Error in Flux Variability Analysis

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Rakesh Mandal

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May 30, 2022, 3:13:19 AM5/30/22
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Hello, 
I am pretty new to cobrapy. My problem is as follows: I ran these specific commands,

from cobra.flux_analysis import flux_variability_analysis
model.summary(fva=0.9)

When I am using cobrapy in a Linux environment, those commands do not generate any error. But when I'm using cobrapy through Spyder-Anaconda in windows, it shows the following error. Please help me resolve this issue.

  File ~\anaconda3\lib\site-packages\cobra\core\model.py:1209 in summary
    return ModelSummary(model=self, solution=solution, fva=fva)

  File ~\anaconda3\lib\site-packages\cobra\summary\model_summary.py:85 in __init__
    self._generate(model, solution, fva)

  File ~\anaconda3\lib\site-packages\cobra\summary\model_summary.py:120 in _generate
    fva = flux_variability_analysis(

  File ~\anaconda3\lib\site-packages\cobra\flux_analysis\variability.py:239 in flux_variability_analysis
    with ProcessPool(

  File ~\anaconda3\lib\site-packages\cobra\util\process_pool.py:56 in __init__
    pickle.dump((initializer,) + initargs, handle)

TypeError: cannot pickle 'SwigPyObject' object


Version details:
conda version: 4.12.0
conda-build version: 3.21.8
python version: 3.9.12.final.0

Thanks,
Rakesh


Moritz Beber

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May 30, 2022, 3:27:23 AM5/30/22
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Hi Rakesh,

Thanks for the info. I haven't seen this problem before. Can you please open an issue on GitHub https://github.com/opencobra/cobrapy/issues with the same information.

Thanks in advance,
Moritz
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