daleroberts / hdmedians Goto Github PK

$ 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