BUG: Combining SciPy 1.14.1 and statsmodels 0.14.2 on OSX causes "symbol not found in flat namespace '_npy_cabs'" #9333

nickodell · 2024-08-22T18:18:14Z

Describe the bug

When importing statsmodels.api, the following error appears:

Traceback (most recent call last):
  File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/test.py", line 1, in <module>
    import statsmodels.api as sm
  File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/api.py", line 136, in <module>
    from .regression.recursive_ls import RecursiveLS
  File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/regression/recursive_ls.py", line 14, in <module>
    from statsmodels.tsa.statespace.mlemodel import (
  File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/mlemodel.py", line 33, in <module>
    from .simulation_smoother import SimulationSmoother
  File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/simulation_smoother.py", line 11, in <module>
    from .kalman_smoother import KalmanSmoother
  File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/kalman_smoother.py", line 11, in <module>
    from statsmodels.tsa.statespace.representation import OptionWrapper
  File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/representation.py", line 10, in <module>
    from .tools import (
  File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/tools.py", line 14, in <module>
    from . import (_initialization, _representation, _kalman_filter,
  File "statsmodels/tsa/statespace/_initialization.pyx", line 1, in init statsmodels.tsa.statespace._initialization
ImportError: dlopen(/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/_representation.cpython-312-darwin.so, 0x0002): symbol not found in flat namespace '_npy_cabs'

This issue was originally reported on StackOverflow. I have independently reproduced the failure on OSX, but failed to reproduce it on Linux.

Curiously, this issue only shows up when SciPy 1.14.1 is installed. If SciPy 1.14.0 is installed, this error does not show up. Similarly, if statsmodels 0.14.1 is installed, the issue also goes away. Strangely, downgrading from statsmodels 0.14.2 to 0.14.1 and upgrading back to 0.14.2 also fixes the issue.

I'm unsure if this is a bug in statsmodels or SciPy - it seems very strange that a change in another package could cause this kind of error.

Code Sample, a copy-pastable example if possible

import statsmodels.api as sm

If you are using a released version, have you verified that the bug exists in the main branch of this repository? It helps the limited resources if we know problems exist in the current main branch so that they do not need to check whether the code sample produces a bug in the next release.

I was unable to verify whether this issue has been fixed in main, because building the package from source also makes the issue go away.

For example, if I install scipy and statsmodels like this:

pip install scipy==1.14.1 git+https://github.com/statsmodels/[email protected]

the error goes away, despite being the same version that breaks when I use pre-built binaries.

Expected Output

I expected that the latest version of SciPy and statsmodels could be used together.

Output of `import statsmodels.api as sm; sm.show_versions()`

This is the output of import statsmodels.api as sm; sm.show_versions() for the working version of SciPy. After installing SciPy 1.14.1, import statsmodels.api as sm no longer works.

import statsmodels.api as sm; sm.show_versions()

INSTALLED VERSIONS

Python: 3.12.5.final.0
OS: Darwin 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:54 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T6030 arm64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8

statsmodels

Installed: 0.14.2 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels)

Required Dependencies

cython: Not installed
numpy: 2.1.0 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/numpy)
scipy: 1.14.0 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/scipy)
pandas: 2.2.2 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/pandas)
dateutil: 2.9.0.post0 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/dateutil)
patsy: 0.5.6 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/patsy)

Optional Dependencies

matplotlib: Not installed
cvxopt: Not installed
joblib: Not installed

Developer Tools

IPython: Not installed
jinja2: Not installed
sphinx: Not installed
pygments: Not installed
pytest: Not installed
virtualenv: Not installed

Additional details:

x-ref scipy/scipy#21434

Original report from StackOverflow

The text was updated successfully, but these errors were encountered:

bashtage · 2024-08-22T18:22:26Z

What happens if you downgrade to NumPy 2.0.x?

