Can't Install scopen

[MayaTalukdar]

I am trying to install scopen with the given instructions, but am having trouble successfully installing it.

I am installing scopen in a fresh conda environment created with the command:

mamba create -n scOPEN_new_env python=3.8 anaconda

I then run the command pip install scopen.

However, I am getting this output: ollecting scopen Downloading scOpen-0.1.7.tar.gz (117 kB) |████████████████████████████████| 117 kB 2.1 MB/s
Preparing metadata (setup.py) ... done Requirement already satisfied: numpy in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scopen) (1.20.3) Requirement already satisfied: h5py in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scopen) (3.3.0) Requirement already satisfied: six in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scopen) (1.16.0) Requirement already satisfied: pandas in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scopen) (1.3.3) Requirement already satisfied: scipy in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scopen) (1.5.3) Requirement already satisfied: tables in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scopen) (3.6.1) Requirement already satisfied: matplotlib in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scopen) (3.4.3) Requirement already satisfied: scikit-learn in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scopen) (1.0) Requirement already satisfied: kneed in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scopen) (0.7.0) Requirement already satisfied: pillow>=6.2.0 in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from matplotlib->scopen) (8.3.2) Requirement already satisfied: pyparsing>=2.2.1 in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from matplotlib->scopen) (2.4.7) Requirement already satisfied: python-dateutil>=2.7 in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from matplotlib->scopen) (2.8.2) Requirement already satisfied: cycler>=0.10 in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from matplotlib->scopen) (0.10.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from matplotlib->scopen) (1.3.2) Requirement already satisfied: pytz>=2017.3 in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from pandas->scopen) (2021.3) Requirement already satisfied: threadpoolctl>=2.0.0 in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scikit-learn->scopen) (3.0.0) Requirement already satisfied: joblib>=0.11 in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from scikit-learn->scopen) (1.1.0) Requirement already satisfied: numexpr>=2.6.2 in ./.conda/envs/scOPEN_new_env/lib/python3.8/site-packages (from tables->scopen) (2.7.3) Building wheels for collected packages: scopen Building wheel for scopen (setup.py) ... error ERROR: Command errored out with exit status 1: command: /PHShome/mt1036/.conda/envs/scOPEN_new_env/bin/python3.8 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/setup.py'"'"'; file='"'"'/tmp/pip-install-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-laj4v41z cwd: /tmp/pip-install-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/ 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-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/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: /PHShome/mt1036/.conda/envs/scOPEN_new_env/bin/python3.8 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/setup.py'"'"'; file='"'"'/tmp/pip-install-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-j427poti/install-record.txt --single-version-externally-managed --compile --install-headers /PHShome/mt1036/.conda/envs/scOPEN_new_env/include/python3.8/scopen cwd: /tmp/pip-install-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/ 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-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/scopen/cdnmf_fast.pyx

ERROR: Command errored out with exit status 1: /PHShome/mt1036/.conda/envs/scOPEN_new_env/bin/python3.8 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/setup.py'"'"'; file='"'"'/tmp/pip-install-g9cehiwo/scopen_f0e95588906e44808732495d2f7d01cd/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-j427poti/install-record.txt --single-version-externally-managed --compile --install-headers /PHShome/mt1036/.conda/envs/scOPEN_new_env/include/python3.8/scopen Check the logs for full command output.

Any input would be appreciated!

[lzj1769]

Hi @MayaTalukdar

I just released a new version of scopen (v1.0.1), can you try again? simply by running the following command: pip install scopen

best, Li

[MayaTalukdar]

