%load_ext rpy2.ipython causes "The kernel appears to have died. It will restart automatically"

Question

In a jupyter notebook

%load_ext rpy2.ipython

causes the kernel to crash.

"The kernel appears to have died. It will restart automatically."

with the following console message

Error in `::`(base, quote) : could not find function "::"
Error in `::`(base, quote) : could not find function "::"
Error in `:::`(compiler, checkCompilerOptions) : 
  could not find function ":::"
Fatal error: unable to initialize the JIT

Any clues on this? I've tried cleaning out my R installation and starting from scratch. Same error, every time.

Mac OS 10.14.6 python 3.8 R version 4.1.0 (2021-05-18) rpy2-3.4.4 jupyter-1.0.0

When you start the R interpreter from command line, does it work? — krassowski, Jun 02 '21 at 10:06
R starts fine...R version 4.1.0 (2021-05-18) -- "Camp Pontanezen" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) — Mike Yearworth, Jun 02 '21 at 10:17
`python3 -m rpy2.situation` `/opt/local/bin/python3: Error while finding module specification for 'rpy2.situation' (ModuleNotFoundError: No module named 'rpy2')` — Mike Yearworth, Jun 02 '21 at 10:19
```pip install rpy2 Requirement already satisfied: rpy2 in /usr/local/lib/python3.8/site-packages (3.4.4)``` — Mike Yearworth, Jun 02 '21 at 10:22
`/usr/local/lib/python3.8 -m rpy2.situation` should work then — krassowski, Jun 02 '21 at 10:30

score 0 · Answer 1 · answered Jun 02 '21 at 13:09

0

Thanks @krassowski my python38 installation was messed up. Uninstalled python and all packages installed by pip and started again with python39. Fixed the problem.

answered Jun 02 '21 at 13:09

Mike Yearworth

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%load_ext rpy2.ipython causes "The kernel appears to have died. It will restart automatically"

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