force rpy2 in conda environment to use the R outside of the conda environment

Question

I started using conda environments. I know that I can open and use R jupiter notebook, but my preferred workflow is to use R within a python notebook, when necessary, with rpy2 and push/pull data between the two languages

%R push data
%R run something
%R pull output

however now when I run rpy2 in a conda environment, it searches for all packages in the R folder within the conda environment. I would like to use the packages installed in my home directory or those from the machine I work on, without the need to reinstall everything for each conda environment. Is that possible?

did you figured out how to do that? – Nielsen Rechia Apr 26 '18 at 14:14 — Nielsen Rechia, Apr 26 '18 at 14:14

score 1 · Answer 1 · answered Nov 15 '17 at 21:59

1

There are several ways to tell R about package directories (http://stat.ethz.ch/R-manual/R-devel/library/base/html/libPaths.html).

Try setting the environment variable R_LIBS or R_LIBS_USER (before %load_ext rpy2.ipython in the notebook).

answered Nov 15 '17 at 21:59

lgautier

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this is a hack that will not always work (the R process will still dynamically load shared libraries [=\= R packages] from the conda environment) – jan-glx Feb 06 '19 at 13:24

force rpy2 in conda environment to use the R outside of the conda environment

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