Help!

[Heporis]

Help me please! wuwuwu~ Building wheel for h5py (setup.py) ... error

[Heporis]

How can I install h5py for macOS 10.15.7?

[Heporis]

how can I install hdf5 correctly? Building wheel for h5py (setup.py) ... error

[Heporis]

Loading library to get version: libhdf5.dylib error: dlopen(libhdf5.dylib, 6): image not found

[qiuqiangkong]

Try pip install h5py?

[Heporis]

Try pip install h5py?

pip install h5py没问题，但是pip install bytesep不行 每次都是Building wheel for h5py (setup.py) ... error 加了HDF5_DIR=/usr/local/Cellar/hdf5/1.12.1后

building 'h5py.defs' extension
creating build/temp.macosx-10.15-x86_64-3.9
creating build/temp.macosx-10.15-x86_64-3.9/private
creating build/temp.macosx-10.15-x86_64-3.9/private/var
creating build/temp.macosx-10.15-x86_64-3.9/private/var/folders
creating build/temp.macosx-10.15-x86_64-3.9/private/var/folders/x1
creating build/temp.macosx-10.15-x86_64-3.9/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn
creating build/temp.macosx-10.15-x86_64-3.9/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T
creating build/temp.macosx-10.15-x86_64-3.9/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po
creating build/temp.macosx-10.15-x86_64-3.9/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823
creating build/temp.macosx-10.15-x86_64-3.9/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -DH5_USE_16_API -I./h5py -I/usr/local/Cellar/hdf5/1.12.1/include -I/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/lzf -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c /private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.c -o build/temp.macosx-10.15-x86_64-3.9/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.o
In file included from /private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.c:725:
In file included from ./h5py/api_compat.h:26:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/usr/local/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with "          "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
 ^
/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.c:16550:56: error: too few arguments to function call, expected 3, have 2
  __pyx_t_1 = H5Oget_info(__pyx_v_loc_id, __pyx_v_oinfo); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1509, __pyx_L1_error)
              ~~~~~~~~~~~                              ^
/usr/local/Cellar/hdf5/1.12.1/include/H5Opublic.h:497:8: note: 'H5Oget_info3' declared here
H5_DLL herr_t H5Oget_info3(hid_t loc_id, H5O_info2_t *oinfo, unsigned fields);
       ^
/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.c:16665:95: error: too few arguments to function call, expected 5, have 4
  __pyx_t_1 = H5Oget_info_by_name(__pyx_v_loc_id, __pyx_v_name, __pyx_v_oinfo, __pyx_v_lapl_id); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1520, __pyx_L1_error)
              ~~~~~~~~~~~~~~~~~~~                                                             ^
/usr/local/Cellar/hdf5/1.12.1/include/H5Opublic.h:557:8: note: 'H5Oget_info_by_name3' declared here
H5_DLL herr_t H5Oget_info_by_name3(hid_t loc_id, const char *name, H5O_info2_t *oinfo, unsigned fields,
       ^
/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.c:16780:144: error: too few arguments to function call, expected 8, have 7
  __pyx_t_1 = H5Oget_info_by_idx(__pyx_v_loc_id, __pyx_v_group_name, __pyx_v_idx_type, __pyx_v_order, __pyx_v_n, __pyx_v_oinfo, __pyx_v_lapl_id); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1531, __pyx_L1_error)
              ~~~~~~~~~~~~~~~~~~                                                                                                               ^
/usr/local/Cellar/hdf5/1.12.1/include/H5Opublic.h:631:8: note: 'H5Oget_info_by_idx3' declared here
H5_DLL herr_t H5Oget_info_by_idx3(hid_t loc_id, const char *group_name, H5_index_t idx_type,
       ^
/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.c:17815:100: error: too few arguments to function call, expected 6, have 5
  __pyx_t_1 = H5Ovisit(__pyx_v_obj_id, __pyx_v_idx_type, __pyx_v_order, __pyx_v_op, __pyx_v_op_data); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1630, __pyx_L1_error)
              ~~~~~~~~                                                                             ^
/usr/local/Cellar/hdf5/1.12.1/include/H5Opublic.h:1326:8: note: 'H5Ovisit3' declared here
H5_DLL herr_t H5Ovisit3(hid_t obj_id, H5_index_t idx_type, H5_iter_order_t order, H5O_iterate2_t op,
       ^
/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.c:17930:143: error: too few arguments to function call, expected 8, have 7
  __pyx_t_1 = H5Ovisit_by_name(__pyx_v_loc_id, __pyx_v_obj_name, __pyx_v_idx_type, __pyx_v_order, __pyx_v_op, __pyx_v_op_data, __pyx_v_lapl_id); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 1641, __pyx_L1_error)
              ~~~~~~~~~~~~~~~~                                                                                                                ^
/usr/local/Cellar/hdf5/1.12.1/include/H5Opublic.h:1492:8: note: 'H5Ovisit_by_name3' declared here
H5_DLL herr_t H5Ovisit_by_name3(hid_t loc_id, const char *obj_name, H5_index_t idx_type,
       ^
/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.c:21840:13: warning: assigning to 'void *' from 'const void *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers]
  __pyx_t_1 = H5Pget_driver_info(__pyx_v_plist_id); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 2016, __pyx_L1_error)
            ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/private/var/folders/x1/1fd67kn91pddn94ch27h08th0000gn/T/pip-install-eb0041po/h5py_9578fe6d3dc8408bb773ea988cd77823/h5py/defs.c:34600:68: error: too few arguments to function call, expected 4, have 3
  __pyx_t_1 = H5Sencode(__pyx_v_obj_id, __pyx_v_buf, __pyx_v_nalloc); if (unlikely(PyErr_Occurred())) __PYX_ERR(0, 3303, __pyx_L1_error)
              ~~~~~~~~~                                            ^
/usr/local/Cellar/hdf5/1.12.1/include/H5Spublic.h:373:8: note: 'H5Sencode2' declared here
H5_DLL herr_t H5Sencode2(hid_t obj_id, void *buf, size_t *nalloc, hid_t fapl);
       ^
2 warnings and 6 errors generated.
error: command '/usr/bin/clang' failed with exit code 1

[qiuqiangkong]

Try this? pip install h5py --upgrade

It is suggested to use conda or virtualenv to manage the packages.

On Mon, 6 Dec 2021 at 00:30, Heporis @.***> wrote:

How to specify the path of hdf5, or pkg-config? Help me please! wuwuwu~

[image: 截屏2021-12-06 上午12 29 33] https://user-images.githubusercontent.com/51895154/144754880-978d9e26-dce8-4ac6-87d3-4464f8121260.png

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[Heporis]

Try this? pip install h5py --upgrade It is suggested to use conda or virtualenv to manage the packages. The same error. Tried many times with/without anaconda. I have installed it successfully on windows subsystem for linux. Confused macOS.🙄

[qiuqiangkong]

The installation works on my Mac. It looks like the problem is caused by some environment settings.

On Sat, 11 Dec 2021 at 03:34, Heporis @.***> wrote:

Try this? pip install h5py --upgrade It is suggested to use conda or virtualenv to manage the packages. The same error. Tried many times with/without anaconda. I have installed it successfully on windows subsystem for linux. Confused macOS.🙄

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