NotImplementedError: Conversion 'rpy2py' not defined for objects of type '<class 'rpy2.rinterface.SexpClosure'>' only after I run the code twice

Question

If I run the following code once it works.

import numpy as np
import rpy2.robjects as robjects
x = np.linspace(0, 1, num = 11, endpoint=True)    
y = np.array([-1,1,1, -1,1,0, .5,.5,.4,  .5, -1])

r_x = robjects.FloatVector(x)
r_y = robjects.FloatVector(y)
r_smooth_spline = robjects.r['smooth.spline'] #extract R function
spline_xy = r_smooth_spline(x=r_x, y=r_y)
print('x =', x)
print('ysplined =',np.array(robjects.r['predict'](spline_xy,robjects.FloatVector(x)).rx2('y')))

If I run this cell twice in a Jupyter notebook, I obtain the following error message:

---------------------------------------------------------------------------
NotImplementedError                       Traceback (most recent call last)
<ipython-input-2-5efeb940cd16> in <module>
      6 r_x = robjects.FloatVector(x)
      7 r_y = robjects.FloatVector(y)
----> 8 r_smooth_spline = robjects.r['smooth.spline'] #extract R function
      9 spline_xy = r_smooth_spline(x=r_x, y=r_y)
     10 print('x =', x)

2 frames
/usr/local/lib/python3.8/dist-packages/rpy2/robjects/conversion.py in _rpy2py(obj)
    250     non-rpy2) objects.
    251     """
--> 252     raise NotImplementedError(
    253         "Conversion 'rpy2py' not defined for objects of type '%s'" %
    254         str(type(obj))

NotImplementedError: Conversion 'rpy2py' not defined for objects of type '<class 'rpy2.rinterface.SexpClosure'>'

This code always used to run without problems multiple times. Probably a new version of python or rpy2 is the problem? How can I fix the problem such that I am able to run this code multiple times within one Jupyter notebook.

This bug occurs for the vollowing version: ipykernel version 5.3.4,

!jupyter --version

Selected Jupyter core packages...
IPython          : 7.9.0
ipykernel        : 5.3.4
ipywidgets       : 7.7.1
jupyter_client   : 6.1.12
jupyter_core     : 4.11.2
jupyter_server   : not installed
jupyterlab       : not installed
nbclient         : not installed
nbconvert        : 5.6.1
nbformat         : 5.7.0
notebook         : 5.7.16
qtconsole        : not installed
traitlets        : 5.1.1

in combination with rpy2 version 3.5.5

import rpy2
print(rpy2.__version__)

3.5.5

Asked By: Jakob

||

Source

Answer 1

The easiest fix is to run once:

!pip install -Iv rpy2==3.4.2

at the start of the Jupyter-notebook in order to rollback to version 3.4.2, where this problem did not occur (see Rpy2 Error depends on execution method: NotImplementedError: Conversion "rpy2py" not defined). For more information how to change the version of a python package see Rollback to specific version of a python package in Goolge Colab and Installing specific package version with pip)

It would still be interesting to understand how one could use the latest version of rpy2 correctly.

Answered By: Jakob

Answer 2

This is caused by an issue in older releases of ipykernel. I’d recommend to upgrade it rather than downgrade rpy2.

See https://github.com/rpy2/rpy2/issues/952

Answered By: lgautier

NotImplementedError: Conversion 'rpy2py' not defined for objects of type '<class 'rpy2.rinterface.SexpClosure'>' only after I run the code twice

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