PyTables: Pip install errors on m1 python 3.11
I’ve reached a dead end trying to get tables to install on Mac m1 python 3.11.0rc2 (in preparation for 3.11 release). I was previously using 3.9.13 and recall having issues with this library.
I brew installed and exported the vars for a few things but looks like it gets stuck on tables/utilsextension.c and I’m not sure where to go with it now.
✗ uname -a
Darwin Jamess-Air 21.2.0 Darwin Kernel Version 21.2.0: Sun Nov 28 20:29:10 PST 2021; root:xnu-8019.61.5~1/RELEASE_ARM64_T8101 arm64
✗ python --version
Python 3.11.0rc2
✗ pip install -U tables
Collecting tables
Using cached tables-3.7.0.tar.gz (8.2 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy>=1.19.0 in ./.venv/lib/python3.11/site-packages (from tables) (1.23.4)
Requirement already satisfied: numexpr>=2.6.2 in ./.venv/lib/python3.11/site-packages (from tables) (2.8.3)
Requirement already satisfied: packaging in ./.venv/lib/python3.11/site-packages (from tables) (21.3)
Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in ./.venv/lib/python3.11/site-packages (from packaging->tables) (3.0.9)
Building wheels for collected packages: tables
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
╰─> [293 lines of output]
cpuinfo failed, assuming no CPU features: No module named 'cpuinfo'
* Using Python 3.11.0rc2 (main, Oct 25 2022, 15:27:23) [Clang 13.1.6 (clang-1316.0.21.2.5)]
* Found cython 0.29.32
* USE_PKGCONFIG: True
* Found HDF5 headers at ``/opt/homebrew/opt/hdf5/include``, library at ``/opt/homebrew/opt/hdf5/lib``.
* Found LZO 2 headers at ``/opt/homebrew/opt/lzo/include``, library at ``/opt/homebrew/opt/lzo/lib``.
* 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``.
* pkg-config header dirs for blosc: /opt/homebrew/Cellar/c-blosc/1.21.1/include
* pkg-config library dirs for blosc: /opt/homebrew/Cellar/c-blosc/1.21.1/lib
* Found blosc headers at ``/opt/homebrew/Cellar/c-blosc/1.21.1/include``, library at ``/opt/homebrew/Cellar/c-blosc/1.21.1/lib``.
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-12.1-arm64-cpython-311
creating build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/link.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/description.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/index.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/attributeset.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/registry.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/leaf.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/carray.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/__init__.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/unimplemented.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/req_versions.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/conditions.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/file.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/indexes.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/utils.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/undoredo.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/group.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/parameters.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/exceptions.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/table.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/idxutils.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/node.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/array.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/path.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/expression.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/atom.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/filters.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/earray.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/vlarray.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/flavor.py -> build/lib.macosx-12.1-arm64-cpython-311/tables
creating build/lib.macosx-12.1-arm64-cpython-311/tables/misc
copying tables/misc/__init__.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/misc
copying tables/misc/proxydict.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/misc
copying tables/misc/enum.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/misc
creating build/lib.macosx-12.1-arm64-cpython-311/tables/nodes
copying tables/nodes/__init__.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/nodes
copying tables/nodes/filenode.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/nodes
creating build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_utils.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_tree.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_all.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_basics.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_tables.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_expression.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/check_leaks.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_do_undo.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_timetype.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_backcompat.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_array.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_aux.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/__init__.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_earray.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/create_backcompat_indexes.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_index_backcompat.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/common.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_timestamps.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_queries.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_suite.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_lists.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_create.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_indexes.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_indexvalues.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_vlarray.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_garbage.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_tablesMD.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_carray.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_links.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_numpy.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_hdf5compat.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_attributes.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_types.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_enum.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_nestedtypes.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
