theislab/anndata2ri

import error

Closed this issue · 7 comments

iosonofabio commented

Hi and thanks for the nice package.

I cannot import anndata2ri. I just created a new conda environment with python3.8 and installed R. I also installed anndata2ri with pip (conda failed AND failed to backtrace the error...). When trying to import the package, I get a long backtrace that ends with:

...

~/anaconda3/envs/scconvert/lib/python3.8/site-packages/rpy2/rinterface_lib/sexp.py in __getitem__(self, key)
    353         # TODO: move check of R_UnboundValue to _rinterface
    354         if res == openrlib.rlib.R_UnboundValue:
--> 355             raise KeyError("'%s' not found" % key)
    356         return res
    357 

KeyError: "'str2lang' not found"

Any help to get this to work would be greatly appreciated.

flying-sheep commented

Can you please give me a minimal reproducible example as well as the full stack trace? Otherwise I can’t help you.

iosonofabio commented

Thank you, here the code of how I got this:

$ conda create -n myenv python=3.8
$ conda activate myenv
$ conda install R
$ conda install -c bioconda anndata2ri 

Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

then I tried to install with pip:

$ pip install anndata2ri
python
Python 3.8.2 (default, Mar 26 2020, 15:53:00) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import anndata2ri
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/fabio/anaconda3/envs/myenv/lib/python3.8/site-packages/anndata2ri/__init__.py", line 20, in <module>
    from .conv import converter, activate, deactivate
  File "/home/fabio/anaconda3/envs/myenv/lib/python3.8/site-packages/anndata2ri/conv.py", line 3, in <module>
    from rpy2.robjects import conversion, numpy2ri, pandas2ri, default_converter, SexpVector
  File "/home/fabio/anaconda3/envs/myenv/lib/python3.8/site-packages/rpy2/robjects/__init__.py", line 27, in <module>
    from . import language
  File "/home/fabio/anaconda3/envs/myenv/lib/python3.8/site-packages/rpy2/robjects/language.py", line 16, in <module>
    _str2lang = ri.baseenv['str2lang']
  File "/home/fabio/anaconda3/envs/myenv/lib/python3.8/site-packages/rpy2/rinterface_lib/conversion.py", line 44, in _
    cdata = function(*args, **kwargs)
  File "/home/fabio/anaconda3/envs/myenv/lib/python3.8/site-packages/rpy2/rinterface_lib/_rinterface_capi.py", line 282, in _
    robj = function(*args, **kwargs)
  File "/home/fabio/anaconda3/envs/myenv/lib/python3.8/site-packages/rpy2/rinterface_lib/sexp.py", line 355, in __getitem__
    raise KeyError("'%s' not found" % key)
KeyError: "'str2lang' not found"

Now since you are not testing python 3.8 on Travis, I repeated the spiel on Python 3.7.7, same errors (both on the conda install and on the import after pip install).

My guess is that this package should require a specific version of rpy2 and/or R to go be paired with?

Maybe you could extend your Travis build matrix to include installing R within a conda environment instead of globally?

Having semi-insulated environment is one major reason why people use conda in the first place, since having to juggle 5 different versions of R on the same server is not great.

If you are interested you can have a look at how I usually do these things using manylinux2010 and OSX + conda, could be useful here too: https://travis-ci.org/github/htseq/htseq/builds/677026670

flying-sheep commented

Conda is being weird; after “The following specifications were found to be incompatible with each other:” should be something, you should probably report that bug with them.

For the pip route, the error happens when importing rpy2, so

  1. please check where the problem happens before reporting a bug somewhere. the stack trace clearly tells you that the last anndata2ri line that’s involved is

    rpy2.robjects import conversion, numpy2ri, pandas2ri, default_converter, SexpVector

    which clearly means that it’s not a anndata2ri bug.

  2. if you google “str2lang”, you’ll find that it has been added in R 3.6.0. I strongly assume that you should simply update your R to make rpy2 work. If you think rpy2 should work with older R versions, please report an issue there

iosonofabio commented
flying-sheep commented

done: https://github.com/theislab/anndata2ri#troubleshooting

If you have any ideas how to make it more helpful, I’d be happy about that PR.

I think the rpy2 project would be happy to accept a PR for the R version requirement, as it is the one requiring it. I just require a working rpy2 version, however that comes to be.

iosonofabio commented
flying-sheep commented

I’m sure rpy2 could be fixed to not use that specific function (and possible other 3.6+ features) if you ask/try!