$ python -m pip install tables
stops with
Error: compiling Cython file
Environment (I am within a virtual environment, created with pyenv. )
Only few packages installed atm
Package Version
---------- -------
Cython 3.0.0
numpy 1.25.1
pip 23.2.1
setuptools 65.5.0
wheel 0.41.0
My exports
export HDF5_DIR="$(brew --prefix hdf5)"
export BLOSC_DIR="$(brew --prefix c-blosc)"
export C_INCLUDE_PATH=/opt/homebrew/Cellar/lzo/2.10/include/lzo:/opt/homebrew/Cellar/lzo/2.10/include/
export LIBRARY_PATH=/opt/homebrew/lib
Here is the complete error message:
$ python -m pip install tables ─╯
Collecting tables
Using cached tables-3.8.0.tar.gz (8.0 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [51 lines of output]
<string>:19: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
Error compiling Cython file:
------------------------------------------------------------
...
def _dump_h5_backtrace():
cdef object bt = []
if H5Ewalk(H5E_DEFAULT, H5E_WALK_DOWNWARD, e_walk_cb, <void*>bt) < 0:
^
------------------------------------------------------------
tables/utilsextension.pyx:384:47: Cannot assign type 'herr_t (unsigned int, const H5E_error_t *, void *) except? -1 nogil' to 'H5E_walk_t'
cpuinfo failed, assuming no CPU features: 'flags'
* Using Python 3.11.4 (main, Jul 27 2023, 14:26:12) [Clang 14.0.3 (clang-1403.0.22.14.1)]
* Found cython 3.0.0
* USE_PKGCONFIG: False
* Found HDF5 headers at ``/opt/homebrew/opt/hdf5/include``, library at ``/opt/homebrew/opt/hdf5/lib``.
* Found LZO 2 headers at ``/opt/homebrew/Cellar/lzo/2.10/include``, the library is located in the standard system search dirs.
* Skipping detection of LZO 1 since LZO 2 has already been found.
* Found bzip2 headers at ``/opt/homebrew/opt/bzip2/include``, library at ``/opt/homebrew/opt/bzip2/lib``.
* Found blosc headers at ``/opt/homebrew/opt/c-blosc/include``, library at ``/opt/homebrew/opt/c-blosc/lib``.
* Found blosc2 headers at ``/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-n4mpp65u/overlay/include``, library at ``/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-n4mpp65u/overlay/lib``.
* Copying blosc2 runtime library to 'tables' dir because it was not found in standard locations
Compiling tables/utilsextension.pyx because it changed.
[1/1] Cythonizing tables/utilsextension.pyx
Traceback (most recent call last):
File "/Users/mario.theuermann/.pyenv/versions/i4SEE-sandbox/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/Users/mario.theuermann/.pyenv/versions/i4SEE-sandbox/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/mario.theuermann/.pyenv/versions/i4SEE-sandbox/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 118, in get_requires_for_build_wheel
return hook(config_settings)
^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-n4mpp65u/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_wheel
return self._get_build_requires(config_settings, requirements=['wheel'])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-n4mpp65u/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 323, in _get_build_requires
self.run_setup()
File "/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-n4mpp65u/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 338, in run_setup
exec(code, locals())
File "<string>", line 928, in <module>
File "<string>", line 923, in get_cython_extfiles
File "/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-n4mpp65u/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
cythonize_one(*args)
File "/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-n4mpp65u/overlay/lib/python3.11/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: tables/utilsextension.pyx
[end of output]
What I investigated so far
H5Ewalk() was renamed to H5Ewalk1() and deprecated in 1.8.0 as stated here: https://docs.hdfgroup.org/hdf5/develop/group___h5_e.html#title29
I use 1.14.1, so I don't really understand that the build seems to to use this deprecated function?
