def _install(self, name, version, repos):
'''Check existence and version match of R library.
cran and bioc packages are unique yet might overlap with github.
Therefore if the input name is {repo}/{pkg} the package will be
installed from github if not available, else from cran or bioc
'''
from sos.pattern import glob_wildcards
import tempfile
import subprocess
output_file = tempfile.NamedTemporaryFile(mode='w+t',
suffix='.txt',
delete=False).name
script_file = tempfile.NamedTemporaryFile(mode='w+t',
suffix='.R',
delete=False).name
if len(glob_wildcards('{repo}@{pkg}', [name])['repo']):
# package is from github
self._install('devtools', None, repos)
install_script = f'''
options(warn=-1)
package_repo <-strsplit("{name}", split="@")[[1]][2]
package <-strsplit("{name}", split="@")[[1]][1]
if (suppressMessages(require(package, character.only=TRUE, quietly=TRUE))) {{
write(paste(package, packageVersion(package), "AVAILABLE"), file="{output_file}")
}} else {{
devtools::install_github(package_repo)
# if it still does not exist, write the package name to output
if (suppressMessages(require(package, character.only=TRUE, quietly=TRUE))) {{
write(paste(package, packageVersion(package), "INSTALLED"), file="{output_file}")
}} else {{
write(paste(package, "NA", "MISSING"), file="{output_file}")
quit("no")
}}
}}
cur_version <- packageVersion(package)
'''
else:
# package is from cran or bioc
install_script = f'''
options(warn=-1)
package <- "{name}"
if (suppressMessages(require(package, character.only=TRUE, quietly=TRUE))) {{
write(paste(package, packageVersion(package), "AVAILABLE"), file={output_file!r})
}} else {{
install.packages(package, repos="{repos}",
quiet=FALSE)
# if the package still does not exist
if (!suppressMessages(require(package, character.only=TRUE, quietly=TRUE))) {{
source("http://bioconductor.org/biocLite.R")
biocLite(package, suppressUpdates=TRUE, suppressAutoUpdate=TRUE, ask=FALSE)
}}
# if it still does not exist, write the package name to output
if (suppressMessages(require(package, character.only=TRUE, quietly=TRUE))) {{
write(paste(package, packageVersion(package), "INSTALLED"), file={output_file!r})
}} else {{
write(paste(package, "NA", "MISSING"), file={output_file!r})
quit("no")
}}
}}
cur_version <- packageVersion(package)
'''
version_script = ''
if version is not None:
version = list(version)
operators = []
for idx, value in enumerate(version):
value = str(value)
if value.endswith('+'):
operators.append('>=')
version[idx] = value[:-1]
elif value.endswith('-'):
operators.append('<')
version[idx] = value[:-1]
else:
operators.append('==')
# check version and mark version mismatch
# if current version satisfies any of the
# requirement the check program quits
for x, y in zip(version, operators):
version_script += f'''
if (cur_version {y} {repr(x)}) {{
quit("no")
}}
'''
version_script += f'write(paste(package, cur_version, "VERSION_MISMATCH"), file = {repr(output_file)})'
# temporarily change the run mode to run to execute script
try:
with open(script_file, 'w') as sfile:
sfile.write(install_script + version_script)
#
p = subprocess.Popen(
['Rscript', '--default-packages=utils', script_file])
ret = p.wait()
if ret != 0:
env.logger.warning('Failed to detect or install R library')
return False
except Exception as e:
env.logger.error(f'Failed to execute script: {e}')
return False
finally:
os.remove(script_file)
ret_val = False
with open(output_file) as tmp:
for line in tmp:
lib, version, status = line.split()
if status.strip() == "MISSING":
env.logger.warning(
f'R Library {lib} is not available and cannot be installed.'
)
elif status.strip() == 'AVAILABLE':
env.logger.debug(
f'R library {lib} ({version}) is available')
ret_val = True
elif status.strip() == 'INSTALLED':
env.logger.debug(
f'R library {lib} ({version}) has been installed')
ret_val = True
elif status.strip() == 'VERSION_MISMATCH':
env.logger.warning(
f'R library {lib} ({version}) does not satisfy version requirement!'
)
else:
raise RuntimeError(f'This should not happen: {line}')
try:
os.remove(output_file)
except Exception:
pass
return ret_val
def _install(self, name, version, repos):
"""Check existence and version match of R library.
cran and bioc packages are unique yet might overlap with github.
