如何在Azure笔记本中使用rmagic？

Question

I am trying to get some data out of R snippet to Azure Python 3 Jupyter notebook (hosting is available for free at http://notebooks.azure.com ).

I tried the following in Python 3 notebook:

%load_ext rmagic

then tried to embed R:

%%R -o x
x <- 1

then

x

Here I get Python error: name 'x' is not defined – see the picture below. What is the right way to embed R into Python 3 and exchange data using Azure Notebooks?

Azure Notebooks http://nogin.info/R2Py.png

Answer 1

@DmitryNogin, I reproduced the issue successfully. And according to the descprition below from here , you need to use %load_ext rpy2.ipython instead of %load_ext rmagic in jupyter notebook now.

The rmagic extension has been moved to rpy2 as rpy2.interactive.ipython.

However, I got some other errors below when I tried %load_ext rpy2.ipython in notebook.

ImportError: libRblas.so: cannot open shared object file: No such file or directory

I searched a solution which need to set an environment variable LD_LIBRARY_PATH with export LD_LIBRARY_PATH=/usr/lib64/MR0-3.3.0/R-3.3.0/lib/R/lib (the path value which I found via the command which R ) on Azure notebook server. However, the host Ubuntu OS not be installed vi or vim and I don't know the sudo password for nbuser in the terminal, so although the solution works for ipython in the terminal of notebook server, it can't make the jupyter works.

My final work solution is that using the terminal of notebook server to command ln -s /usr/lib64/MR0-3.3.0/R-3.3.0/lib/R/lib/* ~/anaconda3_410/lib/ .

Then, when you enter %load_ext rpy2.ipython , you will get an error ImportError ..../libreadline.so.6: undefined symbol: PC . You only need to enter import readline to solve it before %load_ext rpy2.ipython .

Finally, you can load rpy2.ipython for %R xxx with some warning information.

Hope it helps.