$ brew info hdf5
==> hdf5: stable 1.14.1 (bottled)
Test tables 3.7.0
This version does not result in the above error, but in the following step of my requirements.txt file package installation:
Building wheels for collected packages: lxml, python-pptx, simplekml, tables, timezonefinder
Building wheel for lxml (setup.py) ... done
Created wheel for lxml: filename=lxml-4.9.2-cp311-cp311-macosx_13_0_arm64.whl size=1642538 sha256=00fdcd8bd9a533750afc5c27015d13fc99e25cad31f7f8d91b200cd4806ca7ef
Stored in directory: /Users/mario.theuermann/Library/Caches/pip/wheels/fb/5b/f7/0a27880b4a007daeff53a196d01901627f640392b7e76e76e5
Building wheel for python-pptx (setup.py) ... done
Created wheel for python-pptx: filename=python_pptx-0.6.21-py3-none-any.whl size=470934 sha256=05c7f46456d4ab5df20c574b3b051386e6965af187d1b31ee469b01d5e42f144
Stored in directory: /Users/mario.theuermann/Library/Caches/pip/wheels/f4/c7/af/d1d91f3decfaa7621033f30b69a29bf0b1206005663d233e7a
Building wheel for simplekml (setup.py) ... done
Created wheel for simplekml: filename=simplekml-1.3.6-py3-none-any.whl size=65860 sha256=1c1b2052ef80cfc795ba6a281a718c7a338a10723bd388c18b6910ce40356f0c
Stored in directory: /Users/mario.theuermann/Library/Caches/pip/wheels/72/3e/80/c3e5c354c3cbe62d8c5e4fb63d9e7cdccc7f93399997ae465f
Building wheel for tables (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for tables (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [296 lines of output]
<string>:18: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
cpuinfo failed, assuming no CPU features: No module named 'cpuinfo'
* Using Python 3.11.4 (main, Jul 27 2023, 14:26:12) [Clang 14.0.3 (clang-1403.0.22.14.1)]
* Found cython 3.0.0
* USE_PKGCONFIG: False
* Found HDF5 headers at ``/opt/homebrew/opt/hdf5/include``, library at ``/opt/homebrew/opt/hdf5/lib``.
* Found LZO 2 headers at ``/opt/homebrew/Cellar/lzo/2.10/include``, the library is located in the standard system search dirs.
* Skipping detection of LZO 1 since LZO 2 has already been found.
* Found bzip2 headers at ``/opt/homebrew/opt/bzip2/include``, library at ``/opt/homebrew/opt/bzip2/lib``.
* Found blosc headers at ``/opt/homebrew/opt/c-blosc/include``, library at ``/opt/homebrew/opt/c-blosc/lib``.
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-13.4-arm64-cpython-311
creating build/lib.macosx-13.4-arm64-cpython-311/tables
copying tables/link.py -> build/lib.macosx-13.4-arm64-cpython-311/tables
copying tables/description.py -> build/lib.macosx-13.4-arm64-cpython-311/tables
copying tables/index.py -> build/lib.macosx-13.4-arm64-cpython-311/tables
copying tables/attributeset.py -> build/lib.macosx-13.4-arm64-cpython-311/tables
copying tables/registry.py -> build/lib.macosx-13.4-arm64-cpython-311/tables
copying tables/leaf.py -> build/lib.macosx-13.4-arm64-cpython-311/tables
copying tables/carray.py -> build/lib.macosx-13.4-arm64-cpython-311/tables
copying tables/__init__.py -> build/lib.macosx-13.4-arm64-cpython-311/tables
copying tables/unimplemented.py -> build/lib.macosx-13.4-arm64-cpython-311/tables
.
.
.
.
.
