scikit-bio

seg_fault.txt

❯ nosetests --with-doctest -v
test_degap (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_distances (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_init_equal_lengths (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_init_not_equal_lengths (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_init_validate (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_iter_positions (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_k_word_frequencies (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_majority_consensus (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_omit_gap_positions (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_omit_gap_sequences (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_position_counters (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_position_entropies (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_position_frequencies (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_position_frequencies_floating_point_precision (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_score (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_sequence_length (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_start_end_positions (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_subalignment (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_subalignment_filter_out_everything (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_validate_lengths (skbio.alignment.tests.test_alignment.AlignmentTests) ... ok
test_contains (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_degap (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_distances (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_distribution_stats (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_eq (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_get_seq (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_getitem (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_ids (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_init (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_init_fail (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_init_validate (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_is_empty (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_is_valid (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_iter (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_iteritems (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_k_word_frequencies (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_len (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_lower (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_ne (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_repr (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_reversed (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_sequence_count (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_sequence_lengths (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_str (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_update_ids_default_behavior (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_update_ids_fn_parameter (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_update_ids_ids_parameter (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_update_ids_invalid_ids (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_update_ids_invalid_parameter_combos (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_update_ids_prefix (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_update_ids_sequence_attributes_propagated (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_upper (skbio.alignment.tests.test_alignment.SequenceCollectionTests) ... ok
test_from_file_GC (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_from_file_GF (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_from_file_GR (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_from_file_GS (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_from_file_alignment (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_from_file_multi (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gc_info_malformed (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gc_info_nongf (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gc_info_strict_duplicate (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gc_info_strict_len (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gf_info_malformed (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gf_info_nongf (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gf_multiline_cc (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gf_multiline_nh (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gs_gr_info_malformed (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gs_gr_info_mixed (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_parse_gs_gr_info_strict (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_retrieve_metadata (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_str (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_str_gc (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_str_gf (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_str_gr (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_str_gs (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_str_trees (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_to_file (skbio.alignment.tests.test_alignment.StockholmAlignmentTests) ... ok
test_compute_score_and_traceback_matrices (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_compute_score_and_traceback_matrices_invalid (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_compute_substitution_score (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_first_largest (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_get_seq_id (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_global_pairwise_align_nucleotide (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_global_pairwise_align_nucleotide_penalize_terminal_gaps (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_global_pairwise_align_protein (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_global_pairwise_align_protein_penalize_terminal_gaps (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_init_matrices_nw (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_init_matrices_sw (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_local_pairwise_align_nucleotide (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_local_pairwise_align_protein (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_make_identity_substitution_matrix (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_nucleotide_aligners_use_substitution_matrices (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_traceback (skbio.alignment.tests.test_pairwise.PairwiseAlignmentTests) ... ok
test_kwargs_are_usable (skbio.alignment.tests.test_ssw.TestAlignStripedSmithWaterman) ...
[1]    23166 segmentation fault (core dumped)