Source: python-skbio
Version: 0.5.6-6
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20221220 ftbfs-bookworm
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:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build;
> python3.11 -m pytest
> ============================= test session starts
> ==============================
> platform linux -- Python 3.11.1, pytest-7.2.0, pluggy-1.0.0+repack
> rootdir: /<<PKGBUILDDIR>>
> collected 2352 items
>
> skbio/alignment/tests/test_pairwise.py ......................... [
> 1%]
> skbio/alignment/tests/test_ssw.py ........................... [
> 2%]
> skbio/alignment/tests/test_tabular_msa.py .............................. [
> 3%]
> ........................................................................ [
> 6%]
> ........................................................................ [
> 9%]
> ........................................................................ [
> 12%]
> ........................................................................ [
> 15%]
> ........................................................................ [
> 18%]
> ............ [
> 19%]
> skbio/diversity/alpha/tests/test_ace.py .. [
> 19%]
> skbio/diversity/alpha/tests/test_base.py .................F...... [
> 20%]
> skbio/diversity/alpha/tests/test_chao1.py ... [
> 20%]
> skbio/diversity/alpha/tests/test_faith_pd.py ........ [
> 20%]
> skbio/diversity/alpha/tests/test_gini.py ... [
> 21%]
> skbio/diversity/alpha/tests/test_lladser.py ............ [
> 21%]
> skbio/diversity/beta/tests/test_unifrac.py ............................ [
> 22%]
> skbio/diversity/tests/test_block.py ........... [
> 23%]
> skbio/diversity/tests/test_driver.py .................................. [
> 24%]
> skbio/diversity/tests/test_util.py .......... [
> 25%]
> skbio/io/format/tests/test_base.py ................................ [
> 26%]
> skbio/io/format/tests/test_blast6.py ........... [
> 26%]
> skbio/io/format/tests/test_blast7.py .............. [
> 27%]
> skbio/io/format/tests/test_clustal.py ............. [
> 28%]
> skbio/io/format/tests/test_embl.py ............................... [
> 29%]
> skbio/io/format/tests/test_emptyfile.py .. [
> 29%]
> skbio/io/format/tests/test_fasta.py ................ [
> 30%]
> skbio/io/format/tests/test_fastq.py ............... [
> 30%]
> skbio/io/format/tests/test_genbank.py ..................... [
> 31%]
> skbio/io/format/tests/test_gff3.py ........................ [
> 32%]
> skbio/io/format/tests/test_lsmat.py ....... [
> 32%]
> skbio/io/format/tests/test_newick.py ....... [
> 33%]
> skbio/io/format/tests/test_ordination.py ..... [
> 33%]
> skbio/io/format/tests/test_phylip.py ....... [
> 33%]
> skbio/io/format/tests/test_qseq.py ...... [
> 34%]
> skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [
> 34%]
> skbio/io/format/tests/test_stockholm.py ................................ [
> 35%]
> ........................................... [
> 37%]
> skbio/io/tests/test_iosources.py .......... [
> 37%]
> skbio/io/tests/test_registry.py ........................................ [
> 39%]
> ...................................................... [
> 41%]
> skbio/io/tests/test_util.py .........................................sss [
> 43%]
> sssssssssssssssssssssssssss............................................. [
> 46%]
> ........................................................................ [
> 49%]
> ................................ [
> 51%]
> skbio/metadata/tests/test_intersection.py ............... [
> 51%]
> skbio/metadata/tests/test_interval.py .................................. [
> 53%]
> ..................................... [
> 54%]
> skbio/metadata/tests/test_mixin.py ..................................... [
> 56%]
> ............................................................. [
> 58%]
> skbio/sequence/tests/test_distance.py .......................... [
> 60%]
> skbio/sequence/tests/test_dna.py .... [
> 60%]
> skbio/sequence/tests/test_genetic_code.py .......................... [
> 61%]
> skbio/sequence/tests/test_grammared_sequence.py ........................ [
> 62%]
> ................... [
