pyarrow breaks the install.py using python3.9

[shyamalschandra]

What should I do? Is there some timeline for a diff and patch?

[shyamalschandra]

root@77d2c138cf98:/home/shyamal/deepdrive# python3.9 -m pip install -r requirements.txt 
Collecting scipy
  Using cached scipy-1.5.4-cp39-cp39-manylinux1_x86_64.whl (25.8 MB)
Requirement already satisfied: numpy in /usr/local/lib/python3.9/dist-packages (from -r requirements.txt (line 2)) (1.19.4)
Collecting h5py
  Using cached h5py-3.1.0-cp39-cp39-manylinux1_x86_64.whl (4.4 MB)
Collecting gym
  Using cached gym-0.17.3.tar.gz (1.6 MB)
Collecting arrow
  Using cached arrow-0.17.0-py2.py3-none-any.whl (50 kB)
Requirement already satisfied: pytest-xdist in /usr/local/lib/python3.9/dist-packages (from -r requirements.txt (line 6)) (2.1.0)
Collecting requests
  Using cached requests-2.24.0-py2.py3-none-any.whl (61 kB)
Collecting clint
  Using cached clint-0.5.1.tar.gz (29 kB)
Requirement already satisfied: Pillow in /usr/lib/python3/dist-packages (from -r requirements.txt (line 9)) (3.1.2)
Collecting boto
  Using cached boto-2.49.0-py2.py3-none-any.whl (1.4 MB)
Collecting future
  Using cached future-0.18.2.tar.gz (829 kB)
Collecting pyzmq
  Using cached pyzmq-19.0.2-cp39-cp39-manylinux1_x86_64.whl (1.1 MB)
Collecting gputil
  Using cached GPUtil-1.4.0.tar.gz (5.5 kB)
Collecting joblib
  Using cached joblib-0.17.0-py3-none-any.whl (301 kB)
Collecting cloudpickle
  Using cached cloudpickle-1.6.0-py3-none-any.whl (23 kB)
Collecting pyarrow
  Using cached pyarrow-1.0.1.tar.gz (1.3 MB)
  Installing build dependencies ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3.9 /usr/local/lib/python3.9/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-888juo_9/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'cython >= 0.29' 'numpy==1.14.5; python_version<'"'"'3.7'"'"'' 'numpy==1.16.0; python_version>='"'"'3.7'"'"'' setuptools setuptools_scm wheel
       cwd: None
  Complete output (710 lines):
  Ignoring numpy: markers 'python_version < "3.7"' don't match your environment
  Collecting cython>=0.29
    Using cached Cython-0.29.21-cp39-cp39-manylinux1_x86_64.whl (1.9 MB)
  Collecting numpy==1.16.0
    Using cached numpy-1.16.0.zip (5.1 MB)
  Collecting setuptools
    Using cached setuptools-50.3.2-py3-none-any.whl (785 kB)
  Collecting setuptools_scm
    Using cached setuptools_scm-4.1.2-py2.py3-none-any.whl (27 kB)
  Collecting wheel
    Using cached wheel-0.35.1-py2.py3-none-any.whl (33 kB)
  Building wheels for collected packages: numpy
    Building wheel for numpy (setup.py): started
    Building wheel for numpy (setup.py): finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-sl6959pr
         cwd: /tmp/pip-install-ma35s7ou/numpy/
    Complete output (336 lines):
    Running from numpy source directory.
    /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/misc_util.py:476: SyntaxWarning: "is" with a literal. Did you mean "=="?
      return is_string(s) and ('*' in s or '?' is s)
    /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'python_requires'
      warnings.warn(msg)
    blas_opt_info:
    blas_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    blis_info:
    customize UnixCCompiler
      libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    openblas_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_3_10_blas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries tatlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_3_10_blas_info:
    customize UnixCCompiler
      libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_blas_info:
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    accelerate_info:
      NOT AVAILABLE
  
    /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Atlas (http://math-atlas.sourceforge.net/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [atlas]) or by setting
        the ATLAS environment variable.
      self.calc_info()
    blas_info:
    customize UnixCCompiler
      libraries blas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Blas (http://www.netlib.org/blas/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [blas]) or by setting
        the BLAS environment variable.
      self.calc_info()
    blas_src_info:
      NOT AVAILABLE
  