Hi Li,

Thank you very much for your fast reply! Unfortunately, I am still getting a similar error: Collecting scopen Downloading scOpen-1.0.1.tar.gz (126 kB) |████████████████████████████████| 126 kB 2.2 MB/s
Preparing metadata (setup.py) ... done Requirement already satisfied: numpy in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scopen) (1.20.3) Requirement already satisfied: h5py in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scopen) (3.4.0) Requirement already satisfied: six in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scopen) (1.16.0) Requirement already satisfied: pandas in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scopen) (1.3.3) Requirement already satisfied: scipy in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scopen) (1.7.1) Requirement already satisfied: tables in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scopen) (3.6.1) Requirement already satisfied: matplotlib in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scopen) (3.4.3) Requirement already satisfied: scikit-learn in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scopen) (1.0) Collecting kneed Using cached kneed-0.7.0-py2.py3-none-any.whl (9.4 kB) Requirement already satisfied: cached-property in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from h5py->scopen) (1.5.2) Requirement already satisfied: pillow>=6.2.0 in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from matplotlib->scopen) (8.3.2) Requirement already satisfied: python-dateutil>=2.7 in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from matplotlib->scopen) (2.8.2) Requirement already satisfied: kiwisolver>=1.0.1 in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from matplotlib->scopen) (1.3.2) Requirement already satisfied: cycler>=0.10 in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from matplotlib->scopen) (0.10.0) Requirement already satisfied: pyparsing>=2.2.1 in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from matplotlib->scopen) (2.4.7) Requirement already satisfied: pytz>=2017.3 in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from pandas->scopen) (2021.3) Requirement already satisfied: threadpoolctl>=2.0.0 in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scikit-learn->scopen) (3.0.0) Requirement already satisfied: joblib>=0.11 in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from scikit-learn->scopen) (1.1.0) Requirement already satisfied: numexpr>=2.6.2 in ./.conda/envs/scopen_env/lib/python3.7/site-packages (from tables->scopen) (2.7.3) Building wheels for collected packages: scopen Building wheel for scopen (setup.py) ... error ERROR: Command errored out with exit status 1: command: /PHShome/mt1036/.conda/envs/scopen_env/bin/python3.7 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/setup.py'"'"'; file='"'"'/tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-di0qgnto cwd: /tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/ Complete output (14 lines): running bdist_wheel running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/scopen copying scopen/MF.py -> build/lib.linux-x86_64-3.7/scopen copying scopen/Main.py -> build/lib.linux-x86_64-3.7/scopen copying scopen/Utils.py -> build/lib.linux-x86_64-3.7/scopen copying scopen/init.py -> build/lib.linux-x86_64-3.7/scopen copying scopen/version.py -> build/lib.linux-x86_64-3.7/scopen running build_ext cythoning ./scopen/cdnmf_fast.pyx to ./scopen/cdnmf_fast.c error: /tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/scopen/cdnmf_fast.pyx

ERROR: Failed building wheel for scopen Running setup.py clean for scopen Failed to build scopen Installing collected packages: kneed, scopen Running setup.py install for scopen ... error ERROR: Command errored out with exit status 1: command: /PHShome/mt1036/.conda/envs/scopen_env/bin/python3.7 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/setup.py'"'"'; file='"'"'/tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-rntjthxv/install-record.txt --single-version-externally-managed --compile --install-headers /PHShome/mt1036/.conda/envs/scopen_env/include/python3.7m/scopen cwd: /tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/ Complete output (14 lines): running install running build running build_py creating build creating build/lib.linux-x86_64-3.7 creating build/lib.linux-x86_64-3.7/scopen copying scopen/MF.py -> build/lib.linux-x86_64-3.7/scopen copying scopen/Main.py -> build/lib.linux-x86_64-3.7/scopen copying scopen/Utils.py -> build/lib.linux-x86_64-3.7/scopen copying scopen/init.py -> build/lib.linux-x86_64-3.7/scopen copying scopen/version.py -> build/lib.linux-x86_64-3.7/scopen running build_ext cythoning ./scopen/cdnmf_fast.pyx to ./scopen/cdnmf_fast.c error: /tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/scopen/cdnmf_fast.pyx

ERROR: Command errored out with exit status 1: /PHShome/mt1036/.conda/envs/scopen_env/bin/python3.7 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/setup.py'"'"'; file='"'"'/tmp/pip-install-1sijzu8m/scopen_9959595dd054491e888c848128e39679/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-rntjthxv/install-record.txt --single-version-externally-managed --compile --install-headers /PHShome/mt1036/.conda/envs/scopen_env/include/python3.7m/scopen Check the logs for full command output.

[lzj1769]

Hi,

I am still trying to figure out what the problem is. Meanwhile, you can try to install it from the source.

git clone git@github.com:CostaLab/scopen.git
cd scopen
pip install ./

In my case, I could reproduce the error, and here is what I did:

conda create -n scopen python=3.8
pip install scopen

It works pretty well.

Best, Li

[MayaTalukdar]

Thank you very much, Li! This seems to work!

[rvinas]

Encountering the same error

[lzj1769]

@rvinas

Can you provide your python version? also which system are you using?

[rvinas]

I'm using Python 3.8.5 on a Ubuntu machine (16.04)

[lzj1769]

Hi,

Can you try to install scopen from source?

git clone git@github.com:CostaLab/scopen.git
cd scopen
pip install ./

I tested it with the Conda environment of python3.8, but couldn't reproduce the error.

best, Li

[lzj1769]

Closed with no further comments.

[alexlenail]

I also had this installation issue, and also solved it by downloading from github