Я пытаюсь заставить Cellprofiler снова работать с экземплярами ARM64 EC2 в AWS. Раньше это работало, но в последней версии Ubuntu 22.04 LTS оно больше не будет успешно устанавливаться. Я свел это к пакету (надеюсь, последнему), который необходимо установить: h5py v3.6.0
К сожалению, при запуске pip install h5py все проходит гладко, но при запуске pip install cellprofiler пытается установить h5py=1.14.5 in ./.local/lib/python3.10/site-packages (from h5py==3.6.0) (1.26.4)
Building wheels for collected packages: h5py
Building wheel for h5py (pyproject.toml): started
Building wheel for h5py (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error
× Building wheel for h5py (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [532 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-aarch64-cpython-310
creating build/lib.linux-aarch64-cpython-310/h5py
copying h5py/ipy_completer.py -> build/lib.linux-aarch64-cpython-310/h5py
copying h5py/version.py -> build/lib.linux-aarch64-cpython-310/h5py
copying h5py/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py
copying h5py/h5py_warnings.py -> build/lib.linux-aarch64-cpython-310/h5py
creating build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/datatype.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/group.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/dataset.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/compat.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/base.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/filters.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/selections2.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/attrs.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/files.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/selections.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/vds.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
copying h5py/_hl/dims.py -> build/lib.linux-aarch64-cpython-310/h5py/_hl
creating build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/common.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_dataset.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_h5f.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_dtype.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_h5.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_base.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_file_image.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_datatype.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_h5t.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_dimension_scales.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_h5o.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_errors.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/conftest.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_attrs.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_slicing.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_attribute_create.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_completions.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_objects.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_big_endian_file.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_h5pl.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_file2.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_group.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_file.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_h5p.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_filters.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_attrs_data.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_selections.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-aarch64-cpython-310/h5py/tests
creating build/lib.linux-aarch64-cpython-310/h5py/tests/data_files
copying h5py/tests/data_files/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files
creating build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds
copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds
copying h5py/tests/test_vds/__init__.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds
copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds
copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-aarch64-cpython-310/h5py/tests/test_vds
copying h5py/tests/data_files/vlen_string_dset.h5 -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files
copying h5py/tests/data_files/vlen_string_s390x.h5 -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files
copying h5py/tests/data_files/vlen_string_dset_utc.h5 -> build/lib.linux-aarch64-cpython-310/h5py/tests/data_files
running build_ext
warning: h5py/defs.pxd:15:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
...(shortened it due to a character limit on StackOverflow)
warning: h5py/defs.pxd:385:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
warning: h5py/api_types_hdf5.pxd:48:2: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
...(shortened it due to a character limit on StackOverflow)
warning: h5py/api_types_ext.pxd:52:4: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
warning: h5py/_conv.pyx:161:8: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
warning: h5py/_conv.pyx:422:8: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
warning: h5py/h5r.pxd:17:0: The 'IF' statement is deprecated and will be removed in a future Cython version. Consider using runtime conditions or C macros instead. See https://github.com/cython/cython/issues/4310
Error compiling Cython file:
------------------------------------------------------------
...
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
from .defs cimport *
from ._objects cimport class ObjectID
^
------------------------------------------------------------
h5py/h5t.pxd:13:23: Expected an identifier
Error compiling Cython file:
------------------------------------------------------------
...
from logging import getLogger
from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^
------------------------------------------------------------
h5py/_conv.pyx:21:0: 'h5py/h5t/H5PY_OBJ.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
from logging import getLogger
from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^
------------------------------------------------------------
h5py/_conv.pyx:21:0: 'h5py/h5t/typewrap.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
from logging import getLogger
from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^
------------------------------------------------------------
h5py/_conv.pyx:21:0: 'h5py/h5t/py_create.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
from logging import getLogger
from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^
------------------------------------------------------------
h5py/_conv.pyx:21:0: 'h5py/h5t/TypeID.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
from logging import getLogger
from .h5 import get_config
from .h5r cimport Reference, RegionReference, hobj_ref_t, hdset_reg_ref_t
from .h5t cimport H5PY_OBJ, typewrap, py_create, TypeID, H5PY_PYTHON_OPAQUE_TAG
^
------------------------------------------------------------
h5py/_conv.pyx:21:0: 'h5py/h5t/H5PY_PYTHON_OPAQUE_TAG.pxd' not found
Error compiling Cython file:
------------------------------------------------------------
...
void* ptr
cdef int conv_vlen2ndarray(void* ipt,
void* opt,
cnp.dtype elem_dtype,
TypeID intype,
^
------------------------------------------------------------
h5py/_conv.pyx:687:27: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef int conv_vlen2ndarray(void* ipt,
void* opt,
cnp.dtype elem_dtype,
TypeID intype,
TypeID outtype) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:688:27: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
cdef int conv_ndarray2vlen(void* ipt,
void* opt,
TypeID intype,
^
------------------------------------------------------------
h5py/_conv.pyx:820:27: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef int conv_ndarray2vlen(void* ipt,
void* opt,
TypeID intype,
TypeID outtype) except -1:
^
------------------------------------------------------------
h5py/_conv.pyx:821:27: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
:return: error-code
"""
cdef:
int command = cdata[0].command
size_t src_size, dst_size
TypeID supertype
^
------------------------------------------------------------
h5py/_conv.pyx:629:8: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
"""
cdef:
int command = cdata[0].command
size_t src_size, dst_size
TypeID supertype
TypeID outtype
^
------------------------------------------------------------
h5py/_conv.pyx:630:8: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
void *bkg_i,
hid_t dxpl) except -1 with gil:
cdef:
int command = cdata[0].command
size_t src_size, dst_size
TypeID supertype
^
------------------------------------------------------------
h5py/_conv.pyx:752:8: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
hid_t dxpl) except -1 with gil:
cdef:
int command = cdata[0].command
size_t src_size, dst_size
TypeID supertype
TypeID outtype
^
------------------------------------------------------------
h5py/_conv.pyx:753:8: 'TypeID' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef char* ctag = NULL
try:
if H5Tget_class(obj) == H5T_OPAQUE:
ctag = H5Tget_tag(obj)
if ctag != NULL:
if strcmp(ctag, H5PY_PYTHON_OPAQUE_TAG) == 0:
^
------------------------------------------------------------
h5py/_conv.pyx:157:32: 'H5PY_PYTHON_OPAQUE_TAG' is not a constant, variable or function identifier
warning: h5py/_conv.pyx:157:32: Obtaining 'const char *' from externally modifiable global Python value
Error compiling Cython file:
------------------------------------------------------------
...
