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theislab / scib

Benchmarking analysis of data integration tools
MIT License
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Import Error #320

Closed liujilei156231 closed 2 years ago

liujilei156231 commented 2 years ago

I have installed my R-4.1.0 to conda base env. It may be a reason for my Import Error. So how to repair this error? Thanks!

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/scib/__init__.py", line 8, in <module>
    from . import integration, metrics, preprocessing
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/scib/metrics/__init__.py", line 1, in <module>
    from .metrics import *
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/scib/metrics/metrics.py", line 7, in <module>
    from .cell_cycle import cell_cycle
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/scib/metrics/cell_cycle.py", line 4, in <module>
    from ..preprocessing import score_cell_cycle
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/scib/preprocessing.py", line 6, in <module>
    import anndata2ri
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/anndata2ri/__init__.py", line 39, in <module>
    from .conv import converter, activate, deactivate
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/anndata2ri/conv.py", line 3, in <module>
    from rpy2.robjects import conversion, numpy2ri, pandas2ri
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/rpy2/robjects/__init__.py", line 20, in <module>
    import rpy2.robjects.functions
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/rpy2/robjects/functions.py", line 12, in <module>
    from rpy2.robjects import help
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/rpy2/robjects/help.py", line 46, in <module>
    quiet_require('tools')
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/rpy2/robjects/help.py", line 41, in quiet_require
    expr = rinterface.parse(expr_txt)
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _
    cdata = function(*args, **kwargs)
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/rpy2/rinterface.py", line 100, in parse
    res = _rinterface._parse(robj.__sexp__._cdata, num, rmemory)
  File "/home/liujilei/miniconda3/envs/scvi-env/lib/python3.9/site-packages/rpy2/rinterface_lib/_rinterface_capi.py", line 640, in _parse
    openrlib.rlib.R_tryCatchError(
ffi.error: symbol 'R_tryCatchError' not found in library '/usr/lib/R/lib/libR.so': /usr/lib/R/lib/libR.so: undefined symbol: R_tryCatchError
>>>