Tests are failing because the optimization process is not converging:
sccaf -i Zeisel_reg.h5 --optimise --skip-assessment -o output.h5 -s louvain -a 0.89 --produce-rounds-summary
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.index is deprecated and will be removed in a future version. The public classes are available in the top-level namespace.
from pandas.core.index import RangeIndex
INFO:root:Read ann data file: DONE
INFO:root:Run louvain for starting point: DONE
R1norm_cutoff: 0.500000
R2norm_cutoff: 0.050000
Accuracy: 0.000000
======================
Round1 ...
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
/home/travis/virtualenv/python3.6.7/lib/python3.6/site-packages/sklearn/linear_model/_sag.py:330: ConvergenceWarning: The max_iter was reached which means the coef_ did not converge
"the coef_ did not converge", ConvergenceWarning)
The job exceeded the maximum time limit for jobs, and has been terminated.
pcm32
commented
4 years ago
Tests are failing because the optimization process is not converging: