note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for velocyto
Running setup.py clean for velocyto
Failed to build velocyto
Installing collected packages: velocyto
Running setup.py install for velocyto ... error
error: subprocess-exited-with-error
Hi, I've been having trouble installing velocyto. Please help as I was unable to solve this error! This is what I'm doing:
Dependencies:
conda install numpy scipy cython numba matplotlib scikit-learn h5py click pip install pysam
Installation:
pip install velocyto
Error:
(base) TS261@PHS024050 ~ % pip install velocyto Collecting velocyto Using cached velocyto-0.17.17.tar.gz (198 kB) Preparing metadata (setup.py) ... done Requirement already satisfied: numpy in ./miniconda3/lib/python3.9/site-packages (from velocyto) (1.21.5) Requirement already satisfied: scipy in ./miniconda3/lib/python3.9/site-packages (from velocyto) (1.8.1) Requirement already satisfied: cython in ./miniconda3/lib/python3.9/site-packages (from velocyto) (0.29.32) Requirement already satisfied: numba in ./miniconda3/lib/python3.9/site-packages (from velocyto) (0.55.1) Requirement already satisfied: matplotlib in ./miniconda3/lib/python3.9/site-packages (from velocyto) (3.5.2) Requirement already satisfied: scikit-learn in ./miniconda3/lib/python3.9/site-packages (from velocyto) (1.0.2) Requirement already satisfied: h5py in ./miniconda3/lib/python3.9/site-packages (from velocyto) (2.10.0) Requirement already satisfied: loompy in ./miniconda3/lib/python3.9/site-packages (from velocyto) (3.0.7) Requirement already satisfied: pysam in ./miniconda3/lib/python3.9/site-packages (from velocyto) (0.19.1) Requirement already satisfied: Click in ./miniconda3/lib/python3.9/site-packages (from velocyto) (8.1.3) Requirement already satisfied: pandas in ./miniconda3/lib/python3.9/site-packages (from velocyto) (1.4.4) Requirement already satisfied: six in ./miniconda3/lib/python3.9/site-packages (from h5py->velocyto) (1.16.0) Requirement already satisfied: numpy-groupies in ./miniconda3/lib/python3.9/site-packages (from loompy->velocyto) (0.9.19) Requirement already satisfied: setuptools in ./miniconda3/lib/python3.9/site-packages (from loompy->velocyto) (61.2.0) Requirement already satisfied: pillow>=6.2.0 in ./miniconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (9.2.0) Requirement already satisfied: python-dateutil>=2.7 in ./miniconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (2.8.2) Requirement already satisfied: cycler>=0.10 in ./miniconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (0.11.0) Requirement already satisfied: packaging>=20.0 in ./miniconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (21.3) Requirement already satisfied: pyparsing>=2.2.1 in ./miniconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (3.0.9) Requirement already satisfied: fonttools>=4.22.0 in ./miniconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (4.25.0) Requirement already satisfied: kiwisolver>=1.0.1 in ./miniconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (1.4.2) Requirement already satisfied: llvmlite<0.39,>=0.38.0rc1 in ./miniconda3/lib/python3.9/site-packages (from numba->velocyto) (0.38.0) Requirement already satisfied: pytz>=2020.1 in ./miniconda3/lib/python3.9/site-packages (from pandas->velocyto) (2022.2.1) Requirement already satisfied: joblib>=0.11 in ./miniconda3/lib/python3.9/site-packages (from scikit-learn->velocyto) (1.1.0) Requirement already satisfied: threadpoolctl>=2.0.0 in ./miniconda3/lib/python3.9/site-packages (from scikit-learn->velocyto) (2.2.0) Building wheels for collected packages: velocyto Building wheel for velocyto (setup.py) ... error error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [43 lines of output] ['/private/var/folders/zk/t3gx7blx4mn670hvn9brp00m0000gq/T/pip-install-oj8_pdzt/velocyto_04916a0ba16b45fbb69f1e1fc3cc19a2/setup.py', 'bdist_wheel', '-d', '/private/var/folders/zk/t3gx7blx4mn670hvn9brp00m0000gq/T/pip-wheel-ocp3ye9e'] running bdist_wheel running build running build_py creating build creating build/lib.macosx-10.9-x86_64-3.9 creating build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/transcript_model.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/diffusion.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/metadata.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/analysis.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/molitem.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/_version.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/neighbors.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/constants.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/estimation.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/init.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/feature.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/logic.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/indexes.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/utils.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/gene_info.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/r_interface.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/segment_match.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/counter.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/serialization.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/read.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto creating build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/velocyto.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/run.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/init.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/run_smartseq2.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/dropest_bc_correct.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/run_dropest.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/run10x.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/_run.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands running build_ext building 'velocyto.speedboosted' extension creating build/temp.macosx-10.9-x86_64-3.9 creating build/temp.macosx-10.9-x86_64-3.9/velocyto clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/TS261/miniconda3/include -arch x86_64 -I/Users/TS261/miniconda3/include -fPIC -O2 -isystem /Users/TS261/miniconda3/include -arch x86_64 -I/Users/TS261/miniconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/TS261/miniconda3/include/python3.9 -c velocyto/speedboosted.c -o build/temp.macosx-10.9-x86_64-3.9/velocyto/speedboosted.o -fopenmp -ffast-math clang: error: unsupported option '-fopenmp' 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 velocyto Running setup.py clean for velocyto Failed to build velocyto Installing collected packages: velocyto Running setup.py install for velocyto ... error error: subprocess-exited-with-error
× Running setup.py install for velocyto did not run successfully. │ exit code: 1 ╰─> [45 lines of output] ['/private/var/folders/zk/t3gx7blx4mn670hvn9brp00m0000gq/T/pip-install-oj8_pdzt/velocyto_04916a0ba16b45fbb69f1e1fc3cc19a2/setup.py', 'install', '--record', '/private/var/folders/zk/t3gx7blx4mn670hvn9brp00m0000gq/T/pip-record-xw8svpyk/install-record.txt', '--single-version-externally-managed', '--compile', '--install-headers', '/Users/TS261/miniconda3/include/python3.9/velocyto'] running install /Users/TS261/miniconda3/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_64-3.9 creating build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/transcript_model.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/diffusion.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/metadata.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/analysis.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/molitem.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/_version.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/neighbors.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/constants.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/estimation.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/init.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/feature.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/logic.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/indexes.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/utils.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/gene_info.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/r_interface.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/segment_match.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/counter.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/serialization.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto copying velocyto/read.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto creating build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/velocyto.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/run.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/init.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/run_smartseq2.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/dropest_bc_correct.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/run_dropest.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/run10x.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands copying velocyto/commands/_run.py -> build/lib.macosx-10.9-x86_64-3.9/velocyto/commands running build_ext building 'velocyto.speedboosted' extension creating build/temp.macosx-10.9-x86_64-3.9 creating build/temp.macosx-10.9-x86_64-3.9/velocyto clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/TS261/miniconda3/include -arch x86_64 -I/Users/TS261/miniconda3/include -fPIC -O2 -isystem /Users/TS261/miniconda3/include -arch x86_64 -I/Users/TS261/miniconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/TS261/miniconda3/include/python3.9 -c velocyto/speedboosted.c -o build/temp.macosx-10.9-x86_64-3.9/velocyto/speedboosted.o -fopenmp -ffast-math clang: error: unsupported option '-fopenmp' 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. ╰─> velocyto
note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.