running install
running bdist_egg
running egg_info
writing h5py.egg-info/PKG-INFO
writing dependency_links to h5py.egg-info/dependency_links.txt
writing requirements to h5py.egg-info/requires.txt
writing top-level names to h5py.egg-info/top_level.txt
reading manifest file 'h5py.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'AUTHORS'
no previously-included directories found matching 'docs/_build'
no previously-included directories found matching 'docs_api/_build'
warning: no previously-included files matching '.DS_Store' found under directory '*'
warning: no previously-included files found matching 'ci'
warning: no previously-included files found matching 'other'
warning: no previously-included files found matching '.github'
warning: no previously-included files matching '*' found under directory 'ci'
warning: no previously-included files matching '*' found under directory 'other'
warning: no previously-included files matching '*' found under directory '.github'
warning: no previously-included files found matching '*.yml'
warning: no previously-included files found matching '*.yaml'
warning: no previously-included files matching '__pycache__' found under directory '*'
warning: no previously-included files matching '*.py[co]' found under directory '*'
warning: no previously-included files found matching '.coveragerc'
warning: no previously-included files found matching '.coverage_dir'
warning: no previously-included files matching '*' found under directory '.coverage_dir'
warning: no previously-included files found matching '.mailmap'
warning: no previously-included files found matching 'github_deploy_key_h5py_h5py.enc'
warning: no previously-included files found matching 'rever.xsh'
no previously-included directories found matching 'news'
writing manifest file 'h5py.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
Loading library to get build settings and version: libhdf5.so
********************************************************************************
Summary of the h5py configuration
HDF5 include dirs: []
HDF5 library dirs: []
HDF5 Version: (1, 12, 0)
MPI Enabled: False
ROS3 VFD Enabled: False
Rebuild Required: True
********************************************************************************
Executing cythonize()
Traceback (most recent call last):
File "setup.py", line 156, in <module>
setup(
File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 144, in setup
return distutils.core.setup(**attrs)
File "/usr/lib/python3.8/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.8/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 67, in run
self.do_egg_install()
File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 109, in do_egg_install
self.run_command('bdist_egg')
File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 172, in run
cmd = self.call_command('install_lib', warn_dir=0)
File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 158, in call_command
self.run_command(cmdname)
File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/setuptools/command/install_lib.py", line 23, in run
self.build()
File "/usr/lib/python3.8/distutils/command/install_lib.py", line 109, in build
self.run_command('build_ext')
File "/usr/lib/python3.8/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.8/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/winash12/libPython/h5py-3.4.0/setup_build.py", line 170, in run
self.extensions = cythonize(self._make_extensions(config),
File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Build/Dependencies.py", line 963, in cythonize
ctx = c_options.create_context()
File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/Main.py", line 596, in create_context
return Context(self.include_path, self.compiler_directives,
File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/Main.py", line 80, in __init__
from . import Builtin, CythonScope
File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/CythonScope.py", line 5, in <module>
from .UtilityCode import CythonUtilityCode
File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/UtilityCode.py", line 3, in <module>
from .TreeFragment import parse_from_strings, StringParseContext
File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/TreeFragment.py", line 17, in <module>
from .Visitor import VisitorTransform
File "Cython/Compiler/Visitor.py", line 16, in init Cython.Compiler.Visitor
File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/Nodes.py", line 31, in <module>
from .Pythran import has_np_pythran, pythran_type, is_pythran_buffer
File "/usr/local/lib/python3.8/dist-packages/Cython-0.29.24-py3.8-linux-x86_64.egg/Cython/Compiler/Pythran.py", line 10, in <module>
import pythran
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/__init__.py", line 41, in <module>
from pythran.toolchain import (generate_cxx, compile_cxxfile, compile_cxxcode,
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/toolchain.py", line 6, in <module>
from pythran.backend import Cxx, Python
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/backend.py", line 7, in <module>
from pythran.analyses import LocalNodeDeclarations, GlobalDeclarations, Scope
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/analyses/__init__.py", line 12, in <module>
from .aliases import Aliases, StrictAliases
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/analyses/aliases.py", line 6, in <module>
from pythran.syntax import PythranSyntaxError
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/syntax.py", line 7, in <module>
from pythran.tables import MODULES
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/tables.py", line 4580, in <module>
save_arguments((), MODULES)
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/tables.py", line 4547, in save_arguments
save_arguments(module_name + (elem,), signature)
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/tables.py", line 4547, in save_arguments
save_arguments(module_name + (elem,), signature)
File "/usr/local/lib/python3.8/dist-packages/pythran-0.9.12.post1-py3.8.egg/pythran/tables.py", line 4551, in save_arguments
themodule = __import__(".".join(module_name))
File "/usr/local/lib/python3.8/dist-packages/scipy-1.7.1-py3.8-linux-x86_64.egg/scipy/special/__init__.py", line 643, in <module>
from . import _ufuncs
File "_ufuncs.pyx", line 1, in init scipy.special._ufuncs
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject
To assist reproducing bugs, please include the following:
Windows) system python
I am getting this error when I type python3.8 setup.py install