Fail to install velocyto

[sjwu571]

Hi,

I have trouble installing velocyto. See the screenshot below. Any idea how to fix that? I have a Macbook with A1 chip.

Thanks!

pip install velocyto
Collecting velocyto
Downloading velocyto-0.17.17.tar.gz (198 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 198.9/198.9 kB 2.8 MB/s eta 0:00:00
Preparing metadata (setup.py) ... done
Requirement already satisfied: numpy in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from velocyto) (1.23.5)
Requirement already satisfied: scipy in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from velocyto) (1.7.1)
Requirement already satisfied: cython in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from velocyto) (0.29.33)
Requirement already satisfied: numba in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from velocyto) (0.56.4)
Requirement already satisfied: matplotlib in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from velocyto) (3.7.0)
Requirement already satisfied: scikit-learn in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from velocyto) (1.2.1)
Requirement already satisfied: h5py in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from velocyto) (3.7.0)
Collecting loompy
Downloading loompy-3.0.7.tar.gz (4.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.8/4.8 MB 9.7 MB/s eta 0:00:00
Preparing metadata (setup.py) ... done
Collecting pysam
Downloading pysam-0.20.0-cp39-cp39-macosx_10_9_x86_64.whl (3.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 10.3 MB/s eta 0:00:00
Requirement already satisfied: Click in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from velocyto) (8.0.4)
Collecting pandas
Downloading pandas-1.5.3-cp39-cp39-macosx_10_9_x86_64.whl (12.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.0/12.0 MB 10.6 MB/s eta 0:00:00
Requirement already satisfied: setuptools in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from loompy->velocyto) (65.6.3)
Collecting numpy-groupies
Downloading numpy_groupies-0.9.20-py3-none-any.whl (25 kB)
Requirement already satisfied: packaging>=20.0 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (22.0)
Requirement already satisfied: pyparsing>=2.3.1 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (3.0.9)
Requirement already satisfied: pillow>=6.2.0 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (9.4.0)
Requirement already satisfied: importlib-resources>=3.2.0 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (5.2.0)
Requirement already satisfied: python-dateutil>=2.7 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (2.8.2)
Requirement already satisfied: fonttools>=4.22.0 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (4.25.0)
Requirement already satisfied: contourpy>=1.0.1 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (1.0.5)
Requirement already satisfied: cycler>=0.10 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (0.11.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from matplotlib->velocyto) (1.4.4)
Requirement already satisfied: llvmlite<0.40,>=0.39.0dev0 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from numba->velocyto) (0.39.1)
Requirement already satisfied: pytz>=2020.1 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from pandas->velocyto) (2022.7)
Requirement already satisfied: joblib>=1.1.1 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn->velocyto) (1.1.1)
Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from scikit-learn->velocyto) (2.2.0)
Collecting numpy
Downloading numpy-1.22.4-cp39-cp39-macosx_10_15_x86_64.whl (17.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 17.7/17.7 MB 2.1 MB/s eta 0:00:00
Requirement already satisfied: zipp>=3.1.0 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from importlib-resources>=3.2.0->matplotlib->velocyto) (3.11.0)
Requirement already satisfied: six>=1.5 in /Users/jsong/opt/anaconda3/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib->velocyto) (1.16.0)
Building wheels for collected packages: velocyto, loompy
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/vl/x9ks4zqx3vx6jg0zgg1kzt780000gn/T/pip-install-r6ybq1f6/velocyto_0bad0e9ae1c543ce8c2238dcf18b0f0e/setup.py', 'bdist_wheel', '-d', '/private/var/folders/vl/x9ks4zqx3vx6jg0zgg1kzt780000gn/T/pip-wheel-xriwvgjl']
running bdist_wheel
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/velocyto
copying velocyto/transcript_model.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/diffusion.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/metadata.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/analysis.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/molitem.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/_version.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/neighbors.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/constants.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/estimation.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/init.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/feature.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/logic.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/indexes.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/utils.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/gene_info.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/r_interface.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/segment_match.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/counter.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/serialization.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/read.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
