Skip to content

Unable to install h5py 3.4 #1955

@winash12

Description

@winash12

To assist reproducing bugs, please include the following:

  • Operating System (e.g. Windows 10, MacOS 10.11, Ubuntu 16.04.2 LTS, CentOS 7) Ubuntu 20.04 LTS
  • Python version (e.g. 2.7, 3.5) 3.8
  • Where Python was acquired (e.g. system Python on MacOS or Linux, Anaconda on
    Windows) system python
  • h5py version (e.g. 2.6) 3.4
  • HDF5 version (e.g. 1.8.17) 1.12.0
  • The full traceback/stack trace shown (if it appears)
    I am getting this error when I type python3.8 setup.py install
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

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions