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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
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.
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