…

On Thu, Aug 22, 2024, 19:18 Nick ODell ***@***.***> wrote: Describe the bug When importing statsmodels.api, the following error appears: Traceback (most recent call last): File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/test.py", line 1, in <module> import statsmodels.api as sm File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/api.py", line 136, in <module> from .regression.recursive_ls import RecursiveLS File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/regression/recursive_ls.py", line 14, in <module> from statsmodels.tsa.statespace.mlemodel import ( File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/mlemodel.py", line 33, in <module> from .simulation_smoother import SimulationSmoother File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/simulation_smoother.py", line 11, in <module> from .kalman_smoother import KalmanSmoother File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/kalman_smoother.py", line 11, in <module> from statsmodels.tsa.statespace.representation import OptionWrapper File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/representation.py", line 10, in <module> from .tools import ( File "/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/tools.py", line 14, in <module> from . import (_initialization, _representation, _kalman_filter, File "statsmodels/tsa/statespace/_initialization.pyx", line 1, in init statsmodels.tsa.statespace._initialization ImportError: dlopen(/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels/tsa/statespace/_representation.cpython-312-darwin.so, 0x0002): symbol not found in flat namespace '_npy_cabs' This issue was originally reported on StackOverflow <https://stackoverflow.com/questions/78900274/scipy-1-14-1-breaks-statsmodels-0-14-2>. I have independently reproduced the failure on OSX, but failed to reproduce it on Linux. Curiously, this issue only shows up when SciPy 1.14.1 is installed. If SciPy 1.14.0 is installed, this error does not show up. Similarly, if statsmodels 0.14.1 is installed, the issue also goes away. Strangely, downgrading from statsmodels 0.14.2 to 0.14.1 and upgrading back to 0.14.2 also fixes the issue. I'm unsure if this is a bug in statsmodels or SciPy - it seems very strange that a change in another package could cause this kind of error. Code Sample, a copy-pastable example if possible import statsmodels.api as sm If you are using a released version, have you verified that the bug exists in the main branch of this repository? It helps the limited resources if we know problems exist in the current main branch so that they do not need to check whether the code sample produces a bug in the next release. I was unable to verify whether this issue has been fixed in main, because building the package from source also makes the issue go away. For example, if I install scipy and statsmodels like this: pip install scipy==1.14.1 ***@***.*** the error goes away, despite being the same version that breaks when I use pre-built binaries. Expected Output I expected that the latest version of SciPy and statsmodels could be used together. Output of import statsmodels.api as sm; sm.show_versions() This is the output of import statsmodels.api as sm; sm.show_versions() for the working version of SciPy. After installing SciPy 1.14.1, import statsmodels.api as sm no longer works. import statsmodels.api as sm; sm.show_versions() INSTALLED VERSIONS Python: 3.12.5.final.0 OS: Darwin 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:54 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T6030 arm64 byteorder: little LC_ALL: None LANG: en_US.UTF-8 statsmodels Installed: 0.14.2 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/statsmodels) Required Dependencies cython: Not installed numpy: 2.1.0 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/numpy) scipy: 1.14.0 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/scipy) pandas: 2.2.2 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/pandas) dateutil: 2.9.0.post0 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/dateutil) patsy: 0.5.6 (/private/var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh/venv/lib/python3.12/site-packages/patsy) Optional Dependencies matplotlib: Not installed cvxopt: Not installed joblib: Not installed Developer Tools IPython: Not installed jinja2: Not installed sphinx: Not installed pygments: Not installed pytest: Not installed virtualenv: Not installed Additional details: x-ref scipy/scipy#21434 <scipy/scipy#21434> — Reply to this email directly, view it on GitHub <#9333>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABKTSRKGBYOFVWDEFQ3XME3ZSYTQHAVCNFSM6AAAAABM6VWXQKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DCNBUGI4TQNI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

bashtage · 2024-08-22T18:23:54Z

Should have nothing to do with SciPy, but perhaps SciPy 1.14 is bumping NumPy to 2.1.0, while SciPy 1.13 is happy with NumPy 2.0.x.

nickodell · 2024-08-22T18:38:21Z

What happens if you downgrade to NumPy 2.0.x?

Curiously, the configuration pip install scipy==1.14.1 statsmodels==0.14.2 numpy==2.0.1 works.

