search

TuragaLab / malis

MALIS structured loss function for supervised learning of segmentation and clustering
MIT License
18 stars 13 forks source link

Issue in building #9

Open QianChris opened 3 years ago

QianChris commented 3 years ago

After 'pip install malis', see: malis/malis_cpp.cpp(4): fatal error C1083: Cannot open include file: 'boost/pending/disjoint_sets.hpp': No such file or directory

Haoxin22 commented 2 years ago

Hi Chris,

Have you solved it? I met the same issue as yours. Thanks!

After 'pip install malis', see: malis/malis_cpp.cpp(4): fatal error C1083: Cannot open include file: 'boost/pending/disjoint_sets.hpp': No such file or directory

liulianni1688 commented 2 years ago

Hello，I also encounter this problem: you can install boost c++ library (https://www.boost.org/), and then link the library with malis code.

dreamhasany commented 1 year ago

@liulianni1688 Hello,can you explain how to link the library with malis code

ysairaaj commented 1 year ago

Hello , I encountered this error too . I extracted the boost files and pasted it in C:\Program Files (x86)\Windows Kits\10\include\10.0.22000.0\winrt . This solved the "No such file or directory " problem . However , I got a new error

Collecting malis Using cached malis-1.0.tar.gz (7.0 kB) Preparing metadata (setup.py) ... done Requirement already satisfied: cython in d:\anaconda\lib\site-packages (from malis) (0.29.35) Requirement already satisfied: numpy in d:\anaconda\lib\site-packages (from malis) (1.23.5) Requirement already satisfied: h5py in d:\anaconda\lib\site-packages (from malis) (3.7.0) Requirement already satisfied: scipy in d:\anaconda\lib\site-packages (from malis) (1.10.0) Building wheels for collected packages: malis Building wheel for malis (setup.py) ... error error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [86 lines of output] running bdist_wheel running build running build_py creating build creating build\lib.win-amd64-cpython-310 creating build\lib.win-amd64-cpython-310\malis copying malis\setup.py -> build\lib.win-amd64-cpython-310\malis copying malis\test_malis.py -> build\lib.win-amd64-cpython-310\malis copying malis__init__.py -> build\lib.win-amd64-cpython-310\malis running build_ext cythoning malis/malis.pyx to malis\malis.cpp D:\anaconda\lib\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: C:\Users\hp\AppData\Local\Temp\pip-install-0445dqsf\malis_72140fde1c5b4c1fa11fface29426005\malis\malis.pyx tree = Parsing.p_module(s, pxd, full_module_name) building 'malis.malis' extension creating build\temp.win-amd64-cpython-310 creating build\temp.win-amd64-cpython-310\Release creating build\temp.win-amd64-cpython-310\Release\malis "C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.36.32532\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -IC:\Users\hp\AppData\Local\Temp\pip-install-0445dqsf\malis_72140fde1c5b4c1fa11fface29426005\malis -ID:\anaconda -ID:\anaconda\include -ID:\anaconda\include -ID:\anaconda\Include -ID:\anaconda\lib\site-packages\numpy\core\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" /EHsc /Tpmalis/malis_cpp.cpp /Fobuild\temp.win-amd64-cpython-310\Release\malis/malis_cpp.obj -std=c++11 -w cl : Command line warning D9025 : overriding '/W3' with '/w' cl : Command line warning D9002 : ignoring unknown option '-std=c++11' malis_cpp.cpp "C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.36.32532\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -IC:\Users\hp\AppData\Local\Temp\pip-install-0445dqsf\malis_72140fde1c5b4c1fa11fface29426005\malis -ID:\anaconda -ID:\anaconda\include -ID:\anaconda\include -ID:\anaconda\Include -ID:\anaconda\lib\site-packages\numpy\core\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" /EHsc /Tpmalis\malis.cpp /Fobuild\temp.win-amd64-cpython-310\Release\malis\malis.obj -std=c++11 -w cl : Command line warning D9025 : overriding '/W3' with '/w' cl : Command line warning D9002 : ignoring unknown option '-std=c++11' malis.cpp D:\anaconda\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 Traceback (most recent call last): File "", line 2, in File "", line 34, in File "C:\Users\hp\AppData\Local\Temp\pip-install-0445dqsf\malis_72140fde1c5b4c1fa11fface29426005\setup.py", line 30, in setup(name='malis', File "D:\anaconda\lib\site-packages\setuptools__init__.py", line 87, in setup return distutils.core.setup(*attrs) File "D:\anaconda\lib\site-packages\setuptools_distutils\core.py", line 185, in setup return run_commands(dist) File "D:\anaconda\lib\site-packages\setuptools_distutils\core.py", line 201, in run_commands dist.run_commands() File "D:\anaconda\lib\site-packages\setuptools_distutils\dist.py", line 969, in run_commands self.run_command(cmd) File "D:\anaconda\lib\site-packages\setuptools\dist.py", line 1208, in run_command super().run_command(command) File "D:\anaconda\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command cmd_obj.run() File "D:\anaconda\lib\site-packages\wheel\bdist_wheel.py", line 325, in run self.run_command("build") File "D:\anaconda\lib\site-packages\setuptools_distutils\cmd.py", line 318, in run_command self.distribution.run_command(command) File "D:\anaconda\lib\site-packages\setuptools\dist.py", line 1208, in run_command super().run_command(command) File "D:\anaconda\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command cmd_obj.run() File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build.py", line 132, in run self.run_command(cmd_name) File "D:\anaconda\lib\site-packages\setuptools_distutils\cmd.py", line 318, in run_command self.distribution.run_command(command) File "D:\anaconda\lib\site-packages\setuptools\dist.py", line 1208, in run_command super().run_command(command) File "D:\anaconda\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command cmd_obj.run() File "D:\anaconda\lib\site-packages\setuptools\command\build_ext.py", line 84, in run _build_ext.run(self) File "D:\anaconda\lib\site-packages\Cython\Distutils\old_build_ext.py", line 186, in run _build_ext.build_ext.run(self) File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build_ext.py", line 346, in run self.build_extensions() File "D:\anaconda\lib\site-packages\Cython\Distutils\old_build_ext.py", line 195, in build_extensions _build_ext.build_ext.build_extensions(self) File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build_ext.py", line 468, in build_extensions self._build_extensions_serial() File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build_ext.py", line 494, in _build_extensions_serial self.build_extension(ext) File "D:\anaconda\lib\site-packages\setuptools\command\build_ext.py", line 246, in build_extension _build_ext.build_extension(self, ext) File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build_ext.py", line 573, in build_extension self.compiler.link_shared_object( File "D:\anaconda\lib\site-packages\setuptools_distutils\ccompiler.py", line 751, in link_shared_object self.link( File "D:\anaconda\lib\site-packages\setuptools_distutils_msvccompiler.py", line 484, in link lib_opts = gen_lib_options(self, library_dirs, runtime_library_dirs, libraries) File "D:\anaconda\lib\site-packages\setuptools\msvc.py", line 230, in msvc14_gen_lib_options return get_unpatched(msvc14_gen_lib_options)(args, **kwargs) File "D:\anaconda\lib\site-packages\setuptools_distutils\ccompiler.py", line 1193, in gen_lib_options lib_opts.append(compiler.library_dir_option(dir)) File "D:\anaconda\lib\site-packages\setuptools_distutils_msvccompiler.py", line 555, in library_dir_option return "/LIBPATH:" + dir TypeError: can only concatenate str (not "NoneType") to str [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for malis Running setup.py clean for malis Failed to build malis Installing collected packages: malis Running setup.py install for malis ... error error: subprocess-exited-with-error

