R notebook not executing with `jupyter nbconvert --execute`

[Jonathan Taylor]

I am trying to execute and save a notebook with the "ir" kernel but am getting an error. It runs find under `jupyter notebook` Here is a notebook that fails

https://gist.github.com/jonathan-taylor/3201952fcf518edfc21cbed4cc12e105

~/git-repos/datascience_101 (master) $ jupyter nbconvert --execute --to notebook --allow-errors modules/intro/intro-lab01.ipynb

[NbConvertApp] Converting notebook modules/intro/intro-lab01.ipynb to notebook

[NbConvertApp] Executing notebook with kernel: ir

Traceback (most recent call last):

  File "/Users/jonathantaylor/anaconda/bin/jupyter-nbconvert", line 6, in <module>

    main()

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/jupyter_core/application.py", line 267, in launch_instance

    return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/traitlets/config/application.py", line 589, in launch_instance

    app.start()

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/nbconvertapp.py", line 289, in start

    self.convert_notebooks()

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/nbconvertapp.py", line 412, in convert_notebooks

    self.convert_single_notebook(notebook_filename)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/nbconvertapp.py", line 383, in convert_single_notebook

    output, resources = self.export_single_notebook(notebook_filename, resources)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/nbconvertapp.py", line 335, in export_single_notebook

    output, resources = self.exporter.from_filename(notebook_filename, resources=resources)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/exporters/exporter.py", line 165, in from_filename

    return self.from_notebook_node(nbformat.read(f, as_version=4), resources=resources, **kw)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/exporters/notebook.py", line 26, in from_notebook_node

    nb_copy, resources = super(NotebookExporter, self).from_notebook_node(nb, resources, **kw)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/exporters/exporter.py", line 130, in from_notebook_node

    nb_copy, resources = self._preprocess(nb_copy, resources)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/exporters/exporter.py", line 302, in _preprocess

    nbc, resc = preprocessor(nbc, resc)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/preprocessors/base.py", line 47, in __call__

    return self.preprocess(nb,resources)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py", line 83, in preprocess

    nb, resources = super(ExecutePreprocessor, self).preprocess(nb, resources)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/preprocessors/base.py", line 70, in preprocess

    nb.cells[index], resources = self.preprocess_cell(cell, resources, index)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py", line 97, in preprocess_cell

    outputs = self.run_cell(cell)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbconvert/preprocessors/execute.py", line 183, in run_cell

    out = output_from_msg(msg)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbformat/v4/nbbase.py", line 77, in output_from_msg

    data=content['data'],

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbformat/v4/nbbase.py", line 42, in new_output

    validate(output, output_type)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbformat/v4/nbbase.py", line 23, in validate

    return validate(node, ref=ref, version=nbformat)

  File "/Users/jonathantaylor/anaconda/lib/python2.7/site-packages/nbformat/validator.py", line 156, in validate

    raise better_validation_error(e, version, version_minor)

jsonschema.exceptions.ValidationError: None is not valid under any of the given schemas

Failed validating u'oneOf' in schema[u'properties'][u'data'][u'patternProperties'][u'^(?!application/json$)[a-zA-Z0-9]+/[a-zA-Z0-9\\-\\+\\.]+$']:

    {u'oneOf': [{u'type': u'string'},

                {u'items': {u'type': u'string'}, u'type': u'array'}]}

On instance[u'data'][u'text/latex']:

    None

Others work fine: https://gist.github.com/jonathan-taylor/764d10c8029730b359afcc5db81c6351

~/git-repos/datascience_101 (master) $ jupyter nbconvert --execute --to notebook --allow-errors modules/intro/intro-lab02.ipynb

[NbConvertApp] Converting notebook modules/intro/intro-lab02.ipynb to notebook

[NbConvertApp] Executing notebook with kernel: ir

[NbConvertApp] Writing 623234 bytes to intro-lab02.nbconvert.ipynb

~/git-repos/datascience_101 (master) $ 

(The second one has some data files I could include if necessary).

[Jonathan Taylor]

I should probably add that these notebooks were generated by subclassing notedown's MarkdownReader and manually inserting metadata to set the kernel to "ir".

That said, `jupyter notebook` works fine on these notebooks.

[Thomas Kluyver]

Hi Jonathan,

It looks like somewhere in the json it has an output with:

'text/latex': null

I don't know exactly how it occurred, but if you can find that, remove that key-value pair and it should be OK.

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[Jonathan Taylor]

Thanks for the reply. It seems like a cell like this would be the problem? I didn't find exactly  ''' "text/latex": null ''' in the file, though.

    {
     "data": {
      "text/html": [],
      "text/latex": [],
      "text/markdown": [],
      "text/plain": [
       "logical(0)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },

I guess I will try to see how that got inserted in the notebook from (subclassed) notedown...

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[luck]

Hi Jonathan,

did you find a solution to your problem? If yes, what was your solution.

I seem to have the same problem when trying to use RunNotebook to include a R notebook via sphinx.  

I have 2 R notebooks and only one has this problem.

Luc