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PIP installation error, same error appears in both Win10 system and Ubuntu 20.04 #22

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wanghanruibaba opened this issue Feb 24, 2024 · 11 comments
Open

PIP installation error, same error appears in both Win10 system and Ubuntu 20.04 #22

wanghanruibaba opened this issue Feb 24, 2024 · 11 comments

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@wanghanruibaba
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wanghanruibaba commented Feb 24, 2024 •
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An error occurred during the installation process；windows10 aconoda virtually variable‘skeletor’

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

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [181 lines of output]
C:\Users\Administrator\AppData\Local\Temp\pip-install-796duxqi\mistree_24fe46a7bfa14acaa559369759895f4b\setup.py:4: DeprecationWarning:

    `numpy.distutils` is deprecated since NumPy 1.23.0, as a result
    of the deprecation of `distutils` itself. It will be removed for
    Python >= 3.12. For older Python versions it will remain present.
    It is recommended to use `setuptools < 60.0` for those Python versions.
    For more details, see:
      https://numpy.org/devdocs/reference/distutils_status_migration.html


    from numpy.distutils.core import setup, Extension
  running bdist_wheel
  running build
  running config_cc
  INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
  running config_fc
  INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
  running build_src
  INFO: build_src
  INFO: building extension "mistree.levy_flight.utility_random_walk" sources
  INFO: f2py options: []
  INFO:   adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight\fortranobject.c' to sources.
  INFO:   adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight' to include_dirs.
  copying D:\Anaconda3\envs\skeletor\lib\site-packages\numpy\f2py\src\fortranobject.c -> build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight
  copying D:\Anaconda3\envs\skeletor\lib\site-packages\numpy\f2py\src\fortranobject.h -> build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight
  INFO:   adding 'build\src.win-amd64-3.9\mistree\levy_flight\utility_random_walk-f2pywrappers.f' to sources.
  INFO: building extension "mistree.mst.utility_density" sources
  INFO: f2py options: []
  INFO:   adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst\fortranobject.c' to sources.
  INFO:   adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst' to include_dirs.
  copying D:\Anaconda3\envs\skeletor\lib\site-packages\numpy\f2py\src\fortranobject.c -> build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst
  copying D:\Anaconda3\envs\skeletor\lib\site-packages\numpy\f2py\src\fortranobject.h -> build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst
  INFO:   adding 'build\src.win-amd64-3.9\mistree\mst\utility_density-f2pywrappers.f' to sources.
  INFO: building extension "mistree.mst.utility_mst" sources
  INFO: f2py options: []
  INFO:   adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst\fortranobject.c' to sources.
  INFO:   adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst' to include_dirs.
  copying D:\Anaconda3\envs\skeletor\lib\site-packages\numpy\f2py\src\fortranobject.c -> build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst
  copying D:\Anaconda3\envs\skeletor\lib\site-packages\numpy\f2py\src\fortranobject.h -> build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst
  INFO:   adding 'build\src.win-amd64-3.9\mistree\mst\utility_mst-f2pywrappers.f' to sources.
  INFO: build_src: building npy-pkg config files
  D:\Anaconda3\envs\skeletor\lib\site-packages\setuptools\_distutils\cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
  !!

          ********************************************************************************
          Please avoid running ``setup.py`` directly.
          Instead, use pypa/build, pypa/installer or other
          standards-based tools.

          See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
          ********************************************************************************

