Zymo-Research / figaro

An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
GNU General Public License v3.0
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Error installing FIGARO #56

Open jibarozzo opened 1 year ago

jibarozzo commented 1 year ago

Hi,

I have tried installing FIGARO multiples times on Windows and Linux and I get an error that it is either missing "numpy' and/or "Cython". Once I take care of that it returns the following (or similar on Linux):

 Building wheels for collected packages: figaro

Building wheel for figaro (setup.py) ... error
  error: subprocess-exited-with-error

  × python setup.py bdist_wheel did not run successfully.
  │ exit code: 1
  ╰─> [49 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build\lib.win-amd64-3.7
      creating build\lib.win-amd64-3.7\figaro
      creating build\lib.win-amd64-3.7\figaro\pipelines
      copying figaro/pipelines/probability_density.py -> build\lib.win-amd64-3.7\figaro/pipelines
      copying figaro/pipelines/hierarchical_inference.py -> build\lib.win-amd64-3.7\figaro/pipelines
      copying figaro/pipelines/create_glade.py -> build\lib.win-amd64-3.7\figaro/pipelines
      copying figaro/pipelines/ppplot.py -> build\lib.win-amd64-3.7\figaro/pipelines
      copying figaro/pipelines/gen_mock_data.py -> build\lib.win-amd64-3.7\figaro/pipelines
      copying figaro/pipelines/entropy.py -> build\lib.win-amd64-3.7\figaro/pipelines
      copying figaro\coordinates.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\credible_regions.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\decorators.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\diagnostic.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\exceptions.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\likelihood.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\load.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\marginal.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\mixture.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\montecarlo.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\plot.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\plot_settings.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\threeDvolume.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\transform.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\utils.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\__init__.py -> build\lib.win-amd64-3.7\figaro
      copying figaro\cosmology.c -> build\lib.win-amd64-3.7\figaro
      copying figaro\cumulative.c -> build\lib.win-amd64-3.7\figaro
      copying figaro\cosmology.pyx -> build\lib.win-amd64-3.7\figaro
      copying figaro\cumulative.pyx -> build\lib.win-amd64-3.7\figaro
      copying figaro\cosmology.pxd -> build\lib.win-amd64-3.7\figaro
      running build_ext
      building 'figaro.cumulative' extension
      creating build\temp.win-amd64-3.7
      creating build\temp.win-amd64-3.7\Release
      creating build\temp.win-amd64-3.7\Release\figaro
      C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.36.32532\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ifigaro -Ic:\users\boloq\anaconda3\lib\site-packages\numpy\core\include -Ifigaro -Ic:\users\boloq\anaconda3\lib\site-packages\numpy\core\include -Ic:\users\boloq\anaconda3\include -Ic:\users\boloq\anaconda3\include "-IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.36.32532\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.36.32532\ATLMFC\include" "-IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Auxiliary\VS\include" "-IC:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\ucrt" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\um" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\shared" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\winrt" "-IC:\Program Files (x86)\Windows Kits\10\\include\10.0.22000.0\\cppwinrt" /Tcfigaro\cumulative.c /Fobuild\temp.win-amd64-3.7\Release\figaro\cumulative.obj -O3 -ffast-math
      cl : Command line warning D9002 : ignoring unknown option '-O3'
      cl : Command line warning D9002 : ignoring unknown option '-ffast-math'
      cumulative.c
      c:\users\boloq\anaconda3\lib\site-packages\numpy\core\include\numpy\npy_1_7_deprecated_api.h(14) : Warning Msg: Using deprecated NumPy API, disable it with #define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
      figaro\cumulative.c(1940): warning C4244: '=': conversion from 'npy_intp' to 'unsigned int', possible loss of data
      figaro\cumulative.c(2281): warning C4244: '=': conversion from 'npy_intp' to 'unsigned int', possible loss of data
      C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.36.32532\bin\HostX86\x64\link.exe /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:c:\users\boloq\anaconda3\libs /LIBPATH:c:\users\boloq\anaconda3\PCbuild\amd64 "/LIBPATH:C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.36.32532\lib\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\lib\10.0.22000.0\ucrt\x64" "/LIBPATH:C:\Program Files (x86)\Windows Kits\10\\lib\10.0.22000.0\\um\x64" m.lib /EXPORT:PyInit_cumulative build\temp.win-amd64-3.7\Release\figaro\cumulative.obj /OUT:build\lib.win-amd64-3.7\figaro\cumulative.cp37-win_amd64.pyd /IMPLIB:build\temp.win-amd64-3.7\Release\figaro\cumulative.cp37-win_amd64.lib
      LINK : fatal error LNK1181: cannot open input file 'm.lib'
      error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio\\2022\\BuildTools\\VC\\Tools\\MSVC\\14.36.32532\\bin\\HostX86\\x64\\link.exe' failed with exit status 1181
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for figaro
  Running setup.py clean for figaro
Failed to build figaro
ERROR: Could not build wheels for figaro, which is required to install pyproject.toml-based projects

I have also tried installing in a virtual environment and the same error occurs. Anyone have any suggestions?