daleroberts / hdmedians Goto Github PK
View Code? Open in Web Editor NEWHigh-dimensional medians (medoid, geometric median, etc.). Fast implementations in Python.
License: Apache License 2.0
High-dimensional medians (medoid, geometric median, etc.). Fast implementations in Python.
License: Apache License 2.0
Hello, we get an error when trying to install via pip in a virtualenv. "ERROR: Failed building wheel for hdmedians". Full traceback follows. Thank you for your help
$ python3.8 -m pip install hdmedians
Collecting hdmedians
Using cached hdmedians-0.14.2.tar.gz (7.6 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... done
Collecting numpy
Using cached numpy-1.22.3-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB)
Collecting Cython>=0.23
Using cached Cython-0.29.28-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (1.9 MB)
Building wheels for collected packages: hdmedians
Building wheel for hdmedians (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for hdmedians (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [30 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.8
creating build/lib.linux-x86_64-3.8/hdmedians
copying hdmedians/__init__.py -> build/lib.linux-x86_64-3.8/hdmedians
copying hdmedians/medoid.py -> build/lib.linux-x86_64-3.8/hdmedians
creating build/lib.linux-x86_64-3.8/hdmedians/tests
copying hdmedians/tests/test_medoid.py -> build/lib.linux-x86_64-3.8/hdmedians/tests
copying hdmedians/tests/test_geomedian.py -> build/lib.linux-x86_64-3.8/hdmedians/tests
copying hdmedians/tests/__init__.py -> build/lib.linux-x86_64-3.8/hdmedians/tests
running build_ext
cythoning hdmedians/geomedian.pyx to hdmedians/geomedian.c
building 'hdmedians.geomedian' extension
creating build/temp.linux-x86_64-3.8
creating build/temp.linux-x86_64-3.8/hdmedians
/home/user/.conda/envs/py38/bin/x86_64-conda-linux-gnu-cc -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/user/.conda/envs/py38/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/user/.conda/envs/py38/include -fPIC -I/scratch/user/pip-build-env-gcmtcp8a/overlay/lib/python3.8/site-packages/numpy/core/include -I/home/user/scanpy/scanpy_env2/include -I/home/user/.conda/envs/py38/include/python3.8 -c hdmedians/geomedian.c -o build/temp.linux-x86_64-3.8/hdmedians/geomedian.o
In file included from /scratch/user/pip-build-env-gcmtcp8a/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1830,
from /scratch/user/pip-build-env-gcmtcp8a/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /scratch/user/pip-build-env-gcmtcp8a/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from hdmedians/geomedian.c:688:
/scratch/user/pip-build-env-gcmtcp8a/overlay/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
gcc -pthread -shared -B /home/user/.conda/envs/py38/compiler_compat -L/home/user/.conda/envs/py38/lib -Wl,-rpath=/home/user/.conda/envs/py38/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/user/.conda/envs/py38/lib -Wl,-rpath-link,/home/user/.conda/envs/py38/lib -L/home/user/.conda/envs/py38/lib -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/user/.conda/envs/py38/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/user/.conda/envs/py38/include build/temp.linux-x86_64-3.8/hdmedians/geomedian.o -o build/lib.linux-x86_64-3.8/hdmedians/geomedian.cpython-38-x86_64-linux-gnu.so
gcc: error: unrecognized command line option ‘-fno-plt’
/scratch/user/pip-build-env-gcmtcp8a/overlay/lib/python3.8/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: /scratch/user/pip-install-b_2ajirb/hdmedians_a6d88b5d918246fcbca4200687f7dc4d/hdmedians/geomedian.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
error: command '/bin/gcc' 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 hdmedians
Failed to build hdmedians
ERROR: Could not build wheels for hdmedians, which is required to install pyproject.toml-based projects
We are considering using this package in scikit-bio (a BSD 3-clause licensed package), but the GPL license would require us to change our package to a GPL-like license. Can you consider double-licensing hdmedians, or grant us permission to use this without the need to change our license?
Hi,
Great package, thanks for putting this together. Do you know how you would like the repository to be cited?
Thanks
Hi,
I intend to package hdmedians for official Debian. It would help if you would consider adding release tags to enable users to decide what is just a develoment commit and what is a real release fit for distribution.
Thanks a lot for considering, Andreas.
The hdmedians/tests
directory is not a module, and thus does not end up in the sdist
, making it a bit tough to test the package when distributing it. I'd be happy to make a PR to address this if acceptable.
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