.uns['neighbors'] crashes conversion of pbmc3k_processed() demo data

[ktpolanski]

Tried to pass sc.datasets.pbmc3k_processed() through the Jupyter %%R -i adata syntax, encountered wall of error pasted below. Deleted .uns['neighbors'], the object went through just fine.

anndata 0.7.5, anndata2ri 1.1.0, rpy2 3.4.3 if relevant

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-5-4f83d5b8882a> in <module>
----> 1 get_ipython().run_cell_magic('R', '-i adata', 'adata\n')

/opt/conda/envs/teichlab/lib/python3.8/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
   2397             with self.builtin_trap:
   2398                 args = (magic_arg_s, cell)
-> 2399                 result = fn(*args, **kwargs)
   2400             return result
   2401 

<decorator-gen-121> in R(self, line, cell, local_ns)

/opt/conda/envs/teichlab/lib/python3.8/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

/opt/conda/envs/teichlab/lib/python3.8/site-packages/rpy2/ipython/rmagic.py in R(self, line, cell, local_ns)
    773                                                'consolewrite_print',
    774                                                self.write_console_regular))
--> 775                         cell_display(result, args)
    776                         text_output += self.flush()
    777 

/opt/conda/envs/teichlab/lib/python3.8/site-packages/rpy2/ipython/rmagic.py in CELL_DISPLAY_DEFAULT(res, args)
    108 
    109 def CELL_DISPLAY_DEFAULT(res, args):
--> 110     return ro.r.show(res)
    111 
    112 

/opt/conda/envs/teichlab/lib/python3.8/site-packages/rpy2/robjects/functions.py in __call__(self, *args, **kwargs)
    196                 v = kwargs.pop(k)
    197                 kwargs[r_k] = v
--> 198         return (super(SignatureTranslatedFunction, self)
    199                 .__call__(*args, **kwargs))
    200 

/opt/conda/envs/teichlab/lib/python3.8/site-packages/rpy2/robjects/functions.py in __call__(self, *args, **kwargs)
    115 
    116     def __call__(self, *args, **kwargs):
--> 117         new_args = [conversion.py2rpy(a) for a in args]
    118         new_kwargs = {}
    119         for k, v in kwargs.items():

/opt/conda/envs/teichlab/lib/python3.8/site-packages/rpy2/robjects/functions.py in <listcomp>(.0)
    115 
    116     def __call__(self, *args, **kwargs):
--> 117         new_args = [conversion.py2rpy(a) for a in args]
    118         new_kwargs = {}
    119         for k, v in kwargs.items():

/opt/conda/envs/teichlab/lib/python3.8/functools.py in wrapper(*args, **kw)
    873                             '1 positional argument')
    874 
--> 875         return dispatch(args[0].__class__)(*args, **kw)
    876 
    877     funcname = getattr(func, '__name__', 'singledispatch function')

/opt/conda/envs/teichlab/lib/python3.8/site-packages/anndata2ri/py2r.py in py2rpy_anndata(obj)
     69         # Convert everything we know
     70         with localconverter(full_converter() + dict_converter):
---> 71             metadata = ListVector(obj.uns.items())
     72 
     73         rd_args = {conv_name.scanpy2sce(k): mat_converter.py2rpy(obj.obsm[k]) for k in obj.obsm.keys()}

/opt/conda/envs/teichlab/lib/python3.8/site-packages/rpy2/robjects/vectors.py in __init__(self, tlist)
    639                 raise ValueError('tlist should have a /method/ __iter__ '
    640                                  '(not an attribute)')
--> 641             kv = [(str(k), conversion.py2rpy(v)) for k, v in tlist]
    642             kv = tuple(kv)
    643             df = baseenv_ri.find("list").rcall(kv, globalenv_ri)

/opt/conda/envs/teichlab/lib/python3.8/site-packages/rpy2/robjects/vectors.py in <listcomp>(.0)
    639                 raise ValueError('tlist should have a /method/ __iter__ '
    640                                  '(not an attribute)')
--> 641             kv = [(str(k), conversion.py2rpy(v)) for k, v in tlist]
    642             kv = tuple(kv)
    643             df = baseenv_ri.find("list").rcall(kv, globalenv_ri)

/opt/conda/envs/teichlab/lib/python3.8/functools.py in wrapper(*args, **kw)
    873                             '1 positional argument')
    874 
--> 875         return dispatch(args[0].__class__)(*args, **kw)
    876 
    877     funcname = getattr(func, '__name__', 'singledispatch function')

/opt/conda/envs/teichlab/lib/python3.8/site-packages/anndata2ri/py2r.py in py2rpy_dict(obj)
     31     """Try converting everything. For nested dicts, this needs itself to be registered"""
     32     converted = {}
---> 33     for k, v in obj.items():
     34         try:
     35             converted[str(k)] = conversion.py2rpy(v)

/opt/conda/envs/teichlab/lib/python3.8/_collections_abc.py in __iter__(self)
    742     def __iter__(self):
    743         for key in self._mapping:
--> 744             yield (key, self._mapping[key])
    745 
    746 ItemsView.register(dict_items)

/opt/conda/envs/teichlab/lib/python3.8/site-packages/anndata/compat/_overloaded_dict.py in __getitem__(self, key)
     98             return self.overloaded[key].get()
     99         else:
--> 100             return self.data[key]
    101 
    102     def __setitem__(self, key, value):

/opt/conda/envs/teichlab/lib/python3.8/site-packages/rpy2/robjects/vectors.py in __getitem__(self, i)
    263 
    264     def __getitem__(self, i):
--> 265         res = super().__getitem__(i)
    266 
    267         if isinstance(res, Sexp):

/opt/conda/envs/teichlab/lib/python3.8/site-packages/rpy2/rinterface_lib/sexp.py in __getitem__(self, i)
    639             )
    640         else:
--> 641             raise TypeError(
    642                 'Indices must be integers or slices, not %s' % type(i))
    643         return res

TypeError: Indices must be integers or slices, not <class 'rpy2.robjects.vectors.ListVector'>