dependency related errors during make-entities step.

[sujeetvkulkarni]

MacBook Pro:
removed nohup so that can see errors in command line.

docker exec -t running_glycositeminer python make-entities.py &

Should docker container not have all required libraries/dependencies etc below dependency related errors?

Error output

[1]   Exit 1                  docker exec -t running_glycositeminer python make-entities.py
(base) Sujeets-MacBook-Pro:Users sujeet$ OpenBLAS blas_thread_init: pthread_create failed for thread 1 of 6: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 2 of 6: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 3 of 6: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 4 of 6: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
OpenBLAS blas_thread_init: pthread_create failed for thread 5 of 6: Operation not permitted
OpenBLAS blas_thread_init: RLIMIT_NPROC -1 current, -1 max
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/numpy/_core/__init__.py", line 23, in <module>
    from . import multiarray
  File "/usr/local/lib/python3.9/site-packages/numpy/_core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/usr/local/lib/python3.9/site-packages/numpy/_core/overrides.py", line 8, in <module>
    from numpy._core._multiarray_umath import (
ImportError: PyCapsule_Import could not import module "datetime"

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/numpy/__init__.py", line 114, in <module>
    from numpy.__config__ import show as show_config
  File "/usr/local/lib/python3.9/site-packages/numpy/__config__.py", line 4, in <module>
    from numpy._core._multiarray_umath import (
  File "/usr/local/lib/python3.9/site-packages/numpy/_core/__init__.py", line 49, in <module>
    raise ImportError(msg)
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.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.9 from "/usr/local/bin/python"
  * The NumPy version is: "2.0.2"

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

Original error was: PyCapsule_Import could not import module "datetime"


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

Traceback (most recent call last):
  File "/app/make-entities.py", line 3, in <module>
    import util
  File "/app/util.py", line 6, in <module>
    import numpy
  File "/usr/local/lib/python3.9/site-packages/numpy/__init__.py", line 119, in <module>
    raise ImportError(msg) from e
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.