You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I'm trying to use mnnpy through scanpy, but I seem to have hit an installation error. When I run pip install mnnpy in the command line, I get the following error:
`ERROR: Failed building wheel for mnnpy
Running setup.py clean for mnnpy
Failed to build mnnpy
Installing collected packages: mnnpy
Running setup.py install for mnnpy ... error
ERROR: Command errored out with exit status 1:`
I can see other posts about installation issues, but none with the same error. I'd appreciate any advice!
The full output is below:
Collecting mnnpy
Using cached mnnpy-0.1.9.5.tar.gz (117 kB)
Requirement already satisfied: numpy in /opt/anaconda3/lib/python3.8/site-packages (from mnnpy) (1.20.1)
Requirement already satisfied: scipy in /opt/anaconda3/lib/python3.8/site-packages (from mnnpy) (1.6.2)
Requirement already satisfied: anndata in /opt/anaconda3/lib/python3.8/site-packages (from mnnpy) (0.7.8)
Requirement already satisfied: pandas in /opt/anaconda3/lib/python3.8/site-packages (from mnnpy) (1.2.4)
Requirement already satisfied: numba in /opt/anaconda3/lib/python3.8/site-packages (from mnnpy) (0.53.1)
Requirement already satisfied: natsort in /opt/anaconda3/lib/python3.8/site-packages (from anndata->mnnpy) (8.1.0)
Requirement already satisfied: packaging>=20 in /opt/anaconda3/lib/python3.8/site-packages (from anndata->mnnpy) (21.3)
Requirement already satisfied: xlrd<2.0 in /opt/anaconda3/lib/python3.8/site-packages (from anndata->mnnpy) (1.2.0)
Requirement already satisfied: h5py in /opt/anaconda3/lib/python3.8/site-packages (from anndata->mnnpy) (2.10.0)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /opt/anaconda3/lib/python3.8/site-packages (from packaging>=20->anndata->mnnpy) (2.4.7)
Requirement already satisfied: python-dateutil>=2.7.3 in /opt/anaconda3/lib/python3.8/site-packages (from pandas->mnnpy) (2.8.1)
Requirement already satisfied: pytz>=2017.3 in /opt/anaconda3/lib/python3.8/site-packages (from pandas->mnnpy) (2021.1)
Requirement already satisfied: six>=1.5 in /opt/anaconda3/lib/python3.8/site-packages (from python-dateutil>=2.7.3->pandas->mnnpy) (1.15.0)
Requirement already satisfied: setuptools in /opt/anaconda3/lib/python3.8/site-packages (from numba->mnnpy) (60.9.3)
Requirement already satisfied: llvmlite<0.37,>=0.36.0rc1 in /opt/anaconda3/lib/python3.8/site-packages (from numba->mnnpy) (0.36.0)
Building wheels for collected packages: mnnpy
Building wheel for mnnpy (setup.py) ... error
ERROR: Command errored out with exit status 1:
command: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-install-o44s9l6l/mnnpy_5acf7cd472394e3c882895e763f55a6c/setup.py'"'"'; __file__='"'"'/private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-install-o44s9l6l/mnnpy_5acf7cd472394e3c882895e763f55a6c/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 /private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-wheel-ehg150g1
cwd: /private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-install-o44s9l6l/mnnpy_5acf7cd472394e3c882895e763f55a6c/
Complete output (23 lines):
running bdist_wheel
running build
running build_py
file irlb.py (for module irlb) not found
file mnn.py (for module mnn) not found
file utils.py (for module utils) not found
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/irlb.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/utils.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/mnn.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/settings.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
file irlb.py (for module irlb) not found
file mnn.py (for module mnn) not found
file utils.py (for module utils) not found
running build_ext
building 'mnnpy._utils' extension
creating build/temp.macosx-10.9-x86_64-3.8
creating build/temp.macosx-10.9-x86_64-3.8/mnnpy
/usr/local/Cellar/gcc/8.2.0/bin/gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/include -arch x86_64 -Imnnpy -I/opt/anaconda3/include/python3.8 -c mnnpy/_utils.c -o build/temp.macosx-10.9-x86_64-3.8/mnnpy/_utils.o -O2 -ffast-math -march=native -fopenmp
error: command '/usr/local/Cellar/gcc/8.2.0/bin/gcc-8' failed: No such file or directory
----------------------------------------
ERROR: Failed building wheel for mnnpy
Running setup.py clean for mnnpy
Failed to build mnnpy
Installing collected packages: mnnpy
Running setup.py install for mnnpy ... error
ERROR: Command errored out with exit status 1:
command: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-install-o44s9l6l/mnnpy_5acf7cd472394e3c882895e763f55a6c/setup.py'"'"'; __file__='"'"'/private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-install-o44s9l6l/mnnpy_5acf7cd472394e3c882895e763f55a6c/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-record-wm0ufrhh/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/include/python3.8/mnnpy
cwd: /private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-install-o44s9l6l/mnnpy_5acf7cd472394e3c882895e763f55a6c/
Complete output (25 lines):
running install
/opt/anaconda3/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
file irlb.py (for module irlb) not found
file mnn.py (for module mnn) not found
file utils.py (for module utils) not found
creating build
creating build/lib.macosx-10.9-x86_64-3.8
creating build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/irlb.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/__init__.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/utils.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/mnn.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
copying mnnpy/settings.py -> build/lib.macosx-10.9-x86_64-3.8/mnnpy
file irlb.py (for module irlb) not found
file mnn.py (for module mnn) not found
file utils.py (for module utils) not found
running build_ext
building 'mnnpy._utils' extension
creating build/temp.macosx-10.9-x86_64-3.8
creating build/temp.macosx-10.9-x86_64-3.8/mnnpy
/usr/local/Cellar/gcc/8.2.0/bin/gcc-8 -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/include -arch x86_64 -Imnnpy -I/opt/anaconda3/include/python3.8 -c mnnpy/_utils.c -o build/temp.macosx-10.9-x86_64-3.8/mnnpy/_utils.o -O2 -ffast-math -march=native -fopenmp
error: command '/usr/local/Cellar/gcc/8.2.0/bin/gcc-8' failed: No such file or directory
----------------------------------------
ERROR: Command errored out with exit status 1: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-install-o44s9l6l/mnnpy_5acf7cd472394e3c882895e763f55a6c/setup.py'"'"'; __file__='"'"'/private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-install-o44s9l6l/mnnpy_5acf7cd472394e3c882895e763f55a6c/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/sz/s_8c7lv974x_rxczn323lc_c0000gn/T/pip-record-wm0ufrhh/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/include/python3.8/mnnpy Check the logs for full command output.
The text was updated successfully, but these errors were encountered:
I'm trying to use mnnpy through scanpy, but I seem to have hit an installation error. When I run
pip install mnnpy
in the command line, I get the following error:`ERROR: Failed building wheel for mnnpy
Running setup.py clean for mnnpy
Failed to build mnnpy
Installing collected packages: mnnpy
Running setup.py install for mnnpy ... error
ERROR: Command errored out with exit status 1:`
I can see other posts about installation issues, but none with the same error. I'd appreciate any advice!
The full output is below:
The text was updated successfully, but these errors were encountered: