Dec 07 22:42:16.992 INFO testing bio-0.24.0 against master#906deae0790bd18681b937fe9a141a3c26cf1855 for pr-56514 Dec 07 22:42:16.992 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-5/master#906deae0790bd18681b937fe9a141a3c26cf1855:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-56514/master#906deae0790bd18681b937fe9a141a3c26cf1855:/source:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/source" "-e" "USER_ID=1000" "-e" "CMD=cargo +906deae0790bd18681b937fe9a141a3c26cf1855-alt build --frozen" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"` Dec 07 22:42:17.469 INFO [stdout] 509e1444e9d7c950dc4ce21630762aab2ae57f1bcf232826f009cd04b6cf68b5 Dec 07 22:42:17.471 INFO running `"docker" "start" "-a" "509e1444e9d7c950dc4ce21630762aab2ae57f1bcf232826f009cd04b6cf68b5"` Dec 07 22:42:19.016 INFO [stderr] usermod: no changes Dec 07 22:42:19.281 INFO [stderr] Compiling feature-probe v0.1.1 Dec 07 22:42:19.289 INFO [stderr] Compiling bio v0.24.0 (/source) Dec 07 22:42:19.316 INFO [stderr] Compiling approx v0.3.0 Dec 07 22:42:19.316 INFO [stderr] Compiling multimap v0.4.0 Dec 07 22:42:19.316 INFO [stderr] Compiling vec_map v0.8.1 Dec 07 22:42:19.316 INFO [stderr] Compiling bio-types v0.4.0 Dec 07 22:42:21.596 INFO [stderr] Compiling bv v0.10.0 Dec 07 22:42:34.424 INFO [stderr] warning: unused import: `std::ops::Deref` Dec 07 22:42:34.424 INFO [stderr] --> src/data_structures/bwt.rs:15:5 Dec 07 22:42:34.424 INFO [stderr] | Dec 07 22:42:34.424 INFO [stderr] 15 | use std::ops::Deref; Dec 07 22:42:34.424 INFO [stderr] | ^^^^^^^^^^^^^^^ Dec 07 22:42:34.424 INFO [stderr] | Dec 07 22:42:34.424 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 07 22:42:34.424 INFO [stderr] Dec 07 22:42:36.416 INFO [stderr] warning: use of deprecated item 'ndarray::impl_methods::>::subview': renamed to `index_axis` Dec 07 22:42:36.416 INFO [stderr] --> src/stats/hmm.rs:266:22 Dec 07 22:42:36.416 INFO [stderr] | Dec 07 22:42:36.416 INFO [stderr] 266 | .subview(Axis(0), i - 1) Dec 07 22:42:36.416 INFO [stderr] | ^^^^^^^ Dec 07 22:42:36.416 INFO [stderr] | Dec 07 22:42:36.416 INFO [stderr] = note: #[warn(deprecated)] on by default Dec 07 22:42:36.416 INFO [stderr] Dec 07 22:42:42.730 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 23.68s Dec 07 22:42:42.740 INFO [stderr] su: No module specific data is present Dec 07 22:42:43.242 INFO running `"docker" "inspect" "509e1444e9d7c950dc4ce21630762aab2ae57f1bcf232826f009cd04b6cf68b5"` Dec 07 22:42:43.426 INFO running `"docker" "rm" "-f" "509e1444e9d7c950dc4ce21630762aab2ae57f1bcf232826f009cd04b6cf68b5"` Dec 07 22:42:43.589 INFO [stdout] 509e1444e9d7c950dc4ce21630762aab2ae57f1bcf232826f009cd04b6cf68b5 Dec 07 22:42:43.594 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-5/master#906deae0790bd18681b937fe9a141a3c26cf1855:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-56514/master#906deae0790bd18681b937fe9a141a3c26cf1855:/source:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/source" "-e" "USER_ID=1000" "-e" "CMD=cargo +906deae0790bd18681b937fe9a141a3c26cf1855-alt test --frozen --no-run" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"` Dec 07 22:42:43.967 INFO [stdout] 783d1404c3ebd08cd1d4de412129289d89bcddad1bc2937f80216101396cb81c Dec 07 22:42:43.974 INFO running `"docker" "start" "-a" "783d1404c3ebd08cd1d4de412129289d89bcddad1bc2937f80216101396cb81c"` Dec 07 22:42:44.766 INFO [stderr] usermod: no changes Dec 07 22:42:44.928 INFO [stderr] Compiling bio v0.24.0 (/source) Dec 07 22:42:49.144 INFO [stderr] warning: unused import: `std::ops::Deref` Dec 07 22:42:49.144 INFO [stderr] --> src/data_structures/bwt.rs:15:5 Dec 07 22:42:49.144 INFO [stderr] | Dec 07 22:42:49.144 INFO [stderr] 15 | use std::ops::Deref; Dec 07 22:42:49.144 INFO [stderr] | ^^^^^^^^^^^^^^^ Dec 07 22:42:49.144 INFO [stderr] | Dec 07 22:42:49.144 INFO [stderr] = note: #[warn(unused_imports)] on by default Dec 07 22:42:49.144 INFO [stderr] Dec 07 22:42:52.546 INFO [stderr] warning: use of deprecated item 'ndarray::impl_methods::>::subview': renamed to `index_axis` Dec 07 22:42:52.546 INFO [stderr] --> src/stats/hmm.rs:266:22 Dec 07 22:42:52.546 INFO [stderr] | Dec 07 22:42:52.546 INFO [stderr] 266 | .subview(Axis(0), i - 1) Dec 07 22:42:52.546 INFO [stderr] | ^^^^^^^ Dec 07 22:42:52.546 INFO [stderr] | Dec 07 22:42:52.546 INFO [stderr] = note: #[warn(deprecated)] on by default Dec 07 22:42:52.546 INFO [stderr] Dec 07 22:43:10.484 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 25.68s Dec 07 22:43:10.492 INFO [stderr] su: No module specific data is present Dec 07 22:43:11.322 INFO running `"docker" "inspect" "783d1404c3ebd08cd1d4de412129289d89bcddad1bc2937f80216101396cb81c"` Dec 07 22:43:11.602 INFO running `"docker" "rm" "-f" "783d1404c3ebd08cd1d4de412129289d89bcddad1bc2937f80216101396cb81c"` Dec 07 22:43:11.899 INFO [stdout] 783d1404c3ebd08cd1d4de412129289d89bcddad1bc2937f80216101396cb81c Dec 07 22:43:11.902 INFO running `"docker" "create" "-v" "/mnt/big/crater/work/local/target-dirs/pr-56514/worker-5/master#906deae0790bd18681b937fe9a141a3c26cf1855:/target:rw,Z" "-v" "/mnt/big/crater/work/local/test-source/worker-5/pr-56514/master#906deae0790bd18681b937fe9a141a3c26cf1855:/source:ro,Z" "-v" "/mnt/big/crater/work/local/cargo-home:/cargo-home:ro,Z" "-v" "/mnt/big/crater/work/local/rustup-home:/rustup-home:ro,Z" "-e" "USER_ID=1000" "-e" "SOURCE_DIR=/source" "-e" "USER_ID=1000" "-e" "CMD=cargo +906deae0790bd18681b937fe9a141a3c26cf1855-alt test --frozen" "-e" "CARGO_TARGET_DIR=/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/cargo-home" "-e" "RUSTUP_HOME=/rustup-home" "-m" "1536M" "--network" "none" "crater"` Dec 07 22:43:12.322 INFO [stdout] 6ff5405be8e9fe5c703c1d92ed792147ab1502d84e89fedde6ea02d05e34dd0e Dec 07 22:43:12.326 INFO running `"docker" "start" "-a" "6ff5405be8e9fe5c703c1d92ed792147ab1502d84e89fedde6ea02d05e34dd0e"` Dec 07 22:43:14.115 INFO [stderr] usermod: no changes Dec 07 22:43:14.253 INFO [stderr] Finished dev [unoptimized + debuginfo] target(s) in 0.12s Dec 07 22:43:14.268 INFO [stderr] Running /target/debug/deps/bio-0fc1973696b56612 Dec 07 22:43:14.272 INFO [stdout] Dec 07 22:43:14.272 INFO [stdout] running 245 tests Dec 07 22:43:14.288 INFO [stdout] test alignment::pairwise::banded::banded::test_aligner_new ... ok Dec 07 22:43:14.288 INFO [stdout] test alignment::pairwise::banded::banded::test_band_add_entry ... ok Dec 07 22:43:14.288 INFO [stdout] test alignment::pairwise::banded::banded::test_band_add_kmer ... ok Dec 07 22:43:14.288 INFO [stdout] test alignment::distance::tests::test_hamming_dist_good ... ok Dec 07 22:43:14.288 INFO [stdout] test alignment::distance::tests::test_levenshtein_dist ... ok Dec 07 22:43:14.320 INFO [stdout] test alignment::pairwise::banded::banded::test_global ... ok Dec 07 22:43:14.351 INFO [stdout] test alignment::pairwise::banded::banded::test_global_affine_ins ... ok Dec 07 22:43:14.351 INFO [stdout] test alignment::pairwise::banded::banded::test_blosum62 ... ok Dec 07 22:43:14.364 INFO [stdout] test alignment::pairwise::banded::banded::test_global_affine_ins2 ... ok Dec 07 22:43:14.392 INFO [stdout] test alignment::pairwise::banded::banded::test_global_right_del ... ok Dec 07 22:43:14.392 INFO [stdout] test alignment::pairwise::banded::banded::test_insert_in_between_semiglobal ... ok Dec 07 22:43:14.421 INFO [stdout] test alignment::pairwise::banded::banded::test_insert_only_semiglobal ... ok Dec 07 22:43:14.421 INFO [stdout] test alignment::pairwise::banded::banded::test_band_ends_inside ... ok Dec 07 22:43:14.484 INFO [stdout] test alignment::pairwise::banded::banded::test_deletion ... ok Dec 07 22:43:14.484 INFO [stdout] test alignment::pairwise::banded::banded::test_issue11 ... ok Dec 07 22:43:14.484 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_1 ... ok Dec 07 22:43:14.492 INFO [stdout] test alignment::pairwise::banded::banded::test_band_starts_inside ... ok Dec 07 22:43:14.492 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_2 ... ok Dec 07 22:43:14.492 INFO [stdout] test alignment::pairwise::banded::banded::test_left_aligned_ins ... ok Dec 07 22:43:14.492 INFO [stdout] test alignment::pairwise::banded::banded::test_local ... ok Dec 07 22:43:14.501 INFO [stdout] test alignment::pairwise::banded::banded::test_issue12_3 ... ok Dec 07 22:43:14.524 INFO [stdout] test alignment::pairwise::banded::banded::test_left_aligned_del ... ok Dec 07 22:43:14.524 INFO [stdout] test alignment::pairwise::banded::banded::test_insertion ... ok Dec 07 22:43:14.540 INFO [stdout] test alignment::pairwise::banded::banded::test_longer_string_all_operations ... ok Dec 07 22:43:14.540 INFO [stdout] test alignment::pairwise::banded::banded::test_local_affine_ins2 ... ok Dec 07 22:43:14.556 INFO [stdout] test alignment::pairwise::banded::banded::test_local_empty ... ok Dec 07 22:43:14.592 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs3 ... ok Dec 07 22:43:14.616 