在Jupyter Notebook中使用rpy2进行内联rmagic

Question

I am trying to use inline rmagic with jupyter notebook, but have had an extremely difficult time trying to get it to work.

Whenever I try to load %load_ext rpy2.ipython , I get the following error:

ImportError: dlopen(/Users/MyName/anaconda/lib/python2.7/site
   packages/rpy2/rinterface/_rinterface.so, 2): Library not loaded: liblzma.5.dylib
   Referenced from: /Users/MyName/anaconda/lib/python2.7/site-
   packages/rpy2/rinterface/_rinterface.so
   Reason: image not found

I have tried installing it with pip , tried installing it with conda install -cr rpy2 .

Beside this rpy2 issue, I was able to set up R and Jupyter notebook so that I can create a new notebook with R, so it doesn't seem to be an R/Jupyter communication issue.

I am running:

OS X (El Capitan)
Python 2.7.12 :: Anaconda 4.1.1 (x86_64)
R version 3.3.1 (2016-06-21) (located as in /Users/myName/anaconda/bin)
rpy2 2.8.3 (located in /Users/myName/anaconda/lib/python2.7/site-packages/)

Is there any way to get rpy2 to work with Jupyter notebook these days?

Answer 1

This is looking like a conda issue to me (lzma present at build time, but missing at run time).

Is there any way to get rpy2 to work with Jupyter notebook these days?

Probably more than one way to achieve it, but the docker container mentioned on the front page ( http://rpy2.bitbucket.org/ ) is getting all pieces together in one step.

Answer 2

I was able to get this to work by reinstalling anaconda, and installing rpy2 through conda:

conda install rpy2

This will install R and lots of dependencies for anaconda. Use this R and not the system R . The PATH should be automatically updated after anaconda is installed, but just in case, make sure to prepend anaconda:

setenv PATH /Users/myName/anaconda2/bin:$PATH

It critical that rpy2 be able to find the Renviron file, which should be newly installed within anaconda. I found mine here (I just searched for it using spotlight):

/Users/myName/anaconda2/lib/R/

which I then made into the R_HOME variable that rpy2 requires to find Renviron . I also specified my username:

setenv R_HOME /Users/myName/anaconda2/lib/R/
setenv R_USER myName

(note that which R will return /Users/myName/anaconda2/bin/R/ , but this is NOT R_HOME . This tripped me up for ages).