  !!
    self.initialize_options()
  running build_py
  creating build\lib.win-amd64-cpython-39
  creating build\lib.win-amd64-cpython-39\mistree
  copying mistree\__init__.py -> build\lib.win-amd64-cpython-39\mistree
  creating build\lib.win-amd64-cpython-39\mistree\coordinates
  copying mistree\coordinates\coordinate_utility.py -> build\lib.win-amd64-cpython-39\mistree\coordinates
  copying mistree\coordinates\__init__.py -> build\lib.win-amd64-cpython-39\mistree\coordinates
  creating build\lib.win-amd64-cpython-39\mistree\levy_flight
  copying mistree\levy_flight\levy_flight.py -> build\lib.win-amd64-cpython-39\mistree\levy_flight
  copying mistree\levy_flight\__init__.py -> build\lib.win-amd64-cpython-39\mistree\levy_flight
  creating build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\branches.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\construct.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\density.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\get_mst_class.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\graph.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\hist_mst.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\partition.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\plot_mst.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\scale_cut.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\stats.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\tomo.py -> build\lib.win-amd64-cpython-39\mistree\mst
  copying mistree\mst\__init__.py -> build\lib.win-amd64-cpython-39\mistree\mst
  running build_ext
  INFO: No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils
  INFO: customize MSVCCompiler
  INFO: customize MSVCCompiler using build_ext
  INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (/O2)
  creating C:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3
  creating C:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs
  creating C:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor
  creating C:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib
  creating C:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib\site-packages
  creating C:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib\site-packages\numpy
  creating C:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils
  creating C:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks
  INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (/WX)
  WARN: CCompilerOpt.__init__[1253] : feature 'AVX512_KNL' is disabled, MSVC compiler doesn't support it
  WARN: CCompilerOpt.__init__[1253] : feature 'AVX512_KNM' is disabled, MSVC compiler doesn't support it
  WARN: CCompilerOpt.__init__[1253] : feature 'AVX512_SPR' is disabled, MSVC compiler doesn't support it
  INFO: CCompilerOpt.__init__[1795] : check requested baseline
  INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE2' with flags ()
  WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\bin\HostX86\x64\cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -ID:\Anaconda3\envs\skeletor\include -ID:\Anaconda3\envs\skeletor\Include -ID:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include -ID:\Microsoft\VisualStudio\IDE\VC\Auxiliary\VS\include /TcD:\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_sse2.c /FoC:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_sse2.obj /WX) failed with exit status 2 output ->
  cpu_sse2.c
  D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include\xmmintrin.h(79): fatal error C1083: 无法打开包括文件: “malloc.h”: No such file or directory

  WARN: CCompilerOpt.feature_test[1576] : testing failed
  INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE' with flags ()
  WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\bin\HostX86\x64\cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -ID:\Anaconda3\envs\skeletor\include -ID:\Anaconda3\envs\skeletor\Include -ID:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include -ID:\Microsoft\VisualStudio\IDE\VC\Auxiliary\VS\include /TcD:\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_sse.c /FoC:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_sse.obj /WX) failed with exit status 2 output ->
  cpu_sse.c
  D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include\xmmintrin.h(79): fatal error C1083: 无法打开包括文件: “malloc.h”: No such file or directory

  WARN: CCompilerOpt.feature_test[1576] : testing failed
  INFO: CCompilerOpt.__init__[1804] : check requested dispatch-able features
  INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (/arch:AVX)
  INFO: CCompilerOpt.cc_test_flags[1086] : testing flags (/arch:AVX2)
  INFO: CCompilerOpt.feature_test[1560] : testing feature 'FMA3' with flags (/arch:AVX2)
  WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\bin\HostX86\x64\cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -ID:\Anaconda3\envs\skeletor\include -ID:\Anaconda3\envs\skeletor\Include -ID:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include -ID:\Microsoft\VisualStudio\IDE\VC\Auxiliary\VS\include /TcD:\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_fma3.c /FoC:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_fma3.obj /arch:AVX2 /WX) failed with exit status 2 output ->
  cpu_fma3.c
  D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include\xmmintrin.h(79): fatal error C1083: 无法打开包括文件: “malloc.h”: No such file or directory

  WARN: CCompilerOpt.feature_test[1576] : testing failed
  INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE42' with flags ()
  WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\bin\HostX86\x64\cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -ID:\Anaconda3\envs\skeletor\include -ID:\Anaconda3\envs\skeletor\Include -ID:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include -ID:\Microsoft\VisualStudio\IDE\VC\Auxiliary\VS\include /TcD:\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_sse42.c /FoC:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_sse42.obj /WX) failed with exit status 2 output ->
  cpu_sse42.c
  D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include\xmmintrin.h(79): fatal error C1083: 无法打开包括文件: “malloc.h”: No such file or directory

