Installation error due to pybind11 #19

ghost · 2021-05-06T22:33:35Z

When installing oceanmesh personalized python library with pip install -U -e . in the oceanmeshmater directorym I get a long big thread of errors due to pybind11.
I already installed the requirements sudo apt install libcgal-dev python3-pybind11.

The log with the errors from the installation of oceanmesh with pip is bellow. Did you get the same kind of errors? How could I solve this?

Installing collected packages: oceanmesh
  Running setup.py develop for oceanmesh
    ERROR: Command errored out with exit status 1:
     command: /home/nuno/resources/miniconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/setup.py'"'"'; __file__='"'"'/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
         cwd: /home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/
    Complete output (107 lines):
    running develop
    running egg_info
    writing oceanmesh.egg-info/PKG-INFO
    writing dependency_links to oceanmesh.egg-info/dependency_links.txt
    writing requirements to oceanmesh.egg-info/requires.txt
    writing top-level names to oceanmesh.egg-info/top_level.txt
    reading manifest file 'oceanmesh.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'oceanmesh.egg-info/SOURCES.txt'
    running build_ext
    -- OS detected: Linux
    -- CXX Compiler detected: GNU
    -- CMake additional search path for libraries:
    -- Using header-only CGAL
    -- Targetting Unix Makefiles
    -- Using /usr/bin/c++ compiler.
    -- Boost version: 1.65.1
    -- Boost include dirs: /usr/include
    -- Boost libraries:
    -- Using gcc version 4 or later. Adding -frounding-math
    -- CGAL version: 5.00.0.100
    -- Build type: Release
    -- USING CXXFLAGS = '-DVERSION_INFO=\"0.0.1\" -O3 -DNDEBUG'
    -- USING EXEFLAGS = ' '
    -- Requested component: MPFR
    -- Requested component: GMP
    -- Found pybind11 v2.0.1: /usr/include;/home/nuno/resources/miniconda3/include/python3.8
    -- Configuring done
    -- Generating done
    -- Build files have been written to: /home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/build/temp.linux-x86_64-3.8
    [ 25%] Building CXX object CMakeFiles/fast_geometry.dir/oceanmesh/cpp/fast_geometry.cpp.o
    [ 50%] Building CXX object CMakeFiles/delaunay_class.dir/oceanmesh/cpp/delaunay_class.cpp.o
    /home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/oceanmesh/cpp/fast_geometry.cpp: In function ‘pybind11::array unique_edges(pybind11::array_t<int, 17>)’:
    /home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/oceanmesh/cpp/fast_geometry.cpp:76:23: error: no matching function for call to ‘pybind11::buffer_info::buffer_info(int*, long unsigned int, std::__cxx11::string, int, std::vector<long int>&, std::vector<long int>&)’
                           ));
                           ^
    In file included from /usr/include/pybind11/pytypes.h:12:0,
                     from /usr/include/pybind11/cast.h:13,
                     from /usr/include/pybind11/attr.h:13,
                     from /usr/include/pybind11/pybind11.h:36,
                     from /usr/include/pybind11/complex.h:12,
                     from /home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/oceanmesh/cpp/fast_geometry.cpp:2:
    /usr/include/pybind11/common.h:287:5: note: candidate: pybind11::buffer_info::buffer_info(pybind11::buffer_info&&)
         buffer_info(buffer_info &&other) {
         ^~~~~~~~~~~
    /usr/include/pybind11/common.h:287:5: note:   candidate expects 1 argument, 6 provided
    /usr/include/pybind11/common.h:274:14: note: candidate: pybind11::buffer_info::buffer_info(Py_buffer*, bool)
         explicit buffer_info(Py_buffer *view, bool ownview = true)
                  ^~~~~~~~~~~
    /usr/include/pybind11/common.h:274:14: note:   candidate expects 2 arguments, 6 provided
    /usr/include/pybind11/common.h:270:5: note: candidate: pybind11::buffer_info::buffer_info(void*, pybind11::size_t, const string&, pybind11::size_t)
         buffer_info(void *ptr, size_t itemsize, const std::string &format, size_t size)
         ^~~~~~~~~~~
    /usr/include/pybind11/common.h:270:5: note:   candidate expects 4 arguments, 6 provided
    /usr/include/pybind11/common.h:262:5: note: candidate: pybind11::buffer_info::buffer_info(void*, pybind11::size_t, const string&, pybind11::size_t, const std::vector<long unsigned int>&, const std::vector<long unsigned int>&)
         buffer_info(void *ptr, size_t itemsize, const std::string &format, size_t ndim,
         ^~~~~~~~~~~
    /usr/include/pybind11/common.h:262:5: note:   no known conversion for argument 5 from ‘std::vector<long int>’ to ‘const std::vector<long unsigned int>&’
    /usr/include/pybind11/common.h:260:5: note: candidate: pybind11::buffer_info::buffer_info()
         buffer_info() { }
         ^~~~~~~~~~~
    /usr/include/pybind11/common.h:260:5: note:   candidate expects 0 arguments, 6 provided
    /home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/oceanmesh/cpp/fast_geometry.cpp: At global scope:
    /home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/oceanmesh/cpp/fast_geometry.cpp:79:16: error: expected constructor, destructor, or type conversion before ‘(’ token
     PYBIND11_MODULE(fast_geometry, m) {
                    ^
    CMakeFiles/fast_geometry.dir/build.make:62: recipe for target 'CMakeFiles/fast_geometry.dir/oceanmesh/cpp/fast_geometry.cpp.o' failed
    make[2]: *** [CMakeFiles/fast_geometry.dir/oceanmesh/cpp/fast_geometry.cpp.o] Error 1
    CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/fast_geometry.dir/all' failed
    make[1]: *** [CMakeFiles/fast_geometry.dir/all] Error 2
    make[1]: *** Waiting for unfinished jobs....
    /home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/oceanmesh/cpp/delaunay_class.cpp:66:16: error: expected constructor, destructor, or type conversion before ‘(’ token
     PYBIND11_MODULE(delaunay_class, m) {
                    ^
    CMakeFiles/delaunay_class.dir/build.make:62: recipe for target 'CMakeFiles/delaunay_class.dir/oceanmesh/cpp/delaunay_class.cpp.o' failed
    make[2]: *** [CMakeFiles/delaunay_class.dir/oceanmesh/cpp/delaunay_class.cpp.o] Error 1
    CMakeFiles/Makefile2:104: recipe for target 'CMakeFiles/delaunay_class.dir/all' failed
    make[1]: *** [CMakeFiles/delaunay_class.dir/all] Error 2
    Makefile:83: recipe for target 'all' failed
    make: *** [all] Error 2
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/setup.py", line 81, in <module>
        setup(
      File "/home/nuno/resources/miniconda3/lib/python3.8/site-packages/setuptools/__init__.py", line 153, in setup
        return distutils.core.setup(**attrs)
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/home/nuno/resources/miniconda3/lib/python3.8/site-packages/setuptools/command/develop.py", line 34, in run
        self.install_for_development()
      File "/home/nuno/resources/miniconda3/lib/python3.8/site-packages/setuptools/command/develop.py", line 136, in install_for_development
        self.run_command('build_ext')
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/setup.py", line 44, in run
        self.build_extension(ext)
      File "/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/setup.py", line 76, in build_extension
        subprocess.check_call(
      File "/home/nuno/resources/miniconda3/lib/python3.8/subprocess.py", line 364, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '--build', '.', '--config', 'Release', '--', '-j2']' returned non-zero exit status 2.
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/nuno/resources/miniconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/setup.py'"'"'; __file__='"'"'/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-master/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.

