jupyter
Error output suppressed using IRkernel
Using Jupyter 5.0.0.dev (built from master a few days ago) with an R kernel (IRkernel), important error output is suppressed when code is run in the notebook. The error messages are reported normally when run in a standard R shell.
The notebook I am running is here.
The first screen shot shows the model code run in an R session (this was exported directly from the notebook's export facility), with the key error message shown in red:
However, when run as a notebook, the error line is missing
Session information: Python 3.5.1 |Continuum Analytics, Inc.| (default, Dec 7 2015, 11:24:55) [GCC 4.2.1 (Apple Inc. build 5577)] R version 3.2.5 (2016-04-14)
This also might be an issue with the R kernel itself. Could you open an issue on this repo as well: https://github.com/IRkernel/IRkernel
On Mon, May 16, 2016 at 6:34 PM, Chris Fonnesbeck [email protected] wrote:
Using Jupyter 5.0.0.dev (built from master a few days ago) with an R kernel (IRkernel), important error output is suppressed when code is run in the notebook. The error messages are reported normally when run in a standard R shell.
The notebook I am running is here https://gist.github.com/a025f78ad1bdff0835232523273a56b3.
The first screen shot shows the model code run in an R session (this was exported directly from the notebook's export facility), with the key error message shown in red:
[image: screenshot 2016-05-16 20 32 59] https://cloud.githubusercontent.com/assets/81476/15308675/690618ca-1ba5-11e6-8d6c-a64b23ec737d.png
However, when run as a notebook, the error line is missing
[image: screenshot 2016-05-16 20 33 47] https://cloud.githubusercontent.com/assets/81476/15308689/8554f7e4-1ba5-11e6-9577-bf36b47246c6.png
Session information: Python 3.5.1 |Continuum Analytics, Inc.| (default, Dec 7 2015, 11:24:55) [GCC 4.2.1 (Apple Inc. build 5577)] R version 3.2.5 (2016-04-14)
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Brian E. Granger Associate Professor of Physics and Data Science Cal Poly State University, San Luis Obispo @ellisonbg on Twitter and GitHub [email protected] and [email protected]
I would guess that the error message is being written to stderr at a lower level than our capturing works - this also comes up in some cases in Python. Once the kernel nanny machinery (jupyter/enhancement-proposals#14) lands, it should fix cases like this (assuming IRkernel opts in to the output capturing part of that spec).
Having error seen in notebooks would be important. This (very old) issue is still open - is there a workaround maybe?
