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zcang / COMMOT

MIT License
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unable to install commot #2

Closed ayusyarif closed 1 year ago

ayusyarif commented 1 year ago

Dear Developer,

I made several attempts to install commit using jupyter and spyder. However, it kept giving me an error message.

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for rvlib Running setup.py clean for rvlib Failed to build rvlib Installing collected packages: python-louvain, Levenshtein, rvlib, requests-futures, rasterio, quantecon, python-Levenshtein, python-igraph, pygsp, pot, pandas, leidenalg, inequality, fiona, deprecation, aws-requests-auth, rasterstats, pynndescent, mapclassify, libpysal, karateclub, geopandas, anndata, umap-learn, tobler, spreg, pointpats, momepy, esda, access, spvcm, spglm, spaghetti, scanpy, quilt3, giddy, spopt, splot, spint, segregation, mgwr, pysal, commot Running setup.py install for rvlib ... error error: subprocess-exited-with-error

× Running setup.py install for rvlib did not run successfully. │ exit code: 1 ╰─> [32 lines of output] running install /Users/ayuhutamisyarif/opt/anaconda3/lib/python3.9/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 creating build creating build/lib.macosx-10.9-x86_64-cpython-39 creating build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/univariate.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/version.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib copying rvlib/specials.py -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib running egg_info writing rvlib.egg-info/PKG-INFO writing dependency_links to rvlib.egg-info/dependency_links.txt writing requirements to rvlib.egg-info/requires.txt writing top-level names to rvlib.egg-info/top_level.txt reading manifest file 'rvlib.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE.txt' writing manifest file 'rvlib.egg-info/SOURCES.txt' copying rvlib/metadata.yaml -> build/lib.macosx-10.9-x86_64-cpython-39/rvlib running build_ext generating cffi module 'build/temp.macosx-10.9-x86_64-cpython-39/rvlib._rmath_ffi.c' creating build/temp.macosx-10.9-x86_64-cpython-39 building 'rvlib._rmath_ffi' extension creating build/temp.macosx-10.9-x86_64-cpython-39/build creating build/temp.macosx-10.9-x86_64-cpython-39/build/temp.macosx-10.9-x86_64-cpython-39 creating build/temp.macosx-10.9-x86_64-cpython-39/src clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/ayuhutamisyarif/opt/anaconda3/include -arch x86_64 -I/Users/ayuhutamisyarif/opt/anaconda3/include -fPIC -O2 -isystem /Users/ayuhutamisyarif/opt/anaconda3/include -arch x86_64 -Isrc -Iinclude -I/Users/ayuhutamisyarif/opt/anaconda3/include/python3.9 -c build/temp.macosx-10.9-x86_64-cpython-39/rvlib._rmath_ffi.c -o build/temp.macosx-10.9-x86_64-cpython-39/build/temp.macosx-10.9-x86_64-cpython-39/rvlib._rmath_ffi.o -DMATHLIB_STANDALONE -std=c99 xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun error: command '/usr/bin/clang' failed with exit code 1 [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure

× Encountered error while trying to install package. ╰─> rvlib

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

I am very new to python and have no idea about this error. Any advice would be so much appreciated

Best, Ayu

zcang commented 1 year ago

Hi, does installing other packages like scanpy result in the same error? It seems xcrun is missing. I am not familiar with macOS but a search of the first line of the error message gives me this solution: https://developer.apple.com/forums/thread/711512