Source: python-skbio Version: 0.6.1-2 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu...@debian.org Usertags: ftbfs-20240702 ftbfs-trixie
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[1]: Entering directory '/<<PKGBUILDDIR>>' > echo No testing for the -doc package > No testing for the -doc package > make[1]: Leaving directory '/<<PKGBUILDDIR>>' > dh_auto_test -O--buildsystem=pybuild -Npython-skbio-doc > I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build; > python3.11 -m pytest > ============================= test session starts > ============================== > platform linux -- Python 3.11.9, pytest-8.2.2, pluggy-1.5.0 > rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build > configfile: pyproject.toml > collected 2761 items > > skbio/alignment/tests/test_pairwise.py ......................... [ > 0%] > skbio/alignment/tests/test_path.py ................. [ > 1%] > skbio/alignment/tests/test_ssw.py ........................... [ > 2%] > skbio/alignment/tests/test_tabular_msa.py .............................. [ > 3%] > ........................................................................ [ > 6%] > ........................................................................ [ > 8%] > ........................................................................ [ > 11%] > ........................................................................ [ > 14%] > ........................................................................ [ > 16%] > ........... [ > 17%] > skbio/diversity/alpha/tests/test_ace.py .. [ > 17%] > skbio/diversity/alpha/tests/test_base.py .....................F...... [ > 18%] > skbio/diversity/alpha/tests/test_chao1.py ... [ > 18%] > skbio/diversity/alpha/tests/test_gini.py .... [ > 18%] > skbio/diversity/alpha/tests/test_lladser.py ............ [ > 18%] > skbio/diversity/alpha/tests/test_pd.py ................ [ > 19%] > skbio/diversity/beta/tests/test_unifrac.py ............................ [ > 20%] > skbio/diversity/tests/test_block.py ........... [ > 20%] > skbio/diversity/tests/test_driver.py ................................... [ > 22%] > .. [ > 22%] > skbio/diversity/tests/test_util.py ................ [ > 22%] > skbio/embedding/tests/test_embedding.py ................... [ > 23%] > skbio/embedding/tests/test_protein.py .............. [ > 23%] > skbio/io/format/tests/test_base.py ................................ [ > 25%] > skbio/io/format/tests/test_binary_dm.py ......... [ > 25%] > skbio/io/format/tests/test_biom.py ... [ > 25%] > skbio/io/format/tests/test_blast6.py ........... [ > 25%] > skbio/io/format/tests/test_blast7.py .............. [ > 26%] > skbio/io/format/tests/test_clustal.py ............. [ > 26%] > skbio/io/format/tests/test_embed.py ........ [ > 27%] > skbio/io/format/tests/test_embl.py ............................... [ > 28%] > skbio/io/format/tests/test_emptyfile.py .. [ > 28%] > skbio/io/format/tests/test_fasta.py ................ [ > 28%] > skbio/io/format/tests/test_fastq.py ............... [ > 29%] > skbio/io/format/tests/test_genbank.py ..................... [ > 30%] > skbio/io/format/tests/test_gff3.py ........................ [ > 31%] > skbio/io/format/tests/test_lsmat.py ....... [ > 31%] > skbio/io/format/tests/test_newick.py ....... [ > 31%] > skbio/io/format/tests/test_ordination.py ..... [ > 31%] > skbio/io/format/tests/test_phylip.py ....... [ > 32%] > skbio/io/format/tests/test_qseq.py ...... [ > 32%] > skbio/io/format/tests/test_sample_metadata.py .... [ > 32%] > skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [ > 32%] > skbio/io/format/tests/test_stockholm.py ................................ [ > 33%] > ........................................... [ > 35%] > skbio/io/format/tests/test_taxdump.py ...... [ > 35%] > skbio/io/tests/test_iosources.py .......... [ > 35%] > skbio/io/tests/test_registry.py ........................................ [ > 37%] > ...................................................... [ > 39%] > skbio/io/tests/test_util.py .......................................XXsss [ > 40%] > sssssssssssssssssssssssssss..................................XX......... [ > 43%] > .........................XX..................................XX......... [ > 46%] > .........................XX..... [ > 47%] > skbio/metadata/tests/test_enan.py ... [ > 47%] > skbio/metadata/tests/test_intersection.py ............... [ > 47%] > skbio/metadata/tests/test_interval.py .................................. [ > 49%] > ..................................... [ > 50%] > skbio/metadata/tests/test_io.py ........................................ [ > 51%] > .................................................................. [ > 54%] > skbio/metadata/tests/test_metadata.py .................................. [ > 55%] > .......................... [ > 56%] > skbio/metadata/tests/test_metadata_column.py ........................... [ > 57%] > .............................................. [ > 59%] > skbio/metadata/tests/test_missing.py ................ [ > 59%] > skbio/metadata/tests/test_mixin.py ..................................... [ > 61%] > ............................................................. [ > 63%] > skbio/sequence/tests/test_alphabet.py ..... [ > 63%] > skbio/sequence/tests/test_distance.py .......................... [ > 64%] > skbio/sequence/tests/test_dna.py ... [ > 64%] > skbio/sequence/tests/test_genetic_code.py .......................... [ > 65%] > skbio/sequence/tests/test_grammared_sequence.py ........................ [ > 66%] > ......................... [ > 67%] > skbio/sequence/tests/test_nucleotide_sequences.py ...................... [ > 67%] > ....... [ > 68%] > skbio/sequence/tests/test_protein.py ........... [ > 68%] > skbio/sequence/tests/test_rna.py ... [ > 68%] > skbio/sequence/tests/test_sequence.py .................................. [ > 69%] > ........................................................................ [ > 72%] > ........................................................................ [ > 75%] > ........................................................................ [ > 77%] > ............. [ > 78%] > skbio/sequence/tests/test_substitution.py ........ [ > 78%] > skbio/stats/distance/tests/test_anosim.py .... [ > 78%] > skbio/stats/distance/tests/test_base.py ................................ [ > 79%] > ............................................................... [ > 82%] > skbio/stats/distance/tests/test_bioenv.py ................. [ > 82%] > skbio/stats/distance/tests/test_mantel.py .............................. [ > 83%] > .............. [ > 84%] > skbio/stats/distance/tests/test_permanova.py ..... [ > 84%] > skbio/stats/distance/tests/test_permdisp.py .............. [ > 85%] > skbio/stats/evolve/tests/test_hommola.py ............ [ > 85%] > skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ > 85%] > ..... [ > 85%] > skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ > 85%] > skbio/stats/ordination/tests/test_ordination_results.py ............ [ > 86%] > skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ > 86%] > ....... [ > 86%] > skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ > 86%] > skbio/stats/ordination/tests/test_util.py .......... [ > 87%] > skbio/stats/tests/test_composition.py .................................. [ > 88%] > ................................................. [ > 90%] > skbio/stats/tests/test_gradient.py .......................... [ > 91%] > skbio/stats/tests/test_misc.py ... [ > 91%] > skbio/stats/tests/test_power.py ........................................ [ > 92%] > ... [ > 92%] > skbio/stats/tests/test_subsample.py ............ [ > 93%] > skbio/table/tests/test_base.py . [ > 93%] > skbio/tests/test_base.py ..... [ > 93%] > skbio/tests/test_workflow.py ................. [ > 94%] > skbio/tree/tests/test_majority_rule.py ...... [ > 94%] > skbio/tree/tests/test_nj.py ........... [ > 94%] > skbio/tree/tests/test_tree.py .......................................... [ > 96%] > ................................................... [ > 98%] > skbio/util/tests/test_decorator.py ........ [ > 98%] > skbio/util/tests/test_misc.py .................... [ > 99%] > skbio/util/tests/test_plotting.py ...... [ > 99%] > skbio/util/tests/test_testing.py ............... > [100%] > > =================================== FAILURES > =================================== > ____________________________ BaseTests.test_shannon > ____________________________ > > self = <skbio.diversity.alpha.tests.test_base.BaseTests > testMethod=test_shannon> > > def test_shannon(self): > self.assertAlmostEqual(shannon([5, 5]), 0.693147181) > self.assertEqual(shannon([5, 5], base=2), 1) > self.assertAlmostEqual(shannon([5, 5], base=10), 0.301029996) > > # taxa with 0 counts are excluded from calculation > self.assertAlmostEqual(shannon([1, 2, 3, 4]), 1.279854226) > self.assertAlmostEqual(shannon([0, 1, 2, 3, 4]), 1.279854226) > > # Shannon index of a single-taxon community is always 0 > self.assertEqual(shannon(np.array([5])), 0) > > # Shannon index cannot be calculated for an empty community > self.assertTrue(np.isnan(shannon([0, 0]))) > > # NaN still holds if input is empty (instead of 0's), this behavior is > # different from scipy.stats.entropy, which would return 0.0. > self.assertTrue(np.isnan(shannon([]))) > > # Exponential of Shannon index > self.assertAlmostEqual(shannon([1, 2, 3, 4], exp=True), 3.596115467) > > # Equally abundant taxa, exp(H) = # taxa > > self.assertEqual(shannon([5, 5, 5], exp=True), 3.0) > E AssertionError: 3.000000000000001 != 3.0 > > skbio/diversity/alpha/tests/test_base.py:319: AssertionError > =============================== warnings summary > =============================== > skbio/alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:56: > DeprecationWarning: make_identity_substitution_matrix is deprecated as of > 0.4.0. It