> 63%]
> skbio/sequence/tests/test_nucleotide_sequences.py ...................... [
> 64%]
> ....... [
> 64%]
> skbio/sequence/tests/test_protein.py .......... [
> 64%]
> skbio/sequence/tests/test_rna.py .... [
> 65%]
> skbio/sequence/tests/test_sequence.py .................................. [
> 66%]
> ........................................................................ [
> 69%]
> ........................................................................ [
> 72%]
> ........................................................................ [
> 75%]
> ....... [
> 75%]
> skbio/stats/distance/tests/test_anosim.py .... [
> 76%]
> skbio/stats/distance/tests/test_base.py ................................ [
> 77%]
> ............................................................... [
> 80%]
> skbio/stats/distance/tests/test_bioenv.py ................. [
> 80%]
> skbio/stats/distance/tests/test_mantel.py .............................. [
> 82%]
> ......... [
> 82%]
> skbio/stats/distance/tests/test_permanova.py .... [
> 82%]
> skbio/stats/distance/tests/test_permdisp.py ............ [
> 83%]
> skbio/stats/evolve/tests/test_hommola.py ............ [
> 83%]
> skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [
> 83%]
> ..... [
> 83%]
> skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [
> 84%]
> skbio/stats/ordination/tests/test_ordination_results.py ................ [
> 84%]
> [
> 84%]
> skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [
> 85%]
> ...... [
> 85%]
> skbio/stats/ordination/tests/test_redundancy_analysis.py .... [
> 85%]
> skbio/stats/ordination/tests/test_util.py ......... [
> 86%]
> skbio/stats/tests/test_composition.py .................................. [
> 87%]
> ........................ [
> 88%]
> skbio/stats/tests/test_gradient.py .......................... [
> 89%]
> skbio/stats/tests/test_misc.py ... [
> 89%]
> skbio/stats/tests/test_power.py ........................................ [
> 91%]
> ... [
> 91%]
> skbio/stats/tests/test_subsample.py ............ [
> 92%]
> skbio/tests/test_base.py ..... [
> 92%]
> skbio/tests/test_workflow.py ................. [
> 92%]
> skbio/tree/tests/test_majority_rule.py ...... [
> 93%]
> skbio/tree/tests/test_nj.py ........... [
> 93%]
> skbio/tree/tests/test_tree.py .......................................... [
> 95%]
> ................................................. [
> 97%]
> skbio/util/tests/test_decorator.py ....................... [
> 98%]
> skbio/util/tests/test_misc.py ................... [
> 99%]
> skbio/util/tests/test_testing.py ...............
> [100%]
>
> =================================== FAILURES
> ===================================
> ___________________________ BaseTests.test_pielou_e
> ____________________________
>
> self = <skbio.diversity.alpha.tests.test_base.BaseTests
> testMethod=test_pielou_e>
>
> def test_pielou_e(self):
> # Calculate "by hand".
> arr = np.array([1, 2, 3, 1])
> h = shannon(arr, np.e)
> s = 4
> expected = h / np.log(s)
> self.assertAlmostEqual(pielou_e(arr), expected)
>
> self.assertAlmostEqual(pielou_e(self.counts), 0.92485490560)
>
> > self.assertEqual(pielou_e([1, 1]), 1.0)
> E AssertionError: 1.0000000000000002 != 1.0
>
> skbio/diversity/alpha/tests/test_base.py:218: AssertionError
> =============================== warnings summary
> ===============================
> skbio/stats/ordination/tests/test_redundancy_analysis.py:12
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_redundancy_analysis.py:12:
> FutureWarning: pandas.util.testing is deprecated. Use the functions in the
> public API at pandas.testing instead.
> import pandas.util.testing as pdt
>
> .pybuild/cpython3_3.11_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis
> .pybuild/cpython3_3.11_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis_empty_selection
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment/_indexing.py:116:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-tuple of lists-or-tuples-or ndarrays with different
> lengths or shapes) is deprecated. If you meant to do this, you must specify
> 'dtype=object' when creating the ndarray.