  WARN: CCompilerOpt.feature_test[1576] : testing failed
  INFO: CCompilerOpt.feature_test[1560] : testing feature 'SSE41' with flags ()
  WARN: CCompilerOpt.dist_test[637] : CCompilerOpt._dist_test_spawn[771] : Command (D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\bin\HostX86\x64\cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -ID:\Anaconda3\envs\skeletor\include -ID:\Anaconda3\envs\skeletor\Include -ID:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include -ID:\Microsoft\VisualStudio\IDE\VC\Auxiliary\VS\include /TcD:\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_sse41.c /FoC:\Users\ADMINI~1\AppData\Local\Temp\tmpm4iligww\Anaconda3\envs\skeletor\Lib\site-packages\numpy\distutils\checks\cpu_sse41.obj /WX) failed with exit status 2 output ->
  cpu_sse41.c
  D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include\xmmintrin.h(79): fatal error C1083: 无法打开包括文件: “malloc.h”: No such file or directory

  WARN: CCompilerOpt.feature_test[1576] : testing failed
  INFO: CCompilerOpt.__init__[1820] : initialize targets groups
  INFO: CCompilerOpt.__init__[1822] : parse target group simd_test
  INFO: CCompilerOpt._parse_target_tokens[2033] : skip targets (SSE42 VXE2 VXE NEON VX AVX512F SSE2 ASIMD (AVX2 FMA3) AVX512_SKX VSX2 XOP VSX FMA4 VSX4 VSX3) not part of baseline or dispatch-able features
  INFO: CCompilerOpt.generate_dispatch_header[2366] : generate CPU dispatch header: (build\src.win-amd64-3.9\numpy\distutils\include\npy_cpu_dispatch_config.h)
  WARN: CCompilerOpt.generate_dispatch_header[2375] : dispatch header dir build\src.win-amd64-3.9\numpy\distutils\include does not exist, creating it
  INFO: get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv', 'intelev', 'gnu95', 'g95', 'intelvem', 'intelem', 'flang']'
  INFO: customize GnuFCompiler
  WARN: Could not locate executable g77
  WARN: Could not locate executable f77
  INFO: customize IntelVisualFCompiler
  WARN: Could not locate executable ifort
  WARN: Could not locate executable ifl
  INFO: customize AbsoftFCompiler
  WARN: Could not locate executable f90
  INFO: customize CompaqVisualFCompiler
  WARN: Could not locate executable DF
  INFO: customize IntelItaniumVisualFCompiler
  WARN: Could not locate executable efl
  INFO: customize Gnu95FCompiler
  INFO: Found executable e:\rosa\mingw64\mingw64\mingw64\bin\gfortran.exe
  INFO: customize Gnu95FCompiler
  INFO: customize Gnu95FCompiler using build_ext
  INFO: building 'mistree.levy_flight.utility_random_walk' extension
  INFO: compiling C sources
  creating build\temp.win-amd64-cpython-39\Release\build
  creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9
  creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\mistree
  creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\mistree\levy_flight
  creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\build
  creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\build\src.win-amd64-3.9
  creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree
  creating build\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight
  INFO: D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\bin\HostX86\x64\cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight -ID:\Anaconda3\envs\skeletor\lib\site-packages\numpy\core\include -Ibuild\src.win-amd64-3.9\numpy\distutils\include -ID:\Anaconda3\envs\skeletor\include -ID:\Anaconda3\envs\skeletor\Include -ID:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include -ID:\Microsoft\VisualStudio\IDE\VC\Auxiliary\VS\include /Tcbuild\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.c /Fobuild\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.obj
  utility_random_walkmodule.c
  D:\Anaconda3\envs\skeletor\include\pyconfig.h(59): fatal error C1083: 无法打开包括文件: “io.h”: No such file or directory
  error: Command "D:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\bin\HostX86\x64\cl.exe /c /nologo /O2 /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight -ID:\Anaconda3\envs\skeletor\lib\site-packages\numpy\core\include -Ibuild\src.win-amd64-3.9\numpy\distutils\include -ID:\Anaconda3\envs\skeletor\include -ID:\Anaconda3\envs\skeletor\Include -ID:\Microsoft\VisualStudio\IDE\VC\Tools\MSVC\14.33.31629\include -ID:\Microsoft\VisualStudio\IDE\VC\Auxiliary\VS\include /Tcbuild\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.c /Fobuild\temp.win-amd64-cpython-39\Release\build\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.obj" failed with exit status 2
  INFO:
  ########### EXT COMPILER OPTIMIZATION ###########
  INFO: Platform      :
    Architecture: x64
    Compiler    : msvc

