r - Error when installing rpy2 module in Python with easy_install

Question

I've been trying to install the rpy2 module so I can use R functions inside my Python script, but I'm getting an error after following the advice from these pages:

1) Tried to guess R's HOME but no R command in the PATH. OsX 10.6

2) http://rpy.sourceforge.net/rpy2/doc-dev/html/overview.html

---

What I've done so far:

1) Edited my path environment variable to include "C:Program FilesRR-3.1.0inx64;"

2) Created a new environment variable called "R_HOME" and set its value to "C:Program FilesRR-3.1.0"

3) Created a new environment variable called "R_USER" and set its value to "Hefin" (my windows username)

Then in my command prompt I type:

easy_install rpy2

As far as I'm aware, easy_install is setup and installed correctly.

The output I get is:

Searching for rpy2
Reading https://pypi.python.org/simple/rpy2/
Best match: rpy2 2.5.5
Downloading https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.5.tar.gz#md5=c874bebbe775e3cdc926a1da00252c37
Processing rpy2-2.5.5.tar.gz
Writing C:UsersHefinAppDataLocalTempeasy_install-98mu0_xn
py2-2.5.5setup.cfg
Running rpy2-2.5.5setup.py -q bdist_egg --dist-dir C:UsersHefinAppDataLocalTempeasy_install-98mu0_xn
py2-2.5.5egg-dist-tmp-00qpf_z8
The system cannot find the path specified.
Traceback (most recent call last):
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 150, in save_modules
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 191, in setup_context
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 235, in run_setup
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 265, in run

  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 234, in runner
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 46, in _execfile
  File "C:UsersHefinAppDataLocalTempeasy_install-98mu0_xn
py2-2.5.5setup.py", line 282, in <module>
  File "C:UsersHefinAppDataLocalTempeasy_install-98mu0_xn
py2-2.5.5setup.py", line 185, in getRinterface_ext
  File "C:UsersHefinAppDataLocalTempeasy_install-98mu0_xn
py2-2.5.5setup.py", line 106, in version
  File "C:Python34libsubprocess.py", line 620, in check_output
    raise CalledProcessError(retcode, process.args, output=output)
subprocess.CalledProcessError: Command '('C:\PROGRA~1\R\R-31~1.0\bin\R', '--version')' returned non-zero exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:Python34Scriptseasy_install-script.py", line 9, in <module>
    load_entry_point('setuptools==12.0.5', 'console_scripts', 'easy_install')()
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolscommandeasy_install.py", line 2244, in main
  File "C:Python34libdistutilscore.py", line 148, in setup
    dist.run_commands()
  File "C:Python34libdistutilsdist.py", line 955, in run_commands
    self.run_command(cmd)
  File "C:Python34libdistutilsdist.py", line 974, in run_command
    cmd_obj.run()
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolscommandeasy_install.py", line 374, in run
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolscommandeasy_install.py", line 623, in easy_install
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolscommandeasy_install.py", line 653, in install_item
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolscommandeasy_install.py", line 838, in install_eggs
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolscommandeasy_install.py", line 1066, in build_and_install
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolscommandeasy_install.py", line 1052, in run_setup
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 238, in run_setup
  File "C:Python34libcontextlib.py", line 77, in __exit__
    self.gen.throw(type, value, traceback)
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 191, in setup_context
  File "C:Python34libcontextlib.py", line 77, in __exit__
    self.gen.throw(type, value, traceback)
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 162, in save_modules
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 137, in resume
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolscompat.py", line 65, in reraise
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 150, in save_modules
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 191, in setup_context
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 235, in run_setup
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 265, in run
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 234, in runner
  File "C:Python34libsite-packagessetuptools-12.0.5-py3.4.eggsetuptoolssandbox.py", line 46, in _execfile
  File "C:UsersHefinAppDataLocalTempeasy_install-98mu0_xn
py2-2.5.5setup.py", line 282, in <module>
  File "C:UsersHefinAppDataLocalTempeasy_install-98mu0_xn
py2-2.5.5setup.py", line 185, in getRinterface_ext
  File "C:UsersHefinAppDataLocalTempeasy_install-98mu0_xn
py2-2.5.5setup.py", line 106, in version
  File "C:Python34libsubprocess.py", line 620, in check_output
    raise CalledProcessError(retcode, process.args, output=output)
subprocess.CalledProcessError: Command '('C:\PROGRA~1\R\R-31~1.0\bin\R', '--version')' returned non-zero exit status 1

C:UsersHefin>

Sorry it's so verbose! If I then invoke python and try to import the rpy module, I get:

>>> import python
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named 'python'
>>>

I'm afraid I'm new to Python and I don't know what I'm doing wrong. I've searched through previous forum posts, but none seem to have this problem. I'm using a 64bit machine with Windows 7, Python3.4 and R3.1.0.

Any help or thoughts would be much appreciated as I'm sure it's just something simple I'm doing wrong.

Thank you!

Hefin

Answer 1

There's a much easier way to go about this - install rpy2 from Christoph Gohlke's Python Extension Packages for Windows repository here. Download the rpy2?2.5.5?cp34?none?win_amd64.whl file (the current version at the time of this writing), change to the download folder on the command line, and run

pip install rpy2?2.5.5?cp34?none?win_amd64.whl

pip is already included in Python 3.4, and should be used instead of easy_install when installing new modules, as easy_install is deprecated.