creating build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/velocyto.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/run.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/init.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/run_smartseq2.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/dropest_bc_correct.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/run_dropest.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/run10x.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/_run.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
running build_ext
building 'velocyto.speedboosted' extension
creating build/temp.macosx-10.9-x86_64-cpython-39
creating build/temp.macosx-10.9-x86_64-cpython-39/velocyto
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/jsong/opt/anaconda3/include -arch x86_64 -I/Users/jsong/opt/anaconda3/include -fPIC -O2 -isystem /Users/jsong/opt/anaconda3/include -arch x86_64 -I/Users/jsong/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/jsong/opt/anaconda3/include/python3.9 -c velocyto/speedboosted.c -o build/temp.macosx-10.9-x86_64-cpython-39/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
Building wheel for loompy (setup.py) ... done
Created wheel for loompy: filename=loompy-3.0.7-py3-none-any.whl size=52018 sha256=0750011c1332a24b6160f3ecf61261bd9c19fe590c93b65046904228e61ee8e7
Stored in directory: /Users/jsong/Library/Caches/pip/wheels/8b/5b/87/3eabb82aa3b53152c1f25646389ceb6f083e614d928836c341
Successfully built loompy
Failed to build velocyto
Installing collected packages: pysam, numpy, pandas, numpy-groupies, loompy, velocyto
Attempting uninstall: numpy
Found existing installation: numpy 1.23.5
Uninstalling numpy-1.23.5:
Successfully uninstalled numpy-1.23.5
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
╰─> [49 lines of output]
['/private/var/folders/vl/x9ks4zqx3vx6jg0zgg1kzt780000gn/T/pip-install-r6ybq1f6/velocyto_0bad0e9ae1c543ce8c2238dcf18b0f0e/setup.py', 'install', '--record', '/private/var/folders/vl/x9ks4zqx3vx6jg0zgg1kzt780000gn/T/pip-record-aia4f9hi/install-record.txt', '--single-version-externally-managed', '--compile', '--install-headers', '/Users/jsong/opt/anaconda3/include/python3.9/velocyto']
Compiling velocyto/speedboosted.pyx because it depends on /Users/jsong/opt/anaconda3/lib/python3.9/site-packages/numpy/init.pxd.
[1/1] Cythonizing velocyto/speedboosted.pyx
/Users/jsong/opt/anaconda3/lib/python3.9/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /private/var/folders/vl/x9ks4zqx3vx6jg0zgg1kzt780000gn/T/pip-install-r6ybq1f6/velocyto_0bad0e9ae1c543ce8c2238dcf18b0f0e/velocyto/speedboosted.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
running install
/Users/jsong/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/velocyto
copying velocyto/transcript_model.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/diffusion.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/metadata.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/analysis.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/molitem.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/_version.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/neighbors.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/constants.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/estimation.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/init.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/feature.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/logic.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/indexes.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/utils.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/gene_info.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/r_interface.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/segment_match.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/counter.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/serialization.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
copying velocyto/read.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto
creating build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/velocyto.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/run.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/init.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/run_smartseq2.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/dropest_bc_correct.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/run_dropest.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/run10x.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
copying velocyto/commands/_run.py -> build/lib.macosx-10.9-x86_64-cpython-39/velocyto/commands
running build_ext
building 'velocyto.speedboosted' extension
creating build/temp.macosx-10.9-x86_64-cpython-39
creating build/temp.macosx-10.9-x86_64-cpython-39/velocyto
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /Users/jsong/opt/anaconda3/include -arch x86_64 -I/Users/jsong/opt/anaconda3/include -fPIC -O2 -isystem /Users/jsong/opt/anaconda3/include -arch x86_64 -I/Users/jsong/opt/anaconda3/lib/python3.9/site-packages/numpy/core/include -I/Users/jsong/opt/anaconda3/include/python3.9 -c velocyto/speedboosted.c -o build/temp.macosx-10.9-x86_64-cpython-39/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.