Bug 2232463 - h5py: FTBFS in Fedora 39
Summary: h5py: FTBFS in Fedora 39
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: h5py
Version: 39
Hardware: Unspecified
OS: Linux
unspecified
medium
Target Milestone: ---
Assignee: Terje Røsten
QA Contact: Fedora Extras Quality Assurance
URL: https://koschei.fedoraproject.org/pac...
Whiteboard:
Depends On:
Blocks:
TreeView+ depends on / blocked
 
Reported: 2023-08-17 03:12 UTC by Orion Poplawski
Modified: 2023-11-07 01:39 UTC (History)
3 users (show)

Fixed In Version: h5py-3.10.0-1.fc39
Clone Of:
Environment:
Last Closed: 2023-11-07 01:39:10 UTC
Type: ---
Embargoed:


Attachments (Terms of Use)

Description Orion Poplawski 2023-08-17 03:12:53 UTC
Error compiling Cython file:
------------------------------------------------------------
...
    # First, extract the major & minor error codes from the top of the
    # stack, along with the top-level error description
    err.n = -1
    if H5Ewalk(<hid_t>H5E_DEFAULT, H5E_WALK_UPWARD, walk_cb, &err) < 0:
                                                    ^
------------------------------------------------------------
h5py/_errors.pyx:123:52: Cannot assign type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil' to 'H5E_walk_t'
Error compiling Cython file:
------------------------------------------------------------
...
    # Second, retrieve the bottom-most error description for additional info
    err.n = -1
    if H5Ewalk(<hid_t>H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_cb, &err) < 0:
                                                      ^
------------------------------------------------------------
h5py/_errors.pyx:140:54: Cannot assign type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil' to 'H5E_walk_t'
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, 1)
        MPI Enabled: False
   ROS3 VFD Enabled: False
 DIRECT VFD Enabled: False
   Rebuild Required: True
     MS-MPI Enabled: False
MS-MPI include dirs: []
MS-MPI library dirs: []
********************************************************************************
Updated /builddir/build/BUILD/h5py-3.8.0/serial/h5py/config.pxi
Executing cythonize()
[ 1/24] Cythonizing /builddir/build/BUILD/h5py-3.8.0/serial/h5py/_conv.pyx
[ 2/24] Cythonizing /builddir/build/BUILD/h5py-3.8.0/serial/h5py/_errors.pyx
Traceback (most recent call last):
  File "/builddir/build/BUILD/h5py-3.8.0/serial/setup.py", line 68, in <module>
    setup(
  File "/usr/lib/python3.12/site-packages/setuptools/__init__.py", line 107, in setup
    return distutils.core.setup(**attrs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 185, in setup
    return run_commands(dist)
           ^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
    dist.run_commands()
  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python3.12/site-packages/setuptools/dist.py", line 1244, in run_command
    super().run_command(command)
  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/command/build.py", line 131, in run
    self.run_command(cmd_name)
  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python3.12/site-packages/setuptools/dist.py", line 1244, in run_command
    super().run_command(command)
  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/builddir/build/BUILD/h5py-3.8.0/serial/setup_build.py", line 171, in run
    self.extensions = cythonize(self._make_extensions(config),
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib64/python3.12/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
    cythonize_one(*args)
  File "/usr/lib64/python3.12/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
    raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: /builddir/build/BUILD/h5py-3.8.0/serial/h5py/_errors.pyx


Reproducible: Always

Comment 1 Fedora Update System 2023-10-29 12:14:44 UTC
FEDORA-2023-d5a7283d1c has been submitted as an update to Fedora 39. https://bodhi.fedoraproject.org/updates/FEDORA-2023-d5a7283d1c

Comment 2 Fedora Update System 2023-10-30 01:47:09 UTC
FEDORA-2023-d5a7283d1c has been pushed to the Fedora 39 testing repository.
Soon you'll be able to install the update with the following command:
`sudo dnf upgrade --enablerepo=updates-testing --refresh --advisory=FEDORA-2023-d5a7283d1c`
You can provide feedback for this update here: https://bodhi.fedoraproject.org/updates/FEDORA-2023-d5a7283d1c

See also https://fedoraproject.org/wiki/QA:Updates_Testing for more information on how to test updates.

Comment 3 Fedora Update System 2023-11-07 01:39:10 UTC
FEDORA-2023-d5a7283d1c has been pushed to the Fedora 39 stable repository.
If problem still persists, please make note of it in this bug report.


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