INFO [stdout] test alignment::pairwise::banded::banded::test_band_is_fully_inside ... ok Dec 07 22:43:14.616 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs1 ... ok Dec 07 22:43:14.616 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs2 ... ok Dec 07 22:43:14.628 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs4 ... ok Dec 07 22:43:14.628 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal ... ok Dec 07 22:43:14.628 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal_gap_open_lt_mismatch ... ok Dec 07 22:43:14.644 INFO [stdout] test alignment::pairwise::banded::banded::test_semiglobal_simple ... ok Dec 07 22:43:14.656 INFO [stdout] test alignment::pairwise::banded::banded::test_xclip_prefix_custom ... ok Dec 07 22:43:14.656 INFO [stdout] test alignment::pairwise::banded::banded::test_yclip_prefix_custom ... ok Dec 07 22:43:14.656 INFO [stdout] test alignment::pairwise::banded::banded::test_yclip_suffix_custom ... ok Dec 07 22:43:14.657 INFO [stdout] test alignment::pairwise::tests::test_aligner_new ... ok Dec 07 22:43:14.670 INFO [stdout] test alignment::pairwise::tests::test_blosum62 ... ok Dec 07 22:43:14.670 INFO [stdout] test alignment::pairwise::tests::test_global ... ok Dec 07 22:43:14.672 INFO [stdout] test alignment::pairwise::banded::banded::test_xclip_suffix_custom ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_global_right_del ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_insert_in_between_semiglobal ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_global_affine_ins2 ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_insert_only_semiglobal ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_global_affine_ins ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_issue11 ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_issue12_1 ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_left_aligned_del ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_issue12_3 ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_issue12_2 ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_left_aligned_ins ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_local ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_local_affine_ins2 ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_semiglobal ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_semiglobal_gap_open_lt_mismatch ... ok Dec 07 22:43:14.676 INFO [stdout] test alignment::pairwise::tests::test_semiglobal_simple ... ok Dec 07 22:43:14.684 INFO [stdout] test alignment::pairwise::tests::test_xclip_prefix_custom ... ok Dec 07 22:43:14.684 INFO [stdout] test alignment::pairwise::tests::test_longer_string_all_operations ... ok Dec 07 22:43:14.684 INFO [stdout] test alignment::pairwise::tests::test_scoring_from_scores ... ok Dec 07 22:43:14.684 INFO [stdout] test alignment::pairwise::tests::test_xclip_suffix_custom ... ok Dec 07 22:43:14.691 INFO [stdout] test alignment::pairwise::tests::traceback_cell ... ok Dec 07 22:43:14.691 INFO [stdout] test alignment::pairwise::tests::test_yclip_suffix_custom ... ok Dec 07 22:43:14.691 INFO [stdout] test alignment::pairwise::tests::test_yclip_prefix_custom ... ok Dec 07 22:43:14.691 INFO [stdout] test alignment::sparse::sparse_alignment::test_expanded_matches ... ok Dec 07 22:43:14.691 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp0 ... ok Dec 07 22:43:14.692 INFO [stdout] test alignment::sparse::sparse_alignment::test_find_kmer_matches ... ok Dec 07 22:43:14.694 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp1 ... ok Dec 07 22:43:14.694 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp2 ... ok Dec 07 22:43:14.704 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp_same ... ok Dec 07 22:43:14.704 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp ... ok Dec 07 22:43:14.705 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp1 ... ok Dec 07 22:43:14.706 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdpkpp_same ... ok Dec 07 22:43:14.706 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdp2 ... ok Dec 07 22:43:14.711 INFO [stdout] test alignment::pairwise::banded::banded::test_overhangs5 ... ok Dec 07 22:43:14.712 INFO [stdout] test alphabets::protein::tests::is_no_word ... ok Dec 07 22:43:14.716 INFO [stdout] test alignment::distance::tests::test_hamming_dist_bad ... ok Dec 07 22:43:14.716 INFO [stdout] test alphabets::protein::tests::is_word ... ok Dec 07 22:43:14.716 INFO [stdout] test