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build_failure.osx-64.yaml
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build_failure.osx-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: |-
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/conda-bld/unifrac_1717780701288/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.12/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/mambaforge/envs/bioconda/conda-bld/unifrac_1717780701288/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.12/site-packages/skbio/diversity/_driver.py", line 439, in beta_diversity
taxa, tree, kwargs = _get_phylogenetic_kwargs(counts, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/mambaforge/envs/bioconda/conda-bld/unifrac_1717780701288/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/lib/python3.12/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 4.773s
FAILED (errors=4)
WARNING: Tests failed for unifrac-1.3-py312h68c8633_1.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken
TESTS FAILED: unifrac-1.3-py312h68c8633_1.tar.bz2
export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/unifrac_1717780701288/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p
export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/unifrac_1717780701288/test_tmp
import: 'unifrac'
import: 'unifrac'
usage: ssu -i <biom> -o <out.dm> -m [METHOD] -t <newick> [-a alpha] [-f] [--vaw]
[--mode MODE] [--start starting-stripe] [--stop stopping-stripe] [--partial-pattern <glob>]
[--n-partials number_of_partitions] [--report-bare] [--format|-r out-mode]
[--n-substeps n] [--pcoa dims] [--diskbuf path]
-i The input BIOM table.
-t The input phylogeny in newick.
-m The method, [unweighted | weighted_normalized | weighted_unnormalized | generalized |
unweighted_fp64 | weighted_normalized_fp64 | weighted_unnormalized_fp64 | generalized_fp64 |
unweighted_fp32 | weighted_normalized_fp32 | weighted_unnormalized_fp32 | generalized_fp32].
-o The output distance matrix.
-g [OPTIONAL] The input grouping in TSV.
-c [OPTIONAL] The columns(s) to use for grouping, multiple values comma separated.
-a [OPTIONAL] Generalized UniFrac alpha, default is 1.
-f [OPTIONAL] Bypass tips, reduces compute by about 50%.
--vaw [OPTIONAL] Variance adjusted, default is to not adjust for variance.
--mode [OPTIONAL] Mode of operation:
one-off : [DEFAULT] compute UniFrac.
partial : Compute UniFrac over a subset of stripes.
partial-report : Start and stop suggestions for partial compute.
merge-partial : Merge partial UniFrac results.
check-partial : Check partial UniFrac results.
multi : compute UniFrac multiple times.
--start [OPTIONAL] If mode==partial, the starting stripe.
--stop [OPTIONAL] If mode==partial, the stopping stripe.
--partial-pattern [OPTIONAL] If mode==merge-partial or check-partial, a glob pattern for partial outputs to merge.
--n-partials [OPTIONAL] If mode==partial-report, the number of partitions to compute.
--report-bare [OPTIONAL] If mode==partial-report, produce barebones output.
--n-substeps [OPTIONAL] Internally split the problem in n substeps for reduced memory footprint, default is 1.
--format|-r [OPTIONAL] Output format:
ascii : Original ASCII format. (default if mode==one-off)
hdf5 : HFD5 format. May be fp32 or fp64, depending on method.
hdf5_fp32 : HFD5 format, using fp32 precision.
hdf5_fp64 : HFD5 format, using fp64 precision.
hdf5_nodist : HFD5 format, no distance matrix. (default if mode==multi)
--subsample-depth Depth of subsampling of the input BIOM before computing unifrac (required for mode==multi, optional for one-off)
--subsample-replacement [OPTIONAL] Subsample with or without replacement (default is with)
--n-subsamples [OPTIONAL] if mode==multi, number of subsampled UniFracs to compute (default: 100)
--permanova [OPTIONAL] Number of PERMANOVA permutations to compute (default: 999 with -g, do not compute if 0)
--pcoa [OPTIONAL] Number of PCoA dimensions to compute (default: 10, do not compute if 0)
--seed [OPTIONAL] Seed to use for initializing the random gnerator
--diskbuf [OPTIONAL] Use a disk buffer to reduce memory footprint. Provide path to a fast partition (ideally NVMe).
-n [OPTIONAL] DEPRECATED, no-op.
Environment variables:
CPU parallelism is controlled by OMP_NUM_THREADS. If not defined, all detected core will be used.
GPU offload can be disabled with UNIFRAC_USE_GPU=N. By default, if a NVIDIA GPU is detected, it will be used.
A specific GPU can be selected with ACC_DEVICE_NUM. If not defined, the first GPU will be used.
Citations:
For UniFrac, please see:
Sfiligoi et al. mSystems 2022; DOI: 10.1128/msystems.00028-22
McDonald et al. Nature Methods 2018; DOI: 10.1038/s41592-018-0187-8
Lozupone and Knight Appl Environ Microbiol 2005; DOI: 10.1128/AEM.71.12.8228-8235.2005
Lozupone et al. Appl Environ Microbiol 2007; DOI: 10.1128/AEM.01996-06
Hamady et al. ISME 2010; DOI: 10.1038/ismej.2009.97
Lozupone et al. ISME 2011; DOI: 10.1038/ismej.2010.133
For Generalized UniFrac, please see:
Chen et al. Bioinformatics 2012; DOI: 10.1093/bioinformatics/bts342
For Variance Adjusted UniFrac, please see:
Chang et al. BMC Bioinformatics 2011; DOI: 10.1186/1471-2105-12-118
Runtime progress can be obtained by issuing a SIGUSR1 signal. If running with
multiple threads, this signal will only be honored if issued to the master PID.
The report will yield the following information:
tid:<thread ID> start:<starting stripe> stop:<stopping stripe> k:<postorder node index> total:<number of nodes>
The proportion of the tree that has been evaluated can be determined from (k / total).
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
# Last 100 lines of the build log.