    /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Blas (http://www.netlib.org/blas/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [blas_src]) or by setting
        the BLAS_SRC environment variable.
      self.calc_info()
      NOT AVAILABLE
  
    /bin/sh: 1: svnversion: not found
    non-existing path in 'numpy/distutils': 'site.cfg'
    lapack_opt_info:
    lapack_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    openblas_lapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    openblas_clapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE
  
    atlas_3_10_info:
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE
  
    atlas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE
  
    atlas_info:
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE
  
    lapack_info:
    customize UnixCCompiler
      libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
  
    /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Lapack (http://www.netlib.org/lapack/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [lapack]) or by setting
        the LAPACK environment variable.
      self.calc_info()
    lapack_src_info:
      NOT AVAILABLE
  
    /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
        Lapack (http://www.netlib.org/lapack/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [lapack_src]) or by setting
        the LAPACK_SRC environment variable.
      self.calc_info()
      NOT AVAILABLE
  
    /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'python_requires'
      warnings.warn(msg)
    /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
      warnings.warn(msg)
    running bdist_wheel
    running build
    running config_cc
    unifing config_cc, config, build_clib, build_ext, build commands --compiler options
    running config_fc
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
    running build_src
    build_src
    building py_modules sources
    creating build
    creating build/src.linux-x86_64-3.9
    creating build/src.linux-x86_64-3.9/numpy
    creating build/src.linux-x86_64-3.9/numpy/distutils
    building library "npymath" sources
    get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
    customize Gnu95FCompiler
    Could not locate executable gfortran
    Could not locate executable f95
    customize IntelFCompiler
    Could not locate executable ifort
    Could not locate executable ifc
    customize LaheyFCompiler
    Could not locate executable lf95
    customize PGroupFCompiler
    Could not locate executable pgfortran
    customize AbsoftFCompiler
    Could not locate executable f90
    Could not locate executable f77
    customize NAGFCompiler
    customize VastFCompiler
    customize CompaqFCompiler
    Could not locate executable fort
    customize IntelItaniumFCompiler
    Could not locate executable efort
    Could not locate executable efc
    customize IntelEM64TFCompiler
    customize GnuFCompiler
    Could not locate executable g77
    customize G95FCompiler
    Could not locate executable g95
    customize PathScaleFCompiler
    Could not locate executable pathf95
    customize NAGFORCompiler
    Could not locate executable nagfor
    don't know how to compile Fortran code on platform 'posix'
    C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
  
    compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.9 -c'
    x86_64-linux-gnu-gcc: _configtest.c
    x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
    success!
    removing: _configtest.c _configtest.o _configtest.o.d _configtest
    C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
  
    compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.9 -c'
    x86_64-linux-gnu-gcc: _configtest.c
    _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
     int exp (void);
         ^
    x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
    _configtest.o: In function `main':
    /tmp/pip-install-ma35s7ou/numpy/_configtest.c:6: undefined reference to `exp'
    collect2: error: ld returned 1 exit status
    failure.
    removing: _configtest.c _configtest.o _configtest.o.d
    C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
  
    compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.9 -c'
    x86_64-linux-gnu-gcc: _configtest.c
    _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
     int exp (void);
         ^
    x86_64-linux-gnu-gcc -pthread _configtest.o -lm -o _configtest
    success!
    removing: _configtest.c _configtest.o _configtest.o.d _configtest
    creating build/src.linux-x86_64-3.9/numpy/core
    creating build/src.linux-x86_64-3.9/numpy/core/src
    creating build/src.linux-x86_64-3.9/numpy/core/src/npymath
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h
      adding 'build/src.linux-x86_64-3.9/numpy/core/src/npymath' to include_dirs.
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npymath/ieee754.c
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_complex.c
    None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h']
    building library "npysort" sources
    creating build/src.linux-x86_64-3.9/numpy/core/src/common
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/common/npy_sort.h
      adding 'build/src.linux-x86_64-3.9/numpy/core/src/common' to include_dirs.
    creating build/src.linux-x86_64-3.9/numpy/core/src/npysort
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/quicksort.c
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/mergesort.c
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/heapsort.c
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/common/npy_partition.h
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/selection.c
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/common/npy_binsearch.h
    conv_template:> build/src.linux-x86_64-3.9/numpy/core/src/npysort/binsearch.c
    None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/common/npy_sort.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_partition.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_binsearch.h']
    building extension "numpy.core._dummy" sources
    Generating build/src.linux-x86_64-3.9/numpy/core/include/numpy/config.h
    C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
  
    compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.9 -c'
    x86_64-linux-gnu-gcc: _configtest.c
    _configtest.c:1:20: fatal error: Python.h: No such file or directory
    compilation terminated.
    failure.
    removing: _configtest.c _configtest.o
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-ma35s7ou/numpy/setup.py", line 415, in <module>
        setup_package()
      File "/tmp/pip-install-ma35s7ou/numpy/setup.py", line 407, in setup_package
        setup(**metadata)
      File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/core.py", line 171, in setup
        return old_setup(**new_attr)
      File "/usr/lib/python3.9/distutils/core.py", line 148, in setup
        dist.run_commands()
      File "/usr/lib/python3.9/distutils/dist.py", line 966, in run_commands
        self.run_command(cmd)
      File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/usr/lib/python3/dist-packages/wheel/bdist_wheel.py", line 179, in run
        self.run_command('build')
      File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build.py", line 47, in run
        old_build.run(self)
      File "/usr/lib/python3.9/distutils/command/build.py", line 135, in run
        self.run_command(cmd_name)
      File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
        self.distribution.run_command(command)
      File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
        cmd_obj.run()
      File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 148, in run
        self.build_sources()
      File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 165, in build_sources
        self.build_extension_sources(ext)
      File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 322, in build_extension_sources
        sources = self.generate_sources(sources, ext)
      File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 375, in generate_sources
        source = func(extension, build_dir)
      File "numpy/core/setup.py", line 423, in generate_config_h
        moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
      File "numpy/core/setup.py", line 47, in check_types
        out = check_types(*a, **kw)
      File "numpy/core/setup.py", line 279, in check_types
        raise SystemError(
    SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
    ----------------------------------------
    ERROR: Failed building wheel for numpy
    Running setup.py clean for numpy
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
         cwd: /tmp/pip-install-ma35s7ou/numpy
    Complete output (10 lines):
    Running from numpy source directory.
  
    `setup.py clean` is not supported, use one of the following instead:
  
      - `git clean -xdf` (cleans all files)
      - `git clean -Xdf` (cleans all versioned files, doesn't touch
                          files that aren't checked into the git repo)
  
    Add `--force` to your command to use it anyway if you must (unsupported).
  
    ----------------------------------------
    ERROR: Failed cleaning build dir for numpy
  Failed to build numpy
  Installing collected packages: cython, numpy, setuptools, setuptools-scm, wheel
      Running setup.py install for numpy: started
      Running setup.py install for numpy: finished with status 'error'
      ERROR: Command errored out with exit status 1:
       command: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-40loq39b/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-888juo_9/overlay --compile --install-headers /tmp/pip-build-env-888juo_9/overlay/include/python3.9/numpy
           cwd: /tmp/pip-install-ma35s7ou/numpy/
      Complete output (327 lines):
      Running from numpy source directory.
  
      Note: if you need reliable uninstall behavior, then install
      with pip instead of using `setup.py install`:
  
        - `pip install .`       (from a git repo or downloaded source
                                 release)
        - `pip install numpy`   (last NumPy release on PyPi)
  
  
      /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'python_requires'
        warnings.warn(msg)
      blas_opt_info:
      blas_mkl_info:
      customize UnixCCompiler
        libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      blis_info:
      customize UnixCCompiler
        libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      openblas_info:
      customize UnixCCompiler
      customize UnixCCompiler
        libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      atlas_3_10_blas_threads_info:
      Setting PTATLAS=ATLAS
      customize UnixCCompiler
        libraries tatlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      atlas_3_10_blas_info:
      customize UnixCCompiler
        libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      atlas_blas_threads_info:
      Setting PTATLAS=ATLAS
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      atlas_blas_info:
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      accelerate_info:
        NOT AVAILABLE
  