alphabets::protein::tests::number_is_no_word ... ok Dec 07 22:43:14.720 INFO [stdout] test alphabets::rna::tests::is_word ... ok Dec 07 22:43:14.732 INFO [stdout] test alphabets::rna::tests::number_is_no_word ... ok Dec 07 22:43:14.732 INFO [stdout] test alphabets::rna::tests::is_no_word ... ok Dec 07 22:43:14.732 INFO [stdout] test alphabets::protein::tests::symbol_is_no_word ... ok Dec 07 22:43:14.732 INFO [stdout] test alphabets::rna::tests::test_reverse_complement ... ok Dec 07 22:43:14.732 INFO [stdout] test alphabets::rna::tests::symbol_is_no_word ... ok Dec 07 22:43:14.732 INFO [stdout] test data_structures::annot_map::tests::overlaps ... ok Dec 07 22:43:14.732 INFO [stdout] test data_structures::bit_tree::test_bit_tree::test_bit_tree ... ok Dec 07 22:43:14.732 INFO [stdout] test data_structures::bitenc::tests::test_bitenc ... ok Dec 07 22:43:14.732 INFO [stdout] test data_structures::annot_map::tests::lookup ... ok Dec 07 22:43:14.732 INFO [stdout] test data_structures::bwt::tests::test_bwtfind ... ok Dec 07 22:43:14.732 INFO [stdout] test data_structures::bwt::tests::test_invert_bwt ... ok Dec 07 22:43:14.737 INFO [stdout] test data_structures::bwt::tests::test_occ ... ok Dec 07 22:43:14.744 INFO [stdout] test data_structures::bitenc::tests::test_push_values ... ok Dec 07 22:43:14.744 INFO [stdout] test data_structures::fmindex::tests::test_fmindex ... ok Dec 07 22:43:14.744 INFO [stdout] test data_structures::bitenc::tests::test_issue29 ... ok Dec 07 22:43:14.744 INFO [stdout] test alignment::pairwise::banded::banded::test_substitutions ... ok Dec 07 22:43:14.744 INFO [stdout] test alignment::sparse::sparse_alignment::test_lcskpp_tandem_repeat ... ok Dec 07 22:43:14.756 INFO [stdout] test alignment::sparse::sparse_alignment::test_sdpkpp_tandem_repeat ... ok Dec 07 22:43:14.765 INFO [stdout] test data_structures::interval_tree::tests::from_iterator ... ok Dec 07 22:43:14.765 INFO [stdout] test data_structures::fmindex::tests::test_init_interval ... ok Dec 07 22:43:14.773 INFO [stdout] test data_structures::fmindex::tests::test_smems ... ok Dec 07 22:43:14.784 INFO [stdout] test data_structures::interval_tree::tests::test_insertion_and_intersection ... ok Dec 07 22:43:14.788 INFO [stdout] test data_structures::qgram_index::tests::test_exact_matches ... ok Dec 07 22:43:14.788 INFO [stdout] test data_structures::qgram_index::tests::test_exact_matches_self ... ok Dec 07 22:43:14.788 INFO [stdout] test data_structures::qgram_index::tests::test_matches ... ok Dec 07 22:43:14.789 INFO [stdout] test data_structures::qgram_index::tests::test_qgram_matches ... ok Dec 07 22:43:14.789 INFO [stdout] test data_structures::rank_select::tests::test_rank_select ... ok Dec 07 22:43:14.789 INFO [stdout] test data_structures::rank_select::tests::test_select ... ok Dec 07 22:43:14.789 INFO [stdout] test data_structures::rank_select::tests::test_single_select ... ok Dec 07 22:43:14.792 INFO [stdout] test data_structures::suffix_array::tests::test_buckets ... ok Dec 07 22:43:14.802 INFO [stdout] test data_structures::suffix_array::tests::test_handles_sentinels_properly ... ok Dec 07 22:43:14.802 INFO [stdout] test data_structures::suffix_array::tests::test_issue10_1 ... ok Dec 07 22:43:14.802 INFO [stdout] test data_structures::suffix_array::tests::test_issue10_2 ... ok Dec 07 22:43:14.802 INFO [stdout] test data_structures::suffix_array::tests::test_lms_pos ... ok Dec 07 22:43:14.802 INFO [stdout] test data_structures::suffix_array::tests::test_pos ... ok Dec 07 22:43:14.803 INFO [stdout] test data_structures::suffix_array::tests::test_pos_types ... ok Dec 07 22:43:14.813 INFO [stdout] test data_structures::interval_tree::tests::zero_width_ranges ... ok Dec 07 22:43:14.813 INFO [stdout] test data_structures::interval_tree::tests::iter_mut ... ok Dec 07 22:43:14.824 INFO [stdout] test io::bed::tests::test_reader ... ok Dec 07 22:43:14.824 INFO [stdout] test io::bed::tests::spliced_to_bed ... ok Dec 07 22:43:14.829 INFO [stdout] test io::fasta::tests::test_index_sequences ... ok Dec 07 22:43:14.830 INFO [stdout] test io::bed::tests::test_writer ... ok Dec 07 22:43:14.830 INFO [stdout] test alignment::pairwise::banded::banded::test_same ... ok Dec 07 22:43:14.831 INFO [stdout] test data_structures::suffix_array::tests::test_sorts_lexically ... ok Dec 07 22:43:14.833 INFO [stdout] test io::fasta::tests::test_indexed_reader_all ... ok Dec 07 22:43:14.834 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf ... ok Dec 07 22:43:14.844 INFO [stdout] test io::fasta::tests::test_indexed_reader ... ok Dec 07 22:43:14.844 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf_all ... ok Dec 07 22:43:14.844 INFO [stdout] test io::fasta::tests::test_indexed_reader_bad_reader ... ok Dec 07 22:43:14.844 INFO [stdout] test io::fasta::tests::test_indexed_reader_by_rid_all ... ok Dec 07 22:43:14.856 INFO [stdout] test io::fasta::tests::test_indexed_reader_crlf_by_rid_all ... ok Dec 07 22:43:14.856 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_all ... ok Dec 07 22:43:14.856 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_by_rid_all ... ok Dec 07 22:43:14.856 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf ... ok Dec 07 22:43:14.856 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf_by_rid_all ... ok Dec 07 22:43:14.856 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_crlf_all ... ok Dec 07 22:43:14.856 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_seek_fails ... ok Dec 07 22:43:14.856 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_read_fails ... ok Dec 07 22:43:14.856 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter_size_hint ... ok Dec 07 22:43:14.888 INFO [stdout] test io::fasta::tests::test_indexed_reader_iter ... ok Dec 07 22:43:14.888 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_fetch_read_iter_fails ... ok Dec 07 22:43:14.888 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_fetch_read_fails ... ok Dec 07 22:43:14.888 INFO [stdout] test io::fasta::tests::test_indexed_reader_no_trailing_lf ... ok Dec 07 22:43:14.888 INFO [stdout] test io::fasta::tests::test_indexed_reader_read_read_fails ... ok Dec 07 22:43:14.888 INFO [stdout] test io::fasta::tests::test_indexed_reader_read_seek_fails ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fasta::tests::test_indexed_reader_reused_buffer ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fasta::tests::test_reader ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fasta::tests::test_reader_non_ascii_sequence ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fasta::tests::test_reader_no_id ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fasta::tests::test_reader_wrong_header ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fasta::tests::test_record_with_attrs ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fasta::tests::test_writer ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fastq::tests::test_reader ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fastq::tests::test_record_with_attrs ... ok Dec 07 22:43:14.891 INFO [stdout] test io::fastq::tests::test_writer ... ok Dec 07 22:43:14.891 INFO [stdout] test alignment::pairwise::banded::banded::test_big ... ok Dec 07 22:43:14.903 INFO [stdout] test data_structures::interval_tree::tests::test_insertion_and_intersection_2 ... ok Dec 07 22:43:14.903 INFO [stdout] test io::gff::tests::test_reader_gtf2_2 ... ok Dec 07 22:43:14.903 INFO [stdout] test io::gff::tests::test_reader_gtf2_dup_attr_keys ... ok Dec 07 22:43:14.903 INFO [stdout] test io::gff::tests::test_writer_gff3 ... ok Dec 07 22:43:14.903 INFO [stdout] test io::gff::tests::test_reader_gtf2 ... ok Dec 07 22:43:14.903 INFO [stdout] test io::fasta::tests::test_reader_read_fails ... ok Dec 07 22:43:14.903 INFO [stdout] test io::fasta::tests::test_reader_read_fails_iter ... ok Dec 07 22:43:14.909 INFO [stdout] test pattern_matching::bndm::tests::test_find_all ... ok Dec 07 22:43:14.909 INFO [stdout] test pattern_matching::bom::tests::test_delta ... ok Dec 07 22:43:14.909 INFO [stdout] test io::gff::tests::test_reader_gff3 ... ok Dec 07 22:43:14.909 INFO [stdout] test io::gff::tests::test_convert_gtf2_to_gff3 ... ok Dec 07 22:43:14.924 INFO [stdout] test pattern_matching::horspool::tests::test_find_all ... ok Dec 07 22:43:14.924 INFO [stdout] test pattern_matching::horspool::tests::test_shift ... ok Dec 07 22:43:14.924 INFO [stdout] test pattern_matching::kmp::tests::test_find_all_at_start ... ok Dec 07 22:43:14.924 INFO [stdout] test pattern_matching::kmp::tests::test_lps ... ok Dec 07 22:43:14.944 INFO [stdout] test pattern_matching::myers::tests::test_alignment ... ok Dec 07 22:43:14.944 INFO [stdout] test pattern_matching::kmp::tests::test_delta ... ok Dec 07 22:43:14.944 INFO [stdout] test pattern_matching::kmp::tests::test_find_all ... ok Dec 07 22:43:14.944 INFO [stdout] test io::gff::tests::test_writer_gtf2 ... ok