Installation fail Mac OSX 10.9.3

Issue #208 resolved
c n created an issue

Hi. I'm trying to install rpy2-2.4.2 on OSX10.9.3 runing python 2.7.3 and R3.1.0. Basically nothing is working for a legit install of Rpy2.

easy_install rpy2 #runs to completion, but then when importing the testing modules... ImportError: dlopen(.../site-packages/rpy2-2.4.2-py2.7-macosx-10.5-i386.egg/rpy2/rinterface/_rinterface.so, 2): Symbol not found: _R_BaseEnv ... Expected in: dynamic lookup

after uninstalling pip install rpy2 #also fails Downloading/unpacking rpy2 Cannot fetch index base URL https://pypi.python.org/simple/ Could not find any downloads that satisfy the requirement rpy2

rpy2 --upgrade #also fails Cannot fetch index base URL https://pypi.python.org/simple/ Could not find any downloads that satisfy the requirement rpy2 in /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages Downloading/unpacking rpy2 Cleaning up... No distributions at all found for rpy2 in /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-packages Storing debug log for failure in /Users/chrisnelson/.pip/pip.log

python setup.py install # gives much the same behavior as the easy install route, even when I use rpy2.1.9

Could somebody point me to an easier version to install?

Comments (5)

  1. Matthew Wakefield

    I think this is the same as #196. There are two installs of R3.1 for OSX, one that is more backwards compatible and a newer, cleaner install with more modern compiler, libraries and optimisations.

    Laurent, I would suggest a check for the presence of the library in the install script with a more verbose error.

    3.1 for OS X 10.9 Mavericks (the binary package installer) is going catch a lot of people with these fortran library issues. The first many users are going to notice is that loading libraries fails. Tracing this back into R showed that compiling the same libraries from source also fails. This is because R3.1 for OS X 10.9 Mavericks is compiled against gFortran 4.8 and these libraries are not included in Xcode 5.1 or by the binary installer. The fix (thanks to thecoatlessprofessor) is to add the libraries - easily done with: curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2 sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /

    Really this is a bug in the R installer, it should install, or at least prompt to install, these libraries.

  2. c n reporter

    I'm getting similar issues on a machine running R 3.0.1

    import rpy2.tests

    cannot find system Renviron; Error in getLoadedDLLs() : not a BUILTIN function; Error in checkConflicts(value) : 7 arguments passed to .Internal(identical) which requires 6 Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Python/2.7/site-packages/rpy2-2.3.6-py2.7-macosx-10.7-intel.egg/rpy2/tests.py", line 9, in <module> import rpy2.robjects.tests File "/Library/Python/2.7/site-packages/rpy2-2.3.6-py2.7-macosx-10.7-intel.egg/rpy2/robjects/init.py", line 18, in <module> from rpy2.robjects.robject import RObjectMixin, RObject File "/Library/Python/2.7/site-packages/rpy2-2.3.6-py2.7-macosx-10.7-intel.egg/rpy2/robjects/robject.py", line 9, in <module> class RObjectMixin(object): File "/Library/Python/2.7/site-packages/rpy2-2.3.6-py2.7-macosx-10.7-intel.egg/rpy2/robjects/robject.py", line 22, in RObjectMixin __show = rpy2.rinterface.baseenv.get("show") LookupError: 'show' not found

  3. c n reporter

    I had been working with Enthought python release 7.3.

    I migrated over to the continuum anaconda release of python http://continuum.io/downloads, installed, added it to the beginning of $PATH, and did a clean:

    pip install rpy2

    That seems to have worked around the issue.

  4. Laurent Gautier

    There has been issues with Enthought's Python and rpy2. All were resolved by using an other Python (except the OS X system's Python).

  5. Laurent Gautier

    The issue initially reported is probably a problem upstream (R & tools on OS X), and the second issue likely specific to Enthought's Python. The resolution was: use an other Python

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