'packagename': 'r-' + package.lower(),
'patches': '',
'build_number': 0,
'build_depends': '',
'host_depends': '',
'run_depends': '',
# CRAN doesn't seem to have this metadata :(
'home_comment': '#',
'homeurl': '',
'summary_comment': '#',
'summary': '',
})
d = package_dicts[package.lower()]
d['binary1'] = ''
d['binary2'] = ''
if version:
d['version'] = version
raise NotImplementedError("Package versions from CRAN are not yet implemented")
d['cran_version'] = cran_package['Version']
# Conda versions cannot have -. Conda (verlib) will treat _ as a .
d['conda_version'] = d['cran_version'].replace('-', '_')
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 = int(m.get_value('build/number', 0))
build_number += 1 if update_policy == 'merge-incr-build-num' else 0
if add_maintainer:
new_maintainer = "{indent}{add_maintainer}".format(indent=INDENT,
add_maintainer=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 = {'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': 'bin/windows/contrib/{}/'.format(use_binaries_ver),
'ext': '.zip',
'use_this': True if use_binaries_ver else False},
'osx-64': {'selector': 'osx',
'dir': 'bin/macosx/el-capitan/contrib/{}/'.format(
use_binaries_ver),
'ext': '.tgz',
'use_this': True if use_binaries_ver else False}}
available = {}
for archive_type, archive_details in iteritems(cran_layout):
contrib_url = ''
if archive_details['use_this']:
if is_tarfile:
filename = basename(location)
contrib_url = relpath(location, dir_path)
contrib_url_rendered = package_url = contrib_url
sha256 = hashlib.sha256()
cached_path = location
elif not is_github_url:
filename_rendered = '{}_{}{}'.format(
package, d['cran_version'], archive_details['ext'])
filename = '{}_{{{{ version }}}}'.format(package) + 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
sha256 = hashlib.sha256()
print("Downloading {} from {}".format(archive_type, package_url))
# We may need to inspect the file later to determine which compilers are needed.
cached_path, _ = source.download_to_cache(
config.src_cache, '',
{'url': package_url, 'fn': archive_type + '-' + filename_rendered})
available_details = {}
available_details['selector'] = archive_details['selector']
if cached_path:
sha256.update(open(cached_path, 'rb').read())
available_details['filename'] = filename
available_details['contrib_url'] = contrib_url
available_details['contrib_url_rendered'] = contrib_url_rendered
available_details['cranurl'] = package_url
available_details['hash_entry'] = 'sha256: {}'.format(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['fn_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['fn_key'] = 'fn:'
available_details['git_url_key'] = ''
available_details['git_tag_key'] = ''
available_details['cranurl'] = ' ' + contrib_url + filename
available_details['git_url'] = ''
available_details['git_tag'] = ''
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 iteritems(available):
if archive_type != 'source':
sel = archive_details['selector']
from_source.remove(sel)
binary_id += 1
else:
for k, v in iteritems(archive_details):
d[k] = v
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')) + ']'
d['sel_src'] = sel_src
d['sel_src_and_win'] = sel_src_and_win
d['sel_src_not_win'] = sel_src_not_win
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)
else:
available_details['cranurl'] = (INDENT + contrib_url +
filename + sel_src + INDENT + contrib_url +
'Archive/{}/'.format(package) + filename + sel_src)
else:
available_details['cranurl'] = ' ' + contrib_url + filename + sel_src
if not is_github_url:
available_details['archive_keys'] = '{fn_key} {filename} {sel}\n' \
' {url_key}{sel}' \
' {cranurl}\n' \
' {hash_entry}{sel}'.format(
**available_details)
d['cran_metadata'] = '\n'.join(['# %s' % l for l in
cran_package['orig_lines'] if l])
# Render the source and binaryN keys
binary_id = 1
for archive_type, archive_details in iteritems(available):
if archive_type == 'source':
d['source'] = SOURCE_META.format(**archive_details)
else:
archive_details['sel'] = ' # [' + archive_details['selector'] + ']'
