#1129897 python-hmmlearn: FTBFS: FAILED hmmlearn/tests/test_gaussian_hmm.py::TestGaussianHMMWithTiedCovars::test_fit_with_priors[scaling]

#1129897#5
Date:
2026-03-05 23:49:14 UTC
From:
To:
Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202603/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:python-hmmlearn, so that this is still
visible in the BTS web page for this package.

Thanks.
--------------------------------------------------------------------------------
[...]
 debian/rules clean
dh clean --buildsystem=pybuild
   dh_auto_clean -O--buildsystem=pybuild
   dh_autoreconf_clean -O--buildsystem=pybuild
   dh_clean -O--buildsystem=pybuild
 debian/rules binary
dh binary --buildsystem=pybuild
   dh_update_autotools_config -O--buildsystem=pybuild
   dh_autoreconf -O--buildsystem=pybuild
   dh_auto_configure -O--buildsystem=pybuild
   dh_auto_build -O--buildsystem=pybuild
I: pybuild plugin_pyproject:142: Building wheel for python3.14 with "build" module
I: pybuild base:384: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn
* Building wheel...
/usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.

[... snipped ...]

hmmlearn/tests/test_kl_divergence.py .....                               [ 76%]
hmmlearn/tests/test_multinomial_hmm.py ................                  [ 81%]
hmmlearn/tests/test_poisson_hmm.py ............                          [ 85%]
hmmlearn/tests/test_utils.py ...                                         [ 86%]
hmmlearn/tests/test_variational_categorical.py ............              [ 90%]
hmmlearn/tests/test_variational_gaussian.py ............................ [ 98%]
....                                                                     [100%]

=============================== warnings summary ===============================
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gaussian_hmm.py: 1 warning
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_multisequence.py: 5 warnings
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py: 12 warnings
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_poisson_hmm.py: 1 warning
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 27 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/base.py:509: RuntimeWarning: underflow encountered in multiply
    posteriors = fwdlattice * bwdlattice

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_multisequence.py: 4 warnings
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py: 13 warnings
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_poisson_hmm.py: 1 warning
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 27 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/utils.py:29: RuntimeWarning: underflow encountered in divide
    a /= a_sum

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithSphericalCovars::test_fit_zero_variance[scaling]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/base.py:598: RuntimeWarning: overflow encountered in exp
    return np.exp(self._compute_log_likelihood(X))

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithSphericalCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithSphericalCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/utils.py:55: RuntimeWarning: invalid value encountered in subtract
    a -= a_lse

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/hmm.py:744: RuntimeWarning: invalid value encountered in divide
    self.weights_ = w_n / w_d

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/hmm.py:756: RuntimeWarning: invalid value encountered in divide
    self.means_ = m_n / m_d[:, :, None]

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[log]
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithFullCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithFullCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/hmm.py:809: RuntimeWarning: invalid value encountered in divide
    self.covars_ = c_n / c_d

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[log]
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithFullCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithFullCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/_emissions.py:208: RuntimeWarning: divide by zero encountered in log
    log_cur_weights = np.log(self.weights_[i_comp])

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_categorical.py: 10 warnings
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 20 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/base.py:1215: RuntimeWarning: underflow encountered in exp
    self.startprob_subnorm_ = np.exp(startprob_log_subnorm)

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_categorical.py: 8 warnings
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 12 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/base.py:1220: RuntimeWarning: underflow encountered in exp
    self.transmat_subnorm_ = np.exp(transmat_log_subnorm)

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_categorical.py: 1 warning
.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 31 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/base.py:1153: RuntimeWarning: underflow encountered in exp
    return np.exp(self._compute_subnorm_log_likelihood(X))

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 30 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/_emissions.py:153: RuntimeWarning: underflow encountered in matmul
    stats['obs'] += posteriors.T @ X

