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.

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