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I'm brand new to Python (and programming in general) I come from a finance background, so please bear with me. I just started using Python (Enthought's Pylab/Scipy/Numpy) and R for statistical analysis. I'm trying to install rpy2 into Python to integrate R, but I get the error:
Tried to guess R's HOME but no R command in the PATH.
I'm not sure what this means. The path to my R.exe is "C:\Program Files\R\R-2.12.1\bin" if that's useful. Any help would be much appreciated!
Here's setup.py's code
import os, os.path, sys, shutil, re, itertools
from distutils.command.build_ext import build_ext as _build_ext
from distutils.command.build import build as _build
from distutils.core import setup
from distutils.core import Extension
pack_name = 'rpy2'
pack_version = __import__('rpy').__version__
class build(_build):
user_options = _build.user_options + \
[
#('r-autoconfig', None,
# "guess all configuration paths from " +\
# "the R executable found in the PATH " +\
# "(this overrides r-home)"),
('r-home=', None,
"full path for the R home to compile against " +\
"(see r-autoconfig for an automatic configuration)"),
('r-home-lib=', None,
"full path for the R shared lib/ directory " +\
"(<r-home>/lib otherwise)"),
('r-home-modules=', None,
"full path for the R shared modules/ directory " +\
"(<r-home>/modules otherwise)")
]
boolean_options = _build.boolean_options #+ \
#['r-autoconfig', ]
def initialize_options(self):
_build.initialize_options(self)
self.r_autoconfig = None
self.r_home = None
self.r_home_lib = None
self.r_home_modules = None
class build_ext(_build_ext):
"""
-DRPY_VERBOSE
-DRPY_DEBUG_PRESERV
-DRPY_DEBUG_PROMISE : evaluation of promises
-DRPY_DEBUG_OBJECTINIT : initialization of PySexpObject
-DRPY_DEBUG_CONSOLE : console I/O
-DRPY_DEBUG_COBJECT : SexpObject passed as a CObject
-DRPY_DEBUG_GRDEV
"""
user_options = _build_ext.user_options + \
[
#('r-autoconfig', None,
# "guess all configuration paths from " +\
# "the R executable found in the PATH " +\
# "(this overrides r-home)"),
('r-home=', None,
"full path for the R home to compile against " +\
"(see r-autoconfig for an automatic configuration)"),
('r-home-lib=', None,
"full path for the R shared lib/ directory" +\
"(<r-home>/lib otherwise)"),
('r-home-modules=', None,
"full path for the R shared modules/ directory" +\
"(<r-home>/modules otherwise)")]
boolean_options = _build_ext.boolean_options #+ \
#['r-autoconfig', ]
def initialize_options(self):
_build_ext.initialize_options(self)
self.r_autoconfig = None
self.r_home = None
self.r_home_lib = None
self.r_home_modules = None
def finalize_options(self):
self.set_undefined_options('build',
#('r_autoconfig', 'r_autoconfig'),
('r_home', 'r_home'))
_build_ext.finalize_options(self)
if self.r_home is None:
self.r_home = os.popen("R RHOME").readlines()
if len(self.r_home) == 0:
raise SystemExit("Error: Tried to guess R's HOME but no R command in the PATH.")
#Twist if 'R RHOME' spits out a warning
if self.r_home[0].startswith("WARNING"):
self.r_home = self.r_home[1]
else:
self.r_home = self.r_home[0]
#self.r_home = [self.r_home, ]
if self.r_home is None:
raise SystemExit("Error: --r-home not specified.")
else:
self.r_home = self.r_home.split(os.pathsep)
rversions = []
for r_home in self.r_home:
r_home = r_home.strip()
rversion = get_rversion(r_home)
if cmp_version(rversion[:2], [2, 8]) == -1:
raise SystemExit("Error: R >= 2.8 required.")