Therefore if the input name is {repo}/{pkg} the package will be
installed from github if not available, else from cran or bioc
"""
from sos.pattern import glob_wildcards
import tempfile
import subprocess
output_file = tempfile.NamedTemporaryFile(mode="w+t",
suffix=".txt",
delete=False).name
script_file = tempfile.NamedTemporaryFile(mode="w+t",
suffix=".R",
delete=False).name
#
package_loaded = (
"suppressMessages(require(package, character.only=TRUE, quietly=TRUE))"
)
version_satisfied = "TRUE"
for opt in ("==", ">=", ">", "<=", "<", "!="):
if opt in name:
if version is not None:
raise ValueError(
f"Specifying 'version=' option in addition to '{name}' is not allowed"
)
name, version = [x.strip() for x in name.split(opt, 1)]
if "," in version:
raise ValueError(
f"SoS does not yet support multiple version comparisons. {version} provided"
)
version = (opt + version, )
break
if version is not None:
version = list(version)
operators = []
for idx, value in enumerate(version):
value = str(value)
if value.startswith(">="):
operators.append(">=")
version[idx] = value[2:]
elif value.startswith(">"):
operators.append(">")
version[idx] = value[1:]
elif value.startswith("<="):
operators.append("<=")
version[idx] = value[2:]
elif value.startswith("<"):
operators.append("<")
version[idx] = value[1:]
elif value.startswith("=="):
operators.append("==")
version[idx] = value[2:]
elif value.startswith("!="):
operators.append("!=")
version[idx] = value[2:]
else:
operators.append("==")
# check version and mark version mismatch
# if current version satisfies any of the
# requirement the check program quits
version_satisfied = "||".join([
f"(cur_version {y} {repr(x)})"
for x, y in zip(version, operators)
])
#
if len(glob_wildcards("{repo}@{pkg}", [name])["repo"]):
# package is from github
self._install("remotes>=2.0.0", None, repos)
install_script = f"""
options(warn=-1)
package_repo <-strsplit("{name}", split="@")[[1]][2]
package <-strsplit("{name}", split="@")[[1]][1]
if ({package_loaded}) cur_version <- packageVersion(package) else cur_version <- NULL
if (!is.null(cur_version) && {version_satisfied}) {{
write(paste(package, cur_version, "AVAILABLE"), file={repr(output_file)})
}} else if ({"TRUE" if self._autoinstall else "FALSE"}) {{
remotes::install_github(package_repo, force=TRUE, upgrade="never")
if ({package_loaded}) cur_version <- packageVersion(package) else cur_version <- NULL
# if it still does not exist, write the package name to output
if (!is.null(cur_version)) {{
if ({version_satisfied}) write(paste(package, cur_version, "INSTALLED"), file={repr(output_file)})
else write(paste(package, cur_version, "VERSION_MISMATCH"), file={repr(output_file)})
}} else {{
write(paste(package, "NA", "MISSING"), file={repr(output_file)})
quit("no")
}}
}} else {{
if (!is.null(cur_version)) write(paste(package, cur_version, "VERSION_MISMATCH"), file={repr(output_file)}) else write(paste(package, cur_version, "UNAVAILABLE"), file={repr(output_file)})
}}
"""
else:
# package is from cran or bioc
install_script = f"""
options(warn=-1)
package <- "{name}"
if ({package_loaded}) cur_version <- packageVersion(package) else cur_version <- NULL
if (!is.null(cur_version) && {version_satisfied}) {{
write(paste(package, cur_version, "AVAILABLE"), file={repr(output_file)})
}} else if ({"TRUE" if self._autoinstall else "FALSE"}) {{
install.packages(package, repos="{repos}", quiet=FALSE)
# if the package still does not exist
if (!{package_loaded}) {{
source("http://bioconductor.org/biocLite.R")
biocLite(package, suppressUpdates=TRUE, suppressAutoUpdate=TRUE, ask=FALSE)
}}
if ({package_loaded}) cur_version <- packageVersion(package) else cur_version <- NULL
# if it still does not exist, write the package name to output
if (!is.null(cur_version)) {{
if ({version_satisfied}) write(paste(package, cur_version, "INSTALLED"), file={repr(output_file)}) else write(paste(package, cur_version, "VERSION_MISMATCH"), file={repr(output_file)})
}} else {{
write(paste(package, "NA", "MISSING"), file={repr(output_file)})
quit("no")
}}
}} else {{
if (!is.null(cur_version)) write(paste(package, cur_version, "VERSION_MISMATCH"), file={repr(output_file)}) else write(paste(package, cur_version, "UNAVAILABLE"), file={repr(output_file)})
}}
"""
# temporarily change the run mode to run to execute script
try:
with open(script_file, "w") as sfile:
sfile.write(install_script)
#
p = subprocess.Popen(
["Rscript", "--default-packages=utils", script_file])
ret = p.wait()
if ret != 0:
env.logger.warning(
f"Failed to detect or install R library {name}")
return False
except Exception as e:
env.logger.error(f"Failed to execute script: {e}")
return False
finally:
os.remove(script_file)
ret_val = False
with open(output_file) as tmp:
for line in tmp:
lib, cur_version, status = line.split(" ", 2)
if status.strip() == "MISSING":
env.logger.error(
f"R library {lib} is not available and cannot be installed."
