--- Begin Message ---
Source: python-skbio
Version: 0.6.1-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: [email protected]
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%]
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> .. [
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> 31%]
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> 32%]
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> ........................................... [
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> skbio/sequence/tests/test_distance.py .......................... [
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> 64%]
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> ......................... [
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> 67%]
> ....... [
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> skbio/sequence/tests/test_rna.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 ................. [
> 82%]
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> .............. [
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> 84%]
> skbio/stats/distance/tests/test_permdisp.py .............. [
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> skbio/stats/ordination/tests/test_canonical_correspondence_analysis.py . [
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> ..... [
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> skbio/stats/ordination/tests/test_principal_coordinate_analysis.py ..... [
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> ....... [
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> 86%]
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> 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;[email protected]
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240702&[email protected]&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.
--- End Message ---
pgpBTtt5KH8bJ.pgp