d['binary' + str(binary_id)] = BINARY_META.format(**archive_details)
binary_id += 1
# XXX: We should maybe normalize these
d['license'] = cran_package.get("License", "None")
d['license_family'] = guess_license_family(d['license'], allowed_license_families)
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'] = ' {}'.format(location)
else:
d['homeurl'] = ' https://CRAN.R-project.org/package={}'.format(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:
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("Could not parse version from dependency of %s: %s" %
(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 "
"package %s: %s" % (package, s))
dep_dict[name] = '{relop}{version}'.format(relop=relop, version=ver)
if 'R' not in dep_dict:
dep_dict['R'] = ''
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')) 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("{indent}{{{{ compiler('c') }}}} {sel}".format(
indent=INDENT, sel=sel_src_not_win))
if need_cxx:
deps.append("{indent}{{{{ compiler('cxx') }}}} {sel}".format(
indent=INDENT, sel=sel_src_not_win))
if need_f:
deps.append("{indent}{{{{ compiler('fortran') }}}}{sel}".format(
indent=INDENT, sel=sel_src_not_win))
if use_rtools_win:
need_c = need_cxx = need_f = need_autotools = need_make = False
deps.append("{indent}{{{{native}}}}rtools {sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{native}}}}extsoft {sel}".format(
indent=INDENT, sel=sel_src_and_win))
if need_c or need_cxx or need_f:
deps.append("{indent}{{{{native}}}}toolchain {sel}".format(
indent=INDENT, sel=sel_src_and_win))
if need_autotools or need_make or need_git:
deps.append("{indent}{{{{posix}}}}filesystem {sel}".format(
indent=INDENT, sel=sel_src_and_win))
if need_git:
deps.append("{indent}{{{{posix}}}}git".format(indent=INDENT))
if need_autotools:
deps.append("{indent}{{{{posix}}}}sed {sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{posix}}}}grep {sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{posix}}}}autoconf {sel}".format(
indent=INDENT, sel=sel_src))
deps.append("{indent}{{{{posix}}}}automake-wrapper{sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{posix}}}}automake {sel}".format(
indent=INDENT, sel=sel_src_and_win))
deps.append("{indent}{{{{posix}}}}pkg-config".format(indent=INDENT))
if need_make:
deps.append("{indent}{{{{posix}}}}make {sel}".format(
indent=INDENT, sel=sel_src))
elif dep_type == 'run':
if need_c or need_cxx or need_f:
deps.append("{indent}{{{{native}}}}gcc-libs {sel}".format(
indent=INDENT, sel=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, '{indent}{r_name}'.format(indent=INDENT, r_name=r_interp))
else:
conda_name = 'r-' + name.lower()
if dep_dict[name]:
deps.append('{indent}{name} {version}'.format(name=conda_name,
version=dep_dict[name], indent=INDENT))
else:
deps.append('{indent}{name}'.format(name=conda_name,
indent=INDENT))
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)
assert lower_name == inputs_dict['pkg-name'], \
"name %s != inputs_dict['pkg-name'] %s" % (
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)
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' and up_to_date(cran_metadata,
d['inputs']['old-metadata']):
continue
elif update_policy == 'skip-existing' and d['inputs']['old-metadata']:
continue
# Normalize the metadata values
d = {k: unicodedata.normalize("NFKD", text_type(v)).encode('ascii', 'ignore')
.decode() for k, v in iteritems(d)}
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'), 'w') as f:
if from_source == all:
f.write(CRAN_BUILD_SH_SOURCE.format(**d))
elif from_source == []:
f.write(CRAN_BUILD_SH_BINARY.format(**d))
else:
tpbt = [target_platform_bash_test_by_sel[t] for t in from_source]
d['source_pf_bash'] = ' || '.join(['[[ $target_platform ' + s + ' ]]'
for s in tpbt])
f.write(CRAN_BUILD_SH_MIXED.format(**d))
if not exists(join(dir_path, 'bld.bat')) or update_policy == 'overwrite':
with open(join(dir_path, 'bld.bat'), 'w') as f:
if len([fs for fs in from_source if fs.startswith('win')]) == 2:
f.write(CRAN_BLD_BAT_SOURCE.format(**d))
else:
f.write(CRAN_BLD_BAT_MIXED.format(**d))