has been replaced by the SubstitutionMatrix class. Additional > details at https://github.com/scikit-bio/scikit-bio/pull/1913. > warn( > > skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:56: > DeprecationWarning: local_pairwise_align_ssw is deprecated as of 0.5.8. It > will be removed in favor of more general purpose and performant aligners. > Additional details at https://github.com/scikit-bio/scikit-bio/issues/1814. > warn( > > skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment/_tabular_msa.py:1648: > RuntimeWarning: invalid value encountered in divide > gap_freqs /= length > > skbio/diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:56: > DeprecationWarning: partial_beta_diversity is deprecated as of 0.5.0. The > return type is unstable. Developer caution is advised. The resulting > DistanceMatrix object will include zeros when distance has not been > calculated, and therefore can be misleading. > warn( > > skbio/metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing > skbio/metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true > skbio/metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/_metadata.py:1102: > FutureWarning: Setting an item of incompatible dtype is deprecated and will > raise in a future error of pandas. Value '['missing']' has dtype incompatible > with float64, please explicitly cast to a compatible dtype first. > series[missing.index] = missing > > skbio/metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object > skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_missing.py:53: > FutureWarning: Mismatched null-like values nan and None found. In a future > version, pandas equality-testing functions (e.g. assert_frame_equal) will > consider these not-matching and raise. > pdt.assert_series_equal(missing, series.astype(object)) > > skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool > skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/metadata/tests/test_missing.py:31: > FutureWarning: Mismatched null-like values nan and None found. In a future > version, pandas equality-testing functions (e.g. assert_frame_equal) will > consider these not-matching and raise. > pdt.assert_series_equal(missing, series[1:].astype(object)) > > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/_grammared_sequence.py:639: > DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0 > warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning) > > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars > skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars > skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars > skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars > skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars > skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars > skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/_grammared_sequence.py:313: > DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0 > warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning) > > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/_grammared_sequence.py:572: > DeprecationWarning: nondenengerates is deprecated as of 0.5.0. > warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning) > > skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/_sequence.py:1824: > RuntimeWarning: invalid value encountered in divide > obs_counts = obs_counts / len(self) > > skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/_mantel.py:364: > ConstantInputWarning: All values in data are exactly equal; results may not > be reliable. > warnings.warn(ConstantInputWarning()) > > skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/_mantel.py:483: > ConstantInputWarning: All values in data are exactly equal; results may not > be reliable. > warnings.warn(ConstantInputWarning()) > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: > RuntimeWarning: The result contains negative eigenvalues. Please compare > their magnitude with the magnitude of some of the largest positive > eigenvalues. If the negative ones are smaller, it's probably safe to ignore > them, but if they are large in magnitude, the results won't be useful. See > the Notes section for more details. The smallest eigenvalue is > -0.006573677549550485 and the largest is 0.17668321589384078. > warn( > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: > RuntimeWarning: The result contains negative eigenvalues. Please compare > their magnitude with the magnitude of some of the largest positive > eigenvalues. If the negative ones are smaller, it's probably safe to ignore > them, but if they are large in magnitude, the results won't be useful. See > the Notes section for more details. The smallest eigenvalue is > -13.54184654426961 and the largest is 16.5872013747859. > warn( > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: > RuntimeWarning: The result contains negative eigenvalues. Please