trouble installing rpy2 on win7 (R 2.12, Python 2.

Question

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 = "[e-mail]",
    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]
    )

Answer 1

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.

Answer 2

I've encountered a somewhat different but related installation problem and finally found a solution at http://www.mail-archive.com/[e-mail]/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.

Answer 3

I had exactly the same problem running rpy2 in python under win32 "WINBLOW :)" XP ; but I got this to work , FINALLY !!.

Here's how I did it :

1. Same as Guillaume, I had to copy all the files from C:\Program Files\R\R-2.15.0\bin\i386 to R\R-2.15.0

2. I had to set an environment variable

Go to My Computer>properties>Advanced>Environment Variables> Variable : "PATH" , adding ;C:\Program Files\R\R-2.15.0 at the end of the "Value"

1. rerun python setup.py build install under command prompt C:\Python27\rpy2>

Hope This help, and please let me know if this work for you.

Answer 4

I too had a problem with RPy2, and I never actually got it to work - after days and days of trying all different sorts of solutions. I encourage you to try all of the great ideas people are telling you, and I'm interested to see if any of them work!

If you fail as I did, you may be able to use a workaround in the following way depending on your purposes:

1. Write R code with all of the functions you would like to use which also calls the libraries you want to use. Put all of these functions and library calls into one file (temp.r). For example, maybe my file looks like
   

   
   CurrentYear <- function(birth.year,age) { 
      year <- birth.year + age
      return(year)
   }
   

2. Use python to prompt for user input to do function calls. I did this with a GUI, you can probably just do it with script in the terminal.

3. Use python to create a string with the R function calls. For example, we might have

    stuff = '\nCurrentYear("%(birth.year)d", "%(age)d")\n' %vars() 

   where birth.year and age have been input by the user in the python program.

4. Add stuff to the end of temp.r using python:

   
   # Creates a copy of temp.r, so as not to disturb its contents for future use.
   tocall = copyfile("C:\My Documents\temp.r", "C:\My Documents\tocall.r")
   # Open the copy with the intent to append it (hence the "a")
   inp = open("C:\tocall.r", "a")
   # Adds the function call to the R script
   inp.write(stuff)
   inp.close()
   # Navigate to the correct directory, use "Rscript" to
   # run the code in the shell
   dostuff = call('cd C:\My Documents &Rscript temp.r', shell = True)
   

5. Profit

I'm not sure what the disadvantages of this method are, but it works for me. Hope this helps if you fail with the whole RPy2 thing!

Answer 5

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

Answer 6

Got rpy2 to work finally with Windows 7 from source code. If it doesn't work for you like it didn't for me. See rpy2 install on windows 7.

Hope this helps!!