--- Begin Message ---
Source: python-skbio
Version: 0.5.6-5
Severity: important
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-numpy121
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64, using numpy 1.21 currently in experimental. This version
will soon be uploaded to unstable.
If you have questions about this, please contact Sandro Tosi
<mo...@debian.org>.
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:232: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build;
> python3.9 -m pytest
> ============================= test session starts
> ==============================
> platform linux -- Python 3.9.7, pytest-6.2.5, py-1.10.0, pluggy-0.13.0
> rootdir: /<<PKGBUILDDIR>>
> collected 2348 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 ........................ [
> 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 ....... [
> 33%]
> 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%]
> ............................................................. [
> 59%]
> 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%]
> ....... [
> 76%]
> skbio/stats/distance/tests/test_anosim.py .... [
> 76%]
> skbio/stats/distance/tests/test_base.py ................................ [
> 77%]
> ............................................................... [
> 80%]
> skbio/stats/distance/tests/test_bioenv.py ................. [
> 81%]
> 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 ......... [
> 85%]
> skbio/stats/tests/test_composition.py ......F........................... [
> 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
> ===================================
> ________________________ CompositionTests.test_clr_inv
> _________________________
>
> self = <skbio.stats.tests.test_composition.CompositionTests
> testMethod=test_clr_inv>
>
> def test_clr_inv(self):
> npt.assert_allclose(clr_inv(self.rdata1), self.ortho1)
> > npt.assert_allclose(clr(clr_inv(self.rdata1)), self.rdata1)
> E AssertionError:
> E Not equal to tolerance rtol=1e-07, atol=0
> E
> E Mismatched elements: 2 / 12 (16.7%)
> E Max absolute difference: 2.5000001e-09
> E Max relative difference: 8.66025451e-09
> E x: array([[ 7.071068e-01, -7.071068e-01, 2.220446e-16,
> 2.220446e-16],
> E [ 4.082483e-01, 4.082483e-01, -8.164966e-01, 0.000000e+00],
> E [ 2.886751e-01, 2.886751e-01, 2.886751e-01, -8.660254e-01]])
> E y: array([[ 0.707107, -0.707107, 0. , 0. ],
> E [ 0.408248, 0.408248, -0.816497, 0. ],
> E [ 0.288675, 0.288675, 0.288675, -0.866025]])
>
> skbio/stats/tests/test_composition.py:259: AssertionError
> =============================== warnings summary
> ===============================
> skbio/util/_testing.py:15
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/util/_testing.py:15:
> FutureWarning: pandas.util.testing is deprecated. Use the functions in the
> public API at pandas.testing instead.
> import pandas.util.testing as pdt
>
> skbio/sequence/_sequence.py:28
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:28:
> DeprecationWarning: Using or importing the ABCs from 'collections' instead
> of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will
> stop working
> collections.Sequence, SkbioObject):
>
> skbio/io/format/gff3.py:217
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/gff3.py:217:
> DeprecationWarning: Using or importing the ABCs from 'collections' instead
> of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will
> stop working
> from collections import Iterable
>
> skbio/util/_exception.py:10
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/util/_exception.py:10:
> PytestCollectionWarning: cannot collect test class 'TestingUtilError'
> because it has a __init__ constructor (from:
> .pybuild/cpython3_3.9_skbio/build/skbio/io/tests/test_registry.py)
> class TestingUtilError(Exception):
>
> skbio/sequence/tests/test_sequence.py:14
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py:14:
> DeprecationWarning: Using or importing the ABCs from 'collections' instead
> of from 'collections.abc' is deprecated since Python 3.3, and in 3.10 it will
> stop working
> from collections import Hashable
>
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_ssw.py: 18
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py:
> 5622 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_base.py: 14
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_clustal.py: 57
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_embl.py: 40
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 1632
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 652
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_genbank.py: 34
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_gff3.py: 6
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_phylip.py: 55
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_qseq.py: 108
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_stockholm.py: 58
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/tests/test_registry.py: 6 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_distance.py: 251
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_dna.py: 29
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_genetic_code.py:
> 1818 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py:
> 104 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py:
> 264 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_protein.py: 6
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_rna.py: 29
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 1377
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:427:
> DeprecationWarning: tostring() is deprecated. Use tobytes() instead.
> return self._bytes.tostring()
>
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_ssw.py: 6
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py:
> 3712 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_clustal.py: 18
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 30
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 83
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_phylip.py: 34
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_stockholm.py: 79
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_tabular_msa.py:784:
> DeprecationWarning: The default dtype for empty Series will be 'object'
> instead of 'float64' in a future version. Specify a dtype explicitly to
> silence this warning.