creating build/lib.macosx-12.1-arm64-cpython-311/tables/scripts
copying tables/scripts/ptrepack.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/scripts
copying tables/scripts/pttree.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/scripts
copying tables/scripts/__init__.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/scripts
copying tables/scripts/pt2to3.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/scripts
copying tables/scripts/ptdump.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/scripts
creating build/lib.macosx-12.1-arm64-cpython-311/tables/nodes/tests
copying tables/nodes/tests/__init__.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/nodes/tests
copying tables/nodes/tests/test_filenode.py -> build/lib.macosx-12.1-arm64-cpython-311/tables/nodes/tests
running egg_info
writing tables.egg-info/PKG-INFO
writing dependency_links to tables.egg-info/dependency_links.txt
writing entry points to tables.egg-info/entry_points.txt
writing requirements to tables.egg-info/requires.txt
writing top-level names to tables.egg-info/top_level.txt
reading manifest file 'tables.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'VERSION'
warning: no files found matching '*.inc' under directory 'c-blosc/blosc'
warning: no files found matching '*.conf' under directory 'doc'
warning: no files found matching '*.*_t' under directory 'doc'
warning: no files found matching '*.gif' under directory 'doc/html'
warning: no files found matching '*' under directory 'doc/sphinxext'
warning: no previously-included files matching '*' found under directory 'doc/build'
warning: no files found matching '*.h5' under directory 'bench'
adding license file 'LICENSE.txt'
writing manifest file 'tables.egg-info/SOURCES.txt'
copying tables/_comp_bzip2.c -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/_comp_bzip2.pyx -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/_comp_lzo.c -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/_comp_lzo.pyx -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/definitions.pxd -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/hdf5extension.c -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/hdf5extension.pxd -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/hdf5extension.pyx -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/indexesextension.c -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/indexesextension.pyx -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/linkextension.c -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/linkextension.pyx -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/lrucacheextension.c -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/lrucacheextension.pxd -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/lrucacheextension.pyx -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/tableextension.c -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/tableextension.pyx -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/utilsextension.c -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/utilsextension.pxd -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/utilsextension.pyx -> build/lib.macosx-12.1-arm64-cpython-311/tables
copying tables/tests/Table2_1_lzo_nrv2e_shuffle.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/Tables_lzo1.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/Tables_lzo1_shuffle.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/Tables_lzo2.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/Tables_lzo2_shuffle.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/array_mdatom.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/attr-u16.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/blosc_bigendian.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/bug-idx.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/create-nested-type.c -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/elink.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/elink2.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/ex-noattr.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/flavored_vlarrays-format1.6.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/float.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/idx-std-1.x.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/indexes_2_0.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/indexes_2_1.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/issue_368.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/issue_560.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/itemsize.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/matlab_file.mat -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/nested-type-with-gaps.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/non-chunked-table.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/oldflavor_numeric.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/out_of_order_types.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/python2.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/python3.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/scalar.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/slink.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_SDSextendible.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_compound_chunked.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_enum.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_f64be.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_f64le.