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:
Details
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.