      /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
          Atlas (http://math-atlas.sourceforge.net/) libraries not found.
          Directories to search for the libraries can be specified in the
          numpy/distutils/site.cfg file (section [atlas]) or by setting
          the ATLAS environment variable.
        self.calc_info()
      blas_info:
      customize UnixCCompiler
        libraries blas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
          Blas (http://www.netlib.org/blas/) libraries not found.
          Directories to search for the libraries can be specified in the
          numpy/distutils/site.cfg file (section [blas]) or by setting
          the BLAS environment variable.
        self.calc_info()
      blas_src_info:
        NOT AVAILABLE
  
      /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
          Blas (http://www.netlib.org/blas/) sources not found.
          Directories to search for the sources can be specified in the
          numpy/distutils/site.cfg file (section [blas_src]) or by setting
          the BLAS_SRC environment variable.
        self.calc_info()
        NOT AVAILABLE
  
      /bin/sh: 1: svnversion: not found
      non-existing path in 'numpy/distutils': 'site.cfg'
      lapack_opt_info:
      lapack_mkl_info:
      customize UnixCCompiler
        libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      openblas_lapack_info:
      customize UnixCCompiler
      customize UnixCCompiler
        libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      openblas_clapack_info:
      customize UnixCCompiler
      customize UnixCCompiler
        libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      atlas_3_10_threads_info:
      Setting PTATLAS=ATLAS
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries tatlas,tatlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries tatlas,tatlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
      customize UnixCCompiler
        libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
      <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
        NOT AVAILABLE
  
      atlas_3_10_info:
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries satlas,satlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries satlas,satlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
      customize UnixCCompiler
        libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
      <class 'numpy.distutils.system_info.atlas_3_10_info'>
        NOT AVAILABLE
  
      atlas_threads_info:
      Setting PTATLAS=ATLAS
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
      <class 'numpy.distutils.system_info.atlas_threads_info'>
        NOT AVAILABLE
  
      atlas_info:
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
      <class 'numpy.distutils.system_info.atlas_info'>
        NOT AVAILABLE
  
      lapack_info:
      customize UnixCCompiler
        libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
        NOT AVAILABLE
  
      /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
          Lapack (http://www.netlib.org/lapack/) libraries not found.
          Directories to search for the libraries can be specified in the
          numpy/distutils/site.cfg file (section [lapack]) or by setting
          the LAPACK environment variable.
        self.calc_info()
      lapack_src_info:
        NOT AVAILABLE
  
      /tmp/pip-install-ma35s7ou/numpy/numpy/distutils/system_info.py:625: UserWarning:
          Lapack (http://www.netlib.org/lapack/) sources not found.
          Directories to search for the sources can be specified in the
          numpy/distutils/site.cfg file (section [lapack_src]) or by setting
          the LAPACK_SRC environment variable.
        self.calc_info()
        NOT AVAILABLE
  
      /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'python_requires'
        warnings.warn(msg)
      /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
        warnings.warn(msg)
      running install
      running build
      running config_cc
      unifing config_cc, config, build_clib, build_ext, build commands --compiler options
      running config_fc
      unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
      running build_src
      build_src
      building py_modules sources
      building library "npymath" sources
      get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']'
      customize Gnu95FCompiler
      Could not locate executable gfortran
      Could not locate executable f95
      customize IntelFCompiler
      Could not locate executable ifort
      Could not locate executable ifc
      customize LaheyFCompiler
      Could not locate executable lf95
      customize PGroupFCompiler
      Could not locate executable pgfortran
      customize AbsoftFCompiler
      Could not locate executable f90
      Could not locate executable f77
      customize NAGFCompiler
      customize VastFCompiler
      customize CompaqFCompiler
      Could not locate executable fort
      customize IntelItaniumFCompiler
      Could not locate executable efort
      Could not locate executable efc
      customize IntelEM64TFCompiler
      customize GnuFCompiler
      Could not locate executable g77
      customize G95FCompiler
      Could not locate executable g95
      customize PathScaleFCompiler
      Could not locate executable pathf95
      customize NAGFORCompiler
      Could not locate executable nagfor
      don't know how to compile Fortran code on platform 'posix'
      C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
  
      compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.9 -c'
      x86_64-linux-gnu-gcc: _configtest.c
      x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
      success!
      removing: _configtest.c _configtest.o _configtest.o.d _configtest
      C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
  
      compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.9 -c'
      x86_64-linux-gnu-gcc: _configtest.c
      _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
       int exp (void);
           ^
      x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest
      _configtest.o: In function `main':
      /tmp/pip-install-ma35s7ou/numpy/_configtest.c:6: undefined reference to `exp'
      collect2: error: ld returned 1 exit status
      failure.
      removing: _configtest.c _configtest.o _configtest.o.d
      C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
  
      compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.9 -c'
      x86_64-linux-gnu-gcc: _configtest.c
      _configtest.c:1:5: warning: conflicting types for built-in function ‘exp’
       int exp (void);
           ^
      x86_64-linux-gnu-gcc -pthread _configtest.o -lm -o _configtest
      success!
      removing: _configtest.c _configtest.o _configtest.o.d _configtest
        adding 'build/src.linux-x86_64-3.9/numpy/core/src/npymath' to include_dirs.
      None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/npymath/npy_math_internal.h']
      building library "npysort" sources
        adding 'build/src.linux-x86_64-3.9/numpy/core/src/common' to include_dirs.
      None - nothing done with h_files = ['build/src.linux-x86_64-3.9/numpy/core/src/common/npy_sort.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_partition.h', 'build/src.linux-x86_64-3.9/numpy/core/src/common/npy_binsearch.h']
      building extension "numpy.core._dummy" sources
      Generating build/src.linux-x86_64-3.9/numpy/core/include/numpy/config.h
      C compiler: x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
  
      compile options: '-Inumpy/core/src/common -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/usr/include/python3.9 -c'
      x86_64-linux-gnu-gcc: _configtest.c
      _configtest.c:1:20: fatal error: Python.h: No such file or directory
      compilation terminated.
      failure.
      removing: _configtest.c _configtest.o
      Traceback (most recent call last):
        File "<string>", line 1, in <module>
        File "/tmp/pip-install-ma35s7ou/numpy/setup.py", line 415, in <module>
          setup_package()
        File "/tmp/pip-install-ma35s7ou/numpy/setup.py", line 407, in setup_package
          setup(**metadata)
        File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/core.py", line 171, in setup
          return old_setup(**new_attr)
        File "/usr/lib/python3.9/distutils/core.py", line 148, in setup
          dist.run_commands()
        File "/usr/lib/python3.9/distutils/dist.py", line 966, in run_commands
          self.run_command(cmd)
        File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/install.py", line 62, in run
          r = self.setuptools_run()
        File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/install.py", line 36, in setuptools_run
          return distutils_install.run(self)
        File "/usr/lib/python3.9/distutils/command/install.py", line 590, in run
          self.run_command('build')
        File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build.py", line 47, in run
          old_build.run(self)
        File "/usr/lib/python3.9/distutils/command/build.py", line 135, in run
          self.run_command(cmd_name)
        File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
          self.distribution.run_command(command)
        File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
          cmd_obj.run()
        File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 148, in run
          self.build_sources()
        File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 165, in build_sources
          self.build_extension_sources(ext)
        File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 322, in build_extension_sources
          sources = self.generate_sources(sources, ext)
        File "/tmp/pip-install-ma35s7ou/numpy/numpy/distutils/command/build_src.py", line 375, in generate_sources
          source = func(extension, build_dir)
        File "numpy/core/setup.py", line 423, in generate_config_h
          moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
        File "numpy/core/setup.py", line 47, in check_types
          out = check_types(*a, **kw)
        File "numpy/core/setup.py", line 279, in check_types
          raise SystemError(
      SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
      ----------------------------------------
  ERROR: Command errored out with exit status 1: /usr/bin/python3.9 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-ma35s7ou/numpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-40loq39b/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-888juo_9/overlay --compile --install-headers /tmp/pip-build-env-888juo_9/overlay/include/python3.9/numpy Check the logs for full command output.
  ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3.9 /usr/local/lib/python3.9/dist-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-888juo_9/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'cython >= 0.29' 'numpy==1.14.5; python_version<'"'"'3.7'"'"'' 'numpy==1.16.0; python_version>='"'"'3.7'"'"'' setuptools setuptools_scm wheel Check the logs for full command output.

[Rookie-81]

i have the same issue

[rahulbhadani]

I have the same issue with python 3.8

[mfaccin]

same here. does anyone have a fix for it?