Processed: HDF 4.3.1 uploaded to unstable
Antonio Valentino
antonio.valentino at tiscali.it
Sat Aug 16 11:23:26 BST 2025
Dear Bas,
Il 10/08/25 16:44, Antonio Valentino ha scritto:
> Il 10/08/25 16:39, Sebastiaan Couwenberg ha scritto:
>> On 8/10/25 4:25 PM, Antonio Valentino wrote:
>>> Il 10/08/25 13:59, Debian Bug Tracking System ha scritto:
>>>> Processing control commands:
>>>>
>>>>> severity -1 serious
>>>> Bug #1108651 [src:python-hdf4] python-hdf4: FTBFS with HDF 4.3.1
>>>> Severity set to 'serious' from 'important'
>>>>
>>>
>>> Should we use a versioned dependency?
>>>
>>> libhdf4-dev (>= 4.3.1-1)
>>>
>>> ... or also the unversioned one is fine?
>>
>> The change I have ready uses an unversioned B-D, this requires waiting
>> for libhdf4 (4.3.1-1) package to built & installed on all (release)
>> architectures:
>>
>> https://buildd.debian.org/status/package.php?p=libhdf4
>>
>> If you don't want to wait, you need to use a versioned dependency
>> (without the debian revision):
>>
>> libhdf4-dev (>= 4.3.1)
>>
>> The changes I have ready have not been pushed to Salsa yet as those
>> will trigger CI failures as long as libhdf4 (4.3.1-1) is not installed
>> on amd64 & i386 yet.
>>
>> You don't have to worry about python-hdf4, I intent to upload gdal,
>> python-hdf4, and libpdl-io-hdf-perl once libhdf4 (4.3.1-1) is built &
>> installed everywhere.
>>
>> I may also do team uploads of the affected Debian Science packages
>> that are uptodate on Salsa, but I prefer Alastair doing those.
>>
>> Kind Regards,
>>
>> Bas
>>
>
> OK, thanks
>
I started having some HDF4 related failures when I build satpy locally.
Current thread 0x00007c4262336100 (most recent call first):
File "/usr/lib/python3/dist-packages/pyhdf/hdfext.py", line 348 in
SDendaccess
File "/usr/lib/python3/dist-packages/pyhdf/SD.py", line 1835 in endaccess
File "/usr/lib/python3/dist-packages/pyhdf/SD.py", line 1770 in __del__
File "/usr/lib/python3.13/unittest/case.py", line 603 in _callSetUp
File "/usr/lib/python3.13/unittest/case.py", line 647 in run
File "/usr/lib/python3.13/unittest/case.py", line 707 in __call__
File "/usr/lib/python3/dist-packages/_pytest/unittest.py", line 351
in runtest
Full log attached.
Strangely all the checks are green on the python-hdf4 tracker [1], so
I'm not totally sure that it is not something related to by environment,
although I'm using
$ git-pbuilder update
$ gbp buildpackage --git-pbuilder
Also in Debian CI [2] there seems to be some recent failure.
I still didn't have the time for a deep investigation (not sure I will
be able to do it soon).
I was just wondering how to proceed in this case.
Do you have the chance to confirm my findings?
Should I file an bug report against python-hdf4 (or maybe satpy)?
[1] https://tracker.debian.org/pkg/python-hdf4
[2] https://ci.debian.net/packages/s/satpy/unstable/amd64/
kind regards
--
Antonio Valentino
-------------- next part --------------
make[1]: Leaving directory '/build/satpy-0.55.0'
dh_auto_test -O--buildsystem=pybuild
I: pybuild base:311: cd /build/satpy-0.55.0/.pybuild/cpython3_3.13_satpy/build; python3.13 -m pytest -k "not test__slice and not test_init and not test_strip_invalid_lat and not test_retrieve and not test_offline_retrieve and not test_retrieve_all and not test_download_script and not test_basic_default_not_provided and not test_rayleigh_corrector and not test_rayleigh_with_angles and not test_median and not test_no_downloads_in_tests and not test_convert_remote_files_to_fsspec_fsfile and not test_convert_remote_files_to_fsspec_filename_dict and not test_convert_remote_files_to_fsspec_mixed_sources and not test_hvplot_basic_with_area and not test_hvplot_basic_with_swath and not test_hvplot_rgb_with_area and not test_loading_lon_lat and not test_loading_sensor_angles and not test_loading_solar_angles and not test_get_ti_lon_lats and not test_distributed and not test_correct_area_clearsky_different_resolutions and not test_available_reader and not test_find_registerable and not test_filenames_as_path and not test_no_parameters and not test_bad_sensor and not test_sensor and not