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Roshan1992 / RedeFISH

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Issues about installation ImportError: numpy.core.multiarray failed to import #2

Open Bio-MingChen opened 4 months ago

Bio-MingChen commented 4 months ago

Hi, I am trying to install the package as steps of introduction,but after I set the environment , I run the redefish and get the conflict error like below,do you have any idea about it ? Thanks. /TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/init.py:143: UserWarning: A NumPy version >=1.19.5 and <1.27.0 is required for this version of SciPy (detected version 2.0.0) warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"

A module that was compiled using NumPy 1.x cannot be run in NumPy 2.0.0 as it may crash. To support both 1.x and 2.x versions of NumPy, modules must be compiled with NumPy 2.0. Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to downgrade to 'numpy<2' or try to upgrade the affected module. We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last): File "/TJPROJ6/SC/personal_dir/chenming/research/cell_segmentation_for_spatial/scripts/redfish_test.py", line 1, in import scanpy as sc File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scanpy/init.py", line 6, in from ._utils import check_versions File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scanpy/_utils/init.py", line 20, in from scipy import sparse File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/init.py", line 200, in getattr return _importlib.import_module(f'scipy.{name}') File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/sparse/init.py", line 267, in from ._csr import File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/sparse/_csr.py", line 10, in from ._sparsetools import (csr_tocsc, csr_tobsr, csr_count_blocks, AttributeError: _ARRAY_API not found Traceback (most recent call last): File "/TJPROJ6/SC/personal_dir/chenming/research/cell_segmentation_for_spatial/scripts/redfish_test.py", line 1, in import scanpy as sc File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scanpy/init.py", line 6, in from ._utils import check_versions File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scanpy/_utils/init.py", line 20, in from scipy import sparse File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/init.py", line 200, in getattr return _importlib.import_module(f'scipy.{name}') File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/sparse/init.py", line 267, in from ._csr import File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/sparse/_csr.py", line 10, in from ._sparsetools import (csr_tocsc, csr_tobsr, csr_count_blocks, ImportError: numpy.core.multiarray failed to import

Liyongheng-03 commented 8 hours ago

Hi, I am trying to install the package as steps of introduction,but after I set the environment , I run the redefish and get the conflict error like below,do you have any idea about it ? Thanks. /TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/init.py:143: UserWarning: A NumPy version >=1.19.5 and <1.27.0 is required for this version of SciPy (detected version 2.0.0) warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"

A module that was compiled using NumPy 1.x cannot be run in NumPy 2.0.0 as it may crash. To support both 1.x and 2.x versions of NumPy, modules must be compiled with NumPy 2.0. Some module may need to rebuild instead e.g. with 'pybind11>=2.12'.

If you are a user of the module, the easiest solution will be to downgrade to 'numpy<2' or try to upgrade the affected module. We expect that some modules will need time to support NumPy 2.

Traceback (most recent call last): File "/TJPROJ6/SC/personal_dir/chenming/research/cell_segmentation_for_spatial/scripts/redfish_test.py", line 1, in import scanpy as sc File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scanpy/init.py", line 6, in from ._utils import check_versions File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scanpy/_utils/init.py", line 20, in from scipy import sparse File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/init.py", line 200, in getattr return _importlib.import_module(f'scipy.{name}') File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/sparse/init.py", line 267, in from ._csr import File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/sparse/_csr.py", line 10, in from ._sparsetools import (csr_tocsc, csr_tobsr, csr_count_blocks, AttributeError: _ARRAY_API not found Traceback (most recent call last): File "/TJPROJ6/SC/personal_dir/chenming/research/cell_segmentation_for_spatial/scripts/redfish_test.py", line 1, in import scanpy as sc File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scanpy/init.py", line 6, in from ._utils import check_versions File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scanpy/_utils/init.py", line 20, in from scipy import sparse File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/init.py", line 200, in getattr return _importlib.import_module(f'scipy.{name}') File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/importlib/init.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/sparse/init.py", line 267, in from ._csr import File "/TJPROJ6/SC/personal_dir/chenming/software/Miniconda/miniconda202012/envs/RedeFISH_env/lib/python3.9/site-packages/scipy/sparse/_csr.py", line 10, in from ._sparsetools import (csr_tocsc, csr_tobsr, csr_count_blocks, ImportError: numpy.core.multiarray failed to import

这是我的包的版本，其他的跟给出的要求保持一致 ：