> self._seqs = pd.Series([])
>
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py:
> 498 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_clustal.py: 1
> warning
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 9
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 12
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_phylip.py: 2
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_stockholm.py: 47
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_tabular_msa.py:1991:
> DeprecationWarning: The default dtype for empty Series will be 'object'
> instead of 'float64' in a future version. Specify a dtype explicitly to
> silence this warning.
> self._seqs = pd.Series(sequences, index=index)
>
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py:
> 26 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_blast6.py: 6
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_blast7.py: 8
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/metadata/tests/test_mixin.py: 22
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py:
> 2 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 29
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py: 3
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_bioenv.py:
> 8 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_mantel.py:
> 9 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py: 21
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_gradient.py: 4
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py: 2 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/util/_testing.py:304:
> FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is
> deprecated and will be removed in a future version. You can stop passing
> 'check_less_precise' to silence this warning.
> pdt.assert_frame_equal(left, right,
>
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestLoc::test_multiindex_complicated_axis_empty_selection
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestExtend::test_non_empty_msa_empty_iterable
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestExtend::test_reset_index_non_empty_msa_empty_iterable
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_tabular_msa.py:1986:
> DeprecationWarning: The default dtype for empty Series will be 'object'
> instead of 'float64' in a future version. Specify a dtype explicitly to
> silence this warning.
> self._seqs = self._seqs.append(pd.Series(sequences, index=index))
>
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py:
> 62 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_embl.py: 14
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 18
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:1815:
> DeprecationWarning: tostring() is deprecated. Use tobytes() instead.
> chars = indices.astype(np.uint8).tostring().decode('ascii')
>
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py:
> 4 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 52
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 75
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py:
> 4 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_protein.py: 1
> warning
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 126
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:2135:
> DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`.
> To silence this warning, use `bool` by itself. Doing this will not modify any
> behavior and is safe. If you specifically wanted the numpy scalar type, use
> `np.bool_` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> if sliceable.dtype == np.bool:
>
> .pybuild/cpython3_3.9_skbio/build/skbio/alignment/tests/test_tabular_msa.py::TestGapFrequencies::test_no_positions_relative
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/alignment/_tabular_msa.py:1653:
> RuntimeWarning: invalid value encountered in true_divide
> gap_freqs /= length
>
> .pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/_base.py:793:
> RuntimeWarning: invalid value encountered in double_scalars
> return shannon(counts, base=np.e) / np.log(observed_otus(counts))
>
> .pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/_base.py:869:
> RuntimeWarning: invalid value encountered in true_divide
> freqs = counts / counts.sum()
>
> .pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/tests/test_base.py::BaseTests::test_pielou_e
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/alpha/_base.py:793:
> RuntimeWarning: divide by zero encountered in log
> return shannon(counts, base=np.e) / np.log(observed_otus(counts))
>
> .pybuild/cpython3_3.9_skbio/build/skbio/diversity/beta/tests/test_unifrac.py::UnifracTests::test_invalid_input
> .pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests/test_util.py::ValidationTests::test_validate_counts_matrix_unequal_lengths
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/diversity/_util.py:52:
> 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_3.9_skbio/build/skbio/diversity/tests/test_block.py: 2
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests/test_driver.py: 35
> warnings
> /usr/lib/python3/dist-packages/sklearn/metrics/pairwise.py:58:
> DeprecationWarning: `np.float` is a deprecated alias for the builtin `float`.
> To silence this warning, use `float` by itself. Doing this will not modify
> any behavior and is safe. If you specifically wanted the numpy scalar type,
> use `np.float64` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> dtype = np.float
>
> .pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests/test_block.py: 3
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests/test_driver.py: 9
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/diversity/tests/test_driver.py: 7
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py: 4
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py: 2 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/util/_testing.py:322:
> FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is
> deprecated and will be removed in a future version. You can stop passing
> 'check_less_precise' to silence this warning.
> pdt.assert_series_equal(left, right,
>
> .pybuild/cpython3_3.9_skbio/build/skbio/diversity/tests/test_driver.py::BetaDiversityTests::test_qualitative_bug_issue_1549
> /usr/lib/python3/dist-packages/sklearn/metrics/pairwise.py:1765:
> DataConversionWarning: Data was converted to boolean for metric jaccard
> warnings.warn(msg, DataConversionWarning)
>
> .pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 52
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 75
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 5
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:2105:
> DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`.
> To silence this warning, use `bool` by itself. Doing this will not modify any
> behavior and is safe. If you specifically wanted the numpy scalar type, use
> `np.bool_` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> if self.positional_metadata[sliceable].dtype == np.bool:
>
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 52
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fastq.py: 75
> warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 3
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:1308:
> DeprecationWarning: tostring() is deprecated. Use tobytes() instead.