  CPU baseline  :
    Requested   : 'min'
    Enabled     : none
    Flags       : none
    Extra checks: none

  CPU dispatch  :
    Requested   : 'max -xop -fma4'
    Enabled     : none
    Generated   : none
  INFO: CCompilerOpt.cache_flush[864] : write cache to path -> C:\Users\Administrator\AppData\Local\Temp\pip-install-796duxqi\mistree_24fe46a7bfa14acaa559369759895f4b\build\temp.win-amd64-cpython-39\Release\ccompiler_opt_cache_ext.py
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for mistree
Running setup.py clean for mistree
Failed to build mistree
ERROR: Could not build wheels for mistree, which is required to install pyproject.toml-based projects
@WS517
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WS517 commented Mar 12, 2024

When I install mistree separately in python 3.8 as well as 3.9 environments, using the command pip install mistree, the following problem occurs:
NOTE: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for mistree
Running setup.py clean for mistree
Building wheel for wget (setup.py) ... done
Created wheel for wget: filename=wget-3.2-py3-none-any.whl size=9655 sha256= 518c49bf89ba6d614190095777a1e8e417c2a21bf6f932322a6b3d7c5cc1b0fc
Stored in directory: /home/ws/.cache/pip/wheels/04/5f/3e/46cc37c5d698415694d83f607f833f83f0149e49b3af9d0f38
Successfully built wget
Failed to build mistree
ERROR: Could not build wheels for mistree, which is required to install pyproject.toml-based projects
How to solve this problem?Thank you very much.

@meyerls
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Owner

meyerls commented Mar 12, 2024

Currently, I am busy but I hope I can help you in 2-3 weeks

@WS517
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WS517 commented Mar 12, 2024

Thank you very much for your help and look forward to hearing from you again!

@albertpaolobugayong
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Hello any followup from this?

@meyerls
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Owner

meyerls commented Apr 12, 2024

In several issues, I refer to my fork of mistree. Please clone this repo and install it with pip install -e .

Did it solve your problem?