> indexable = np.asarray(list(indexable))
>
> .pybuild/cpython3_3.11_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/alignment/_tabular_msa.py:1653:
> RuntimeWarning: invalid value encountered in divide
> gap_freqs /= length
>
> .pybuild/cpython3_3.11_skbio/build/skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_invalid_input
> .pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_matrix_unequal_lengths
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/diversity/_util.py:56:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-tuple of lists-or-tuples-or ndarrays with different
> lengths or shapes) is deprecated. If you meant to do this, you must specify
> 'dtype=object' when creating the ndarray.
> counts = np.asarray(counts)
>
> .pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_block.py: 3
> warnings
> .pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_driver.py: 9
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: partial_beta_diversity is deprecated as of scikit-bio
> version 0.5.0, and will be removed in version 0.6.0. 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.
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> .pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_qualitative_bug_issue_1549
> /usr/lib/python3/dist-packages/sklearn/metrics/pairwise.py:2008:
> DataConversionWarning: Data was converted to boolean for metric jaccard
> warnings.warn(msg, DataConversionWarning)
>
> .pybuild/cpython3_3.11_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_vector_invalid_input
> /usr/lib/python3/dist-packages/numpy/lib/type_check.py:300: FutureWarning:
> elementwise comparison failed; returning scalar instead, but in the future
> will perform elementwise comparison
> return imag(x) == 0
>
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: has_nondegenerates is deprecated as of scikit-bio
> version 0.5.0, and will be removed in version 0.6.0. Renamed to has_definites
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: nondegenerate_chars is deprecated as of scikit-bio
> version 0.5.0, and will be removed in version 0.6.0. Renamed to definite_chars
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: nondegenerates is deprecated as of scikit-bio version
> 0.5.0, and will be removed in version 0.6.0. Renamed to definites
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/_sequence.py:1819:
> RuntimeWarning: invalid value encountered in divide
> obs_counts = obs_counts / len(self)
>
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_init_invalid_sequence
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_sequence.py:461:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-tuple of lists-or-tuples-or ndarrays with different
> lengths or shapes) is deprecated. If you meant to do this, you must specify
> 'dtype=object' when creating the ndarray.
> Sequence(np.array([1, {}, ()]))
>
> .pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_munge_to_index_array_valid_iterable
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/sequence/tests/test_sequence.py:2214:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-tuple of lists-or-tuples-or ndarrays with different
> lengths or shapes) is deprecated. If you meant to do this, you must specify
> 'dtype=object' when creating the ndarray.
> for c in (lambda x: x, list, tuple, lambda x: np.array(tuple(x)),
>
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson
> /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4068:
> PearsonRConstantInputWarning: An input array is constant; the correlation
> coefficient is not defined.
> warnings.warn(PearsonRConstantInputWarning())
>
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman
> /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4529:
> SpearmanRConstantInputWarning: An input array is constant; the correlation
> coefficient is not defined.
> warnings.warn(SpearmanRConstantInputWarning())
>
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups
> .pybuild/cpython3_3.11_skbio/build/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:143:
> 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
> -13.541846544269621 and the largest is 16.5872013747859.
> warn(
>
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups
> .pybuild/cpython3_3.11_skbio/build/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:143:
> 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
> -15.629533932395216 and the largest is 20.90315427793891.
> warn(
>
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_not_distance_matrix
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:188:
> RuntimeWarning: invalid value encountered in divide
> proportion_explained = eigvals / sum_eigenvalues
>
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal
> /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:3659:
> F_onewayConstantInputWarning: Each of the input arrays is constant;the F
> statistic is not defined or infinite
> warnings.warn(F_onewayConstantInputWarning())
>
> .pybuild/cpython3_3.11_skbio/build/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:143:
> 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
> -0.007758325147780645 and the largest is 2.7077929489469246.
