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bm2-lab / scMVP

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installation issue wrong scikit-learn version #7

Open hamidsta opened 2 years ago

hamidsta commented 2 years ago

Hello, I'm currently trying to analyze multiomics scRNA-ATACseq data . However when i run this following line > python setup.py install I get this error 

                `> No local packages or working download links found for scikit-learn==0.22.2`
                `> error: Could not find suitable distribution for Requirement.parse('scikit-learn==0.22.2') `

my current version of scikit-learn : 

                    (base) C:\Users\User\ATAC-scMVP\scMVP>conda list scikit-learn
                    # packages in environment at C:\Users\User\anaconda3:
                    # Name                    Version                   Build  Channel
                    scikit-learn              0.24.2           py39hcf78d83_2

however i can't downgrade the version since 0.22.2 don't seem to be present 

    (base) C:\Users\User\ATAC-scMVP\scMVP>conda search scikit-learn
                  scikit-learn                  0.20.2  py36h343c172_0  pkgs/main
                  scikit-learn                  0.20.2  py37h343c172_0  pkgs/main
                  scikit-learn                  0.20.3  py27hf381715_0  pkgs/main
                  scikit-learn                  0.20.3  py36h343c172_0  pkgs/main
                  scikit-learn                  0.20.3  py37h343c172_0  pkgs/main
                  scikit-learn                  0.21.1  py36h6288b17_0  pkgs/main
                  scikit-learn                  0.21.1  py37h6288b17_0  pkgs/main
                  scikit-learn                  0.22.1  py38h6288b17_0  pkgs/main
                  scikit-learn                  0.23.1  py36h25d0782_0  pkgs/main

here is some information : (base) C:\Users\User\ATAC-scMVP\scMVP>conda info

               active environment : base
              active env location : C:\Users\User\anaconda3
                      shell level : 1
                 user config file : C:\Users\User\.condarc
           populated config files : C:\Users\User\.condarc
                    conda version : 4.12.0
              conda-build version : 3.21.6
                   python version : 3.9.7.final.0
                 virtual packages : __win=0=0
                                    __archspec=1=x86
                 base environment : C:\Users\User\anaconda3  (writable)
                conda av data dir : C:\Users\User\anaconda3\etc\conda
            conda av metadata url : None
                     channel URLs : https://conda.anaconda.org/bioconda/win-32
                                    https://conda.anaconda.org/bioconda/noarch
                                    https://repo.anaconda.com/pkgs/main/win-32
                                    https://repo.anaconda.com/pkgs/main/noarch
                                    https://repo.anaconda.com/pkgs/r/win-32
                                    https://repo.anaconda.com/pkgs/r/noarch
                                    https://repo.anaconda.com/pkgs/msys2/win-32
                                    https://repo.anaconda.com/pkgs/msys2/noarch
                                    https://conda.anaconda.org/conda-forge/win-32
                                    https://conda.anaconda.org/conda-forge/noarch
                    package cache : C:\Users\User\anaconda3\pkgs
                                    C:\Users\User\.conda\pkgs
                                    C:\Users\User\AppData\Local\conda\conda\pkgs
                 envs directories : C:\Users\User\anaconda3\envs
                                    C:\Users\User\.conda\envs
                                    C:\Users\User\AppData\Local\conda\conda\envs
                         platform : win-32
                       user-agent : conda/4.12.0 requests/2.26.0 CPython/3.9.7 Windows/10 Windows/10.0.22000
                    administrator : False
                       netrc file : None
                     offline mode : False

Thanks you very much , I'm a bit lost with this issue .

adamtongji commented 2 years ago

It seems that the version of "scikit-learn" pip requirement may differ from version "scikit-learn" already in your conda environment. Can you try pip install scikit-learn=0.22.2 or install use a new conda env?