@yangfeng-Lyu
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Hello! I built mistree according to your instructions. I downloaded gcc and put it into the environment variable, but it still failed to compile successfully. I hope you can provide some help.
PS E:\LYF_data\code\pc-skeletor-main> cd mistree-master
PS E:\LYF_data\code\pc-skeletor-main\mistree-master> python setup.py build
running build
running config_cc
INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
INFO: build_src
INFO: building extension "mistree.levy_flight.utility_random_walk" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight' to include_dirs.
INFO: building extension "mistree.mst.utility_density" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst' to include_dirs.
INFO: building extension "mistree.mst.utility_mst" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst' to include_dirs.
INFO: build_src: building npy-pkg config files
running build_py
running build_ext
INFO: No module named 'numpy.distutils.msvccompiler' in numpy.distutils; trying from distutils
INFO: customize MSVCCompiler
INFO: customize MSVCCompiler using build_ext
INFO: CCompilerOpt.init[781] : load cache from file -> E:\LYF_data\code\pc-skeletor-main\mistree-master\build\temp.win-amd64-3.9\Release\ccompiler_opt_cache_ext.py
INFO: CCompilerOpt.init[792] : hit the file cache
INFO: get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv', 'intelev', 'gnu95', 'g95', 'intelvem', 'intelem', 'flang']'
INFO: customize GnuFCompiler
WARN: Could not locate executable g77
WARN: Could not locate executable f77
INFO: customize IntelVisualFCompiler
WARN: Could not locate executable ifort
WARN: Could not locate executable ifl
INFO: customize AbsoftFCompiler
WARN: Could not locate executable f90
INFO: customize CompaqVisualFCompiler
WARN: Could not locate executable DF
INFO: customize IntelItaniumVisualFCompiler
WARN: Could not locate executable efl
INFO: customize Gnu95FCompiler
INFO: Found executable C:\Users\Admin\gcc\bin\gfortran.exe
Built by Equation Solution http://www.Equation.com.
Using built-in specs.
COLLECT_GCC=C:\Users\Admin\gcc\bin\gfortran.exe
COLLECT_LTO_WRAPPER=C:/Users/Admin/gcc/bin/../libexec/gcc/x86_64-w64-mingw32/13.2.0/lto-wrapper.exe
Target: x86_64-w64-mingw32
Configured with: ../gcc-13.2.0/configure --host=x86_64-w64-mingw32 --build=x86_64-unknown-linux-gnu --target=x86_64-w64-mingw32 --prefix=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/gcc/13.
2.0 --with-sysroot=/home/gfortran/gcc-home/binary/mingw32/cross/x86_64/gcc/13.2.0 --with-gcc --with-gnu-ld --with-gnu-as --with-ld64=no --with-gmp=/home/gfortran/gcc-home/binary/mingw32/native/x86
64/gmp --with-mpfr=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/mpfr --with-mpc=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/mpc --with-cloog=/home/gfortran/gcc-home/binary/mingw32/
native/x86_64/cloog --with-libiconv-prefix=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/libiconv --with-diagnostics-color=auto --enable-cloog-backend=isl --enable-targets=i686-w64-mingw32,x
86_64-w64-mingw32 --enable-lto --enable-languages=c,c++,fortran --enable-threads=win32 --enable-static --enable-shared=lto-plugin --enable-plugins --enable-ld=yes --enable-libquadmath --enable-libquadmath-support --enable-libgomp --disable-checking --disable-nls --disable-tls --disable-win32-registry
Thread model: win32
Supported LTO compression algorithms: zlib
gcc version 13.2.0 (GCC)
INFO: customize Gnu95FCompiler
Built by Equation Solution http://www.Equation.com.
Using built-in specs.
COLLECT_GCC=C:\Users\Admin\gcc\bin\gfortran.exe
COLLECT_LTO_WRAPPER=C:/Users/Admin/gcc/bin/../libexec/gcc/x86_64-w64-mingw32/13.2.0/lto-wrapper.exe
Target: x86_64-w64-mingw32
Configured with: ../gcc-13.2.0/configure --host=x86_64-w64-mingw32 --build=x86_64-unknown-linux-gnu --target=x86_64-w64-mingw32 --prefix=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/gcc/13.
2.0 --with-sysroot=/home/gfortran/gcc-home/binary/mingw32/cross/x86_64/gcc/13.2.0 --with-gcc --with-gnu-ld --with-gnu-as --with-ld64=no --with-gmp=/home/gfortran/gcc-home/binary/mingw32/native/x86_
64/gmp --with-mpfr=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/mpfr --with-mpc=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/mpc --with-cloog=/home/gfortran/gcc-home/binary/mingw32/
native/x86_64/cloog --with-libiconv-prefix=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/libiconv --with-diagnostics-color=auto --enable-cloog-backend=isl --enable-targets=i686-w64-mingw32,x
86_64-w64-mingw32 --enable-lto --enable-languages=c,c++,fortran --enable-threads=win32 --enable-static --enable-shared=lto-plugin --enable-plugins --enable-ld=yes --enable-libquadmath --enable-libquadmath-support --enable-libgomp --disable-checking --disable-nls --disable-tls --disable-win32-registry
Thread model: win32
Supported LTO compression algorithms: zlib
gcc version 13.2.0 (GCC)
INFO: customize Gnu95FCompiler using build_ext
INFO: building 'mistree.levy_flight.utility_random_walk' extension
INFO: compiling C sources
INFO: C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.39.33519\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\src.win-amd
64-3.9\mistree\levy_flight -IE:\LYF_data\code\pythonProject\venv\lib\site-packages\numpy\core\include -Ibuild\src.win-amd64-3.9\numpy\distutils\include -IE:\LYF_data\code\pythonProject\venv\include
-IC:\Users\Admin\AppData\Local\Programs\Python\Python39\include -IC:\Users\Admin\AppData\Local\Programs\Python\Python39\include -IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC
Tools\MSVC\14.39.33519\include -IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Auxiliary\VS\include /Tcbuild\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.c /Fobuild\temp.win-amd64-3.9\Release\build\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.obj
utility_random_walkmodule.c
C:\Users\Admin\AppData\Local\Programs\Python\Python39\include\pyconfig.h(59): fatal error C1083: �޷��򿪰����ļ�: ��io.h��: No such file or directory
error: Command "C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.39.33519\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\s
rc.win-amd64-3.9\mistree\levy_flight -IE:\LYF_data\code\pythonProject\venv\lib\site-packages\numpy\core\include -Ibuild\src.win-amd64-3.9\numpy\distutils\include -IE:\LYF_data\code\pythonProject\ve
nv\include -IC:\Users\Admin\AppData\Local\Programs\Python\Python39\include -IC:\Users\Admin\AppData\Local\Programs\Python\Python39\include -IC:\Program Files (x86)\Microsoft Visual Studio\2022\Buil
dTools\VC\Tools\MSVC\14.39.33519\include -IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Auxiliary\VS\include /Tcbuild\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.c /Fobuild\temp.win-amd64-3.9\Release\build\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.obj" failed with exit status 2
INFO:
########### EXT COMPILER OPTIMIZATION ###########
INFO: Platform :
Architecture: x64
Compiler : msvc