> return str(outbytes.tostring().decode('ascii'))
>
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_fasta.py: 49
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/fasta.py:781:
> DeprecationWarning: `np.str` is a deprecated alias for the builtin `str`. To
> silence this warning, use `str` by itself. Doing this will not modify any
> behavior and is safe. If you specifically wanted the numpy scalar type, use
> `np.str_` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> qual_str = ' '.join(np.asarray(qual_scores, dtype=np.str))
>
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_lsmat.py: 46
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/lsmat.py:228:
> DeprecationWarning: `np.str` is a deprecated alias for the builtin `str`. To
> silence this warning, use `str` by itself. Doing this will not modify any
> behavior and is safe. If you specifically wanted the numpy scalar type, use
> `np.str_` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> fh.write(delimiter.join(np.asarray(vals, dtype=np.str)))
>
> .pybuild/cpython3_3.9_skbio/build/skbio/io/format/tests/test_ordination.py:
> 164 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/io/format/ordination.py:414:
> DeprecationWarning: `np.str` is a deprecated alias for the builtin `str`. To
> silence this warning, use `str` by itself. Doing this will not modify any
> behavior and is safe. If you specifically wanted the numpy scalar type, use
> `np.str_` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> formatted_vector = '\t'.join(np.asarray(vector, dtype=np.str))
>
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_has_nondegenerates
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py:
> 19 warnings
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 2
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_grammared_sequence.py:348:
> DeprecationWarning: tostring() is deprecated. Use tobytes() instead.
> [str(b.tostring().decode("ascii")) for b in bad] if
>
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_nucleotide_sequences.py::TestNucleotideSequence::test_nondegenerate_chars
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_protein.py::TestProtein::test_nondegenerate_chars
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_grammared_sequence.py::TestGrammaredSequence::test_nondegenerates
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_frequencies_empty_sequence
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:1819:
> RuntimeWarning: invalid value encountered in true_divide
> obs_counts = obs_counts / len(self)
>
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_init_invalid_sequence
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/sequence/tests/test_sequence.py: 20
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/sequence/_sequence.py:2124:
> DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`.
> To silence this warning, use `bool` by itself. Doing this will not modify any
> behavior and is safe. If you specifically wanted the numpy scalar type, use
> `np.bool_` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> hasattr(s, 'dtype') and s.dtype != np.bool):
>
> .pybuild/cpython3_3.9_skbio/build/skbio/sequence/tests/test_sequence.py::TestSequence::test_munge_to_index_array_valid_iterable
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/_base.py:550:
> DeprecationWarning: The default dtype for empty Series will be 'object'
> instead of 'float64' in a future version. Specify a dtype explicitly to
> silence this warning.
> i = pd.Series(i, name='i')
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DissimilarityMatrixTests::test_subset_to_dataframe
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/_base.py:551:
> DeprecationWarning: The default dtype for empty Series will be 'object'
> instead of 'float64' in a future version. Specify a dtype explicitly to
> silence this warning.
> j = pd.Series(j, name='j')
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py::DistanceMatrixTests::test_to_series_1x1
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_base.py:938:
> DeprecationWarning: The default dtype for empty Series will be 'object'
> instead of 'float64' in a future version. Specify a dtype explicitly to
> silence this warning.
> exp = pd.Series([], index=[])
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_mantel.py:
> 71 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/_mantel.py:285:
> DeprecationWarning: `np.float` is a deprecated alias for the builtin
> `float`. To silence this warning, use `float` by itself. Doing this will not
> modify any behavior and is safe. If you specifically wanted the numpy scalar
> type, use `np.float64` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> permuted_stats = np.fromiter(perm_gen, np.float, count=permutations)
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_pearson
> /usr/lib/python3/dist-packages/scipy/stats/stats.py:4023:
> PearsonRConstantInputWarning: An input array is constant; the correlation
> coefficient is not defined.
> warnings.warn(PearsonRConstantInputWarning())
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_mantel.py::MantelTests::test_no_variation_spearman
> /usr/lib/python3/dist-packages/scipy/stats/stats.py:4484:
> SpearmanRConstantInputWarning: An input array is constant; the correlation
> coefficient is not defined.
> warnings.warn(SpearmanRConstantInputWarning())
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_confirm_betadispr_results
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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
> -0.007758325147780715 and the largest is 2.707792948946925.
> warn(
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_no_permuations
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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
> -13.541846544269625 and the largest is 16.5872013747859.
