Question

utf-8 codec can't decode byte 0xd5

0

Entering edit mode

yuhang • 0

@1b2a94a4

Last seen 8 months ago

Hong Kong

Hi, I am learning to analyze bulk RNA-Seq data using Python. I am using Python3.6 and R 4.2.3.


    import pandas as pd
    import rpy2.robjects as robjects
    from rpy2.robjects import pandas2ri, Formula
    pandas2ri.activate()
    from rpy2.robjects.packages import importr

Everything went well and an error hit me.


    deseq = importr('DESeq2')

## 

    error
    D:\Files\Python\PXF_H_L\venv\Scripts\python.exe D:/Files/Python/PXF_H_L/deseq2_2.py
    From cffi callback <function _consolewrite_ex at 0x164A4AE0>:
    Traceback (most recent call last):
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\callbacks.py", line 132, in _consolewrite_ex
        s = conversion._cchar_to_str_with_maxlen(buf, n, _CCHAR_ENCODING)
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\conversion.py", line 133, in _cchar_to_str_with_maxlen
        s = ffi.string(c, maxlen).decode(encoding)
    UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd5 in position 223: invalid continuation byte
    R[write to console]: Failed with error:  
    R[write to console]: 
    From cffi callback <function _consolewrite_ex at 0x164A4AE0>:
    Traceback (most recent call last):
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\callbacks.py", line 132, in _consolewrite_ex
        s = conversion._cchar_to_str_with_maxlen(buf, n, _CCHAR_ENCODING)
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\conversion.py", line 133, in _cchar_to_str_with_maxlen
        s = ffi.string(c, maxlen).decode(encoding)
    UnicodeDecodeError: 'utf-8' codec can't decode byte 0xce in position 1: invalid continuation byte
    R[write to console]: 
    R[write to console]: 

    From cffi callback <function _consolewrite_ex at 0x164A4AE0>:
    Traceback (most recent call last):
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\callbacks.py", line 132, in _consolewrite_ex
        s = conversion._cchar_to_str_with_maxlen(buf, n, _CCHAR_ENCODING)
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\conversion.py", line 133, in _cchar_to_str_with_maxlen
        s = ffi.string(c, maxlen).decode(encoding)
    UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd5 in position 180: invalid continuation byte
    Traceback (most recent call last):
      File "D:/Files/Python/PXF_H_L/deseq2_2.py", line 6, in <module>
        deseq = importr('DESeq2')
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\robjects\packages.py", line 484, in importr
        env = _get_namespace(name)
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\conversion.py", line 45, in _
        cdata = function(*args, **kwargs)
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface.py", line 680, in __call__
        raise embedded.RRuntimeError(_rinterface._geterrmessage())
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\_rinterface_capi.py", line 438, in _geterrmessage
        res = _string_getitem(res, 0)
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\_rinterface_capi.py", line 286, in _string_getitem
        conversion._R_ENC_PY[openrlib.rlib.Rf_getCharCE(elt)]
      File "D:\Files\Python\PXF_H_L\venv\lib\site-packages\rpy2\rinterface_lib\conversion.py", line 127, in _cchar_to_str
        s = ffi.string(c).decode(encoding)
    UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd5 in position 180: invalid continuation byte
    During startup - Warning message:
    package 'stats' in options("defaultPackages") was not found

I think this error may suggests that there is an issue with decoding a string using the 'utf-8' codec due to an invalid byte sequence.

importr DESeq2 • 693 views

ADD COMMENT • link updated 9 months ago by Michael Love 42k • written 9 months ago by yuhang • 0

score 0 · Answer 1 · 2024-02-20

0

Entering edit mode

Michael Love 42k

@mikelove

Last seen 8 hours ago

United States

Sorry, this seems like an issue with importr, not DESeq2, which is supported for R's release and devel branches.

You might instead try pydeseq2:

https://pydeseq2.readthedocs.io/en/latest/

ADD COMMENT • link 9 months ago Michael Love 42k

0

Entering edit mode

Thanks! I tried to install PyDESeq2 within a conda environment following the official instruction

 conda env create -n pydeseq2

An error hit me

SpecNotFound: Invalid name, try the format: user/package

Then I googled the error and changed the code

conda create -n pydeseq2

Another error hit me

Solving environment: done

CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://repo.anaconda.com/pkgs/free/noarch/repodata.json.bz2>
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.

If your current network has https://www.anaconda.com blocked, please file
a support request with your network engineering team.

ConnectionError(MaxRetryError('HTTPSConnectionPool(host=\'repo.anaconda.com\', port=443): Max retries exceeded with url: /pkgs/free/noarch/repodata.json.bz2 (Caused by ReadTimeoutError("HTTPSConnectionPool(host=\'repo.anaconda.com\', p
ort=443): Read timed out. (read timeout=9.15)"))'))

It seems that there's a problem with the connection between my system and the Anaconda repository.