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POtrouble installing rpy2 on win7 (R 2.12, Python 2.5)
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  1. POtrouble installing rpy2 on win7 (R 2.12, Python 2.5)
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    copied!<p>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:</p> <blockquote> <p>Tried to guess R's HOME but no R command in the PATH.</p> </blockquote> <p>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!</p> <p>Here's setup.py's code</p> <pre><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 " +\ "(&lt;r-home&gt;/lib otherwise)"), ('r-home-modules=', None, "full path for the R shared modules/ directory " +\ "(&lt;r-home&gt;/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" +\ "(&lt;r-home&gt;/lib otherwise)"), ('r-home-modules=', None, "full path for the R shared modules/ directory" +\ "(&lt;r-home&gt;/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 &gt;= 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 ([^ ]+) .+$', rversion) rversion = m.groups()[0] rversion = rversion.split('.') rversion[0] = int(rversion[0]) rversion[1] = int(rversion[1]) return rversion def cmp_version(x, y): if (x[0] &lt; y[0]): return -1 if (x[0] &gt; y[0]): return 1 if (x[0] == y[0]): if len(x) == 1 or len(y) == 1: return 0 return cmp_version(x[1:], y[1:]) class RConfig(object): _include_dirs = None _libraries = None _library_dirs = None _extra_link_args = None _frameworks = None _framework_dirs = None def __init__(self, include_dirs = tuple(), libraries = tuple(), library_dirs = tuple(), extra_link_args = tuple(), frameworks = tuple(), framework_dirs = tuple()): for k in ('include_dirs', 'libraries', 'library_dirs', 'extra_link_args'): v = locals()[k] if not isinstance(v, tuple): if isinstance(v, str): v = [v, ] v = tuple(set(v)) self.__dict__['_'+k] = v # frameworks are specific to OSX for k in ('framework_dirs', 'frameworks'): v = locals()[k] if not isinstance(v, tuple): if isinstance(v, str): v = [v, ] v = tuple(set(v)) self.__dict__['_'+k] = v self.__dict__['_'+'extra_link_args'] = tuple(set(v + self.__dict__['_'+'extra_link_args'])) def __repr__(self): s = 'Configuration for R as a library:' + os.linesep s += os.linesep.join( [' ' + x + ': ' + self.__dict__['_'+x].__repr__() \ for x in ('include_dirs', 'libraries', 'library_dirs', 'extra_link_args')]) s += os.linesep + ' # OSX-specific (included in extra_link_args)' + os.linesep s += os.linesep.join( [' ' + x + ': ' + self.__dict__['_'+x].__repr__() \ for x in ('framework_dirs', 'frameworks')] ) return s def __add__(self, config): assert isinstance(config, RConfig) res = RConfig(include_dirs = self._include_dirs + \ config._include_dirs, libraries = self._libraries + config._libraries, library_dirs = self._library_dirs + \ config._library_dirs, extra_link_args = self._extra_link_args + \ config._extra_link_args) return res @staticmethod def from_string(string, allow_empty = False): possible_patterns = ('^-L(?P&lt;library_dirs&gt;[^ ]+)$', '^-l(?P&lt;libraries&gt;[^ ]+)$', '^-I(?P&lt;include_dirs&gt;[^ ]+)$', '^(?P&lt;framework_dirs&gt;-F[^ ]+?)$', '^(?P&lt;frameworks&gt;-framework [^ ]+)$') 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('(?&lt;!-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 = "lgautier@gmail.com", 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] ) </code></pre>
 

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