The text was updated successfully, but these errors were encountered:

krober10nd · 2021-05-06T22:45:31Z

Hey @nunormont probably you need to use a newer C++ compiler. What version of C++ did you use?

I don't actively develop this code here at the currently due to other projects but I can of course help out if you want to achieve a particular goal.

ghost · 2021-05-06T23:09:36Z

So here are my versions of cpp and g++ (the compiler is g++ isn't it?)

cpp (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

g++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I have to update g++ and cpp? I use the Ubuntu 18.04 OS by the way.

krober10nd · 2021-05-06T23:19:28Z

Looks like you're using

    -- Using /usr/bin/c++ compiler.
    -- Using gcc version 4 or later. Adding -frounding-math

I would set the CXX variable to point to your C++ compiler that supports std14

ghost · 2021-05-06T23:25:41Z

Sorry if I'm not understanding, but the CXX variable is defined in ~/.bashrc or in other specific CMake of oceanmesh?

krober10nd · 2021-05-06T23:35:44Z

It's alright,

export CXX=/path/to/cpp/compiler

ghost · 2021-05-06T23:40:55Z

Yes I actually did that and I sourced the bashrc. In my case I did this: export CXX=/usr/bin/g++ but got the same error. I also tried export CXX=/usr/bin/cpp but it didn't solve the problem either. Before that, I updated the CPP compiler from g++-7 to g++-8, with the methodology here: https://www.bojankomazec.com/2020/03/upgrading-gnu-cc-compilers-on-ubuntu.html.

krober10nd · 2021-05-07T00:47:54Z

Hmm I'll have to take a closer look then tomorrow when I have a chance. Maybe something changed in the new pybind11

ghost · 2021-05-07T10:38:09Z

Thank you, I'll also try to dive deep into that.

krober10nd · 2021-05-08T03:22:45Z

Okay could you try to uninstall the apt-get version of pybind11 and try to use pip install pybind11 -U instead? It seems this is a common problem with installations of pybind11 by searching the error message:

 error: expected constructor, destructor, or type conversion before ‘(’ token

ghost · 2021-05-11T10:14:09Z

I uninstalled and purged python3-pybind11 and did pip install pybind11 -U as you instructed, and I still get errors:
(...)

