Bizzarre issue trying to make Rpy2 2.1.9 work with R 2.12.1, using Python 2.6 under Windows xp - Rpy can't find the R.dll?

Question

I've been having a real issue trying to make Rpy2 play nice with my R install. I first tried installing the rpy2 MSI package, and this didn't appear to work. When I ran the recommended tests, it was giving me an error saying that it couldn't find the R.dll, because the new R installs (post 2.11) install the DLLs into an i386 folder, where rpy2 can't find them because its looking in the bin folder instead of the bin/i386 folder.

Then I tried to build the install from scratch myself using the command line tools (distutils) included with python. This didn't work, because setup.py claimed to be unable to find the R_home location. But I did work out that editing an environment variable (PATH) might show the rpy2 setup where to find the R installation. I then made a couple of edits to the environment, adding the "R_home" variable pointing to the bin/i386 directory, and made a new entry under the PATH variable, pointing to the same spot.

Unfortunately, when it found the R path, I got this issue instead:

running build
running build_py
running build_ext
Traceback (most recent call last):
  File "setup.py", line 372, in <module>
    [os.path.join('doc', 'source', 'rpy2_logo.png')])]
  File "C:\Python26\lib\distutils\core.py", line 152, in setup
    dist.run_commands()
  File "C:\Python26\lib\distutils\dist.py", line 975, in run_commands
    self.run_command(cmd)
  File "C:\Python26\lib\distutils\dist.py", line 995, in run_command
    cmd_obj.run()
  File "C:\Python26\lib\distutils\command\build.py", line 134, in run
    self.run_command(cmd_name)
  File "C:\Python26\lib\distutils\cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "C:\Python26\lib\distutils\dist.py", line 994, in run_command
    cmd_obj.ensure_finalized()
  File "C:\Python26\lib\distutils\cmd.py", line 117, in ensure_finalized
    self.finalize_options()
  File "setup.py", line 111, in finalize_options
    config += get_rconfig(r_home, about)
  File "setup.py", line 264, in get_rconfig
    rc = RConfig.from_string(rconfig)
  File "setup.py", line 252, in from_string
    + '\nin string\n' + string)
ValueError: Invalid substring in string

So I went back to trying to use the premade install, thinking that maybe the new edits to the environment might work but got this issue here

 Traceback (most recent call last):
      File "<string>", line 245, in run_nodebug
      File "C:\Documents and Settings\User\Desktop\rpy2-2.1.9\rpy\tests.py", line 3, in <module>
        import rpy2.robjects.tests
      File "C:\Python26\lib\site-packages\rpy2\robjects\__init__.py", line 12, in <module>
        import rpy2.rinterface as rinterface
      File "C:\Python26\lib\site-packages\rpy2\rinterface\__init__.py", line 56, in <module>
        raise RuntimeError("Unable to locate R.dll within %s" % R_HOME)
    RuntimeError: Unable to locate R.dll within C:\Program Files\R\R-2.12.1\bin\i386

This is REALLY weird, because (as anyone can check on their own install) R installs R.dll into "C:\Program Files\R\R-2.12.1\bin\i386" and I've checked and verified that its in there, and I've pointed rpy2 to this directory in the windows default PATH! I know for a fact that rpy2 is looking in the right place, but can't understand why its not seeing R.dll.

So why can't rpy2 find it? And does anyone know a way to get rpy2 working with R 2.12? Perhaps I should try the newer rpy2 2.2.0 version? Its still in development though, and 1.9 is supposed to be able to handle R 2.12 according to this website so I don't know what to do...

Thanks to anyone who can help out...

[EDIT] I've also tried these instructions over here but they return the same "can't find DLL" error... Unless you change the environment variable "R_home" to point straight at the c/program files/R/R 2.12 directory instead of into the i386 subdirectory.

If it points at the right place, you get these errors back. This looks a bit more promising... But its still pretty bad!

.......................F....................................F.FFF...F....................................................................F..................................
======================================================================
FAIL: testNewWithoutInit (rpy2.rinterface.tests.test_SexpVector.SexpVectorTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\rpy2\rinterface\tests\test_SexpVector.py", line 43, in testNewWithoutInit
    self.assertTrue(False) # worked when tested, but calling endEmbeddedR causes trouble
AssertionError

======================================================================
FAIL: testCallErrorWhenEndedR (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\rpy2\rinterface\tests\test_EmbeddedR.py", line 122, in testCallErrorWhenEndedR
    self.assertTrue(False) # worked when tested, but calling endEmbeddedR causes trouble
AssertionError

======================================================================
FAIL: testReadConsoleWithError (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\rpy2\rinterface\tests\test_EmbeddedR.py", line 117, in testReadConsoleWithError
    self.assertTrue(errorstring.startswith('Traceback'))
AssertionError

======================================================================
FAIL: testSetReadConsole (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\rpy2\rinterface\tests\test_EmbeddedR.py", line 97, in testSetReadConsole
    self.assertEquals(yes.strip(), res[0])
AssertionError: 'yes' != ''

======================================================================
FAIL: testSetWriteConsole (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\rpy2\rinterface\tests\test_EmbeddedR.py", line 36, in testSetWriteConsole
    self.assertEquals('[1] "3"\n', str.join('', buf))
AssertionError: '[1] "3"\n' != ''

======================================================================
FAIL: testWriteConsoleWithError (rpy2.rinterface.tests.test_EmbeddedR.EmbeddedRTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\rpy2\rinterface\tests\test_EmbeddedR.py", line 55, in testWriteConsoleWithError
    self.assertTrue(errorstring.startswith('Traceback'))
AssertionError

======================================================================
FAIL: testVectorUnicodeCharacter (rpy2.robjects.tests.testNumpyConversions.NumpyConversionsTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "C:\Python26\lib\site-packages\rpy2\robjects\tests\testNumpyConversions.py", line 54, in testVectorUnicodeCharacter
    self.assertTrue(False) # arrays of unicode characters causing segfault
AssertionError

----------------------------------------------------------------------
Ran 172 tests in 0.407s

FAILED (failures=7)
Exit code:  True

Answer 1

After many hours of searching on the web and trying out many different things, amongst others encountering the same issues as above, I finally got Rpy2 working on my windows 7 computer!

Basically, the crucial help came from this thread: http://www.mail-archive.com/[email protected]/msg03348.html.

Summarized, these were the steps to get rpy2 up and running on Windows7:

1. Install rpy2 from this link: https://bitbucket.org/breisfeld/rpy2_w32_fix/issue/1/binary-installer-for-win32
2. Add the path to R.dll to the environment variable PATH (C:\Program Files\R\R-2.12.1\bin\i386 in my case)
3. Add an environment variable R_HOME (C:\Program Files\R\R-2.12.1 in my case)
4. Add an environment variable R_USER (simply my username in Windows)
5. Restart your Python IDE (otherwise the environment variables are not reloaded!)