> warn(
>
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg
> .pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/stats/ordination/_ordination_results.py:285:
> UserWarning: Tight layout not applied. The left and right margins cannot be
> made large enough to accommodate all axes decorations.
> fig.tight_layout()
>
> .pybuild/cpython3_3.11_skbio/build/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)
>
> .pybuild/cpython3_3.11_skbio/build/skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: f is deprecated as of scikit-bio version 0.1.0, and will
> be removed in version 0.1.4. You should now use skbio.g().
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> -- 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_pielou_e -
> A...
> ====== 1 failed, 2321 passed, 30 skipped, 65 warnings in 67.53s (0:01:07)
> ======
> E: pybuild pybuild:386: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_skbio/build; python3.11 -m pytest
> I: pybuild base:240: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build;
> python3.10 -m pytest
> ============================= test session starts
> ==============================
> platform linux -- Python 3.10.9, pytest-7.2.0, pluggy-1.0.0+repack
> rootdir: /<<PKGBUILDDIR>>
> collected 2352 items
>
> skbio/alignment/tests/test_pairwise.py ......................... [
> 1%]
> skbio/alignment/tests/test_ssw.py ........................... [
> 2%]
> skbio/alignment/tests/test_tabular_msa.py .............................. [
> 3%]
> ........................................................................ [
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> ........................................................................ [
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> skbio/diversity/alpha/tests/test_ace.py .. [
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> skbio/diversity/alpha/tests/test_base.py .................F...... [
> 20%]
> skbio/diversity/alpha/tests/test_chao1.py ... [
> 20%]
> skbio/diversity/alpha/tests/test_faith_pd.py ........ [
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> skbio/diversity/alpha/tests/test_gini.py ... [
> 21%]
> skbio/diversity/alpha/tests/test_lladser.py ............ [
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> skbio/diversity/beta/tests/test_unifrac.py ............................ [
> 22%]
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> skbio/diversity/tests/test_driver.py .................................. [
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> skbio/diversity/tests/test_util.py .......... [
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> skbio/io/format/tests/test_base.py ................................ [
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> skbio/io/format/tests/test_blast6.py ........... [
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> skbio/io/format/tests/test_embl.py ............................... [
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> skbio/io/format/tests/test_fasta.py ................ [
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> skbio/io/format/tests/test_genbank.py ..................... [
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> 33%]
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> skbio/io/format/tests/test_qseq.py ...... [
> 34%]
> skbio/io/format/tests/test_sequence_feature_vocabulary.py .... [
> 34%]
> skbio/io/format/tests/test_stockholm.py ................................ [
> 35%]
> ........................................... [
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> skbio/io/tests/test_iosources.py .......... [
> 37%]
> skbio/io/tests/test_registry.py ........................................ [
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> ...................................................... [
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> skbio/io/tests/test_util.py .........................................sss [
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> ........................................................................ [
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> ................................ [
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> ..................................... [
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> skbio/metadata/tests/test_mixin.py ..................................... [
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> ............................................................. [
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> skbio/sequence/tests/test_distance.py .......................... [
> 60%]
> skbio/sequence/tests/test_dna.py .... [
> 60%]
> skbio/sequence/tests/test_genetic_code.py .......................... [
> 61%]
> skbio/sequence/tests/test_grammared_sequence.py ........................ [
> 62%]
> ................... [
> 63%]
> skbio/sequence/tests/test_nucleotide_sequences.py ...................... [
> 64%]
> ....... [
> 64%]
> skbio/sequence/tests/test_protein.py .......... [
> 64%]
> skbio/sequence/tests/test_rna.py .... [