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_i32be.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_i32le.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_i64be.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_i64le.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/smpl_unsupptype.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_ref_array1.mat -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_ref_array2.mat -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/test_szip.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/time-table-vlarray-1_x.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/times-nested-be.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/vlstr_attr.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/vlunicode_endian.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/zerodim-attrs-1.3.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/tests/zerodim-attrs-1.4.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/tests
copying tables/nodes/tests/test_filenode.dat -> build/lib.macosx-12.1-arm64-cpython-311/tables/nodes/tests
copying tables/nodes/tests/test_filenode.xbm -> build/lib.macosx-12.1-arm64-cpython-311/tables/nodes/tests
copying tables/nodes/tests/test_filenode_v1.h5 -> build/lib.macosx-12.1-arm64-cpython-311/tables/nodes/tests
running build_ext
building 'tables.utilsextension' extension
creating build/temp.macosx-12.1-arm64-cpython-311
creating build/temp.macosx-12.1-arm64-cpython-311/hdf5-blosc
creating build/temp.macosx-12.1-arm64-cpython-311/hdf5-blosc/src
creating build/temp.macosx-12.1-arm64-cpython-311/src
creating build/temp.macosx-12.1-arm64-cpython-311/tables
clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.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/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/lzo/include -I/opt/homebrew/Cellar/c-blosc/1.21.1/include -I/private/var/folders/21/vb8hxzps7h5djnckkr81z61h0000gn/T/pip-build-env-9uppalzm/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/james/code/xs-shogun/.venv/include -I/Users/james/.pyenv/versions/3.11.0rc2/include/python3.11 -c hdf5-blosc/src/blosc_filter.c -o build/temp.macosx-12.1-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/MacOSX12.1.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.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/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/lzo/include -I/opt/homebrew/Cellar/c-blosc/1.21.1/include -I/private/var/folders/21/vb8hxzps7h5djnckkr81z61h0000gn/T/pip-build-env-9uppalzm/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/james/code/xs-shogun/.venv/include -I/Users/james/.pyenv/versions/3.11.0rc2/include/python3.11 -c src/H5ARRAY.c -o build/temp.macosx-12.1-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/MacOSX12.1.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.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/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/lzo/include -I/opt/homebrew/Cellar/c-blosc/1.21.1/include -I/private/var/folders/21/vb8hxzps7h5djnckkr81z61h0000gn/T/pip-build-env-9uppalzm/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/james/code/xs-shogun/.venv/include -I/Users/james/.pyenv/versions/3.11.0rc2/include/python3.11 -c src/H5ATTR.c -o build/temp.macosx-12.1-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/MacOSX12.1.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.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/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/lzo/include -I/opt/homebrew/Cellar/c-blosc/1.21.1/include -I/private/var/folders/21/vb8hxzps7h5djnckkr81z61h0000gn/T/pip-build-env-9uppalzm/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/james/code/xs-shogun/.venv/include -I/Users/james/.pyenv/versions/3.11.0rc2/include/python3.11 -c src/utils.c -o build/temp.macosx-12.1-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
clang -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.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/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/lzo/include -I/opt/homebrew/Cellar/c-blosc/1.21.1/include -I/private/var/folders/21/vb8hxzps7h5djnckkr81z61h0000gn/T/pip-build-env-9uppalzm/overlay/lib/python3.11/site-packages/numpy/core/include -I/Users/james/code/xs-shogun/.venv/include -I/Users/james/.pyenv/versions/3.11.0rc2/include/python3.11 -c tables/utilsextension.c -o build/temp.macosx-12.1-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/james/.pyenv/versions/3.11.0rc2/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/james/.pyenv/versions/3.11.0rc2/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/james/.pyenv/versions/3.11.0rc2/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/james/.pyenv/versions/3.11.0rc2/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/james/.pyenv/versions/3.11.0rc2/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
Failed to build tables
ERROR: Could not build wheels for tables, which is required to install pyproject.toml-based projects```About this issue
- Original URL
- State: closed
- Created 2 years ago
- Comments: 32 (13 by maintainers)
This is not an issue with PyTables, rather it is a problem with the generated C files for cython extensions that are packed in the source tarball on PyPi. This is usually done to remove the dependency from cython on the user side but has the drawback that it is not future compatible. In this case there was clearly a change in the Python API form 3.10 to 3.11, so pre generated C files for cython extensions are no longer valid for 3.11.
The workaround, at the moment is to remove manually the .c files and let cython re-generate them. An alternative is to pip install firm the v3.7.0 tag on github. The following perfectly works on Ubuntu 22.10 with Python 3.11rc2:
OK, I will prepare a PR ASAP if it is OK for you.
you can do
pip install git+https://github.com/PyTables/PyTables.gitas temporary bypassI suggest to use the v3.7.0 tag. The command is in the comments above:
It happens on Linux as well, so it’s just a PyTables problem with CPython 3.11
@Mouradost no need to apologise. I’m glad to hear that your problem is now solved.