Dec 07 22:43:14.944 INFO [stdout] test pattern_matching::bom::tests::test_find_all ... ok Dec 07 22:43:14.952 INFO [stdout] test pattern_matching::myers::tests::test_distance ... ok Dec 07 22:43:14.952 INFO [stdout] test pattern_matching::myers::tests::test_find_all_end ... ok Dec 07 22:43:14.952 INFO [stdout] test pattern_matching::myers::tests::test_find_best_end ... ok Dec 07 22:43:14.952 INFO [stdout] test pattern_matching::myers::tests::test_full_position ... ok Dec 07 22:43:14.952 INFO [stdout] test pattern_matching::myers::tests::test_large_dist ... ok Dec 07 22:43:14.952 INFO [stdout] test pattern_matching::myers::tests::test_long_shorter ... ok Dec 07 22:43:14.963 INFO [stdout] test pattern_matching::myers::tests::test_path_at ... ok Dec 07 22:43:14.963 INFO [stdout] test pattern_matching::myers::tests::test_longest_possible ... ok Dec 07 22:43:14.963 INFO [stdout] test pattern_matching::myers::tests::test_ambig ... ok Dec 07 22:43:14.972 INFO [stdout] test pattern_matching::myers::tests::test_shorter ... ok Dec 07 22:43:14.976 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::find_motif ... ok Dec 07 22:43:14.980 INFO [stdout] test pattern_matching::myers::tests::test_traceback_path ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::myers::tests::test_traceback_path2 ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_inconsist_err ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::simple_pssm ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_info_content ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::pssm::dnamotif::tests::test_mono_err ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_inconsist_err ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_info_content ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_mono_err ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::pssm::protmotif::tests::test_scoring ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::shift_and::tests::test_find_all ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::ukkonen::tests::test_find_all_end ... ok Dec 07 22:43:15.000 INFO [stdout] test pattern_matching::ukkonen::tests::test_find_start ... ok Dec 07 22:43:15.000 INFO [stdout] test scores::blosum62::tests::test_blosum62 ... ok Dec 07 22:43:15.000 INFO [stdout] test scores::pam120::tests::test_pam120 ... ok Dec 07 22:43:15.000 INFO [stdout] test scores::pam200::tests::test_pam200 ... ok Dec 07 22:43:15.000 INFO [stdout] test scores::pam250::tests::test_pam250 ... ok Dec 07 22:43:15.000 INFO [stdout] test scores::pam40::tests::test_pam40 ... ok Dec 07 22:43:15.000 INFO [stdout] test seq_analysis::orf::tests::test_orf ... ok Dec 07 22:43:15.000 INFO [stdout] test stats::bayesian::tests::test_expected_fdr ... ok Dec 07 22:43:15.000 INFO [stdout] test stats::combinatorics::tests::test_comb ... ok Dec 07 22:43:15.000 INFO [stdout] test stats::combinatorics::tests::test_comb_scaled ... ok Dec 07 22:43:15.000 INFO [stdout] test stats::hmm::tests::test_discrete_backward_toy_example ... ok Dec 07 22:43:15.000 INFO [stdout] test stats::hmm::tests::test_discrete_forward_toy_example ... ok Dec 07 22:43:15.001 INFO [stdout] test stats::hmm::tests::test_discrete_viterbi_toy_example ... ok Dec 07 22:43:15.001 INFO [stdout] test stats::hmm::tests::test_gaussian_backward_simple_example ... ok Dec 07 22:43:15.012 INFO [stdout] test pattern_matching::myers::tests::test_position_cmp ... ok Dec 07 22:43:15.020 INFO [stdout] test pattern_matching::myers::tests::test_pattern_too_long_builder ... ok Dec 07 22:43:15.024 INFO [stdout] test stats::pairhmm::tests::test_deletion ... ok Dec 07 22:43:15.024 INFO [stdout] test stats::hmm::tests::test_gaussian_forward_equals_backward_simple_example ... ok Dec 07 22:43:15.024 INFO [stdout] test stats::hmm::tests::test_gaussian_forward_simple_example ... ok Dec 07 22:43:15.040 INFO [stdout] test stats::hmm::tests::test_gaussian_viterbi_simple_example ... ok Dec 07 22:43:15.040 INFO [stdout] test stats::pairhmm::tests::test_insertion ... ok Dec 07 22:43:15.040 INFO [stdout] test stats::pairhmm::tests::test_mismatch ... ok Dec 07 22:43:15.044 INFO [stdout] test stats::pairhmm::tests::test_same ... ok Dec 07 22:43:15.048 INFO [stdout] test stats::probs::tests::test_cap_numerical_overshoot ... ok Dec 07 22:43:15.048 INFO [stdout] test pattern_matching::myers::tests::test_pattern_too_long ... ok Dec 07 22:43:15.048 INFO [stdout] test stats::probs::cdf::test::test_cdf ... ok