rversions.append(rversion)
config = RConfig()
for about in ('--ldflags', '--cppflags',
'LAPACK_LIBS', 'BLAS_LIBS'):
config += get_rconfig(r_home, about)
print(config.__repr__())
self.include_dirs.extend(config._include_dirs)
self.libraries.extend(config._libraries)
self.library_dirs.extend(config._library_dirs)
if self.r_home_modules is None:
self.library_dirs.extend([os.path.join(r_home, 'modules'), ])
else:
self.library_dirs.extends([self.r_home_modules, ])
#for e in self.extensions:
# self.extra_link_args.extra_link_args(config.extra_link_args)
# e.extra_compile_args.extend(extra_compile_args)
def run(self):
_build_ext.run(self)
def get_rversion(r_home):
r_exec = os.path.join(r_home, 'bin', 'R')
# Twist if Win32
if sys.platform == "win32":
rp = os.popen3('"'+r_exec+'" --version')[2]
else:
rp = os.popen('"'+r_exec+'" --version')
rversion = rp.readline()
#Twist if 'R RHOME' spits out a warning
if rversion.startswith("WARNING"):
rversion = rp.readline()
m = re.match('^R version ([^ ]+) .+$', rversion)
rversion = m.groups()[0]
rversion = rversion.split('.')
rversion[0] = int(rversion[0])
rversion[1] = int(rversion[1])
return rversion
def cmp_version(x, y):
if (x[0] < y[0]):
return -1
if (x[0] > y[0]):
return 1
if (x[0] == y[0]):
if len(x) == 1 or len(y) == 1:
return 0
return cmp_version(x[1:], y[1:])
class RConfig(object):
_include_dirs = None
_libraries = None
_library_dirs = None
_extra_link_args = None
_frameworks = None
_framework_dirs = None
def __init__(self,
include_dirs = tuple(), libraries = tuple(),
library_dirs = tuple(), extra_link_args = tuple(),
frameworks = tuple(),
framework_dirs = tuple()):
for k in ('include_dirs', 'libraries',
'library_dirs', 'extra_link_args'):
v = locals()[k]
if not isinstance(v, tuple):
if isinstance(v, str):
v = [v, ]
v = tuple(set(v))
self.__dict__['_'+k] = v
# frameworks are specific to OSX
for k in ('framework_dirs', 'frameworks'):
v = locals()[k]
if not isinstance(v, tuple):
if isinstance(v, str):
v = [v, ]
v = tuple(set(v))
self.__dict__['_'+k] = v
self.__dict__['_'+'extra_link_args'] = tuple(set(v + self.__dict__['_'+'extra_link_args']))
def __repr__(self):
s = 'Configuration for R as a library:' + os.linesep
s += os.linesep.join(
[' ' + x + ': ' + self.__dict__['_'+x].__repr__() \
for x in ('include_dirs', 'libraries',
'library_dirs', 'extra_link_args')])
s += os.linesep + ' # OSX-specific (included in extra_link_args)' + os.linesep
s += os.linesep.join(
[' ' + x + ': ' + self.__dict__['_'+x].__repr__() \
for x in ('framework_dirs', 'frameworks')]
)
return s
def __add__(self, config):
assert isinstance(config, RConfig)
res = RConfig(include_dirs = self._include_dirs + \
config._include_dirs,
libraries = self._libraries + config._libraries,
library_dirs = self._library_dirs + \
config._library_dirs,
extra_link_args = self._extra_link_args + \
config._extra_link_args)
return res
@staticmethod
def from_string(string, allow_empty = False):
possible_patterns = ('^-L(?P<library_dirs>[^ ]+)$',
'^-l(?P<libraries>[^ ]+)$',
'^-I(?P<include_dirs>[^ ]+)$',
'^(?P<framework_dirs>-F[^ ]+?)$',
'^(?P<frameworks>-framework [^ ]+)$')
pp = [re.compile(x) for x in possible_patterns]
# sanity check of what is returned into rconfig
rconfig_m = None
span = (0, 0)
rc = RConfig()
for substring in re.split('(?<!-framework) ', string):
ok = False
for pattern in pp:
rconfig_m = pattern.match(substring)
if rconfig_m is not None:
rc += RConfig(**rconfig_m.groupdict())
span = rconfig_m.span()