Should have nothing to do with SciPy, but perhaps SciPy 1.14 is bumping NumPy to 2.1.0

According to pip freeze, both working and non-working configurations have the same NumPy version. The only package that differs is SciPy.

Working:

numpy==2.1.0
packaging==24.1
pandas==2.2.2
patsy==0.5.6
python-dateutil==2.9.0.post0
pytz==2024.1
scipy==1.14.0
six==1.16.0
statsmodels==0.14.2
tzdata==2024.1

Failing:

numpy==2.1.0
packaging==24.1
pandas==2.2.2
patsy==0.5.6
python-dateutil==2.9.0.post0
pytz==2024.1
scipy==1.14.1
six==1.16.0
statsmodels==0.14.2
tzdata==2024.1

nickodell · 2024-08-22T19:00:50Z

I've done a test of all combinations of SciPy 1.14.0/1.14.1, NumPy 2.0.1/2.1.0, and statsmodels 0.14.1/0.14.2.

The result is that the only failing configuration is latest SciPy plus latest NumPy plus latest statsmodels.

`scipy` Version	`statsmodels` Version	`numpy` Version	Compatibility
1.14.0	0.14.1	2.0.1	incompatible (statsmodels requires numpy < 2)
1.14.0	0.14.1	2.1.0	incompatible (statsmodels requires numpy < 2)
1.14.0	0.14.1	1.26.4	works
1.14.0	0.14.2	2.0.1	works
1.14.0	0.14.2	2.1.0	works
1.14.1	0.14.1	2.0.1	incompatible (statsmodels requires numpy < 2)
1.14.1	0.14.1	2.1.0	incompatible (statsmodels requires numpy < 2)
1.14.1	0.14.1	1.26.4	works
1.14.1	0.14.2	2.0.1	works
1.14.1	0.14.2	2.1.0	fails

Everything else either works, or pip refuses to install that combination of packages.

bashtage · 2024-08-22T19:38:04Z

Sounds like the both used to export the symbol but have both stopped.

…

On Thu, Aug 22, 2024, 20:01 Nick ODell ***@***.***> wrote: I've done a test of all combinations of SciPy 1.14.0/1.14.1, NumPy 2.0.1/2.1.0, and statsmodels 0.14.1/0.14.2. The result is that the only failing configuration is latest SciPy plus latest NumPy plus latest statsmodels. scipy Version statsmodels Version numpy Version Compatibility 1.14.0 0.14.1 2.0.1 incompatible (statsmodels requires numpy < 2) 1.14.0 0.14.1 2.1.0 incompatible (statsmodels requires numpy < 2) 1.14.0 0.14.1 1.26.4 works 1.14.0 0.14.2 2.0.1 works 1.14.0 0.14.2 2.1.0 works 1.14.1 0.14.1 2.0.1 incompatible (statsmodels requires numpy < 2) 1.14.1 0.14.1 2.1.0 incompatible (statsmodels requires numpy < 2) 1.14.1 0.14.1 1.26.4 works 1.14.1 0.14.2 2.0.1 works 1.14.1 0.14.2 2.1.0 fails Everything else either works, or pip refuses to install that combination of packages. — Reply to this email directly, view it on GitHub <#9333 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABKTSRMFUBBZUVROO5YV5SLZSYYPTAVCNFSM6AAAAABM6VWXQKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMBVGQZTQNRQGU> . You are receiving this because you commented.Message ID: ***@***.***>

nickodell · 2024-08-22T20:53:24Z

You're right. It took me a bit of googling to work out how to view the symbol tables, but NumPy 2.1.0 no longer exports this symbol, and SciPy 1.14.1 no longer exports it either.