elif command == H5T_CONV_FREE:
pass
elif command == H5T_CONV_CONV:
# need to pass element dtype to converter
supertype = typewrap(H5Tget_super(src_id))
^
------------------------------------------------------------
h5py/_conv.pyx:645:20: 'typewrap' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
elif command == H5T_CONV_CONV:
# need to pass element dtype to converter
supertype = typewrap(H5Tget_super(src_id))
dt = supertype.dtype
outtype = py_create(dt)
^
------------------------------------------------------------
h5py/_conv.pyx:647:18: 'py_create' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
PyObject *pdata_elem
char* buf = buf_i
if command == H5T_CONV_INIT:
cdata[0].need_bkg = H5T_BKG_NO
if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
^
------------------------------------------------------------
h5py/_conv.pyx:761:32: 'H5PY_OBJ' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
if command == H5T_CONV_INIT:
cdata[0].need_bkg = H5T_BKG_NO
if not H5Tequal(src_id, H5PY_OBJ) or H5Tget_class(dst_id) != H5T_VLEN:
return -2
supertype = typewrap(H5Tget_super(dst_id))
^
------------------------------------------------------------
h5py/_conv.pyx:763:20: 'typewrap' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
return -2
supertype = typewrap(H5Tget_super(dst_id))
for i in range(nl):
# smells a lot
memcpy(&pdata_elem, pdata+i, sizeof(pdata_elem))
if supertype != py_create(( pdata_elem).dtype, 1):
^
------------------------------------------------------------
h5py/_conv.pyx:767:28: 'py_create' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
if nl == 0:
return 0
# need to pass element dtype to converter
pdata_elem = pdata[0]
supertype = py_create(( pdata_elem).dtype)
^
------------------------------------------------------------
h5py/_conv.pyx:784:20: 'py_create' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
return 0
# need to pass element dtype to converter
pdata_elem = pdata[0]
supertype = py_create(( pdata_elem).dtype)
outtype = typewrap(H5Tget_super(dst_id))
^
------------------------------------------------------------
h5py/_conv.pyx:785:18: 'typewrap' is not a constant, variable or function identifier
Error compiling Cython file:
------------------------------------------------------------
...
enum = H5Tenum_create(H5T_STD_I32LE)
vlentype = H5Tvlen_create(H5T_STD_I32LE)
pyobj = H5PY_OBJ
^
------------------------------------------------------------
h5py/_conv.pyx:894:12: 'H5PY_OBJ' is not a constant, variable or function identifier
Loading library to get build settings and version: /usr/lib/aarch64-linux-gnu/hdf5/serial/libhdf5.so
********************************************************************************
Summary of the h5py configuration
HDF5 include dirs: [
'/usr/include/hdf5/serial'
]
HDF5 library dirs: [
'/usr/lib/aarch64-linux-gnu/hdf5/serial'
]
HDF5 Version: (1, 10, 7)
MPI Enabled: False
ROS3 VFD Enabled: True
Rebuild Required: True
********************************************************************************
Executing api_gen rebuild of defs
Executing cythonize()
[ 1/24] Cythonizing /tmp/pip-req-build-dhg1ew8t/h5py/_conv.pyx
Traceback (most recent call last):
File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
main()
File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/build_meta.py", line 415, in build_wheel
return self._build_with_temp_dir(
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/build_meta.py", line 397, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/build_meta.py", line 313, in run_setup
exec(code, locals())
File "", line 104, in
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/__init__.py", line 103, in setup
return distutils.core.setup(**attrs)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/_distutils/core.py", line 184, in setup
return run_commands(dist)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/_distutils/core.py", line 200, in run_commands
dist.run_commands()
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/dist.py", line 976, in run_command
super().run_command(command)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/command/bdist_wheel.py", line 373, in run
self.run_command("build")
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/dist.py", line 976, in run_command
super().run_command(command)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/_distutils/command/build.py", line 132, in run
self.run_command(cmd_name)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/dist.py", line 976, in run_command
super().run_command(command)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/tmp/pip-req-build-dhg1ew8t/setup_build.py", line 170, in run
self.extensions = cythonize(self._make_extensions(config),
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
cythonize_one(*args)
File "/tmp/pip-build-env-rmuz9tpt/overlay/local/lib/python3.10/dist-packages/Cython/Build/Dependencies.py", line 1321, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: /tmp/pip-req-build-dhg1ew8t/h5py/_conv.pyx
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for h5py
Failed to build h5py
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (h5py)
[/code]
Эти ошибки могут быть вызваны запуском pip3 install "h5py
Подробнее здесь: https://stackoverflow.com/questions/786 ... r-packages