ok = True
break
elif rconfig_m is None:
if allow_empty and (rconfig == ''):
print(cmd + '\nreturned an empty string.\n')
rc += RConfig()
ok = True
break
else:
# if the configuration points to an existing library,
# use it
if os.path.exists(string):
rc += RConfig(library = substring)
ok = True
break
if not ok:
raise ValueError('Invalid substring\n' + substring
+ '\nin string\n' + string)
return rc
def get_rconfig(r_home, about, allow_empty = False):
r_exec = os.path.join(r_home, 'bin', 'R')
cmd = '"'+r_exec+'" CMD config '+about
rp = os.popen(cmd)
rconfig = rp.readline()
#Twist if 'R RHOME' spits out a warning
if rconfig.startswith("WARNING"):
rconfig = rp.readline()
rconfig = rconfig.strip()
rc = RConfig.from_string(rconfig)
return rc
def getRinterface_ext():
#r_libs = [os.path.join(RHOME, 'lib'), os.path.join(RHOME, 'modules')]
r_libs = []
extra_link_args = []
#FIXME: crude way (will break in many cases)
#check how to get how to have a configure step
define_macros = []
if sys.platform == 'win32':
define_macros.append(('Win32', 1))
else:
define_macros.append(('R_INTERFACE_PTRS', 1))
define_macros.append(('HAVE_POSIX_SIGJMP', 1))
define_macros.append(('CSTACK_DEFNS', 1))
define_macros.append(('RIF_HAS_RSIGHAND', 1))
include_dirs = []
rinterface_ext = Extension(
name = pack_name + '.rinterface.rinterface',
sources = [ \
#os.path.join('rpy', 'rinterface', 'embeddedr.c'),
#os.path.join('rpy', 'rinterface', 'r_utils.c'),
#os.path.join('rpy', 'rinterface', 'buffer.c'),
#os.path.join('rpy', 'rinterface', 'sequence.c'),
#os.path.join('rpy', 'rinterface', 'sexp.c'),
os.path.join('rpy', 'rinterface', 'rinterface.c')
],
depends = [os.path.join('rpy', 'rinterface', 'embeddedr.h'),
os.path.join('rpy', 'rinterface', 'r_utils.h'),
os.path.join('rpy', 'rinterface', 'buffer.h'),
os.path.join('rpy', 'rinterface', 'sequence.h'),
os.path.join('rpy', 'rinterface', 'sexp.h'),
os.path.join('rpy', 'rinterface', 'rpy_rinterface.h')
],
include_dirs = [os.path.join('rpy', 'rinterface'),] + include_dirs,
libraries = ['R', ],
library_dirs = r_libs,
define_macros = define_macros,
runtime_library_dirs = r_libs,
#extra_compile_args=['-O0', '-g'],
#extra_link_args = extra_link_args
)
rpy_device_ext = Extension(
pack_name + '.rinterface.rpy_device',
[
os.path.join('rpy', 'rinterface', 'rpy_device.c'),
],
include_dirs = include_dirs +
[os.path.join('rpy', 'rinterface'), ],
libraries = ['R', ],
library_dirs = r_libs,
define_macros = define_macros,
runtime_library_dirs = r_libs,
#extra_compile_args=['-O0', '-g'],
extra_link_args = extra_link_args
)
return [rinterface_ext, rpy_device_ext]
rinterface_exts = []
ri_ext = getRinterface_ext()
rinterface_exts.append(ri_ext)
pack_dir = {pack_name: 'rpy'}
import distutils.command.install
for scheme in distutils.command.install.INSTALL_SCHEMES.values():
scheme['data'] = scheme['purelib']
setup(
#install_requires=['distribute'],
cmdclass = {'build': build,
'build_ext': build_ext},
name = pack_name,
version = pack_version,
description = "Python interface to the R language",
url = "http://rpy.sourceforge.net",
license = "AGPLv3.0 (except rpy2.rinterface: LGPL)",
author = "Laurent Gautier",
author_email = "[email protected]",
ext_modules = rinterface_exts[0],
package_dir = pack_dir,
packages = [pack_name,
pack_name + '.rlike',
pack_name + '.rlike.tests',
pack_name + '.rinterface',
pack_name + '.rinterface.tests',
pack_name + '.robjects',
pack_name + '.robjects.tests',
pack_name + '.robjects.lib',
],