Dec 07 22:43:15.048 INFO [stdout] test stats::probs::tests::test_cap_numerical_overshoot_panic ... ok Dec 07 22:43:15.048 INFO [stdout] test stats::probs::tests::test_empty_sum ... ok Dec 07 22:43:15.048 INFO [stdout] test stats::probs::tests::test_one_minus ... ok Dec 07 22:43:15.049 INFO [stdout] test stats::probs::tests::test_sub ... ok Dec 07 22:43:15.049 INFO [stdout] test stats::probs::tests::test_sum_one_zero ... ok Dec 07 22:43:15.060 INFO [stdout] test stats::probs::tests::test_simpsons_integrate ... ok Dec 07 22:43:15.060 INFO [stdout] test stats::probs::tests::test_cumsum ... ok Dec 07 22:43:15.060 INFO [stdout] test stats::probs::tests::test_sum ... ok Dec 07 22:43:15.068 INFO [stdout] test utils::interval::tests::negative_width_range ... ok Dec 07 22:43:15.068 INFO [stdout] test data_structures::fmindex::tests::test_issue39 ... ok Dec 07 22:43:15.068 INFO [stdout] test stats::probs::tests::test_trapezoidal_integrate ... ok Dec 07 22:43:15.068 INFO [stdout] test utils::interval::tests::range_interval_conversions ... ok Dec 07 22:43:15.068 INFO [stdout] test utils::text::tests::test_print_sequence ... ok Dec 07 22:43:15.068 INFO [stdout] test utils::tests::test_prescan ... ok Dec 07 22:43:15.068 INFO [stdout] test utils::tests::test_scan ... ok Dec 07 22:43:15.082 INFO [stdout] test utils::fastexp::tests::test_fastexp ... ok Dec 07 22:43:15.084 INFO [stdout] test stats::probs::tests::test_zero ... ok Dec 07 22:43:15.092 INFO [stdout] test stats::pairhmm::tests::test_large ... ok Dec 07 22:43:15.140 INFO [stdout] test data_structures::interpolation_table::tests::test_interpolation_table ... ok Dec 07 22:43:15.179 INFO [stdout] test stats::hmm::tests::test_discrete_forward_equals_backward_toy_example ... ok Dec 07 22:43:15.179 INFO [stdout] Dec 07 22:43:15.179 INFO [stdout] test result: ok. 245 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 07 22:43:15.179 INFO [stdout] Dec 07 22:43:15.188 INFO [stderr] Doc-tests bio Dec 07 22:43:20.724 INFO [stdout] Dec 07 22:43:20.724 INFO [stdout] running 58 tests Dec 07 22:44:05.349 INFO [stdout] test src/alignment/sparse.rs - alignment::sparse (line 18) ... ok Dec 07 22:44:07.748 INFO [stdout] test src/alignment/distance.rs - alignment::distance::hamming (line 16) ... ok Dec 07 22:44:10.365 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::PHREDProb (line 46) ... ok Dec 07 22:44:11.180 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::LogProb (line 50) ... ok Dec 07 22:44:11.268 INFO [stdout] test src/alignment/distance.rs - alignment::distance::levenshtein (line 48) ... ok Dec 07 22:44:13.837 INFO [stdout] test src/alignment/pairwise/banded.rs - alignment::pairwise::banded (line 20) ... ok Dec 07 22:44:13.964 INFO [stdout] test src/alignment/pairwise/mod.rs - alignment::pairwise (line 13) ... ok Dec 07 22:44:14.244 INFO [stdout] test <::custom_derive::custom_derive macros> - stats::probs::Prob (line 46) ... ok Dec 07 22:44:59.296 INFO [stdout] test src/alphabets/dna.rs - alphabets::dna (line 10) ... ok Dec 07 22:45:04.942 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::find (line 92) ... ok Dec 07 22:45:05.126 INFO [stdout] test src/alphabets/mod.rs - alphabets (line 10) ... ok Dec 07 22:45:06.053 INFO [stdout] test src/alphabets/rna.rs - alphabets::rna (line 10) ... ok Dec 07 22:45:08.700 INFO [stdout] test src/alphabets/protein.rs - alphabets::protein (line 10) ... ok Dec 07 22:45:10.492 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::insert_at (line 58) ... ok Dec 07 22:45:11.604 INFO [stdout] test src/data_structures/annot_map.rs - data_structures::annot_map::AnnotMap::new (line 39) ... ok Dec 07 22:45:13.607 INFO [stdout] test src/data_structures/bit_tree.rs - data_structures::bit_tree (line 12) ... ok Dec 07 22:45:52.880 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex (line 12) ... ok Dec 07 22:45:55.160 INFO [stdout] test src/data_structures/bwt.rs - data_structures::bwt::bwt (line 33) ... ok Dec 07 22:45:55.612 INFO [stdout] test src/data_structures/bitenc.rs - data_structures::bitenc (line 11) ... ok Dec 07 22:45:58.176 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex (line 32) ... ok Dec 07 22:46:06.208 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex::FMIndexable::backward_search (line 96) ... ok Dec 07 22:46:07.529 INFO [stdout] test src/data_structures/interval_tree.rs - data_structures::interval_tree (line 14) ... ok Dec 07 22:46:08.697 