.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 12 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_hmmlearn/build/hmmlearn/_emissions.py:157: RuntimeWarning: underflow encountered in matmul
    stats['obs**2'] += posteriors.T @ X**2

            sorted(orig.ravel().tolist()),
            sorted(h_learn._covars_.ravel().tolist()),
            10)
E       AssertionError:
E       Not equal to tolerance rtol=10, atol=0
E
E       Mismatched elements: 2 / 9 (22.2%)
E       Max absolute difference among violations: 0.02119294
E       Max relative difference among violations: 48.39799969
E        ACTUAL: array([-0.215859, -0.215859, -0.020755, -0.020755,  0.370281,  0.370281,
E               0.624374,  0.679083,  3.635532])
E        DESIRED: array([-1.927959e-01, -1.927959e-01,  4.378887e-04,  4.378887e-04,
E               3.559196e-01,  3.559196e-01,  6.293362e-01,  6.718302e-01,
E               3.494150e+00])

hmmlearn/tests/test_gaussian_hmm.py:251: AssertionError
=============================== warnings summary ===============================
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gaussian_hmm.py: 2 warnings
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_multisequence.py: 4 warnings
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py: 13 warnings
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_poisson_hmm.py: 1 warning
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 27 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/utils.py:29: RuntimeWarning: underflow encountered in divide
    a /= a_sum

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gaussian_hmm.py: 2 warnings
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 30 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/_emissions.py:153: RuntimeWarning: underflow encountered in matmul
    stats['obs'] += posteriors.T @ X

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gaussian_hmm.py: 1 warning
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_multisequence.py: 5 warnings
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py: 12 warnings
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_poisson_hmm.py: 1 warning
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 27 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/base.py:509: RuntimeWarning: underflow encountered in multiply
    posteriors = fwdlattice * bwdlattice

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gaussian_hmm.py::TestGaussianHMMWithFullCovars::test_fit_zero_variance[scaling]
  /usr/lib/python3/dist-packages/numpy/_core/numeric.py:995: RuntimeWarning: underflow encountered in multiply
    return multiply(a.ravel()[:, newaxis], b.ravel()[newaxis, :], out)

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithSphericalCovars::test_fit_zero_variance[scaling]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/base.py:598: RuntimeWarning: overflow encountered in exp
    return np.exp(self._compute_log_likelihood(X))

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithSphericalCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithSphericalCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/utils.py:55: RuntimeWarning: invalid value encountered in subtract
    a -= a_lse

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/hmm.py:744: RuntimeWarning: invalid value encountered in divide
    self.weights_ = w_n / w_d

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/hmm.py:756: RuntimeWarning: invalid value encountered in divide
    self.means_ = m_n / m_d[:, :, None]

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[log]
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithFullCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithFullCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/hmm.py:809: RuntimeWarning: invalid value encountered in divide
    self.covars_ = c_n / c_d

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithDiagCovars::test_fit_zero_variance[log]
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithFullCovars::test_fit_zero_variance[scaling]
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_gmm_hmm_new.py::TestGMMHMMWithFullCovars::test_fit_zero_variance[log]
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/_emissions.py:208: RuntimeWarning: divide by zero encountered in log
    log_cur_weights = np.log(self.weights_[i_comp])

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_categorical.py: 10 warnings
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 20 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/base.py:1215: RuntimeWarning: underflow encountered in exp
    self.startprob_subnorm_ = np.exp(startprob_log_subnorm)

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_categorical.py: 8 warnings
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 12 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/base.py:1220: RuntimeWarning: underflow encountered in exp
    self.transmat_subnorm_ = np.exp(transmat_log_subnorm)

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_categorical.py: 1 warning
.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 31 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/base.py:1153: RuntimeWarning: underflow encountered in exp
    return np.exp(self._compute_subnorm_log_likelihood(X))

.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/tests/test_variational_gaussian.py: 12 warnings
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_hmmlearn/build/hmmlearn/_emissions.py:157: RuntimeWarning: underflow encountered in matmul
    stats['obs**2'] += posteriors.T @ X**2