After upgrading MacOS to 15.4. the import failed: Exception has occurred: ImportError Error importing numpy: you should not try to import numpy from its source directory; please exit the numpy source tree, and relaunch your python interpreter from there.

Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.
ImportError: dlopen(/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <0B9C315B-A1DD-3527-88DB-4B90531D343F> /opt/miniconda3/envs/ho/lib/libopenblas.0.dylib
  Reason: tried: '/opt/miniconda3/envs/ho/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    .html

Please note and check the following:

  * The Python version is: Python3.12 from "/opt/miniconda3/envs/ho/bin/python"
  * The NumPy version is: "2.0.0"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: dlopen(/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <0B9C315B-A1DD-3527-88DB-4B90531D343F> /opt/miniconda3/envs/ho/lib/libopenblas.0.dylib
  Reason: tried: '/opt/miniconda3/envs/ho/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)


The above exception was the direct cause of the following exception:

  File "/Users/yf/Library/CloudStorage/OneDrive-Personal/Documents/Projects/hohoho/playground.py", line 1, in <module>
    import numpy as np
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

Everything was OK yesterday. The environment is created by miniconda. Python is 3.12.4, numpy is 2.0.0

I tried all ways below, but cannot solve the exception:

1. Delete and recreate the environment, install the same package backup in yaml file before.
2. Clean all conda cache, reinstall miniconda, recreate the environment, reinstall the packages.
3. search and delete the numpy path in the sys.path before import: sys.path = [p for p in sys.path if not os.path.basename(p).lower() == "numpy"]
4. Clone a new environment, upgrade all packages the latest version.
5. I have a packed .app file created by the pyinstaller before, which worked well before upgrading the OS, but cannot run now and report the same error.
6. Another Mac also installed the .app before, but cannot run after upgrading the OS.

Any other way I can solve the problem please..

More details:

1. previously OS version is 15.3
2. Macbook Pro M1
3. upgrade to NumPy 2.2.4 but not solve the problem:numpy 2.0.0-py312hb544834_0 --> 2.2.4-py312h7c1f314_0
4. no gfortran in conda list
5. another Macbook Air M1, which works fine with the pyinstaller build .app, and not any other python environment outside the .app, raise the same error after upgrade OS to 15.4

After upgrading MacOS to 15.4. the import failed: Exception has occurred: ImportError Error importing numpy: you should not try to import numpy from its source directory; please exit the numpy source tree, and relaunch your python interpreter from there.

Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.
ImportError: dlopen(/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <0B9C315B-A1DD-3527-88DB-4B90531D343F> /opt/miniconda3/envs/ho/lib/libopenblas.0.dylib
  Reason: tried: '/opt/miniconda3/envs/ho/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)

During handling of the above exception, another exception occurred:

ImportError: 

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy./devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.12 from "/opt/miniconda3/envs/ho/bin/python"
  * The NumPy version is: "2.0.0"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: dlopen(/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/_multiarray_umath.cpython-312-darwin.so, 0x0002): Library not loaded: @rpath/libgfortran.5.dylib
  Referenced from: <0B9C315B-A1DD-3527-88DB-4B90531D343F> /opt/miniconda3/envs/ho/lib/libopenblas.0.dylib
  Reason: tried: '/opt/miniconda3/envs/ho/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/lib/python3.12/site-packages/numpy/_core/../../../../libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/opt/miniconda3/envs/ho/bin/../lib/libgfortran.5.dylib' (duplicate LC_RPATH '@loader_path'), '/usr/local/lib/libgfortran.5.dylib' (no such file), '/usr/lib/libgfortran.5.dylib' (no such file, not in dyld cache)


The above exception was the direct cause of the following exception:

  File "/Users/yf/Library/CloudStorage/OneDrive-Personal/Documents/Projects/hohoho/playground.py", line 1, in <module>
    import numpy as np
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.

Everything was OK yesterday. The environment is created by miniconda. Python is 3.12.4, numpy is 2.0.0

I tried all ways below, but cannot solve the exception:

1. Delete and recreate the environment, install the same package backup in yaml file before.
2. Clean all conda cache, reinstall miniconda, recreate the environment, reinstall the packages.
3. search and delete the numpy path in the sys.path before import: sys.path = [p for p in sys.path if not os.path.basename(p).lower() == "numpy"]
4. Clone a new environment, upgrade all packages the latest version.
5. I have a packed .app file created by the pyinstaller before, which worked well before upgrading the OS, but cannot run now and report the same error.
6. Another Mac also installed the .app before, but cannot run after upgrading the OS.

Any other way I can solve the problem please..

More details:

1. previously OS version is 15.3
2. Macbook Pro M1
3. upgrade to NumPy 2.2.4 but not solve the problem:numpy 2.0.0-py312hb544834_0 --> 2.2.4-py312h7c1f314_0
4. no gfortran in conda list
5. another Macbook Air M1, which works fine with the pyinstaller build .app, and not any other python environment outside the .app, raise the same error after upgrade OS to 15.4

• python
• macos
• numpy

• What version was your OS previously? 15.3, or 14.6? – 9769953 Commented 2 days ago
• What is your architecture? M1, M2, M3, M4, older Intel? – 9769953 Commented 2 days ago
• You can also try to relax the NumPy constraints (note: 2.0.0 is really the very first release of a major new NumPy version, so that could be flakey in ways as well), like using 2.0.x, or even allowing 2.x.y (currently 2.2.0). – 9769953 Commented 2 days ago
• If you co conda list in your environment, can you see (lib)gfortran in that list? If so, what version & package ID? – 9769953 Commented 2 days ago
• I'm getting the same error with a pyinstaller packaged app that was working fine with MacOS 15.3. So, it seems that MacOS 15.4 has broken something related to Numpy preventing it from running. – LozzerJP Commented yesterday

2 Answers 2

I create a fresh new conda environment, install only numpy, swich to the env, no error raised!

I had the same issue. Even had an issue when recreating the same environment using a requirements.txt file. Ended up having to recreate the environment from scratch to resolve the error unfortunately.