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex::FMDIndex::smems (line 260) ... test src/data_structures/fmindex.rs - data_structures::fmindex::FMDIndex::smems (line 260) has been running for over 60 seconds Dec 07 22:46:09.555 INFO [stdout] test src/data_structures/qgram_index.rs - data_structures::qgram_index (line 10) ... ok Dec 07 22:46:10.301 INFO [stdout] test src/data_structures/fmindex.rs - data_structures::fmindex::FMDIndex::smems (line 260) ... ok Dec 07 22:46:43.576 INFO [stdout] test src/data_structures/rank_select.rs - data_structures::rank_select (line 11) ... ok Dec 07 22:46:44.340 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::shortest_unique_substrings (line 304) ... ok Dec 07 22:46:50.360 INFO [stdout] test src/io/bed.rs - io::bed::Record (line 314) ... ok Dec 07 22:46:51.044 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::lcp (line 239) ... ok Dec 07 22:46:53.585 INFO [stdout] test src/data_structures/smallints.rs - data_structures::smallints (line 13) ... ok Dec 07 22:46:55.760 INFO [stdout] test src/io/bed.rs - io::bed (line 10) ... ok Dec 07 22:47:00.960 INFO [stdout] test src/io/bed.rs - io::bed::annot::contig::Contig::from (line 237) ... ok Dec 07 22:47:02.912 INFO [stdout] test src/data_structures/suffix_array.rs - data_structures::suffix_array::suffix_array (line 198) ... ok Dec 07 22:47:33.156 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::new (line 49) ... ok Dec 07 22:47:37.008 INFO [stdout] test src/io/fasta.rs - io::fasta (line 10) ... ok Dec 07 22:47:37.084 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::read (line 69) ... ok Dec 07 22:47:40.704 INFO [stdout] test src/io/fastq.rs - io::fastq (line 10) ... ok Dec 07 22:47:41.590 INFO [stdout] test src/io/fasta.rs - io::fasta::Reader::records (line 127) ... ok Dec 07 22:47:43.528 INFO [stdout] test src/io/gff.rs - io::gff (line 14) ... ok Dec 07 22:47:46.316 INFO [stdout] test src/lib.rs - (line 54) ... ok Dec 07 22:47:50.384 INFO [stdout] test src/lib.rs - (line 31) ... ok Dec 07 22:48:01.552 INFO [stdout] test src/pattern_matching/horspool.rs - pattern_matching::horspool (line 32) ... ok Dec 07 22:48:01.604 INFO [stdout] test src/pattern_matching/bom.rs - pattern_matching::bom (line 12) ... ok Dec 07 22:48:02.552 INFO [stdout] test src/pattern_matching/bndm.rs - pattern_matching::bndm (line 12) ... ok Dec 07 22:48:03.748 INFO [stdout] test src/pattern_matching/kmp.rs - pattern_matching::kmp (line 16) ... ok Dec 07 22:48:06.448 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::build (line 142) ... ok Dec 07 22:48:08.769 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::ambig (line 63) ... ok Dec 07 22:48:11.068 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder (line 9) ... ok Dec 07 22:48:12.589 INFO [stdout] test src/pattern_matching/myers/builder.rs - pattern_matching::myers::builder::MyersBuilder::text_wildcard (line 98) ... ok Dec 07 22:48:23.156 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 41) ... ok Dec 07 22:48:25.683 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 124) ... ok Dec 07 22:48:26.396 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 168) ... ok Dec 07 22:48:27.684 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 15) ... ok Dec 07 22:48:30.876 INFO [stdout] test src/pattern_matching/myers/mod.rs - pattern_matching::myers (line 61) ... ok Dec 07 22:48:31.584 INFO [stdout] test src/pattern_matching/shift_and.rs - pattern_matching::shift_and (line 12) ... ok Dec 07 22:48:34.498 INFO [stdout] test src/pattern_matching/ukkonen.rs - pattern_matching::ukkonen (line 17) ... ok Dec 07 22:48:36.253 INFO [stdout] test src/seq_analysis/orf.rs - seq_analysis::orf (line 12) ... ok Dec 07 22:48:39.472 INFO [stdout] test src/stats/hmm.rs - stats::hmm (line 15) ... ok Dec 07 22:48:40.028 INFO [stdout] test src/stats/hmm.rs - stats::hmm (line 37) ... ok Dec 07 22:48:40.028 INFO [stdout] Dec 07 22:48:40.028 INFO [stdout] test result: ok. 58 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out Dec 07 22:48:40.028 INFO [stdout] Dec 07 22:48:40.072 INFO [stderr] su: No module specific data is present Dec 07 22:48:40.318 INFO running `"docker" "inspect" "6ff5405be8e9fe5c703c1d92ed792147ab1502d84e89fedde6ea02d05e34dd0e"` Dec 07 22:48:40.526 INFO running `"docker" "rm" "-f" "6ff5405be8e9fe5c703c1d92ed792147ab1502d84e89fedde6ea02d05e34dd0e"` Dec 07 22:48:40.721 INFO [stdout] 6ff5405be8e9fe5c703c1d92ed792147ab1502d84e89fedde6ea02d05e34dd0e