classifiers = ['Programming Language :: Python',
'License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)',
'License :: OSI Approved :: GNU Affero General Public License v3',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'Development Status :: 5 - Production/Stable'
],
data_files = [(os.path.join('rpy2', 'images'),
[os.path.join('doc', 'source', 'rpy2_logo.png')])]
#[pack_name + '.rinterface_' + x for x in rinterface_rversions] + \
#[pack_name + '.rinterface_' + x + '.tests' for x in rinterface_rversions]
)
990
I know I'm a little late to the party, but I had the same problem and got it working on Windows 7 by doing the install via conda
conda install --channel https://conda.binstar.org/joshadel rpy2
I have encountered a similar problem trying to use rpy2 with R 2.12 and Python 2.6 (as recommended by the rpy2 documentation).
It seems that windows binaries from http://cran.r-project.org/bin/windows/base/R-2.12.1-win.exe install the required R.dll in a directory not expected by rpy2.
I have copied all the files from R\R-2.12.1\bin\i386 to the bin directory, set an environnement variable R_HOME pointing to R\R-2.12.1 and it then worked.
24
I've encountered a somewhat different but related installation problem and finally found a solution at http://www.mail-archive.com/[email protected]/msg02817.html
After I installed rpy2 2.0.8 via rpy2-2.0.8.win32-py2.6.msi (windows 7 (64bit), python 2.6, R 2.14 (both 32bit and 64bit, via RAndFriendsSetup2140V3.2-1-1.exe)), and tried to import rpy2 within python console, I got the exception:
Unable to locate R.dll
Adding the following lines to rinterface/__init__.py made it work:
if os.path.exists(os.path.join(R_HOME, 'lib')): ## ADDED ##
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'bin')
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'modules')
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'lib')
else: ## ADDED ##
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'bin', 'i386') ## ADDED ##
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'modules', 'i386') ## ADDED ##
os.environ['PATH'] += ';' + os.path.join(R_HOME, 'library') ## ADDED ##
# Load the R dll using the explicit path
# First try the bin dir:
Rlib = os.path.join(R_HOME, 'bin', 'R.dll')
# Try bin/i386 subdirectory seen in R 2.12.0 ## ADDED ##
if not os.path.exists(Rlib): ## ADDED ##
Rlib = os.path.join(R_HOME, 'bin', 'i386', 'R.dll') ## ADDED ##
# Then the lib dir:
if not os.path.exists(Rlib):
Rlib = os.path.join(R_HOME, 'lib', 'R.dll')
# Otherwise fail out!
if not os.path.exists(Rlib):
raise RuntimeError("Unable to locate R.dll within %s" % R_HOME)
It turns out that the R.dll is moved but the __init__.py is not updated accordingly. So simply editing the __init__.py file will get things right.
Then I tried to replicate Taj G's situation, and I did it. After adding "your_R_installation_dir\bin\i386" into the windows environment variable PATH, the old error disappeared but new one came:
ValueError: Invalid substring in string
It seems that some additional pieces need to be installed and a C/C++ compiler needs to be correctly configured. I gave up here. Using easy_install to build rpy2 from source seems really tricky on windows and not officially support at present.
Although rpy2 2.0.8 is not a full-fledged version compared with 2.2.4, it is the latest version with standard windows installer on sourceforge. For now, it is the easy choice.
30
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