running build_ext
building 'tables.utilsextension' extension
creating build/temp.macosx-13.4-arm64-cpython-311/hdf5-blosc
creating build/temp.macosx-13.4-arm64-cpython-311/hdf5-blosc/src
creating build/temp.macosx-13.4-arm64-cpython-311/src
creating build/temp.macosx-13.4-arm64-cpython-311/tables
clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/opt/homebrew/opt/bzip2/include -DNDEBUG=1 -DHAVE_LZO2_LIB=1 -DHAVE_BZ2_LIB=1 -DHAVE_BLOSC_LIB=1 -Ihdf5-blosc/src -I/opt/homebrew/Cellar/lzo/2.10/include/lzo -I/opt/homebrew/Cellar/lzo/2.10/include -I/opt/homebrew/opt/bzip2/include -I/usr/local/include -I/sw/include -I/opt/include -I/opt/local/include -I/usr/include -I/include -I/opt/homebrew/opt/hdf5/include -I/opt/homebrew/opt/c-blosc/include -I/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-kvflwhff/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/mario.theuermann/.pyenv/versions/i4SEE-sandbox/include -I/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11 -c hdf5-blosc/src/blosc_filter.c -o build/temp.macosx-13.4-arm64-cpython-311/hdf5-blosc/src/blosc_filter.o -Isrc -DH5_USE_18_API -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5E_auto_t_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Tarray_create_vers=2 -DH5Tget_array_dims_vers=2 -DH5Z_class_t_vers=2 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/opt/homebrew/opt/bzip2/include -DNDEBUG=1 -DHAVE_LZO2_LIB=1 -DHAVE_BZ2_LIB=1 -DHAVE_BLOSC_LIB=1 -Ihdf5-blosc/src -I/opt/homebrew/Cellar/lzo/2.10/include/lzo -I/opt/homebrew/Cellar/lzo/2.10/include -I/opt/homebrew/opt/bzip2/include -I/usr/local/include -I/sw/include -I/opt/include -I/opt/local/include -I/usr/include -I/include -I/opt/homebrew/opt/hdf5/include -I/opt/homebrew/opt/c-blosc/include -I/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-kvflwhff/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/mario.theuermann/.pyenv/versions/i4SEE-sandbox/include -I/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11 -c src/H5ARRAY.c -o build/temp.macosx-13.4-arm64-cpython-311/src/H5ARRAY.o -Isrc -DH5_USE_18_API -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5E_auto_t_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Tarray_create_vers=2 -DH5Tget_array_dims_vers=2 -DH5Z_class_t_vers=2 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/opt/homebrew/opt/bzip2/include -DNDEBUG=1 -DHAVE_LZO2_LIB=1 -DHAVE_BZ2_LIB=1 -DHAVE_BLOSC_LIB=1 -Ihdf5-blosc/src -I/opt/homebrew/Cellar/lzo/2.10/include/lzo -I/opt/homebrew/Cellar/lzo/2.10/include -I/opt/homebrew/opt/bzip2/include -I/usr/local/include -I/sw/include -I/opt/include -I/opt/local/include -I/usr/include -I/include -I/opt/homebrew/opt/hdf5/include -I/opt/homebrew/opt/c-blosc/include -I/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-kvflwhff/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/mario.theuermann/.pyenv/versions/i4SEE-sandbox/include -I/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11 -c src/H5ATTR.c -o build/temp.macosx-13.4-arm64-cpython-311/src/H5ATTR.o -Isrc -DH5_USE_18_API -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5E_auto_t_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Tarray_create_vers=2 -DH5Tget_array_dims_vers=2 -DH5Z_class_t_vers=2 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
src/H5ATTR.c:453:8: warning: explicitly assigning value of variable of type 'hid_t' (aka 'long long') to itself [-Wself-assign]
loc_id=loc_id;
~~~~~~^~~~~~~
1 warning generated.
clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/opt/homebrew/opt/bzip2/include -DNDEBUG=1 -DHAVE_LZO2_LIB=1 -DHAVE_BZ2_LIB=1 -DHAVE_BLOSC_LIB=1 -Ihdf5-blosc/src -I/opt/homebrew/Cellar/lzo/2.10/include/lzo -I/opt/homebrew/Cellar/lzo/2.10/include -I/opt/homebrew/opt/bzip2/include -I/usr/local/include -I/sw/include -I/opt/include -I/opt/local/include -I/usr/include -I/include -I/opt/homebrew/opt/hdf5/include -I/opt/homebrew/opt/c-blosc/include -I/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-kvflwhff/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/mario.theuermann/.pyenv/versions/i4SEE-sandbox/include -I/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11 -c src/utils.c -o build/temp.macosx-13.4-arm64-cpython-311/src/utils.o -Isrc -DH5_USE_18_API -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5E_auto_t_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Tarray_create_vers=2 -DH5Tget_array_dims_vers=2 -DH5Z_class_t_vers=2 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
src/utils.c:290:14: warning: variable 'namedtypes' set but not used [-Wunused-but-set-variable]
int namedtypes = 0;
^
1 warning generated.
clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/opt/homebrew/opt/bzip2/include -DNDEBUG=1 -DHAVE_LZO2_LIB=1 -DHAVE_BZ2_LIB=1 -DHAVE_BLOSC_LIB=1 -Ihdf5-blosc/src -I/opt/homebrew/Cellar/lzo/2.10/include/lzo -I/opt/homebrew/Cellar/lzo/2.10/include -I/opt/homebrew/opt/bzip2/include -I/usr/local/include -I/sw/include -I/opt/include -I/opt/local/include -I/usr/include -I/include -I/opt/homebrew/opt/hdf5/include -I/opt/homebrew/opt/c-blosc/include -I/private/var/folders/h2/tcw923v140sbnqcz0p0xp3y80000gp/T/pip-build-env-kvflwhff/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/mario.theuermann/.pyenv/versions/i4SEE-sandbox/include -I/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11 -c tables/utilsextension.c -o build/temp.macosx-13.4-arm64-cpython-311/tables/utilsextension.o -Isrc -DH5_USE_18_API -DH5Acreate_vers=2 -DH5Aiterate_vers=2 -DH5Dcreate_vers=2 -DH5Dopen_vers=2 -DH5Eclear_vers=2 -DH5Eprint_vers=2 -DH5Epush_vers=2 -DH5Eset_auto_vers=2 -DH5Eget_auto_vers=2 -DH5Ewalk_vers=2 -DH5E_auto_t_vers=2 -DH5Gcreate_vers=2 -DH5Gopen_vers=2 -DH5Pget_filter_vers=2 -DH5Pget_filter_by_id_vers=2 -DH5Tarray_create_vers=2 -DH5Tget_array_dims_vers=2 -DH5Z_class_t_vers=2 -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION
tables/utilsextension.c:8032:52: warning: comparison of integers of different signs: 'hsize_t' (aka 'unsigned long long') and 'long long' [-Wsign-compare]
__pyx_t_2 = (((__pyx_v_maxdims[__pyx_v_i]) == -1LL) != 0);
~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~
tables/utilsextension.c:12367:33: warning: comparison of integers of different signs: 'int' and 'hsize_t' (aka 'unsigned long long') [-Wsign-compare]
for (__pyx_t_4 = 0; __pyx_t_4 < __pyx_t_3; __pyx_t_4+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
tables/utilsextension.c:15186:35: warning: comparison of integers of different signs: 'int' and 'size_t' (aka 'unsigned long') [-Wsign-compare]
for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
~~~~~~~~~ ^ ~~~~~~~~~
tables/utilsextension.c:15413:52: warning: comparison of integers of different signs: 'hsize_t' (aka 'unsigned long long') and 'long long' [-Wsign-compare]
__pyx_t_3 = (((__pyx_v_maxdims[__pyx_v_j]) == -1LL) != 0);
~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~
tables/utilsextension.c:22030:23: error: no member named 'exc_type' in 'struct _err_stackitem'
while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
~~~~~~~~ ^
tables/utilsextension.c:22030:53: error: no member named 'exc_type' in 'struct _err_stackitem'
while ((exc_info->exc_type == NULL || exc_info->exc_type == Py_None) &&
~~~~~~~~ ^
tables/utilsextension.c:22044:23: error: no member named 'exc_type' in 'struct _err_stackitem'
*type = exc_info->exc_type;
~~~~~~~~ ^
tables/utilsextension.c:22046:21: error: no member named 'exc_traceback' in 'struct _err_stackitem'
*tb = exc_info->exc_traceback;
~~~~~~~~ ^
tables/utilsextension.c:22060:26: error: no member named 'exc_type' in 'struct _err_stackitem'
tmp_type = exc_info->exc_type;
~~~~~~~~ ^
tables/utilsextension.c:22062:24: error: no member named 'exc_traceback' in 'struct _err_stackitem'
tmp_tb = exc_info->exc_traceback;
~~~~~~~~ ^
tables/utilsextension.c:22063:15: error: no member named 'exc_type' in 'struct _err_stackitem'
exc_info->exc_type = type;
~~~~~~~~ ^
tables/utilsextension.c:22065:15: error: no member named 'exc_traceback' in 'struct _err_stackitem'
exc_info->exc_traceback = tb;
~~~~~~~~ ^
tables/utilsextension.c:22147:30: error: no member named 'exc_type' in 'struct _err_stackitem'
tmp_type = exc_info->exc_type;
~~~~~~~~ ^
tables/utilsextension.c:22149:28: error: no member named 'exc_traceback' in 'struct _err_stackitem'
tmp_tb = exc_info->exc_traceback;
~~~~~~~~ ^
tables/utilsextension.c:22150:19: error: no member named 'exc_type' in 'struct _err_stackitem'
exc_info->exc_type = local_type;
~~~~~~~~ ^
tables/utilsextension.c:22152:19: error: no member named 'exc_traceback' in 'struct _err_stackitem'
exc_info->exc_traceback = local_tb;
~~~~~~~~ ^
tables/utilsextension.c:22201:43: warning: 'ob_shash' is deprecated [-Wdeprecated-declarations]
hash1 = ((PyBytesObject*)s1)->ob_shash;
^
/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11/cpython/bytesobject.h:7:5: note: 'ob_shash' has been explicitly marked deprecated here
Py_DEPRECATED(3.11) Py_hash_t ob_shash;
^
/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11/pyport.h:336:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
tables/utilsextension.c:22202:43: warning: 'ob_shash' is deprecated [-Wdeprecated-declarations]
hash2 = ((PyBytesObject*)s2)->ob_shash;
^
/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11/cpython/bytesobject.h:7:5: note: 'ob_shash' has been explicitly marked deprecated here
Py_DEPRECATED(3.11) Py_hash_t ob_shash;
^
/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11/pyport.h:336:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
tables/utilsextension.c:22347:26: error: no member named 'exc_type' in 'struct _err_stackitem'
tmp_type = exc_info->exc_type;
~~~~~~~~ ^
tables/utilsextension.c:22349:24: error: no member named 'exc_traceback' in 'struct _err_stackitem'
tmp_tb = exc_info->exc_traceback;
~~~~~~~~ ^
tables/utilsextension.c:22350:15: error: no member named 'exc_type' in 'struct _err_stackitem'
exc_info->exc_type = *type;
~~~~~~~~ ^
tables/utilsextension.c:22352:15: error: no member named 'exc_traceback' in 'struct _err_stackitem'
exc_info->exc_traceback = *tb;
~~~~~~~~ ^
tables/utilsextension.c:23020:5: error: incomplete definition of type 'struct _frame'
__Pyx_PyFrame_SetLineNumber(py_frame, py_line);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
tables/utilsextension.c:445:62: note: expanded from macro '__Pyx_PyFrame_SetLineNumber'
#define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno)
~~~~~~~^
/Users/mario.theuermann/.pyenv/versions/3.11.4/include/python3.11/pytypedefs.h:22:16: note: forward declaration of 'struct _frame'
typedef struct _frame PyFrameObject;
^
6 warnings and 17 errors generated.
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for tables
Building wheel for timezonefinder (pyproject.toml) ... done
Following the Github issue I tried building and installing the latest version of tables like so:
python setup.py build --hdf5=/opt/homebrew/opt/hdf5 --use-pkgconfig=FALSE --blosc=/opt/homebrew/opt/c-blosc --lzo=/opt/homebrew/Cellar/lzo/2.10 --bzip2=/opt/homebrew/Cellar/bzip2/1.0.8
python setup.py install --hdf5=/opt/homebrew/opt/hdf5
Then, the test suite of tables fails with:
python3 -m tables.tests.test_all ─╯
Traceback (most recent call last):
File "<frozen runpy>", line 189, in _run_module_as_main
File "<frozen runpy>", line 112, in _get_module_details
File "/Users/xyz/projects-my/PyTables/tables/__init__.py", line 42, in <module>
from .utilsextension import get_hdf5_version as _get_hdf5_version
ModuleNotFoundError: No module named 'tables.utilsextension'
I managed to reproduce your issue, the problem seems to be installing the package from PyPi. From the error message it seems the Cython cannot find lzo libraries.
The solution of the mentioned GitHub thread seems to be installing c-blosc, which also did not fix the problem for me.
There are two options that worked for me:
pip3 install git+https://github.com/PyTables/PyTables
conda install -c anaconda pytables