× Running setup.py install for malis did not run successfully. │ exit code: 1 ╰─> [88 lines of output] running install D:\anaconda\lib\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.win-amd64-cpython-310 creating build\lib.win-amd64-cpython-310\malis copying malis\setup.py -> build\lib.win-amd64-cpython-310\malis copying malis\test_malis.py -> build\lib.win-amd64-cpython-310\malis copying malis__init.py -> build\lib.win-amd64-cpython-310\malis running build_ext skipping 'malis\malis.cpp' Cython extension (up-to-date) building 'malis.malis' extension creating build\temp.win-amd64-cpython-310 creating build\temp.win-amd64-cpython-310\Release creating build\temp.win-amd64-cpython-310\Release\malis "C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.36.32532\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -IC:\Users\hp\AppData\Local\Temp\pip-install-0445dqsf\malis_72140fde1c5b4c1fa11fface29426005\malis -ID:\anaconda -ID:\anaconda\include -ID:\anaconda\include -ID:\anaconda\Include -ID:\anaconda\lib\site-packages\numpy\core\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" /EHsc /Tpmalis/malis_cpp.cpp /Fobuild\temp.win-amd64-cpython-310\Release\malis/malis_cpp.obj -std=c++11 -w cl : Command line warning D9025 : overriding '/W3' with '/w' cl : Command line warning D9002 : ignoring unknown option '-std=c++11' malis_cpp.cpp "C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.36.32532\bin\HostX86\x64\cl.exe" /c /nologo /O2 /W3 /GL /DNDEBUG /MD -IC:\Users\hp\AppData\Local\Temp\pip-install-0445dqsf\malis_72140fde1c5b4c1fa11fface29426005\malis -ID:\anaconda -ID:\anaconda\include -ID:\anaconda\include -ID:\anaconda\Include -ID:\anaconda\lib\site-packages\numpy\core\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" /EHsc /Tpmalis\malis.cpp /Fobuild\temp.win-amd64-cpython-310\Release\malis\malis.obj -std=c++11 -w cl : Command line warning D9025 : overriding '/W3' with '/w' cl : Command line warning D9002 : ignoring unknown option '-std=c++11' malis.cpp D:\anaconda\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 Traceback (most recent call last): File "", line 2, in File "", line 34, in File "C:\Users\hp\AppData\Local\Temp\pip-install-0445dqsf\malis_72140fde1c5b4c1fa11fface29426005\setup.py", line 30, in setup(name='malis', File "D:\anaconda\lib\site-packages\setuptools\init__.py", line 87, in setup return distutils.core.setup(*attrs) File "D:\anaconda\lib\site-packages\setuptools_distutils\core.py", line 185, in setup return run_commands(dist) File "D:\anaconda\lib\site-packages\setuptools_distutils\core.py", line 201, in run_commands dist.run_commands() File "D:\anaconda\lib\site-packages\setuptools_distutils\dist.py", line 969, in run_commands self.run_command(cmd) File "D:\anaconda\lib\site-packages\setuptools\dist.py", line 1208, in run_command super().run_command(command) File "D:\anaconda\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command cmd_obj.run() File "D:\anaconda\lib\site-packages\setuptools\command\install.py", line 68, in run return orig.install.run(self) File "D:\anaconda\lib\site-packages\setuptools_distutils\command\install.py", line 698, in run self.run_command('build') File "D:\anaconda\lib\site-packages\setuptools_distutils\cmd.py", line 318, in run_command self.distribution.run_command(command) File "D:\anaconda\lib\site-packages\setuptools\dist.py", line 1208, in run_command super().run_command(command) File "D:\anaconda\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command cmd_obj.run() File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build.py", line 132, in run self.run_command(cmd_name) File "D:\anaconda\lib\site-packages\setuptools_distutils\cmd.py", line 318, in run_command self.distribution.run_command(command) File "D:\anaconda\lib\site-packages\setuptools\dist.py", line 1208, in run_command super().run_command(command) File "D:\anaconda\lib\site-packages\setuptools_distutils\dist.py", line 988, in run_command cmd_obj.run() File "D:\anaconda\lib\site-packages\setuptools\command\build_ext.py", line 84, in run _build_ext.run(self) File "D:\anaconda\lib\site-packages\Cython\Distutils\old_build_ext.py", line 186, in run _build_ext.build_ext.run(self) File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build_ext.py", line 346, in run self.build_extensions() File "D:\anaconda\lib\site-packages\Cython\Distutils\old_build_ext.py", line 195, in build_extensions _build_ext.build_ext.build_extensions(self) File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build_ext.py", line 468, in build_extensions self._build_extensions_serial() File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build_ext.py", line 494, in _build_extensions_serial self.build_extension(ext) File "D:\anaconda\lib\site-packages\setuptools\command\build_ext.py", line 246, in build_extension _build_ext.build_extension(self, ext) File "D:\anaconda\lib\site-packages\setuptools_distutils\command\build_ext.py", line 573, in build_extension self.compiler.link_shared_object( File "D:\anaconda\lib\site-packages\setuptools_distutils\ccompiler.py", line 751, in link_shared_object self.link( File "D:\anaconda\lib\site-packages\setuptools_distutils_msvccompiler.py", line 484, in link lib_opts = gen_lib_options(self, library_dirs, runtime_library_dirs, libraries) File "D:\anaconda\lib\site-packages\setuptools\msvc.py", line 230, in msvc14_gen_lib_options return get_unpatched(msvc14_gen_lib_options)(args, **kwargs) File "D:\anaconda\lib\site-packages\setuptools_distutils\ccompiler.py", line 1193, in gen_lib_options lib_opts.append(compiler.library_dir_option(dir)) File "D:\anaconda\lib\site-packages\setuptools_distutils_msvccompiler.py", line 555, in library_dir_option return "/LIBPATH:" + dir TypeError: can only concatenate str (not "NoneType") to str [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. ╰─> malis

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure.

Please can anyone help me with this issue??