$ pip install numpy==2.1.0                                                                                          1 ↵
(venv) nick@Nicks-MacBook-Pro /var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh 
$ pip install scipy==1.14.0                                                                                       130 ↵
Collecting scipy==1.14.0
  Using cached scipy-1.14.0-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)
Requirement already satisfied: numpy<2.3,>=1.23.5 in ./venv/lib/python3.12/site-packages (from scipy==1.14.0) (2.1.0)
Using cached scipy-1.14.0-cp312-cp312-macosx_14_0_arm64.whl (23.1 MB)
Installing collected packages: scipy
  Attempting uninstall: scipy
    Found existing installation: scipy 1.14.1
    Uninstalling scipy-1.14.1:
      Successfully uninstalled scipy-1.14.1
Successfully installed scipy-1.14.0
(venv) nick@Nicks-MacBook-Pro /var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh 
$ nm -gU venv/lib/python3.12/site-packages/scipy/special/_ufuncs.cpython-312-darwin.so | grep cabs     
000000000007c248 T _npy_cabs
000000000007c204 T _npy_cabsf
000000000007c28c T _npy_cabsl
(venv) nick@Nicks-MacBook-Pro /var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh 
$ pip install scipy==1.14.1                                                                       
Collecting scipy==1.14.1
  Using cached scipy-1.14.1-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)
Requirement already satisfied: numpy<2.3,>=1.23.5 in ./venv/lib/python3.12/site-packages (from scipy==1.14.1) (2.1.0)
Using cached scipy-1.14.1-cp312-cp312-macosx_14_0_arm64.whl (23.1 MB)
Installing collected packages: scipy
  Attempting uninstall: scipy
    Found existing installation: scipy 1.14.0
    Uninstalling scipy-1.14.0:
      Successfully uninstalled scipy-1.14.0
Successfully installed scipy-1.14.1
(venv) nick@Nicks-MacBook-Pro /var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh 
$ nm -gU venv/lib/python3.12/site-packages/scipy/special/_ufuncs.cpython-312-darwin.so | grep cabs
(venv) nick@Nicks-MacBook-Pro /var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh 
$ pip install numpy==2.0.1                                                                                          1 ↵
Collecting numpy==2.0.1
  Using cached numpy-2.0.1-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)
Using cached numpy-2.0.1-cp312-cp312-macosx_14_0_arm64.whl (5.0 MB)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 2.1.0
    Uninstalling numpy-2.1.0:
      Successfully uninstalled numpy-2.1.0
Successfully installed numpy-2.0.1
(venv) nick@Nicks-MacBook-Pro /var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh 
$ nm -gU venv/lib/python3.12/site-packages/scipy/special/_ufuncs.cpython-312-darwin.so | grep cabs
(venv) nick@Nicks-MacBook-Pro /var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh 
$ nm -gU venv/lib/python3.12/site-packages/numpy/linalg/_umath_linalg.cpython-312-darwin.so | grep cabs             1 ↵
00000000000148c0 T _npy_cabs
000000000001487c T _npy_cabsf
0000000000014904 T _npy_cabsl
(venv) nick@Nicks-MacBook-Pro /var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh 
$ pip install numpy==2.1.0                                                                             
Collecting numpy==2.1.0
  Using cached numpy-2.1.0-cp312-cp312-macosx_14_0_arm64.whl.metadata (60 kB)
Using cached numpy-2.1.0-cp312-cp312-macosx_14_0_arm64.whl (5.1 MB)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 2.0.1
    Uninstalling numpy-2.0.1:
      Successfully uninstalled numpy-2.0.1
Successfully installed numpy-2.1.0
(venv) nick@Nicks-MacBook-Pro /var/folders/7v/pg90myg55bs218ff8dpkrfrc0000gn/T/tmp.8CjfzJEYnh 
$ nm -gU venv/lib/python3.12/site-packages/numpy/linalg/_umath_linalg.cpython-312-darwin.so | grep cabs

SciPy used to export the symbol via scipy/special/_ufuncs.cpython-312-darwin.so, and NumPy used to export it via numpy/linalg/_umath_linalg.cpython-312-darwin.so.