CPU baseline :
Requested : 'min'
Enabled : none
Flags : none
Extra checks: none

CPU dispatch :
Requested : 'max -xop -fma4'
Enabled : none
Generated : none
INFO: CCompilerOpt.cache_flush[825] : write cache to path -> E:\LYF_data\code\pc-skeletor-main\mistree-master\build\temp.win-amd64-3.9\Release\ccompiler_opt_cache_ext.py
PS E:\LYF_data\code\pc-skeletor-main\mistree-master> python setup.py install
running install
running bdist_egg
running egg_info
running build_src
INFO: build_src
INFO: building extension "mistree.levy_flight.utility_random_walk" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\levy_flight' to include_dirs.
INFO: building extension "mistree.mst.utility_density" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst' to include_dirs.
INFO: building extension "mistree.mst.utility_mst" sources
INFO: f2py options: []
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst\fortranobject.c' to sources.
INFO: adding 'build\src.win-amd64-3.9\build\src.win-amd64-3.9\mistree\mst' to include_dirs.
INFO: build_src: building npy-pkg config files
writing mistree.egg-info\PKG-INFO
writing dependency_links to mistree.egg-info\dependency_links.txt
writing requirements to mistree.egg-info\requires.txt
writing top-level names to mistree.egg-info\top_level.txt
reading manifest file 'mistree.egg-info\SOURCES.txt'
adding license file 'LICENSE.txt'
writing manifest file 'mistree.egg-info\SOURCES.txt'
installing library code to build\bdist.win-amd64\egg
running install_lib
running build_py
running build_ext
INFO: No module named 'numpy.distutils.msvccompiler' in numpy.distutils; trying from distutils
INFO: customize MSVCCompiler
INFO: customize MSVCCompiler using build_ext
INFO: CCompilerOpt.init[781] : load cache from file -> E:\LYF_data\code\pc-skeletor-main\mistree-master\build\temp.win-amd64-3.9\Release\ccompiler_opt_cache_ext.py
INFO: CCompilerOpt.init[792] : hit the file cache
INFO: get_default_fcompiler: matching types: '['gnu', 'intelv', 'absoft', 'compaqv', 'intelev', 'gnu95', 'g95', 'intelvem', 'intelem', 'flang']'
INFO: customize GnuFCompiler
WARN: Could not locate executable g77
WARN: Could not locate executable f77
INFO: customize IntelVisualFCompiler
WARN: Could not locate executable ifort
WARN: Could not locate executable ifl
INFO: customize AbsoftFCompiler
WARN: Could not locate executable f90
INFO: customize CompaqVisualFCompiler
WARN: Could not locate executable DF
INFO: customize IntelItaniumVisualFCompiler
WARN: Could not locate executable efl
INFO: customize Gnu95FCompiler
INFO: Found executable C:\Users\Admin\gcc\bin\gfortran.exe
Built by Equation Solution http://www.Equation.com.
Using built-in specs.
COLLECT_GCC=C:\Users\Admin\gcc\bin\gfortran.exe
COLLECT_LTO_WRAPPER=C:/Users/Admin/gcc/bin/../libexec/gcc/x86_64-w64-mingw32/13.2.0/lto-wrapper.exe
Target: x86_64-w64-mingw32
Configured with: ../gcc-13.2.0/configure --host=x86_64-w64-mingw32 --build=x86_64-unknown-linux-gnu --target=x86_64-w64-mingw32 --prefix=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/gcc/13.
2.0 --with-sysroot=/home/gfortran/gcc-home/binary/mingw32/cross/x86_64/gcc/13.2.0 --with-gcc --with-gnu-ld --with-gnu-as --with-ld64=no --with-gmp=/home/gfortran/gcc-home/binary/mingw32/native/x86
64/gmp --with-mpfr=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/mpfr --with-mpc=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/mpc --with-cloog=/home/gfortran/gcc-home/binary/mingw32/
native/x86_64/cloog --with-libiconv-prefix=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/libiconv --with-diagnostics-color=auto --enable-cloog-backend=isl --enable-targets=i686-w64-mingw32,x
86_64-w64-mingw32 --enable-lto --enable-languages=c,c++,fortran --enable-threads=win32 --enable-static --enable-shared=lto-plugin --enable-plugins --enable-ld=yes --enable-libquadmath --enable-libquadmath-support --enable-libgomp --disable-checking --disable-nls --disable-tls --disable-win32-registry