compare > their magnitude with the magnitude of some of the largest positive > eigenvalues. If the negative ones are smaller, it's probably safe to ignore > them, but if they are large in magnitude, the results won't be useful. See > the Notes section for more details. The smallest eigenvalue is > -15.629533932395208 and the largest is 20.90315427793891. > warn( > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:190: > RuntimeWarning: invalid value encountered in divide > proportion_explained = eigvals / sum_eigenvalues > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/_permdisp.py:304: > ConstantInputWarning: Each of the input arrays is constant; the F statistic > is not defined or infinite > stat, _ = f_oneway(*groups) > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: > RuntimeWarning: The result contains negative eigenvalues. Please compare > their magnitude with the magnitude of some of the largest positive > eigenvalues. If the negative ones are smaller, it's probably safe to ignore > them, but if they are large in magnitude, the results won't be useful. See > the Notes section for more details. The smallest eigenvalue is > -0.007758325147780521 and the largest is 2.7077929489469237. > warn( > > skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape > /usr/lib/python3.11/unittest/case.py:678: DeprecationWarning: It is > deprecated to return a value that is not None from a test case (<bound method > TestRDAErrors.test_shape of > <skbio.stats.ordination.tests.test_redundancy_analysis.TestRDAErrors > testMethod=test_shape>>) > return self.run(*args, **kwds) > > skbio/stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:60: > UserWarning: multiplicative_replacement is deprecated as of 0.6.0. > warn(f"{func.__name__} is deprecated as of {ver}.") > > skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test > /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:531: > RuntimeWarning: Precision loss occurred in moment calculation due to > catastrophic cancellation. This occurs when the data are nearly identical. > Results may be unreliable. > res = hypotest_fun_out(*samples, **kwds) > > skbio/stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_warning.py:60: > UserWarning: ancom is deprecated as of 0.6.0. > warn(f"{func.__name__} is deprecated as of {ver}.") > > skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/composition.py:1654: > ConstantInputWarning: Each of the input arrays is constant; the F statistic > is not defined or infinite > return test(*[x[cats == k] for k in cs]) > > skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/composition.py:945: > RuntimeWarning: divide by zero encountered in log > X_log = np.log(mat) > > skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr > /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: > RuntimeWarning: invalid value encountered in subtract > X -= avg[:, None] > > skbio/stats/tests/test_composition.py::VLRTests::test_vlr > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/composition.py:829: > RuntimeWarning: divide by zero encountered in log > x = np.log(x) > > skbio/stats/tests/test_composition.py::VLRTests::test_vlr > /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: > invalid value encountered in subtract > x = asanyarray(arr - arrmean) > > skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/gradient.py:167: > FutureWarning: Setting an item of incompatible dtype is deprecated and will > raise in a future error of pandas. Value '6.357142857142857' has dtype > incompatible with int64, please explicitly cast to a compatible dtype first. > trajectories.loc[idx] = ( > > -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html > =========================== short test summary info > ============================ > FAILED skbio/diversity/alpha/tests/test_base.py::BaseTests::test_shannon - > As... > = 1 failed, 2720 passed, 30 skipped, 10 xpassed, 56 warnings in 96.32s > (0:01:36) = > E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build; python3.11 -m pytest > I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build; > python3.12 -m pytest > ============================= test session starts > ============================== > platform linux -- Python 3.12.4, pytest-8.2.2, pluggy-1.5.0 > rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build > configfile: pyproject.toml > collected 2761 items > > skbio/alignment/tests/test_pairwise.py ......................... [ > 0%] > skbio/alignment/tests/test_path.py ................. [ > 1%] > skbio/alignment/tests/test_ssw.py ........................... [ > 2%] > skbio/alignment/tests/test_tabular_msa.py .............................. [ > 3%] > ........................................................................ [ > 6%] > ........................................................................ [ > 8%] > ........................................................................ [ > 11%] > ........................................................................ [ > 14%] > ........................................................................ [ > 16%] > ........... [ > 17%] > skbio/diversity/alpha/tests/test_ace.py .. [ > 17%] > skbio/diversity/alpha/tests/test_base.py .....................F...... [ > 18%] > skbio/diversity/alpha/tests/test_chao1.py ... [ > 18%] > skbio/diversity/alpha/tests/test_gini.py .... [ > 18%] > skbio/diversity/alpha/tests/test_lladser.py ............ [ > 18%] > skbio/diversity/alpha/tests/test_pd.py ................ [ > 19%] > skbio/diversity/beta/tests/test_unifrac.py ............................ [ > 20%] > skbio/diversity/tests/test_block.py ........... [ > 20%] > skbio/diversity/tests/test_driver.py ................................... [ > 22%] > .. [ > 22%] > skbio/diversity/tests/test_util.py ................ [ > 22%] > skbio/embedding/tests/test_embedding.py ................... [ > 23%] > skbio/embedding/tests/test_protein.py .............. [ > 23%] > skbio/io/format/tests/test_base.py ................................ [ > 25%] > skbio/io/format/tests/test_binary_dm.py ......... [ > 25%] > skbio/io/format/tests/test_biom.py ... [ > 25%] > skbio/io/format/tests/test_blast6.py ........... [ > 25%] > skbio/io/format/tests/test_blast7.py .............. [ > 26%] > skbio/io/format/tests/test_clustal.py ............. [ > 26%] > skbio/io/format/tests/test_embed.py ........ [ > 27%] > skbio/io/format/tests/test_embl.py ............................... [ > 28%] > skbio/io/format/tests/test_emptyfile.py .. [ > 28%] > skbio/io/format/tests/test_fasta.py ................ [ > 28%] > skbio/io/format/tests/test_fastq.py ............... [ > 29%] > skbio/io/format/tests/test_genbank.py ..................... [ > 30%] > skbio/io/format/tests/test_gff3.py ........................ [ > 31%] > skbio/io/format/tests/test_lsmat.py ....... [ > 31%] > skbio/io/format/tests/test_newick.py ....... [ > 31%] > skbio/io/format/tests/test_ordination.py ..... [ > 31%] > skbio/io/format/tests/test_phylip.py ....... [ > 32%] > skbio/io/format/tests/test_qseq.py ...... [ > 32%] > skbio/io/format/tests/test_sample_metadata.py .... [ > 32%] > skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [ > 32%] > skbio/io/format/tests/test_stockholm.py ................................ [ > 33%] > ........................................... [ > 35%] > skbio/io/format/tests/test_taxdump.py ...... [ > 35%] > skbio/io/tests/test_iosources.py .......... [ > 35%] > skbio/io/tests/test_registry.py ........................................ [ > 37%] > ...................................................... [ > 39%] > skbio/io/tests/test_util.py .......................................XXsss [ > 40%] > sssssssssssssssssssssssssss..................................XX......... [ > 43%] > .........................XX..................................XX......... [ > 46%] > .........................XX..... [ > 47%] > skbio/metadata/tests/test_enan.py ... [ > 47%] > skbio/metadata/tests/test_intersection.py ............... [ > 47%] > skbio/metadata/tests/test_interval.py .................................. [ > 49%] > ..................................... [ > 50%] > skbio/metadata/tests/test_io.py ........................................ [ > 51%] > .................................................................. [ > 54%] > skbio/metadata/tests/test_metadata.py .................................. [ > 55%] > .......................... [ > 56%] > skbio/metadata/tests/test_metadata_column.py ........................... [ > 57%] > .............................................. [ > 59%] > skbio/metadata/tests/test_missing.py ................ [ > 59%] > skbio/metadata/tests/test_mixin.py ..................................... [ > 61%] > ............................................................. [ > 63%] > skbio/sequence/tests/test_alphabet.py ..... [ > 63%] > skbio/sequence/tests/test_distance.py .......................... [ > 64%] > skbio/sequence/tests/test_dna.py ... [ > 64%] > skbio/sequence/tests/test_genetic_code.py .......................... [ > 65%] > skbio/sequence/tests/test_grammared_sequence.py ........................ [ > 66%] > ......................... [ > 67%] > skbio/sequence/tests/test_nucleotide_sequences.py ...................... [ > 67%] > ....... [ > 68%] > skbio/sequence/tests/test_protein.py ........... [ > 68%] > skbio/sequence/tests/test_rna.py ... [ > 68%] > skbio/sequence/tests/test_sequence.py .................................. [ > 69%] > ........................................................................ [ > 72%] > ........................................................................ [ > 75%] > ........................................................................ [ > 77%] > ............. [ > 78%] > skbio/sequence/tests/test_substitution.py ........ [ > 78%] > skbio/stats/distance/tests/test_anosim.py .... [ > 78%] > skbio/stats/distance/tests/test_base.py ................................ [ > 79%] > ............................................................... [ > 82%] > skbio/stats/distance/tests/test_bioenv.py ................. [ > 82%] > skbio/stats/distance/tests/test_mantel.py .............................. [ > 83%] > .............. [ > 84%] > skbio/stats/distance/tests/test_permanova.py ..... [ > 84%] > skbio/stats/distance/tests/test_permdisp.py .............. [ > 85%] > skbio/stats/evolve/tests/test_hommola.py ............ [ > 85%] > skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [ > 85%] > ..... [ > 85%] > skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [ > 85%] > skbio/stats/ordination/tests/test_ordination_results.py ............ [ > 86%] > skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [ > 86%] > ....... [ > 86%] > skbio/stats/ordination/tests/test_redundancy_analysis.py .... [ > 86%] > skbio/stats/ordination/tests/test_util.py .......... [ > 87%] > skbio/stats/tests/test_composition.py .................................. [ > 88%] > ................................................. [ > 90%] > skbio/stats/tests/test_gradient.py .......................... [ > 91%] > skbio/stats/tests/test_misc.py ... [ > 91%] > skbio/stats/tests/test_power.py ........................................ [ > 92%] > ... [ > 92%] > skbio/stats/tests/test_subsample.py ............ [ > 93%] > skbio/table/tests/test_base.py . [ > 93%] > skbio/tests/test_base.py ..... [ > 93%] > skbio/tests/test_workflow.py ................. [ > 94%] > skbio/tree/tests/test_majority_rule.py ...... [ > 94%] > skbio/tree/tests/test_nj.py ........... [ > 94%] > skbio/tree/tests/test_tree.py .......................................... [ > 96%] > ................................................... [ > 98%] > skbio/util/tests/test_decorator.py ........ [ > 98%] > skbio/util/tests/test_misc.py .................... [ > 99%] > skbio/util/tests/test_plotting.py ...... [ > 99%] > skbio/util/tests/test_testing.py ............... > [100%] > > =================================== FAILURES > =================================== > ____________________________ BaseTests.test_shannon > ____________________________ > > self = <skbio.diversity.alpha.tests.test_base.BaseTests > testMethod=test_shannon> > > def test_shannon(self): > self.assertAlmostEqual(shannon([5, 5]), 0.693147181) > self.assertEqual(shannon([5, 5], base=2), 1) > self.assertAlmostEqual(shannon([5, 5], base=10), 0.301029996) > > # taxa with 0 counts are excluded from calculation > self.assertAlmostEqual(shannon([1, 2, 3, 4]), 1.279854226) > self.assertAlmostEqual(shannon([0, 1, 2, 3, 4]), 1.279854226) > > # Shannon index of a single-taxon community is always 0 > self.assertEqual(shannon(np.array([5])), 0) > > # Shannon index cannot be calculated for an empty community > self.assertTrue(np.isnan(shannon([0, 0]))) > > # NaN still holds if input is empty (instead of 0's), this behavior is > # different from scipy.stats.entropy, which would return 0.0. > self.assertTrue(np.isnan(shannon([]))) > > # Exponential of Shannon index > self.assertAlmostEqual(shannon([1, 2, 3, 4], exp=True), 3.596115467) > > # Equally abundant taxa, exp(H) = # taxa > > self.assertEqual(shannon([5, 5, 5], exp=True), 3.0) > E AssertionError: 3.000000000000001 != 3.0 > > skbio/diversity/alpha/tests/test_base.py:319: AssertionError > =============================== warnings summary > =============================== > skbio/alignment/tests/test_pairwise.py::PairwiseAlignmentTests::test_compute_score_and_traceback_matrices > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:56: > DeprecationWarning: make_identity_substitution_matrix is deprecated as of > 0.4.0. It has been replaced by the SubstitutionMatrix class. Additional > details at https://github.com/scikit-bio/scikit-bio/pull/1913. > warn( > > skbio/alignment/tests/test_ssw.py::TestAlignStripedSmithWaterman::test_invalid_type > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:56: > DeprecationWarning: local_pairwise_align_ssw is deprecated as of 0.5.8. It > will be removed in favor of more general purpose and performant aligners. > Additional details at https://github.com/scikit-bio/scikit-bio/issues/1814. > warn( > > skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/alignment/_tabular_msa.py:1648: > RuntimeWarning: invalid value encountered in divide > gap_freqs /= length > > skbio/diversity/tests/test_block.py::ParallelBetaDiversity::test_block_beta_diversity > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:56: > DeprecationWarning: partial_beta_diversity is deprecated as of 0.5.0. The > return type is unstable. Developer caution is advised. The resulting > DistanceMatrix object will include zeros when distance has not been > calculated, and therefore can be misleading. > warn( > > skbio/metadata/tests/test_io.py::TestSave::test_numeric_metadata_column_insdc_missing > skbio/metadata/tests/test_metadata_column.py::TestToSeries::test_encode_missing_true > skbio/metadata/tests/test_metadata_column.py::TestToDataframe::test_encode_missing_true > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/metadata/_metadata.py:1102: > FutureWarning: Setting an item of incompatible dtype is deprecated and will > raise in a future error of pandas. Value '['missing']' has dtype incompatible > with float64, please explicitly cast to a compatible dtype first. > series[missing.index] = missing > > skbio/metadata/tests/test_missing.py::TestISNDC::test_roundtrip_all_missing_object > skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_all_missing_object > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/metadata/tests/test_missing.py:53: > FutureWarning: Mismatched null-like values nan and None found. In a future > version, pandas equality-testing functions (e.g. assert_frame_equal) will > consider these not-matching and raise. > pdt.assert_series_equal(missing, series.astype(object)) > > skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_bool > skbio/metadata/tests/test_missing.py::TestOmitted::test_roundtrip_string > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/metadata/tests/test_missing.py:31: > FutureWarning: Mismatched null-like values nan and None found. In a future > version, pandas equality-testing functions (e.g. assert_frame_equal) will > consider these not-matching and raise. > pdt.assert_series_equal(missing, series[1:].astype(object)) > > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/sequence/_grammared_sequence.py:639: > DeprecationWarning: has_nondegenerates is deprecated as of 0.5.0 > warn("has_nondegenerates is deprecated as of 0.5.0", DeprecationWarning) > > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars > skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars > skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars > skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars > skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars > skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars > skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/sequence/_grammared_sequence.py:313: > DeprecationWarning: nondegenerate_chars is deprecated as of 0.5.0 > warn("nondegenerate_chars is deprecated as of 0.5.0", DeprecationWarning) > > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/sequence/_grammared_sequence.py:572: > DeprecationWarning: nondenengerates is deprecated as of 0.5.0. > warn("nondenengerates is deprecated as of 0.5.0.", DeprecationWarning) > > skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/sequence/_sequence.py:1824: > RuntimeWarning: invalid value encountered in divide > obs_counts = obs_counts / len(self) > > skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/distance/_mantel.py:364: > ConstantInputWarning: All values in data are exactly equal; results may not > be reliable. > warnings.warn(ConstantInputWarning()) > > skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/distance/_mantel.py:483: > ConstantInputWarning: All values in data are exactly equal; results may not > be reliable. > warnings.warn(ConstantInputWarning()) > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_call_via_series > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: > RuntimeWarning: The result contains negative eigenvalues. Please compare > their magnitude with the magnitude of some of the largest positive > eigenvalues. If the negative ones are smaller, it's probably safe to ignore > them, but if they are large in magnitude, the results won't be useful. See > the Notes section for more details. The smallest eigenvalue is > -0.006573677549550485 and the largest is 0.17668321589384078. > warn( > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: > RuntimeWarning: The result contains negative eigenvalues. Please compare > their magnitude with the magnitude of some of the largest positive > eigenvalues. If the negative ones are smaller, it's probably safe to ignore > them, but if they are large in magnitude, the results won't be useful. See > the Notes section for more details. The smallest eigenvalue is > -13.54184654426961 and the largest is 16.5872013747859. > warn( > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: > RuntimeWarning: The result contains negative eigenvalues. Please compare > their magnitude with the magnitude of some of the largest positive > eigenvalues. If the negative ones are smaller, it's probably safe to ignore > them, but if they are large in magnitude, the results won't be useful. See > the Notes section for more details. The smallest eigenvalue is > -15.629533932395208 and the largest is 20.90315427793891. > warn( > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:190: > RuntimeWarning: invalid value encountered in divide > proportion_explained = eigvals / sum_eigenvalues > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/distance/_permdisp.py:304: > ConstantInputWarning: Each of the input arrays is constant; the F statistic > is not defined or infinite > stat, _ = f_oneway(*groups) > > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results > skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:146: > RuntimeWarning: The result contains negative eigenvalues. Please compare > their magnitude with the magnitude of some of the largest positive > eigenvalues. If the negative ones are smaller, it's probably safe to ignore > them, but if they are large in magnitude, the results won't be useful. See > the Notes section for more details. The smallest eigenvalue is > -0.007758325147780521 and the largest is 2.7077929489469237. > warn( > > skbio/stats/ordination/tests/test_redundancy_analysis.py::TestRDAErrors::test_shape > /usr/lib/python3.12/unittest/case.py:690: DeprecationWarning: It is > deprecated to return a value that is not None from a test case (<bound method > TestRDAErrors.test_shape of > <skbio.stats.ordination.tests.test_redundancy_analysis.TestRDAErrors > testMethod=test_shape>>) > return self.run(*args, **kwds) > > skbio/stats/tests/test_composition.py::CompositionTests::test_multiplicative_replacement > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:60: > UserWarning: multiplicative_replacement is deprecated as of 0.6.0. > warn(f"{func.__name__} is deprecated as of {ver}.") > > skbio/stats/tests/test_composition.py::AncomTests::test_ancom_alternative_test > /usr/lib/python3/dist-packages/scipy/stats/_axis_nan_policy.py:531: > RuntimeWarning: Precision loss occurred in moment calculation due to > catastrophic cancellation. This occurs when the data are nearly identical. > Results may be unreliable. > res = hypotest_fun_out(*samples, **kwds) > > skbio/stats/tests/test_composition.py::AncomTests::test_ancom_multiple_comparisons_deprecated > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/util/_warning.py:60: > UserWarning: ancom is deprecated as of 0.6.0. > warn(f"{func.__name__} is deprecated as of {ver}.") > > skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/composition.py:1654: > ConstantInputWarning: Each of the input arrays is constant; the F statistic > is not defined or infinite > return test(*[x[cats == k] for k in cs]) > > skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/composition.py:945: > RuntimeWarning: divide by zero encountered in log > X_log = np.log(mat) > > skbio/stats/tests/test_composition.py::VLRTests::test_pairwise_vlr > /usr/lib/python3/dist-packages/numpy/lib/function_base.py:2742: > RuntimeWarning: invalid value encountered in subtract > X -= avg[:, None] > > skbio/stats/tests/test_composition.py::VLRTests::test_vlr > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/composition.py:829: > RuntimeWarning: divide by zero encountered in log > x = np.log(x) > > skbio/stats/tests/test_composition.py::VLRTests::test_vlr > /usr/lib/python3/dist-packages/numpy/core/_methods.py:173: RuntimeWarning: > invalid value encountered in subtract > x = asanyarray(arr - arrmean) > > skbio/stats/tests/test_gradient.py::GradientTests::test_weight_by_vector > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build/skbio/stats/gradient.py:167: > FutureWarning: Setting an item of incompatible dtype is deprecated and will > raise in a future error of pandas. Value '6.357142857142857' has dtype > incompatible with int64, please explicitly cast to a compatible dtype first. > trajectories.loc[idx] = ( > > skbio/util/tests/test_plotting.py::TestPlottableMixin::test_figure_data > skbio/util/tests/test_plotting.py::TestPlottableMixin::test_repr_svg > skbio/util/tests/test_plotting.py::TestPlottableMixin::test_svg > /usr/lib/python3/dist-packages/matplotlib/backends/backend_svg.py:413: > DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and > scheduled for removal in a future version. Use timezone-aware objects to > represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, > datetime.UTC). > date = datetime.datetime.utcfromtimestamp(int(date)) > > -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html > =========================== short test summary info > ============================ > FAILED skbio/diversity/alpha/tests/test_base.py::BaseTests::test_shannon - > As... > = 1 failed, 2720 passed, 30 skipped, 10 xpassed, 59 warnings in 90.16s > (0:01:30) = > E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_skbio/build; python3.12 -m pytest > dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.11 > 3.12" returned exit code 13 The full build log is available from: http://qa-logs.debian.net/2024/07/02/python-skbio_0.6.1-2_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240702;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240702&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please mark it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
