rmagic not displaying output in jupyter python notebook

[mikekaminsky]

(Apologies if this is not the right the repo for this issue, or if I'm missing something obvious in the ecosystem.)

When I'm using rmagic to run models in R in the midst of my python notebook, the R output is getting sent to stdout (visible where my notebook server is running) but I can't get it to display the output in my notebook.

A notebook with these two cells should reproduce the issue.

# Setup
import rpy2
%load_ext rpy2.ipython

Run a model:

%%R
X <-c(1,4,5,7)
Y <- c(2,4,3,9)
summary(lm(Y~X))

[takluyver]

This may be something that rpy2 can improve more easily in the short term. We're working on a mechanism to capture output at the OS level, which would fix this, but it's an idea we've had for years that gets bogged down in discussion every time we try to drive it forwards.

[mikekaminsky]

I see some chatter about jupyter in the rpy2 repo. @takluyver If you give me some more of an idea of what you're thinking about I can try to run this down a bit farther over there.

[takluyver]

Are you on Windows? If so, I think this is the issue: https://bitbucket.org/rpy2/rpy2/issues/125/set_writeconsole-not-working-on-windows

If you're on another platform, I'd recommend opening a new issue about it. Feel free to link to this issue and tag me (I'm takluyver on bitbucket as well).

[mikekaminsky]

macOS unfortunately. I've tagged you over there. Thanks for the help!

[lgautier]

Repeating comment in https://bitbucket.org/rpy2/rpy2/issues/416/rmagic-not-displaying-output-in-jupyter.

The callbacks are properly function in ipython:

In [1]: import rpy2.robjects as ro                                              

In [2]: ro.r('library("dplyr")')                                                
R[write to console]: 
Attaching package: ‘dplyr’


R[write to console]: The following objects are masked from ‘package:stats’:

    filter, lag


R[write to console]: The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


Out[2]: 
R object with classes: ('character',) mapped to:
['dplyr', 'tools', 'stats', 'graphics', ..., 'utils', 'datasets', 'methods', 'base']

[lgautier]

Actually I cannot reproduce the issue on Linux. I am expecting that the discussion will continue in the issue tracker for rpy2, and I'll come back here if this is believed to be an issue with Jupyter.

[joseph-allen]

This still appears to be an issue

%%R
x <- c(0,1,2,3,4)
print(x)