Thread model: win32
Supported LTO compression algorithms: zlib
gcc version 13.2.0 (GCC)
INFO: customize Gnu95FCompiler
Built by Equation Solution http://www.Equation.com.
Using built-in specs.
COLLECT_GCC=C:\Users\Admin\gcc\bin\gfortran.exe
COLLECT_LTO_WRAPPER=C:/Users/Admin/gcc/bin/../libexec/gcc/x86_64-w64-mingw32/13.2.0/lto-wrapper.exe
Target: x86_64-w64-mingw32
Configured with: ../gcc-13.2.0/configure --host=x86_64-w64-mingw32 --build=x86_64-unknown-linux-gnu --target=x86_64-w64-mingw32 --prefix=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/gcc/13.
2.0 --with-sysroot=/home/gfortran/gcc-home/binary/mingw32/cross/x86_64/gcc/13.2.0 --with-gcc --with-gnu-ld --with-gnu-as --with-ld64=no --with-gmp=/home/gfortran/gcc-home/binary/mingw32/native/x86_
64/gmp --with-mpfr=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/mpfr --with-mpc=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/mpc --with-cloog=/home/gfortran/gcc-home/binary/mingw32/
native/x86_64/cloog --with-libiconv-prefix=/home/gfortran/gcc-home/binary/mingw32/native/x86_64/libiconv --with-diagnostics-color=auto --enable-cloog-backend=isl --enable-targets=i686-w64-mingw32,x
86_64-w64-mingw32 --enable-lto --enable-languages=c,c++,fortran --enable-threads=win32 --enable-static --enable-shared=lto-plugin --enable-plugins --enable-ld=yes --enable-libquadmath --enable-libquadmath-support --enable-libgomp --disable-checking --disable-nls --disable-tls --disable-win32-registry
Thread model: win32
Supported LTO compression algorithms: zlib
gcc version 13.2.0 (GCC)
INFO: customize Gnu95FCompiler using build_ext
INFO: building 'mistree.levy_flight.utility_random_walk' extension
INFO: compiling C sources
INFO: C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.39.33519\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\src.win-amd
64-3.9\mistree\levy_flight -IE:\LYF_data\code\pythonProject\venv\lib\site-packages\numpy\core\include -Ibuild\src.win-amd64-3.9\numpy\distutils\include -IE:\LYF_data\code\pythonProject\venv\include
-IC:\Users\Admin\AppData\Local\Programs\Python\Python39\include -IC:\Users\Admin\AppData\Local\Programs\Python\Python39\include -IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC
Tools\MSVC\14.39.33519\include -IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Auxiliary\VS\include /Tcbuild\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.c /Fobuild\temp.win-amd64-3.9\Release\build\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.obj
utility_random_walkmodule.c
C:\Users\Admin\AppData\Local\Programs\Python\Python39\include\pyconfig.h(59): fatal error C1083: �޷��򿪰����ļ�: ��io.h��: No such file or directory
error: Command "C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.39.33519\bin\HostX86\x64\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MD -Ibuild\src.win-amd64-3.9\build\s
rc.win-amd64-3.9\mistree\levy_flight -IE:\LYF_data\code\pythonProject\venv\lib\site-packages\numpy\core\include -Ibuild\src.win-amd64-3.9\numpy\distutils\include -IE:\LYF_data\code\pythonProject\ve
nv\include -IC:\Users\Admin\AppData\Local\Programs\Python\Python39\include -IC:\Users\Admin\AppData\Local\Programs\Python\Python39\include -IC:\Program Files (x86)\Microsoft Visual Studio\2022\Buil
dTools\VC\Tools\MSVC\14.39.33519\include -IC:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Auxiliary\VS\include /Tcbuild\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.c /Fobuild\temp.win-amd64-3.9\Release\build\src.win-amd64-3.9\mistree\levy_flight\utility_random_walkmodule.obj" failed with exit status 2
INFO:
########### EXT COMPILER OPTIMIZATION ###########
INFO: Platform :
Architecture: x64
Compiler : msvc

