SystemError encountered for app that has been working for months due to Numpy Numba dependency issue

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1

Hi, 2 of my apps suddenly stopped working, even though they have been working for the previous few months. This is the error

SystemError: initialization of _internal failed without raising an exception

From this link and this link and this link, it appears that it is because of a dependency issue with numpy and numba.

It appears that one needs to reinstall numba, which will then install the right version of numpy. But how do I do that when deploying onto the cloud?

I also tried manually editing my requirements.txt to the correct versions (numpy==1.23.1, numba==0.56.4) but it still shows, which indicates the incorrect versions are installed:

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.

numba 0.56.4 requires numpy<1.24,>=1.18, but you have numpy 1.24.3 which is incompatible.

Successfully installed MarkupSafe-2.1.2 altair-4.2.2 attrs-23.1.0 entrypoints-0.4 jinja2-3.1.2 jsonschema-4.17.3 numpy-1.24.3 pandas-2.0.1 pyrsistent-0.19.3 python-dateutil-2.8.2 pytz-2023.3 six-1.16.0 toolz-0.12.0 tzdata-2023.3

I am able to run the app on my local windows device though. So the problem appears to be specific for the linux environment when deploying to streamlit cloud.

Please help!

2

Can you share your requirements.txt file that you are using?

4

Here is the requirements.txt for 1 of my project. The other one is way longer so sharing this instead.

scikit-learn==1.0.2
pandas==1.3.5
shap==0.41.0
matplotlib==3.5.1
pydeck==0.7.1
streamlit==1.11.1
joblib==1.1.0
requests==2.27.1
geopy==2.2.0
numba==0.56.4
numpy==1.23.1
gdown

5

This is for the other project. Apologies for the long list.

absl-py==1.2.0
altair==4.2.0
appdirs==1.4.4
asttokens==2.0.8
astunparse==1.6.3
attrs==22.1.0
audioread==3.0.0
backcall==0.2.0
black==22.10.0
blinker==1.5
cachetools==5.2.0
certifi==2022.9.24
cffi==1.15.1
charset-normalizer==2.1.1
click==8.1.3
colorama==0.4.5
coloredlogs==15.0.1
commonmark==0.9.1
contourpy==1.0.5
cycler==0.11.0
debugpy==1.6.3
decorator==5.1.1
entrypoints==0.4
executing==1.1.1
ffmpeg==1.4
flatbuffers==22.9.24
fonttools==4.37.4
future==0.18.2
gast==0.4.0
gitdb==4.0.9
GitPython==3.1.29
google-auth==2.12.0
google-auth-oauthlib==0.4.6
google-pasta==0.2.0
grpcio==1.49.1
h5py==3.7.0
humanfriendly==10.0
idna==3.4
importlib-metadata==5.0.0
imutils==0.5.4
ipykernel==6.16.0
ipython==8.5.0
jedi==0.18.1
Jinja2==3.1.2
joblib==1.2.0
jsonschema==4.16.0
jupyter-core==4.11.1
jupyter_client==7.4.2
keras==2.10.0
Keras-Preprocessing==1.1.2
kiwisolver==1.4.4
libclang==14.0.6
librosa==0.9.2
llvmlite==0.39.1
loguru==0.6.0
Markdown==3.4.1
MarkupSafe==2.1.1
matplotlib==3.6.0
matplotlib-inline==0.1.6
mpmath==1.2.1
mypy-extensions==0.4.3
nest-asyncio==1.5.6
ninja==1.10.2.4
numba==0.56.3
numpy==1.23.3
oauthlib==3.2.1
onnx==1.12.0
onnxruntime==1.12.1
opencv-python==4.6.0.66
opt-einsum==3.3.0
packaging==21.3
pafy==0.5.5
pandas==1.5.0
parso==0.8.3
pathspec==0.10.1
pickleshare==0.7.5
pilgram==1.2.1
Pillow==9.2.0
platformdirs==2.5.2
pooch==1.6.0
prompt-toolkit==3.0.31
protobuf==3.19.6
psutil==5.9.2
pure-eval==0.2.2
pyarrow==9.0.0
pyasn1==0.4.8
pyasn1-modules==0.2.8
pycocotools==2.0.5
pycparser==2.21
pydeck==0.8.0b4
pydub==0.25.1
pyee==9.0.4
Pygments==2.13.0
Pympler==1.0.1
pyparsing==3.0.9
pyreadline3==3.4.1
pyrsistent==0.18.1
python-dateutil==2.8.2
pytz==2022.4
pytz-deprecation-shim==0.1.0.post0
pyzmq==24.0.1
requests==2.28.1
requests-oauthlib==1.3.1
resampy==0.4.2
rich==12.6.0
rsa==4.9
scikit-learn==1.1.2
scipy==1.9.2
semver==2.13.0
six==1.16.0
smmap==5.0.0
soundfile==0.11.0
stack-data==0.5.1
streamlit==1.13.0
sympy==1.11.1
tabulate==0.9.0
tenacity==8.1.0
tensorboard==2.10.1
tensorboard-data-server==0.6.1
tensorboard-plugin-wit==1.8.1
tensorflow-estimator==2.10.0
tensorflow-hub==0.12.0
tensorflow-io-gcs-filesystem==0.27.0
termcolor==2.0.1
thop==0.1.1.post2209072238
threadpoolctl==3.1.0
toml==0.10.2
tomli==2.0.1
toolz==0.12.0
torch==1.12.1
torchvision==0.13.1
tornado==6.2
tqdm==4.64.1
traitlets==5.4.0
typing_extensions==4.3.0
tzdata==2022.5
tzlocal==4.2
urllib3==1.26.12
validators==0.20.0
watchdog==2.1.9
wcwidth==0.2.5
Werkzeug==2.2.2
win32-setctime==1.1.0
wrapt==1.14.1
youtube-dl==2021.12.17
zipp==3.9.0

6
  • Please share your github repo links
  • You probably don’t need most of the packages, clean it up
  • You also have windows-only packages, which will not run on streamlit cloud
7

Here are the github repo links:

Thanks for the advice on cleaning up the required packages. Will do so!

8

I got it to work.

  1. Deleted my virtual environment and created a new one.
  2. Updated streamlit package to latest.
  3. Installed only necessary packages for app to work.

That solves the issue. Not sure what was the problem though. Might be a clash in dependencies of some of the packages.

9

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