Could not install rpy2 correctly: undefined symbol omp_get_num_procs

Question

I try to install rpy2 on my computer with R 3.1.2 from the source using

python setup.py install --user

It output success, but when I try to test it using

python -m rpy2.tests

It give me the following output:

rpy2 version: 2.6.0
- built against R version: 3-1.2--66913
- running linked to R version: R version 3.1.2 (2014-10-31)
/scratch/opt/python-2.7.9/lib/python2.7/site-packages/rpy2-2.6.0-py2.7-linux-x86_64.egg/rpy2/robjects/lib/ggplot2.py:59: UserWarning: This was designed againt ggplot2 version 1.0.1 but you have 1.0.0
  warnings.warn('This was designed againt ggplot2 version %s but you have %s' % (TARGET_VERSION, ggplot2.__version__))
....../tmp/tmp05nvfc.py:17: UserWarning:

  ri.baseenv['eval'](ri.parse(rcode))
............................................................................................................................................................................................................python: symbol lookup error: /usr/lib64/RRO-8.0.2/R-3.1.2/lib64/R/lib/libmkl_gnu_thread.so: undefined symbol: omp_get_num_procs

I have the full Installation Log stored here:

https://bitbucket.org/Tamaki_Sakura/labscript/src/4cf05da1e19fca5b539c0ffb96c4334c6afe850d/stackoverflowtemp.txt?at=default

This one is kind of related to my old question here:

Could not install rpy2 correctly

However they're not the same. It happens on different machines and the one I have here now does have R built as a library.

Answer 1

Issue is likely related to openmp and /or Intel's MKL in relation with the way R was compiled (and this is different when you are running rpy2). There are likely environment variables to be set...