Installing collected packages: oceanmesh
  Running setup.py develop for oceanmesh
    ERROR: Command errored out with exit status 1:
     command: /home/nuno/resources/miniconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/setup.py'"'"'; __file__='"'"'/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
         cwd: /home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/
    Complete output (77 lines):
    running develop
    running egg_info
    writing oceanmesh.egg-info/PKG-INFO
    writing dependency_links to oceanmesh.egg-info/dependency_links.txt
    writing requirements to oceanmesh.egg-info/requires.txt
    writing top-level names to oceanmesh.egg-info/top_level.txt
    reading manifest file 'oceanmesh.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    writing manifest file 'oceanmesh.egg-info/SOURCES.txt'
    running build_ext
    -- OS detected: Linux
    -- CXX Compiler detected: GNU
    -- CMake additional search path for libraries:
    -- Using header-only CGAL
    -- Targetting Unix Makefiles
    -- Using /usr/bin/c++ compiler.
    -- Boost version: 1.65.1
    -- Boost include dirs: /usr/include
    -- Boost libraries:
    -- Using gcc version 4 or later. Adding -frounding-math
    -- CGAL version: 5.00.0.100
    -- Build type: Release
    -- USING CXXFLAGS = ' -O3 -DNDEBUG'
    -- USING EXEFLAGS = ' '
    -- Requested component: MPFR
    -- Requested component: GMP
    CMake Warning at CMakeLists.txt:31 (find_package):
      By not providing "Findpybind11.cmake" in CMAKE_MODULE_PATH this project has
      asked CMake to find a package configuration file provided by "pybind11",
      but CMake did not find one.
    
      Could not find a package configuration file provided by "pybind11" with any
      of the following names:
    
        pybind11Config.cmake
        pybind11-config.cmake
    
      Add the installation prefix of "pybind11" to CMAKE_PREFIX_PATH or set
      "pybind11_DIR" to a directory containing one of the above files.  If
      "pybind11" provides a separate development package or SDK, be sure it has
      been installed.
    
    
    -- Found pybind11 v:
    CMake Error at CMakeLists.txt:35 (pybind11_add_module):
      Unknown CMake command "pybind11_add_module".
    
    
    -- Configuring incomplete, errors occurred!
    See also "/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/CMakeFiles/CMakeOutput.log".
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/setup.py", line 78, in <module>
        setup(
      File "/home/nuno/resources/miniconda3/lib/python3.8/site-packages/setuptools/__init__.py", line 153, in setup
        return distutils.core.setup(**attrs)
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/home/nuno/resources/miniconda3/lib/python3.8/site-packages/setuptools/command/develop.py", line 34, in run
        self.install_for_development()
      File "/home/nuno/resources/miniconda3/lib/python3.8/site-packages/setuptools/command/develop.py", line 136, in install_for_development
        self.run_command('build_ext')
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/home/nuno/resources/miniconda3/lib/python3.8/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/setup.py", line 42, in run
        self.build_extension(ext)
      File "/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/setup.py", line 71, in build_extension
        subprocess.check_call(
      File "/home/nuno/resources/miniconda3/lib/python3.8/subprocess.py", line 364, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['cmake', '/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/oceanmesh/cpp', '-DPYTHON_EXECUTABLE=/home/nuno/resources/miniconda3/bin/python', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/nuno/resources/miniconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/setup.py'"'"'; __file__='"'"'/home/nuno/universidade/tese/unst_grid_generation/oceanmesh-python/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.

krober10nd · 2021-05-11T12:40:07Z

Sorry, not sure, I don't have Ubuntu. Maybe build then pybind11 by source.

My other package uses the same build system and this is what one user recommended.

krober10nd/SeismicMesh#161

ghost · 2021-05-12T00:22:48Z

I solved my problem with those links. Thanks!

ghost closed this as completed May 12, 2021

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Installation error due to pybind11 #19

Installation error due to pybind11 #19

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Installation error due to pybind11 #19

Installation error due to pybind11 #19

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