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build_failure.linux-64.yaml
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build_failure.linux-64.yaml
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recipe_sha: 0c3fb5d570dc4b66dc35de9ba850a12bc8cf40c159b78490d6fc3af5302176ca # The hash of the recipe's meta.yaml at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
category: test failure
log: |-
usage: faithpd -i <biom> -t <newick> -o <out.txt>
-i The input BIOM table.
-t The input phylogeny in newick.
-o The output series.
Citations:
For Faith's PD, please see:
Faith Biological Conservation 1992; DOI: 10.1016/0006-3207(92)91201-3
python -m unittest unifrac.tests.test_methods
.........
----------------------------------------------------------------------
Ran 9 tests in 0.018s
OK
python -m unittest unifrac.tests.test_api
....................................EEEE
======================================================================
ERROR: test_unweighted_fp32_inmem (unifrac.tests.test_api.UnifracAPITests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_util.py", line 137, in _get_phylogenetic_kwargs
taxa = kwargs.pop("taxa")
KeyError: 'taxa'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/unifrac/tests/test_api.py", line 59, in test_unweighted_fp32_inmem
exp = skbio.diversity.beta_diversity('unweighted_unifrac', cnts,
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_driver.py", line 439, in beta_diversity
taxa, tree, kwargs = _get_phylogenetic_kwargs(counts, **kwargs)
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_util.py", line 139, in _get_phylogenetic_kwargs
raise ValueError("taxa is required for phylogenetic diversity " "metrics.")
ValueError: taxa is required for phylogenetic diversity metrics.
======================================================================
ERROR: test_unweighted_fp64_inmem (unifrac.tests.test_api.UnifracAPITests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_util.py", line 137, in _get_phylogenetic_kwargs
taxa = kwargs.pop("taxa")
KeyError: 'taxa'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/unifrac/tests/test_api.py", line 79, in test_unweighted_fp64_inmem
exp = skbio.diversity.beta_diversity('unweighted_unifrac', cnts,
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_driver.py", line 439, in beta_diversity
taxa, tree, kwargs = _get_phylogenetic_kwargs(counts, **kwargs)
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_util.py", line 139, in _get_phylogenetic_kwargs
raise ValueError("taxa is required for phylogenetic diversity " "metrics.")
ValueError: taxa is required for phylogenetic diversity metrics.
======================================================================
ERROR: test_unweighted_inmem (unifrac.tests.test_api.UnifracAPITests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_util.py", line 137, in _get_phylogenetic_kwargs
taxa = kwargs.pop("taxa")
KeyError: 'taxa'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/unifrac/tests/test_api.py", line 39, in test_unweighted_inmem
exp = skbio.diversity.beta_diversity('unweighted_unifrac', cnts,
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_driver.py", line 439, in beta_diversity
taxa, tree, kwargs = _get_phylogenetic_kwargs(counts, **kwargs)
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_util.py", line 139, in _get_phylogenetic_kwargs
raise ValueError("taxa is required for phylogenetic diversity " "metrics.")
ValueError: taxa is required for phylogenetic diversity metrics.
======================================================================
ERROR: test_unweighted_root_eval_issue_46 (unifrac.tests.test_api.UnifracAPITests)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_util.py", line 137, in _get_phylogenetic_kwargs
taxa = kwargs.pop("taxa")
KeyError: 'taxa'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/unifrac/tests/test_api.py", line 104, in test_unweighted_root_eval_issue_46
exp = skbio.diversity.beta_diversity('unweighted_unifrac', cnts,
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_driver.py", line 439, in beta_diversity
taxa, tree, kwargs = _get_phylogenetic_kwargs(counts, **kwargs)
File "/opt/conda/conda-bld/unifrac_1717780005364/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/python3.8/site-packages/skbio/diversity/_util.py", line 139, in _get_phylogenetic_kwargs
raise ValueError("taxa is required for phylogenetic diversity " "metrics.")
ValueError: taxa is required for phylogenetic diversity metrics.
----------------------------------------------------------------------
Ran 40 tests in 3.379s
FAILED (errors=4)
WARNING: Tests failed for unifrac-1.3-py38h0020b31_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken
TESTS FAILED: unifrac-1.3-py38h0020b31_1.tar.bz2
# Last 100 lines of the build log.