hamidsta commented 2 years ago

thank you ,it work now ! However i have a new error :/ here is the error TypeError: _getfullpathname: path should be string, bytes or os.PathLike, not int

here is my session info `(myenv) C:\Users\User\ATAC-scMVP\scMVP>conda info

       active environment : myenv
      active env location : C:\Users\User\miniconda3\envs\myenv
              shell level : 2
         user config file : C:\Users\User\.condarc
    populated config files : C:\Users\User\.condarc
            conda version : 4.12.0
      conda-build version : not installed
           python version : 3.7.12.final.0
         virtual packages : __win=0=0
                            __archspec=1=x86_64
         base environment : C:\Users\User\miniconda3  (writable)
        conda av data dir : C:\Users\User\miniconda3\etc\conda
    conda av metadata url : None
             channel URLs : https://conda.anaconda.org/bioconda/win-64
                            https://conda.anaconda.org/bioconda/noarch
                            https://repo.anaconda.com/pkgs/main/win-64
                            https://repo.anaconda.com/pkgs/main/noarch
                            https://repo.anaconda.com/pkgs/r/win-64
                            https://repo.anaconda.com/pkgs/r/noarch
                            https://repo.anaconda.com/pkgs/msys2/win-64
                            https://repo.anaconda.com/pkgs/msys2/noarch
                            https://conda.anaconda.org/conda-forge/win-64
                            https://conda.anaconda.org/conda-forge/noarch
            package cache : C:\Users\User\miniconda3\pkgs
                            C:\Users\User\.conda\pkgs
                            C:\Users\User\AppData\Local\conda\conda\pkgs
         envs directories : C:\Users\User\miniconda3\envs
                            C:\Users\User\.conda\envs
                            C:\Users\User\AppData\Local\conda\conda\envs
                 platform : win-64
               user-agent : conda/4.12.0 requests/2.27.1 CPython/3.7.12 Windows/10 Windows/10.0.22000
            administrator : False
               netrc file : None
             offline mode : False

` Also when i first run python setup.py install 2 errors messages comes up , du to module cython and NumPy not being installed. So i had to installed them directly . Maybe the error is due to a wrong version i just download ? Name Version Build Channel cython 0.29.28 py37hd77b12b_0 Name Version Build Channel numpy 1.21.5 py37ha4e8547_0 numpy-base 1.21.5 py37hc2deb75_0

and here is a part of the error traceback :

Traceback (most recent call last): File "setup.py", line 90, in zip_safe=False, File "C:\Users\User\miniconda3\envs\myenv\lib\site-packages\setuptools__init.py", line 153, in setup return distutils.core.setup(**attrs) File "C:\Users\User\miniconda3\envs\myenv\lib\distutils\core.py", line 148, in setup dist.run_commands() File "C:\Users\User\miniconda3\envs\myenv\lib\distutils\dist.py", line 966, in run_commands self.run_command(cmd) File "C:\Users\User\miniconda3\envs\myenv\lib\distutils\dist.py", line 985, in run_command cmd_obj.run() File "C:\Users\User\miniconda3\envs\myenv\lib\site-packages\setuptools\command\install.py", line 67, in run self.do_egg_install() File "C:\Users\User\miniconda3\envs\myenv\lib\site-packages\setuptools\command\easy_install.py", line 650, in easy_install return self.install_item(None, spec, tmpdir, deps, True) File "C:\Users\User\miniconda3\envs\myenv\lib\multiprocessing\process.py", line 112, in start self._popen = self._Popen(self) File "C:\Users\User\miniconda3\envs\myenv\lib\multiprocessing\context.py", line 322, in _Popen return Popen(process_obj) File "C:\Users\User\miniconda3\envs\myenv\lib\multiprocessing\popen_spawn_win32.py", line 67, in init__ with open(wfd, 'wb', closefd=True) as to_child: File "C:\Users\User\miniconda3\envs\myenv\lib\site-packages\setuptools\sandbox.py", line 453, in _open if mode not in ('r', 'rt', 'rb', 'rU', 'U') and not self._ok(path): File "C:\Users\User\miniconda3\envs\myenv\lib\site-packages\setuptools\sandbox.py", line 464, in _ok realpath = os.path.normcase(os.path.realpath(path)) File "C:\Users\User\miniconda3\envs\myenv\lib\ntpath.py", line 526, in abspath return normpath(_getfullpathname(path)) TypeError: _getfullpathname: path should be string, bytes or os.PathLike, not int