test_sensor_no_files and not test_no_reader and not test_basic_check_satpy and not test_plugin_reader_available_readers and not test_filenames_only and not test_add_grid_mapping_oblique_mercator and not test_palettize and not test_viirs and not test_basic_default_provided and not test_scene_dynamic_available_datasets and not test_read_real_segment and not test_read_physical_seviri_nat_file" --ignore=satpy/tests/reader_tests/gms/test_gms5_vissr_l1b.py --ignore=satpy/tests/reader_tests/gms/test_gms5_vissr_navigation.py --ignore=satpy/tests/reader_tests/test_viirs_edr_active_fires.py --ignore=satpy/tests/reader_tests/test_mviri_l1b_fiduceo_nc.py satpy/tests
============================= test session starts ==============================
platform linux -- Python 3.13.6, pytest-8.4.1, pluggy-1.6.0
rootdir: /build/satpy-0.55.0/.pybuild/cpython3_3.13_satpy/build
configfile: pyproject.toml
plugins: remotedata-0.4.1, typeguard-4.4.2, mock-3.14.0, astropy-0.11.0, doctestplus-1.4.0, filter-subpackage-0.2.0, cov-5.0.0, astropy-header-0.2.2, arraydiff-0.6.1, hypothesis-6.138.0, lazy-fixtures-0.0.0
collected 2805 items / 274 deselected / 2531 selected
satpy/tests/cf_tests/test_area.py ......... [ 0%]
satpy/tests/cf_tests/test_attrs.py . [ 0%]
satpy/tests/cf_tests/test_coords.py ....... [ 0%]
satpy/tests/cf_tests/test_dataaarray.py .... [ 0%]
satpy/tests/cf_tests/test_datasets.py .... [ 0%]
satpy/tests/cf_tests/test_decoding.py .. [ 1%]
satpy/tests/cf_tests/test_encoding.py ... [ 1%]
satpy/tests/compositor_tests/test_abi.py .. [ 1%]
satpy/tests/compositor_tests/test_agri.py .. [ 1%]
satpy/tests/compositor_tests/test_ahi.py . [ 1%]
satpy/tests/compositor_tests/test_glm.py .. [ 1%]
satpy/tests/compositor_tests/test_lightning.py ... [ 1%]
satpy/tests/compositor_tests/test_sar.py .. [ 1%]
satpy/tests/compositor_tests/test_spectral.py ........ [ 1%]
satpy/tests/enhancement_tests/test_abi.py . [ 2%]
satpy/tests/enhancement_tests/test_enhancements.py ..................... [ 2%]
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satpy/tests/modifier_tests/test_angles.py .............................. [ 7%]
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satpy/tests/modifier_tests/test_crefl.py ............. [ 8%]
satpy/tests/modifier_tests/test_parallax.py ............................ [ 9%]
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satpy/tests/multiscene_tests/test_blend.py ............................. [ 12%]
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satpy/tests/multiscene_tests/test_misc.py .... [ 12%]
satpy/tests/multiscene_tests/test_save_animation.py ....... [ 12%]
satpy/tests/reader_tests/modis_tests/test_modis_l1b.py ............. [ 13%]
satpy/tests/reader_tests/modis_tests/test_modis_l2.py ........... [ 13%]
satpy/tests/reader_tests/modis_tests/test_modis_l3.py ... [ 13%]
satpy/tests/reader_tests/modis_tests/test_modis_l3_mcd12q1.py ... [ 14%]
satpy/tests/reader_tests/test_aapp_l1b.py ........ [ 14%]
satpy/tests/reader_tests/test_aapp_mhs_amsub_l1c.py .... [ 14%]
satpy/tests/reader_tests/test_abi_l1b.py ............................... [ 15%]
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satpy/tests/reader_tests/test_abi_l2_nc.py ........ [ 16%]
satpy/tests/reader_tests/test_acspo.py . [ 16%]
satpy/tests/reader_tests/test_agri_l1.py ............... [ 17%]
satpy/tests/reader_tests/test_ahi_hrit.py ......... [ 17%]
satpy/tests/reader_tests/test_ahi_hsd.py ............................ [ 18%]
satpy/tests/reader_tests/test_ahi_l1b_gridded_bin.py ........... [ 18%]
satpy/tests/reader_tests/test_ahi_l2_nc.py .... [ 19%]
satpy/tests/reader_tests/test_ami_l1b.py ............. [ 19%]
satpy/tests/reader_tests/test_amsr2_l1b.py .. [ 19%]
satpy/tests/reader_tests/test_amsr2_l2.py . [ 19%]
satpy/tests/reader_tests/test_amsr2_l2_gaasp.py ........................ [ 20%]
[ 20%]
satpy/tests/reader_tests/test_ascat_l2_soilmoisture_bufr.py ... [ 20%]
satpy/tests/reader_tests/test_atms_l1b_nc.py ..................... [ 21%]
satpy/tests/reader_tests/test_atms_sdr_hdf5.py .. [ 21%]
satpy/tests/reader_tests/test_avhrr_l0_hrpt.py ........... [ 22%]
