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CostaLab / scopen

scOpen: single-cell open chromatin analysis via NMF modelling
GNU General Public License v3.0
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installation did not work #21

Open fahmadimoughari opened 1 year ago

fahmadimoughari commented 1 year ago

Hi,

I tried to install the package but it stopped. Any ideas what the problem is?

`pip install scopen

Defaulting to user installation because normal site-packages is not writeable

Collecting scopen

Using cached scOpen-1.0.1.tar.gz (126 kB)

Requirement already satisfied: numpy in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from scopen) (1.18.5)

Requirement already satisfied: h5py in ./.local/lib/python3.8/site-packages (from scopen) (3.8.0)

Requirement already satisfied: six in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from scopen) (1.15.0)

Requirement already satisfied: pandas in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from scopen) (1.0.5)

Requirement already satisfied: scipy in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from scopen) (1.5.0)

Requirement already satisfied: tables in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from scopen) (3.6.1)

Requirement already satisfied: matplotlib in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from scopen) (3.2.2)

Requirement already satisfied: scikit-learn in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from scopen) (0.23.1)

Requirement already satisfied: kneed in ./.local/lib/python3.8/site-packages (from scopen) (0.8.3)

Requirement already satisfied: pytz>=2017.2 in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from pandas->scopen) (2020.1)

Requirement already satisfied: python-dateutil>=2.6.1 in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from pandas->scopen) (2.8.1)

Requirement already satisfied: numexpr>=2.6.2 in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from tables->scopen) (2.7.1)

Requirement already satisfied: cycler>=0.10 in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from matplotlib->scopen) (0.10.0)

Requirement already satisfied: kiwisolver>=1.0.1 in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from matplotlib->scopen) (1.2.0)

Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from matplotlib->scopen) (2.4.7)

Requirement already satisfied: threadpoolctl>=2.0.0 in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from scikit-learn->scopen) (2.1.0)

Requirement already satisfied: joblib>=0.11 in /opt/software/applications/anaconda/3/lib/python3.8/site-packages (from scikit-learn->scopen) (0.16.0)

Building wheels for collected packages: scopen

Building wheel for scopen (setup.py) ... error

ERROR: Command errored out with exit status 1:

command: /opt/software/applications/anaconda/3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-clzr77nz/scopen/setup.py'"'"'; file='"'"'/tmp/pip-install-clzr77nz/scopen/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-r3fynsqu

   cwd: /tmp/pip-install-clzr77nz/scopen/

Complete output (14 lines):

running bdist_wheel

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.8

creating build/lib.linux-x86_64-3.8/scopen

copying scopen/MF.py -> build/lib.linux-x86_64-3.8/scopen

copying scopen/Main.py -> build/lib.linux-x86_64-3.8/scopen

copying scopen/Utils.py -> build/lib.linux-x86_64-3.8/scopen

copying scopen/init.py -> build/lib.linux-x86_64-3.8/scopen

copying scopen/version.py -> build/lib.linux-x86_64-3.8/scopen

running build_ext

cythoning ./scopen/cdnmf_fast.pyx to ./scopen/cdnmf_fast.c

error: /tmp/pip-install-clzr77nz/scopen/scopen/cdnmf_fast.pyx

ERROR: Failed building wheel for scopen

Running setup.py clean for scopen

Failed to build scopen

Installing collected packages: scopen

Running setup.py install for scopen ... error

ERROR: Command errored out with exit status 1:

 command: /opt/software/applications/anaconda/3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-clzr77nz/scopen/setup.py'"'"'; __file__='"'"'/tmp/pip-install-clzr77nz/scopen/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-0splnvqi/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/shaider/.local/include/python3.8/scopen

     cwd: /tmp/pip-install-clzr77nz/scopen/

Complete output (14 lines):

running install

running build

running build_py

creating build

creating build/lib.linux-x86_64-3.8

creating build/lib.linux-x86_64-3.8/scopen

copying scopen/MF.py -> build/lib.linux-x86_64-3.8/scopen

copying scopen/Main.py -> build/lib.linux-x86_64-3.8/scopen

copying scopen/Utils.py -> build/lib.linux-x86_64-3.8/scopen

copying scopen/__init__.py -> build/lib.linux-x86_64-3.8/scopen

copying scopen/__version__.py -> build/lib.linux-x86_64-3.8/scopen

running build_ext

cythoning ./scopen/cdnmf_fast.pyx to ./scopen/cdnmf_fast.c

error: /tmp/pip-install-clzr77nz/scopen/scopen/cdnmf_fast.pyx

----------------------------------------

ERROR: Command errored out with exit status 1: /opt/software/applications/anaconda/3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-clzr77nz/scopen/setup.py'"'"'; file='"'"'/tmp/pip-install-clzr77nz/scopen/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-0splnvqi/install-record.txt --single-version-externally-managed --user --prefix= --compile --install-headers /home/shaider/.local/include/python3.8/scopen Check the logs for full command output.`

lzj1769 commented 1 year ago

Hi,

This seems to be related to cython.

Did you first install cython?

fahmadimoughari commented 1 year ago

Hi,

Previously, I did not install "cython" before installing "scopen". Now, I installed "cython", and then, tried to install "scopen" and I got exactly the same error log.

shycheng commented 11 months ago

Hi, you can install an older version of Cython with the command pip install Cython==0.29.36, and then install scopen using pip install scopen --no-build-isolation. If this doesn't work, you can download the package files and install them locally using the following commands: git clone https://github.com/CostaLab/scopen.git, cd scopen/, and pip install ..