prete
commented
1 year ago Hi @nadiacneto the command for installing (or updating) CellPhoneDB is:
pip3 install -U cellphonedb
only after the install has completed you need to download the latest database with:
cellphonedb database download
Can I check you are actually running both commands separately?
I'm going to guess that you're running this on an M1 Mac laptop, those devices have shown issues while installing older versions of some packages. In this case, the needed numpy version is 1.19.5 and may no be compatible with your architecture/compiler. However, if you've already got the requirements installed, then you may want to try installing CellPhoneDB without dependencies using:
pip3 install --no-dependencies cellphonedbkeep in mind that running cellphonedb will only work if you've got the dependencies installed on your own.
nadiacneto
sinanugur
Hi team,
I am trying to install cellphone DB on my machine: macOS Monterey Python 3.9.13 pip 22.1.1
pip install -U cellphonedb cellphonedb database downloadWhen I do this I get the following error:
error: Command "clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.sdk -I/opt/homebrew/opt/hdf5@1.8/include -DNPY_INTERNAL_BUILD=1 -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=3 -DHAVE_CBLAS -Ibuild/src.macosx-12-arm64-3.9/numpy/core/src/umath -Ibuild/src.macosx-12-arm64-3.9/numpy/core/src/npymath -Ibuild/src.macosx-12-arm64-3.9/numpy/core/src/common -Inumpy/core/include -Ibuild/src.macosx-12-arm64-3.9/numpy/core/include/numpy -Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/opt/homebrew/Cellar/python@3.9/3.9.13_1/Frameworks/Python.framework/Versions/3.9/include/python3.9 -Ibuild/src.macosx-12-arm64-3.9/numpy/core/src/common -Ibuild/src.macosx-12-arm64-3.9/numpy/core/src/npymath -c numpy/core/src/multiarray/array_assign_scalar.c -o build/temp.macosx-12-arm64-cpython-39/numpy/core/src/multiarray/array_assign_scalar.o -MMD -MF build/temp.macosx-12-arm64-cpython-39/numpy/core/src/multiarray/array_assign_scalar.o.d -faltivec -I/System/Library/Frameworks/vecLib.framework/Headers" failed with exit status 1note: This error originates from a subprocess, and is likely not a problem with pip.ERROR: Failed building wheel for numpyFailed to build scikit-learn numpyERROR: Could not build wheels for numpy, which is required to install pyproject.toml-based projectsI am able to locate numpy on my machine:
pip3 show numpyName: numpy Version: 1.23.1 Summary: NumPy is the fundamental package for array computing with Python. Home-page: https://www.numpy.org Author: Travis E. Oliphant et al. Author-email: License: BSD Location: /opt/homebrew/lib/python3.9/site-packages Requires: Required-by: scikit-learn, scipyPlease let me know if I am missing any other dependency or if there's anything else I should be doing beforehand. Thank you kindly for your help