> warn(
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/distance/tests/test_permdisp.py::testPERMDISP::test_not_distance_matrix
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/_principal_coordinate_analysis.py:188:
> RuntimeWarning: invalid value encountered in true_divide
> proportion_explained = eigvals / sum_eigenvalues
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_no_metadata
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_categorical_metadata_and_plot_options
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_plot_with_numeric_metadata_and_plot_options
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_png
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_png
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_repr_svg
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_ordination_results.py::TestOrdinationResults::test_svg
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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_3.9_skbio/build/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py::TestPCoA::test_fsvd
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py::TestPCoA::test_fsvd_inplace
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py::TestPCoA::test_fsvd_inplace
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_util.py::TestUtils::test_center_distance_matrix_inplace
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_util.py::TestUtils::test_e_matrix_inplace
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/_utils.py:240:
> DeprecationWarning: `np.float` is a deprecated alias for the builtin
> `float`. To silence this warning, use `float` by itself. Doing this will not
> modify any behavior and is safe. If you specifically wanted the numpy scalar
> type, use `np.float64` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> distance_matrix = distance_matrix.astype(np.float)
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py::TestPCoA::test_fsvd
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py::TestPCoA::test_fsvd_inplace
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_principal_coordinate_analysis.py::TestPCoA::test_fsvd_inplace
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_util.py::TestUtils::test_center_distance_matrix_inplace
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/tests/test_util.py::TestUtils::test_f_matrix_inplace
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/ordination/_utils.py:262:
> DeprecationWarning: `np.float` is a deprecated alias for the builtin
> `float`. To silence this warning, use `float` by itself. Doing this will not
> modify any behavior and is safe. If you specifically wanted the numpy scalar
> type, use `np.float64` here.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> e_matrix = e_matrix.astype(np.float)
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py: 37
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py:524:
> DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To
> silence this warning, use `int` by itself. Doing this will not modify any
> behavior and is safe. When replacing `np.int`, you may wish to use e.g.
> `np.int64` or `np.int32` to specify the precision. If you wish to review your
> current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.table2 = pd.DataFrame(self.table2.astype(np.int).T)
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py: 37
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py:557:
> DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To
> silence this warning, use `int` by itself. Doing this will not modify any
> behavior and is safe. When replacing `np.int`, you may wish to use e.g.
> `np.int64` or `np.int32` to specify the precision. If you wish to review your
> current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.table4 = pd.DataFrame(self.table4.astype(np.int).T)
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py: 37
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py:638:
> DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To
> silence this warning, use `int` by itself. Doing this will not modify any
> behavior and is safe. When replacing `np.int`, you may wish to use e.g.
> `np.int64` or `np.int32` to specify the precision. If you wish to review your
> current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.table9 = pd.DataFrame(self.table9.astype(np.int).T)
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py: 37
> warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py:672:
> DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To
> silence this warning, use `int` by itself. Doing this will not modify any
> behavior and is safe. When replacing `np.int`, you may wish to use e.g.
> `np.int64` or `np.int32` to specify the precision. If you wish to review your
> current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> self.table10 = pd.DataFrame(self.table10.astype(np.int).T)
>
> .pybuild/cpython3_3.9_skbio/build/skbio/stats/tests/test_composition.py::AncomTests::test_ancom_no_signal
> /usr/lib/python3/dist-packages/scipy/stats/stats.py:3650:
> F_onewayConstantInputWarning: Each of the input arrays is constant;the F
> statistic is not defined or infinite
> warnings.warn(F_onewayConstantInputWarning())
>
> .pybuild/cpython3_3.9_skbio/build/skbio/tree/tests/test_tree.py: 18 warnings
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/tree/_tree.py:2189:
> DeprecationWarning: `np.int` is a deprecated alias for the builtin `int`. To
> silence this warning, use `int` by itself. Doing this will not modify any
> behavior and is safe. When replacing `np.int`, you may wish to use e.g.
> `np.int64` or `np.int32` to specify the precision. If you wish to review your
> current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance:
> https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> mid = np.int(np.trunc((lo + hi) / 2))
>
> .pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_decorator.py::TestDeprecated::test_function_output
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_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 '
>
> .pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py::TestAssertSeriesAlmostEqual::test_equal
> .pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py::TestAssertSeriesAlmostEqual::test_not_equal
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build/skbio/util/tests/test_testing.py:231:
> DeprecationWarning: The default dtype for empty Series will be 'object'
> instead of 'float64' in a future version. Specify a dtype explicitly to
> silence this warning.
> pd.Series(),
>
> -- Docs: https://docs.pytest.org/en/stable/warnings.html
> =========================== short test summary info
> ============================
> FAILED skbio/stats/tests/test_composition.py::CompositionTests::test_clr_inv
> ========= 1 failed, 2317 passed, 30 skipped, 18143 warnings in 50.28s
> ==========
> E: pybuild pybuild:354: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_skbio/build; python3.9 -m pytest
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.9
> returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2021/11/numpy-matplotlib/numpy-exp/python-skbio_0.5.6-5_unstable_numpy-exp.log
If you reassign this bug to another package, please marking 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 ---