bashtage · 2024-08-23T18:03:47Z

We can't reproduce on CI:

https://dev.azure.com/statsmodels/statsmodels-testing/_build/results?buildId=5869&view=logs&j=ff02c0bf-a6da-574b-cd48-e6a8a9d1f05d
Configuration:

build           1.2.1
certifi         2024.7.4
colorama        0.4.6
contourpy       1.2.1
coverage        7.6.1
cycler          0.12.1
Cython          3.0.11
execnet         2.1.1
flake8          7.1.1
fonttools       4.53.1
iniconfig       2.0.0
isort           5.13.2
joblib          1.4.2
kiwisolver      1.4.5
matplotlib      3.9.2
mccabe          0.7.0
numpy           2.1.0
packaging       24.1
pandas          2.2.2
patsy           0.5.6
pillow          10.4.0
pip             24.2
pluggy          1.5.0
pycodestyle     2.12.1
pyflakes        3.2.0
pyparsing       3.1.2
pyproject_hooks 1.1.0
pytest          7.4.4
pytest-cov      5.0.0
pytest-randomly 3.15.0
pytest-xdist    3.6.1
python-dateutil 2.9.0.post0
pytz            2024.1
scipy           1.14.1
setuptools      73.0.1
setuptools-scm  8.1.0
six             1.16.0
statsmodels     0.15.0.dev334+gde18b6fbb /Users/runner/work/1/s
tzdata          2024.1
wheel           0.44.0

I wonder if it matters that the CI one is built against scipy 1.14.1 - not 100% but could imagine that since SciPy doesn't have the symbol anymore, it is finding it from NumPy and so is happy. The release 0.14.2 was built against SciPy 1.13 and probably expects to find the symbol there. At least this is my working hypothesis.

…9333

joegasewicz · 2024-08-28T18:18:28Z

0.15.0.dev334+gde18b6fbb

I just tried running with a Pipfile -

[[source]]
url = "https://pypi.org/simple"
verify_ssl = true
name = "pypi"

[packages]
jupyter = "*"
pandas = "2.2.2"
matplotlib = "*"
scipy = "1.14.1"
numpy = "2.1.0"
statsmodels = "0.14.2"

[dev-packages]

[requires]
python_version = "3.12"

Output:

ImportError: dlopen(/Users/$USER/.local/share/virtualenvs/machine_learning_course-oXhJl1U5/lib/python3.12/site-packages/statsmodels/tsa/statespace/_representation.cpython-312-darwin.so, 0x0002): symbol not found in flat namespace '_npy_cabs'

MAC:

Chip	Apple M1 Pro
Memory	32G
MacOS	14.5

EwoutH · 2024-09-09T20:07:49Z

We have a similar issue in our CI, see this run for example. Numpy 2.1.1, SciPy 1.14.1 and statsmodels 0.14.2. Also happening only on macOS.

karrmagadgeteer2 · 2024-09-10T21:55:25Z

Also on macOS. this run. Numpy 2.1.0, SciPy 1.14.1 and statsmodels 0.14.2.

dsdanielko · 2024-09-11T17:57:00Z

I am having the same problem while using any combinations of python==3.10.15, scipy==1.14.0/1.14.1/1.14.2, numpy==2.0.1/2.1.1 and statsmodels==0.14.2

bashtage · 2024-09-11T23:10:45Z

There seems to be a decent bug here that isn't easy to fix. It appears in the 0.14.2 code even if built against SciPy 1.14.1.

Simplify setup since NumPy wikk always be installed when using pip install. Standardize library usage xref statsmodels#9333

bashtage · 2024-09-13T07:35:27Z

The source of the issue has been found. It is due to some changes in the arch used by the GitHub MaxOS runners, which were previously x86_64 and have moved to arm64. This means that the x86_64 wheels were not correctly linked. The fix is in place, although there are a number of bugs due to changes in other libraries (probably pandas) that need to be addressed before we can release 0.14.3.

https://github.com/MacPython/statsmodels-wheels/actions/runs/10844514094

bashtage · 2024-09-13T15:21:33Z

Appears to be fixed now. Will need a release note and then likely to release early next week.

https://github.com/MacPython/statsmodels-wheels/actions/runs/10848683287

bashtage · 2024-09-16T10:01:20Z

Wheels are on PyPi (excluding a couple that are slow building). Closing. Please let us know if there continues to be a problem.