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> skbio/sequence/tests/test_sequence.py .................................. [
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> ........................................................................ [
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> skbio/stats/distance/tests/test_base.py ................................ [
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> ............................................................... [
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> skbio/stats/distance/tests/test_bioenv.py ................. [
> 80%]
> skbio/stats/distance/tests/test_mantel.py .............................. [
> 82%]
> ......... [
> 82%]
> skbio/stats/distance/tests/test_permanova.py .... [
> 82%]
> skbio/stats/distance/tests/test_permdisp.py ............ [
> 83%]
> skbio/stats/evolve/tests/test_hommola.py ............ [
> 83%]
> skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [
> 83%]
> ..... [
> 83%]
> skbio/stats/ordination/tests/test_correspondence_analysis.py ........ [
> 84%]
> skbio/stats/ordination/tests/test_ordination_results.py ................ [
> 84%]
> [
> 84%]
> skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [
> 85%]
> ...... [
> 85%]
> skbio/stats/ordination/tests/test_redundancy_analysis.py .... [
> 85%]
> skbio/stats/ordination/tests/test_util.py ......... [
> 86%]
> skbio/stats/tests/test_composition.py .................................. [
> 87%]
> ........................ [
> 88%]
> skbio/stats/tests/test_gradient.py .......................... [
> 89%]
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> 89%]
> skbio/stats/tests/test_power.py ........................................ [
> 91%]
> ... [
> 91%]
> skbio/stats/tests/test_subsample.py ............ [
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> skbio/tests/test_base.py ..... [
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> skbio/tests/test_workflow.py ................. [
> 92%]
> skbio/tree/tests/test_majority_rule.py ...... [
> 93%]
> skbio/tree/tests/test_nj.py ........... [
> 93%]
> skbio/tree/tests/test_tree.py .......................................... [
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> ................................................. [
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> skbio/util/tests/test_decorator.py ....................... [
> 98%]
> skbio/util/tests/test_misc.py ................... [
> 99%]
> skbio/util/tests/test_testing.py ...............
> [100%]
>
> =================================== FAILURES
> ===================================
> ___________________________ BaseTests.test_pielou_e
> ____________________________
>
> self = <skbio.diversity.alpha.tests.test_base.BaseTests
> testMethod=test_pielou_e>
>
> def test_pielou_e(self):
> # Calculate "by hand".
> arr = np.array([1, 2, 3, 1])
> h = shannon(arr, np.e)
> s = 4
> expected = h / np.log(s)
> self.assertAlmostEqual(pielou_e(arr), expected)
>
> self.assertAlmostEqual(pielou_e(self.counts), 0.92485490560)
>
> > self.assertEqual(pielou_e([1, 1]), 1.0)
> E AssertionError: 1.0000000000000002 != 1.0
>
> skbio/diversity/alpha/tests/test_base.py:218: AssertionError
> =============================== warnings summary
> ===============================
> skbio/stats/ordination/tests/test_redundancy_analysis.py:12
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_redundancy_analysis.py:12:
> FutureWarning: pandas.util.testing is deprecated. Use the functions in the
> public API at pandas.testing instead.
> import pandas.util.testing as pdt
>
> .pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis
> .pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis_empty_selection
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_indexing.py:116:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-tuple of lists-or-tuples-or ndarrays with different
> lengths or shapes) is deprecated. If you meant to do this, you must specify
> 'dtype=object' when creating the ndarray.
> indexable = np.asarray(list(indexable))
>
> .pybuild/cpython3_3.10_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/alignment/_tabular_msa.py:1653:
> RuntimeWarning: invalid value encountered in divide
> gap_freqs /= length
>
> .pybuild/cpython3_3.10_skbio/build/skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_invalid_input
> .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_matrix_unequal_lengths
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/diversity/_util.py:56:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-tuple of lists-or-tuples-or ndarrays with different
> lengths or shapes) is deprecated. If you meant to do this, you must specify
> 'dtype=object' when creating the ndarray.
> counts = np.asarray(counts)
>
> .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_block.py: 3
> warnings
> .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_driver.py: 9
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: partial_beta_diversity is deprecated as of scikit-bio
> version 0.5.0, and will be removed in version 0.6.0. 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.