)
elif status.strip() == "UNAVAILABLE":
env.logger.error(f"R library {lib} is not available.")
elif status.strip() == "AVAILABLE":
env.logger.debug(
f"R library {lib} ({cur_version}) is available")
ret_val = True
elif status.strip() == "INSTALLED":
env.logger.debug(
f"R library {lib} ({cur_version}) has been installed")
ret_val = True
elif status.strip() == "VERSION_MISMATCH":
env.logger.error(
f'R library {lib} ({cur_version}) does not satisfy version requirement ({"/".join(version)})!'
)
else:
raise RuntimeError(f"This should not happen: {line}")
try:
os.remove(output_file)
except Exception:
pass
return ret_val
def _install(self, name, version, repos):
'''Check existence and version match of R library.
cran and bioc packages are unique yet might overlap with github.
Therefore if the input name is {repo}/{pkg} the package will be
installed from github if not available, else from cran or bioc
'''
from sos.pattern import glob_wildcards
from sos.sos_eval import interpolate
import tempfile
import shlex
import subprocess
output_file = tempfile.NamedTemporaryFile(mode='w+t', suffix='.txt', delete=False).name
script_file = tempfile.NamedTemporaryFile(mode='w+t', suffix='.R', delete=False).name
if len(glob_wildcards('{repo}/{pkg}', [name])['repo']):
# package is from github
self._intall('devtools', version, repos)
install_script = interpolate('''
options(warn=-1)
package_repo <- ${name!r}
package <- basename(package_repo)
if (require(package, character.only=TRUE, quietly=TRUE)) {
write(paste(package, packageVersion(package), "AVAILABLE"), file="${output_file}")
} else {
devtools::install_github(package_repo)
# if it still does not exist, write the package name to output
if (require(package, character.only=TRUE, quietly=TRUE)) {
write(paste(package, packageVersion(package), "INSTALLED"), file="${output_file}")
} else {
write(paste(package, "NA", "MISSING"), file="${output_file}")
quit("no")
}
}
cur_version <- packageVersion(package)
''', '${ }', locals())
else:
# package is from cran or bioc
install_script = interpolate('''
options(warn=-1)
package <- ${name!r}
if (require(package, character.only=TRUE, quietly=TRUE)) {
write(paste(package, packageVersion(package), "AVAILABLE"), file="${output_file}")
} else {
install.packages(package, repos="${repos}",
quiet=FALSE)
# if the package still does not exist
if (!require(package, character.only=TRUE, quietly=TRUE)) {
source("http://bioconductor.org/biocLite.R")
biocLite(package, suppressUpdates=TRUE, suppressAutoUpdate=TRUE, ask=FALSE)
}
# if it still does not exist, write the package name to output
if (require(package, character.only=TRUE, quietly=TRUE)) {
write(paste(package, packageVersion(package), "INSTALLED"), file="${output_file}")
} else {
write(paste(package, "NA", "MISSING"), file="${output_file}")
quit("no")
}
}
cur_version <- packageVersion(package)
''', '${ }', locals())
version_script = ''
if version is not None:
version = [version] if isinstance(version, str) else version
operators = []
for idx, value in enumerate(version):
value = str(value)
if value.endswith('+'):
operators.append('>=')
version[idx] = value[:-1]
elif value.endswith('-'):
operators.append('<')
version[idx] = value[:-1]
else:
operators.append('==')
# check version and mark version mismatch
# if current version satisfies any of the
# requirement the check program quits
for x, y in zip(version, operators):
version_script += '''
if (cur_version {1} {0}) {{
quit("no")
}}
'''.format(repr(x), y)
version_script += 'write(paste(package, cur_version, "VERSION_MISMATCH"), file = {})'.\
format(repr(output_file))
# temporarily change the run mode to run to execute script
try:
with open(script_file, 'w') as sfile:
sfile.write(install_script + version_script)
cmd = 'Rscript --default-packages=utils ' + shlex.quote(script_file)
#
p = subprocess.Popen(cmd, shell=True)
ret = p.wait()
if ret != 0:
env.logger.warning('Failed to detect or install R library')
return False
except Exception as e:
env.logger.error('Failed to execute script: {}'.format(e))
return False
finally:
os.remove(script_file)
ret_val = False
with open(output_file) as tmp:
for line in tmp:
lib, version, status = line.split()
if status.strip() == "MISSING":
env.logger.warning('R Library {} is not available and cannot be installed.'.format(lib))
elif status.strip() == 'AVAILABLE':
env.logger.debug('R library {} ({}) is available'.format(lib, version))
ret_val = True
elif status.strip() == 'INSTALLED':
env.logger.debug('R library {} ({}) has been installed'.format(lib, version))
ret_val = True
elif status.strip() == 'VERSION_MISMATCH':
env.logger.warning('R library {} ({}) does not satisfy version requirement!'.format(lib, version))
else:
raise RuntimeError('This should not happen: {}'.format(line))
try:
os.remove(output_file)
except:
pass
return ret_val