EwoutH · 2024-09-16T10:09:10Z

I can confirm statsmodels 0.14.3 resolves this bug for us, and our CI now passes again!

Thanks a lot for the time and effort to crack this complex bug!

nickodell · 2024-09-18T15:59:30Z

Hi, original reporter here, I can confirm the issue is fixed on my computer with statmodels 0.14.3.

nickodell mentioned this issue Aug 22, 2024

BUG: Combining SciPy 1.14.1 and statsmodels 0.14.2 on OSX causes "symbol not found in flat namespace '_npy_cabs'" scipy/scipy#21434

Closed

rgommers mentioned this issue Aug 23, 2024

BUG: _npy_cabs is no longer exported in 2.1.0 numpy/numpy#27270

Closed

karrmagadgeteer2 added a commit to CaptorAB/openseries that referenced this issue Aug 24, 2024

Limited scipy version due to statsmodels bug statsmodels/statsmodels#…

874d98e

…9333

karrmagadgeteer2 mentioned this issue Aug 24, 2024

Bump scipy from 1.14.0 to 1.14.1 CaptorAB/openseries#173

Closed

cookpa mentioned this issue Aug 26, 2024

COMP: downgrade numpy for arm64 ANTsX/ANTsPy#702

Merged

ckdckd145 mentioned this issue Sep 2, 2024

[REVIEW]: Statmanager-kr: A user-friendly statistical package for python in pandas openjournals/joss-reviews#6642

Closed

bashtage added a commit to bashtage/statsmodels that referenced this issue Sep 12, 2024

MAINT: Simplify and standardize setup

5a1dd21

Simplify setup since NumPy wikk always be installed when using pip install. Standardize library usage xref statsmodels#9333

bashtage mentioned this issue Sep 12, 2024

MAINT: Simplify and standardize setup #9354

Merged

4 tasks

bashtage mentioned this issue Sep 13, 2024

MAINT: Backport changes needed for 0.14.3 release #9356

Merged

2 tasks

r-spiewak mentioned this issue Sep 15, 2024

Workflow failure due to bug in Statsmodels for which the fix hasn't yet been released. r-spiewak/sync_project#1

Closed

bashtage closed this as completed Sep 16, 2024

This was referenced Sep 18, 2024

Importing ridgeplot fails with scipy 1.14.1 with "symbol not found in flat namespace '_npy_cabs'" tpvasconcelos/ridgeplot#197

Closed

[Bug]: Version conflict between scipy 1.14.1 and statsmodels 0.14.2 MeteoSwiss/ampycloud#139

Closed

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BUG: Combining SciPy 1.14.1 and statsmodels 0.14.2 on OSX causes "symbol not found in flat namespace '_npy_cabs'" #9333

BUG: Combining SciPy 1.14.1 and statsmodels 0.14.2 on OSX causes "symbol not found in flat namespace '_npy_cabs'" #9333

nickodell commented Aug 22, 2024 •

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INSTALLED VERSIONS

statsmodels

Required Dependencies

Optional Dependencies

Developer Tools

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nickodell commented Sep 18, 2024

BUG: Combining SciPy 1.14.1 and statsmodels 0.14.2 on OSX causes "symbol not found in flat namespace '_npy_cabs'" #9333

BUG: Combining SciPy 1.14.1 and statsmodels 0.14.2 on OSX causes "symbol not found in flat namespace '_npy_cabs'" #9333

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nickodell commented Aug 22, 2024 • edited Loading

Describe the bug

Code Sample, a copy-pastable example if possible

Expected Output

Output of import statsmodels.api as sm; sm.show_versions()

INSTALLED VERSIONS

statsmodels

Required Dependencies

Optional Dependencies

Developer Tools

Additional details:

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MAC:

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nickodell commented Aug 22, 2024 •

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Output of `import statsmodels.api as sm; sm.show_versions()`

bashtage commented Aug 22, 2024 •

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