satpy/tests/reader_tests/test_avhrr_l1b_gaclac.py .......... [ 22%]
satpy/tests/reader_tests/test_aws1_mwr_l1b.py ........... [ 22%]
satpy/tests/reader_tests/test_aws1_mwr_l1c.py ....... [ 23%]
satpy/tests/reader_tests/test_camel_l3_nc.py ...... [ 23%]
satpy/tests/reader_tests/test_clavrx/test_clavrx_geohdf.py ... [ 23%]
satpy/tests/reader_tests/test_clavrx/test_clavrx_nc.py ..... [ 23%]
satpy/tests/reader_tests/test_clavrx/test_clavrx_polarhdf.py ... [ 23%]
satpy/tests/reader_tests/test_cmsaf_claas.py ................... [ 24%]
satpy/tests/reader_tests/test_electrol_hrit.py .... [ 24%]
satpy/tests/reader_tests/test_epic_l1b_h5.py ..... [ 25%]
satpy/tests/reader_tests/test_eps_l1b.py ............ [ 25%]
satpy/tests/reader_tests/test_eps_sterna_mwr_l1b.py .... [ 25%]
satpy/tests/reader_tests/test_eum_base.py ............ [ 26%]
satpy/tests/reader_tests/test_eum_l2_bufr.py ........................... [ 27%]
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satpy/tests/reader_tests/test_eum_l2_grib.py .. [ 28%]
satpy/tests/reader_tests/test_fci_base.py . [ 28%]
satpy/tests/reader_tests/test_fci_l1c_nc.py ............................ [ 29%]
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satpy/tests/reader_tests/test_fci_l2_nc.py .......................... [ 38%]
satpy/tests/reader_tests/test_fy4_base.py ... [ 38%]
satpy/tests/reader_tests/test_generic_image.py ............. [ 38%]
satpy/tests/reader_tests/test_geocat.py ... [ 38%]
satpy/tests/reader_tests/test_geos_area.py ....... [ 39%]
satpy/tests/reader_tests/test_gerb_l2_hr_h5.py .... [ 39%]
satpy/tests/reader_tests/test_ghi_l1.py ........ [ 39%]
satpy/tests/reader_tests/test_ghrsst_l2.py ..... [ 39%]
satpy/tests/reader_tests/test_gld360_ualf2.py .......................... [ 40%]
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satpy/tests/reader_tests/test_glm_l2.py .... [ 41%]
satpy/tests/reader_tests/test_goci2_l2_nc.py ............ [ 41%]
satpy/tests/reader_tests/test_goes_imager_hrit.py .... [ 41%]
satpy/tests/reader_tests/test_goes_imager_nc_eum.py .... [ 41%]
satpy/tests/reader_tests/test_goes_imager_nc_noaa.py ................... [ 42%]
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satpy/tests/reader_tests/test_gpm_imerg.py . [ 42%]
satpy/tests/reader_tests/test_grib.py ......... [ 43%]
satpy/tests/reader_tests/test_hdf4_utils.py Fatal Python error: Segmentation fault
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File "<frozen runpy>", line 88 in _run_code
File "<frozen runpy>", line 198 in _run_module_as_main
Extension modules: numpy._core._multiarray_umath, numpy.linalg._umath_linalg, yaml._yaml, psutil._psutil_linux, psutil._psutil_posix, markupsafe._speedups, scipy._lib._ccallback_c, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, charset_normalizer.md, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg._matfuncs_expm, scipy.linalg._linalg_pythran, scipy.linalg.cython_blas, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy._lib._uarray._uarray, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.fftpack.convolve, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, bottleneck.move, bottleneck.nonreduce, bottleneck.nonreduce_axis, bottleneck.reduce, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, cftime._cftime, PIL._imaging, numcodecs.compat_ext, numcodecs.blosc, numcodecs.zstd, numcodecs.lz4, numcodecs._shuffle, numcodecs.jenkins, crc32c._crc32c, numcodecs.vlen, numcodecs.fletcher32, msgpack._cmsgpack, pyproj._compat, pyproj._context, pyproj._network, pyproj._version, pyproj._geod, pyproj.list, pyproj._crs, pyproj.database, pyproj._transformer, pyproj._sync, pykdtree.kdtree, pyresample.ewa._fornav, pyresample.ewa._ll2cr, shapely.lib, shapely._geos, shapely._geometry_helpers, pyresample.gradient._gradient_search, trollimage._colorspaces, tornado.speedups, lz4._version, lz4.block._block, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._cython_nnls, scipy.linalg._decomp_interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, _brotli, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, netCDF4._netCDF4, pyhdf._hdfext, h5py._debian_h5py_serial._errors, h5py._debian_h5py_serial.defs, h5py._debian_h5py_serial._objects, h5py._debian_h5py_serial.h5, h5py._debian_h5py_serial.utils, h5py._debian_h5py_serial.h5t, h5py._debian_h5py_serial.h5s, h5py._debian_h5py_serial.h5ac, h5py._debian_h5py_serial.h5p, h5py._debian_h5py_serial.h5r, h5py._debian_h5py_serial._proxy, h5py._debian_h5py_serial._conv, h5py._debian_h5py_serial.h5z, h5py._debian_h5py_serial.h5a, h5py._debian_h5py_serial.h5d, h5py._debian_h5py_serial.h5ds, h5py._debian_h5py_serial.h5g, h5py._debian_h5py_serial.h5i, h5py._debian_h5py_serial.h5o, h5py._debian_h5py_serial.h5f, h5py._debian_h5py_serial.h5fd, h5py._debian_h5py_serial.h5pl, h5py._debian_h5py_serial.h5l, h5py._debian_h5py_serial._selector, h5py.atexit, h5py._errors, h5py.defs, h5py._objects, h5py.h5, h5py.utils, h5py.h5t, h5py.h5s, h5py.h5ac, h5py.h5p, h5py.h5r, h5py._proxy, h5py._conv, h5py.h5z, h5py.h5a, h5py.h5d, h5py.h5ds, h5py.h5g, h5py.h5i, h5py.h5o, h5py.h5f, h5py.h5fd, h5py.h5pl, h5py.h5l, h5py._selector, scipy.interpolate._fitpack, scipy.interpolate._dfitpack, scipy.interpolate._dierckx, scipy.interpolate._ppoly, scipy.interpolate._interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.interpolate._bspl, rasterio._err, rasterio._filepath, rasterio._version, rasterio._env, rasterio.crs, rasterio._transform, rasterio._base, rasterio._features, rasterio._warp, rasterio._io, rasterio._vsiopener, lz4.frame._frame, scipy.signal._sigtools, scipy.signal._max_len_seq_inner, scipy.signal._upfirdn_apply, scipy.signal._spline, scipy.ndimage._nd_image, scipy.ndimage._rank_filter_1d, _ni_label, scipy.ndimage._ni_label, scipy.signal._sosfilt, scipy.special.cython_special, scipy.stats._stats, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._biasedurn, scipy.stats._stats_pythran, scipy.stats._levy_stable.levyst, scipy.stats._ansari_swilk_statistics, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.signal._peak_finding_utils, erfa.ufunc, geotiepoints._modis_utils, geotiepoints._simple_modis_interpolator, geotiepoints._modis_interpolator, _cffi_backend, PIL._imagingmath, PIL._webp, pygrib._pygrib (total: 256)
Segmentation fault (core dumped)
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=139: cd /build/satpy-0.55.0/.pybuild/cpython3_3.13_satpy/build; python3.13 -m pytest -k "not test__slice and not test_init and not test_strip_invalid_lat and not test_retrieve and not test_offline_retrieve and not test_retrieve_all and not test_download_script and not test_basic_default_not_provided and not test_rayleigh_corrector and not test_rayleigh_with_angles and not test_median and not test_no_downloads_in_tests and not test_convert_remote_files_to_fsspec_fsfile and not test_convert_remote_files_to_fsspec_filename_dict and not test_convert_remote_files_to_fsspec_mixed_sources and not test_hvplot_basic_with_area and not test_hvplot_basic_with_swath and not test_hvplot_rgb_with_area and not test_loading_lon_lat and not test_loading_sensor_angles and not test_loading_solar_angles and not test_get_ti_lon_lats and not test_distributed and not test_correct_area_clearsky_different_resolutions and not test_available_reader and not test_find_registerable and not test_filenames_as_path and not test_no_parameters and not test_bad_sensor and not test_sensor and not test_sensor_no_files and not test_no_reader and not test_basic_check_satpy and not test_plugin_reader_available_readers and not test_filenames_only and not test_add_grid_mapping_oblique_mercator and not test_palettize and not test_viirs and not test_basic_default_provided and not test_scene_dynamic_available_datasets and not test_read_real_segment and not test_read_physical_seviri_nat_file" --ignore=satpy/tests/reader_tests/gms/test_gms5_vissr_l1b.py --ignore=satpy/tests/reader_tests/gms/test_gms5_vissr_navigation.py --ignore=satpy/tests/reader_tests/test_viirs_edr_active_fires.py --ignore=satpy/tests/reader_tests/test_mviri_l1b_fiduceo_nc.py satpy/tests
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13
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