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_qualitative_bug_issue_1549
> /usr/lib/python3/dist-packages/sklearn/metrics/pairwise.py:2008:
> DataConversionWarning: Data was converted to boolean for metric jaccard
> warnings.warn(msg, DataConversionWarning)
>
> .pybuild/cpython3_3.10_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_vector_invalid_input
> /usr/lib/python3/dist-packages/numpy/lib/type_check.py:300: FutureWarning:
> elementwise comparison failed; returning scalar instead, but in the future
> will perform elementwise comparison
> return imag(x) == 0
>
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: has_nondegenerates is deprecated as of scikit-bio
> version 0.5.0, and will be removed in version 0.6.0. Renamed to has_definites
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: nondegenerate_chars is deprecated as of scikit-bio
> version 0.5.0, and will be removed in version 0.6.0. Renamed to definite_chars
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: nondegenerates is deprecated as of scikit-bio version
> 0.5.0, and will be removed in version 0.6.0. Renamed to definites
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/_sequence.py:1819:
> RuntimeWarning: invalid value encountered in divide
> obs_counts = obs_counts / len(self)
>
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_init_invalid_sequence
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py:461:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-tuple of lists-or-tuples-or ndarrays with different
> lengths or shapes) is deprecated. If you meant to do this, you must specify
> 'dtype=object' when creating the ndarray.
> Sequence(np.array([1, {}, ()]))
>
> .pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_munge_to_index_array_valid_iterable
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/sequence/tests/test_sequence.py:2214:
> VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences
> (which is a list-or-tuple of lists-or-tuples-or ndarrays with different
> lengths or shapes) is deprecated. If you meant to do this, you must specify
> 'dtype=object' when creating the ndarray.
> for c in (lambda x: x, list, tuple, lambda x: np.array(tuple(x)),
>
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson
> /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4068:
> PearsonRConstantInputWarning: An input array is constant; the correlation
> coefficient is not defined.
> warnings.warn(PearsonRConstantInputWarning())
>
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman
> /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:4529:
> SpearmanRConstantInputWarning: An input array is constant; the correlation
> coefficient is not defined.
> warnings.warn(SpearmanRConstantInputWarning())
>
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_eq_groups
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143:
> 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
> -13.541846544269621 and the largest is 16.5872013747859.
> warn(
>
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_mixedgroups
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_uneq_groups
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143:
> 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
> -15.629533932395216 and the largest is 20.90315427793891.
> warn(
>
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_not_distance_matrix
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:188:
> RuntimeWarning: invalid value encountered in divide
> proportion_explained = eigvals / sum_eigenvalues
>
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_centroids_null
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal
> /usr/lib/python3/dist-packages/scipy/stats/_stats_py.py:3659:
> F_onewayConstantInputWarning: Each of the input arrays is constant;the F
> statistic is not defined or infinite
> warnings.warn(F_onewayConstantInputWarning())
>
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:143:
> 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
> -0.007758325147780645 and the largest is 2.7077929489469246.
> warn(
>
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg
> .pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/stats/ordination/_ordination_results.py:285:
> UserWarning: Tight layout not applied. The left and right margins cannot be
> made large enough to accommodate all axes decorations.
> fig.tight_layout()
>
> .pybuild/cpython3_3.10_skbio/build/skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build/skbio/util/_decorator.py:254:
> DeprecationWarning: f is deprecated as of scikit-bio version 0.1.0, and will
> be removed in version 0.1.4. You should now use skbio.g().
> warnings.warn('%s is deprecated as of scikit-bio version %s, and '
>
> -- 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_pielou_e -
> A...
> =========== 1 failed, 2321 passed, 30 skipped, 64 warnings in 45.64s
> ===========
> E: pybuild pybuild:386: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_skbio/build; python3.10 -m pytest
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.11
> 3.10" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2022/12/20/python-skbio_0.5.6-6_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221220;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221220&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.