CPU baseline :
Requested : 'min'
Enabled : none
Flags : none
Extra checks: none

CPU dispatch :
Requested : 'max -xop -fma4'
Enabled : none
Generated : none
INFO: CCompilerOpt.cache_flush[825] : write cache to path -> E:\LYF_data\code\pc-skeletor-main\mistree-master\build\temp.win-amd64-3.9\Release\ccompiler_opt_cache_ext.py
PS E:\LYF_data\code\pc-skeletor-main\mistree-master>

@pedrozamboni
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Hi, Im having the same issu during installation. Does somebody know how to fix?

@Lixiao-bai
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If you guys have problem when installing mistree or the pc-skeletor, please check the version of dgl in your virtual environment, try to change the dgl version to 1.1.2 ,maybe the problem will gone, though I do not know why, but it works on my windows11, ubuntu and macOS.

@unicorn186
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I installed an MSYS2 and configured it, and thenI installed a compiler by typing commands in the MSYS2 window

@wanghanruibaba
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Author

您好，感谢[meyerls]伟大的工作，我已经解决了出现的错误，初步实现了骨架效果，多问一句，是否后面继续更新point2skeleton.py以及L1.py，期待您的工作，祝福，感激

@lukasuz
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lukasuz commented Oct 10, 2024

The problem seems to be with the setup tools version and numpy see the issue here. I could fix it by downgrading, i.e. conda install "setuptools<74".

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@meyerls @lukasuz @albertpaolobugayong @pedrozamboni @Lixiao-bai @wanghanruibaba @unicorn186 @WS517 @yangfeng-Lyu